TY - JOUR
T1 - Capturing the most wanted taxa through cross-sample correlations
JF - The ISME Journal
Y1 - 2016
A1 - Almeida, Mathieu
A1 - Pop, Mihai
A1 - Le Chatelier, Emmanuelle
A1 - Prifti, Edi
A1 - Pons, Nicolas
A1 - Ghozlane, Amine
A1 - Ehrlich, S Dusko
UR - http://www.nature.com/doifinder/10.1038/ismej.2016.35
J1 - ISME J
M3 - 10.1038/ismej.2016.35
ER -
TY - JOUR
T1 - Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures
JF - mBio
Y1 - 2016
A1 - Fernandes, Maria Cecilia
A1 - Dillon, Laura A. L.
A1 - Belew, Ashton Trey
A1 - Bravo, Héctor Corrada
A1 - Mosser, David M.
A1 - El-Sayed, Najib M.
VL - 7
UR - http://mbio.asm.org/lookup/doi/10.1128/mBio.00027-16https://syndication.highwire.org/content/doi/10.1128/mBio.00027-16
CP - 3
J1 - mBio
M3 - 10.1128/mBio.00027-16
ER -
TY - JOUR
T1 - The fruRBA operon is necessary for Group A Streptococcal growth in fructose and for resistance to neutrophil killing during growth in whole human blood.
JF - Infect Immun
Y1 - 2016
A1 - Valdes, Kayla M
A1 - Sundar, Ganesh S
A1 - Vega, Luis A
A1 - Belew, Ashton T
A1 - Islam, Emrul
A1 - Binet, Rachel
A1 - El-Sayed, Najib M
A1 - Le Breton, Yoann
A1 - McIver, Kevin S
AB -
Bacterial pathogens rely on the availability of nutrients for survival in the host environment. The phosphoenolpyruvate-phosphotransferase system (PTS) is a global regulatory network connecting sugar uptake with signal transduction. Since the fructose PTS has been shown to impact virulence in several Streptococci, including the human pathogen S. pyogenes (the group A Streptococcus, GAS), we characterized its role in carbon metabolism and pathogenesis in the M1T1 strain 5448. Growth in fructose as a sole carbon source resulted in 103 genes affected transcriptionally, where the fru locus (fruRBA) was the most induced. RT-PCR showed that fruRBA formed an operon, which was repressed by FruR in the absence of fructose, in addition to being under carbon catabolic repression. Growth assays and carbon utilization profiles revealed that although the entire fru operon was required for growth in fructose, FruA was the main transporter for fructose and was also involved in the utilization of three additional PTS sugars: cellobiose, mannitol, and N-acetyl-D-galactosamine. Inactivation of sloR, a fruA homolog that was also up regulated in presence of fructose, failed to reveal a role as a secondary fructose transporter. Whereas the ability of both ΔfruR and ΔfruB mutants to survive in the presence of whole human blood or neutrophils was impaired, the phenotype was not reproduced in murine whole blood, nor were those mutants attenuated in a mouse intraperitoneal infection. Since the ΔfruA mutant exhibited no phenotype in the human or mouse assays, we propose that FruR and FruB are important for GAS survival in a human-specific environment.
M3 - 10.1128/IAI.01296-15
ER -
TY - JOUR
T1 - Identification guide to the heterobranch sea slugs (Mollusca: Gastropoda) from Bocas del Toro, Panama
JF - Marine Biodiversity Records
Y1 - 2016
A1 - Goodheart, Jessica
A1 - Ellingson, Ryan A.
A1 - Vital, Xochitl G.
A1 - ão Filho, Hilton C.
A1 - McCarthy, Jennifer B.
A1 - Medrano, Sabrina M.
A1 - Bhave, Vishal J.
A1 - ía-Méndez, Kimberly
A1 - énez, Lina M.
A1 - ópez, Gina
A1 - Hoover, Craig A.
A1 - Awbrey, Jaymes D.
A1 - De Jesus, Jessika M.
A1 - Gowacki, William
A1 - Krug, Patrick J.
A1 - és, Ángel
VL - 96737453830254034557880541418411912544728739317415779780725696418782226404216145163412560451520488424050829677
UR - http://mbr.biomedcentral.com/articles/10.1186/s41200-016-0048-zhttp://link.springer.com/content/pdf/10.1186/s41200-016-0048-z
CP - 12343–4
J1 - Mar Biodivers Rec
M3 - 10.1186/s41200-016-0048-z
ER -
TY - JOUR
T1 - The fruRBA Operon Is Necessary for Group A Streptococcal Growth in Fructose and for Resistance to Neutrophil Killing during Growth in Whole Human Blood
JF - Infection and Immunity
Y1 - 2016
A1 - Valdes, Kayla M.
A1 - Sundar, Ganesh S.
A1 - Vega, Luis A.
A1 - Belew, Ashton T.
A1 - Islam, Emrul
A1 - Binet, Rachel
A1 - El-Sayed, Najib M.
A1 - Le Breton, Yoann
A1 - McIver, Kevin S.
ED - Camilli, A.
VL - 84
UR - http://iai.asm.org/lookup/doi/10.1128/IAI.01296-15
CP - 4
J1 - Infect. Immun.
M3 - 10.1128/IAI.01296-15
ER -
TY - JOUR
T1 - Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection.
JF - PLoS Pathog
Y1 - 2016
A1 - Li, Yuan
A1 - Shah-Simpson, Sheena
A1 - Okrah, Kwame
A1 - Belew, A Trey
A1 - Choi, Jungmin
A1 - Caradonna, Kacey L
A1 - Padmanabhan, Prasad
A1 - Ndegwa, David M
A1 - Temanni, M Ramzi
A1 - Corrada Bravo, Hector
A1 - El-Sayed, Najib M
A1 - Burleigh, Barbara A
AB - Intracellular colonization and persistent infection by the kinetoplastid protozoan parasite, Trypanosoma cruzi, underlie the pathogenesis of human Chagas disease. To obtain global insights into the T. cruzi infective process, transcriptome dynamics were simultaneously captured in the parasite and host cells in an infection time course of human fibroblasts. Extensive remodeling of the T. cruzi transcriptome was observed during the early establishment of intracellular infection, coincident with a major developmental transition in the parasite. Contrasting this early response, few additional changes in steady state mRNA levels were detected once mature T. cruzi amastigotes were formed. Our findings suggest that transcriptome remodeling is required to establish a modified template to guide developmental transitions in the parasite, whereas homeostatic functions are regulated independently of transcriptomic changes, similar to that reported in related trypanosomatids. Despite complex mechanisms for regulation of phenotypic expression in T. cruzi, transcriptomic signatures derived from distinct developmental stages mirror known or projected characteristics of T. cruzi biology. Focusing on energy metabolism, we were able to validate predictions forecast in the mRNA expression profiles. We demonstrate measurable differences in the bioenergetic properties of the different mammalian-infective stages of T. cruzi and present additional findings that underscore the importance of mitochondrial electron transport in T. cruzi amastigote growth and survival. Consequences of T. cruzi colonization for the host include dynamic expression of immune response genes and cell cycle regulators with upregulation of host cholesterol and lipid synthesis pathways, which may serve to fuel intracellular T. cruzi growth. Thus, in addition to the biological inferences gained from gene ontology and functional enrichment analysis of differentially expressed genes in parasite and host, our comprehensive, high resolution transcriptomic dataset provides a substantially more detailed interpretation of T. cruzi infection biology and offers a basis for future drug and vaccine discovery efforts.
VL - 12
CP - 4
M3 - 10.1371/journal.ppat.1005511
ER -
TY - JOUR
T1 - Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis
JF - Nature
Y1 - 2015
A1 - Rabinovich, Shiran
A1 - Adler, Lital
A1 - Yizhak, Keren
A1 - Sarver, Alona
A1 - Silberman, Alon
A1 - Agron, Shani
A1 - Stettner, Noa
A1 - Sun, Qin
A1 - Brandis, Alexander
A1 - Helbling, Daniel
A1 - Korman, Stanley
A1 - Itzkovitz, Shalev
A1 - Dimmock, David
A1 - Ulitsky, Igor
A1 - Nagamani, Sandesh C. S.
A1 - Ruppin, Eytan
A1 - Erez, Ayelet
VL - 527
UR - http://www.nature.com/doifinder/10.1038/nature15529
CP - 7578
J1 - Nature
M3 - 10.1038/nature15529
ER -
TY - JOUR
T1 - Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes.
JF - Sci Rep
Y1 - 2015
A1 - Le Breton, Yoann
A1 - Belew, Ashton T
A1 - Valdes, Kayla M
A1 - Islam, Emrul
A1 - Curry, Patrick
A1 - Tettelin, Hervé
A1 - Shirtliff, Mark E
A1 - El-Sayed, Najib M
A1 - McIver, Kevin S
AB - Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major public health burden worldwide, infecting over 750 million people leading to over 500,000 deaths annually. GAS pathogenesis is complex, involving genetically distinct GAS strains and multiple infection sites. To overcome fastidious genetic manipulations and accelerate pathogenesis investigations in GAS, we developed a mariner-based system (Krmit) for en masse monitoring of complex mutant pools by transposon sequencing (Tn-seq). Highly saturated transposant libraries (Krmit insertions in ca. every 25 nucleotides) were generated in two distinct GAS clinical isolates, a serotype M1T1 invasive strain 5448 and a nephritogenic serotype M49 strain NZ131, and analyzed using a Bayesian statistical model to predict GAS essential genes, identifying sets of 227 and 241 of those genes in 5448 and NZ131, respectively. A large proportion of GAS essential genes corresponded to key cellular processes and metabolic pathways, and 177 were found conserved within the GAS core genome established from 20 available GAS genomes. Selected essential genes were validated using conditional-expression mutants. Finally, comparison to previous essentiality analyses in S. sanguinis and S. pneumoniae revealed significant overlaps, providing valuable insights for the development of new antimicrobials to treat infections by GAS and other pathogenic streptococci.
VL - 5
M3 - 10.1038/srep09838
ER -
TY - Generic
T1 - Fumarate induces redox-dependent senescence by modifying glutathione metabolism.
Y1 - 2015
A1 - Zheng, Liang
A1 - Cardaci, Simone
A1 - Jerby, Livnat
A1 - MacKenzie, Elaine D
A1 - Sciacovelli, Marco
A1 - Johnson, T Isaac
A1 - Gaude, Edoardo
A1 - King, Ayala
A1 - Leach, Joshua D G
A1 - Edrada-Ebel, RuAngelie
A1 - Hedley, Ann
A1 - Morrice, Nicholas A
A1 - Kalna, Gabriela
A1 - Blyth, Karen
A1 - Ruppin, Eytan
A1 - Frezza, Christian
A1 - Gottlieb, Eyal
AB - Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) are associated with a highly malignant form of renal cancer. We combined analytical chemistry and metabolic computational modelling to investigate the metabolic implications of FH loss in immortalized and primary mouse kidney cells. Here, we show that the accumulation of fumarate caused by the inactivation of FH leads to oxidative stress that is mediated by the formation of succinicGSH, a covalent adduct between fumarate and glutathione. Chronic succination of GSH, caused by the loss of FH, or by exogenous fumarate, leads to persistent oxidative stress and cellular senescence in vitro and in vivo. Importantly, the ablation of p21, a key mediator of senescence, in Fh1-deficient mice resulted in the transformation of benign renal cysts into a hyperplastic lesion, suggesting that fumarate-induced senescence needs to be bypassed for the initiation of renal cancers.
JA - Nat Commun
VL - 6
M3 - 10.1038/ncomms7001
ER -
TY - Generic
T1 - The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.
Y1 - 2015
A1 - Fleming, Bryan D
A1 - Chandrasekaran, Prabha
A1 - Dillon, Laura A L
A1 - Dalby, Elizabeth
A1 - Suresh, Rahul
A1 - Sarkar, Arup
A1 - El-Sayed, Najib M
A1 - Mosser, David M
AB - Macrophages readily change their phenotype in response to exogenous stimuli. In this work, macrophages were stimulated under a variety of experimental conditions, and phenotypic alterations were correlated with changes in gene expression. We identified 3 transcriptionally related populations of macrophages with immunoregulatory activity. They were generated by stimulating cells with TLR ligands in the presence of 3 different "reprogramming" signals: high-density ICs, PGE2, or Ado. All 3 of these cell populations produced high levels of transcripts for IL-10 and growth and angiogenic factors. They also secreted reduced levels of inflammatory cytokines IL-1β, IL-6, and IL-12. All 3 macrophage phenotypes could partially rescue mice from lethal endotoxemia, and therefore, we consider each to have anti-inflammatory activity. This ability to regulate innate-immune responses occurred equally well in macrophages from STAT6-deficient mice. The lack of STAT6 did not affect the ability of macrophages to change cytokine production reciprocally or to rescue mice from lethal endotoxemia. Furthermore, treatment of macrophages with IL-4 failed to induce similar phenotypic or transcriptional alterations. This work demonstrates that there are multiple ways to generate macrophages with immunoregulatory activity. These anti-inflammatory macrophages are transcriptionally and functionally related to each other and are quite distinct from macrophages treated with IL-4.
JA - J Leukoc Biol
VL - 98
CP - 3
M3 - 10.1189/jlb.2A1114-560R
ER -
TY - Generic
T1 - Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.
Y1 - 2015
A1 - Patella, Francesca
A1 - Schug, Zachary T
A1 - Persi, Erez
A1 - Neilson, Lisa J
A1 - Erami, Zahra
A1 - Avanzato, Daniele
A1 - Maione, Federica
A1 - Hernandez-Fernaud, Juan R
A1 - Mackay, Gillian
A1 - Zheng, Liang
A1 - Reid, Steven
A1 - Frezza, Christian
A1 - Giraudo, Enrico
A1 - Fiorio Pla, Alessandra
A1 - Anderson, Kurt
A1 - Ruppin, Eytan
A1 - Gottlieb, Eyal
A1 - Zanivan, Sara
AB - Endothelial cells (ECs) play a key role to maintain the functionality of blood vessels. Altered EC permeability causes severe impairment in vessel stability and is a hallmark of pathologies such as cancer and thrombosis. Integrating label-free quantitative proteomics data into genome-wide metabolic modeling, we built up a model that predicts the metabolic fluxes in ECs when cultured on a tridimensional matrix and organize into a vascular-like network. We discovered how fatty acid oxidation increases when ECs are assembled into a fully formed network that can be disrupted by inhibiting CPT1A, the fatty acid oxidation rate-limiting enzyme. Acute CPT1A inhibition reduces cellular ATP levels and oxygen consumption, which are restored by replenishing the tricarboxylic acid cycle. Remarkably, global phosphoproteomic changes measured upon acute CPT1A inhibition pinpointed altered calcium signaling. Indeed, CPT1A inhibition increases intracellular calcium oscillations. Finally, inhibiting CPT1A induces hyperpermeability in vitro and leakage of blood vessel in vivo, which were restored blocking calcium influx or replenishing the tricarboxylic acid cycle. Fatty acid oxidation emerges as central regulator of endothelial functions and blood vessel stability and druggable pathway to control pathological vascular permeability.
JA - Mol Cell Proteomics
VL - 14
CP - 3
M3 - 10.1074/mcp.M114.045575
ER -
TY - JOUR
T1 - Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions.
JF - BMC Genomics
Y1 - 2015
A1 - Dillon, Laura A L
A1 - Suresh, Rahul
A1 - Okrah, Kwame
A1 - Corrada Bravo, Hector
A1 - Mosser, David M
A1 - El-Sayed, Najib M
AB - BACKGROUND: Parasites of the genus Leishmania are the causative agents of leishmaniasis, a group of diseases that range in manifestations from skin lesions to fatal visceral disease. The life cycle of Leishmania parasites is split between its insect vector and its mammalian host, where it resides primarily inside of macrophages. Once intracellular, Leishmania parasites must evade or deactivate the host's innate and adaptive immune responses in order to survive and replicate.
RESULTS: We performed transcriptome profiling using RNA-seq to simultaneously identify global changes in murine macrophage and L. major gene expression as the parasite entered and persisted within murine macrophages during the first 72 h of an infection. Differential gene expression, pathway, and gene ontology analyses enabled us to identify modulations in host and parasite responses during an infection. The most substantial and dynamic gene expression responses by both macrophage and parasite were observed during early infection. Murine genes related to both pro- and anti-inflammatory immune responses and glycolysis were substantially upregulated and genes related to lipid metabolism, biogenesis, and Fc gamma receptor-mediated phagocytosis were downregulated. Upregulated parasite genes included those aimed at mitigating the effects of an oxidative response by the host immune system while downregulated genes were related to translation, cell signaling, fatty acid biosynthesis, and flagellum structure.
CONCLUSIONS: The gene expression patterns identified in this work yield signatures that characterize multiple developmental stages of L. major parasites and the coordinated response of Leishmania-infected macrophages in the real-time setting of a dual biological system. This comprehensive dataset offers a clearer and more sensitive picture of the interplay between host and parasite during intracellular infection, providing additional insights into how pathogens are able to evade host defenses and modulate the biological functions of the cell in order to survive in the mammalian environment.
VL - 16
CP - 1
M3 - 10.1186/s12864-015-2237-2
ER -
TY - Generic
T1 - Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.
Y1 - 2015
A1 - Dillon, Laura A L
A1 - Okrah, Kwame
A1 - Hughitt, V Keith
A1 - Suresh, Rahul
A1 - Li, Yuan
A1 - Fernandes, Maria Cecilia
A1 - Belew, A Trey
A1 - Corrada Bravo, Hector
A1 - Mosser, David M
A1 - El-Sayed, Najib M
AB - Protozoan parasites of the genus Leishmania are the etiological agents of leishmaniasis, a group of diseases with a worldwide incidence of 0.9-1.6 million cases per year. We used RNA-seq to conduct a high-resolution transcriptomic analysis of the global changes in gene expression and RNA processing events that occur as L. major transforms from non-infective procyclic promastigotes to infective metacyclic promastigotes. Careful statistical analysis across multiple biological replicates and the removal of batch effects provided a high quality framework for comprehensively analyzing differential gene expression and transcriptome remodeling in this pathogen as it acquires its infectivity. We also identified precise 5' and 3' UTR boundaries for a majority of Leishmania genes and detected widespread alternative trans-splicing and polyadenylation. An investigation of possible correlations between stage-specific preferential trans-splicing or polyadenylation sites and differentially expressed genes revealed a lack of systematic association, establishing that differences in expression levels cannot be attributed to stage-regulated alternative RNA processing. Our findings build on and improve existing expression datasets and provide a substantially more detailed view of L. major biology that will inform the field and potentially provide a stronger basis for drug discovery and vaccine development efforts.
JA - Nucleic Acids Res
VL - 43
CP - 14
M3 - 10.1093/nar/gkv656
ER -
TY - JOUR
T1 - Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923
JF - Genome announcements
Y1 - 2014
A1 - Treangen, Todd J
A1 - Maybank, Rosslyn A
A1 - Enke, Sana
A1 - Friss, Mary Beth
A1 - Diviak, Lynn F
A1 - Karaolis, David KR
A1 - Koren, Sergey
A1 - Ondov, Brian
A1 - Phillippy, Adam M
A1 - Bergman, Nicholas H
VL - 2
ER -
TY - JOUR
T1 - Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products
JF - BMC GenomicsBMC Genomics
Y1 - 2014
A1 - Almeida, Mathieu
A1 - Hebert, Agnes
A1 - Abraham, Anne-Laure
A1 - Rasmussen, Simon
A1 - Monnet, Christophe
A1 - Pons, Nicolas
A1 - Delbes, Celine
A1 - Loux, Valentin
A1 - Batto, Jean-Michel
A1 - Leonard, Pierre
A1 - Kennedy, Sean
A1 - Ehrlich, Stanislas
A1 - Pop, Mihai
A1 - Montel, Marie-Christine
A1 - Irlinger, Francoise
A1 - Renault, Pierre
AB - BACKGROUND:Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.RESULTS:We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.CONCLUSIONS:Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.
VL - 15
SN - 1471-2164
ER -
TY - JOUR
T1 - CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
JF - Nucleic Acids ResNucleic Acids ResNucleic Acids Res
Y1 - 2014
A1 - Plasschaert, R. N.
A1 - Vigneau, S.
A1 - Tempera, I.
A1 - Gupta, R.
A1 - Maksimoska, J.
A1 - Everett, L.
A1 - Davuluri, R.
A1 - Mamorstein, R.
A1 - Lieberman, P. M.
A1 - Schultz, D.
A1 - Sridhar Hannenhalli
A1 - Bartolomei, M. S.
KW - *Gene Expression Regulation
KW - *Regulatory Elements, Transcriptional
KW - Animals
KW - Binding Sites
KW - Cell Differentiation/*genetics
KW - Cells, Cultured
KW - Embryonic Stem Cells/cytology/*metabolism
KW - Mice
KW - Nucleotide Motifs
KW - Protein Binding
KW - Repressor Proteins/*metabolism
AB - CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18(th) position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site.
VL - 42
SN - 1362-4962 (Electronic)
0305-1048 (Linking)
N1 - Plasschaert, Robert N
Vigneau, Sebastien
Tempera, Italo
Gupta, Ravi
Maksimoska, Jasna
Everett, Logan
Davuluri, Ramana
Mamorstein, Ronen
Lieberman, Paul M
Schultz, David
Hannenhalli, Sridhar
Bartolomei, Marisa S
eng
K99AI099153/AI/NIAID NIH HHS/
P30 CA10815/CA/NCI NIH HHS/
R01 CA140652/CA/NCI NIH HHS/
R01-GM052880/GM/NIGMS NIH HHS/
R01CA140652/CA/NCI NIH HHS/
R01GM085226/GM/NIGMS NIH HHS/
R01HD042026/HD/NICHD NIH HHS/
T32GM008216/GM/NIGMS NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
England
2013/10/15 06:00
Nucleic Acids Res. 2014 Jan;42(2):774-89. doi: 10.1093/nar/gkt910. Epub 2013 Oct 10.
U2 - 3902912
J1 - Nucleic acids researchNucleic acids research
ER -
TY - Generic
T1 - Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.
Y1 - 2014
A1 - Pop, Mihai
A1 - Walker, Alan W
A1 - Paulson, Joseph
A1 - Lindsay, Brianna
A1 - Antonio, Martin
A1 - Hossain, M Anowar
A1 - Oundo, Joseph
A1 - Tamboura, Boubou
A1 - Mai, Volker
A1 - Astrovskaya, Irina
A1 - Corrada Bravo, Hector
A1 - Rance, Richard
A1 - Stares, Mark
A1 - Levine, Myron M
A1 - Panchalingam, Sandra
A1 - Kotloff, Karen
A1 - Ikumapayi, Usman N
A1 - Ebruke, Chinelo
A1 - Adeyemi, Mitchell
A1 - Ahmed, Dilruba
A1 - Ahmed, Firoz
A1 - Alam, Meer Taifur
A1 - Amin, Ruhul
A1 - Siddiqui, Sabbir
A1 - Ochieng, John B
A1 - Ouma, Emmanuel
A1 - Juma, Jane
A1 - Mailu, Euince
A1 - Omore, Richard
A1 - Morris, J Glenn
A1 - Breiman, Robert F
A1 - Saha, Debasish
A1 - Parkhill, Julian
A1 - Nataro, James P
A1 - Stine, O Colin
KW - Bangladesh
KW - Base Sequence
KW - Case-Control Studies
KW - Child, Preschool
KW - Diarrhea, Infantile
KW - Dysentery
KW - Feces
KW - Female
KW - Gambia
KW - HUMANS
KW - Infant
KW - Infant, Newborn
KW - Intestines
KW - Kenya
KW - Male
KW - Mali
KW - Microbiota
KW - Molecular Typing
KW - Poverty
KW - RNA, Bacterial
KW - RNA, Ribosomal, 16S
AB - BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.
RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.
CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.
JA - Genome Biol
VL - 15
CP - 6
M3 - 10.1186/gb-2014-15-6-r76
ER -
TY - Generic
T1 - Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations
Y1 - 2014
A1 - Eilam, O.
A1 - Zarecki, R.
A1 - Oberhardt, M.
A1 - Ursell, L. K.
A1 - Kupiec, M.
A1 - Knight, R.
A1 - Gophna, U.
A1 - Ruppin, E.
JA - mBio
VL - 5
UR - http://mbio.asm.org/cgi/doi/10.1128/mBio.01526-14
CP - 4
J1 - mBio
M3 - 10.1128/mBio.01526-14
ER -
TY - Generic
T1 - Correlated evolution of positions within mammalian cis elements
Y1 - 2013
A1 - R. Mukherjee
A1 - L. N. S. Singh
A1 - Evans, P.
A1 - Sridhar Hannenhalli
JA - Plos One
VL - 8
ER -
TY - Generic
T1 - Genomic analysis of sequence-dependent DNA curvature in Leishmania.
Y1 - 2013
A1 - Smircich, Pablo
A1 - Forteza, Diego
A1 - El-Sayed, Najib M
A1 - Garat, Beatriz
KW - Chromosome mapping
KW - Comparative Genomic Hybridization
KW - Computational Biology
KW - DNA, Protozoan
KW - Genome, Protozoan
KW - Genomics
KW - HUMANS
KW - Leishmania
KW - Nucleic Acid Conformation
AB - Leishmania major is a flagellated protozoan parasite of medical importance. Like other members of the Trypanosomatidae family, it possesses unique mechanisms of gene expression such as constitutive polycistronic transcription of directional gene clusters, gene amplification, mRNA trans-splicing, and extensive editing of mitochondrial transcripts. The molecular signals underlying most of these processes remain under investigation. In order to investigate the role of DNA secondary structure signals in gene expression, we carried out a genome-wide in silico analysis of the intrinsic DNA curvature. The L. major genome revealed a lower frequency of high intrinsic curvature regions as well as inter- and intra- chromosomal distribution heterogeneity, when compared to prokaryotic and eukaryotic organisms. Using a novel method aimed at detecting region-integrated intrinsic curvature (RIIC), high DNA curvature was found to be associated with regions implicated in transcription initiation. Those include divergent strand-switch regions between directional gene clusters and regions linked to markers of active transcription initiation such as acetylated H3 histone, TRF4 and SNAP50. These findings suggest a role for DNA curvature in transcription initiation in Leishmania supporting the relevance of DNA secondary structures signals.
JA - PLoS One
VL - 8
CP - 4
M3 - 10.1371/journal.pone.0063068
ER -
TY - JOUR
T1 - Functional genomics of trypanosomatids.
JF - Parasite Immunol
Y1 - 2012
A1 - Choi, J
A1 - El-Sayed, N M
KW - Animals
KW - Genome, Protozoan
KW - Genomics
KW - HUMANS
KW - Proteome
KW - Protozoan Proteins
KW - Transcriptome
KW - Trypanosomatina
AB - The decoding of the Tritryp reference genomes nearly 7 years ago provided a first peek into the biology of pathogenic trypanosomatids and a blueprint that has paved the way for genome-wide studies. Although 60-70% of the predicted protein coding genes in Trypanosoma brucei, Trypanosoma cruzi and Leishmania major remain unannotated, the functional genomics landscape is rapidly changing. Facilitated by the advent of next-generation sequencing technologies, improved structural and functional annotation and genes and their products are emerging. Information is also growing for the interactions between cellular components as transcriptomes, regulatory networks and metabolomes are characterized, ushering in a new era of systems biology. Simultaneously, the launch of comparative sequencing of multiple strains of kinetoplastids will finally lead to the investigation of a vast, yet to be explored, evolutionary and pathogenomic space.
VL - 34
CP - 2-3
M3 - 10.1111/j.1365-3024.2011.01347.x
ER -
TY - Generic
T1 - Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.
Y1 - 2012
A1 - Waisberg, Michael
A1 - Cerqueira, Gustavo C
A1 - Yager, Stephanie B
A1 - Francischetti, Ivo M B
A1 - Lu, Jinghua
A1 - Gera, Nidhi
A1 - Srinivasan, Prakash
A1 - Miura, Kazutoyo
A1 - Rada, Balazs
A1 - Lukszo, Jan
A1 - Barbian, Kent D
A1 - Leto, Thomas L
A1 - Porcella, Stephen F
A1 - Narum, David L
A1 - El-Sayed, Najib
A1 - Miller, Louis H
A1 - Pierce, Susan K
KW - Amino Acid Sequence
KW - Animals
KW - Calcium-Binding Proteins
KW - Chromatography, Gel
KW - Electrophoresis, Polyacrylamide Gel
KW - Enzyme-Linked Immunosorbent Assay
KW - HUMANS
KW - Merozoite Surface Protein 1
KW - Microscopy, Confocal
KW - Molecular Sequence Data
KW - Neoplasm Proteins
KW - Plasmodium falciparum
KW - Sequence Homology, Amino Acid
KW - Surface Plasmon Resonance
AB - The malaria parasite, Plasmodium falciparum, and the human immune system have coevolved to ensure that the parasite is not eliminated and reinfection is not resisted. This relationship is likely mediated through a myriad of host-parasite interactions, although surprisingly few such interactions have been identified. Here we show that the 33-kDa fragment of P. falciparum merozoite surface protein 1 (MSP1(33)), an abundant protein that is shed during red blood cell invasion, binds to the proinflammatory protein, S100P. MSP1(33) blocks S100P-induced NFκB activation in monocytes and chemotaxis in neutrophils. Remarkably, S100P binds to both dimorphic alleles of MSP1, estimated to have diverged >27 Mya, suggesting an ancient, conserved relationship between these parasite and host proteins that may serve to attenuate potentially damaging inflammatory responses.
JA - Proc Natl Acad Sci U S A
VL - 109
CP - 14
M3 - 10.1073/pnas.1202689109
ER -
TY - JOUR
T1 - Role of Shrimp Chitin in the Ecology of Toxigenic Vibrio cholerae and Cholera Transmission
JF - Frontiers in MicrobiologyFront MicrobiolFrontiers in MicrobiologyFront Microbiol
Y1 - 2012
A1 - Nahar, Shamsun
A1 - Sultana, Marzia
A1 - Naser, M. Niamul
A1 - Nair, Gopinath B.
A1 - Watanabe, Haruo
A1 - Ohnishi, Makoto
A1 - Yamamoto, Shouji
A1 - Endtz, Hubert
A1 - Cravioto, Alejandro
A1 - Sack, R. Bradley
A1 - Hasan, Nur A.
A1 - Sadique, Abdus
A1 - Huq, Anwar
A1 - Rita R. Colwell
A1 - Alam, Munirul
AB - Seasonal plankton blooms correlate with occurrence of cholera in Bangladesh, although the mechanism of how dormant Vibrio cholerae, enduring interepidemic period in biofilms and plankton, initiates seasonal cholera is not fully understood. In this study, laboratory microcosms prepared with estuarine Mathbaria water (MW) samples supported active growth of toxigenic V. cholerae O1 up to 7 weeks as opposed to 6 months when microcosms were supplemented with dehydrated shrimp chitin chips (CC) as the single source of nutrient. Bacterial counting and detection of wbe and ctxA genes were done employing culture, direct fluorescent antibody (DFA) assay, and multiplex-polymerase chain reaction methods. In MW microcosm, the aqueous phase became clear as the non-culturable cells settled, whereas the aqueous phase of the MW–CC microcosm became turbid from bacterial growth stimulated by chitin. Bacterial chitin degradation and biofilm formation proceeded from an initial steady state to a gradually declining bacterial culturable count. V. cholerae within the microenvironments of chitin and chitin-associated biofilms remained metabolically active even in a high acidic environment without losing either viability or virulence. It is concluded that the abundance of chitin that occurs during blooms plays an important role in the aquatic life cycle of V. cholerae and, ultimately, in the seasonal transmission of cholera.
VL - 2
SN - 1664-302X
ER -
TY - JOUR
T1 - Structure, function and diversity of the healthy human microbiome
JF - NatureNature
Y1 - 2012
A1 - Huttenhower, C.
A1 - Gevers, D.
A1 - Knight, R.
A1 - Abubucker, S.
A1 - Badger, J. H.
A1 - Chinwalla, A. T.
A1 - Creasy, H. H.
A1 - Earl, A. M.
A1 - Fitzgerald, M. G.
A1 - Fulton, R. S.
A1 - others,
VL - 486
ER -
TY - JOUR
T1 - Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
JF - Genome biology
Y1 - 2011
A1 - Enk, Jacob
A1 - Devault, Alison
A1 - Debruyne, Regis
A1 - King, Christine E
A1 - Todd Treangen
A1 - O'Rourke, Dennis
A1 - Salzberg, Steven L
A1 - Fisher, Daniel
A1 - MacPhee, Ross
A1 - Poinar, Hendrik
VL - 12
ER -
TY - Generic
T1 - Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization
Y1 - 2011
A1 - Korpal, Manav
A1 - Ell, Brian J
A1 - Buffa, Francesca M
A1 - Ibrahim, Toni
A1 - Blanco, Mario A
A1 - à-Terrassa, Toni
A1 - Mercatali, Laura
A1 - Khan, Zia
A1 - Goodarzi, Hani
A1 - Hua, Yuling
A1 - Wei, Yong
A1 - Hu, Guohong
A1 - Garcia, Benjamin A
A1 - Ragoussis, Jiannis
A1 - Amadori, Dino
A1 - Harris, Adrian L
A1 - Kang, Yibin
JA - Nature Medicine
VL - 17
UR - http://www.nature.com/doifinder/10.1038/nm.2401
CP - 9
J1 - Nat Med
M3 - 10.1038/nm.2401
ER -
TY - JOUR
T1 - Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.
JF - Nat Med
Y1 - 2011
A1 - Korpal, Manav
A1 - Ell, Brian J
A1 - Buffa, Francesca M
A1 - Ibrahim, Toni
A1 - Blanco, Mario A
A1 - Celià-Terrassa, Toni
A1 - Mercatali, Laura
A1 - Khan, Zia
A1 - Goodarzi, Hani
A1 - Hua, Yuling
A1 - Wei, Yong
A1 - Hu, Guohong
A1 - Garcia, Benjamin A
A1 - Ragoussis, Jiannis
A1 - Amadori, Dino
A1 - Harris, Adrian L
A1 - Kang, Yibin
KW - Animals
KW - Cadherins
KW - Cell Line, Tumor
KW - Female
KW - Gene Expression Profiling
KW - Gene Expression Regulation, Neoplastic
KW - HUMANS
KW - Mass Spectrometry
KW - Mice
KW - Mice, Inbred BALB C
KW - Microarray Analysis
KW - MicroRNAs
KW - Neoplasm Metastasis
KW - Statistics, Nonparametric
KW - Vesicular Transport Proteins
AB - Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin-dependent epithelial traits and Sec23a-mediated tumor cell secretome.
VL - 17
CP - 9
M3 - 10.1038/nm.2401
ER -
TY - JOUR
T1 - The genome and its implications.
JF - Adv Parasitol
Y1 - 2011
A1 - Teixeira, Santuza M
A1 - El-Sayed, Najib M
A1 - Araújo, Patrícia R
KW - Animals
KW - Antigens, Protozoan
KW - Chagas Disease
KW - Chromosomes
KW - Comparative Genomic Hybridization
KW - DNA, Protozoan
KW - Gene Expression Regulation
KW - Genetic Variation
KW - Genome, Protozoan
KW - Host-Parasite Interactions
KW - HUMANS
KW - Species Specificity
KW - Synteny
KW - Transcription, Genetic
KW - Transfection
KW - Trypanosoma cruzi
AB - Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.
VL - 75
M3 - 10.1016/B978-0-12-385863-4.00010-1
ER -
TY - JOUR
T1 - Identification of Schistosoma mansoni microRNAs.
JF - BMC Genomics
Y1 - 2011
A1 - Simões, Mariana C
A1 - Lee, Jonathan
A1 - Djikeng, Appolinaire
A1 - Cerqueira, Gustavo C
A1 - Zerlotini, Adhemar
A1 - da Silva-Pereira, Rosiane A
A1 - Dalby, Andrew R
A1 - LoVerde, Philip
A1 - El-Sayed, Najib M
A1 - Oliveira, Guilherme
KW - Animals
KW - Computational Biology
KW - Genome, Helminth
KW - MicroRNAs
KW - Schistosoma mansoni
AB - BACKGROUND: MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples.
RESULTS: Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni.
CONCLUSION: Evidence for the presence of miRNAs in S. mansoni is presented. The number of miRNAs detected by homology-based computational methods in S. mansoni is limited due to the lack of close relatives in the miRNA repository. In spite of this, the computational approach described here can likely be applied to the identification of pre-miRNA hairpins in other organisms. Construction and analysis of a small RNA library led to the experimental identification of 14 novel miRNAs from S. mansoni through a combination of molecular cloning, DNA sequencing and expression studies. Our results significantly expand the set of known miRNAs in multicellular parasites and provide a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites.
VL - 12
M3 - 10.1186/1471-2164-12-47
ER -
TY - JOUR
T1 - Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem
JF - Bangladesh Journal of MicrobiologyBangladesh Journal of Microbiology
Y1 - 2011
A1 - Hasan, Nur A.
A1 - Chowdhury, W. Bari
A1 - Rahim, Niaz
A1 - Sultana, Marzia
A1 - Shabnam, S. Antara
A1 - Mai, Volker
A1 - Ali, Afsar
A1 - Morris, Glen J.
A1 - Sack, R. Bradley
A1 - Huq, Anwar
A1 - Rita R. Colwell
A1 - Endtz, Hubert Ph
A1 - Cravioto, Alejandro
A1 - Alam, Munirul
AB - Bacterial numbers in surface water samples, collected randomly from six different water bodies, were estimated by acridine orange direct counting (AODC) and conventional culture-based heterotrophic plate counting (HPC). Bacterial genomic DNA was prepared from water samples by employing methods used for stool samples, including the population dynamics, were determined by primer extension of the 16S rDNA (V6/V8 region) using polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE), a metagenomic tool that is capable of separating unrelated DNAs based on the differences in their sequences and GC contents. The bacterial numbers in water samples ranged from 103 – 106 CFU/ mL for HPC and 104 – 107 cells/ mL for AODC, showing that a great majority of bacteria prevail as uncultivable which do not respond to culture methods that are used widely for tracking bacterial pathogens. The acridine orange-stained bacteria varied in sizes and shapes, and appeared either as planktonic (solitary) cells or as clusters of biofilms, showing the presence of diverse community under the epifluorescence microscope. The DGGE of the ca. 457 bp amplicons, as confirmed by agarose gel electrophoresis, produced bands that ranged in intensities and numbers from 18 to 31, with each band possibly indicating the presence of one or more closely related bacterial species. The enrichment of pathogenic bacteria in the aquatic ecosystem is known to precede the seasonal diarrhoeal outbreaks; therefore, bacterial community dynamics determined by Metagenomic 16S PCR-DGGE during pre-epidemic enrichment appears promising in predicting the upcoming diarrheal outbreaks.
VL - 27
SN - 1011-9981
ER -
TY - JOUR
T1 - Transcriptional Regulation Via TF-Modifying Enzymes: An Integrative Model-Based Analysis
JF - Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.
Y1 - 2011
A1 - Everett, Logan J.
A1 - Jensen, Shane T.
A1 - Sridhar Hannenhalli
AB - Transcription factor activity is largely regulated through post-translational modification. Here, we report the first integrative model of transcription that includes both interactions between transcription factors and promoters, and between transcription factors and modifying enzymes. Simulations indicate that our method is robust against noise. We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription.
VL - 39
SN - 0305-1048, 1362-4962
ER -
TY - JOUR
T1 - The Alveolate Perkinsus marinus: biological insights from EST gene discovery.
JF - BMC Genomics
Y1 - 2010
A1 - Joseph, Sandeep J
A1 - Fernández-Robledo, José A
A1 - Gardner, Malcolm J
A1 - El-Sayed, Najib M
A1 - Kuo, Chih-Horng
A1 - Schott, Eric J
A1 - Wang, Haiming
A1 - Kissinger, Jessica C
A1 - Vasta, Gerardo R
KW - Alveolata
KW - Animals
KW - Expressed Sequence Tags
KW - Ostreidae
KW - Phylogeny
AB - BACKGROUND: Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified as a member of the Perkinsozoa, a recently established phylum considered close to the ancestor of ciliates, dinoflagellates, and apicomplexans, and a key taxon for understanding unique adaptations (e.g. parasitism) within the Alveolata. Despite intense parasite pressure, no disease-resistant oysters have been identified and no effective therapies have been developed to date.
RESULTS: To gain insight into the biological basis of the parasite's virulence and pathogenesis mechanisms, and to identify genes encoding potential targets for intervention, we generated>31,000 5' expressed sequence tags (ESTs) derived from four trophozoite libraries generated from two P. marinus strains. Trimming and clustering of the sequence tags yielded 7,863 unique sequences, some of which carry a spliced leader. Similarity searches revealed that 55% of these had hits in protein sequence databases, of which 1,729 had their best hit with proteins from the chromalveolates (E-valueCONCLUSIONS: Our transcriptome analysis of P. marinus, the first for any member of the Perkinsozoa, contributes new insight into its biology and taxonomic position. It provides a very informative, albeit preliminary, glimpse into the expression of genes encoding functionally relevant proteins as potential targets for chemotherapy, and evidence for the presence of a relict plastid. Further, although P. marinus sequences display significant similarity to those from both apicomplexans and dinoflagellates, the presence of trans-spliced transcripts confirms the previously established affinities with the latter. The EST analysis reported herein, together with the recently completed sequence of the P. marinus genome and the development of transfection methodology, should result in improved intervention strategies against dermo disease.
VL - 11
M3 - 10.1186/1471-2164-11-228
ER -
TY - CHAP
T1 - Genetics of Trypanosoma cruzi in American Trypanosomiasis: Chagas Disease One hundred Years of Research
Y1 - 2010
A1 - Bartholomeu, D.
A1 - Buck, G.
A1 - Teixeira, S.
A1 - El-Sayed, N.M.
PB - Elsevier Press
CY - Burlington
ER -
TY - JOUR
T1 - Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans.
JF - PLoS Genet
Y1 - 2010
A1 - Severance, Scott
A1 - Rajagopal, Abbhirami
A1 - Rao, Anita U
A1 - Cerqueira, Gustavo C
A1 - Mitreva, Makedonka
A1 - El-Sayed, Najib M
A1 - Krause, Michael
A1 - Hamza, Iqbal
KW - Animals
KW - Caenorhabditis elegans
KW - Dose-Response Relationship, Drug
KW - Gene Expression Profiling
KW - Gene Expression Regulation
KW - genes
KW - Genome-Wide Association Study
KW - Heme
KW - Homeostasis
KW - HUMANS
KW - Leishmania
KW - Nematoda
KW - Trypanosoma
AB - Heme is a cofactor in proteins that function in almost all sub-cellular compartments and in many diverse biological processes. Heme is produced by a conserved biosynthetic pathway that is highly regulated to prevent the accumulation of heme--a cytotoxic, hydrophobic tetrapyrrole. Caenorhabditis elegans and related parasitic nematodes do not synthesize heme, but instead require environmental heme to grow and develop. Heme homeostasis in these auxotrophs is, therefore, regulated in accordance with available dietary heme. We have capitalized on this auxotrophy in C. elegans to study gene expression changes associated with precisely controlled dietary heme concentrations. RNA was isolated from cultures containing 4, 20, or 500 microM heme; derived cDNA probes were hybridized to Affymetrix C. elegans expression arrays. We identified 288 heme-responsive genes (hrgs) that were differentially expressed under these conditions. Of these genes, 42% had putative homologs in humans, while genomes of medically relevant heme auxotrophs revealed homologs for 12% in both Trypanosoma and Leishmania and 24% in parasitic nematodes. Depletion of each of the 288 hrgs by RNA-mediated interference (RNAi) in a transgenic heme-sensor worm strain identified six genes that regulated heme homeostasis. In addition, seven membrane-spanning transporters involved in heme uptake were identified by RNAi knockdown studies using a toxic heme analog. Comparison of genes that were positive in both of the RNAi screens resulted in the identification of three genes in common that were vital for organismal heme homeostasis in C. elegans. Collectively, our results provide a catalog of genes that are essential for metazoan heme homeostasis and demonstrate the power of C. elegans as a genetic animal model to dissect the regulatory circuits which mediate heme trafficking in both vertebrate hosts and their parasites, which depend on environmental heme for survival.
VL - 6
CP - 7
M3 - 10.1371/journal.pgen.1001044
ER -
TY - JOUR
T1 - Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation
JF - Developmental CellDevelopmental Cell
Y1 - 2010
A1 - Trivedi, Chinmay M.
A1 - Zhu, Wenting
A1 - Wang, Qiaohong
A1 - Jia, Cheng
A1 - Kee, Hae Jin
A1 - Li, Li
A1 - Sridhar Hannenhalli
A1 - Epstein, Jonathan A.
AB - SummaryRegulation of chromatin structure via histone modification has recently received intense attention. Here, we demonstrate that the chromatin-modifying enzyme histone deacetylase 2 (Hdac2) functions with a small homeodomain factor, Hopx, to mediate deacetylation of Gata4, which is expressed by cardiac progenitor cells and plays critical roles in the regulation of cardiogenesis. In the absence of Hopx and Hdac2 in mouse embryos, Gata4 hyperacetylation is associated with a marked increase in cardiac myocyte proliferation, upregulation of Gata4 target genes, and perinatal lethality. Hdac2 physically interacts with Gata4, and this interaction is stabilized by Hopx. The ability of Gata4 to transactivate cell cycle genes is impaired by Hopx/Hdac2-mediated deacetylation, and this effect is abrogated by loss of Hdac2-Gata4 interaction. These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development.
VL - 19
SN - 1534-5807
ER -
TY - JOUR
T1 - Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
JF - Algorithms for Molecular BiologyAlgorithms for Molecular Biology
Y1 - 2010
A1 - Hansen, Matthew
A1 - Everett, Logan
A1 - Singh, Larry
A1 - Sridhar Hannenhalli
AB - Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation.
VL - 5
SN - 1748-7188
ER -
TY - JOUR
T1 - A model for using a concept inventory as a tool for students' assessment and faculty professional development.
JF - CBE Life Sci Educ
Y1 - 2010
A1 - Marbach-Ad, Gili
A1 - McAdams, Katherine C
A1 - Benson, Spencer
A1 - Briken, Volker
A1 - Cathcart, Laura
A1 - Chase, Michael
A1 - El-Sayed, Najib M
A1 - Frauwirth, Kenneth
A1 - Fredericksen, Brenda
A1 - Joseph, Sam W
A1 - Lee, Vincent
A1 - McIver, Kevin S
A1 - Mosser, David
A1 - Quimby, B Booth
A1 - Shields, Patricia
A1 - Song, Wenxia
A1 - Stein, Daniel C
A1 - Stewart, Richard
A1 - Thompson, Katerina V
A1 - Smith, Ann C
KW - Curriculum
KW - Faculty
KW - Models, Theoretical
KW - Research
KW - Students
KW - Teaching
AB - This essay describes how the use of a concept inventory has enhanced professional development and curriculum reform efforts of a faculty teaching community. The Host Pathogen Interactions (HPI) teaching team is composed of research and teaching faculty with expertise in HPI who share the goal of improving the learning experience of students in nine linked undergraduate microbiology courses. To support evidence-based curriculum reform, we administered our HPI Concept Inventory as a pre- and postsurvey to approximately 400 students each year since 2006. The resulting data include student scores as well as their open-ended explanations for distractor choices. The data have enabled us to address curriculum reform goals of 1) reconciling student learning with our expectations, 2) correlating student learning with background variables, 3) understanding student learning across institutions, 4) measuring the effect of teaching techniques on student learning, and 5) demonstrating how our courses collectively form a learning progression. The analysis of the concept inventory data has anchored and deepened the team's discussions of student learning. Reading and discussing students' responses revealed the gap between our understanding and the students' understanding. We provide evidence to support the concept inventory as a tool for assessing student understanding of HPI concepts and faculty development.
VL - 9
CP - 4
M3 - 10.1187/cbe.10-05-0069
ER -
TY - JOUR
T1 - Regulating the regulators: modulators of transcription factor activity
JF - Methods Mol. BiolMethods Mol. Biol
Y1 - 2010
A1 - Everett, L.
A1 - Hansen, M.
A1 - Sridhar Hannenhalli
PB - Springer
VL - 674
ER -
TY - JOUR
T1 - Assessing Student Understanding of Host Pathogen Interactions Using a Concept Inventory
JF - J. Microbiol. Biol. Ed.
Y1 - 2009
A1 - Marbach-Ad, G.
A1 - Briken, V.
A1 - El-Sayed, N.M.
A1 - Frauwirth, K.
A1 - Fredericksen, B.
A1 - Hutcheson, S.
A1 - Gao, L.-Y.
A1 - Joseph, S.
A1 - Lee, V.
A1 - McIver, K.S.
A1 - Mosser, D.
A1 - Quimby, B.B.
A1 - Shields, P.
A1 - Song, W.
A1 - Stein, D.C.
A1 - Yuan, R.T.
A1 - Smith, A.C.
VL - 10
ER -
TY - JOUR
T1 - CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features
JF - Genome BiologyGenome Biology
Y1 - 2009
A1 - Essien, Kobby
A1 - Vigneau, Sebastien
A1 - Apreleva, Sofia
A1 - Singh, Larry N.
A1 - Bartolomei, Marisa S.
A1 - Sridhar Hannenhalli
AB - CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role.
VL - 10
SN - 1465-6906
ER -
TY - JOUR
T1 - Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming
JF - J Mach Learn Res
Y1 - 2009
A1 - Corrada Bravo, Hector
A1 - Wright, Stephen
A1 - Eng, Kevin H.
A1 - Keles, Sündüz
A1 - Wahba, Grace
VL - 5
ER -
TY - JOUR
T1 - Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development
JF - Sci Transl MedSci Transl Med
Y1 - 2009
A1 - Takala, S. L.
A1 - Coulibaly, D.
A1 - Thera, M. A.
A1 - Batchelor, A. H.
A1 - Michael P. Cummings
A1 - Escalante, A. A.
A1 - Ouattara, A.
A1 - Traoré, K.
A1 - Niangaly, A.
A1 - Djimdé, A. A.
A1 - Doumbo, O. K.
A1 - Plowe, C. V.
AB - Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine.
VL - 1
ER -
TY - JOUR
T1 - The genome of the blood fluke Schistosoma mansoni.
JF - Nature
Y1 - 2009
A1 - Berriman, Matthew
A1 - Haas, Brian J
A1 - LoVerde, Philip T
A1 - Wilson, R Alan
A1 - Dillon, Gary P
A1 - Cerqueira, Gustavo C
A1 - Mashiyama, Susan T
A1 - Al-Lazikani, Bissan
A1 - Andrade, Luiza F
A1 - Ashton, Peter D
A1 - Aslett, Martin A
A1 - Bartholomeu, Daniella C
A1 - Blandin, Gaëlle
A1 - Caffrey, Conor R
A1 - Coghlan, Avril
A1 - Coulson, Richard
A1 - Day, Tim A
A1 - Delcher, Art
A1 - DeMarco, Ricardo
A1 - Djikeng, Appolinaire
A1 - Eyre, Tina
A1 - Gamble, John A
A1 - Ghedin, Elodie
A1 - Gu, Yong
A1 - Hertz-Fowler, Christiane
A1 - Hirai, Hirohisha
A1 - Hirai, Yuriko
A1 - Houston, Robin
A1 - Ivens, Alasdair
A1 - Johnston, David A
A1 - Lacerda, Daniela
A1 - Macedo, Camila D
A1 - McVeigh, Paul
A1 - Ning, Zemin
A1 - Oliveira, Guilherme
A1 - Overington, John P
A1 - Parkhill, Julian
A1 - Pertea, Mihaela
A1 - Pierce, Raymond J
A1 - Protasio, Anna V
A1 - Quail, Michael A
A1 - Rajandream, Marie-Adèle
A1 - Rogers, Jane
A1 - Sajid, Mohammed
A1 - Salzberg, Steven L
A1 - Stanke, Mario
A1 - Tivey, Adrian R
A1 - White, Owen
A1 - Williams, David L
A1 - Wortman, Jennifer
A1 - Wu, Wenjie
A1 - Zamanian, Mostafa
A1 - Zerlotini, Adhemar
A1 - Fraser-Liggett, Claire M
A1 - Barrell, Barclay G
A1 - El-Sayed, Najib M
KW - Animals
KW - Biological Evolution
KW - Exons
KW - Genes, Helminth
KW - Genome, Helminth
KW - Host-Parasite Interactions
KW - Introns
KW - Molecular Sequence Data
KW - Physical Chromosome Mapping
KW - Schistosoma mansoni
KW - Schistosomiasis mansoni
AB - Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
VL - 460
CP - 7253
M3 - 10.1038/nature08160
ER -
TY - JOUR
T1 - Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi.
JF - Nucleic Acids Res
Y1 - 2009
A1 - Bartholomeu, Daniella C
A1 - Cerqueira, Gustavo C
A1 - Leão, Ana Carolina A
A1 - daRocha, Wanderson D
A1 - Pais, Fabiano S
A1 - Macedo, Camila
A1 - Djikeng, Appolinaire
A1 - Teixeira, Santuza M R
A1 - El-Sayed, Najib M
KW - 3' Flanking Region
KW - 5' Flanking Region
KW - Amino Acid Sequence
KW - Animals
KW - Base Sequence
KW - Conserved Sequence
KW - Gene Expression Profiling
KW - Genes, Protozoan
KW - Genome, Protozoan
KW - Membrane Proteins
KW - Molecular Sequence Data
KW - Mucins
KW - Multigene Family
KW - Protozoan Proteins
KW - RNA, Messenger
KW - Trypanosoma cruzi
AB - A novel large multigene family was recently identified in the human pathogen Trypanosoma cruzi, causative agent of Chagas disease, and corresponds to approximately 6% of the parasite diploid genome. The predicted gene products, mucin-associated surface proteins (MASPs), are characterized by highly conserved N- and C-terminal domains and a strikingly variable and repetitive central region. We report here an analysis of the genomic organization and expression profile of masp genes. Masps are not randomly distributed throughout the genome but instead are clustered with genes encoding mucin and other surface protein families. Masp transcripts vary in size, are preferentially expressed during the trypomastigote stage and contain highly conserved 5' and 3' untranslated regions. A sequence analysis of a trypomastigote cDNA library reveals the expression of multiple masp variants with a bias towards a particular masp subgroup. Immunofluorescence assays using antibodies generated against a MASP peptide reveals that the expression of particular MASPs at the cell membrane is limited to subsets of the parasite population. Western blots of phosphatidylinositol-specific phospholipase C (PI-PLC)-treated parasites suggest that MASP may be GPI-anchored and shed into the medium culture, thus contributing to the large repertoire of parasite polypeptides that are exposed to the host immune system.
VL - 37
CP - 10
M3 - 10.1093/nar/gkp172
ER -
TY - JOUR
T1 - Mimosa: mixture model of co-expression to detect modulators of regulatory interaction
JF - Algorithms in BioinformaticsAlgorithms in Bioinformatics
Y1 - 2009
A1 - Hansen, M.
A1 - Everett, L.
A1 - Singh, L.
A1 - Sridhar Hannenhalli
PB - Springer Berlin/Heidelberg
ER -
TY - JOUR
T1 - A phylogenetic mixture model for the evolution of gene expression
JF - Molecular biology and evolutionMolecular biology and evolution
Y1 - 2009
A1 - Eng, K. H.
A1 - Héctor Corrada Bravo
A1 - Keles, S.
VL - 26
ER -
TY - JOUR
T1 - PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
JF - Nucleic acids researchNucleic Acids Research
Y1 - 2009
A1 - Everett, L.
A1 - Vo, A.
A1 - Sridhar Hannenhalli
PB - Oxford Univ Press
VL - 37
ER -
TY - CHAP
T1 - Salient Frame Detection for Molecular Dynamics Simulations
T2 - Scientific VisualizationScientific Visualization
Y1 - 2009
A1 - Kim, Youngmin
A1 - Patro, Robert
A1 - Ip, Cheuk Yiu
A1 - O'Leary, Dianne P.
A1 - Anishkin, Andriy
A1 - Sukharev, Sergei
A1 - Varshney, Amitabh
ED - Ebert, D. S.
ED - Gr,
ED - x6f,
ED - x,
ED - ller, E.
ED - Hagen, H.
ED - Kaufman, A.
JA - Scientific VisualizationScientific Visualization
PB - Dagstuhl Seminar Proceedings 09251
ER -
TY - JOUR
T1 - Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh
JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.
Y1 - 2009
A1 - Alam, Munirul
A1 - Chowdhury, Wasimul B.
A1 - Bhuiyan, N. A.
A1 - Islam, Atiqul
A1 - Hasan, Nur A.
A1 - Nair, G. Balakrish
A1 - Watanabe, H.
A1 - Siddique, A. K.
A1 - Huq, Anwar
A1 - Sack, R. Bradley
A1 - Akhter, M. Z.
A1 - Grim, Christopher J.
A1 - Kam, K. M.
A1 - Luey, C. K. Y.
A1 - Endtz, Hubert P.
A1 - Cravioto, Alejandro
A1 - Rita R. Colwell
AB - Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., “clonal cluster,” as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.
VL - 75
SN - 0099-2240, 1098-5336
ER -
TY - JOUR
T1 - Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study
JF - BMC Evol BiolBMC Evol Biol
Y1 - 2009
A1 - Regier, J. C.
A1 - Zwick, A.
A1 - Michael P. Cummings
A1 - Kawahara, A. Y.
A1 - Cho, S.
A1 - Weller, S.
A1 - Roe, A.
A1 - Baixeras, J.
A1 - Brown, J. W.
A1 - Parr, C.
A1 - Davis, D. R.
A1 - Epstein, M.
A1 - Hallwachs, W.
A1 - Hausmann, A.
A1 - Janzen, D. H.
A1 - Kitching, I. J.
A1 - Solis, M. A.
A1 - Yen, S. H.
A1 - Adam L. Bazinet
A1 - Mitter, C.
AB - BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.
VL - 9
ER -
TY - JOUR
T1 - Computational Analysis of Constraints on Noncoding Regions, Coding Regions and Gene Expression in Relation to Plasmodium Phenotypic Diversity
JF - PLoS ONEPLoS ONEPLoS ONEPLoS ONE
Y1 - 2008
A1 - Essien, Kobby
A1 - Sridhar Hannenhalli
A1 - Stoeckert, Christian J.
AB - Malaria-causing Plasmodium species exhibit marked differences including host choice and preference for invading particular cell types. The genetic bases of phenotypic differences between parasites can be understood, in part, by investigating constraints on gene expression and genic sequences, both coding and regulatory.We investigated the evolutionary constraints on sequence and expression of parasitic genes by applying comparative genomics approaches to 6 Plasmodium genomes and 2 genome-wide expression studies. We found that the coding regions of Plasmodium transcription factor and sexual development genes are relatively less constrained, as are those of genes encoding CCCH zinc fingers and invasion proteins, which all play important roles in these parasites. Transcription factors and genes with stage-restricted expression have conserved upstream regions and so do several gene classes critical to the parasite's lifestyle, namely, ion transport, invasion, chromatin assembly and CCCH zinc fingers. Additionally, a cross-species comparison of expression patterns revealed that Plasmodium-specific genes exhibit significant expression divergence. Overall, constraints on Plasmodium's protein coding regions confirm observations from other eukaryotes in that transcription factors are under relatively lower constraint. Proteins relevant to the parasite's unique lifestyle also have lower constraint on their coding regions. Greater conservation between Plasmodium species in terms of promoter motifs suggests tight regulatory control of lifestyle genes. However, an interspecies divergence in expression patterns of these genes suggests that either expression is controlled via genomic or epigenomic features not encoded in the proximal promoter sequence, or alternatively, the combinatorial interactions between motifs confer species-specific expression patterns.
VL - 3
ER -
TY - JOUR
T1 - The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
JF - Nature
Y1 - 2008
A1 - Ming, Ray
A1 - Hou, Shaobin
A1 - Feng, Yun
A1 - Yu, Qingyi
A1 - Dionne-Laporte, Alexandre
A1 - Saw, Jimmy H
A1 - Senin, Pavel
A1 - Wang, Wei
A1 - Ly, Benjamin V
A1 - Lewis, Kanako L T
A1 - Salzberg, Steven L
A1 - Feng, Lu
A1 - Jones, Meghan R
A1 - Skelton, Rachel L
A1 - Murray, Jan E
A1 - Chen, Cuixia
A1 - Qian, Wubin
A1 - Shen, Junguo
A1 - Du, Peng
A1 - Eustice, Moriah
A1 - Tong, Eric
A1 - Tang, Haibao
A1 - Lyons, Eric
A1 - Paull, Robert E
A1 - Michael, Todd P
A1 - Wall, Kerr
A1 - Rice, Danny W
A1 - Albert, Henrik
A1 - Wang, Ming-Li
A1 - Zhu, Yun J
A1 - Schatz, Michael
A1 - Nagarajan, Niranjan
A1 - Acob, Ricelle A
A1 - Guan, Peizhu
A1 - Blas, Andrea
A1 - Wai, Ching Man
A1 - Ackerman, Christine M
A1 - Ren, Yan
A1 - Liu, Chao
A1 - Wang, Jianmei
A1 - Wang, Jianping
A1 - Na, Jong-Kuk
A1 - Shakirov, Eugene V
A1 - Haas, Brian
A1 - Thimmapuram, Jyothi
A1 - Nelson, David
A1 - Wang, Xiyin
A1 - Bowers, John E
A1 - Gschwend, Andrea R
A1 - Delcher, Arthur L
A1 - Singh, Ratnesh
A1 - Suzuki, Jon Y
A1 - Tripathi, Savarni
A1 - Neupane, Kabi
A1 - Wei, Hairong
A1 - Irikura, Beth
A1 - Paidi, Maya
A1 - Jiang, Ning
A1 - Zhang, Wenli
A1 - Presting, Gernot
A1 - Windsor, Aaron
A1 - Navajas-Pérez, Rafael
A1 - Torres, Manuel J
A1 - Feltus, F Alex
A1 - Porter, Brad
A1 - Li, Yingjun
A1 - Burroughs, A Max
A1 - Luo, Ming-Cheng
A1 - Liu, Lei
A1 - Christopher, David A
A1 - Mount, Stephen M
A1 - Moore, Paul H
A1 - Sugimura, Tak
A1 - Jiang, Jiming
A1 - Schuler, Mary A
A1 - Friedman, Vikki
A1 - Mitchell-Olds, Thomas
A1 - Shippen, Dorothy E
A1 - dePamphilis, Claude W
A1 - Palmer, Jeffrey D
A1 - Freeling, Michael
A1 - Paterson, Andrew H
A1 - Gonsalves, Dennis
A1 - Wang, Lei
A1 - Alam, Maqsudul
KW - Arabidopsis
KW - Carica
KW - Contig Mapping
KW - Databases, Genetic
KW - Genes, Plant
KW - Genome, Plant
KW - Molecular Sequence Data
KW - Plants, Genetically Modified
KW - sequence alignment
KW - Sequence Analysis, DNA
KW - Transcription Factors
KW - Tropical Climate
AB - Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.
VL - 452
CP - 7190
M3 - 10.1038/nature06856
ER -
TY - RPRT
T1 - Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression
Y1 - 2008
A1 - Héctor Corrada Bravo
A1 - Eng, K. H.
A1 - Keles, S.
A1 - Wahba, G.
A1 - Wright, S.
AB - We present a novel method for estimating tree-structured covariance matrices directly fromobserved continuous data. A representation of these classes of matrices as linear combinations of rank-one matrices indicating object partitions is used to formulate estimation as instances of well-studied numerical optimization problems. In particular, we present estimation based on projection where the covariance estimate is the nearest tree-structured covariance matrix to an observed sample covariance matrix. The problem is posed as a linear or quadratic mixed-integer program (MIP) where a setting of the integer variables in the MIP specifies a set of tree topologies of the structured covariance matrix. We solve these problems to optimality using efficient and robust existing MIP solvers. We also show that the least squares distance method of Fitch and Margoliash (1967) can be formulated as a quadratic MIP and thus solved exactly using existing, robust branch-and-bound MIP solvers. Our motivation for this method is the discovery of phylogenetic structure directly from gene expression data. Recent studies have adapted traditional phylogenetic comparative anal- ysis methods to expression data. Typically, these methods first estimate a phylogenetic tree from genomic sequence data and subsequently analyze expression data. A covariance matrix constructed from the sequence-derived tree is used to correct for the lack of independence in phy- logenetically related taxa. However, recent results have shown that the hierarchical structure of sequence-derived tree estimates are highly sensitive to the genomic region chosen to build them. To circumvent this difficulty, we propose a stable method for deriving tree-structured covariance matrices directly from gene expression as an exploratory step that can guide investigators in their modelling choices for these types of comparative analysis. We present a case study in phylogenetic analysis of expression in yeast gene families. Our method is able to corroborate the presence of phylogenetic structure in the response of expression in a subset of the gene families under particular experimental conditions. Additionally, when used in conjunction with transcription factor occupancy data, our methods show that alternative modelling choices should be considered when creating sequence-derived trees for this comparative analysis.
PB - Department of Statistics, University of Wisconsin
VL - 1142
ER -
TY - JOUR
T1 - The minimum information about a genome sequence (MIGS) specification
JF - Nature biotechnologyNature biotechnology
Y1 - 2008
A1 - Field, Dawn
A1 - Garrity, George
A1 - Gray, Tanya
A1 - Morrison, Norman
A1 - J. Selengut
A1 - Sterk, Peter
A1 - Tatusova, Tatiana
A1 - Thomson, Nicholas
A1 - Allen, Michael J.
A1 - Angiuoli, Samuel V.
A1 - Ashburner, Michael
A1 - Axelrod, Nelson
A1 - Baldauf, Sandra
A1 - Ballard, Stuart
A1 - Boore, Jeffrey
A1 - Cochrane, Guy
A1 - Cole, James
A1 - Dawyndt, Peter
A1 - De Vos, Paul
A1 - DePamphilis, Claude
A1 - Edwards, Robert
A1 - Faruque, Nadeem
A1 - Feldman, Robert
A1 - Gilbert, Jack
A1 - Gilna, Paul
A1 - Glöckner, Frank Oliver
A1 - Goldstein, Philip
A1 - Guralnick, Robert
A1 - Haft, Dan
A1 - Hancock, David
A1 - Hermjakob, Henning
A1 - Hertz-Fowler, Christiane
A1 - Hugenholtz, Phil
A1 - Joint, Ian
A1 - Kagan, Leonid
A1 - Kane, Matthew
A1 - Kennedy, Jessie
A1 - Kowalchuk, George
A1 - Kottmann, Renzo
A1 - Kolker, Eugene
A1 - Kravitz, Saul
A1 - Kyrpides, Nikos
A1 - Leebens-Mack, Jim
A1 - Lewis, Suzanna E.
A1 - Li, Kelvin
A1 - Lister, Allyson L.
A1 - Lord, Phillip
A1 - Maltsev, Natalia
A1 - Markowitz, Victor
A1 - Martiny, Jennifer
A1 - Methe, Barbara
A1 - Mizrachi, Ilene
A1 - Moxon, Richard
A1 - Nelson, Karen
A1 - Parkhill, Julian
A1 - Proctor, Lita
A1 - White, Owen
A1 - Sansone, Susanna-Assunta
A1 - Spiers, Andrew
A1 - Stevens, Robert
A1 - Swift, Paul
A1 - Taylor, Chris
A1 - Tateno, Yoshio
A1 - Tett, Adrian
A1 - Turner, Sarah
A1 - Ussery, David
A1 - Vaughan, Bob
A1 - Ward, Naomi
A1 - Whetzel, Trish
A1 - San Gil, Ingio
A1 - Wilson, Gareth
A1 - Wipat, Anil
KW - Chromosome mapping
KW - Databases, Factual
KW - information dissemination
KW - Information Storage and Retrieval
KW - Information Theory
KW - Internationality
AB - With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
VL - 26
N1 - http://www.ncbi.nlm.nih.gov/pubmed/18464787?dopt=Abstract
ER -
TY - JOUR
T1 - Role of transposable elements in trypanosomatids
JF - Microbes and InfectionMicrobes and Infection
Y1 - 2008
A1 - Bringaud, Frederic
A1 - Ghedin, Elodie
A1 - Najib M. El‐Sayed
A1 - Papadopoulou, Barbara
KW - Cellular function
KW - Domestication
KW - Evolution
KW - Gene expression
KW - Leishmania
KW - Regulation of mRNA stability
KW - Retroposon
KW - Transposable element
KW - Trypanosoma
AB - Transposable elements constitute 2-5% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.
VL - 10
SN - 1286-4579
ER -
TY - JOUR
T1 - Schistosoma mansoni: Microarray analysis of gene expression induced by host sex.
JF - Exp Parasitol
Y1 - 2008
A1 - Waisberg, M
A1 - Lobo, F P
A1 - Cerqueira, G C
A1 - Passos, L K J
A1 - Carvalho, O S
A1 - El-Sayed, N M
A1 - Franco, G R
KW - Animals
KW - Biomphalaria
KW - Female
KW - Gene expression
KW - Host-Parasite Interactions
KW - Male
KW - Mice
KW - Oligonucleotide Array Sequence Analysis
KW - Reverse Transcriptase Polymerase Chain Reaction
KW - RNA, Helminth
KW - Schistosoma mansoni
KW - Schistosomiasis mansoni
KW - Sex Factors
AB - Schistosoma mansoni is a digenetic trematode and a human parasite responsible for high social and economic impact. Although some authors have studied the effect of host hormones on parasites, not much is known about the effects of host sex on gene expression in Schistosomes. In order to study gene transcripts associated with the host sex, we compared the gene expression profiles of both male and female unisexual adult S. mansoni parasites raised on either male or female hosts, using DNA microarrays. Our results show that host sex caused differential expression of at least 11 genes in female parasites and of 134 in male parasites. Of the differentially expressed genes in female worms, 10 were preferentially expressed in female worms from male mice, while of the 134 differentially expressed genes in male parasites, 79 (59%) were preferentially expressed in worms from female mice. Further investigation of the role of each of those genes will help understand better their importance in the pathogenesis of Schistosomiasis.
VL - 120
CP - 4
M3 - 10.1016/j.exppara.2008.09.005
ER -
TY - JOUR
T1 - Sequence diversity and evolution of multigene families in Trypanosoma cruzi
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 2008
A1 - Cerqueira, Gustavo C.
A1 - Bartholomeu, Daniella C.
A1 - DaRocha, Wanderson D.
A1 - Hou, Lihua
A1 - Freitas-Silva, Danielle M.
A1 - Machado, Carlos Renato
A1 - Najib M. El‐Sayed
A1 - Teixeira, Santuza M. R.
KW - Amastin
KW - Gene conversion
KW - Genetic diversity
KW - Multigene families
KW - Trypanosoma cruzi
AB - Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.
VL - 157
SN - 0166-6851
ER -
TY - JOUR
T1 - Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei
JF - Parasitology researchParasitology research
Y1 - 2007
A1 - Djikeng, A.
A1 - Raverdy, S.
A1 - Foster, Jeffrey S.
A1 - Bartholomeu, D.
A1 - Zhang, Y.
A1 - Najib M. El‐Sayed
A1 - Carlow, C.
VL - 100
ER -
TY - JOUR
T1 - Evolution of genes and genomes on the Drosophila phylogeny
JF - NatureNature
Y1 - 2007
A1 - Clark, Andrew G.
A1 - Eisen, Michael B.
A1 - Smith, Douglas R.
A1 - Bergman, Casey M.
A1 - Oliver, Brian
A1 - Markow, Therese A.
A1 - Kaufman, Thomas C.
A1 - Kellis, Manolis
A1 - Gelbart, William
A1 - Iyer, Venky N.
A1 - Pollard, Daniel A.
A1 - Sackton, Timothy B.
A1 - Larracuente, Amanda M.
A1 - Singh, Nadia D.
A1 - Abad, Jose P.
A1 - Abt, Dawn N.
A1 - Adryan, Boris
A1 - Aguade, Montserrat
A1 - Akashi, Hiroshi
A1 - Anderson, Wyatt W.
A1 - Aquadro, Charles F.
A1 - Ardell, David H.
A1 - Arguello, Roman
A1 - Artieri, Carlo G.
A1 - Barbash, Daniel A.
A1 - Barker, Daniel
A1 - Barsanti, Paolo
A1 - Batterham, Phil
A1 - Batzoglou, Serafim
A1 - Begun, Dave
A1 - Bhutkar, Arjun
A1 - Blanco, Enrico
A1 - Bosak, Stephanie A.
A1 - Bradley, Robert K.
A1 - Brand, Adrianne D.
A1 - Brent, Michael R.
A1 - Brooks, Angela N.
A1 - Brown, Randall H.
A1 - Butlin, Roger K.
A1 - Caggese, Corrado
A1 - Calvi, Brian R.
A1 - Carvalho, A. Bernardo de
A1 - Caspi, Anat
A1 - Castrezana, Sergio
A1 - Celniker, Susan E.
A1 - Chang, Jean L.
A1 - Chapple, Charles
A1 - Chatterji, Sourav
A1 - Chinwalla, Asif
A1 - Civetta, Alberto
A1 - Clifton, Sandra W.
A1 - Comeron, Josep M.
A1 - Costello, James C.
A1 - Coyne, Jerry A.
A1 - Daub, Jennifer
A1 - David, Robert G.
A1 - Delcher, Arthur L.
A1 - Delehaunty, Kim
A1 - Do, Chuong B.
A1 - Ebling, Heather
A1 - Edwards, Kevin
A1 - Eickbush, Thomas
A1 - Evans, Jay D.
A1 - Filipski, Alan
A1 - Findei,
A1 - Sven
A1 - Freyhult, Eva
A1 - Fulton, Lucinda
A1 - Fulton, Robert
A1 - Garcia, Ana C. L.
A1 - Gardiner, Anastasia
A1 - Garfield, David A.
A1 - Garvin, Barry E.
A1 - Gibson, Greg
A1 - Gilbert, Don
A1 - Gnerre, Sante
A1 - Godfrey, Jennifer
A1 - Good, Robert
A1 - Gotea, Valer
A1 - Gravely, Brenton
A1 - Greenberg, Anthony J.
A1 - Griffiths-Jones, Sam
A1 - Gross, Samuel
A1 - Guigo, Roderic
A1 - Gustafson, Erik A.
A1 - Haerty, Wilfried
A1 - Hahn, Matthew W.
A1 - Halligan, Daniel L.
A1 - Halpern, Aaron L.
A1 - Halter, Gillian M.
A1 - Han, Mira V.
A1 - Heger, Andreas
A1 - Hillier, LaDeana
A1 - Hinrichs, Angie S.
A1 - Holmes, Ian
A1 - Hoskins, Roger A.
A1 - Hubisz, Melissa J.
A1 - Hultmark, Dan
A1 - Huntley, Melanie A.
A1 - Jaffe, David B.
A1 - Jagadeeshan, Santosh
A1 - Jeck, William R.
A1 - Johnson, Justin
A1 - Jones, Corbin D.
A1 - Jordan, William C.
A1 - Karpen, Gary H.
A1 - Kataoka, Eiko
A1 - Keightley, Peter D.
A1 - Kheradpour, Pouya
A1 - Kirkness, Ewen F.
A1 - Koerich, Leonardo B.
A1 - Kristiansen, Karsten
A1 - Kudrna, Dave
A1 - Kulathinal, Rob J.
A1 - Kumar, Sudhir
A1 - Kwok, Roberta
A1 - Lander, Eric
A1 - Langley, Charles H.
A1 - Lapoint, Richard
A1 - Lazzaro, Brian P.
A1 - Lee, So-Jeong
A1 - Levesque, Lisa
A1 - Li, Ruiqiang
A1 - Lin, Chiao-Feng
A1 - Lin, Michael F.
A1 - Lindblad-Toh, Kerstin
A1 - Llopart, Ana
A1 - Long, Manyuan
A1 - Low, Lloyd
A1 - Lozovsky, Elena
A1 - Lu, Jian
A1 - Luo, Meizhong
A1 - Machado, Carlos A.
A1 - Makalowski, Wojciech
A1 - Marzo, Mar
A1 - Matsuda, Muneo
A1 - Matzkin, Luciano
A1 - McAllister, Bryant
A1 - McBride, Carolyn S.
A1 - McKernan, Brendan
A1 - McKernan, Kevin
A1 - Mendez-Lago, Maria
A1 - Minx, Patrick
A1 - Mollenhauer, Michael U.
A1 - Montooth, Kristi
A1 - Stephen M. Mount
A1 - Mu, Xu
A1 - Myers, Eugene
A1 - Negre, Barbara
A1 - Newfeld, Stuart
A1 - Nielsen, Rasmus
A1 - Noor, Mohamed A. F.
A1 - O'Grady, Patrick
A1 - Pachter, Lior
A1 - Papaceit, Montserrat
A1 - Parisi, Matthew J.
A1 - Parisi, Michael
A1 - Parts, Leopold
A1 - Pedersen, Jakob S.
A1 - Pesole, Graziano
A1 - Phillippy, Adam M.
A1 - Ponting, Chris P.
A1 - M. Pop
A1 - Porcelli, Damiano
A1 - Powell, Jeffrey R.
A1 - Prohaska, Sonja
A1 - Pruitt, Kim
A1 - Puig, Marta
A1 - Quesneville, Hadi
A1 - Ram, Kristipati Ravi
A1 - Rand, David
A1 - Rasmussen, Matthew D.
A1 - Reed, Laura K.
A1 - Reenan, Robert
A1 - Reily, Amy
A1 - Remington, Karin A.
A1 - Rieger, Tania T.
A1 - Ritchie, Michael G.
A1 - Robin, Charles
A1 - Rogers, Yu-Hui
A1 - Rohde, Claudia
A1 - Rozas, Julio
A1 - Rubenfield, Marc J.
A1 - Ruiz, Alfredo
A1 - Russo, Susan
A1 - Salzberg, Steven L.
A1 - Sanchez-Gracia, Alejandro
A1 - Saranga, David J.
A1 - Sato, Hajime
A1 - Schaeffer, Stephen W.
A1 - Schatz, Michael C.
A1 - Schlenke, Todd
A1 - Schwartz, Russell
A1 - Segarra, Carmen
A1 - Singh, Rama S.
A1 - Sirot, Laura
A1 - Sirota, Marina
A1 - Sisneros, Nicholas B.
A1 - Smith, Chris D.
A1 - Smith, Temple F.
A1 - Spieth, John
A1 - Stage, Deborah E.
A1 - Stark, Alexander
A1 - Stephan, Wolfgang
A1 - Strausberg, Robert L.
A1 - Strempel, Sebastian
A1 - Sturgill, David
A1 - Sutton, Granger
A1 - Sutton, Granger G.
A1 - Tao, Wei
A1 - Teichmann, Sarah
A1 - Tobari, Yoshiko N.
A1 - Tomimura, Yoshihiko
A1 - Tsolas, Jason M.
A1 - Valente, Vera L. S.
A1 - Venter, Eli
A1 - Venter, J. Craig
A1 - Vicario, Saverio
A1 - Vieira, Filipe G.
A1 - Vilella, Albert J.
A1 - Villasante, Alfredo
A1 - Walenz, Brian
A1 - Wang, Jun
A1 - Wasserman, Marvin
A1 - Watts, Thomas
A1 - Wilson, Derek
A1 - Wilson, Richard K.
A1 - Wing, Rod A.
A1 - Wolfner, Mariana F.
A1 - Wong, Alex
A1 - Wong, Gane Ka-Shu
A1 - Wu, Chung- I.
A1 - Wu, Gabriel
A1 - Yamamoto, Daisuke
A1 - Yang, Hsiao-Pei
A1 - Yang, Shiaw-Pyng
A1 - Yorke, James A.
A1 - Yoshida, Kiyohito
A1 - Zdobnov, Evgeny
A1 - Zhang, Peili
A1 - Zhang, Yu
A1 - Zimin, Aleksey V.
A1 - Baldwin, Jennifer
A1 - Abdouelleil, Amr
A1 - Abdulkadir, Jamal
A1 - Abebe, Adal
A1 - Abera, Brikti
A1 - Abreu, Justin
A1 - Acer, St Christophe
A1 - Aftuck, Lynne
A1 - Alexander, Allen
A1 - An, Peter
A1 - Anderson, Erica
A1 - Anderson, Scott
A1 - Arachi, Harindra
A1 - Azer, Marc
A1 - Bachantsang, Pasang
A1 - Barry, Andrew
A1 - Bayul, Tashi
A1 - Berlin, Aaron
A1 - Bessette, Daniel
A1 - Bloom, Toby
A1 - Blye, Jason
A1 - Boguslavskiy, Leonid
A1 - Bonnet, Claude
A1 - Boukhgalter, Boris
A1 - Bourzgui, Imane
A1 - Brown, Adam
A1 - Cahill, Patrick
A1 - Channer, Sheridon
A1 - Cheshatsang, Yama
A1 - Chuda, Lisa
A1 - Citroen, Mieke
A1 - Collymore, Alville
A1 - Cooke, Patrick
A1 - Costello, Maura
A1 - D'Aco, Katie
A1 - Daza, Riza
A1 - Haan, Georgius De
A1 - DeGray, Stuart
A1 - DeMaso, Christina
A1 - Dhargay, Norbu
A1 - Dooley, Kimberly
A1 - Dooley, Erin
A1 - Doricent, Missole
A1 - Dorje, Passang
A1 - Dorjee, Kunsang
A1 - Dupes, Alan
A1 - Elong, Richard
A1 - Falk, Jill
A1 - Farina, Abderrahim
A1 - Faro, Susan
A1 - Ferguson, Diallo
A1 - Fisher, Sheila
A1 - Foley, Chelsea D.
A1 - Franke, Alicia
A1 - Friedrich, Dennis
A1 - Gadbois, Loryn
A1 - Gearin, Gary
A1 - Gearin, Christina R.
A1 - Giannoukos, Georgia
A1 - Goode, Tina
A1 - Graham, Joseph
A1 - Grandbois, Edward
A1 - Grewal, Sharleen
A1 - Gyaltsen, Kunsang
A1 - Hafez, Nabil
A1 - Hagos, Birhane
A1 - Hall, Jennifer
A1 - Henson, Charlotte
A1 - Hollinger, Andrew
A1 - Honan, Tracey
A1 - Huard, Monika D.
A1 - Hughes, Leanne
A1 - Hurhula, Brian
A1 - Husby, M. Erii
A1 - Kamat, Asha
A1 - Kanga, Ben
A1 - Kashin, Seva
A1 - Khazanovich, Dmitry
A1 - Kisner, Peter
A1 - Lance, Krista
A1 - Lara, Marcia
A1 - Lee, William
A1 - Lennon, Niall
A1 - Letendre, Frances
A1 - LeVine, Rosie
A1 - Lipovsky, Alex
A1 - Liu, Xiaohong
A1 - Liu, Jinlei
A1 - Liu, Shangtao
A1 - Lokyitsang, Tashi
A1 - Lokyitsang, Yeshi
A1 - Lubonja, Rakela
A1 - Lui, Annie
A1 - MacDonald, Pen
A1 - Magnisalis, Vasilia
A1 - Maru, Kebede
A1 - Matthews, Charles
A1 - McCusker, William
A1 - McDonough, Susan
A1 - Mehta, Teena
A1 - Meldrim, James
A1 - Meneus, Louis
A1 - Mihai, Oana
A1 - Mihalev, Atanas
A1 - Mihova, Tanya
A1 - Mittelman, Rachel
A1 - Mlenga, Valentine
A1 - Montmayeur, Anna
A1 - Mulrain, Leonidas
A1 - Navidi, Adam
A1 - Naylor, Jerome
A1 - Negash, Tamrat
A1 - Nguyen, Thu
A1 - Nguyen, Nga
A1 - Nicol, Robert
A1 - Norbu, Choe
A1 - Norbu, Nyima
A1 - Novod, Nathaniel
A1 - O'Neill, Barry
A1 - Osman, Sahal
A1 - Markiewicz, Eva
A1 - Oyono, Otero L.
A1 - Patti, Christopher
A1 - Phunkhang, Pema
A1 - Pierre, Fritz
A1 - Priest, Margaret
A1 - Raghuraman, Sujaa
A1 - Rege, Filip
A1 - Reyes, Rebecca
A1 - Rise, Cecil
A1 - Rogov, Peter
A1 - Ross, Keenan
A1 - Ryan, Elizabeth
A1 - Settipalli, Sampath
A1 - Shea, Terry
A1 - Sherpa, Ngawang
A1 - Shi, Lu
A1 - Shih, Diana
A1 - Sparrow, Todd
A1 - Spaulding, Jessica
A1 - Stalker, John
A1 - Stange-Thomann, Nicole
A1 - Stavropoulos, Sharon
A1 - Stone, Catherine
A1 - Strader, Christopher
A1 - Tesfaye, Senait
A1 - Thomson, Talene
A1 - Thoulutsang, Yama
A1 - Thoulutsang, Dawa
A1 - Topham, Kerri
A1 - Topping, Ira
A1 - Tsamla, Tsamla
A1 - Vassiliev, Helen
A1 - Vo, Andy
A1 - Wangchuk, Tsering
A1 - Wangdi, Tsering
A1 - Weiand, Michael
A1 - Wilkinson, Jane
A1 - Wilson, Adam
A1 - Yadav, Shailendra
A1 - Young, Geneva
A1 - Yu, Qing
A1 - Zembek, Lisa
A1 - Zhong, Danni
A1 - Zimmer, Andrew
A1 - Zwirko, Zac
A1 - Jaffe, David B.
A1 - Alvarez, Pablo
A1 - Brockman, Will
A1 - Butler, Jonathan
A1 - Chin, CheeWhye
A1 - Gnerre, Sante
A1 - Grabherr, Manfred
A1 - Kleber, Michael
A1 - Mauceli, Evan
A1 - MacCallum, Iain
AB - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
VL - 450
SN - 0028-0836
N1 - [szlig]
ER -
TY - JOUR
T1 - Evolution of genes and genomes on the Drosophila phylogeny.
JF - Nature
Y1 - 2007
A1 - Clark, Andrew G
A1 - Eisen, Michael B
A1 - Smith, Douglas R
A1 - Bergman, Casey M
A1 - Oliver, Brian
A1 - Markow, Therese A
A1 - Kaufman, Thomas C
A1 - Kellis, Manolis
A1 - Gelbart, William
A1 - Iyer, Venky N
A1 - Pollard, Daniel A
A1 - Sackton, Timothy B
A1 - Larracuente, Amanda M
A1 - Singh, Nadia D
A1 - Abad, Jose P
A1 - Abt, Dawn N
A1 - Adryan, Boris
A1 - Aguade, Montserrat
A1 - Akashi, Hiroshi
A1 - Anderson, Wyatt W
A1 - Aquadro, Charles F
A1 - Ardell, David H
A1 - Arguello, Roman
A1 - Artieri, Carlo G
A1 - Barbash, Daniel A
A1 - Barker, Daniel
A1 - Barsanti, Paolo
A1 - Batterham, Phil
A1 - Batzoglou, Serafim
A1 - Begun, Dave
A1 - Bhutkar, Arjun
A1 - Blanco, Enrico
A1 - Bosak, Stephanie A
A1 - Bradley, Robert K
A1 - Brand, Adrianne D
A1 - Brent, Michael R
A1 - Brooks, Angela N
A1 - Brown, Randall H
A1 - Butlin, Roger K
A1 - Caggese, Corrado
A1 - Calvi, Brian R
A1 - Bernardo de Carvalho, A
A1 - Caspi, Anat
A1 - Castrezana, Sergio
A1 - Celniker, Susan E
A1 - Chang, Jean L
A1 - Chapple, Charles
A1 - Chatterji, Sourav
A1 - Chinwalla, Asif
A1 - Civetta, Alberto
A1 - Clifton, Sandra W
A1 - Comeron, Josep M
A1 - Costello, James C
A1 - Coyne, Jerry A
A1 - Daub, Jennifer
A1 - David, Robert G
A1 - Delcher, Arthur L
A1 - Delehaunty, Kim
A1 - Do, Chuong B
A1 - Ebling, Heather
A1 - Edwards, Kevin
A1 - Eickbush, Thomas
A1 - Evans, Jay D
A1 - Filipski, Alan
A1 - Findeiss, Sven
A1 - Freyhult, Eva
A1 - Fulton, Lucinda
A1 - Fulton, Robert
A1 - Garcia, Ana C L
A1 - Gardiner, Anastasia
A1 - Garfield, David A
A1 - Garvin, Barry E
A1 - Gibson, Greg
A1 - Gilbert, Don
A1 - Gnerre, Sante
A1 - Godfrey, Jennifer
A1 - Good, Robert
A1 - Gotea, Valer
A1 - Gravely, Brenton
A1 - Greenberg, Anthony J
A1 - Griffiths-Jones, Sam
A1 - Gross, Samuel
A1 - Guigo, Roderic
A1 - Gustafson, Erik A
A1 - Haerty, Wilfried
A1 - Hahn, Matthew W
A1 - Halligan, Daniel L
A1 - Halpern, Aaron L
A1 - Halter, Gillian M
A1 - Han, Mira V
A1 - Heger, Andreas
A1 - Hillier, LaDeana
A1 - Hinrichs, Angie S
A1 - Holmes, Ian
A1 - Hoskins, Roger A
A1 - Hubisz, Melissa J
A1 - Hultmark, Dan
A1 - Huntley, Melanie A
A1 - Jaffe, David B
A1 - Jagadeeshan, Santosh
A1 - Jeck, William R
A1 - Johnson, Justin
A1 - Jones, Corbin D
A1 - Jordan, William C
A1 - Karpen, Gary H
A1 - Kataoka, Eiko
A1 - Keightley, Peter D
A1 - Kheradpour, Pouya
A1 - Kirkness, Ewen F
A1 - Koerich, Leonardo B
A1 - Kristiansen, Karsten
A1 - Kudrna, Dave
A1 - Kulathinal, Rob J
A1 - Kumar, Sudhir
A1 - Kwok, Roberta
A1 - Lander, Eric
A1 - Langley, Charles H
A1 - Lapoint, Richard
A1 - Lazzaro, Brian P
A1 - Lee, So-Jeong
A1 - Levesque, Lisa
A1 - Li, Ruiqiang
A1 - Lin, Chiao-Feng
A1 - Lin, Michael F
A1 - Lindblad-Toh, Kerstin
A1 - Llopart, Ana
A1 - Long, Manyuan
A1 - Low, Lloyd
A1 - Lozovsky, Elena
A1 - Lu, Jian
A1 - Luo, Meizhong
A1 - Machado, Carlos A
A1 - Makalowski, Wojciech
A1 - Marzo, Mar
A1 - Matsuda, Muneo
A1 - Matzkin, Luciano
A1 - McAllister, Bryant
A1 - McBride, Carolyn S
A1 - McKernan, Brendan
A1 - McKernan, Kevin
A1 - Mendez-Lago, Maria
A1 - Minx, Patrick
A1 - Mollenhauer, Michael U
A1 - Montooth, Kristi
A1 - Mount, Stephen M
A1 - Mu, Xu
A1 - Myers, Eugene
A1 - Negre, Barbara
A1 - Newfeld, Stuart
A1 - Nielsen, Rasmus
A1 - Noor, Mohamed A F
A1 - O'Grady, Patrick
A1 - Pachter, Lior
A1 - Papaceit, Montserrat
A1 - Parisi, Matthew J
A1 - Parisi, Michael
A1 - Parts, Leopold
A1 - Pedersen, Jakob S
A1 - Pesole, Graziano
A1 - Phillippy, Adam M
A1 - Ponting, Chris P
A1 - Pop, Mihai
A1 - Porcelli, Damiano
A1 - Powell, Jeffrey R
A1 - Prohaska, Sonja
A1 - Pruitt, Kim
A1 - Puig, Marta
A1 - Quesneville, Hadi
A1 - Ram, Kristipati Ravi
A1 - Rand, David
A1 - Rasmussen, Matthew D
A1 - Reed, Laura K
A1 - Reenan, Robert
A1 - Reily, Amy
A1 - Remington, Karin A
A1 - Rieger, Tania T
A1 - Ritchie, Michael G
A1 - Robin, Charles
A1 - Rogers, Yu-Hui
A1 - Rohde, Claudia
A1 - Rozas, Julio
A1 - Rubenfield, Marc J
A1 - Ruiz, Alfredo
A1 - Russo, Susan
A1 - Salzberg, Steven L
A1 - Sanchez-Gracia, Alejandro
A1 - Saranga, David J
A1 - Sato, Hajime
A1 - Schaeffer, Stephen W
A1 - Schatz, Michael C
A1 - Schlenke, Todd
A1 - Schwartz, Russell
A1 - Segarra, Carmen
A1 - Singh, Rama S
A1 - Sirot, Laura
A1 - Sirota, Marina
A1 - Sisneros, Nicholas B
A1 - Smith, Chris D
A1 - Smith, Temple F
A1 - Spieth, John
A1 - Stage, Deborah E
A1 - Stark, Alexander
A1 - Stephan, Wolfgang
A1 - Strausberg, Robert L
A1 - Strempel, Sebastian
A1 - Sturgill, David
A1 - Sutton, Granger
A1 - Sutton, Granger G
A1 - Tao, Wei
A1 - Teichmann, Sarah
A1 - Tobari, Yoshiko N
A1 - Tomimura, Yoshihiko
A1 - Tsolas, Jason M
A1 - Valente, Vera L S
A1 - Venter, Eli
A1 - Venter, J Craig
A1 - Vicario, Saverio
A1 - Vieira, Filipe G
A1 - Vilella, Albert J
A1 - Villasante, Alfredo
A1 - Walenz, Brian
A1 - Wang, Jun
A1 - Wasserman, Marvin
A1 - Watts, Thomas
A1 - Wilson, Derek
A1 - Wilson, Richard K
A1 - Wing, Rod A
A1 - Wolfner, Mariana F
A1 - Wong, Alex
A1 - Wong, Gane Ka-Shu
A1 - Wu, Chung-I
A1 - Wu, Gabriel
A1 - Yamamoto, Daisuke
A1 - Yang, Hsiao-Pei
A1 - Yang, Shiaw-Pyng
A1 - Yorke, James A
A1 - Yoshida, Kiyohito
A1 - Zdobnov, Evgeny
A1 - Zhang, Peili
A1 - Zhang, Yu
A1 - Zimin, Aleksey V
A1 - Baldwin, Jennifer
A1 - Abdouelleil, Amr
A1 - Abdulkadir, Jamal
A1 - Abebe, Adal
A1 - Abera, Brikti
A1 - Abreu, Justin
A1 - Acer, St Christophe
A1 - Aftuck, Lynne
A1 - Alexander, Allen
A1 - An, Peter
A1 - Anderson, Erica
A1 - Anderson, Scott
A1 - Arachi, Harindra
A1 - Azer, Marc
A1 - Bachantsang, Pasang
A1 - Barry, Andrew
A1 - Bayul, Tashi
A1 - Berlin, Aaron
A1 - Bessette, Daniel
A1 - Bloom, Toby
A1 - Blye, Jason
A1 - Boguslavskiy, Leonid
A1 - Bonnet, Claude
A1 - Boukhgalter, Boris
A1 - Bourzgui, Imane
A1 - Brown, Adam
A1 - Cahill, Patrick
A1 - Channer, Sheridon
A1 - Cheshatsang, Yama
A1 - Chuda, Lisa
A1 - Citroen, Mieke
A1 - Collymore, Alville
A1 - Cooke, Patrick
A1 - Costello, Maura
A1 - D'Aco, Katie
A1 - Daza, Riza
A1 - De Haan, Georgius
A1 - DeGray, Stuart
A1 - DeMaso, Christina
A1 - Dhargay, Norbu
A1 - Dooley, Kimberly
A1 - Dooley, Erin
A1 - Doricent, Missole
A1 - Dorje, Passang
A1 - Dorjee, Kunsang
A1 - Dupes, Alan
A1 - Elong, Richard
A1 - Falk, Jill
A1 - Farina, Abderrahim
A1 - Faro, Susan
A1 - Ferguson, Diallo
A1 - Fisher, Sheila
A1 - Foley, Chelsea D
A1 - Franke, Alicia
A1 - Friedrich, Dennis
A1 - Gadbois, Loryn
A1 - Gearin, Gary
A1 - Gearin, Christina R
A1 - Giannoukos, Georgia
A1 - Goode, Tina
A1 - Graham, Joseph
A1 - Grandbois, Edward
A1 - Grewal, Sharleen
A1 - Gyaltsen, Kunsang
A1 - Hafez, Nabil
A1 - Hagos, Birhane
A1 - Hall, Jennifer
A1 - Henson, Charlotte
A1 - Hollinger, Andrew
A1 - Honan, Tracey
A1 - Huard, Monika D
A1 - Hughes, Leanne
A1 - Hurhula, Brian
A1 - Husby, M Erii
A1 - Kamat, Asha
A1 - Kanga, Ben
A1 - Kashin, Seva
A1 - Khazanovich, Dmitry
A1 - Kisner, Peter
A1 - Lance, Krista
A1 - Lara, Marcia
A1 - Lee, William
A1 - Lennon, Niall
A1 - Letendre, Frances
A1 - LeVine, Rosie
A1 - Lipovsky, Alex
A1 - Liu, Xiaohong
A1 - Liu, Jinlei
A1 - Liu, Shangtao
A1 - Lokyitsang, Tashi
A1 - Lokyitsang, Yeshi
A1 - Lubonja, Rakela
A1 - Lui, Annie
A1 - MacDonald, Pen
A1 - Magnisalis, Vasilia
A1 - Maru, Kebede
A1 - Matthews, Charles
A1 - McCusker, William
A1 - McDonough, Susan
A1 - Mehta, Teena
A1 - Meldrim, James
A1 - Meneus, Louis
A1 - Mihai, Oana
A1 - Mihalev, Atanas
A1 - Mihova, Tanya
A1 - Mittelman, Rachel
A1 - Mlenga, Valentine
A1 - Montmayeur, Anna
A1 - Mulrain, Leonidas
A1 - Navidi, Adam
A1 - Naylor, Jerome
A1 - Negash, Tamrat
A1 - Nguyen, Thu
A1 - Nguyen, Nga
A1 - Nicol, Robert
A1 - Norbu, Choe
A1 - Norbu, Nyima
A1 - Novod, Nathaniel
A1 - O'Neill, Barry
A1 - Osman, Sahal
A1 - Markiewicz, Eva
A1 - Oyono, Otero L
A1 - Patti, Christopher
A1 - Phunkhang, Pema
A1 - Pierre, Fritz
A1 - Priest, Margaret
A1 - Raghuraman, Sujaa
A1 - Rege, Filip
A1 - Reyes, Rebecca
A1 - Rise, Cecil
A1 - Rogov, Peter
A1 - Ross, Keenan
A1 - Ryan, Elizabeth
A1 - Settipalli, Sampath
A1 - Shea, Terry
A1 - Sherpa, Ngawang
A1 - Shi, Lu
A1 - Shih, Diana
A1 - Sparrow, Todd
A1 - Spaulding, Jessica
A1 - Stalker, John
A1 - Stange-Thomann, Nicole
A1 - Stavropoulos, Sharon
A1 - Stone, Catherine
A1 - Strader, Christopher
A1 - Tesfaye, Senait
A1 - Thomson, Talene
A1 - Thoulutsang, Yama
A1 - Thoulutsang, Dawa
A1 - Topham, Kerri
A1 - Topping, Ira
A1 - Tsamla, Tsamla
A1 - Vassiliev, Helen
A1 - Vo, Andy
A1 - Wangchuk, Tsering
A1 - Wangdi, Tsering
A1 - Weiand, Michael
A1 - Wilkinson, Jane
A1 - Wilson, Adam
A1 - Yadav, Shailendra
A1 - Young, Geneva
A1 - Yu, Qing
A1 - Zembek, Lisa
A1 - Zhong, Danni
A1 - Zimmer, Andrew
A1 - Zwirko, Zac
A1 - Jaffe, David B
A1 - Alvarez, Pablo
A1 - Brockman, Will
A1 - Butler, Jonathan
A1 - Chin, CheeWhye
A1 - Gnerre, Sante
A1 - Grabherr, Manfred
A1 - Kleber, Michael
A1 - Mauceli, Evan
A1 - MacCallum, Iain
KW - Animals
KW - Codon
KW - DNA Transposable Elements
KW - Drosophila
KW - Drosophila Proteins
KW - Evolution, Molecular
KW - Gene Order
KW - Genes, Insect
KW - Genome, Insect
KW - Genome, Mitochondrial
KW - Genomics
KW - Immunity
KW - Multigene Family
KW - Phylogeny
KW - Reproduction
KW - RNA, Untranslated
KW - sequence alignment
KW - Sequence Analysis, DNA
KW - Synteny
AB - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
VL - 450
CP - 7167
M3 - 10.1038/nature06341
ER -
TY - JOUR
T1 - The Expression of a Plant-type Ferredoxin Redox System provides Molecular Evidence for a Plastid in the Early Dinoflagellate Perkinsus marinus
JF - ProtistProtist
Y1 - 2007
A1 - Stelter, Kathrin
A1 - Najib M. El‐Sayed
A1 - Seeber, Frank
KW - Apicomplexa
KW - ferredoxin
KW - Perkinsozoa
KW - plastid
KW - transit peptide
AB - Perkinsus marinus is a parasitic protozoan with a phylogenetic positioning between Apicomplexa and dinoflagellates. It is thus of interest for reconstructing the early evolution of eukaryotes, especially with regard to the acquisition of secondary plastids in these organisms. It is also an important pathogen of oysters, and the definition of parasite-specific metabolic pathways would be beneficial for the identification of efficient treatments for infected mollusks. Although these different scientific interests have resulted in the start of a genome project for this organism, it is still unknown whether P. marinus contains a plastid or plastid-like organelle like the related dinoflagellates and Apicomplexa. Here, we show that in vitro-cultivated parasites contain transcripts of the plant-type ferredoxin and its associated reductase. Both proteins are nuclear-encoded and possess N-terminal targeting sequences similar to those characterized in dinoflagellates. Since this redox pair is exclusively found in cyanobacteria and plastid-harboring organisms its presence also in P. marinus is highly indicative of a plastid. We also provide additional evidence for such an organelle by demonstrating pharmacological sensitivity to inhibitors of plastid-localized enzymes involved in fatty acid biosynthesis (e.g. acetyl-CoA carboxylase) and by detection of genes for three enzymes of plastid-localized isoprenoid biosynthesis (1-deoxy-D-xylulose 5-phosphate reductoisomerase, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, and (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase).
VL - 158
SN - 1434-4610
ER -
TY - JOUR
T1 - Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.
JF - PLoS Pathog
Y1 - 2007
A1 - Bringaud, Frederic
A1 - Müller, Michaela
A1 - Cerqueira, Gustavo Coutinho
A1 - Smith, Martin
A1 - Rochette, Annie
A1 - el-Sayed, Najib M A
A1 - Papadopoulou, Barbara
A1 - Ghedin, Elodie
KW - 3' Untranslated Regions
KW - Animals
KW - Base Sequence
KW - Biological Evolution
KW - Down-Regulation
KW - Gene Expression Regulation
KW - Genome, Protozoan
KW - Leishmania
KW - Leishmania major
KW - Molecular Sequence Data
KW - Retroelements
KW - RNA, Messenger
KW - sequence alignment
KW - Trypanosoma brucei brucei
KW - Trypanosoma cruzi
AB - Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.
VL - 3
CP - 9
M3 - 10.1371/journal.ppat.0030136
ER -
TY - JOUR
T1 - Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni
JF - BMC GenomicsBMC Genomics
Y1 - 2007
A1 - Waisberg, Michael
A1 - Lobo, Francisco
A1 - Cerqueira, Gustavo
A1 - Passos, Liana
A1 - Carvalho, Omar
A1 - Franco, Gloria
A1 - Najib M. El‐Sayed
AB - BACKGROUND:The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays.RESULTS:For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55% are expressed at higher levels in paired females while the remaining 45% are more expressed in unpaired ones and 56.6% are expressed at higher levels in paired male worms while the remaining 43.4% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis.CONCLUSION:Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of S. mansoni maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes.
VL - 8
SN - 1471-2164
ER -
TY - JOUR
T1 - New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion
JF - Eukaryotic CellEukaryotic Cell
Y1 - 2007
A1 - Souza, Renata T.
A1 - Santos, Marcia R. M.
A1 - Lima, Fabio M.
A1 - Najib M. El‐Sayed
A1 - Myler, Peter J.
A1 - Ruiz, Jeronimo C.
A1 - da Silveira, Jose Franco
AB - A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5' end of the element and a sequence domain of [~]500 bp without a well-defined borderline at the 3' end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of [~]0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be [~]173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.
VL - 6
ER -
TY - JOUR
T1 - Schistosoma mansoni genome: Closing in on a final gene set
JF - Experimental ParasitologyExperimental Parasitology
Y1 - 2007
A1 - Haas, Brian J.
A1 - Berriman, Matthew
A1 - Hirai, Hirohisa
A1 - Cerqueira, Gustavo G.
A1 - LoVerde, Philip T.
A1 - Najib M. El‐Sayed
KW - Annotation
KW - Gene finding
KW - Genome
KW - Schistosoma mansoni
AB - The Schistosoma mansoni genome sequencing consortium has recently released the latest versions of the genome assembly as well as an automated preliminary gene structure annotation. The combined datasets constitute a vast resource for researchers to exploit in a variety of post-genomic studies with an emphasis of transcriptomic and proteomic tools. Here we present an innovative method used for combining diverse sources of evidence including ab initio gene predictions, protein and transcript sequence homologies, and cross-genome sequence homologies between S. mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes.
VL - 117
SN - 0014-4894
ER -
TY - JOUR
T1 - Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans morsitans.
JF - Insect Mol Biol
Y1 - 2006
A1 - Attardo, G M
A1 - Strickler-Dinglasan, P
A1 - Perkin, S A H
A1 - Caler, E
A1 - Bonaldo, M F
A1 - Soares, M B
A1 - El-Sayeed, N
A1 - Aksoy, S
KW - Adipose Tissue
KW - Animals
KW - Base Sequence
KW - Computational Biology
KW - DNA Primers
KW - Egg Proteins
KW - Expressed Sequence Tags
KW - Female
KW - Gene Expression Profiling
KW - Insect Vectors
KW - Male
KW - Molecular Sequence Data
KW - Reverse Transcriptase Polymerase Chain Reaction
KW - Sequence Analysis, DNA
KW - Sex Factors
KW - Tsetse Flies
AB - Tsetse flies (Diptera: Glossinidia) are vectors of pathogenic African trypanosomes. To develop a foundation for tsetse physiology, a normalized expressed sequence tag (EST) library was constructed from fat body tissue of immune-stimulated Glossina morsitans morsitans. Analysis of 20,257 high-quality ESTs yielded 6372 unique genes comprised of 3059 tentative consensus (TC) sequences and 3313 singletons (available at http://aksoylab.yale.edu). We analysed the putative fat body transcriptome based on homology to other gene products with known functions available in the public domain. In particular, we describe the immune-related products, reproductive function related yolk proteins and milk-gland protein, iron metabolism regulating ferritins and transferrin, and tsetse's major energy source proline biosynthesis. Expression analysis of the three yolk proteins indicates that all are detected in females, while only the yolk protein with similarity to lipases, is expressed in males. Milk gland protein, apparently important for larval nutrition, however, is primarily synthesized by accessory milk gland tissue.
VL - 15
CP - 4
M3 - 10.1111/j.1365-2583.2006.00649.x
ER -
TY - JOUR
T1 - Comparative genomics of emerging human ehrlichiosis agents
JF - PLoS geneticsPLoS genetics
Y1 - 2006
A1 - Dunning Hotopp, Julie C.
A1 - Lin, Mingqun
A1 - Madupu, Ramana
A1 - Crabtree, Jonathan
A1 - Angiuoli, Samuel V.
A1 - Eisen, Jonathan A.
A1 - Eisen, Jonathan
A1 - Seshadri, Rekha
A1 - Ren, Qinghu
A1 - Wu, Martin
A1 - Utterback, Teresa R.
A1 - Smith, Shannon
A1 - Lewis, Matthew
A1 - Khouri, Hoda
A1 - Zhang, Chunbin
A1 - Niu, Hua
A1 - Lin, Quan
A1 - Ohashi, Norio
A1 - Zhi, Ning
A1 - Nelson, William
A1 - Brinkac, Lauren M.
A1 - Dodson, Robert J.
A1 - Rosovitz, M. J.
A1 - Sundaram, Jaideep
A1 - Daugherty, Sean C.
A1 - Davidsen, Tanja
A1 - Durkin, Anthony S.
A1 - Gwinn, Michelle
A1 - Haft, Daniel H.
A1 - J. Selengut
A1 - Sullivan, Steven A.
A1 - Zafar, Nikhat
A1 - Zhou, Liwei
A1 - Benahmed, Faiza
A1 - Forberger, Heather
A1 - Halpin, Rebecca
A1 - Mulligan, Stephanie
A1 - Robinson, Jeffrey
A1 - White, Owen
A1 - Rikihisa, Yasuko
A1 - Tettelin, Hervé
KW - Animals
KW - Biotin
KW - DNA Repair
KW - Ehrlichia
KW - Ehrlichiosis
KW - Genome
KW - Genomics
KW - HUMANS
KW - Models, Biological
KW - Phylogeny
KW - Rickettsia
KW - Ticks
AB - Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.
VL - 2
N1 - http://www.ncbi.nlm.nih.gov/pubmed/16482227?dopt=Abstract
ER -
TY - CHAP
T1 - Conservation Patterns in cis-Elements Reveal Compensatory Mutations
T2 - Comparative GenomicsComparative Genomics
Y1 - 2006
A1 - Evans, Perry
A1 - Donahue, Greg
A1 - Sridhar Hannenhalli
ED - Bourque, Guillaume
ED - El-Mabrouk, Nadia
AB - Transcriptional regulation critically depends on proper interactions between transcription factors (TF) and their cognate DNA binding sites or cis elements. A better understanding and modelling of the TF-DNA interaction is an important area of research. The Positional Weight Matrix (PWM) is the most common model of TF-DNA binding and it presumes that the nucleotide preferences at individual positions within the binding site are independent. However, studies have shown that this independence assumption does not always hold. If the nucleotide preference at one position depends on the nucleotide at another position, a chance mutation at one position should exert selection pressures at the other position. By comparing the patterns of evolutionary conservation at individual positions within cis elements, here we show that positional dependence within binding sites is highly prevalent. We also show that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples—Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.
JA - Comparative GenomicsComparative Genomics
T3 - Lecture Notes in Computer Science
PB - Springer Berlin / Heidelberg
VL - 4205
SN - 978-3-540-44529-6
ER -
TY - JOUR
T1 - Dense Subgraph Computation Via Stochastic Search: Application to Detect Transcriptional Modules
JF - BioinformaticsBioinformaticsBioinformaticsBioinformatics
Y1 - 2006
A1 - Everett, Logan
A1 - Wang, Li-San
A1 - Sridhar Hannenhalli
AB - Motivation: In a tri-partite biological network of transcription factors, their putative target genes, and the tissues in which the target genes are differentially expressed, a tightly inter-connected (dense) subgraph may reveal knowledge about tissue specific transcription regulation mediated by a specific set of transcription factors—a tissue-specific transcriptional module. This is just one context in which an efficient computation of dense subgraphs in a multi-partite graph is needed.Result: Here we report a generic stochastic search based method to compute dense subgraphs in a graph with an arbitrary number of partitions and an arbitrary connectivity among the partitions. We then use the tool to explore tissue-specific transcriptional regulation in the human genome. We validate our findings in Skeletal muscle based on literature. We could accurately deduce biological processes for transcription factors via the tri-partite clusters of transcription factors, genes, and the functional annotation of genes. Additionally, we propose a few previously unknown TF-pathway associations and tissue-specific roles for certain pathways. Finally, our combined analysis of Cardiac, Skeletal, and Smooth muscle data recapitulates the evolutionary relationship among the three tissues. Contact:sridharh@pcbi.upenn.edu
VL - 22
SN - 1367-4803, 1460-2059
ER -
TY - JOUR
T1 - Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 2006
A1 - Bringaud, Frederic
A1 - Ghedin, Elodie
A1 - Blandin, Gaëlle
A1 - Bartholomeu, Daniella C.
A1 - Caler, Elisabet
A1 - Levin, Mariano J.
A1 - Baltz, Théo
A1 - Najib M. El‐Sayed
KW - Degenerate retroelement
KW - Evolution
KW - Ingi
KW - L1Tc
KW - Leishmania major
KW - Non-LTR retrotransposon
KW - Retroposon
KW - Trypanosoma brucei
KW - Trypanosoma cruzi
AB - The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5'-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.
VL - 145
SN - 0166-6851
ER -
TY - JOUR
T1 - Metagenomic Analysis of the Human Distal Gut Microbiome
JF - ScienceScienceScienceScience
Y1 - 2006
A1 - Gill, Steven R.
A1 - M. Pop
A1 - DeBoy, Robert T.
A1 - Eckburg, Paul B.
A1 - Turnbaugh, Peter J.
A1 - Samuel, Buck S.
A1 - Gordon, Jeffrey I.
A1 - Relman, David A.
A1 - Fraser-Liggett, Claire M.
A1 - Nelson, Karen E.
AB - The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes as our own genome. We analyzed ∼78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction–amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.
VL - 312
SN - 0036-8075, 1095-9203
ER -
TY - JOUR
T1 - Retroviral DNA integration: viral and cellular determinants of target-site selection
JF - PLoS pathogensPLoS pathogens
Y1 - 2006
A1 - Lewinski, M. K.
A1 - Yamashita, M.
A1 - Emerman, M.
A1 - Ciuffi, A.
A1 - Marshall, H.
A1 - Crawford, G.
A1 - Collins, F.
A1 - Shinn, P.
A1 - Leipzig, J.
A1 - Sridhar Hannenhalli
A1 - others,
PB - Public Library of Science
VL - 2
ER -
TY - JOUR
T1 - Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily
JF - GeneGene
Y1 - 2006
A1 - Wu, Wenjie
A1 - Niles, Edward G.
A1 - Najib M. El‐Sayed
A1 - Berriman, Matthew
A1 - LoVerde, Philip T.
KW - Nuclear receptors
KW - Schistosoma mansoni
AB - Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Sixteen new NRs were identified in the Platyhelminth trematode, Schistosoma mansoni. Three were found to possess novel tandem DNA-binding domains that identify a new subfamily of NR. Two NRs are homologues of the thyroid hormone receptor that previously were thought to be restricted to chordates. This study brings the total number of identified NR in S. mansoni to 21. Phylogenetic and comparative genomic analyses demonstrate that S. mansoni NRs share an evolutionary lineage with that of arthropods and vertebrates. Phylogenic analysis shows that more than half of the S. mansoni nuclear receptors evolved from a second gene duplication. As the second gene duplication of NRs was thought to be specific to vertebrates, our data challenge the current theory of NR evolution.
VL - 366
SN - 0378-1119
ER -
TY - JOUR
T1 - Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure
JF - CirculationCirculation
Y1 - 2006
A1 - Sridhar Hannenhalli
A1 - Putt, Mary E.
A1 - Gilmore, Joan M.
A1 - Wang, Junwen
A1 - Parmacek, Michael S.
A1 - Epstein, Jonathan A.
A1 - Morrisey, Edward E.
A1 - Margulies, Kenneth B.
A1 - Cappola, Thomas P.
AB - Background— Specific transcription factors (TFs) modulate cardiac gene expression in murine models of heart failure, but their relevance in human subjects remains untested. We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure.Methods and Results— RNA isolates from failing (n=196) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays, and differentially expressed heart failure genes were determined. TF binding sites overrepresented in the −5-kb promoter sequences of these heart failure genes were then determined with the use of public genome sequence databases. Binding sites for TFs identified in murine heart failure models (MEF2, NKX, NF-AT, and GATA) were significantly overrepresented in promoters of human heart failure genes (P<0.002; false discovery rate 2% to 4%). In addition, binding sites for FOX TFs showed substantial overrepresentation in both advanced human and early murine heart failure (P<0.002 and false discovery rate <4% for each). A role for FOX TFs was supported further by expression of FOXC1, C2, P1, P4, and O1A in failing human cardiac myocytes at levels similar to established hypertrophic TFs and by abundant FOXP1 protein in failing human cardiac myocyte nuclei.Conclusions— Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans.
VL - 114
ER -
TY - JOUR
T1 - The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion
JF - Molecular biology and evolutionMolecular biology and evolution
Y1 - 2006
A1 - Bringaud, F.
A1 - Bartholomeu, D. C.
A1 - Blandin, G.
A1 - Delcher, A.
A1 - Baltz, T.
A1 - Najib M. El‐Sayed
A1 - Ghedin, E.
VL - 23
ER -
TY - JOUR
T1 - The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion.
JF - Mol Biol Evol
Y1 - 2006
A1 - Bringaud, Frederic
A1 - Bartholomeu, Daniella C
A1 - Blandin, Gaëlle
A1 - Delcher, Arthur
A1 - Baltz, Théo
A1 - el-Sayed, Najib M A
A1 - Ghedin, Elodie
KW - Animals
KW - DNA, Protozoan
KW - DNA-(Apurinic or Apyrimidinic Site) Lyase
KW - Mutagenesis, Insertional
KW - Retroelements
KW - Sequence Deletion
KW - Trypanosoma cruzi
AB - The trypanosomatid protozoan Trypanosoma cruzi contains long autonomous (L1Tc) and short nonautonomous (NARTc) non-long terminal repeat retrotransposons. NARTc (0.25 kb) probably derived from L1Tc (4.9 kb) by 3'-deletion. It has been proposed that their apparent random distribution in the genome is related to the L1Tc-encoded apurinic/apyrimidinic endonuclease (APE) activity, which repairs modified residues. To address this question we used the T. cruzi (CL-Brener strain) genome data to analyze the distribution of all the L1Tc/NARTc elements present in contigs larger than 10 kb. This data set, which represents 0.91x sequence coverage of the haploid nuclear genome ( approximately 55 Mb), contains 419 elements, including 112 full-length L1Tc elements (14 of which are potentially functional) and 84 full-length NARTc. Approximately half of the full-length elements are flanked by a target site duplication, most of them (87%) are 12 bp long. Statistical analyses of sequences flanking the full-length elements show the same highly conserved pattern upstream of both the L1Tc and NARTc retrotransposons. The two most conserved residues are a guanine and an adenine, which flank the site where first-strand cleavage is performed by the element-encoded endonuclease activity. This analysis clearly indicates that the L1Tc and NARTc elements display relative site specificity for insertion, which suggests that the APE activity is not responsible for first-strand cleavage of the target site.
VL - 23
CP - 2
M3 - 10.1093/molbev/msj046
ER -
TY - JOUR
T1 - Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region.
JF - BMC Genomics
Y1 - 2006
A1 - Westenberger, Scott J
A1 - Cerqueira, Gustavo C
A1 - El-Sayed, Najib M
A1 - Zingales, Bianca
A1 - Campbell, David A
A1 - Sturm, Nancy R
KW - Amino Acid Sequence
KW - Animals
KW - Animals, Inbred Strains
KW - Base Composition
KW - Conserved Sequence
KW - DNA, Kinetoplast
KW - Frameshifting, Ribosomal
KW - Gene Deletion
KW - Gene Order
KW - Genetic Variation
KW - Leishmania
KW - Models, Biological
KW - Molecular Sequence Data
KW - Muscle Proteins
KW - NADH Dehydrogenase
KW - Open Reading Frames
KW - Regulatory Elements, Transcriptional
KW - RNA Editing
KW - Sequence Homology, Amino Acid
KW - Species Specificity
KW - Trypanosoma brucei brucei
KW - Trypanosoma cruzi
KW - Ubiquitin-Protein Ligases
KW - Untranslated Regions
AB - BACKGROUND: The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.
RESULTS: We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.
CONCLUSION: The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.
VL - 7
M3 - 10.1186/1471-2164-7-60
ER -
TY - JOUR
T1 - Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region
JF - BMC GenomicsBMC Genomics
Y1 - 2006
A1 - Westenberger, Scott
A1 - Cerqueira, Gustavo
A1 - Najib M. El‐Sayed
A1 - Zingales, Bianca
A1 - Campbell, David
A1 - Sturm, Nancy
AB - BACKGROUND:The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.RESULTS:We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.CONCLUSION:The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.
VL - 7
SN - 1471-2164
ER -
TY - JOUR
T1 - Comparative Genomics of Trypanosomatid Parasitic Protozoa
JF - ScienceScience
Y1 - 2005
A1 - Najib M. El‐Sayed
A1 - Myler, Peter J.
A1 - Blandin, Gaëlle
A1 - Berriman, Matthew
A1 - Crabtree, Jonathan
A1 - Aggarwal, Gautam
A1 - Caler, Elisabet
A1 - Renauld, Hubert
A1 - Worthey, Elizabeth A.
A1 - Hertz-Fowler, Christiane
A1 - Ghedin, Elodie
A1 - Peacock, Christopher
A1 - Bartholomeu, Daniella C.
A1 - Haas, Brian J.
A1 - Tran, Anh-Nhi
A1 - Wortman, Jennifer R.
A1 - Alsmark, U. Cecilia M.
A1 - Angiuoli, Samuel
A1 - Anupama, Atashi
A1 - Badger, Jonathan
A1 - Bringaud, Frederic
A1 - Cadag, Eithon
A1 - Carlton, Jane M.
A1 - Cerqueira, Gustavo C.
A1 - Creasy, Todd
A1 - Delcher, Arthur L.
A1 - Djikeng, Appolinaire
A1 - Embley, T. Martin
A1 - Hauser, Christopher
A1 - Ivens, Alasdair C.
A1 - Kummerfeld, Sarah K.
A1 - Pereira-Leal, Jose B.
A1 - Nilsson, Daniel
A1 - Peterson, Jeremy
A1 - Salzberg, Steven L.
A1 - Shallom, Joshua
A1 - Silva, Joana C.
A1 - Sundaram, Jaideep
A1 - Westenberger, Scott
A1 - White, Owen
A1 - Melville, Sara E.
A1 - Donelson, John E.
A1 - Andersson, Björn
A1 - Stuart, Kenneth D.
A1 - Hall, Neil
AB - A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that—along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions—have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.
VL - 309
ER -
TY - JOUR
T1 - The genetic map and comparative analysis with the physical map of Trypanosoma brucei
JF - Nucleic acids researchNucleic Acids Research
Y1 - 2005
A1 - MacLeod, A.
A1 - Tweedie, A.
A1 - McLellan, S.
A1 - Taylor, S.
A1 - Hall, N.
A1 - Berriman, M.
A1 - Najib M. El‐Sayed
A1 - Hope, M.
A1 - Turner, C. M. R.
A1 - Tait, A.
VL - 33
ER -
TY - JOUR
T1 - The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease
JF - ScienceScience
Y1 - 2005
A1 - Najib M. El‐Sayed
A1 - Myler, P. J.
A1 - Bartholomeu, D. C.
A1 - Nilsson, D.
A1 - Aggarwal, G.
A1 - Tran, A. N.
A1 - Ghedin, E.
A1 - Worthey, E. A.
A1 - Delcher, A. L.
A1 - Blandin, G.
A1 - others,
PB - American Association for the Advancement of Science
VL - 309
ER -
TY - JOUR
T1 - Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription
JF - Journal of VirologyJ. Virol.Journal of VirologyJ. Virol.
Y1 - 2005
A1 - Lewinski, M. K.
A1 - Bisgrove, D.
A1 - Shinn, P.
A1 - Chen, H.
A1 - Hoffmann, C.
A1 - Sridhar Hannenhalli
A1 - Verdin, E.
A1 - Berry, C. C.
A1 - Ecker, J. R.
A1 - Bushman, F. D.
AB - We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.
VL - 79
SN - 0022-538X, 1098-5514
ER -
TY - JOUR
T1 - Promoter architecture and response to a positive regulator of archaeal transcription
JF - Molecular MicrobiologyMolecular Microbiology
Y1 - 2005
A1 - Ouhammouch, Mohamed
A1 - Langham, Geoffrey E.
A1 - Hausner, Winfried
A1 - Simpson, Anjana J.
A1 - Najib M. El‐Sayed
A1 - Geiduschek, E. Peter
AB - The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a ‘one-site’ minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.
VL - 56
SN - 1365-2958
ER -
TY - JOUR
T1 - Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
JF - Genome BiologyGenome Biology
Y1 - 2005
A1 - Salzberg, Steven L.
A1 - Hotopp, Julie C. D.
A1 - Delcher, Arthur L.
A1 - M. Pop
A1 - Smith, Douglas R.
A1 - Eisen, Michael B.
A1 - Nelson, William C.
AB - The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism.
VL - 6
SN - 1465-6906
ER -
TY - JOUR
T1 - Telomere and subtelomere of Trypanosoma cruzi chromosomes are enriched in (pseudo)genes of retrotransposon hot spot and trans-sialidase-like gene families: the origins of T. cruzi telomeres.
JF - Gene
Y1 - 2005
A1 - Kim, Dong
A1 - Chiurillo, Miguel Angel
A1 - El-Sayed, Najib
A1 - Jones, Kristin
A1 - Santos, Márcia R M
A1 - Porcile, Patricio E
A1 - Andersson, Björn
A1 - Myler, Peter
A1 - da Silveira, Jose Franco
A1 - Ramírez, José Luis
KW - Amino Acid Sequence
KW - Animals
KW - Base Sequence
KW - Chromosomes
KW - Chromosomes, Artificial, Bacterial
KW - DNA, Protozoan
KW - Genes, Protozoan
KW - Glycoproteins
KW - Molecular Sequence Data
KW - Multigene Family
KW - Neuraminidase
KW - Pseudogenes
KW - Retroelements
KW - Sequence Homology, Amino Acid
KW - Sequence Homology, Nucleic Acid
KW - Telomere
KW - Trypanosoma cruzi
AB - Here, we sequenced two large telomeric regions obtained from the pathogen protozoan Trypanosoma cruzi. These sequences, together with in silico assembled contigs, allowed us to establish the general features of telomeres and subtelomeres of this parasite. Our findings can be summarized as follows: We confirmed the presence of two types of telomeric ends; subtelomeric regions appeared to be enriched in (pseudo)genes of RHS (retrotransposon hot spot), TS (trans-sialidase)-like proteins, and putative surface protein DGF-1 (dispersed gene family-1). Sequence analysis of the ts-like genes located at the telomeres suggested that T. cruzi chromosomal ends could have been the site for generation of new gp85 variants, an important adhesin molecule involved in the invasion of mammalian cells by T. cruzi. Finally, a mechanism for generation of T. cruzi telomere by chromosome breakage and telomere healing is proposed.
VL - 346
M3 - 10.1016/j.gene.2004.10.014
ER -
TY - JOUR
T1 - Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock.
JF - Environ Microbiol
Y1 - 2005
A1 - Boonyaratanakornkit, Boonchai B
A1 - Simpson, Anjana J
A1 - Whitehead, Timothy A
A1 - Fraser, Claire M
A1 - el-Sayed, Najib M A
A1 - Clark, Douglas S
KW - Adaptation, Physiological
KW - Archaeal Proteins
KW - Cold Temperature
KW - Gene Expression Profiling
KW - Gene Expression Regulation, Archaeal
KW - Heat-Shock Proteins
KW - Hot Temperature
KW - Methanococcus
KW - Temperature
KW - Transcription, Genetic
AB - Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85 degrees C to 65 degrees C and 95 degrees C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95 degrees C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an alpha subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65 degrees C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.
VL - 7
CP - 6
M3 - 10.1111/j.1462-2920.2005.00751.x
ER -
TY - JOUR
T1 - Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non‐lethal cold shock
JF - Environmental MicrobiologyEnvironmental Microbiology
Y1 - 2005
A1 - Boonyaratanakornkit, Boonchai B.
A1 - Simpson, Anjana J.
A1 - Whitehead, Timothy A.
A1 - Fraser, Claire M.
A1 - Najib M. El‐Sayed
A1 - Clark, Douglas S.
AB - Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85°C to 65°C and 95°C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95°C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65°C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.
VL - 7
SN - 1462-2920
ER -
TY - CONF
T1 - What Are the Ants Doing? Vision-Based Tracking and Reconstruction of Control Programs
T2 - 2005 IEEE International Conference on Robotics and AutomationProceedings of the 2005 IEEE International Conference on Robotics and Automation
Y1 - 2005
A1 - Egerstedt, M.
A1 - Balch, T.
A1 - Dellaert, F.
A1 - Delmotte, F.
A1 - Khan, Z.
JA - 2005 IEEE International Conference on Robotics and AutomationProceedings of the 2005 IEEE International Conference on Robotics and Automation
PB - IEEE
CY - Barcelona, Spain
UR - http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1570762
M3 - 10.1109/ROBOT.2005.1570762
ER -
TY - JOUR
T1 - What the genome sequence is revealing about trypanosome antigenic variation.
JF - Biochem Soc Trans
Y1 - 2005
A1 - Barry, J D
A1 - Marcello, L
A1 - Morrison, L J
A1 - Read, A F
A1 - Lythgoe, K
A1 - Jones, N
A1 - Carrington, M
A1 - Blandin, G
A1 - Böhme, U
A1 - Caler, E
A1 - Hertz-Fowler, C
A1 - Renauld, H
A1 - El-Sayed, N
A1 - Berriman, M
KW - Animals
KW - Antigens, Protozoan
KW - Evolution, Molecular
KW - Genetic Variation
KW - Genome
KW - Trypanosomatina
KW - Variant Surface Glycoproteins, Trypanosoma
AB - African trypanosomes evade humoral immunity through antigenic variation, whereby they switch expression of the gene encoding their VSG (variant surface glycoprotein) coat. Switching proceeds by duplication of silent VSG genes into a transcriptionally active locus. The genome project has revealed that most of the silent archive consists of hundreds of subtelomeric VSG tandem arrays, and that most of these are not functional genes. Precedent suggests that they can contribute combinatorially to the formation of expressed, functional genes through segmental gene conversion. These findings from the genome project have major implications for evolution of the VSG archive and for transmission of the parasite in the field.
VL - 33
CP - Pt 5
M3 - 10.1042/BST20050986
ER -
TY - JOUR
T1 - Advances in schistosome genomics
JF - Trends in ParasitologyTrends in Parasitology
Y1 - 2004
A1 - Najib M. El‐Sayed
A1 - Bartholomeu, Daniella
A1 - Ivens, Alasdair
A1 - Johnston, David A.
A1 - LoVerde, Philip T.
AB - In Spring 2004, the first draft of the 270 Mb genome of Schistosoma mansoni will be released. This sequence is based on the assembly and annotation of a >7.5-fold coverage, shotgun sequencing project. The key stages involved in the international collaborative efforts that have led to the generation of these sequencing data for the parasite S. mansoni are discussed here.
VL - 20
SN - 1471-4922
ER -
TY - JOUR
T1 - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America
Y1 - 2004
A1 - Seshadri, Rekha
A1 - Myers, Garry S. A.
A1 - Tettelin, Hervé
A1 - Eisen, Jonathan A.
A1 - Heidelberg, John F.
A1 - Dodson, Robert J.
A1 - Davidsen, Tanja M.
A1 - DeBoy, Robert T.
A1 - Fouts, Derrick E.
A1 - Haft, Dan H.
A1 - J. Selengut
A1 - Ren, Qinghu
A1 - Brinkac, Lauren M.
A1 - Madupu, Ramana
A1 - Kolonay, Jamie
A1 - Durkin, A. Scott
A1 - Daugherty, Sean C.
A1 - Shetty, Jyoti
A1 - Shvartsbeyn, Alla
A1 - Gebregeorgis, Elizabeth
A1 - Geer, Keita
A1 - Tsegaye, Getahun
A1 - Malek, Joel
A1 - Ayodeji, Bola
A1 - Shatsman, Sofiya
A1 - McLeod, Michael P.
A1 - Smajs, David
A1 - Howell, Jerrilyn K.
A1 - Pal, Sangita
A1 - Amin, Anita
A1 - Vashisth, Pankaj
A1 - McNeill, Thomas Z.
A1 - Xiang, Qin
A1 - Sodergren, Erica
A1 - Baca, Ernesto
A1 - Weinstock, George M.
A1 - Norris, Steven J.
A1 - Fraser, Claire M.
A1 - Paulsen, Ian T.
KW - ATP-Binding Cassette Transporters
KW - Bacterial Proteins
KW - Base Sequence
KW - Borrelia burgdorferi
KW - Genes, Bacterial
KW - Genome, Bacterial
KW - Leptospira interrogans
KW - Models, Genetic
KW - Molecular Sequence Data
KW - Mouth
KW - Sequence Homology, Amino Acid
KW - Treponema
KW - Treponema pallidum
AB - We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
VL - 101
N1 - http://www.ncbi.nlm.nih.gov/pubmed/15064399?dopt=Abstract
ER -
TY - JOUR
T1 - Gene synteny and evolution of genome architecture in trypanosomatids.
JF - Mol Biochem Parasitol
Y1 - 2004
A1 - Ghedin, Elodie
A1 - Bringaud, Frederic
A1 - Peterson, Jeremy
A1 - Myler, Peter
A1 - Berriman, Matthew
A1 - Ivens, Alasdair
A1 - Andersson, Björn
A1 - Bontempi, Esteban
A1 - Eisen, Jonathan
A1 - Angiuoli, Sam
A1 - Wanless, David
A1 - Von Arx, Anna
A1 - Murphy, Lee
A1 - Lennard, Nicola
A1 - Salzberg, Steven
A1 - Adams, Mark D
A1 - White, Owen
A1 - Hall, Neil
A1 - Stuart, Kenneth
A1 - Fraser, Claire M
A1 - el-Sayed, Najib M A
KW - Animals
KW - Computational Biology
KW - Evolution, Molecular
KW - Gene Order
KW - Genome, Protozoan
KW - Genomics
KW - Leishmania major
KW - Multigene Family
KW - Recombination, Genetic
KW - Retroelements
KW - Selection, Genetic
KW - Synteny
KW - Trypanosoma brucei brucei
KW - Trypanosoma cruzi
KW - Trypanosomatina
AB - The trypanosomatid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major are related human pathogens that cause markedly distinct diseases. Using information from genome sequencing projects currently underway, we have compared the sequences of large chromosomal fragments from each species. Despite high levels of divergence at the sequence level, these three species exhibit a striking conservation of gene order, suggesting that selection has maintained gene order among the trypanosomatids over hundreds of millions of years of evolution. The few sites of genome rearrangement between these species are marked by the presence of retrotransposon-like elements, suggesting that retrotransposons may have played an important role in shaping trypanosomatid genome organization. A degenerate retroelement was identified in L. major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species.
VL - 134
CP - 2
M3 - 10.1016/j.molbiopara.2003.11.012
ER -
TY - JOUR
T1 - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
JF - NatureNature
Y1 - 2004
A1 - Moran, Mary Ann
A1 - Buchan, Alison
A1 - González, José M.
A1 - Heidelberg, John F.
A1 - Whitman, William B.
A1 - Kiene, Ronald P.
A1 - Henriksen, James R.
A1 - King, Gary M.
A1 - Belas, Robert
A1 - Fuqua, Clay
A1 - Brinkac, Lauren
A1 - Lewis, Matt
A1 - Johri, Shivani
A1 - Weaver, Bruce
A1 - Pai, Grace
A1 - Eisen, Jonathan A.
A1 - Rahe, Elisha
A1 - Sheldon, Wade M.
A1 - Ye, Wenying
A1 - Miller, Todd R.
A1 - Carlton, Jane
A1 - Rasko, David A.
A1 - Paulsen, Ian T.
A1 - Ren, Qinghu
A1 - Daugherty, Sean C.
A1 - DeBoy, Robert T.
A1 - Dodson, Robert J.
A1 - Durkin, A. Scott
A1 - Madupu, Ramana
A1 - Nelson, William C.
A1 - Sullivan, Steven A.
A1 - Rosovitz, M. J.
A1 - Haft, Daniel H.
A1 - J. Selengut
A1 - Ward, Naomi
KW - Adaptation, Physiological
KW - Carrier Proteins
KW - Genes, Bacterial
KW - Genome, Bacterial
KW - marine biology
KW - Molecular Sequence Data
KW - Oceans and Seas
KW - Phylogeny
KW - plankton
KW - RNA, Ribosomal, 16S
KW - Roseobacter
KW - Seawater
AB - Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
VL - 432
N1 - http://www.ncbi.nlm.nih.gov/pubmed/15602564?dopt=Abstract
ER -
TY - JOUR
T1 - The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
JF - Nature biotechnologyNature biotechnology
Y1 - 2004
A1 - Heidelberg, John F.
A1 - Seshadri, Rekha
A1 - Haveman, Shelley A.
A1 - Hemme, Christopher L.
A1 - Paulsen, Ian T.
A1 - Kolonay, James F.
A1 - Eisen, Jonathan A.
A1 - Ward, Naomi
A1 - Methe, Barbara
A1 - Brinkac, Lauren M.
A1 - Daugherty, Sean C.
A1 - DeBoy, Robert T.
A1 - Dodson, Robert J.
A1 - Durkin, A. Scott
A1 - Madupu, Ramana
A1 - Nelson, William C.
A1 - Sullivan, Steven A.
A1 - Fouts, Derrick
A1 - Haft, Daniel H.
A1 - J. Selengut
A1 - Peterson, Jeremy D.
A1 - Davidsen, Tanja M.
A1 - Zafar, Nikhat
A1 - Zhou, Liwei
A1 - Radune, Diana
A1 - Dimitrov, George
A1 - Hance, Mark
A1 - Tran, Kevin
A1 - Khouri, Hoda
A1 - Gill, John
A1 - Utterback, Terry R.
A1 - Feldblyum, Tamara V.
A1 - Wall, Judy D.
A1 - Voordouw, Gerrit
A1 - Fraser, Claire M.
KW - Desulfovibrio vulgaris
KW - Energy Metabolism
KW - Genome, Bacterial
KW - Molecular Sequence Data
AB - Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.
VL - 22
N1 - http://www.ncbi.nlm.nih.gov/pubmed/15077118?dopt=Abstract
ER -
TY - JOUR
T1 - The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei
JF - Molecular biology and evolutionMolecular biology and evolution
Y1 - 2004
A1 - Bringaud, F.
A1 - Biteau, N.
A1 - Zuiderwijk, E.
A1 - Berriman, M.
A1 - Najib M. El‐Sayed
A1 - Ghedin, E.
A1 - Melville, S. E.
A1 - Hall, N.
A1 - Baltz, T.
VL - 21
ER -
TY - JOUR
T1 - The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei.
JF - Mol Biol Evol
Y1 - 2004
A1 - Bringaud, Frederic
A1 - Biteau, Nicolas
A1 - Zuiderwijk, Eduard
A1 - Berriman, Matthew
A1 - El-Sayed, Najib M
A1 - Ghedin, Elodie
A1 - Melville, Sara E
A1 - Hall, Neil
A1 - Baltz, Théo
KW - Amino Acid Sequence
KW - Animals
KW - Base Sequence
KW - Consensus Sequence
KW - Genome, Protozoan
KW - Molecular Sequence Data
KW - Retroelements
KW - Sequence Analysis
KW - Trypanosoma brucei brucei
AB - The ingi (long and autonomous) and RIME (short and nonautonomous) non--long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question, we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/RIME elements analyzed, 60% are complete, and 7% of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5'-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5'-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.
VL - 21
CP - 3
M3 - 10.1093/molbev/msh045
ER -
TY - JOUR
T1 - Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh
JF - Canadian Journal of MicrobiologyCanadian Journal of Microbiology
Y1 - 2004
A1 - Islam, M. S.
A1 - Tasmin, Rizwana
A1 - Khan, Sirajul I. s l a m
A1 - Bakht, Habibul B. M.
A1 - Mahmood, Zahid H. a y a t
A1 - Rahman, M. Z. i a u r
A1 - Bhuiyan, Nurul A. m i n
A1 - Nishibuchi, Mitsuaki
A1 - Nair, G. B. a l a k r i s h
A1 - Sack, R. B. r a d l e y
A1 - Huq, Anwar
A1 - Rita R. Colwell
A1 - Sack, David A.
AB - A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahamolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh.
VL - 50
ER -
TY - JOUR
T1 - Polylysogeny and prophage induction by secondary infection in Vibrio cholerae
JF - Environmental MicrobiologyEnvironmental Microbiology
Y1 - 2004
A1 - Espeland, Eric M.
A1 - Lipp, Erin K.
A1 - Huq, Anwar
A1 - Rita R. Colwell
AB - Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (ΦP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, ΦP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6 days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.
VL - 6
SN - 1462-2920
ER -
TY - JOUR
T1 - Schistosoma mansoni genome project: an update
JF - Parasitology InternationalParasitology International
Y1 - 2004
A1 - LoVerde, Philip T.
A1 - Hirai, Hirohisa
A1 - Merrick, Joseph M.
A1 - Lee, Norman H.
A1 - Najib M. El‐Sayed
KW - Chromosome mapping
KW - Gene discovery
KW - Genomics
KW - Schistosoma mansoni
AB - A schistosome genome project was initiated by the World Health Organization in 1994 with the notion that the best prospects for identifying new targets for drugs, vaccines, and diagnostic development lie in schistosome gene discovery, development of chromosome maps, whole genome sequencing and genome analysis. Schistosoma mansoni has a haploid genome of 270 Mb contained on 8 pairs of chromosomes. It is estimated that the S. mansoni genome contains between 15 000 and 25 000 genes. There are approximately 16 689 ESTs obtained from diverse libraries representing different developmental stages of S. mansoni, deposited in the NCBI EST database. More than half of the deposited sequences correspond to genes of unknown function. Approximately 40-50% of the sequences form unique clusters, suggesting that approximately 20-25% of the total schistosome genes have been discovered. Efforts to develop low resolution chromosome maps are in progress. There is a genome sequencing program underway that will provide 3X sequence coverage of the S. mansoni genome that will result in approximately 95% gene discovery. The genomics era has provided the resources to usher in the era of functional genomics that will involve microarrays to focus on specific metabolic pathways, proteomics to identify relevant proteins and protein-protein interactions to understand critical parasite pathways. Functional genomics is expected to accelerate the development of control and treatment strategies for schistosomiasis.
VL - 53
SN - 1383-5769
ER -
TY - JOUR
T1 - Sequencing strategies for parasite genomes.
JF - Methods Mol Biol
Y1 - 2004
A1 - Bartholomeu, Daniella
A1 - El-Sayed, Najib M
KW - Animals
KW - Chromosome Walking
KW - Chromosomes, Artificial, Bacterial
KW - Genetic Markers
KW - Genome, Protozoan
KW - Plasmodium falciparum
AB - Recent advances in the field of sequencing have enabled the determination of the complete nucleotide sequence of a large number of complex genomes. The complete genome sequence of the parasite Plasmodium falciparum has been published recently, and many other parasite genome initiatives are underway. Parasite genomes vary in size, nucleotide composition, polymorphism level, content, and distribution of repetitive elements. These genomic features affect the performance of sequencing strategies. As a consequence, each of the ongoing parasite genome projects has adopted distinct sequencing approaches. The degree of completeness and accuracy desired as well as available funds should be considered carefully when choosing the most appropriate sequencing strategy.
VL - 270
M3 - 10.1385/1-59259-793-9:001
ER -
TY - JOUR
T1 - Sequencing Strategies for Parasite Genomes
JF - METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-
Y1 - 2004
A1 - Bartholomeu, D.
A1 - Najib M. El‐Sayed
A1 - Melville, S. E.
VL - 270
ER -
TY - JOUR
T1 - Direct Detection of Vibrio Cholerae and ctxA in Peruvian Coastal Water and Plankton by PCR
JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.
Y1 - 2003
A1 - Lipp, Erin K.
A1 - Rivera, Irma N. G.
A1 - Gil, Ana I.
A1 - Espeland, Eric M.
A1 - Choopun, Nipa
A1 - Louis, Valérie R.
A1 - Russek-Cohen, Estelle
A1 - Huq, Anwar
A1 - Rita R. Colwell
AB - Seawater and plankton samples were collected over a period of 17 months from November 1998 to March 2000 along the coast of Peru. Total DNA was extracted from water and from plankton grouped by size into two fractions (64 μm to 202 μm and >202 μm). All samples were assayed for Vibrio cholerae, V. cholerae O1, V. cholerae O139, and ctxA by PCR. Of 50 samples collected and tested, 33 (66.0%) were positive for V. cholerae in at least one of the three fractions. Of these, 62.5% (n = 32) contained V. cholerae O1; ctxA was detected in 25% (n = 20) of the V. cholerae O1-positive samples. None were positive for V. cholerae O139. Thus, PCR was successfully employed in detecting toxigenic V. cholerae directly in seawater and plankton samples and provides evidence for an environmental reservoir for this pathogen in Peruvian coastal waters.
VL - 69
SN - 0099-2240, 1098-5336
ER -
TY - JOUR
T1 - Genome of Geobacter sulfurreducens: metal reduction in subsurface environments
JF - Science (New York, N.Y.)Science (New York, N.Y.)
Y1 - 2003
A1 - Methé, B. A.
A1 - Nelson, K. E.
A1 - Eisen, J. A.
A1 - Paulsen, I. T.
A1 - Nelson, W.
A1 - Heidelberg, J. F.
A1 - Wu, D.
A1 - Wu, M.
A1 - Ward, N.
A1 - Beanan, M. J.
A1 - Dodson, R. J.
A1 - Madupu, R.
A1 - Brinkac, L. M.
A1 - Daugherty, S. C.
A1 - DeBoy, R. T.
A1 - Durkin, A. S.
A1 - Gwinn, M.
A1 - Kolonay, J. F.
A1 - Sullivan, S. A.
A1 - Haft, D. H.
A1 - J. Selengut
A1 - Davidsen, T. M.
A1 - Zafar, N.
A1 - White, O.
A1 - Tran, B.
A1 - Romero, C.
A1 - Forberger, H. A.
A1 - Weidman, J.
A1 - Khouri, H.
A1 - Feldblyum, T. V.
A1 - Utterback, T. R.
A1 - Van Aken, S. E.
A1 - Lovley, D. R.
A1 - Fraser, C. M.
KW - Acetates
KW - Acetyl Coenzyme A
KW - Aerobiosis
KW - Anaerobiosis
KW - Bacterial Proteins
KW - Carbon
KW - Chemotaxis
KW - Chromosomes, Bacterial
KW - Cytochromes c
KW - Electron Transport
KW - Energy Metabolism
KW - Genes, Bacterial
KW - Genes, Regulator
KW - Genome, Bacterial
KW - Geobacter
KW - Hydrogen
KW - Metals
KW - Movement
KW - Open Reading Frames
KW - Oxidation-Reduction
KW - Phylogeny
AB - The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.
VL - 302
N1 - http://www.ncbi.nlm.nih.gov/pubmed/14671304?dopt=Abstract
ER -
TY - JOUR
T1 - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
JF - NatureNature
Y1 - 2003
A1 - Read, Timothy D.
A1 - Peterson, Scott N.
A1 - Tourasse, Nicolas
A1 - Baillie, Les W.
A1 - Paulsen, Ian T.
A1 - Nelson, Karen E.
A1 - Tettelin, Herv
A1 - Fouts, Derrick E.
A1 - Eisen, Jonathan A.
A1 - Gill, Steven R.
A1 - Holtzapple, Erik K.
A1 - kstad, Ole Andreas
A1 - Helgason, Erlendur
A1 - Rilstone, Jennifer
A1 - Wu, Martin
A1 - Kolonay, James F.
A1 - Beanan, Maureen J.
A1 - Dodson, Robert J.
A1 - Brinkac, Lauren M.
A1 - Gwinn, Michelle
A1 - DeBoy, Robert T.
A1 - Madpu, Ramana
A1 - Daugherty, Sean C.
A1 - Durkin, A. Scott
A1 - Haft, Daniel H.
A1 - Nelson, William C.
A1 - Peterson, Jeremy D.
A1 - M. Pop
A1 - Khouri, Hoda M.
A1 - Radune, Diana
A1 - Benton, Jonathan L.
A1 - Mahamoud, Yasmin
A1 - Jiang, Lingxia
A1 - Hance, Ioana R.
A1 - Weidman, Janice F.
A1 - Berry, Kristi J.
A1 - Plaut, Roger D.
A1 - Wolf, Alex M.
A1 - Watkins, Kisha L.
A1 - Nierman, William C.
A1 - Hazen, Alyson
A1 - Cline, Robin
A1 - Redmond, Caroline
A1 - Thwaite, Joanne E.
A1 - White, Owen
A1 - Salzberg, Steven L.
A1 - Thomason, Brendan
A1 - Friedlander, Arthur M.
A1 - Koehler, Theresa M.
A1 - Hanna, Philip C.
A1 - Kolst,
A1 - Anne-Brit
A1 - Fraser, Claire M.
AB - Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax1. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity—including haemolysins, phospholipases and iron acquisition functions—and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax4. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.
VL - 423
SN - 0028-0836
N1 - [eacute]
[Oslash]
ER -
TY - JOUR
T1 - The sequence and analysis of Trypanosoma brucei chromosome II
JF - Nucleic acids researchNucleic Acids Research
Y1 - 2003
A1 - Najib M. El‐Sayed
A1 - Ghedin, E.
A1 - Song, J.
A1 - MacLeod, A.
A1 - Bringaud, F.
A1 - Larkin, C.
A1 - Wanless, D.
A1 - Peterson, J.
A1 - Hou, L.
A1 - Taylor, S.
A1 - others,
VL - 31
ER -
TY - JOUR
T1 - The sequence and analysis of Trypanosoma brucei chromosome II.
JF - Nucleic Acids Res
Y1 - 2003
A1 - el-Sayed, Najib M A
A1 - Ghedin, Elodie
A1 - Song, Jinming
A1 - MacLeod, Annette
A1 - Bringaud, Frederic
A1 - Larkin, Christopher
A1 - Wanless, David
A1 - Peterson, Jeremy
A1 - Hou, Lihua
A1 - Taylor, Sonya
A1 - Tweedie, Alison
A1 - Biteau, Nicolas
A1 - Khalak, Hanif G
A1 - Lin, Xiaoying
A1 - Mason, Tanya
A1 - Hannick, Linda
A1 - Caler, Elisabet
A1 - Blandin, Gaëlle
A1 - Bartholomeu, Daniella
A1 - Simpson, Anjana J
A1 - Kaul, Samir
A1 - Zhao, Hong
A1 - Pai, Grace
A1 - Van Aken, Susan
A1 - Utterback, Teresa
A1 - Haas, Brian
A1 - Koo, Hean L
A1 - Umayam, Lowell
A1 - Suh, Bernard
A1 - Gerrard, Caroline
A1 - Leech, Vanessa
A1 - Qi, Rong
A1 - Zhou, Shiguo
A1 - Schwartz, David
A1 - Feldblyum, Tamara
A1 - Salzberg, Steven
A1 - Tait, Andrew
A1 - Turner, C Michael R
A1 - Ullu, Elisabetta
A1 - White, Owen
A1 - Melville, Sara
A1 - Adams, Mark D
A1 - Fraser, Claire M
A1 - Donelson, John E
KW - Animals
KW - Antigens, Protozoan
KW - Chromosome mapping
KW - Chromosomes
KW - DNA, Protozoan
KW - Gene Duplication
KW - Genes, Protozoan
KW - Molecular Sequence Data
KW - Pseudogenes
KW - Recombination, Genetic
KW - Sequence Analysis, DNA
KW - Trypanosoma brucei brucei
AB - We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.
VL - 31
CP - 16
ER -
TY - JOUR
T1 - Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray.
JF - Mol Biochem Parasitol
Y1 - 2002
A1 - Diehl, Susanne
A1 - Diehl, Frank
A1 - El-Sayed, Najib M
A1 - Clayton, Christine
A1 - Hoheisel, Jörg D
KW - Animals
KW - Blotting, Northern
KW - Escherichia coli
KW - Gene expression
KW - Gene Expression Profiling
KW - Genes, Protozoan
KW - HUMANS
KW - Life Cycle Stages
KW - Molecular Sequence Data
KW - Oligonucleotide Array Sequence Analysis
KW - Polymerase Chain Reaction
KW - Transcription, Genetic
KW - Trypanosoma brucei brucei
AB - A microarray comprising 21,024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.
VL - 123
CP - 2
ER -
TY - JOUR
T1 - Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 2002
A1 - Diehl, Susanne
A1 - Diehl, Frank
A1 - Najib M. El‐Sayed
A1 - Clayton, Christine
A1 - Hoheisel, Jörg D.
KW - Expression
KW - Gene
KW - Microarray
KW - Regulation
KW - Trypanosoma brucei
AB - A microarray comprising 21[punctuation space]024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.
VL - 123
SN - 0166-6851
ER -
TY - CHAP
T1 - Combinatorial Algorithms for Design of DNA Arrays
T2 - Chip TechnologyChip Technology
Y1 - 2002
A1 - Sridhar Hannenhalli
A1 - Hubbell, Earl
A1 - Lipshutz, Robert
A1 - Pevzner, Pavel
ED - Hoheisel, Jörg
ED - Brazma, A.
ED - Büssow, K.
ED - Cantor, C.
ED - Christians, F.
ED - Chui, G.
ED - Diaz, R.
ED - Drmanac, R.
ED - Drmanac, S.
ED - Eickhoff, H.
ED - Fellenberg, K.
ED - Sridhar Hannenhalli
ED - Hoheisel, J.
ED - Hou, A.
ED - Hubbell, E.
ED - Jin, H.
ED - Jin, P.
ED - Jurinke, C.
ED - Konthur, Z.
ED - Köster, H.
ED - Kwon, S.
ED - Lacy, S.
ED - Lehrach, H.
ED - Lipshutz, R.
ED - Little, D.
ED - Lueking, A.
ED - McGall, G.
ED - Moeur, B.
ED - Nordhoff, E.
ED - Nyarsik, L.
ED - Pevzner, P.
ED - Robinson, A.
ED - Sarkans, U.
ED - Shafto, J.
ED - Sohail, M.
ED - Southern, E.
ED - Swanson, D.
ED - Ukrainczyk, T.
ED - van den Boom, D.
ED - Vilo, J.
ED - Vingron, M.
ED - Walter, G.
ED - Xu, C.
AB - Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20–30% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.
JA - Chip TechnologyChip Technology
T3 - Advances in Biochemical Engineering/Biotechnology
PB - Springer Berlin / Heidelberg
VL - 77
SN - 978-3-540-43215-9
ER -
TY - JOUR
T1 - Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
JF - NatureNature
Y1 - 2002
A1 - Carlton, Jane M.
A1 - Angiuoli, Samuel V.
A1 - Suh, Bernard B.
A1 - Kooij, Taco W.
A1 - Pertea, Mihaela
A1 - Silva, Joana C.
A1 - Ermolaeva, Maria D.
A1 - Allen, Jonathan E.
A1 - J. Selengut
A1 - Koo, Hean L.
A1 - Peterson, Jeremy D.
A1 - M. Pop
A1 - Kosack, Daniel S.
A1 - Shumway, Martin F.
A1 - Bidwell, Shelby L.
A1 - Shallom, Shamira J.
A1 - Aken, Susan E. van
A1 - Riedmuller, Steven B.
A1 - Feldblyum, Tamara V.
A1 - Cho, Jennifer K.
A1 - Quackenbush, John
A1 - Sedegah, Martha
A1 - Shoaibi, Azadeh
A1 - Cummings, Leda M.
A1 - Florens, Laurence
A1 - Yates, John R.
A1 - Raine, J. Dale
A1 - Sinden, Robert E.
A1 - Harris, Michael A.
A1 - Cunningham, Deirdre A.
A1 - Preiser, Peter R.
A1 - Bergman, Lawrence W.
A1 - Vaidya, Akhil B.
A1 - Lin, Leo H. van
A1 - Janse, Chris J.
A1 - Waters, Andrew P.
A1 - Smith, Hamilton O.
A1 - White, Owen R.
A1 - Salzberg, Steven L.
A1 - Venter, J. Craig
A1 - Fraser, Claire M.
A1 - Hoffman, Stephen L.
A1 - Gardner, Malcolm J.
A1 - Carucci, Daniel J.
AB - Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.
VL - 419
SN - 0028-0836
ER -
TY - JOUR
T1 - Genome sequence of the human malaria parasite Plasmodium falciparum
JF - NatureNature
Y1 - 2002
A1 - Gardner, Malcolm J.
A1 - Hall, Neil
A1 - Fung, Eula
A1 - White, Owen
A1 - Berriman, Matthew
A1 - Hyman, Richard W.
A1 - Carlton, Jane M.
A1 - Pain, Arnab
A1 - Nelson, Karen E.
A1 - Bowman, Sharen
A1 - Paulsen, Ian T.
A1 - James, Keith
A1 - Eisen, Jonathan A.
A1 - Rutherford, Kim
A1 - Salzberg, Steven L.
A1 - Craig, Alister
A1 - Kyes, Sue
A1 - Chan, Man-Suen
A1 - Nene, Vishvanath
A1 - Shallom, Shamira J.
A1 - Suh, Bernard
A1 - Peterson, Jeremy
A1 - Angiuoli, Sam
A1 - Pertea, Mihaela
A1 - Allen, Jonathan
A1 - J. Selengut
A1 - Haft, Daniel
A1 - Mather, Michael W.
A1 - Vaidya, Akhil B.
A1 - Martin, David M. A.
A1 - Fairlamb, Alan H.
A1 - Fraunholz, Martin J.
A1 - Roos, David S.
A1 - Ralph, Stuart A.
A1 - McFadden, Geoffrey I.
A1 - Cummings, Leda M.
A1 - Subramanian, G. Mani
A1 - Mungall, Chris
A1 - Venter, J. Craig
A1 - Carucci, Daniel J.
A1 - Hoffman, Stephen L.
A1 - Newbold, Chris
A1 - Davis, Ronald W.
A1 - Fraser, Claire M.
A1 - Barrell, Bart
KW - Animals
KW - Chromosome Structures
KW - DNA Repair
KW - DNA Replication
KW - DNA, Protozoan
KW - Evolution, Molecular
KW - Genome, Protozoan
KW - HUMANS
KW - Malaria Vaccines
KW - Malaria, Falciparum
KW - Membrane Transport Proteins
KW - Molecular Sequence Data
KW - Plasmodium falciparum
KW - Plastids
KW - Proteome
KW - Protozoan Proteins
KW - Recombination, Genetic
KW - Sequence Analysis, DNA
AB - The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.
VL - 419
N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368864?dopt=Abstract
ER -
TY - JOUR
T1 - Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 2002
A1 - Bringaud, Frederic
A1 - García-Pérez, José Luis
A1 - Heras, Sara R.
A1 - Ghedin, Elodie
A1 - Najib M. El‐Sayed
A1 - Andersson, Björn
A1 - Baltz, Théo
A1 - Lopez, Manuel C.
KW - Ingi
KW - L1Tc
KW - Non-LTR retrotransposon
KW - RIME
KW - Trypanosoma brucei
KW - Trypanosoma cruzi
AB - As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5'-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.
VL - 124
SN - 0166-6851
ER -
TY - JOUR
T1 - Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi.
JF - Mol Biochem Parasitol
Y1 - 2002
A1 - Bringaud, Frederic
A1 - García-Pérez, José Luis
A1 - Heras, Sara R
A1 - Ghedin, Elodie
A1 - El-Sayed, Najib M
A1 - Andersson, Björn
A1 - Baltz, Théo
A1 - Lopez, Manuel C
KW - Animals
KW - Base Sequence
KW - Computational Biology
KW - Genome, Protozoan
KW - Long Interspersed Nucleotide Elements
KW - Molecular Sequence Data
KW - Retroelements
KW - Short Interspersed Nucleotide Elements
KW - Trypanosoma cruzi
AB - As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5'-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.
VL - 124
CP - 1-2
ER -
TY - JOUR
T1 - A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei
JF - Eukaryotic cellEukaryotic Cell
Y1 - 2002
A1 - Bringaud, F.
A1 - Biteau, N.
A1 - Melville, S. E.
A1 - Hez, S.
A1 - Najib M. El‐Sayed
A1 - Leech, V.
A1 - Berriman, M.
A1 - Hall, N.
A1 - Donelson, J. E.
A1 - Baltz, T.
VL - 1
ER -
TY - JOUR
T1 - A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei.
JF - Eukaryot Cell
Y1 - 2002
A1 - Bringaud, Frederic
A1 - Biteau, Nicolas
A1 - Melville, Sara E
A1 - Hez, Stéphanie
A1 - El-Sayed, Najib M
A1 - Leech, Vanessa
A1 - Berriman, Matthew
A1 - Hall, Neil
A1 - Donelson, John E
A1 - Baltz, Théo
KW - Amino Acid Sequence
KW - Animals
KW - Base Sequence
KW - Cloning, Molecular
KW - DNA Primers
KW - DNA, Protozoan
KW - Escherichia coli
KW - Genes, Protozoan
KW - Molecular Sequence Data
KW - Multigene Family
KW - Mutagenesis, Insertional
KW - Phylogeny
KW - Polymorphism, Genetic
KW - Protozoan Proteins
KW - Pseudogenes
KW - Retroelements
KW - sequence alignment
KW - Sequence Homology, Amino Acid
KW - Telomere
KW - Trypanosoma brucei brucei
KW - Trypanosoma cruzi
AB - We describe a novel gene family that forms clusters in subtelomeric regions of Trypanosoma brucei chromosomes and partially accounts for the observed clustering of retrotransposons. The ingi and ribosomal inserted mobile element (RIME) non-LTR retrotransposons share 250 bp at both extremities and are the most abundant putatively mobile elements, with about 500 copies per haploid genome. From cDNA clones and subsequently in the T. brucei genomic DNA databases, we identified 52 homologous gene and pseudogene sequences, 16 of which contain a RIME and/or ingi retrotransposon inserted at exactly the same relative position. Here these genes are called the RHS family, for retrotransposon hot spot. Comparison of the protein sequences encoded by RHS genes (21 copies) and pseudogenes (24 copies) revealed a conserved central region containing an ATP/GTP-binding motif and the RIME/ingi insertion site. The RHS proteins share between 13 and 96% identity, and six subfamilies, RHS1 to RHS6, can be defined on the basis of their divergent C-terminal domains. Immunofluorescence and Western blot analyses using RHS subfamily-specific immune sera show that RHS proteins are constitutively expressed and occur mainly in the nucleus. Analysis of Genome Survey Sequence databases indicated that the Trypanosoma brucei diploid genome contains about 280 RHS (pseudo)genes. Among the 52 identified RHS (pseudo)genes, 48 copies are in three RHS clusters located in subtelomeric regions of chromosomes Ia and II and adjacent to the active bloodstream form expression site in T. brucei strain TREU927/4 GUTat10.1. RHS genes comprise the remaining sequence of the size-polymorphic "repetitive region" described for T. brucei chromosome I, and a homologous gene family is present in the Trypanosoma cruzi genome.
VL - 1
CP - 1
ER -
TY - JOUR
T1 - Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression
JF - Experimental ParasitologyExperimental Parasitology
Y1 - 2002
A1 - Bartholomeu, Daniella C.
A1 - Silva, Rosiane A.
A1 - Galvão, Lucia M. C.
A1 - Najib M. El‐Sayed
A1 - Donelson, John E.
A1 - Teixeira, Santuza M. R.
AB - Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of [alpha]- and [beta]-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two [beta]-tubulin mRNAs of 1.9 and 2.3 kb were found to differ mainly by an additional 369 nucleotides at the end of the 3' untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, [alpha]- and [beta]-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of [alpha]- and [beta]-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3' UTR plus downstream intergenic region of the [alpha]-tubulin gene and that both positive and negative elements occur in the equivalent regions of the [beta]-tubulin gene.Index Descriptions and Abbreviations: Kinetoplastida; Trypanosoma cruzi; tubulin; gene regulation; PCR, polymerase chain reaction; UTR, untranslated region; IR, intergenic region; SL, spliced leader; BAC, bacterial artificial chromosome.
VL - 102
SN - 0014-4894
ER -
TY - JOUR
T1 - Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression.
JF - Exp Parasitol
Y1 - 2002
A1 - Bartholomeu, Daniella C
A1 - Silva, Rosiane A
A1 - Galvão, Lucia M C
A1 - el-Sayed, Najib M A
A1 - Donelson, John E
A1 - Teixeira, Santuza M R
KW - Animals
KW - Base Sequence
KW - Blotting, Northern
KW - DNA, Complementary
KW - DNA, Protozoan
KW - Gene Expression Regulation
KW - Half-Life
KW - Life Cycle Stages
KW - Molecular Sequence Data
KW - RNA Processing, Post-Transcriptional
KW - RNA, Messenger
KW - RNA, Protozoan
KW - Transcription, Genetic
KW - Transfection
KW - Trypanosoma cruzi
KW - Tubulin
AB - Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of alpha- and beta-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two beta-tubulin mRNAs of 1.9 and 2.3 kb were found to differ mainly by an additional 369 nucleotides at the end of the 3' untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, alpha- and beta-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of alpha- and beta-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3' UTR plus downstream intergenic region of the alpha-tubulin gene and that both positive and negative elements occur in the equivalent regions of the beta-tubulin gene.
VL - 102
CP - 3-4
ER -
TY - JOUR
T1 - Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes
JF - Nucleic acids researchNucleic Acids Research
Y1 - 2001
A1 - LaCount, D. J.
A1 - Najib M. El‐Sayed
A1 - Kaul, S.
A1 - Wanless, D.
A1 - Turner, C. M. R.
A1 - Donelson, J. E.
VL - 29
ER -
TY - JOUR
T1 - The African trypanosome genome
JF - International Journal for ParasitologyInternational Journal for Parasitology
Y1 - 2000
A1 - Najib M. El‐Sayed
A1 - Hegde, Priti
A1 - Quackenbush, John
A1 - Melville, Sara E.
A1 - Donelson, John E.
AB - The haploid nuclear genome of the African trypanosome, Trypanosoma brucei, is about 35 Mb and varies in size among different trypanosome isolates by as much as 25%. The nuclear DNA of this diploid organism is distributed among three size classes of chromosomes: the megabase chromosomes of which there are at least 11 pairs ranging from 1 Mb to more than 6 Mb (numbered I-XI from smallest to largest); several intermediate chromosomes of 200-900 kb and uncertain ploidy; and about 100 linear minichromosomes of 50-150 kb. Size differences of as much as four-fold can occur, both between the two homologues of a megabase chromosome pair in a specific trypanosome isolate and among chromosome pairs in different isolates. The genomic DNA sequences determined to date indicated that about 50% of the genome is coding sequence. The chromosomal telomeres possess TTAGGG repeats and many, if not all, of the telomeres of the megabase and intermediate chromosomes are linked to expression sites for genes encoding variant surface glycoproteins (VSGs). The minichromosomes serve as repositories for VSG genes since some but not all of their telomeres are linked to unexpressed VSG genes. A gene discovery program, based on sequencing the ends of cloned genomic DNA fragments, has generated more than 20 Mb of discontinuous single-pass genomic sequence data during the past year, and the complete sequences of chromosomes I and II (about 1 Mb each) in T. brucei GUTat 10.1 are currently being determined. It is anticipated that the entire genomic sequence of this organism will be known in a few years. Analysis of a test microarray of 400 cDNAs and small random genomic DNA fragments probed with RNAs from two developmental stages of T. brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite.
VL - 30
SN - 0020-7519
ER -
TY - JOUR
T1 - A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity
JF - Molecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol
Y1 - 2000
A1 - Pollock, David D.
A1 - Eisen, Jonathan A.
A1 - Doggett, Norman A.
A1 - Michael P. Cummings
AB - Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.
VL - 17
SN - 0737-4038, 1537-1719
ER -
TY - JOUR
T1 - The genome sequence of Drosophila melanogaster.
JF - Science
Y1 - 2000
A1 - Adams, M D
A1 - Celniker, S E
A1 - Holt, R A
A1 - Evans, C A
A1 - Gocayne, J D
A1 - Amanatides, P G
A1 - Scherer, S E
A1 - Li, P W
A1 - Hoskins, R A
A1 - Galle, R F
A1 - George, R A
A1 - Lewis, S E
A1 - Richards, S
A1 - Ashburner, M
A1 - Henderson, S N
A1 - Sutton, G G
A1 - Wortman, J R
A1 - Yandell, M D
A1 - Zhang, Q
A1 - Chen, L X
A1 - Brandon, R C
A1 - Rogers, Y H
A1 - Blazej, R G
A1 - Champe, M
A1 - Pfeiffer, B D
A1 - Wan, K H
A1 - Doyle, C
A1 - Baxter, E G
A1 - Helt, G
A1 - Nelson, C R
A1 - Gabor, G L
A1 - Abril, J F
A1 - Agbayani, A
A1 - An, H J
A1 - Andrews-Pfannkoch, C
A1 - Baldwin, D
A1 - Ballew, R M
A1 - Basu, A
A1 - Baxendale, J
A1 - Bayraktaroglu, L
A1 - Beasley, E M
A1 - Beeson, K Y
A1 - Benos, P V
A1 - Berman, B P
A1 - Bhandari, D
A1 - Bolshakov, S
A1 - Borkova, D
A1 - Botchan, M R
A1 - Bouck, J
A1 - Brokstein, P
A1 - Brottier, P
A1 - Burtis, K C
A1 - Busam, D A
A1 - Butler, H
A1 - Cadieu, E
A1 - Center, A
A1 - Chandra, I
A1 - Cherry, J M
A1 - Cawley, S
A1 - Dahlke, C
A1 - Davenport, L B
A1 - Davies, P
A1 - de Pablos, B
A1 - Delcher, A
A1 - Deng, Z
A1 - Mays, A D
A1 - Dew, I
A1 - Dietz, S M
A1 - Dodson, K
A1 - Doup, L E
A1 - Downes, M
A1 - Dugan-Rocha, S
A1 - Dunkov, B C
A1 - Dunn, P
A1 - Durbin, K J
A1 - Evangelista, C C
A1 - Ferraz, C
A1 - Ferriera, S
A1 - Fleischmann, W
A1 - Fosler, C
A1 - Gabrielian, A E
A1 - Garg, N S
A1 - Gelbart, W M
A1 - Glasser, K
A1 - Glodek, A
A1 - Gong, F
A1 - Gorrell, J H
A1 - Gu, Z
A1 - Guan, P
A1 - Harris, M
A1 - Harris, N L
A1 - Harvey, D
A1 - Heiman, T J
A1 - Hernandez, J R
A1 - Houck, J
A1 - Hostin, D
A1 - Houston, K A
A1 - Howland, T J
A1 - Wei, M H
A1 - Ibegwam, C
A1 - Jalali, M
A1 - Kalush, F
A1 - Karpen, G H
A1 - Ke, Z
A1 - Kennison, J A
A1 - Ketchum, K A
A1 - Kimmel, B E
A1 - Kodira, C D
A1 - Kraft, C
A1 - Kravitz, S
A1 - Kulp, D
A1 - Lai, Z
A1 - Lasko, P
A1 - Lei, Y
A1 - Levitsky, A A
A1 - Li, J
A1 - Li, Z
A1 - Liang, Y
A1 - Lin, X
A1 - Liu, X
A1 - Mattei, B
A1 - McIntosh, T C
A1 - McLeod, M P
A1 - McPherson, D
A1 - Merkulov, G
A1 - Milshina, N V
A1 - Mobarry, C
A1 - Morris, J
A1 - Moshrefi, A
A1 - Mount, S M
A1 - Moy, M
A1 - Murphy, B
A1 - Murphy, L
A1 - Muzny, D M
A1 - Nelson, D L
A1 - Nelson, D R
A1 - Nelson, K A
A1 - Nixon, K
A1 - Nusskern, D R
A1 - Pacleb, J M
A1 - Palazzolo, M
A1 - Pittman, G S
A1 - Pan, S
A1 - Pollard, J
A1 - Puri, V
A1 - Reese, M G
A1 - Reinert, K
A1 - Remington, K
A1 - Saunders, R D
A1 - Scheeler, F
A1 - Shen, H
A1 - Shue, B C
A1 - Sidén-Kiamos, I
A1 - Simpson, M
A1 - Skupski, M P
A1 - Smith, T
A1 - Spier, E
A1 - Spradling, A C
A1 - Stapleton, M
A1 - Strong, R
A1 - Sun, E
A1 - Svirskas, R
A1 - Tector, C
A1 - Turner, R
A1 - Venter, E
A1 - Wang, A H
A1 - Wang, X
A1 - Wang, Z Y
A1 - Wassarman, D A
A1 - Weinstock, G M
A1 - Weissenbach, J
A1 - Williams, S M
A1 - Worley, K C
A1 - Wu, D
A1 - Yang, S
A1 - Yao, Q A
A1 - Ye, J
A1 - Yeh, R F
A1 - Zaveri, J S
A1 - Zhan, M
A1 - Zhang, G
A1 - Zhao, Q
A1 - Zheng, L
A1 - Zheng, X H
A1 - Zhong, F N
A1 - Zhong, W
A1 - Zhou, X
A1 - Zhu, S
A1 - Zhu, X
A1 - Smith, H O
A1 - Gibbs, R A
A1 - Myers, E W
A1 - Rubin, G M
A1 - Venter, J C
KW - Animals
KW - Biological Transport
KW - Chromatin
KW - Cloning, Molecular
KW - Computational Biology
KW - Contig Mapping
KW - Cytochrome P-450 Enzyme System
KW - DNA Repair
KW - DNA Replication
KW - Drosophila melanogaster
KW - Euchromatin
KW - Gene Library
KW - Genes, Insect
KW - Genome
KW - Heterochromatin
KW - Insect Proteins
KW - Nuclear Proteins
KW - Protein Biosynthesis
KW - Sequence Analysis, DNA
KW - Transcription, Genetic
AB - The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
VL - 287
CP - 5461
ER -
TY - JOUR
T1 - More surprises from Kinetoplastida
JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America
Y1 - 1999
A1 - Donelson, J. E.
A1 - Gardner, M. J.
A1 - Najib M. El‐Sayed
VL - 96
ER -
TY - CHAP
T1 - Multiple mechanisms of immune evasion by African trypanosomes
T2 - The Trypanosome Surface
Y1 - 1999
A1 - Donelson, J.E.
A1 - Hill, K.L.
A1 - El-Sayed, N.M.A.
JA - The Trypanosome Surface
PB - De Boeck & Larcier s.a.
CY - Brussels
ER -
TY - JOUR
T1 - Genetic nomenclature for Trypanosoma and Leishmania.
JF - Mol Biochem Parasitol
Y1 - 1998
A1 - Clayton, C
A1 - Adams, M
A1 - Almeida, R
A1 - Baltz, T
A1 - Barrett, M
A1 - Bastien, P
A1 - Belli, S
A1 - Beverley, S
A1 - Biteau, N
A1 - Blackwell, J
A1 - Blaineau, C
A1 - Boshart, M
A1 - Bringaud, F
A1 - Cross, G
A1 - Cruz, A
A1 - Degrave, W
A1 - Donelson, J
A1 - El-Sayed, N
A1 - Fu, G
A1 - Ersfeld, K
A1 - Gibson, W
A1 - Gull, K
A1 - Ivens, A
A1 - Kelly, J
A1 - Vanhamme, L
KW - Animals
KW - Leishmania
KW - Terminology as Topic
KW - Trypanosoma
VL - 97
CP - 1-2
ER -
TY - JOUR
T1 - Multiple mechanisms of immune evasion by African trypanosomes
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 1998
A1 - Donelson, John E.
A1 - Hill, Kent L.
A1 - Najib M. El‐Sayed
KW - Leishmania
KW - Recombinant cloning
KW - T cell
KW - Trypanosomes
KW - VSG genes
AB - During infection of a mammalian host, African trypanosomes are in constant contact with the host's immune system. These protozoan parasites are infamous for their ability to evade the immune responses by periodically switching their major variant surface glycoprotein (VSG), a phenomenon called antigenic variation. Antigenic variation, however, is likely to be only one of several mechanisms enabling these organisms to thrive in the face of the immune defenses. The ability to grow in high levels of interferon-gamma (IFN-[gamma]) and to avoid complement-mediated destruction may also facilitate the parasite's survival. In this review we summarize (i) the activation of trypanosome genes for three different VSGs during antigenic variation, (ii) the secretion of a trypanosome protein that induces host CD8+ T cells to produce IFN-[gamma], and (iii) the evidence for trypansome protein similar to a surface protease of Leishmania that plays a role in resistance to complement-mediated lysis.
VL - 91
SN - 0166-6851
ER -
TY - JOUR
T1 - Trends in the early careers of life scientists - Preface and executive summary
JF - Mol Biol CellMol Biol Cell
Y1 - 1998
A1 - Tilghman, S.
A1 - Astin, H. S.
A1 - Brinkley, W.
A1 - Chilton, M. D.
A1 - Michael P. Cummings
A1 - Ehrenberg, R. G.
A1 - Fox, M. F.
A1 - Glenn, K.
A1 - Green, P. J.
A1 - Hans, S.
A1 - Kelman, A.
A1 - LaPidus, J.
A1 - Levin, B.
A1 - McIntosh, J. R.
A1 - Riecken, H.
A1 - Stephen, P. E.
VL - 9
ER -
TY - JOUR
T1 - African trypanosomes have differentially expressed genes encoding homologues of the Leishmania GP63 surface protease
JF - Journal of Biological ChemistryJournal of Biological Chemistry
Y1 - 1997
A1 - Najib M. El‐Sayed
A1 - Donelson, J. E.
VL - 272
ER -
TY - CHAP
T1 - Sequencing and mapping the African trypanosome genome
T2 - Trypanosomiasis and Leishmaniasis: Biology and Control
Y1 - 1997
A1 - El-Sayed, N.M.A
A1 - Donelson, J.E.
JA - Trypanosomiasis and Leishmaniasis: Biology and Control
PB - CAB International and the British Society for Parasitology pubs
ER -
TY - JOUR
T1 - A survey of the Trypanosoma brucei rhodesiense genome using shotgun sequencing
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 1997
A1 - Najib M. El‐Sayed
A1 - Donelson, John E.
KW - Expressed sequence tag
KW - Genome survey sequence
KW - Trypanosoma brucei rhodesiense
AB - A comparison of the efficiency of sequencing random genomic DNA fragments versus random cDNAs for the discovery of new genes in African trypanosomes was undertaken. Trypanosome DNA was sheared to a 1.5-2.5 kb size distribution, cloned into a plasmid and the sequences at both ends of 183 cloned fragments determined. Sequences of both kinetoplast and nuclear DNA were identified. New coding regions were discovered for a variety of proteins, including cell division proteins, an RNA-binding protein and a homologue of the Leishmania surface protease GP63. In some cases, each end of a fragment was found to contain a different gene, demonstrating the proximity of those genes and suggesting that the density of genes in the African trypanosome genome is quite high. Repetitive sequence elements found included telomeric hexamer repeats, 76 bp repeats associated with VSG gene expression sites, 177 bp satellite repeats in minichromosomes and the Ingi transposon-like elements. In contrast to cDNA sequencing, no ribosomal protein genes were detected. For the sake of comparison, the sequences of 190 expressed sequence tags (ESTs) were also determined, and a similar number of new trypanosomal homologues were found including homologues of another putative surface protein and a human leucine-rich repeat-containing protein. We conclude from this analysis and our previous work that sequencing random DNA fragments in African trypanosomes is as efficient for gene discovery as is sequencing random cDNA clones.
VL - 84
SN - 0166-6851
ER -
TY - JOUR
T1 - Differential expression of the expression site-associated gene I family in African trypanosomes
JF - Journal of Biological ChemistryJournal of Biological Chemistry
Y1 - 1996
A1 - Morgan, R. W.
A1 - Najib M. El‐Sayed
A1 - Kepa, J. K.
A1 - Pedram, M.
A1 - Donelson, J. E.
VL - 271
ER -
TY - JOUR
T1 - cDNA expressed sequence tags of Trypanosoma brucei rhodesiense provide new insights into the biology of the parasite
JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology
Y1 - 1995
A1 - Najib M. El‐Sayed
A1 - Alarcon, Clara M.
A1 - Beck, John C.
A1 - Sheffield, Val C.
A1 - Donelson, John E.
KW - cDNA
KW - Expressed sequence tag
KW - Trypanosoma brucei rhodesiense
AB - A total of 518 expressed sequence tags (ESTs) have been generated from clones randomly selected from a cDNA library and a spliced leader sub-library of a Trypanosoma brucei rhodesiense bloodstream clone. 205 (39%) of the clones were identified based on matches to 113 unique genes in the public databases. Of these, 71 cDNAs display significant similarities to genes in unrelated organisms encoding metabolic enzymes, signal transduction proteins, transcription factors, ribosomal proteins, histones, a proliferation-associated protein and thimet oligopeptidase, among others. 313 of the cDNAs are not related to any other sequences in the databases. These cDNA ESTs provide new avenues of research for exploring both the novel trypanosome-specific genes and the genome organization of this parasite, as well as a resource for identifying trypanosome homologs to genes expressed in other organisms.
VL - 73
SN - 0166-6851
ER -
TY - JOUR
T1 - Crystallization and preliminary X-ray investigation of the recombinant Trypanosoma brucei rhodesiense calmodulin
JF - Proteins: Structure, Function, and BioinformaticsProteins: Structure, Function, and Bioinformatics
Y1 - 1995
A1 - Najib M. El‐Sayed
A1 - Patton, C. L.
A1 - Harkins, P. C.
A1 - Fox, R. O.
A1 - Anderson, K.
VL - 21
ER -
TY - JOUR
T1 - Detection of alloantigens during preimplantation development and early trophoblast differentiation in the mouse by immunoperoxidase labeling.
JF - J Exp Med
Y1 - 1976
A1 - Searle, R F
A1 - Sellens, M H
A1 - Elson, J
A1 - Jenkinson, E J
A1 - Billington, W D
KW - Animals
KW - Binding Sites, Antibody
KW - Blastocyst
KW - Cell Differentiation
KW - Cell Membrane
KW - Embryo Implantation
KW - Embryonic Development
KW - Epitopes
KW - Female
KW - Histocompatibility Antigens
KW - HLA Antigens
KW - Horseradish Peroxidase
KW - Mice
KW - Mice, Inbred Strains
KW - Pregnancy
KW - Pregnancy, Animal
KW - Trophoblasts
AB - An immunoperoxidase-labeling technique allowing visualization of antibody binding to the cell surface at the electron microscopical level has been employed an an analysis of H-2 and non-H-2 alloantigen expression on the early mouse embryo. The presence of non-H-2 antigenic determinants has been confirmed on eight-cell, morula, and blastocyst stages of development. Contrary to previous reports, however, low levels of H-2 antigen have also been detected on the blastocyst. This is the earliest stage at which H-2 has been shown to be expressed on the fertilized mouse egg and may reflect the greater resolution of the immunoperoxidase technique. Using two different models to study the critical peri-implantation stages, those of experimentally induced blastocyst activation and blastocyst outgrowth in vitro, it has been demonstrated that antigen loss occurs on the trophectoderm at the time of implantation, and that this is not necessarily dependent upon maternal influence. It is suggested that the loss may be an important factor in the prevention of maternal immune rejection during the establishment of the fetal allograft. The two major components of the early postimplantation conceptus display a striking differential in antigenic status. The embryonic sac shows a high degree of peroxidase labeling, while the ectoplacental cone trophoblast is unlabeled. These findings add support to the concept of antigenic neutrality of the early trophoblast and its role in the maintenance of a normal fetomaternal immunological equilibrium.
VL - 143
CP - 2
ER -