@article {49865, title = {Draft Genome Sequences from a Novel Clade of Bacillus cereus sensu lato Strains Isolated from the International Space Station}, volume = {1}, year = {2017}, pages = {1}, author = {Kasthuri Venkateswaran and Aleksandra Checinska-Sielaff and Joy Klubnik and Todd Treangen and M.J. Rosovitz and Nicholas H. Bergman} } @article {49816, title = {Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction}, journal = {PLOS Computational Biology}, volume = {12}, year = {2016}, month = {Mar-09-2018}, pages = {e1005125}, doi = {10.1371/journal.pcbi.1005125}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005125}, author = {Auslander, Noam and Wagner, Allon and Oberhardt, Matthew and Ruppin, Eytan}, editor = {Przytycka, Teresa M.} } @article {49756, title = {Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer}, journal = {BMC Cancer}, volume = {16447943582141728452710921541113181321912}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s12885-016-2128-1}, url = {http://www.biomedcentral.com/1471-2407/16/88http://link.springer.com/content/pdf/10.1186/s12885-016-2128-1}, author = {Sharmin, Mahfuza and Bravo, {\'e}ctor Corrada and Hannenhalli, Sridhar} } @article {49810, title = {Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0160574}, abstract = {

The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B{\textquoteright}a(2-13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0160574}, author = {Davison, Michelle and Todd Treangen and Koren, Sergey and Pop, Mihai and Bhaya, Devaki} } @article {49827, title = {Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures}, journal = {mBio}, volume = {7}, year = {2016}, month = {Jun-07-2016}, pages = {e00027-16}, doi = {10.1128/mBio.00027-16}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00027-16https://syndication.highwire.org/content/doi/10.1128/mBio.00027-16}, author = {Fernandes, Maria Cecilia and Dillon, Laura A. L. and Belew, Ashton Trey and Bravo, H{\'e}ctor Corrada and Mosser, David M. and El-Sayed, Najib M.} } @article {49658, title = {Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis}, journal = {Nature}, volume = {527}, year = {2015}, month = {Nov-11-2015}, pages = {379 - 383}, issn = {0028-0836}, doi = {10.1038/nature15529}, url = {http://www.nature.com/doifinder/10.1038/nature15529}, author = {Rabinovich, Shiran and Adler, Lital and Yizhak, Keren and Sarver, Alona and Silberman, Alon and Agron, Shani and Stettner, Noa and Sun, Qin and Brandis, Alexander and Helbling, Daniel and Korman, Stanley and Itzkovitz, Shalev and Dimmock, David and Ulitsky, Igor and Nagamani, Sandesh C. S. and Ruppin, Eytan and Erez, Ayelet} } @article {49733, title = {Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia.}, journal = {Mol Syst Biol}, volume = {11}, year = {2015}, month = {2015 Mar}, pages = {791}, abstract = {

High-throughput omics have proven invaluable in studying human disease, and yet day-to-day clinical practice still relies on physiological, non-omic markers. The metabolic syndrome, for example, is diagnosed and monitored by blood and urine indices such as blood cholesterol levels. Nevertheless, the association between the molecular and the physiological manifestations of the disease, especially in response to treatment, has not been investigated in a systematic manner. To this end, we studied a mouse model of diet-induced dyslipidemia and atherosclerosis that was subject to various drug treatments relevant to the disease in question. Both physiological data and gene expression data (from the liver and white adipose) were analyzed and compared. We find that treatments that restore gene expression patterns to their norm are associated with the successful restoration of physiological markers to their baselines. This holds in a tissue-specific manner{\textemdash}treatments that reverse the transcriptomic signatures of the disease in a particular tissue are associated with positive physiological effects in that tissue. Further, treatments that introduce large non-restorative gene expression alterations are associated with unfavorable physiological outcomes. These results provide a sound basis to in silico methods that rely on omic metrics for drug repurposing and drug discovery by searching for compounds that reverse a disease{\textquoteright}s omic signatures. Moreover, they highlight the need to develop drugs that restore the global cellular state to its healthy norm rather than rectify particular disease phenotypes.

}, issn = {1744-4292}, author = {Wagner, Allon and Cohen, Noa and Kelder, Thomas and Amit, Uri and Liebman, Elad and Steinberg, David M and Radonjic, Marijana and Ruppin, Eytan} } @article {49596, title = {Determinants of expression variability}, volume = {42}, year = {2014}, month = {Jan-04-2014}, pages = {3503 - 3514}, issn = {0305-1048}, doi = {10.1093/nar/gkt1364}, url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt1364}, author = {Alemu, E. Y. and Carl, J. W. and Corrada Bravo, H. and Hannenhalli, S.} } @article {49595, title = {Developmental expression of chicken FOXN1 and putative target genes during feather development.}, volume = {58}, year = {2014}, month = {2014}, pages = {57-64}, abstract = {

FOXN1 is a member of the forkhead box family of transcription factors. FOXN1 is crucial for hair outgrowth and thymus differentiation in mammals. Unlike the thymus, which is found in all amniotes, hair is an epidermal appendage that arose after the last shared common ancestor between mammals and birds, and hair and feathers differ markedly in their differentiation and gene expression. Here, we show that FOXN1 is expressed in embryonic chicken feathers, nails and thymus, demonstrating an evolutionary conservation that goes beyond obvious homology. At embryonic day (ED) 12, FOXN1 is expressed in some feather buds and at ED13 expression extends along the length of the feather filament. At ED14 FOXN1 mRNA is restricted to the proximal feather filament and is not detectable in distal feather shafts. At the base of the feather, FOXN1 is expressed in the epithelium of the feather sheath and distal barb and marginal plate, whereas in the midsection FOXN1 transcripts are mainly detected in the barb plates of the feather filament. FOXN1 is also expressed in claws; however, no expression was detected in skin or scales. Despite expression of FOXN1 in developing feathers, examination of chick homologs of five putative mammalian FOXN1 target genes shows that, while these genes are expressed in feathers, there is little similarity to the FOXN1 expression pattern, suggesting that some gene regulatory networks may have diverged during evolution of epidermal appendages.

}, keywords = {Amino Acid Sequence, Animals, Biological Evolution, Blotting, Western, Cell Differentiation, Cells, Cultured, Chick Embryo, Chickens, Cloning, Molecular, Embryo, Nonmammalian, Epidermis, Feathers, Forkhead Transcription Factors, Gene Expression Regulation, Developmental, In Situ Hybridization, Molecular Sequence Data, Morphogenesis, Phylogeny, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, RNA, Messenger, Sequence Homology, Amino Acid}, issn = {1696-3547}, doi = {10.1387/ijdb.130023sy}, author = {Darnell, Diana K and Zhang, Li S and Hannenhalli, Sridhar and Yaklichkin, Sergey Y} } @article {49600, title = {Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.}, volume = {15}, year = {2014}, month = {2014}, pages = {R76}, abstract = {

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.

}, keywords = {Bangladesh, Base Sequence, Case-Control Studies, Child, Preschool, Diarrhea, Infantile, Dysentery, Feces, Female, Gambia, HUMANS, Infant, Infant, Newborn, Intestines, Kenya, Male, Mali, Microbiota, Molecular Typing, Poverty, RNA, Bacterial, RNA, Ribosomal, 16S}, issn = {1474-760X}, doi = {10.1186/gb-2014-15-6-r76}, author = {Pop, Mihai and Walker, Alan W and Paulson, Joseph and Lindsay, Brianna and Antonio, Martin and Hossain, M Anowar and Oundo, Joseph and Tamboura, Boubou and Mai, Volker and Astrovskaya, Irina and Corrada Bravo, Hector and Rance, Richard and Stares, Mark and Levine, Myron M and Panchalingam, Sandra and Kotloff, Karen and Ikumapayi, Usman N and Ebruke, Chinelo and Adeyemi, Mitchell and Ahmed, Dilruba and Ahmed, Firoz and Alam, Meer Taifur and Amin, Ruhul and Siddiqui, Sabbir and Ochieng, John B and Ouma, Emmanuel and Juma, Jane and Mailu, Euince and Omore, Richard and Morris, J Glenn and Breiman, Robert F and Saha, Debasish and Parkhill, Julian and Nataro, James P and Stine, O Colin} } @article {38192, title = {De novo likelihood-based measures for comparing genome assemblies}, journal = {BMC research notes}, volume = {6}, year = {2013}, publisher = {BioMed Central Ltd}, author = {Ghodsi, Mohammadreza and Christopher M. Hill and Irina Astrovskaya and Lin, Henry and Sommer, Dan D. and Koren, Sergey and M. Pop} } @conference {45868, title = {De novo likelihood-based measures for comparing metagenomic assemblies}, booktitle = {2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)}, year = {2013}, month = {12/2013}, publisher = {IEEE}, organization = {IEEE}, address = {Shanghai, China}, author = {Hill, Christopher M and Irina Astrovskaya and Huang, Howard and Koren, Sergey and Memon, Atif and Todd Treangen and Pop, Mihai} } @article {38194, title = {A decision-theory approach to interpretable set analysis for high-dimensional data}, journal = {BiometricsBiometrics}, volume = {69}, year = {2013}, note = {http://www.ncbi.nlm.nih.gov/pubmed/23909925?dopt=Abstract}, type = {10.1111/biom.12060}, abstract = {A key problem in high-dimensional significance analysis is to find pre-defined sets that show enrichment for a statistical signal of interest; the classic example is the enrichment of gene sets for differentially expressed genes. Here, we propose a new decision-theory approach to the analysis of gene sets which focuses on estimating the fraction of non-null variables in a set. We introduce the idea of "atoms," non-overlapping sets based on the original pre-defined set annotations. Our approach focuses on finding the union of atoms that minimizes a weighted average of the number of false discoveries and missed discoveries. We introduce a new false discovery rate for sets, called the atomic false discovery rate (afdr), and prove that the optimal estimator in our decision-theory framework is to threshold the afdr. These results provide a coherent and interpretable framework for the analysis of sets that addresses the key issues of overlapping annotations and difficulty in interpreting p values in both competitive and self-contained tests. We illustrate our method and compare it to a popular existing method using simulated examples, as well as gene-set and brain ROI data analyses.}, author = {Boca, Simina M. and H{\'e}ctor Corrada Bravo and Caffo, Brian and Leek, Jeffrey T. and Parmigiani, Giovanni} } @article {38582, title = {Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation}, journal = {BMC CancerBMC CancerBMC Cancer}, volume = {13}, year = {2013}, note = {Kim, Robert
Kulkarni, Prakash
Hannenhalli, Sridhar
eng
R01 GM100335/GM/NIGMS NIH HHS/
R01GM100335/GM/NIGMS NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov{\textquoteright}t
England
2013/03/26 06:00
BMC Cancer. 2013 Mar 22;13:144. doi: 10.1186/1471-2407-13-144.}, pages = {144}, abstract = {BACKGROUND: The Cancer/Testis Antigens (CTAs) are a heterogeneous group of proteins whose expression is typically restricted to the testis. However, they are aberrantly expressed in most cancers that have been examined to date. Broadly speaking, the CTAs can be divided into two groups: the CTX antigens that are encoded by the X-linked genes and the non-X CT antigens that are encoded by the autosomes. Unlike the non-X CTAs, the CTX antigens form clusters of closely related gene families and their expression is frequently associated with advanced disease with poorer prognosis. Regardless however, the mechanism(s) underlying their selective derepression and stage-specific expression in cancer remain poorly understood, although promoter DNA demethylation is believed to be the major driver. METHODS: Here, we report a systematic analysis of DNA methylation profiling data from various tissue types to elucidate the mechanism underlying the derepression of the CTAs in cancer. We analyzed the methylation profiles of 501 samples including sperm, several cancer types, and their corresponding normal somatic tissue types. RESULTS: We found strong evidence for specific DNA hypomethylation of CTA promoters in the testis and cancer cells but not in their normal somatic counterparts. We also found that hypomethylation was clustered on the genome into domains that coincided with nuclear lamina-associated domains (LADs) and that these regions appeared to be insulated by CTCF sites. Interestingly, we did not observe any significant differences in the hypomethylation pattern between the CTAs without CpG islands and the CTAs with CpG islands in the proximal promoter. CONCLUSION: Our results corroborate that widespread DNA hypomethylation appears to be the driver in the derepression of CTA expression in cancer and furthermore, demonstrate that these hypomethylated domains are associated with the nuclear lamina-associated domains (LADS). Taken together, our results suggest that wide-spread methylation changes in cancer are linked to derepression of germ-line-specific genes that is orchestrated by the three dimensional organization of the cancer genome.}, keywords = {*DNA Methylation, *Gene Expression Regulation, Neoplastic, *Genes, X-Linked, Antigens, Neoplasm/*genetics, Binding Sites, Cluster Analysis, CpG Islands, Gene Expression Profiling, HUMANS, Male, Neoplasms/*genetics/*metabolism, Promoter Regions, Genetic, Protein Binding, Protein Interaction Domains and Motifs, Testis/*metabolism}, isbn = {1471-2407 (Electronic)
1471-2407 (Linking)}, author = {Kim, R. and Kulkarni, P. and Sridhar Hannenhalli} } @article {38203, title = {Differential abundance analysis for microbial marker-gene surveys}, journal = {Nature methods}, volume = {10}, year = {2013}, publisher = {Nature Publishing Group}, chapter = {1200}, abstract = {We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling{\textemdash}a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.}, isbn = {1548-7091}, doi = {10.1038/nmeth.2658}, url = {http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html}, author = {Joseph N. Paulson and Stine, O. Colin and H{\'e}ctor Corrada Bravo and M. Pop} } @article {49546, title = {Distinct Rap1 Activity States Control the Extent of Epithelial Invagination via α-Catenin}, volume = {25}, year = {2013}, month = {Jan-05-2013}, pages = {299 - 309}, issn = {15345807}, doi = {10.1016/j.devcel.2013.04.002}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1534580713001937http://api.elsevier.com/content/article/PII:S1534580713001937?httpAccept=text/xmlhttp://api.elsevier.com/content/article/PII:S1534580713001937?httpAccept=text/plain}, author = {Wang, Yu-Chiun and Khan, Zia and Wieschaus, ~F.} } @article {49739, title = {Distinct Rap1 activity states control the extent of epithelial invagination via α-catenin.}, journal = {Dev Cell}, volume = {25}, year = {2013}, month = {2013 May 13}, pages = {299-309}, abstract = {

Localized cell shape change initiates epithelial folding, while neighboring cell invagination determines the final depth of an epithelial fold. The mechanism that controls the extent of invagination remains unknown. During Drosophila gastrulation, a higher number of cells undergo invagination to form the deep posterior dorsal fold, whereas far fewer cells become incorporated into the initially very similar anterior dorsal fold. We find that a decrease in α-catenin activity causes the anterior fold to invaginate as extensively as the posterior fold. In contrast, constitutive activation of the small GTPase Rap1 restricts invagination of both dorsal folds in an α-catenin-dependent manner. Rap1 activity appears spatially modulated by Rapgap1, whose expression levels are high in the cells that flank the posterior fold but low in the anterior fold. We propose a model whereby distinct activity states of Rap1 modulate α-catenin-dependent coupling between junctions and actin to control the extent of epithelial invagination.

}, keywords = {Actins, alpha Catenin, Animals, Cell Adhesion, Cell Adhesion Molecules, Cell Membrane, Cell Shape, Drosophila, Drosophila Proteins, Embryo, Nonmammalian, Enzyme Activation, Epithelial Cells, Genes, Insect, Green Fluorescent Proteins, GTP Phosphohydrolases, GTPase-Activating Proteins, Intercellular Junctions, RNA Interference, Time factors, Time-Lapse Imaging}, issn = {1878-1551}, doi = {10.1016/j.devcel.2013.04.002}, author = {Wang, Yu-Chiun and Khan, Zia and Wieschaus, Eric F} } @article {38195, title = {Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease}, journal = {PloS onePLoS One}, volume = {7}, year = {2012}, publisher = {Public Library of Science}, author = {Liu, B. and Faller, L. L. and Klitgord, N. and Mazumdar, V. and Ghodsi, M. and Sommer, D. D. and Gibbons, T. R. and Todd Treangen and Chang, Y. C. and Li, S. and others,} } @article {49552, title = {Differential positioning of adherens junctions is associated with initiation of epithelial folding}, volume = {484}, year = {2012}, month = {Apr-03-2014}, pages = {390 - 393}, issn = {0028-0836}, doi = {10.1038/nature10938}, url = {http://www.nature.com/doifinder/10.1038/nature10938}, author = {Wang, Yu-Chiun and Khan, Zia and Kaschube, Matthias and Wieschaus, Eric F.} } @article {49742, title = {Differential positioning of adherens junctions is associated with initiation of epithelial folding.}, journal = {Nature}, volume = {484}, year = {2012}, month = {2012 Apr 19}, pages = {390-3}, abstract = {

During tissue morphogenesis, simple epithelial sheets undergo folding to form complex structures. The prevailing model underlying epithelial folding involves cell shape changes driven by myosin-dependent apical constriction. Here we describe an alternative mechanism that requires differential positioning of adherens junctions controlled by modulation of epithelial apical-basal polarity. Using live embryo imaging, we show that before the initiation of dorsal transverse folds during Drosophila gastrulation, adherens junctions shift basally in the initiating cells, but maintain their original subapical positioning in the neighbouring cells. Junctional positioning in the dorsal epithelium depends on the polarity proteins Bazooka and Par-1. In particular, the basal shift that occurs in the initiating cells is associated with a progressive decrease in Par-1 levels. We show that uniform reduction of the activity of Bazooka or Par-1 results in uniform apical or lateral positioning of junctions and in each case dorsal fold initiation is abolished. In addition, an increase in the Bazooka/Par-1 ratio causes formation of ectopic dorsal folds. The basal shift of junctions not only alters the apical shape of the initiating cells, but also forces the lateral membrane of the adjacent cells to bend towards the initiating cells, thereby facilitating tissue deformation. Our data thus establish a direct link between modification of epithelial polarity and initiation of epithelial folding.

}, keywords = {Adherens Junctions, Animals, Cell Polarity, Cell Shape, Choristoma, Drosophila melanogaster, Drosophila Proteins, Epithelial Cells, Epithelium, Gastrula, Gastrulation, Glycogen Synthase Kinase 3, Intracellular Signaling Peptides and Proteins, Protein-Serine-Threonine Kinases}, issn = {1476-4687}, doi = {10.1038/nature10938}, author = {Wang, Yu-Chiun and Khan, Zia and Kaschube, Matthias and Wieschaus, Eric F} } @article {49553, title = {Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size}, volume = {14}, year = {2012}, month = {Jan-03-2014}, pages = {518 - 525}, issn = {1465-7392}, doi = {10.1038/ncb2467}, url = {http://www.nature.com/doifinder/10.1038/ncb2467}, author = {Nelson, Kevin S. and Khan, Zia and {\'a}r, Imre and {\'a}ly, {\'o}zsef and Kaschube, Matthias and Beitel, Greg J.} } @article {49743, title = {Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size.}, journal = {Nat Cell Biol}, volume = {14}, year = {2012}, month = {2012 May}, pages = {518-25}, abstract = {

Networks of epithelial and endothelial tubes are essential for the function of organs such as the lung, kidney and vascular system. The sizes and shapes of these tubes are highly regulated to match their individual functions. Defects in tube size can cause debilitating diseases such as polycystic kidney disease and ischaemia. It is therefore critical to understand how tube dimensions are regulated. Here we identify the tyrosine kinase Src as an instructive regulator of epithelial-tube length in the Drosophila tracheal system. Loss-of-function Src42 mutations shorten tracheal tubes, whereas Src42 overexpression elongates them. Surprisingly, Src42 acts distinctly from known tube-size pathways and regulates both the amount of apical surface growth and, with the conserved formin dDaam, the direction of growth. Quantitative three-dimensional image analysis reveals that Src42- and dDaam-mutant tracheal cells expand more in the circumferential than the axial dimension, resulting in tubes that are shorter in length-but larger in diameter-than wild-type tubes. Thus, Src42 and dDaam control tube dimensions by regulating the direction of anisotropic growth, a mechanism that has not previously been described.

}, keywords = {Animals, Drosophila, Epithelium, src-Family Kinases}, issn = {1476-4679}, doi = {10.1038/ncb2467}, author = {Nelson, Kevin S and Khan, Zia and Moln{\'a}r, Imre and Mih{\'a}ly, J{\'o}zsef and Kaschube, Matthias and Beitel, Greg J} } @article {49556, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization}, volume = {17}, year = {2011}, month = {Jul-08-2011}, pages = {1101 - 1108}, issn = {1078-8956}, doi = {10.1038/nm.2401}, url = {http://www.nature.com/doifinder/10.1038/nm.2401}, author = {Korpal, Manav and Ell, Brian J and Buffa, Francesca M and Ibrahim, Toni and Blanco, Mario A and {\`a}-Terrassa, Toni and Mercatali, Laura and Khan, Zia and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L and Kang, Yibin} } @article {49746, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.}, journal = {Nat Med}, volume = {17}, year = {2011}, month = {2011 Sep}, pages = {1101-8}, abstract = {

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.

}, keywords = {Animals, Cadherins, Cell Line, Tumor, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, HUMANS, Mass Spectrometry, Mice, Mice, Inbred BALB C, Microarray Analysis, MicroRNAs, Neoplasm Metastasis, Statistics, Nonparametric, Vesicular Transport Proteins}, issn = {1546-170X}, doi = {10.1038/nm.2401}, author = {Korpal, Manav and Ell, Brian J and Buffa, Francesca M and Ibrahim, Toni and Blanco, Mario A and Celi{\`a}-Terrassa, Toni and Mercatali, Laura and Khan, Zia and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L and Kang, Yibin} } @article {38213, title = {DNACLUST: accurate and efficient clustering of phylogenetic marker genes}, journal = {BMC BioinformaticsBMC Bioinformatics}, volume = {12}, year = {2011}, type = {10.1186/1471-2105-12-271}, abstract = {Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the rate at which we can generate data, resulting in datasets that cannot be efficiently analyzed by traditional clustering methods.}, isbn = {1471-2105}, author = {Ghodsi, Mohammadreza and Liu, Bo and M. Pop} } @article {38207, title = {Discovery of novel Vibrio cholerae VSP-II genomic islands using comparative genomic analysis}, journal = {FEMS Microbiology LettersFEMS Microbiology Letters}, volume = {308}, year = {2010}, type = {10.1111/j.1574-6968.2010.02008.x}, abstract = {This report describes Vibrio seventh pandemic island II (VSP-II) and three novel variants revealed by comparative genomics of 23 Vibrio cholerae strains and their presence among a large and diverse collection of V. cholerae isolates. Three VSP-II variants were reported previously and our results demonstrate the presence of three novel VSP-II in clinical and environmental V. cholerae marked by major deletions and genetic rearrangements. A new VSP-II cluster was found in the seventh pandemic V. cholerae O1 El Tor strain CIRS101, which is dominant (95\%) among the recent (2004{\textendash}2007) seven pandemic V. cholerae O1 El Tor isolates from two endemic sites, but was not found in older strains from the same region. Two other variants were found in V. cholerae TMA21 and RC385, two environmental strains from coastal Brazil and the Chesapeake Bay, respectively, the latter being prevalent among environmental V. cholerae non-O1/non-O139 and Vibrio mimicus. The results of this study indicate that the VSP-II island has undergone significant rearrangement through a complex evolutionary pathway in V. cholerae. Interestingly, one of the new VSP-II revealed the presence of {\textquoteleft}old{\textquoteright} and {\textquoteleft}new{\textquoteright}V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic.}, keywords = {Vibrio cholerae, Vibrio mimicus, VPS-II}, isbn = {1574-6968}, author = {Taviani, Elisa and Grim, Christopher J. and Choi, Jinna and Jongsik, Chun and Haley, Bradd and Hasan, Nur A. and Huq, Anwar and Rita R. Colwell} } @article {38210, title = {Diversity and distribution of cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae}, journal = {Environmental Microbiology ReportsEnvironmental Microbiology Reports}, volume = {2}, year = {2010}, type = {10.1111/j.1758-2229.2010.00139.x}, abstract = {Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47\% of 83 non-O1, non-O139 strains and 16\% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.}, isbn = {1758-2229}, author = {Purdy, Alexandra E. and Balch, Deborah and Liz{\'a}rraga-Partida, Marcial Leonardo and Islam, Mohammad Sirajul and Martinez-Urtaza, Jaime and Huq, Anwar and Rita R. Colwell and Bartlett, Douglas H.} } @article {38198, title = {Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia}, journal = {Environmental Microbiology ReportsEnvironmental Microbiology Reports}, volume = {2}, year = {2009}, type = {10.1111/j.1758-2229.2009.00073.x}, abstract = {Three freshwater lakes, Lisi Lake, Kumisi Lake and Tbilisi Sea, near Tbilisi, Georgia, were studied from January 2006 to December 2007 to determine the presence of Vibrio cholerae employing both bacteriological culture method and direct detection methods, namely PCR and direct fluorescent antibody (DFA). For PCR, DNA extracted from water samples was tested for presence of V. cholerae and genes coding for selected virulence factors. Vibrio cholerae non-O1/non-O139 was routinely isolated by culture from all three lakes; whereas V. cholerae O1 and O139 were not. Water samples collected during the summer months from Lisi Lake and Kumisi Lake were positive for both V. cholerae and V. cholerae ctxA, tcpA, zot, ompU and toxR by PCR. Water samples collected during the same period from both Lisi and Kumisi Lake were also positive for V. cholerae serogroup O1 by DFA. All of the samples were negative for V. cholerae serotype O139. The results of this study provide evidence for an environmental presence of toxigenic V. cholerae O1, which may represent a potential source of illness as these lakes serve as recreational water in Tbilisi, Georgia.}, isbn = {1758-2229}, author = {Grim, Christopher J. and Jaiani, Ekaterina and Whitehouse, Chris A. and Janelidze, Nino and Kokashvili, Tamuna and Tediashvili, Marina and Rita R. Colwell and Huq, Anwar} } @article {38202, title = {Determination of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor strains from housekeeping gene sequences and ribotype patterns}, journal = {Research in MicrobiologyResearch in Microbiology}, volume = {160}, year = {2009}, type = {10.1016/j.resmic.2008.10.008}, abstract = {Sequencing of three housekeeping genes, mdh, dnaE and recA, and ribotyping for seven non-toxigenic Vibrio cholerae O1 strains isolated from different geographic sources indicate a phylogenetic relationship among the strains. Results of MLST and ribotyping indicate a clear difference between three toxigenic strains (N16961, O395, and 569B) and three non-toxigenic strains from India (GS1, GS2, and GW87) and one Guam strain (X392), the latter of which were similar in both MLST and ribotyping, while two other non-toxigenic strains from the USA and India (2740-80 and OR69) appeared to be more closely related to toxigenic strains than to non-toxigenic strains, although this was not supported by ribotyping. These results provide clues to the emergence of toxigenic strains from a non-toxigenic progenitor by acquisition of virulence gene clusters. Results of split decomposition analysis suggest that widespread recombination occurs among the three housekeeping genes and that recombination plays an important role in the emergence of toxigenic strains of V. cholerae O1.}, keywords = {Housekeeping genes, Ribotyping, sequencing, Vibrio cholerae}, isbn = {0923-2508}, author = {Mohapatra, Saswat S. and Ramachandran, Dhanya and Mantri, Chinmay K. and Rita R. Colwell and Singh, Durg V.} } @article {38211, title = {Diversity and Seasonality of Bioluminescent Vibrio Cholerae Populations in Chesapeake Bay}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, type = {10.1128/AEM.02894-07}, abstract = {Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species.}, isbn = {0099-2240, 1098-5336}, author = {Zo, Young-Gun and Chokesajjawatee, Nipa and Grim, Christopher and Arakawa, Eiji and Watanabe, Haruo and Rita R. Colwell} } @article {38201, title = {Determination of Clonality and Relatedness of Vibrio Cholerae Isolates by Genomic Fingerprinting, Using Long-Range Repetitive Element Sequence-Based PCR}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {74}, year = {2008}, type = {10.1128/AEM.00151-08}, abstract = {A high-throughput method which is applicable for rapid screening, identification, and delineation of isolates of Vibrio cholerae, sensitive to genome variation, and capable of providing phylogenetic inferences enhances environmental monitoring of this bacterium. We have developed and optimized a method for genomic fingerprinting of V. cholerae based on long-range PCR. The method uses a primer set directed to enterobacterial repetitive intergenic consensus sequences, a high-fidelity DNA polymerase, and analysis via conventional agarose gel electrophoresis. Long (\~{}10 kb), highly reproducible amplicons were generated from V. cholerae isolates, including those from different geographical locations and historical strains isolated during the period 1931-2000. The amplicons yielded reduced variability in their densitometric band patterns to <=10\% and clonal distinction at <90\% similarity. Rapid band-matching analysis was accomplished for fingerprints with >=90\% similarity, discriminating O serotypes and biotypes (classical versus El Tor) as well as pathogenic and nonpathogenic strains. Compared to genome similarity measured by DNA-DNA hybridization, the results showed good correlation (r = 0.7; P < 0.001), with five times less measurement error and without bias. The method permits both phylogenetic inference and clonal differentiation of individual V. cholerae strains, enables robust, high-throughput analysis, and does not require specialized equipment to perform. With access to a curated public database furnished with appropriate analytical software applications, the method should prove useful in large-scale multilaboratory surveys, especially those designed to detect specific pathogens in the natural environment.}, isbn = {0099-2240, 1098-5336}, author = {Chokesajjawatee, Nipa and Zo, Young-Gun and Rita R. Colwell} } @article {49676, title = {The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008 Apr 24}, pages = {991-6}, abstract = {

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 {\textquoteright}SunUp{\textquoteright} 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{\textquoteright}s distinguishing morpho-physiological, medicinal and nutritional properties.

}, keywords = {Arabidopsis, Carica, Contig Mapping, Databases, Genetic, Genes, Plant, Genome, Plant, Molecular Sequence Data, Plants, Genetically Modified, sequence alignment, Sequence Analysis, DNA, Transcription Factors, Tropical Climate}, issn = {1476-4687}, doi = {10.1038/nature06856}, author = {Ming, Ray and Hou, Shaobin and Feng, Yun and Yu, Qingyi and Dionne-Laporte, Alexandre and Saw, Jimmy H and Senin, Pavel and Wang, Wei and Ly, Benjamin V and Lewis, Kanako L T and Salzberg, Steven L and Feng, Lu and Jones, Meghan R and Skelton, Rachel L and Murray, Jan E and Chen, Cuixia and Qian, Wubin and Shen, Junguo and Du, Peng and Eustice, Moriah and Tong, Eric and Tang, Haibao and Lyons, Eric and Paull, Robert E and Michael, Todd P and Wall, Kerr and Rice, Danny W and Albert, Henrik and Wang, Ming-Li and Zhu, Yun J and Schatz, Michael and Nagarajan, Niranjan and Acob, Ricelle A and Guan, Peizhu and Blas, Andrea and Wai, Ching Man and Ackerman, Christine M and Ren, Yan and Liu, Chao and Wang, Jianmei and Wang, Jianping and Na, Jong-Kuk and Shakirov, Eugene V and Haas, Brian and Thimmapuram, Jyothi and Nelson, David and Wang, Xiyin and Bowers, John E and Gschwend, Andrea R and Delcher, Arthur L and Singh, Ratnesh and Suzuki, Jon Y and Tripathi, Savarni and Neupane, Kabi and Wei, Hairong and Irikura, Beth and Paidi, Maya and Jiang, Ning and Zhang, Wenli and Presting, Gernot and Windsor, Aaron and Navajas-P{\'e}rez, Rafael and Torres, Manuel J and Feltus, F Alex and Porter, Brad and Li, Yingjun and Burroughs, A Max and Luo, Ming-Cheng and Liu, Lei and Christopher, David A and Mount, Stephen M and Moore, Paul H and Sugimura, Tak and Jiang, Jiming and Schuler, Mary A and Friedman, Vikki and Mitchell-Olds, Thomas and Shippen, Dorothy E and dePamphilis, Claude W and Palmer, Jeffrey D and Freeling, Michael and Paterson, Andrew H and Gonsalves, Dennis and Wang, Lei and Alam, Maqsudul} } @article {38217, title = {Dual role colonization factors connecting Vibrio cholerae{\textquoteright}s lifestyles in human and aquatic environments open new perspectives for combating infectious diseases}, journal = {Current Opinion in BiotechnologyCurrent Opinion in Biotechnology}, volume = {19}, year = {2008}, type = {10.1016/j.copbio.2008.04.002}, abstract = {Vibrio cholerae exhibits two distinctive lifestyles, one inside the milieu of the human intestine and the other in the aquatic environment. Recently, the existence of V. cholerae ligands involved in colonization of both human intestine and environmental chitin surfaces via the same binding specificity has been shown. Such molecules, here named {\textquoteleft}dual role colonization factors (DRCFs){\textquoteright}, are example of a tight connection between the two V. cholerae{\textquoteright}s lifestyles. It is suggested that DRCFs and, more generally, bacterial factors and pathways having roles in pathogenesis and in the out of the human body life may be promising targets for development of novel prophylactic or therapeutic interventions that may also affect V. cholerae fitness in its environmental reservoirs.}, isbn = {0958-1669}, author = {Vezzulli, Luigi and Guzm{\'a}n, Carlos A. and Rita R. Colwell and Pruzzo, Carla} } @article {38215, title = {Draft genome of the filarial nematode parasite Brugia malayi}, journal = {ScienceScience}, volume = {317}, year = {2007}, publisher = {American Association for the Advancement of Science}, author = {Ghedin, E. and Wang, S. and Spiro, D. and Caler, E. and Zhao, Q. and Crabtree, J. and Allen, J. E. and Delcher, A. L. and Guiliano, D. B. and Miranda-Saavedra, D. and others,} } @article {38196, title = {Dense Subgraph Computation Via Stochastic Search: Application to Detect Transcriptional Modules}, journal = {BioinformaticsBioinformaticsBioinformaticsBioinformatics}, volume = {22}, year = {2006}, type = {10.1093/bioinformatics/btl260}, abstract = {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{\textemdash}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}, isbn = {1367-4803, 1460-2059}, author = {Everett, Logan and Wang, Li-San and Sridhar Hannenhalli} } @inbook {38199, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, booktitle = {Current Protocols in MicrobiologyCurrent Protocols in Microbiology}, year = {2006}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, keywords = {culturable, DETECTION, Environment, identification, isolation, nonculturable, viable, Vibrio cholerae}, isbn = {9780471729259}, author = {Huq, Anwar and Grim, Christopher and Rita R. Colwell and Nair, G. Balakrish} } @article {38205, title = {Differential Transcriptional Response to Nonassociative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus}, journal = {Learning \& MemoryLearn. Mem.Learning \& MemoryLearn. Mem.}, volume = {13}, year = {2006}, type = {10.1101/lm.86906}, abstract = {Classical fear conditioning requires the recognition of conditioned stimuli (CS) and the association of the CS with an aversive stimulus. We used Affymetrix oligonucleotide microarrays to characterize changes in gene expression compared to naive mice in both the amygdala and the hippocampus 30 min after classical fear conditioning and 30 min after exposure to the CS in the absence of an aversive stimulus. We found that in the hippocampus, levels of gene regulation induced by classical fear conditioning were not significantly greater than those induced by CS alone, whereas in the amygdala, classical fear conditioning did induce significantly greater levels of gene regulation compared to the CS. Computational studies suggest that transcriptional changes in the hippocampus and amygdala are mediated by large and overlapping but distinct combinations of molecular events. Our results demonstrate that an increase in gene regulation in the amygdala was partially correlated to associative learning and partially correlated to nonassociative components of the task, while gene regulation in the hippocampus was correlated to nonassociative components of classical fear conditioning, including configural learning.}, isbn = {1072-0502, 1549-5485}, author = {Keeley, Michael B. and Wood, Marcelo A. and Isiegas, Carolina and Stein, Joel and Hellman, Kevin and Sridhar Hannenhalli and Abel, Ted} } @article {38191, title = {Data sharing in ecology and evolution}, journal = {Trends in Ecology \& EvolutionTrends in Ecology \& Evolution}, volume = {20}, year = {2005}, type = {10.1016/j.tree.2005.04.023}, isbn = {0169-5347}, author = {Parr, Cynthia S. and Michael P. Cummings} } @article {38219, title = {Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003)}, journal = {Institute for Systems Research Technical ReportsInstitute for Systems Research Technical Reports}, year = {2005}, abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool TimeSearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. TimeSearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. TimeSearcher can be used to search these data sets for candidate splicing signals.}, keywords = {Technical Report}, author = {Hochheiser, Harry and Baehrecke, Eric H. and Stephen M. Mount and Shneiderman, Ben} } @article {38209, title = {Divergent Gene Copies in the Asexual Class Bdelloidea (Rotifera) Separated Before the Bdelloid Radiation or Within Bdelloid Families}, journal = {Proceedings of the National Academy of Sciences of the United States of AmericaPNASProceedings of the National Academy of Sciences of the United States of AmericaPNAS}, volume = {101}, year = {2004}, type = {10.1073/pnas.2136686100}, abstract = {Rotifers of the asexual class Bdelloidea are unusual in possessing two or more divergent copies of every gene that has been examined. Phylogenetic analysis of the heat-shock gene hsp82 and the TATA-box-binding protein gene tbp in multiple bdelloid species suggested that for each gene, each copy belonged to one of two lineages that began to diverge before the bdelloid radiation. Such gene trees are consistent with the two lineages having descended from former alleles that began to diverge after meiotic segregation ceased or from subgenomes of an alloploid ancestor of the bdelloids. However, the original analyses of bdelloid gene-copy divergence used only a single outgroup species and were based on parsimony and neighbor joining. We have now used maximum likelihood and Bayesian inference methods and, for hsp82, multiple outgroups in an attempt to produce more robust gene trees. Here we report that the available data do not unambiguously discriminate between gene trees that root the origin of hsp82 and tbp copy divergence before the bdelloid radiation and those which indicate that the gene copies began to diverge within bdelloid families. The remarkable presence of multiple diverged gene copies in individual genomes is nevertheless consistent with the loss of sex in an ancient ancestor of bdelloids.}, isbn = {0027-8424, 1091-6490}, author = {Welch, David B. Mark and Michael P. Cummings and Hillis, David M. and Meselson, Matthew} } @article {49684, title = {The Drosophila U1-70K protein is required for viability, but its arginine-rich domain is dispensable.}, journal = {Genetics}, volume = {168}, year = {2004}, month = {2004 Dec}, pages = {2059-65}, abstract = {

The conserved spliceosomal U1-70K protein is thought to play a key role in RNA splicing by linking the U1 snRNP particle to regulatory RNA-binding proteins. Although these protein interactions are mediated by repeating units rich in arginines and serines (RS domains) in vitro, tests of this domain{\textquoteright}s importance in intact multicellular organisms have not been carried out. Here we report a comprehensive genetic analysis of U1-70K function in Drosophila. Consistent with the idea that U1-70K is an essential splicing factor, we find that loss of U1-70K function results in lethality during embryogenesis. Surprisingly, and contrary to the current view of U1-70K function, animals carrying a mutant U1-70K protein lacking the arginine-rich domain, which includes two embedded sets of RS dipeptide repeats, have no discernible mutant phenotype. Through double-mutant studies, however, we show that the U1-70K RS domain deletion no longer supports viability when combined with a viable mutation in another U1 snRNP component. Together our studies demonstrate that while the protein interactions mediated by the U1-70K RS domain are not essential for viability, they nevertheless contribute to an essential U1 snRNP function.

}, keywords = {Amino Acid Sequence, Animals, Animals, Genetically Modified, Arginine, Drosophila, Drosophila Proteins, Molecular Sequence Data, Mutation, Protein Structure, Tertiary, Ribonucleoprotein, U1 Small Nuclear, RNA-Binding Proteins}, issn = {0016-6731}, doi = {10.1534/genetics.104.032532}, author = {Salz, Helen K and Mancebo, Ricardo S Y and Nagengast, Alexis A and Speck, Olga and Psotka, Mitchell and Mount, Stephen M} } @article {38206, title = {Direct Detection of Vibrio Cholerae and ctxA in Peruvian Coastal Water and Plankton by PCR}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, type = {10.1128/AEM.69.6.3676-3680.2003}, abstract = {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.}, isbn = {0099-2240, 1098-5336}, author = {Lipp, Erin K. and Rivera, Irma N. G. and Gil, Ana I. and Espeland, Eric M. and Choopun, Nipa and Louis, Val{\'e}rie R. and Russek-Cohen, Estelle and Huq, Anwar and Rita R. Colwell} } @article {38214, title = {The dog genome: survey sequencing and comparative analysis}, journal = {ScienceScience}, volume = {301}, year = {2003}, publisher = {American Association for the Advancement of Science}, author = {Kirkness, E. F. and Bafna, V. and Halpern, A. L. and Levy, S. and Remington, K. and Rusch, D. B. and Delcher, A. L. and M. Pop and Wang, W. and Fraser, C. M. and others,} } @proceedings {38218, title = {Dynamic querying for pattern identification in microarray and genomic data}, volume = {3}, year = {2003}, month = {2003}, publisher = {IEEE}, type = {10.1109/ICME.2003.1221346}, abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals.}, keywords = {Bioinformatics, data sets, Displays, dynamic querying, expression profiles, Frequency, Gene expression, genes, Genetics, genomic data, Genomics, linear ordered sequences, macromolecules, medical signal processing, Mice, Microarray, pattern identification, pattern recognition, premRNA splicing, Query processing, sequences, Signal processing, splicing, TimeSearcher}, isbn = {0-7803-7965-9}, author = {Hochheiser, H. and Baehrecke, E. H. and Stephen M. Mount and Shneiderman, Ben} } @article {38197, title = {Detection of Cytotoxin-Hemolysin mRNA in Nonculturable Populations of Environmental and Clinical Vibrio Vulnificus Strains in Artificial Seawater}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {68}, year = {2002}, type = {10.1128/AEM.68.11.5641-5646.2002}, abstract = {The objective of this study was to develop a molecular detection method that better estimates the potential risk associated with the presence of Vibrio vulnificus. For that purpose, we applied seminested reverse transcription-PCR (RT-PCR) to viable but nonculturable (VBNC) populations of V. vulnificus and targeted the cytotoxin-hemolysin virulence gene vvhA. Three strains, two environmental, IF Vv10 and IF Vv18, and one clinical, C7184, were used in this study. Artificial seawater, inoculated with mid-log-phase cells, was maintained at 4{\textdegree}C. VBNC cells resulted after 3, 6, and 14 days for C7184, IF Vv18, and IF Vv10, respectively. Our data indicate that seminested RT-PCR is sensitive for the detection of vvhA mRNA in artificial seawater when exclusively nonculturable bacteria are present. This is the first report of the expression of a toxin gene in VBNC V. vulnificus. Moreover, vvhA transcripts were shown to persist in nonculturable populations over a 4.5-month period, with a progressive decline of the signal over time. This result indicates that special attention should be given to the presence of potentially pathogenic VBNC cells in environmental samples when assessing public health risk.}, isbn = {0099-2240, 1098-5336}, author = {Fischer-Le Saux, Marion and Hervio-Heath, Dominique and Loaec, Solen and Rita R. Colwell and Pommepuy, Monique} } @article {49687, title = {The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.}, journal = {Science}, volume = {298}, year = {2002}, month = {2002 Dec 13}, pages = {2157-67}, abstract = {

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

}, keywords = {Alleles, Animals, Apoptosis, Base Sequence, Cellulose, Central Nervous System, Ciona intestinalis, Computational Biology, Endocrine System, Gene Dosage, Gene Duplication, genes, Genes, Homeobox, Genome, Heart, Immunity, Molecular Sequence Data, Multigene Family, Muscle Proteins, Organizers, Embryonic, Phylogeny, Polymorphism, Genetic, Proteins, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity, Thyroid Gland, Urochordata, Vertebrates}, issn = {1095-9203}, doi = {10.1126/science.1080049}, author = {Dehal, Paramvir and Satou, Yutaka and Campbell, Robert K and Chapman, Jarrod and Degnan, Bernard and De Tomaso, Anthony and Davidson, Brad and Di Gregorio, Anna and Gelpke, Maarten and Goodstein, David M and Harafuji, Naoe and Hastings, Kenneth E M and Ho, Isaac and Hotta, Kohji and Huang, Wayne and Kawashima, Takeshi and Lemaire, Patrick and Martinez, Diego and Meinertzhagen, Ian A and Necula, Simona and Nonaka, Masaru and Putnam, Nik and Rash, Sam and Saiga, Hidetoshi and Satake, Masanobu and Terry, Astrid and Yamada, Lixy and Wang, Hong-Gang and Awazu, Satoko and Azumi, Kaoru and Boore, Jeffrey and Branno, Margherita and Chin-Bow, Stephen and DeSantis, Rosaria and Doyle, Sharon and Francino, Pilar and Keys, David N and Haga, Shinobu and Hayashi, Hiroko and Hino, Kyosuke and Imai, Kaoru S and Inaba, Kazuo and Kano, Shungo and Kobayashi, Kenji and Kobayashi, Mari and Lee, Byung-In and Makabe, Kazuhiro W and Manohar, Chitra and Matassi, Giorgio and Medina, Monica and Mochizuki, Yasuaki and Mount, Steve and Morishita, Tomomi and Miura, Sachiko and Nakayama, Akie and Nishizaka, Satoko and Nomoto, Hisayo and Ohta, Fumiko and Oishi, Kazuko and Rigoutsos, Isidore and Sano, Masako and Sasaki, Akane and Sasakura, Yasunori and Shoguchi, Eiichi and Shin-i, Tadasu and Spagnuolo, Antoinetta and Stainier, Didier and Suzuki, Miho M and Tassy, Olivier and Takatori, Naohito and Tokuoka, Miki and Yagi, Kasumi and Yoshizaki, Fumiko and Wada, Shuichi and Zhang, Cindy and Hyatt, P Douglas and Larimer, Frank and Detter, Chris and Doggett, Norman and Glavina, Tijana and Hawkins, Trevor and Richardson, Paul and Lucas, Susan and Kohara, Yuji and Levine, Michael and Satoh, Nori and Rokhsar, Daniel S} } @inbook {38193, title = {De-amortization of Algorithms}, booktitle = {Computing and CombinatoricsComputing and Combinatorics}, series = {Lecture Notes in Computer Science}, volume = {1449}, year = {1998}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {De-amortization aims to convert algorithms with excellent overall speed, f ( n ) for performing n operations, into algorithms that take no more than O ( f ( n )/ n ) steps for each operation. The paper reviews several existing techniques for de-amortization of algorithms.}, isbn = {978-3-540-64824-6}, author = {Rao Kosaraju, S. and M. Pop}, editor = {Hsu, Wen-Lian and Kao, Ming-Yang} } @inbook {38216, title = {Drawing of Two-Dimensional Irregular Meshes}, booktitle = {Graph DrawingGraph Drawing}, series = {Lecture Notes in Computer Science}, volume = {1547}, year = {1998}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present a method for transforming two-dimensional irregular meshes into square meshes with only a constant blow up in area. We also explore context invariant transformations of irregular meshes into square meshes and provide a lower bound for the transformation of down-staircases.}, isbn = {978-3-540-65473-5}, author = {Aggarwal, Alok and Rao Kosaraju, S. and M. Pop}, editor = {Whitesides, Sue} } @article {38204, title = {Differential expression of the expression site-associated gene I family in African trypanosomes}, journal = {Journal of Biological ChemistryJournal of Biological Chemistry}, volume = {271}, year = {1996}, author = {Morgan, R. W. and Najib M. El-Sayed and Kepa, J. K. and Pedram, M. and Donelson, J. E.} } @article {38212, title = {DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater {\i}t Cladophora species (Chlorophyta)}, journal = {J PhycolJ Phycol}, volume = {32}, year = {1996}, abstract = {Freshwater species of Cladophora (Chlorophyta) are globally distributed and occupy an unusually wide range of ecological habitats. Delineating species is difficult because most easily observed morphological traits are highly variable and because sexual reproduction has not been clearly documented. Synthesizing ecological data on freshwater Cladophora species is problematic because it is unclear whether freshwater Cladophora species comprise many genetically distinct species or a few ecologically and morphologically variable and / or plastic species. We determined nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron of freshwater Cladophora species from a wide range of habitats and geographic locations. We compared these sequences to those derived from culture collections of C. fracta and C. glomerata, the two most commonly reported freshwater Cladophora species. Cladophora fracta and C. glomerata had very similar ITS sequences (95.3\%). All other sequences were identical to those from the C. fracta or C. glomerata culture collections with the exception of one California sample that was similar to both C. fracta (95.6\%) and C. glomerata (92.4\%). ITS genotypes did not correlate with morphology or geography. This analysis shows that common freshwater Cladophora species comprise very few (possibly one) ecologically and morphologically variable species.}, keywords = {algae, Chlorophyta, Cladophora, diversity, freshwater, genetic, internal, spacer, transcribed}, author = {Marks, J. C. and Michael P. Cummings} } @proceedings {38208, title = {A distributed algorithm for ear decomposition}, year = {1993}, month = {1993}, publisher = {IEEE}, type = {10.1109/ICCI.1993.315382}, abstract = {A distributed algorithm for finding an ear decomposition of an asynchronous communication network with n nodes and m links is presented. At the completion of the algorithm either the ears are correctly labeled or the nodes are informed that there exists no ear decomposition. First we present a novel algorithm to check the existence of an ear decomposition which uses O(m) messages. We also present two other algorithms, one which is time-optimal and the other which is message-optimal to determine the actual ears and their corresponding numbers after determining the existence of an ear decomposition}, keywords = {Asynchronous communication, asynchronous communication network, Automata, Communication networks, computational complexity, Computer networks, Computer science, decomposition graph, distributed algorithm, distributed algorithms, Distributed computing, Ear, ear decomposition, graph theory, message-optimal, network decomposition, sorting, Testing, time-optimal}, isbn = {0-8186-4212-2}, author = {Sridhar Hannenhalli and Perumalla, K. and Chandrasekharan, N. and Sridhar, R.} } @article {49704, title = {Drosophila melanogaster genes for U1 snRNA variants and their expression during development.}, journal = {Nucleic Acids Res}, volume = {18}, year = {1990}, month = {1990 Dec 11}, pages = {6971-9}, abstract = {

We have cloned and characterized a complete set of seven U1-related sequences from Drosophila melanogaster. These sequences are located at the three cytogenetic loci 21D, 82E, and 95C. Three of these sequences have been previously studied: one U1 gene at 21D which encodes the prototype U1 sequence (U1a), one U1 gene at 82E which encodes a U1 variant with a single nucleotide substitution (U1b), and a pseudogene at 82E. The four previously uncharacterized genes are another U1b gene at 82E, two additional U1a genes at 95C, and a U1 gene at 95C which encodes a new variant (U1c) with a distinct single nucleotide change relative to U1a. Three blocks of 5{\textquoteright} flanking sequence similarity are common to all six full length genes. Using specific primer extension assays, we have observed that the U1b RNA is expressed in Drosophila Kc cells and is associated with snRNP proteins, suggesting that the U1b-containing snRNP particles are able to participate in the process of pre-mRNA splicing. We have also examined the expression throughout Drosophila development of the two U1 variants relative to the prototype sequence. The U1c variant is undetectable by our methods, while the U1b variant exhibits a primarily embryonic pattern reminiscent of the expression of certain U1 variants in sea urchin, Xenopus, and mouse.

}, keywords = {Animals, Base Sequence, Blotting, Southern, Cloning, Molecular, Drosophila melanogaster, Gene Expression Regulation, genes, Genetic Variation, Molecular Sequence Data, Nucleic Acid Conformation, Pseudogenes, Restriction Mapping, RNA, Small Nuclear}, issn = {0305-1048}, author = {Lo, P C and Mount, S M} } @article {49628, title = {Detection of alloantigens during preimplantation development and early trophoblast differentiation in the mouse by immunoperoxidase labeling.}, journal = {J Exp Med}, volume = {143}, year = {1976}, month = {1976 Feb 1}, pages = {348-59}, abstract = {

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.

}, keywords = {Animals, Binding Sites, Antibody, Blastocyst, Cell Differentiation, Cell Membrane, Embryo Implantation, Embryonic Development, Epitopes, Female, Histocompatibility Antigens, HLA Antigens, Horseradish Peroxidase, Mice, Mice, Inbred Strains, Pregnancy, Pregnancy, Animal, Trophoblasts}, issn = {0022-1007}, author = {Searle, R F and Sellens, M H and Elson, J and Jenkinson, E J and Billington, W D} }