Genomes and Genes
Experts and Doctors on genetic models in Toronto, Ontario, Canada
Locale: Toronto, Ontario, Canada
Topic: genetic models
- Dorken M, Barrett S. Sex determination and the evolution of dioecy from monoecy in Sagittaria latifolia (Alismataceae). Proc Biol Sci. 2004;271:213-9 pubmed..These results are consistent with predictions for the evolution of dioecy via gynodioecy, rather than the expected monoecy-paradioecy pathway, given the ancestral monoecious condition. ..
- Li J, Liu Y, Dong D, Zhang Z. Evolution of an X-linked primate-specific micro RNA cluster. Mol Biol Evol. 2010;27:671-83 pubmed publisher..Collectively, we argue these miRNAs might play an important role in epididymal morphogenesis and sperm maturation and in establishing primate-specific epididymal characteristics. ..
- Gordon S, Alon N, Buchwald M. FANCC, FANCE, and FANCD2 form a ternary complex essential to the integrity of the Fanconi anemia DNA damage response pathway. J Biol Chem. 2005;280:36118-25 pubmed..Thus, FANCE is shown to be a key mediator of protein interactions both in the architecture of the FA protein complex and in the connection of complex components to the putative downstream targets of complex activity. ..
- Stinchcombe J, Agrawal A, HOHENLOHE P, Arnold S, Blows M. Estimating nonlinear selection gradients using quadratic regression coefficients: double or nothing?. Evolution. 2008;62:2435-40 pubmed publisher..Proper treatment of quadratic regression coefficients is necessary for estimation of fitness surfaces and contour plots, canonical analysis of the gamma matrix, and modeling the evolution of populations on an adaptive landscape. ..
- Riazi A, Takeuchi J, Hornberger L, Zaidi S, Amini F, Coles J, et al. NKX2-5 regulates the expression of beta-catenin and GATA4 in ventricular myocytes. PLoS ONE. 2009;4:e5698 pubmed publisher..This study suggests that NKX2-5 modulates the beta-catenin and GATA4 transcriptional activities in developing human cardiac myocytes. ..
- Gronda M, Arab S, Iafrate B, Suzuki H, Zanke B. Hematopoietic protein tyrosine phosphatase suppresses extracellular stimulus-regulated kinase activation. Mol Cell Biol. 2001;21:6851-8 pubmed
- On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, et al. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 2010;78:2075-89 pubmed publisher..As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems. ..
- Baetz K, Andrews B. Regulation of cell cycle transcription factor Swi4 through auto-inhibition of DNA binding. Mol Cell Biol. 1999;19:6729-41 pubmed..The interaction of the carboxy-terminal region of Swi4 with Swi6 alleviates this inhibition, allowing Swi4 to bind DNA. ..
- Watson C, Bialek P, Anzo M, Khosravi J, Yee S, Han V. Elevated circulating insulin-like growth factor binding protein-1 is sufficient to cause fetal growth restriction. Endocrinology. 2006;147:1175-86 pubmed..5; P < 0.05). Thus, this model of FGR is associated with a larger placenta, but without postnatal catch-up growth. Overall, these data clearly demonstrate that high concentrations of circulating IGFBP-1 are sufficient to cause FGR. ..
- Bonnard M, Mirtsos C, Suzuki S, Graham K, Huang J, Ng M, et al. Deficiency of T2K leads to apoptotic liver degeneration and impaired NF-kappaB-dependent gene transcription. EMBO J. 2000;19:4976-85 pubmed..However, T2K has a unique role in the activation of NF-kappaB-directed transcription, apparently independent of I-kappaB degradation and NF-kappaB DNA binding. ..
- Irwin D, Wong K. Evolution of new hormone function: loss and gain of a receptor. J Hered. 2005;96:205-11 pubmed
- Williams P, Day T. Epidemiological and evolutionary consequences of targeted vaccination. Mol Ecol. 2008;17:485-99 pubmed publisher..They further suggest that accounting for realistic kinds of heterogeneity when contemplating targeted treatment plans and policies might provide a new tool in the design of more effective virulence management strategies. ..
- Dworkin I. Evidence for canalization of Distal-less function in the leg of Drosophila melanogaster. Evol Dev. 2005;7:89-100 pubmed..I discuss the prospects of the evolutionary lability of the Distal-less gene within the context of changes in genetic variation and covariation. ..
- Medvedev P, Brudno M. Maximum likelihood genome assembly. J Comput Biol. 2009;16:1101-16 pubmed publisher..We run our algorithms on simulated read data from Escherichia coli and predict copy counts with extremely high accuracy, while assembling long contigs. ..
- Xu W, Taylor C, Veenstra J, Bull S, Corey M, Greenwood C. Recursive partitioning models for linkage in COGA data. BMC Genet. 2005;6 Suppl 1:S38 pubmed..However, using the RP model, several suggestive regions were found on chromosomes 2, 4, 6, 14, and 20, with detection of associated covariates such as sex and age at onset. ..
- Labonne J, Hilliker A, Shore J. Meiotic recombination in Turnera (Turneraceae): extreme sexual difference in rates, but no evidence for recombination suppression associated with the distyly (S) locus. Heredity (Edinb). 2007;98:411-8 pubmed..We found no significant evidence for recombination suppression...
- Al Kateb H, Mirea L, Xie X, Sun L, Liu M, Chen H, et al. Multiple variants in vascular endothelial growth factor (VEGFA) are risk factors for time to severe retinopathy in type 1 diabetes: the DCCT/EDIC genetics study. Diabetes. 2007;56:2161-8 pubmed..05). These data demonstrate that multiple VEGFA variants are associated with the development of severe retinopathy in type 1 diabetes. ..
- Tavares E, de Kroon G, Baker A. Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, Rallus aquaticus and R. indicus. BMC Evol Biol. 2010;10:226 pubmed publisher..indicus. The use of several independent loci is invaluable in inferring species trees from gene trees and in recognizing species limits. ..
- Liu Y, Snow B, Hande M, Baerlocher G, Kickhoefer V, Yeung D, et al. Telomerase-associated protein TEP1 is not essential for telomerase activity or telomere length maintenance in vivo. Mol Cell Biol. 2000;20:8178-84 pubmed..These results reveal that TEP1 is an RNA binding protein that is not restricted to the telomerase complex and that TEP1 plays a redundant role in the assembly or localization of the telomerase RNP in vivo. ..
- Goobie S, Popovic M, Morrison J, Ellis L, Ginzberg H, Boocock G, et al. Shwachman-Diamond syndrome with exocrine pancreatic dysfunction and bone marrow failure maps to the centromeric region of chromosome 7. Am J Hum Genet. 2001;68:1048-54 pubmed..However, the presence of several different mutations is suggested by the heterogeneity of disease-associated haplotypes in the candidate region. ..
- Baetz K, Moffat J, Haynes J, Chang M, Andrews B. Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4. Mol Cell Biol. 2001;21:6515-28 pubmed..Our results establish a new Slt2-dependent mode of Swi4 regulation and suggest roles for Swi4 beyond its prominent role in controlling cell cycle transcription. ..
- Lakin Thomas P. Transcriptional feedback oscillators: maybe, maybe not. J Biol Rhythms. 2006;21:83-92 pubmed
- Parkinson J, Blaxter M. Expressed sequence tags: an overview. Methods Mol Biol. 2009;533:1-12 pubmed publisher..Chapters are presented which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis of ESTs; and their application to phylogenetics and transcript profiling. ..
- Chen Z, Marsden P, Gorczynski R. Role of a distal enhancer in the transcriptional responsiveness of the human CD200 gene to interferon-gamma and tumor necrosis factor-alpha. Mol Immunol. 2009;46:1951-63 pubmed publisher..All the above findings suggest that IFN-gamma and TNF-alpha induce CD200 expression through a 5' upstream enhancer and that NF-kappaB, STAT1 and IRF-1 play pivotal roles in this process. ..
- Pearce J, Penny G, Rossant J. A mouse cerberus/Dan-related gene family. Dev Biol. 1999;209:98-110 pubmed..All three genes are able to inhibit Bmp4 signaling. These data suggest that the different family members may act to modulate the action of TGFbeta family members during development. ..
- Gao X, Song P. Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments. BMC Bioinformatics. 2005;6:186 pubmed..In the presence of outliers, they are advantageous alternative approaches to the existing parametric F tests due to the robustness feature. ..
- Salahshor S, Goncalves J, Chetty R, Gallinger S, Woodgett J. Differential gene expression profile reveals deregulation of pregnancy specific beta1 glycoprotein 9 early during colorectal carcinogenesis. BMC Cancer. 2005;5:66 pubmed
- Lam M, Urban Grimal D, Bugnicourt A, Greenblatt J, Haguenauer Tsapis R, Emili A. Interaction of the deubiquitinating enzyme Ubp2 and the e3 ligase Rsp5 is required for transporter/receptor sorting in the multivesicular body pathway. PLoS ONE. 2009;4:e4259 pubmed publisher..Taken together, our data suggest a previously overlooked role for Ubp2 as a positive regulator of Rsp5-mediated membrane protein trafficking subsequent to endocytosis. ..
- Haddrath O, Baker A. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc Biol Sci. 2001;268:939-45 pubmed..Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution...
- Boocock G, Marit M, Rommens J. Phylogeny, sequence conservation, and functional complementation of the SBDS protein family. Genomics. 2006;87:758-71 pubmed..These findings link Shwachman-Diamond syndrome to other bone marrow failure syndromes with defects in nucleolus-associated processes, including Diamond-Blackfan anemia, cartilage-hair hypoplasia, and dyskeratosis congenita. ..
- Rogaeva E, Meng Y, Lee J, Gu Y, Kawarai T, Zou F, et al. The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat Genet. 2007;39:168-77 pubmed..These data suggest that inherited or acquired changes in SORL1 expression or function are mechanistically involved in causing Alzheimer disease. ..
- Mnaimneh S, Davierwala A, Haynes J, Moffat J, Peng W, Zhang W, et al. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004;118:31-44 pubmed..We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection. ..
- Moses A. Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites. BMC Evol Biol. 2009;9:286 pubmed publisher..This demonstrates that it is possible to develop tests for selection on regulatory regions based on the specific functional constrains on these sequences...
- Chen F, Gu Y, Hasegawa H, Ruan X, Arawaka S, Fraser P, et al. Presenilin 1 mutations activate gamma 42-secretase but reciprocally inhibit epsilon-secretase cleavage of amyloid precursor protein (APP) and S3-cleavage of notch. J Biol Chem. 2002;277:36521-6 pubmed..They also argue that, although both the gamma-site and the epsilon-site cleavage of APP are presenilin-dependent, they are likely to be independent catalytic events. ..
- Austin R, Provart N, Cutler S. C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families. BMC Genomics. 2007;8:191 pubmed..This approach to background reduction could be expanded for application to protein motif prediction in the protein interior. A parallel N-terminal analysis is presented as supplementary data. ..
- Pang A, Smith A, Nuin P, Tillier E. SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics. 2005;6:236 pubmed
- Mark W, Liao J, Lu Y, Ayed A, Laister R, Szymczyna B, et al. Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions?. J Mol Biol. 2005;345:275-87 pubmed..This supports a model in which the central region may act as a long flexible scaffold for intermolecular interactions, thereby helping to integrate multiple signals in the DNA damage response pathway. ..
- Agrawal A. Differences between selection on sex versus recombination in red queen models with diploid hosts. Evolution. 2009;63:2131-41 pubmed publisher..These results strongly indicate that Red Queen models focusing exclusively on the effects of recombination cannot be used to infer the type of selection on sex that is generated by parasites on diploid hosts. ..
- Yun F, Wong B, Chase M, Shuen A, Canaff L, Thongthai K, et al. Genetic variation at the calcium-sensing receptor (CASR) locus: implications for clinical molecular diagnostics. Clin Biochem. 2007;40:551-61 pubmed..They will assist in the study of CASR polymorphisms as predictors of complex disease states. ..
- Shahbaba B, Neal R. Gene function classification using Bayesian models with hierarchy-based priors. BMC Bioinformatics. 2006;7:448 pubmed..Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information. ..
- Li S, Lakin Thomas P. Effects of prd circadian clock mutations on FRQ-less rhythms in Neurospora. J Biol Rhythms. 2010;25:71-80 pubmed publisher..We propose that prd-1 and prd-2 are good candidates for components of the FRQ-less oscillator and that prd-3 and prd-4 act on the system mainly through effects on FRQ/WCC...
- Larijani M, Yu C, Golub R, Lam Q, Wu G. The role of components of recombination signal sequences in immunoglobulin gene segment usage: a V81x model. Nucleic Acids Res. 1999;27:2304-9 pubmed..Furthermore, the contribution of the heptamer and nonamer to differential VHusage in our assay is correlated inversely with their conservation throughout the VHlocus. ..
- Sheng W, Wang G, Wang Y, Liang J, Wen J, Zheng P, et al. The roles of versican V1 and V2 isoforms in cell proliferation and apoptosis. Mol Biol Cell. 2005;16:1330-40 pubmed..These results were confirmed by silencing the expression of versican V1 with small interfering RNA (siRNA), which abolished V1-enhanced cell proliferation and V1-induced reduction of apoptosis. ..
- Dorval K, Bobechko B, Ahmad K, Bremner R. Transcriptional activity of the paired-like homeodomain proteins CHX10 and VSX1. J Biol Chem. 2005;280:10100-8 pubmed..Therefore, CHX10 and VSX1 may control retinal bipolar cell specification or differentiation by repressing genes required for the development of other cell types. ..
- Fish J, Matouk C, Rachlis A, Lin S, Tai S, D Abreo C, et al. The expression of endothelial nitric-oxide synthase is controlled by a cell-specific histone code. J Biol Chem. 2005;280:24824-38 pubmed..Taken together, these findings provide strong evidence that the endothelial cell-specific expression of eNOS is controlled by cell-specific histone modifications. ..
- Drisaldi B, Coomaraswamy J, Mastrangelo P, Strome B, Yang J, Watts J, et al. Genetic mapping of activity determinants within cellular prion proteins: N-terminal modules in PrPC offset pro-apoptotic activity of the Doppel helix B/B' region. J Biol Chem. 2004;279:55443-54 pubmed..Further implementation of this assay should provide a fuller understanding of the attributes and subcellular localizations required for activity of these enigmatic proteins. ..
- Wong J, Gokgoz N, Alon N, Andrulis I, Buchwald M. Cloning and mutation analysis of ZFP276 as a candidate tumor suppressor in breast cancer. J Hum Genet. 2003;48:668-71 pubmed..One silent polymorphism and two alterations predicted to result in amino acid changes were detected. Absence of the wild-type allele in tumors carrying the E530D variant suggests a possible role for this change in tumorigenesis. ..
- Coulthard A, Nolan N, Bell J, Hilliker A. Transvection at the vestigial locus of Drosophila melanogaster. Genetics. 2005;170:1711-21 pubmed..This physical displacement in the nucleus hinders transvection by disrupting the somatic pairing of homologous chromosomes and gives rise to proximal critical regions. ..
- Bradshaw P, Stavropoulos D, Meyn M. Human telomeric protein TRF2 associates with genomic double-strand breaks as an early response to DNA damage. Nat Genet. 2005;37:193-7 pubmed..Our results implicate TRF2 in an initial stage of DSB recognition and processing that occurs before association of ATM with DSBs and activation of the ATM-dependent DSB response network. ..
- Von Both I, Silvestri C, Erdemir T, Lickert H, Walls J, Henkelman R, et al. Foxh1 is essential for development of the anterior heart field. Dev Cell. 2004;7:331-45 pubmed..Thus, Foxh1 and Nkx2-5 functionally interact and are essential for development of the AHF and its derivatives, the RV and OFT, in response to TGFbeta-like signals. ..
- Petronis A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature. 2010;465:721-7 pubmed publisher..Epigenetics can provide a new framework for the search of aetiological factors in complex traits and diseases. ..
- Savas S, Ozcelik H. Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs. BMC Cancer. 2005;5:107 pubmed
- Haynes J, Garcia B, Stollar E, Rath A, Andrews B, Davidson A. The biologically relevant targets and binding affinity requirements for the function of the yeast actin-binding protein 1 Src-homology 3 domain vary with genetic context. Genetics. 2007;176:193-208 pubmed..We also find that considerable reductions in binding affinity are tolerated by the cell with little effect on growth rate, even when the actin cytoskeletal morphology is significantly perturbed. ..
- Bladt F, Aippersbach E, Gelkop S, Strasser G, Nash P, Tafuri A, et al. The murine Nck SH2/SH3 adaptors are important for the development of mesoderm-derived embryonic structures and for regulating the cellular actin network. Mol Cell Biol. 2003;23:4586-97 pubmed..These data suggest that the Nck SH2/SH3 adaptors have important functions in the development of mesodermal structures during embryogenesis, potentially linked to a role in cell movement and cytoskeletal organization. ..
- Moens P, Kolas N, Tarsounas M, Marcon E, Cohen P, Spyropoulos B. The time course and chromosomal localization of recombination-related proteins at meiosis in the mouse are compatible with models that can resolve the early DNA-DNA interactions without reciprocal recombination. J Cell Sci. 2002;115:1611-22 pubmed
- Nagy A, Rossant J. Chimaeras and mosaics for dissecting complex mutant phenotypes. Int J Dev Biol. 2001;45:577-82 pubmed..Our views on chimaeras presented below definitely contain elements which grew out from this principle. ..
- Talent N. Evolution of gametophytic apomixis in flowering plants: an alternative model from Maloid Rosaceae. Theory Biosci. 2009;128:121-38 pubmed publisher..It is suggested that pollination from other taxa may provide some adaptive advantage to pseudogamous apospory...
- Hudson J, Chen L, Fode C, Binkert C, Dennis J. Sak kinase gene structure and transcriptional regulation. Gene. 2000;241:65-73 pubmed..Using various Sak promoter/luciferase constructs, the core promoter region required for expression was located within 400bp of the message Cap site, and sequence further 5' strongly suppressed transcription. ..
- White K, Nagy P. Advances in the molecular biology of tombusviruses: gene expression, genome replication, and recombination. Prog Nucleic Acid Res Mol Biol. 2004;78:187-226 pubmed..In this review, we compile recent information on each of the aforementioned processes-translation, transcription, replication and recombination-and discuss the significance of the results...
- Cheng E, Collins C, Berru M, Shulman M. A system for precise analysis of transcription-regulating elements of immunoglobulin genes. BMC Biotechnol. 2005;5:27 pubmed..5 fold among independent transfectants, and expression is greatly (> 50 fold) increased by inclusion of the IgH intronic enhancer. This system is suitable for precise analysis of the regulatory elements of the immunoglobulin loci. ..