• These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. (kb.se)
  • To explore the genetics of these and other fly features, the researchers sequenced pooled genomic DNA from six adult female house flies belonging to an inbred strain called aabys. (genomeweb.com)
  • In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
  • Human genetics: The hidden text of genome-wide associations. (ncsu.edu)
  • We are interested in the population genetics and evolutionary genomics of adaptation , mainly by using the fruit fly Drosophila melanogaster as an experimentally tractable model. (unifr.ch)
  • To address these longstanding problems we combine population genetics and population genomics, functional genetics, transcriptomics, physiology, and experimental evolution and apply them to natural and laboratory populations of D. melanogaster that are phenotypically differentiated for fitness-related traits. (unifr.ch)
  • This internship is also an opportunity to discover the Drosophila model, learn its advantages and other techniques used in the lab from Drosophula genetics to connectomics and functional imaging. (cnrs.fr)
  • Combined evidence annotation of transposable elements in genome sequences. (genscript.com)
  • Flybase BLAST -Searches all Drosophila reads and provides links to the individual matched sequences through the NCBI. (bcm.edu)
  • Using these DNA and RNA sequences, the team put together - and annotated - a 691 million base assembly that spans more than three-quarters of the fly's complete genome sequence and contains an estimated 14,810 protein-coding genes. (genomeweb.com)
  • The house fly genome contained sequences for some 771 apparent immune-related genes, for example, including 355 that are not homologous to Drosophila immune genes. (genomeweb.com)
  • My lab studies how the genomic sequences that control gene expression function and evolve. (berkeley.edu)
  • Our ultimate goal is to be able to interpret the regulatory information encoded in genomic DNA, so that we can routinely identify regulatory sequences, discern their function, predict the consequences of their perturbation, and reconstruct how they evolved. (berkeley.edu)
  • We focus on short evolutionary timescales where it is possible to couple specific changes in genome sequences with alterations in gene regulation and expression. (berkeley.edu)
  • For each of the approximately 40 transcription factors critical in shaping anterior-posterior and dorsal-ventral patterns, our goals are to: 1) measure the factor s in vitro affinity to each of its potential target sequences, 2) identify the genomic regions bound by each factor in living embryos, 3) determine the expression pattern of the factor and its targets in three-dimensions at cellular resolution. (berkeley.edu)
  • We now have extensive comparative sequence data for fruitflies (12 Drosophila genomes) and yeasts (many fungal genomes), and are using these data to characterize how the individual building blocks of regulatory sequences (transcription factor binding sites) and higher order structures (e.g. developmental enhancers) evolve. (berkeley.edu)
  • The detailed experimental data we are generating for D. melanogaster , and the genome sequences of 12 Drosophila species are a tremendous resource for studying the evolution of gene regulation. (berkeley.edu)
  • Several methods exist for the prediction of precursor miRNAs (pre-miRNAs) in genomic or sRNA-seq (small RNA sequences) data produced by NGS (Next Generation Sequencing). (biomedcentral.com)
  • We provide a simpler and much faster method with very reasonable sensitivity and precision, which can be applied without special adaptation to the prediction of both animal and plant pre-miRNAs, using as input either genomic sequences or sRNA-seq data. (biomedcentral.com)
  • We suggest that although individuals within a population can be harmed by the deleterious effects of new TE insertions, the presence of TE sequences in a genome is of overall benefit to the population. (blogspot.com)
  • Here, we report that the GA-repeat sequences that recruit the conserved MSL dosage compensation complex to the Drosophila X chromosome are also enriched across mammalian X chromosomes, providing genomic support for the Ohno hypothesis. (marksteinlab.org)
  • However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
  • In the previous funding period, we analyzed the genomes and quantitative phenotypes of 150 families with the 16p12.1 deletion, and tested individual as well as 214 pairwise interactions of homologs of 16p12.1 genes in Drosophila melanogaster and Xenopus laevis models. (psu.edu)
  • The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection. (biomedcentral.com)
  • Here, we investigated, in females of both D. melanogaster and D. nigrosparsa , the gene expression between animals uninfected and infected with w Mel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. (nature.com)
  • Drosophila hydei (mosca casera) is a species of Diptera, or the order of flies, in the family Drosophilidae. (wikipedia.org)
  • The name derives from Dr R. R. Hyde, who first discovered that the species was distinct from Drosophila repleta. (wikipedia.org)
  • Large sperm is a noted phenomenon among Drosophila species, but Drosophila hydei have the largest recorded sperm at over 20 mm long. (wikipedia.org)
  • The North American Species of Drosophila. (wikipedia.org)
  • Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster , including the oldest extant specimens of this species. (biorxiv.org)
  • By comparing historical samples ranging from the early 1800s to 1933 against modern day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of rapidly increasing human activity. (biorxiv.org)
  • Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. (kb.se)
  • Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. (kb.se)
  • Here, using the model species Drosophila melanogaster , we used a combination of Genome Wide Association mapping (GWAS) and transcriptomic profiling to characterize whether genes associated with thermal tolerance are primarily involved in dynamic stress responses or preparatory processes that influence physiological condition at the time of thermal stress. (frontiersin.org)
  • We are a hybrid computational and experimental lab who couple genome-scale computational and experimental analysis of gene regulation in Drosophila melanogaster and Saccharomyces cerevisiae with extensive analysis of comparative sequence data and experimental analysis of species closely related to these model systems. (berkeley.edu)
  • My lab is applying the high-resolution fluorescent imaging methods developed for D. melanogaster to systematically analyze gene expression, and dissect regulatory networks, in other Drosophila species and in several inbred lines of D. melanogaster . (berkeley.edu)
  • While it is impractical to repeat every experiment done in D. melanogaster in every other strain and species, we are extending several classes of experiment to selected strains and species so that we can better understand regulatory variation at each of its multiple levels: how sequence variation affects binding, how binding variation affects expression, and how expression variation affects phenotype. (berkeley.edu)
  • Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. (genomevisualization.com)
  • The analysis demonstrated the presence of multiple copies of retrotransposable elements inside the genome of beech, in accordance with the viral quasi-species theory of retrotransposon evolution. (sisef.it)
  • Among the insects, only the dipterans ( Drosophila and various mosquito species) have been widely investigated for their immune responses towards diverse pathogens. (biomedcentral.com)
  • Starting with a small number of validated and/or predicted cis-regulatory modules (CRMs) in a reference species as a training set, but with no a priori knowledge of the factors acting in trans, we computationally predicted transcription factor binding sites (TFBSs) and genomic CRMs underlying coregulation. (pasteur.fr)
  • Centromeres are genomic regions essential for proper chromosome segregation during cell division. (rochester.edu)
  • The analysis of 50 kb genomic windows identified 23 regions with a high density of TE insertions, most of them located in pericentromeric regions or on chromosome 4 [ 1 ]. (biomedcentral.com)
  • We carried out genome-wide linkage exclusion analysis in 12 families with CdLS and identified four candidate regions, of which chromosome 5p13.1 gave the highest multipoint lod score of 2.7. (nih.gov)
  • Over 50 years ago, Susumo Ohno proposed that dosage compensation in mammals would require upregulation of gene expression on the single active X chromosome, a mechanism which to date is best understood in the fruit fly Drosophila melanogaster. (marksteinlab.org)
  • This study developed a comprehensive approach that combines cytological mapping data of FlyBase-annotated genes and novel tools for predicting cytogenetic features of chromosomes on the basis of their protein composition and determined the genomic coordinates for all black bands of polytene chromosome 2R. (sdbonline.org)
  • . pepo Zucchini genome was published, providing insights into its evolution. (nature.com)
  • Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. (nature.com)
  • Genetic evidence for adaptation-driven incipient speciation of Drosophila melanogaster along a microclimatic contrast in "Evolution Canyon," Israel. (nih.gov)
  • Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel. (nih.gov)
  • They also are among the most rapidly evolving regions of genomes and can play a role in karyotype evolution and speciation. (rochester.edu)
  • Evolution of genes and genomes on the Drosophila phylogeny. (kb.se)
  • The identification of retrotransposable elements in forest trees represents an important step toward the understanding of mechanisms of genome evolution. (sisef.it)
  • Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms ( [44] ), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. (sisef.it)
  • The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy ( [11] ). (sisef.it)
  • it is not surprising that TEs [transposable elements] have a significant influence on the genome organization and evolution. (blogspot.com)
  • Genomic variations, accumulated through mutation, reproduction, and evolution, can contribute to robust differences in the behavior of an animal compared to its peers. (cnrs.fr)
  • To provide a solid experimental foundation for our evolutionary studies, we are working with several other labs in Berkeley to systematically dissect gene expression and regulation in the early D. melanogaster embryo. (berkeley.edu)
  • Gene expression is regulated in part by the interactions of genomic DNA with the packaging histone proteins. (wayne.edu)
  • Research in the Pile laboratory is directed toward understanding how genome packaging affects gene expression. (wayne.edu)
  • A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan amazighs. (ncsu.edu)
  • Their ability to move and/or replicate inside the genome is an important evolutionary force, responsible for the increase of genome size and the regulation of gene expression. (sisef.it)
  • Despite having an identical genome, cells can be regulated differently via epigenetic mechanisms that result in cell specific gene expression patterns. (ccmb.res.in)
  • Using single cell genomic technologies, we analyze the gene expression and epigenetic profiles of various cells to understand cell heterogeneity. (ccmb.res.in)
  • This method was applied to the gene expression program active in Drosophila melanogaster sensory organ precursor cells (SOPs), a specific type of neural progenitor cells. (pasteur.fr)
  • Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. (bcm.edu)
  • To test our hypotheses, we measured the critical thermal minimum (CT min ) and critical thermal maximum (CT max ) of 100 lines of the Drosophila Genetic Reference Panel (DGRP) and used GWAS to identify loci that explain variation in thermal limits. (frontiersin.org)
  • Recurrent insertion of transposable elements in specific genomic regions has been described in the Drosophila melanogaster reference genome. (biomedcentral.com)
  • Associating specific genomic variations with behavioral changes is difficult due to multi-dimensionality and complexity of behavioral measurement as well as the vast number of genomic variations present. (cnrs.fr)
  • One retroelement, G2/Jockey-3, is found at all D. melanogaster centromeres and centromeres in D. simulans . (rochester.edu)
  • We are taking a multi-pronged approach to address these questions in the model organism Drosophila melanogaster and in lung cancer. (wayne.edu)
  • MiRNAs were recognised for controlling, in different organisms, several basic pathways, such as those involved in stress resistance, apoptosis during wing development in D. melanogaster , and cell proliferation in the same organism [ 1 - 3 ]. (biomedcentral.com)
  • Genome Biology. (wikipedia.org)
  • As they reported online today in Genome Biology , the researchers pooled genomic DNA from half a dozen female house flies, using it as a template to generate sequence reads that were then assembled into a 691 million base M. domestica genome. (genomeweb.com)
  • The house fly genome provides a rich resource for enabling work on innovative methods of insect control, for understanding the mechanisms of insecticide resistance, and genetic adaptation to high pathogen loads, and for exploring the basic biology of this important pest," corresponding author Jeffrey Scott, an entomology researcher at Cornell University, and his colleagues wrote. (genomeweb.com)
  • Retrotransposons (RNA mediated Class I TEs) are the most widespread class of eukaryotic TE, particularly relevant in shaping plant genomes ( [10] , [44] ). (sisef.it)
  • The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. (kit.jp)
  • The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource. (kit.jp)
  • Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. (bcm.edu)
  • The transcription units are shown above the genomic DNA, while chromosomal aberrations are shown below (solid triangles indicate insertions of transposable elements and upward arrows indicate breakpoints of translocations and inversions). (nih.gov)
  • Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. (bcm.edu)
  • Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation. (biomedcentral.com)
  • Association of orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila melanogaster. (ncsu.edu)
  • Epidermal growth factor receptor and transforming growth factor-beta signaling contributes to variation for wing shape in Drosophila melanogaster. (ncsu.edu)
  • My lab is interested in understanding how the variation in genomes of Indians predisposes them to disparities in health and disease. (ccmb.res.in)
  • As part of large nation-wide population genomics programs, we map the natural variation in healthy genomes. (ccmb.res.in)
  • To elucidate the connection between genes and behavior, we use tens of thousands of Drosophila melanogaster larvae with sequenced genomes to assess how certain single-nucleotide polymorphisms (SNPs) can influence variation in decision making upon an inducted stimulus. (cnrs.fr)
  • Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. (kb.se)
  • By spelling out protein-coding genes in the genome and comparing the house fly sequence to that of the fruit fly, Drosophila melanogaster , the team has endeavored to unravel genetic factors coinciding with house fly features. (genomeweb.com)
  • These hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions. (biomedcentral.com)
  • Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)
  • To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. (nature.com)
  • We report for the first time whole-genome resequencing of the four subsp. (nature.com)
  • Thus, besides TEs annotated in the reference genome, non-reference TE insertions can now also be analyzed. (biomedcentral.com)
  • In addition, based on the analysis of the reference genome, and on the analysis of 177 DGRP strains, we identified 53 promoter regions that could potentially contain multiple roo insertions. (biomedcentral.com)
  • We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. (kb.se)
  • The modENCODE Project has goal to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes. (rug.nl)
  • Aim 3: Perform functional studies to assess interactions of 16p12.1 genes with second-hits within neuronal cell types in Drosophila and quantitative neurological assays in Danio rerio models. (psu.edu)
  • METHODS We carried out a genome-wide association meta-analysis of 4 QRS traits in up to 73,518 individuals of European ancestry, followed by extensive biological and functional assessment. (uni-muenchen.de)
  • To take advantage of sequence diversity outside of the genus Drosophila, we are sequencing developmentally important loci from several non-Drosophilid fly families to provide insights into the underlying principles of gene regulation. (berkeley.edu)
  • These loci are enriched in regions of open chromatin, histone modifications, and transcription factor binding, suggesting that they represent regions of the genome that are actively transcribed in the human heart. (uni-muenchen.de)
  • We further highlighted 67 candidate genes at the identified loci that are preferentially expressed in cardiac tissue and associated with cardiac abnormalities in Drosophila melanogaster and Mus musculus. (uni-muenchen.de)
  • Comparative validation of the D. melanogaster modENCODE transcriptome annotation. (bcm.edu)
  • The Effects of Weak Genetic Perturbations on the Transcriptome of the Wing Imaginal Disc and Its Association With Wing Shape in Drosophila melanogaster. (ncsu.edu)
  • Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function. (kb.se)
  • Review of A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB]. (ncsu.edu)
  • The student will use existing scripts and programs to process the raw data, extract behavioral features, compare features between genotypes, associate certain features to SNPs using genome wide association studies (GWAS), and present the results in publication-ready visualizations. (cnrs.fr)
  • At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. (biomedcentral.com)
  • Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. (biomedcentral.com)
  • Based on these population analyses, some genes have also been reported to accumulate many TE insertions, such as the 106.5 kb klarsicht , and the 24 kb derailed-2 that were analyzed in 146 strains of the Drosophila Synthetic Population Resource [ 5 , 6 ]. (biomedcentral.com)
  • 2016) [ 10 ] other similar clusters of roo insertions in gene promoter regions are present in the genome. (biomedcentral.com)
  • These opportunities are especially profound in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis. (biorxiv.org)
  • A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. (biomedcentral.com)
  • Because of its large 8 Gb genome, the genomic analysis of rye has lagged behind other cereals. (genomevisualization.com)
  • motif gene sets based on conserved cis-regulatory motifs from a comparative analysis of the human, mouse, rat, and dog genomes. (rug.nl)
  • A genome array-based copy number analysis of 290 NIPBL - , SMC1A -, and SMC3 -negative probands led to identification of the boy with 8q21,4 microdeletion, which included the RAD21 gene. (medscape.com)
  • We characterized the genomic structure of NIPBL and found that it is widely expressed in fetal and adult tissues. (nih.gov)
  • [ 15 ] Ratajska et al found 2 patients with a classic CDLS phenotype and large genomic deletions encompassing NIPBL and some others contiguous genes. (medscape.com)
  • Project Summary Genomic basis of phenotypic variability of complex disorders Extensive phenotypic variability has complicated our understanding of complex disorders. (psu.edu)
  • iii) together with folding, most methods then rely on further information that must be learned from previously validated miRNAs of closely related genomes (at a minimum within the same clade, plant or animal) for the final prediction of new miRNAs in order either to set the parameters of the model or to restrict the search to a limited space. (biomedcentral.com)
  • We found that carrier children were more likely to carry another large CNV or rare deleterious mutation ("second-hit") elsewhere in the genome compared to their carrier parents, indicating that the deletion sensitizes the genome for a range of neurodevelopmental outcomes, and the ultimate phenotype is determined by variants in the genetic background. (psu.edu)
  • These genomic regions appear to have an elevated likelihood of positive selection, based on nucleotide level conservation and transcriptional data. (biomedcentral.com)
  • Assays in transgenes in Drosophila previously identified cis -acting transcriptional regulatory elements from homeotic genes. (nih.gov)
  • Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. (pklab.org)
  • The vast majority of pre-miRNA predictors then rely on further information learned from previously validated miRNAs from the same or a closely related genome for the final prediction of new miRNAs. (biomedcentral.com)
  • However, despite its smaller size, most developmental genes and at least half of the disease- and cancer-causing genes in humans are conserved in Drosophila , making Drosophila an excellent model system for the study of human development and disease. (nih.gov)
  • The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. (biorxiv.org)
  • This symposium will discuss the current understanding of these not-so-long-ago obscure areas of the genome, with special attention to transposable elements' activities and their evolutionary consequences. (blogspot.com)
  • Kugelman JR , Sanchez-Lockhart M , Andersen KG , Gire S , Park DJ , Sealfon R , Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics. (cdc.gov)
  • Spunky Scientific Visualization Safely learn about the plague, ebola and marburg at the deadly genomes depot. (genomevisualization.com)
  • We indeed aimed at better predicting miRNAs at a genome scale, but also from sRNAseq data where in some cases, notably of plants, the current folding methods often infer the wrong structure. (biomedcentral.com)
  • Making sense of genomic data! (pklab.org)
  • Currently we have raw behavioral data from more than 100 genotypes of D. melanogaster, including wild type lines as well as Alzheimer's disease-related genotypes. (cnrs.fr)
  • The Drosophila Genome Project was funded by the National Human Genome Research Institute , National Cancer Institute , and Howard Hughes Medical Institute . (bcm.edu)
  • Together, our results advance the collective knowledge about human genome function in several major areas. (kb.se)
  • In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. (deepdyve.com)
  • The Drosophila genome is about one twentieth the size of the human genome. (nih.gov)
  • The trans -acting factors are also conserved between Drosophila and human and have important functions, not only in development but also in stem-cell maintenance and cancer. (nih.gov)
  • Relative to the fruit fly, the house fly genome contained far more repetitive sequence elements and copy number variants, the researchers noted, along with an especially robust representation of immune system components. (genomeweb.com)