Search results for " genomics"
showing 10 items of 390 documents
Whole-Genome Analyses
2014
Abstract Average nucleotide identity (ANI) was proposed almost 10 years ago as a means to compare genetic relatedness among prokaryotic strains. It was found that values around 95% corresponded to the 70% DNA–DNA hybridization cut-off value that is widely used to delineate archaeal and bacterial species. ANI calculations are one of the many aspects and approaches that can be derived from comparative genomic data and used for taxonomic purposes. Here, an overview about the impact and current usage of ANI values is given together with details of the existing user-friendly package tool, the biology-oriented software package JSpecies, which can be used to generate two types of ANI calculations …
Spectrum of novel mutations found in Waardenburg syndrome types 1 and 2: implications for molecular genetic diagnostics
2013
Objectives Till date, mutations in the genes PAX3 and MITF have been described in Waardenburg syndrome (WS), which is clinically characterised by congenital hearing loss and pigmentation anomalies. Our study intended to determine the frequency of mutations and deletions in these genes, to assess the clinical phenotype in detail and to identify rational priorities for molecular genetic diagnostics procedures. Design Prospective analysis. Patients 19 Caucasian patients with typical features of WS underwent stepwise investigation of PAX3 and MITF . When point mutations and small insertions/deletions were excluded by direct sequencing, copy number analysis by multiplex ligation-dependent probe …
High-throughput Functional Genomics Identifies Genes That Ameliorate Toxicity Due to Oxidative Stress in Neuronal HT-22 Cells
2004
We describe a novel genetic screen that is performed by transfecting every individual clone of an expression clone collection into a separate population of cells in a highthroughput mode. We combined high-throughput functional genomics with experimental validation to discover human genes that ameliorate cytotoxic responses of neuronal HT-22 cells upon exposure to oxidative stress. A collection of 5,000 human cDNAs in mammalian expression vectors were individually transfected into HT-22 cells, which were then exposed to H2O2. Five genes were found that are known to be involved in pathways of detoxification of peroxide (catalase, glutathione peroxidase-1, peroxiredoxin-1, peroxiredoxin-5, and…
A fast algorithm for the exhaustive analysis of 12-nucleotide-long DNA sequences. Applications to human genomics
2004
We have developed a new algorithm that allows the exhaustive determination of words of up to 12 nucleotides in DNA sequences. It is fast enough as to be used at a genomic scale running on a standard personal computer. As an example, we apply the algorithm to compare the number of all 12-nucleotide long words in human chromosomes 21 and 22, each of them more than 33 million nucleotides long. Sequences that are chromosome specific are detected in less than 2 minutes, being analyzed any pair of chromosomes at a rate of 45 millions of nucleotides (45 Mb) per minute. The size of the words is long enough as to allow further analyses of all significant sequences using conventional database searche…
Genetic and Chemical Modifiers Of A CUG Toxicity Model in Drosophila
2007
Non-coding CUG repeat expansions interfere with the activity of human Muscleblind-like (MBNL) proteins contributing to myotonic dystrophy 1 (DM1). To understand this toxic RNA gain-of-function mechanism we developed a Drosophila model expressing 60 pure and 480 interrupted CUG repeats in the context of a non-translatable RNA. These flies reproduced aspects of the DM1 pathology, most notably nuclear accumulation of CUG transcripts, muscle degeneration, splicing misregulation, and diminished Muscleblind function in vivo. Reduced Muscleblind activity was evident from the sensitivity of CUG-induced phenotypes to a decrease in muscleblind genetic dosage and rescue by MBNL1 expression, and furthe…
A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore (Bos indicus) beef cattle
2007
Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2013-08-22T19:04:58Z No. of bitstreams: 1 S1415-47572007000400008.pdf: 85300 bytes, checksum: 7422029b120457123fb366c1bd71e758 (MD5) Made available in DSpace on 2013-08-22T19:04:58Z (GMT). No. of bitstreams: 1 S1415-47572007000400008.pdf: 85300 bytes, checksum: 7422029b120457123fb366c1bd71e758 (MD5) Previous issue date: 2007-01-01 Made available in DSpace on 2013-09-30T20:08:32Z (GMT). No. of bitstreams: 2 S1415-47572007000400008.pdf: 85300 bytes, checksum: 7422029b120457123fb366c1bd71e758 (MD5) S1415-47572007000400008.pdf.txt: 39461 bytes, checksum: 2796161439379a834535eeaff8aac2ba (MD5) Previous issue date: 2007-01-01 Submitt…
The Population Genomics of Anopheles gambiae Species Complex: Progress and Prospects
2021
Anopheles gambiae sensu lato is a species complex containing principal malaria vectors such as An. gambiae sensu stricto, An. coluzzii, and An. arabiensis. Numerous studies have shown dynamic species hybridization among member of this complex makes them an ideal model for studying evolution and speciation as well as for applied vector biology. Applying a population genomics approach to the An. gambiae and An. coluzzii species group has led to a number of important and epidemiologically relevant insights including: (1) organization of genomic divergence into “islands of speciation”; (2) competing models of population origin of An. gambiae and An. Coluzzii; (3) description of asymmetric intro…
Evolutionary Study of Disorder in Protein Sequences
2020
Intrinsically disordered proteins (IDPs) contain regions lacking intrinsic globular structure (intrinsically disordered regions, IDRs). IDPs are present across the tree of life, with great variability of IDR type and frequency even between closely related taxa. To investigate the function of IDRs, we evaluated and compared the distribution of disorder content in 10,695 reference proteomes, confirming its high variability and finding certain correlation along the Euteleostomi (bony vertebrates) lineage to number of cell types. We used the comparison of orthologs to study the function of disorder related to increase in cell types, observing that multiple interacting subunits of protein comple…
Data from: Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits
2015
Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species – the great tit Parus major – at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (< 50 km)…
The transcriptome analysis of Strongyloides stercoralis L3i larvae reveals targets for intervention in a neglected disease.
2012
Background: Strongyloidiasis is one of the most neglected diseases distributed worldwide with endemic areas in developed countries, where chronic infections are life threatening. Despite its impact, very little is known about the molecular biology of the parasite involved and its interplay with its hosts. Next generation sequencing technologies now provide unique opportunities to rapidly address these questions. Principal Findings: Here we present the first transcriptome of the third larval stage of S. stercoralis using 454 sequencing coupled with semi-automated bioinformatic analyses. 253,266 raw sequence reads were assembled into 11,250 contiguous sequences, most of which were novel. 8037…