• Histopathology, in situ hybridization, and western blotting were performed on murine tissues. (molvis.org)
  • Western blot analysis and in situ hybridization confirmed the presence of AND-34 RNA and protein in lens epithelial cells, particularly at the lens equator. (molvis.org)
  • We validated laminar patterning in each block using RNAscope in situ hybridization with Layer I and VI marker genes (RELN and NR4A2). (speakerdeck.com)
  • Fluorescence in situ hybridization to metaphase chromosomes or chromatin fibers in interphase nuclei is a powerful technique in mapping genes and DNA segments to specific chromosome region. (nih.gov)
  • Fluorescence in situ hybridization signals have been detected for sequences separated as close as 21 kilobase pairs and as far as 350 kilobase pairs, with excellent correspondence between the observed and expected distances. (nih.gov)
  • Candidate clusters are cloned into reporter genes, transformed into the genome, and tested for in vivo activity by in situ hybridization experiments. (nyu.edu)
  • Localization of Merkel cell polyomavirus (MCPyV) RNA was confirmed by RNAScope in situ hybridization. (bvsalud.org)
  • Methods for gene identification and analysis of gene structure: cloning, PCR, restriction mapping, in situ hybridisation, DNA sequencing. (lu.se)
  • It also has enormous polytene chromosomes in the salivary glands of larvae that are even bigger than those of Drosophila and were used to develop the method of in situ hybridization. (newswise.com)
  • For cellular localization of SARS-CoV-2 RNA and viral characterization, we performed in-situ hybridization (ISH), subgenomic RNA RT-PCR, and whole genome sequencing. (cdc.gov)
  • 3) Characterize the immunogenic landscape of TNBC through molecular data and in situ analyses combined with image analysis methods. (lu.se)
  • Fluorescence "in situ" hybridization (FISH) technique enables chromosomes to be tagged with fluorescent dyes to highlight genetic traits. (lu.se)
  • He has led genome-wide studies of human genome variation, heritable gene expression variation, human genetic disorders, tumor evolution, mouse strain variation, genome stability in reprogrammed stem cells, and single-neuron somatic mosaicism in the human brain. (yale.edu)
  • His current work is focused on two broad goals: (1) mapping variants and genes that confer risk to human disease, with ongoing projects focused on coronary artery disease and cardiometabolic traits in unique and underrepresented populations, and (2) developing methods for the detection and interpretation of human genome variation, with an emphasis on structural variation and other difficult-to-detect forms, and on comprehensive trait association in human disease studies. (yale.edu)
  • g of input DNA), Ng et al selectively targeted CCDS regions totaling 26.6 Mb of sequence (~0.83% of the human genome). (massgenomics.org)
  • Beyond the simple stream of one-letter characters in the human genome sequence lies a complex, higher-order code. (analytica-world.com)
  • These technologies-reported in the journal "Genome Research" were used to create the first comprehensive map of CNVs in the human genome, concurrently published in Nature. (analytica-world.com)
  • One paper describes a new whole-genome tiling path microarray, which was constructed from the same DNA used to sequence the human genome in 2001. (analytica-world.com)
  • The array covers 93.7% of the euchromatic (gene-containing) regions of the human genome and substantially improves resolution over previous arrays. (analytica-world.com)
  • Data from the array were assessed with a new algorithmic tool, called CNVfinder, which accurately and reliably identified CNVs in the human genome. (analytica-world.com)
  • Accurate and reliable high-throughput detection of copy number variation in the human genome. (analytica-world.com)
  • As of August 10, 2000, draft sequence was available for 87% of the human genome (https://www.ncbi.nlm.nih.gov/genome/seq/), and at least 39 prokaryotic genomes, including those of more than a dozen human pathogens, had been completely sequenced https://www.tigr.org/tdb/mdb/mdbcomplete.html). (medscape.com)
  • In a paper published today in the journal Cell , a team of Princeton researchers detailed a new computational method for detecting Neanderthal ancestry in the human genome. (sciencedaily.com)
  • The Princeton team leveraged the principle of IBD to identify Neanderthal DNA in the human genome by distinguishing sequences that look similar to Neanderthals because we once shared a common ancestor in the very distant past (~500,000 years ago), from those that look similar because we interbred in the more recent present (~50,000 years ago). (sciencedaily.com)
  • Albert Levan, a researcher at Lund University, was the first to establish how many chromosomes there are in the human genome. (lu.se)
  • In the 1950s, Albert Levan and American Joe Hin Tjio improved the method, and in 1956 they established that the human genome is divided into 46 chromosomes, i.e. 23 pairs of chromosomes. (lu.se)
  • Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans 5 and Aspergillus fumigatus 6 . (nature.com)
  • The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
  • The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
  • He has also served as an Associate Editor at Genome Research (2009-2014) and Genes, Genomes and Genetics (2011-2018).Most recently, Dr. Hall has played a leadership role in several large collaborative projects funded by NIH/NHGRI including the Centers for Common Disease Genomics, the AnVIL cloud-based data repository and analysis platform, and the Human Pangenome Project. (yale.edu)
  • To test their hybridization hypothesis, rather than look at individual genes, this time, they used whole-genome sequencing from 80 individual trees that represented 19 of the 22 species of Juglans . (sciencedaily.com)
  • Within species, genomes vary in both gene content (e.g., tandem duplicated genes, CNVs dispersed throughout the genome, and PAVs of genes) and repetitive portions of the genome (e.g., transposable elements, knob repeats, centromere repeats). (biomedcentral.com)
  • Conclusions: Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity. (lu.se)
  • We have contributed to the assembly process by mapping markers/genes to BACs and contigs using overgo hybridization. (kent.ac.uk)
  • First, we use bio-informatics methods and published ChIP-Chip data to identify all clusters of Bicoid-binding sites that are similar to those in the known target genes. (nyu.edu)
  • Analyze full-length infectious clones to determine the genes or gene products involved in replication, systemic movements, and pathogenicity to understand the role of viral pathogen genes in disease development and to identify new targets in the pathogen genome and tools for disease management. (usda.gov)
  • Identify and characterize genes and/or phages affecting virulence and competitiveness of those bacteria to develop effective control methods. (usda.gov)
  • The method utilizes specific primers to amplify target transgenes, and species-specific reference genes in a single duplexed reaction containing thousands of droplets. (usda.gov)
  • The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. (biomedcentral.com)
  • In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. (biomedcentral.com)
  • Plant mitochondrial genomes contain genes for their own rRNA subunits as well as for some of the ribosomal proteins and tRNAs required for translation (Figure 1 ), but many necessary ribosomal protein and tRNA genes are located in the nuclear genome, so their gene products must be imported into the mitochondrion [ 15 ]. (biomedcentral.com)
  • Furthermore, methods to rank the genes according to their importance for the classification are explored. (lu.se)
  • As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)
  • The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)
  • Three specific biomolecular techniques are addressed: polymerase chain reaction, microarray comparative genomic hybridization, and whole-genome sequencing. (umd.edu)
  • For microarray, novel pan-genomic design and analysis methods are presented for the characterization of unknown microbial isolates. (umd.edu)
  • Using microarray technology, scientists can scan for CNVs across the genome in a single experiment. (analytica-world.com)
  • The design and construction of a DNA microarray for any given microbial genome are straightforward. (medscape.com)
  • DNA microarray hybridization analysis stands out for its simplicity, comprehensiveness, data consistency, and high throughput. (medscape.com)
  • Methods for analysis of gene expression: microarray, hybridisation, promoter analyses. (lu.se)
  • Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
  • For designing real-time detection assays, an efficient data structure and search algorithm are presented to identify the most distinguishing sequences of a pathogen that are absent from all other sequenced genomes. (umd.edu)
  • Illumina single nucleotide polymorphism (SNP) chips, kompetitive allele-specific PCR (KASP) assays, genotyping-by-sequencing (GBS)) and sequencing (e.g. (biomedcentral.com)
  • Multiregion hybridization assays (MHA) represent an alternative for a consistent genetic analysis of large numbers of viral strains. (unl.pt)
  • 4-6 The first sequenced and publicly released SARS-CoV-2 genomes helped guide development of diagnostic assays and eventually vaccines. (health.mil)
  • During the early 1990s, breakthroughs in cloning and sequencing of Norwalk virus and Southampton virus ( 15--18 ) led to the development of sensitive molecular assays (e.g., reverse transcription-polymerase chain reaction [RT-PCR]), nucleotide hybridization probes, and enzyme-linked immunosorbent assays (ELISA) that used baculovirus-expressed viral antigens ( 19--33 ). (cdc.gov)
  • These methods emphasize combinations of classical and modern genetic approaches, including isolation and characterization of mutants, two-hybrid analysis, tetrad analysis, complementation, and recombination. (cshlpress.com)
  • Also covered are molecular genetic techniques for genome engineering. (cshlpress.com)
  • Additional experiments introduce fundamental techniques in yeast genomics, including both performance and interpretation of Synthetic Genetic Array analysis, multiplexed whole genome and barcode sequencing, and comparative genomic hybridization to DNA arrays. (cshlpress.com)
  • Using genomic data analyzed with phylogenetic and population genetic approaches, researchers have now cracked this mystery, showing that the Persian walnut is the result of hybridization between two long-extinct species around 3.45 million years ago. (sciencedaily.com)
  • In the end, we characterized the genetic composition of the genomes of not only the Persian walnut, but also the Iron walnut, J. sigillata , and the American butternut, J. cinerea . (sciencedaily.com)
  • However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. (biorxiv.org)
  • Initial efforts to dissect the genetic architecture of traits (e.g., quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS)) and genomic prediction efforts have relied primarily on SNP markers. (biomedcentral.com)
  • We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with Approximate Bayesian Computation (ABC), to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. (clemson.edu)
  • The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. (unl.pt)
  • To identify large genetic differences in pathways within a single species, We performed a genome-wide scan for higher-order genetic interactions in segregants from 16 highly diverse S. cerevisiae crosses grown in 38 different conditions. (escholarship.org)
  • Technical abstract: Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. (usda.gov)
  • To evaluate tumor-specific genetic changes using next-generation sequencing (NGS) panels. (cancerindex.org)
  • Gene technology: basic and applied molecular genetic methods. (lu.se)
  • The method the Princeton researchers developed, IBDmix, draws its name from the genetic principle "identity by descent" (IBD), in which a section of DNA in two individuals is identical because those individuals once shared a common ancestor. (sciencedaily.com)
  • Unlike other viruses, retroviruses must copy their genetic material into the host genome as part of their life cycle. (sciencebulletin.org)
  • Next-generation sequencing technologies have dramatically changed the approach to genetic diagnosis. (msdmanuals.com)
  • This revolutionary and rapidly evolving technology has moved a significant portion of the technical aspects of genetic diagnosis to next-generation sequencing and has become the mainstay of genetic diagnosis. (msdmanuals.com)
  • Detailed genetic and epigenetic sequencing now form the basis of the hunt by cancer researchers for diagnostically useful changes. (lu.se)
  • Sequencing of DNA gives a direct picture of our genetic make-up, while sequencing of the RNA that is naturally present in cells gives a picture of which parts of our non-coding DNA are used and in what way. (lu.se)
  • In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. (mdpi.com)
  • We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)
  • The array was employed in a process known as comparative genomic hybridization (CGH), which involves tagging genomic DNA from two individuals and then co-hybridizing it to the array. (analytica-world.com)
  • Genome structure, comparative genomics, and bioinformatics. (lu.se)
  • Standard chromosome analysis by G-banding has a limited resolution, but molecular cytogenetic techniques, such as multi-subtelomeric FISH, microdeletion FISH, multicolour FISH and comparative genomic hybridisation (CGH), have played an important role for the diagnosis of MR during the past decade. (bmj.com)
  • 2010) Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. (concordia.ca)
  • 4% of probes are specific to YJM789 sequence. (slideserve.com)
  • Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). (unl.pt)
  • We have also demonstrated specific hybridization of fluorescence-labeled probes to single-copy genomic DNA sequences on the free chromatins. (nih.gov)
  • Based on the knowledge and tools developed while identifying and characterizing new viruses and comparisons to previously-characterized viruses, new virus-specific and broad spectrum polyclonal and/or monoclonal antibody reagents, purification protocols, nucleic acid hybridization probes, PCR primers, isothermal amplification methods, and improved associated protocols will be developed. (usda.gov)
  • Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. (usda.gov)
  • Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. (usda.gov)
  • This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species. (usda.gov)
  • This set of tracks shows the genomic positions of probes and targets from a full suite of in-solution-capture target enrichment exome kits for Next Generation Sequencing (NGS) applications. (ucsc.edu)
  • Different types of probes may investigate a broad range of sizes of DNA sequence. (msdmanuals.com)
  • DNA from a patient is compared to a reference genome using many oligonucleotide probes. (msdmanuals.com)
  • Because of the substantial reduction in cost of whole-genome sequencing for bacterial strains, we are entering the era of genomic microbiology ( 8 ). (cdc.gov)
  • To demonstrate the effectiveness of these methods, pan-genomic arrays are applied to the study of multiple strains of the foodborne pathogen, Listeria monocytogenes, revealing new insights into the diversity and evolution of the species. (umd.edu)
  • To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
  • GB virus C (GBV-C) evolutionary patterns revealed by analyses of reference genomes, E2 and NS5B sequences amplified from viral strains circulating in the Lisbon area (Portugal). (unl.pt)
  • The phylogenetic analysis of the 5′-untranslated region (5'UTR) of the GBV-C genome has led to the segregation of viral strains into six genotypes, but incongruent results are frequently obtained depending on the genome region analyzed. (unl.pt)
  • High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. (springer.com)
  • In the last two decades, DNA barcoding, the sequencing of short species-specific amplicons, has considerably simplified community analyses (Hebert et al. (springer.com)
  • All of our genome-wide analyses converged to provide unambiguous evidence of hybridization at the roots of both the American butternut ( J. cinerea ) and the Persian walnut ( J. regia/J. sigillata )," said the authors. (sciencedaily.com)
  • The nuclear and mitochondrial analyses together suggest that the common ancestor of the wisent and CladeX mitochondrial lineages originated from asymmetrical hybridization (or sustained introgression) between male steppe bison and female aurochs. (slashgear.com)
  • BAC fingerprint analyses and alignments of BACs to the pre-existing linkage map have generated a BAC contig physical map of the genome. (kent.ac.uk)
  • Bioinformatic analyses of DNA- and protein sequences. (lu.se)
  • June 18, 2020 -- Illumina has acquired BlueBee, a Dutch genomics analysis software firm that originated as a spinoff from Delft University of Technology, in an effort to boost its next-generation sequencing (NGS) capability. (scienceboard.net)
  • Next-generation sequencing (NGS) of 10 genomes of novel coronavirus (2019-nCoV) from nine patients in China demonstrated that the virus is closely related. (scienceboard.net)
  • Next generation sequencing (NGS) of nucleic acid extracts from plants infected with unknown viruses is expected to yield information about the genomes of previously uncharacterized viruses without any background information on what viruses might be infecting the plant. (usda.gov)
  • We sought to determine the diagnostic yield of aligning off-target reads incidentally obtained during targeted hematolymphoid next-generation sequencing to a large database of viral genomes to screen for viral sequences within tumor specimens. (bvsalud.org)
  • This report describes SARS-CoV-2 genomic surveillance conducted by the Department of Defense (DoD) Global Emerging Infections Surveillance Branch and the Next-Generation Sequencing and Bioinformatics Consortium (NGSBC) in response to the COVID-19 pandemic. (health.mil)
  • The amplicons were pooled by sample and then barcoded and sequenced using Next Generation Sequencing platforms. (cdc.gov)
  • Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae -specific blocks (lacking synteny with A. nidulans and A. fumigatus ) in a mosaic manner throughout the genome of A. oryzae . (nature.com)
  • We performed a genomic study on 48 cases of Enterobacter -caused bloodstream infection by using in silico DNA-DNA hybridization to identify precise species. (cdc.gov)
  • Newly created methods can determine the overall nucleotide identities between genome sequences and therefore enable more precise species identification ( 9 ). (cdc.gov)
  • Calculation of average nucleotide identity (ANI) between genomes is widely used for species identification. (cdc.gov)
  • Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. (biorxiv.org)
  • The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. (biomedcentral.com)
  • Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species. (biomedcentral.com)
  • The ability to produce crops that meet societal needs is enhanced by a thorough understanding of the genome of a species. (biomedcentral.com)
  • Recent innovations are driving a paradigm shift in which the extent and relevance of structural variation within the pan-genome of crop species are now being considered. (biomedcentral.com)
  • In characterizing this variation, the genomic fraction common to all individuals within a species has been termed the "core" genome and the variable fraction the "dispensable" genome. (biomedcentral.com)
  • Methods: We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. (lu.se)
  • Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps, sequences and linkage maps for many species, including other avians. (kent.ac.uk)
  • The polymorphism observed in the organization of the subtelomeric region in the genome of two Penicillium species within the high homogeneous Penicillium subgenus is for the first time reported and perhaps can be employed in future phylogenetic studies. (scielo.br)
  • The results suggest that the endogenisation of a retrovirus may happen frequently and rather rapidly, initially without much change inside the virus and that becoming a part of the genome of all members of a host species takes a very long time" said Prof Alex Greenwood, the principal investigator of the study. (sciencebulletin.org)
  • We will apply this approach to a non-model sparrow study system to answer questions about how hybridization can disrupt evolved miRNA-mRNA interactions, leading to insights about the formation of new species. (lu.se)
  • Illumina 76-bp single-end sequencing was the platform of choice. (massgenomics.org)
  • Our second leukemia genome , which had 23x haploid coverage, took 16.5 Illumina runs to complete. (massgenomics.org)
  • When it comes to Illumina sequencing, UW seems to know what they're doing. (massgenomics.org)
  • Sequence data was collected using Anchored Hybrid Enrichment and sequenced on an Illumina Hi-seq. (clemson.edu)
  • The purchase will also help Illumina lower the cost of storing, sharing, and managing genomic data from the company's installed base of more than 15,000 sequencing systems. (scienceboard.net)
  • Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. (concordia.ca)
  • This dissertation focuses on computational methods for improving the accuracy of commonly used nucleic acid tests for pathogen detection and diagnostics. (umd.edu)
  • His group has developed bioinformatics tools for variant detection, variant interpretation, sequence alignment, data processing, and data integration. (yale.edu)
  • We applied a battery of genome-wide methods for hybridization detection and to test speciation models to infer the time of origin of the Persian walnut," said the Wei-Ning Bai, another senior author. (sciencedaily.com)
  • Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. (analytica-world.com)
  • and, (3) Characterize genomes of bacteria of major significance to ornamental and nursery crops to develop diagnostic tests for accurate pathogen detection. (usda.gov)
  • Improved detection and differentiation methods for these pathogens will enable state and federal regulatory officials to make timely and appropriate recommendations in safeguarding the movement of horticultural and agricultural products into the United States. (usda.gov)
  • In addition to improving detection rates of NLVs in outbreaks of gastroenteritis, advances in laboratory methods have also refined the epidemiologic investigation of these outbreaks. (cdc.gov)
  • In other outbreaks, the detection in the implicated vehicle of NLVs with a sequence identical to that of the strain detected from the patients confirmed the causal link. (cdc.gov)
  • After amplification the samples are typed by hybridization to the typing strips followed by colorimetric detection. (cdc.gov)
  • The genome was confirmed to comprise eight chromosomes (chromosomes 1-8 in decreasing size), the assignment of which is different from a previous report 7 ( Supplementary Table S1 and schematic drawing in Supplementary Fig. S1 ). (nature.com)
  • Transfers of a single gene, a complete metabolic pathway 10 , whole chromosomes 11 or even cases of the integration of almost complete genomes from bacterial endosymbionts into their eukaryotic hosts 12 have been described. (nature.com)
  • This is then followed by exome capture by means of in-solution hybridization. (wikipedia.org)
  • The exome part of the genome consists of exons. (wikipedia.org)
  • This month in Nature , a group from Jay Shendure's lab reported perhaps the most ambitious targeted resequencing study to date - the whole exome sequences of 12 individuals . (massgenomics.org)
  • This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)
  • However, the sheer volume of information generated by sequencing the exome or genome results in a variety of interpretive problems that complicate understanding of the results. (msdmanuals.com)
  • Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. (biomedcentral.com)
  • DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. (medscape.com)
  • DNA microarrays can be used in genome-wide association studies (GWAS) to compare patient and control populations to identify DNA variants that can contribute to disease risk. (msdmanuals.com)
  • Dr. Peter Larson loads an Oxford Nanopore MinION sequencer in support of COVID-19 sequencing assay development at the U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland. (health.mil)
  • Loss of detectable HBV DNA by a solution phase hybridization assay is an earlier indicator of response to antiviral therapy than loss of HBeAg. (medscape.com)
  • the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. (jci.org)
  • Both bacterial artificial chromosome (BAC) and small insert sequencing libraries have been constructed from DNA of a single female inbred Red Jungle Fowl, the nearest wild relative of domestic chickens. (kent.ac.uk)
  • Understanding viral and bacterial genome structures and functions, their mechanisms of pathogenicity and resistance, and conferring virus and bacterial resistance in plants will lead to the development of better disease control measures and increases in both productivity and quality of ornamental plants for industry and the consumer. (usda.gov)
  • Phylogenetic analysis of the three aspergilli using the whole-genome data showed that A. nidulans branched off earlier than A. oryzae and A. fumigatus 5 . (nature.com)
  • Results are presented that show these "signature" sequences can be used to detect pathogens in complex samples and differentiate them from their non-pathogenic, phylogenetic near neighbors. (umd.edu)
  • In Chapter 2, to understand signal evolution across a broad range of taxa, a strongly supported phylogenetic hypothesis is needed and I estimate a new multi-locus phylogeny using Sanger sequencing. (ku.edu)
  • We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments. (lu.se)
  • This work reports the initial characterization, including near full-length sequence analysis, of an ISF which seems to form a divergent lineage within the ISF radiation, as indicated by phylogenetic analysis based on ac multiple sequence alignment of the NS5 flavivirus coding sequence. (unl.pt)
  • One of the methods that does seem to work well is TargetScan, which relies on both pairing of seed sequences (a subset of the 18-23 bp that make up a miRNA) and phylogenetic conservation of sites. (lu.se)
  • Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions. (medscape.com)
  • Genomic sequencing will provide the data needed to unravel the complexities of the host-pathogen interaction. (medscape.com)
  • His interests are in the development and use of molecular methods for pathogen discovery, human microbial ecology, genomewide host and microbial responses to infection, and Bordetella pathogenesis. (medscape.com)
  • An international team of scientists from Europe and North America now applied the technique of hybridisation capture to analyse the entire genome of koala retroviruses and used museum samples to monitor its variation across 130 years. (sciencebulletin.org)
  • This method permits the identification of entire genome sequences of the KoRV, the only known retrovirus currently invading its host germ line, from koala museum skins from the late 19th and across the 20th century and therefore were able to study 130 years of KoRV evolution. (sciencebulletin.org)
  • Using aCGH, the entire genome can be tested (queried). (msdmanuals.com)
  • All HCS alleles are observed to have premature protein destruction before the PEST sequence is fully translated. (wikipedia.org)
  • 3026 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3027. (cdc.gov)
  • The results suggest that for ca. 130 years, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. (sciencebulletin.org)
  • To identify operable lung cancer patients with risk for metastatic relapse we search for new prognostic biomarkers based on analysis of genome-wide gene expression data and conventional protein marker validation based on analysis of primary tumor tissue. (lu.se)
  • The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. (clemson.edu)
  • Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. (clemson.edu)
  • In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia . (biomedcentral.com)
  • Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. (biomedcentral.com)
  • The mitochondrial genomes of flowering plants exhibit a number of characteristics that distinguish them from the mitochondrial genomes of other eukaryotes [ 1 ]. (biomedcentral.com)
  • Angiosperm mitochondrial genomes also contain numerous introns, some of which have been split such that the resulting gene fragments must be transcribed separately and then trans- spliced together [ 7 ]. (biomedcentral.com)
  • The size and complexity of plant mitochondrial genomes, especially when compared with animals and fungi, make them powerful models for exploring the forces affecting eukaryotic genome structure and evolution. (biomedcentral.com)
  • 1) "native" tRNAs encoded in the mitochondrial genome and inherited from the α-proteobacterial progenitor of mitochondria, 2) chloroplast-like tRNAs, which are also encoded in the mitochondrial genome but which were acquired by functional gene transfer from the chloroplast genome during land plant evolution, and 3) nuclear-encoded tRNAs imported from the cytosol. (biomedcentral.com)
  • These rapid adaptations in fungi provide excellent models for studying general processes of eukaryotic genome evolution, including the functional and ecological impact of horizontal gene transfer 1 and changes in metabolism 2 . (nature.com)
  • Finally, multiple methods are presented for the validation of whole-genome sequence assemblies, which are capable of identifying assembly errors in even finished genomes. (umd.edu)
  • These validated assemblies provide the ultimate nucleic acid diagnostic, revealing the entire sequence of a genome. (umd.edu)
  • The project will rely on published whole genome assemblies and gene annotations of various qualities. (lu.se)
  • The Gerbi lab developed the method of Replication Initiation Point (RIP) mapping to map replication origins to the nucleotide level, improving resolution by two orders of magnitude. (newswise.com)
  • Each section was scanned using multispectral imaging and sequenced: whole-genome and targeted gene expression using the 10X Genomics human neuroscience panel. (speakerdeck.com)
  • Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. (biomedcentral.com)
  • Our way of thinking about crop genomics is changing as we gain a deeper understanding of the structural variation within the pan-genome. (biomedcentral.com)
  • Differential hybridization provides a means of detecting polymorphisms, even when only the reference genome sequence is known: SFPs. (slideserve.com)
  • Through sequence analysis and symptom presentation in HCS patients, this proves to be the most definitive method of diagnosis. (wikipedia.org)
  • These methods are potentially the future of diagnostics, but each requires sophisticated computational design or analysis to operate effectively. (umd.edu)
  • I also develop the acoustic analysis pipeline used for acquiring frequency traits from thousands of calls rapidly, where these methods will be used in Chapter 5. (ku.edu)
  • Although array CGH has provided a higher resolution compared to conventional CGH, it has not yet become a widely applied method for the analysis of gene dose alterations in individuals with idiopathic mental retardation. (bmj.com)
  • Methods: This qualitative study was performed using content analysis approach between May-July 2022. (bvsalud.org)
  • By focusing on coding exons, the authors achieved 51x coverage (on average) with just 6.4 Gb of mappable sequence per individual. (massgenomics.org)
  • Do hotspots (binary) or recombination rates (quantitative) correlate with features of DNA sequence or chromatin structure? (slideserve.com)
  • High frequency intra- and intermolecular recombination among large repeated sequences is the rule, generating a heterogeneous pool of genome configurations within a single individual [ 12 - 14 ]. (biomedcentral.com)
  • In the former scenario, reproductive isolation may be unlikely to evolve because the chance that loci under divergent selection will be linked to a trait that causes reproductive isolation is slim, and a genome-wide correlated response to divergent selection is lacking 16 , 17 . (biorxiv.org)
  • Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. (escholarship.org)
  • Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti , and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti -called Wallaby -present as identical fragments at non-homologous loci in P. camemberti and P. rubens . (nature.com)
  • The molecular characterization was based on the RAPD markers, telomeric fingerprinting and ITS sequencing. (scielo.br)
  • To cover the whole genome, genome wide screening for chromosomal imbalances using microsatellite markers has been reported, 17, 18 as well as metaphase CGH. (bmj.com)
  • Several independent high-throughput methods for differential gene expression (including SAGE and differential display) may enable function annotation of sequenced genomes [ 2 ] . (medscape.com)
  • The structural variation that has been uncovered in the pan-genome era necessitates a reevaluation of the determinants of phenotype. (biomedcentral.com)
  • We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. (frontiersin.org)
  • Methods We correlate clinical and molecular data of 25 novel and 23 previously reported patients with FOXP1 defects. (bmj.com)
  • The three objectives of this project are: (1) Characterize viruses of major significance to ornamental and nursery crops, including uncharacterized or emerging viruses affecting key ornamental crops, and develop corresponding diagnostic testing methods. (usda.gov)
  • When the underlying true causal architecture for a simulated gene is a compound heterozygote, our method is better able to capture the signal than the marginal SNP method. (escholarship.org)
  • Implementation of high-throughput and viral capture approaches, such as shotgun and hybridization capture sequencing. (pandasia-project.com)
  • In order to find out how retroviruses invade the germ lines of their hosts, an international team of scientists from the Leibniz Institute for Zoo and Wildlife Research (IZW) in Berlin, the California State University, the Zoo in Vienna, the National Museum of Natural History in Washington and the University of Illinois at Urbana-Champaign applied a technique known as hybridisation capture. (sciencebulletin.org)
  • Using the technique of hybridisation capture, the full retrovirus genome and the location of the retrovirus within the koala genome could be simultaneously examined with far less effort. (sciencebulletin.org)
  • During hybridisation capture, the "library" DNA which contains the sequence of the KoRV is immobilised on beads and serves as bait. (sciencebulletin.org)
  • In the course of her research on DNA replication and amplification, Gerbi has helped develop techniques for mapping replication origins, genome sequencing, and whole organism transformations. (newswise.com)
  • High-throughput methods for assessment of function are clearly required if this wealth of primary sequence information is to be used. (medscape.com)
  • Although outbreaks of nonbacterial gastroenteritis were recognized as a public health concern, electron microscopy (EM) proved to be a tedious and insensitive method for routine examination for enteric viruses in stool specimens collected during outbreak investigations. (cdc.gov)
  • Sequence data were used to monitor transmission dynamics on U.S. Navy ships and at military training centers and installations. (health.mil)
  • We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole genome duplication event. (clemson.edu)
  • Instead, IBDmix uses characteristics of the Neanderthal sequence itself, like the frequency of mutations or the length of the IBD segments, to distinguish shared ancestry from recent interbreeding. (sciencedaily.com)
  • This dissertation presents novel computational methods that unlock the potential of these diagnostics by efficiently analyzing whole-genome DNA sequences. (umd.edu)
  • As a faculty member at the University of Virginia (2007-2014), Washington University (2014-2020) and Yale (2020-present), his work has sought to understand the causes and consequences of genome variation in mammals, with an increasing focus on computational methods development and human genetics. (yale.edu)
  • The equipment and computational methods also continue to improve. (msdmanuals.com)
  • This is the platform on which the Washington University Genome Sequencing Center has assembled a 6.6X draft sequence of the chicken. (kent.ac.uk)
  • 2009) Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. (concordia.ca)
  • We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. (escholarship.org)
  • The main emphasis is on supervised machine learning methods for classification and prediction of tumor gene expression profiles. (lu.se)
  • Using such approaches, studies have already highlighted the prevalence of either strongly differentiated genomic 'islands' of differentiation 5 - 10 or genome-wide polygenic architectures of phenotypic differentiation and ecological speciation 11 - 15 . (biorxiv.org)
  • Gene expression also relies on extensive C-to-U (and sometimes U-to-C) RNA editing, in which substitution of specific pyrimidines in the mRNA sequence restores phylogenetically conserved codons [ 8 ]. (biomedcentral.com)
  • However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)
  • In Chapter 3 I aim to expand upon this dataset and develop a new sequencing technology to obtain thousands of markers affordably. (ku.edu)