• With this new phase we want to understand how the various genes and regulatory elements that make up the genome talk to each other and collaborate together in real-time to influence biology and disease. (umassmed.edu)
  • Depending on the similarity of genomes, segments can be shorter or span several genes and reveal local colinearity. (biomedcentral.com)
  • We sequenced the complete mt genome of W. compar and conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. (nature.com)
  • The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. (nature.com)
  • Genomics is the study of genomes, including large chromosomal segments containing many genes. (slidetodoc.com)
  • Know (close to) all the genes in a genome, and the sequence of the proteins they encode. (slidetodoc.com)
  • Presenting the genes of the human genome in their biological context, Guide to the Human Genome is an extensive online resource (also available in print) that provides easy access to information about human genes and their roles in specific processes. (cshlpress.com)
  • With numerous illustrations and tables, each of the nearly 300 sections of the Guide describes genes involved in a specific pathway, process, or structure from the molecular and cellular levels to developmental and physiological processes. (cshlpress.com)
  • Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. (biomedcentral.com)
  • A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein - coding genes , 8 rRNA genes , 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). (bvsalud.org)
  • Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). (bvsalud.org)
  • An influenza virus' genome consists of all genes that make up the virus. (cdc.gov)
  • A, C, G and T/U) in each of the genes present in the virus's genome. (cdc.gov)
  • Full genome sequencing can reveal the approximately 13,500-letter sequence of all the genes of the influenza virus' genome. (cdc.gov)
  • We observed that M. avium isolates from different sources-human pulmonary infections, human disseminated infections, animals, and natural environments-are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. (cdc.gov)
  • The complete sequence of the HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution. (wikipedia.org)
  • By May 2003, a coronavirus had been identified as the cause of SARS, and the full genome sequence of this new human pathogen, which may have jumped from civet cats to people, had been published. (sciencedaily.com)
  • This element sits at one end of the viral genome, and, as the researchers show, its sequence is highly conserved in related coronaviruses. (sciencedaily.com)
  • This strong sequence conservation indicates that the tertiary structure of s2m could be important for viral function, and when the researchers solved the three-dimensional crystal structure of the element, they found that it had a unique tertiary structure. (sciencedaily.com)
  • With tools such as CRISPR/CAS9, researchers at the center will be able to label specific parts of the genome so that they can be visualized in the microscope, and they will be able to make changes to the DNA sequence so that the 3D folding can be perturbed in a highly targeted manner. (umassmed.edu)
  • The availability of this extended region of contiguous sequence has allowed us to analyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene density. (aaai.org)
  • It's like looking at a protein sequence as a flat structure," co-founder and CEO Danuta Jeziorska told BioCentury. (biocentury.com)
  • The likelihood of interaction was most strongly defined by the three-dimensional (3D) domain structure rather than linear DNA sequence. (elifesciences.org)
  • Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. (biomedcentral.com)
  • Sequence comparison through multiple alignment is an indispensable tool for understanding genomes and their shared histories [ 1 ]. (biomedcentral.com)
  • Over and above, non-colinear multiple global alignments of whole genomes, genome alignments for short, integrate as much sequence similarity information as is available. (biomedcentral.com)
  • Genome alignments, which are the focus of this article, integrate more information than rearrangement studies by combining segmentation and sequence similarity. (biomedcentral.com)
  • This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. (nature.com)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. (peerj.com)
  • The representation of the human reference genome as a linear haploid DNA sequence poses limitations when trying to incorporate the known genetic diversity of human populations. (sevenbridges.com)
  • The initial phase of genomics aims to map and sequence an initial set of entire genomes. (slidetodoc.com)
  • Genome sequencing is a process that determines the order, or sequence, of the nucleotides (i.e. (cdc.gov)
  • Genome sequencing reveals the sequence of the nucleotides in a gene, like alphabet letters in words. (cdc.gov)
  • We recommend taking a plurality consensus sequence for each gene segment, genome, and/or lineage/subtype. (cdc.gov)
  • From the viral genome, researchers have deduced the sequences and structures of the viral proteins, hoping to use this information to develop treatments and vaccines for SARS. (sciencedaily.com)
  • Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. (biomedcentral.com)
  • Structural changes involve longer genomic segments, thereby affecting the structure and order of genomic sequences. (biomedcentral.com)
  • Of the 199 strains submitted to JGI, we received high-quality whole genome sequences for 166. (datadryad.org)
  • We successfully recovered quality S. meliloti genome sequences from 25 of these 33 isolates, for a total of 191 S. meliloti strains analyzed in this study. (datadryad.org)
  • Recent molecular analyses of mt genome sequences have provided selectable hypotheses for the phylogenetic relationships of nematodes based on 18S rRNA. (nature.com)
  • In this chapter, we report on high-resolution structures of single and multi RRM-RNA complexes to explain the numerous strategies used by these domains to interact specifically with a large repertoire of RNA sequences. (nih.gov)
  • Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. (nih.gov)
  • strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)
  • Should continue long after the initial genome sequences have been completed. (slidetodoc.com)
  • This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. (nature.com)
  • In plants, DNA is found in three genomes: plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear genome. (koneensaatio.fi)
  • Consequently, in this project, I will use NGS and other bioinformatic techniques 1) to generate six new complete fern mitochondrial genomes and 2) to infer the fern phylogeny based on mitochondrial DNA data. (koneensaatio.fi)
  • We use a combination of cell-based and in vitro assays to show that the interface of the FluPol A dimer is required for vRNA synthesis during replication of the viral genome. (nature.com)
  • Our study provides high-resolution structures of medically relevant FluPol A , as well as insights into the replication mechanisms of the viral RNA genome. (nature.com)
  • Our findings has provided a new model of gene organization in the human genome, which integrates transcription, replication, and chromatin structure as coordinated determinants of genome architecture. (ens-lyon.fr)
  • Although the structures of rotavirus and other members of the Reoviridae have been extensively studied, little is known about the structures of virus-encoded non-structural proteins that are essential for genome replication and packaging. (nih.gov)
  • Several RNA binding sites, resulting from the quaternary organization of NSP2 monomers, may be required for the helix destabilizing activity of NSP2 and its function during genome replication and packaging. (nih.gov)
  • Emerging coronaviruses: Genome structure, replication, and pathogenesis. (bvsalud.org)
  • Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. (biomedcentral.com)
  • The organisation and evolution of the eukaryotic genomes. (lu.se)
  • Non-colinear alignments, as opposed to colinear alignments, model all kinds of evolutionary changes and thereby enable correct homology prediction for whole genomes with non-colinear changes. (biomedcentral.com)
  • High levels of recombination could confound studies of the gonococcal populations, especially if the studies are based on few genetic loci within strains as compared to the entire genomes. (peerj.com)
  • Furthermore, unlike the rest of the SARS genome, which changes rapidly, the s2m element is absolutely conserved in SARS variants obtained from patients during the SARS epidemic. (sciencedaily.com)
  • Our results demonstrate that statistical interactions between genetic variants and chromatin accessibility are common throughout the genome. (elifesciences.org)
  • GRAF™ Pan Genome Reference - contains both small variants (SNPs and INDELs up to several dozens of base-pairs in length) as well as larger structural variants, which are typically difficult to identify from short-read sequencing data. (sevenbridges.com)
  • GRAF™ Variant Caller - enables integrated calling of SNPs and INDELs, as well as structural variants present in the Genome Graph. (sevenbridges.com)
  • The technology, unlike the chromosome conformation capture technologies that map interactions genome-wide, will allow scientists to zoom in on small, defined regions of the genome and to identify the proteins and other molecules that bind to the genome to facilitate local folding. (umassmed.edu)
  • There are regions of the genome that cannot be sequenced reliably. (cdc.gov)
  • The molecular structure of the viral spike has now been determined by X-ray crystallography and cryo-electron microscopy. (wikipedia.org)
  • We've entered what can be considered the third phase of the human genome project," said Job Dekker, PhD, Howard Hughes Medical Institute Investigator , professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology. (umassmed.edu)
  • However, the details of the molecular interactions and dynamics within these structures is very limited. (gla.ac.uk)
  • To understand the molecular-genetic basis of functional specialization and identify potential drug targets specific to each neuron subtype, we performed a genome wide assessment of both gene expression and splicing across EXC, PV, SST and VIP neurons from male and female mouse brains. (jneurosci.org)
  • Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships. (bvsalud.org)
  • Low-cost exome and genome sequencing technologies, as a group, represent disruptive technologies that in time could supplant- existing molecular diagnostic approaches. (cdc.gov)
  • Tracing the Evolution of Shiitake Mushrooms Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. (doe.gov)
  • Many bacterial symbionts have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmission. (datadryad.org)
  • The mt genome accumulates mutation rates at a faster rate than the nuclear genome and is characterised by fast evolution, maternal inheritance, and a simple structure. (nature.com)
  • An extensive literature documenting physiological and ecological diversity make Daphnia an ideal model to study the genetic architecture of phenotypic variation in natural populations and the evolution of genome structure/function relationships in aquatic environments. (biomedcentral.com)
  • AMR evolution should be considered in the context of the genetic structure of the N. gonorrhoeae population. (peerj.com)
  • Intra-tumor heterogeneity reflects cancer genome evolution and provides key information for diagnosis and treatment. (biomedcentral.com)
  • Ultimately, cancer genome evolution takes place at the single-cell level, and it is the cellular complexity and its dynamics that give rise to both intra- and inter-tumor heterogeneity. (biomedcentral.com)
  • The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. (bvsalud.org)
  • The genome and proteins of HIV (human immunodeficiency virus) have been the subject of extensive research since the discovery of the virus in 1983. (wikipedia.org)
  • The HIV genome encodes a small number of viral proteins, invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. (wikipedia.org)
  • Its innermost region consists of a cone-shaped core that includes two copies of the (positive sense) ssRNA genome, the enzymes reverse transcriptase, integrase and protease, some minor proteins, and the major core protein. (wikipedia.org)
  • The genome of human immunodeficiency virus (HIV) encodes 8 viral proteins playing essential roles during the HIV life cycle. (wikipedia.org)
  • For about a decade, our group has been extending its field of research to the study and modeling of the structure and dynamics of biological molecules (DNA, proteins). (ens-lyon.fr)
  • Complex genomes have roughly 10 x to 30 x more DNA than is required to encode all the RNAs or proteins in the organism. (slidetodoc.com)
  • Genetic variations are important because they affect the structure of an influenza virus' surface proteins. (cdc.gov)
  • Printed in Great Britain Key words: coronaviruses/genome expression/protein structure REVIEW ARTICLE Coronaviruses: Structure and Genome Expression By W. SPAAN, 1. (pdfroom.com)
  • The University of Oxford spinout is applying its target discovery strategy to autoimmune disorders, finding causal links between disease-associated dark genome mutations and functional changes in lymphocytes. (biocentury.com)
  • We carried out genome-wide association studies of 3,144 distinct functional and structural brain imaging derived phenotypes in UK Biobank (discovery dataset 8,428 subjects). (biorxiv.org)
  • We present here the X-ray structure of the functional octamer of NSP2 determined to a resolution of 2.6 A. The NSP2 monomer has two distinct domains. (nih.gov)
  • functional chromosomal elements and chromatin structure. (lu.se)
  • Revolution lauched by full genome sequencing - Many biological problems now have finite (albeit complex) solutions. (slidetodoc.com)
  • The population structure and evolutionary forces within the pathogen population were analyzed. (peerj.com)
  • Early work by O'Rourke & Stevens (1993) using electrophoretic analysis of enzymes of the pathogen and serological methods suggested that gonococci have a non-clonal sexual or panmictic population structure. (peerj.com)
  • Mycoplasma pneumoniae , a major pathogen causing community-acquired pneumonia, has a reduced genome of ≈800 kb, which has been relatively stable over time and geographic distance ( 1 ). (cdc.gov)
  • Here we use whole-genome resequencing of a hierarchically-structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize the population structures of this bacterial symbiont and its host plant Medicago truncatula . (datadryad.org)
  • We used whole-genome sequencing to compare these isolates with a worldwide collection of current and historical clinical strains for characterizing population structures. (cdc.gov)
  • Clonal expansion of macrolide resistance occurred mostly within subtype 1 strains, of which clade T1-2 showed the highest recombination rate and genome diversity. (cdc.gov)
  • P1 adhesin causes antigenic variation between clinical strains as a result of homologous recombination between RepMP2/3 and RepMP4 domains located within their open reading frames and at repetitive DNA elements at other sites in the bacterial genome ( 8 ). (cdc.gov)
  • To study how the M. pneumoniae lineage has evolved as it has spread, we characterized the genomes of 99 M. pneumoniae strains isolated in Taiwan, together with a global collection of 185 M. pneumoniae genomes deposited in public databases. (cdc.gov)
  • Structural MRI measures of brain anatomy include tissue and structure volumes, such as total grey matter volume and hippocampal volume, while other MRI modalities allow the mapping of different biological markers such as venous vasculature, microbleeds and aspects of white matter (WM) micro-structure. (biorxiv.org)
  • Genomes contain all the biological information needed to build and maintain living organisms. (koneensaatio.fi)
  • Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. (mdpi.com)
  • Delve into the labyrinthine complexity of the human genome, a vast biological network underpinning our very existence. (drfournier.com)
  • There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. (psu.edu)
  • We demonstrate that Structure-seq2 can lead to new biological insights. (psu.edu)
  • Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. (elifesciences.org)
  • Here we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. (elifesciences.org)
  • With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. (elifesciences.org)
  • These findings provide evidence that genetic and epigenetic factors operate within the context of three-dimensional chromatin structure. (elifesciences.org)
  • Local regulatory mechanisms within the genome and their interaction with chromatin structure give rise to subtle variations in gene expression. (elifesciences.org)
  • This and other putative roles need to be tested experimentally, but given that the s2m element is absent in the human genome, its unusual structural features could be an attractive target for the design of antiviral therapeutic agents. (sciencedaily.com)
  • Deploying a multi-scale strategy of sharp upwardjump detection in noisy skew profiles, we have identified more than 1000 putative master origins of replications that are central to the Human genome organization. (ens-lyon.fr)
  • Physical distance along a linear genome is a common metric for determining whether a putative regulatory element will affect a given gene's transcription. (elifesciences.org)
  • At the same time, we sought to identify major putative recombination hot spots on a genome wide scale to comprehensively understand the significance of recombination on the evolutionary dynamics of M. pneumoniae . (cdc.gov)
  • All the bocaviruses have been shown to have the same putative intermediate structures. (medscape.com)
  • Together with the prediction of homology, genome alignments provide a segmentation of the genomes originating from large structural changes. (biomedcentral.com)
  • Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. (psu.edu)
  • Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. (bvsalud.org)
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
  • We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)
  • Genome structure, comparative genomics, and bioinformatics. (lu.se)
  • Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. (nature.com)
  • Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology. (psu.edu)
  • We extracted DNA from cultures of S. meliloti grown in liquid TY media using Qiagen DNeasy (Hilden, Germany) and sent samples to the DOE Joint Genome Institute (JGI) for sequencing (Berkeley, CA, USA). (datadryad.org)
  • The generation of complete fern genomes has been hampered for long time by their large size and complex structure, but in the last decade the number of generated genomes has increased thanks to the use of Next Generation Sequencing techniques (NGS). (koneensaatio.fi)
  • Seven Bridges GRAF™ Suite comprises bioinformatics workflows and tools for secondary analysis of next generation sequencing (NGS) data, based on a pan-genome graph reference. (sevenbridges.com)
  • With the advent of advanced technologies, such as gene sequencing and chromosome mapping, scientists are now able to delve deeper into understanding the human genome. (drfournier.com)
  • Here, whole-genome sequencing was used to test whether North Atlantic marine coastal populations of the kelp Alaria esculenta survived in the area of southwestern Greenland during the Last Glacial Maximum. (au.dk)
  • In a typical year, CDC performs whole genome sequencing on about 7,000 influenza viruses from original clinical samples collected through virologic surveillance. (cdc.gov)
  • Genome Sequencing in the Clinic - The question is not whether the glass is half-full or half-empty but whether or not the glass is the right tool. (cdc.gov)
  • A decade ago, sequencing and interpreting even the small portion of the human genome that the exome represents would have been cost-prohibitive. (cdc.gov)
  • The analytic validity and capacity to reliably identify disease-associated variant varies across the genome and are dependent on the effective use of the sequencing instrumentation and subsequent analysis. (cdc.gov)
  • Methods for gene identification and analysis of gene structure: cloning, PCR, restriction mapping, in situ hybridisation, DNA sequencing. (lu.se)
  • The COVID-19 pandemic further exposed these weaknesses and emphasized the urgent need for stronger and coordinated laboratory services, medical imaging, rapid diagnostics, and genome sequencing. (who.int)
  • We establish the extent and structure of genotype-by-epigenotype interaction using embryonic stem cells derived from Diversity Outbred mice. (elifesciences.org)
  • Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPol A from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. (nature.com)
  • Fig. 1: Structures of human H3N2 and avian H5N1 FluPol A . (nature.com)
  • The center is part of the NIH's 4D Nucleome Program , an interdisciplinary effort comprising 29 research teams across the country with the goal of mapping the three-dimensional architecture of the human genome and how this organization changes over time-the fourth dimension. (umassmed.edu)
  • Using chromosome conformation capture technologies in conjunction with advanced computational modeling and a range of imaging methods, the center will generate three-dimensional models of the human genome inside fibroblast cells during metaphase and interphase, as well as in embryonic stem cells in undifferentiated and differentiated states. (umassmed.edu)
  • Brain structure and function are known to vary between individuals in the human population and can be measured non-invasively using Magnetic Resonance Imaging (MRI). (biorxiv.org)
  • Unraveling the mysteries of the human genome begins with an in-depth understanding of its basic architecture. (drfournier.com)
  • The human genome, often referred to as the blueprint of life, holds a vast array of gene functions that play a significant role in shaping our physical and metabolic characteristics. (drfournier.com)
  • Is there anything else From NCBI web site, photo from T. Ried, Natl Human Genome Research Institute, NIH interesting/important? (slidetodoc.com)
  • Human genome has 3. (slidetodoc.com)
  • Miten Generating high-quality reference human genomes using Promethion nanopo. (slideshare.net)
  • Human bocavirus is a small, single-molecule, linear DNA, nonenveloped virus with a nucleocapsid measuring 18-26 nm and a genome length of 4000-6000 nucleotides. (medscape.com)
  • [ 1 , 2 ] Phylogenetic analysis of the complete genome of human bocavirus (see image below) has shown that the virus is most closely related to the significant veterinary pathogens bovine parvovirus and canine minute virus (hence the name, boca virus), which are members of the genus Bocavirus, family Parvoviridae. (medscape.com)
  • He developed the chromosome conformation capture technologies, biochemical techniques for determining how DNA segments interact and are linked to one another, which are the heart of the "3C," "5C," "Hi-C" and "Micro-C" tools used by researchers worldwide to map the structure and organization of chromosomes inside cells. (umassmed.edu)
  • This was particularly true for the two symbiosis elements pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. (datadryad.org)
  • The differences in population structure may result from among-replicon differences in the extent of horizontal gene transfer, although given limited recombination of the chromosome, different levels of purifying or positive selection may also contribute to among-replicon differences. (datadryad.org)
  • b Comparison of 2275 gene pairs from the terminal 150 Mb of short chromosome arms from A and B genomes. (biomedcentral.com)
  • NGS has made possible to produce around 222 complete fern plastomes, two mitogenomes and two nuclear genomes. (koneensaatio.fi)
  • Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N 1 -methyladenosine (m 1 A) in a nuclear-encoded Oryza sativa rRNA. (psu.edu)
  • If not specified, "genome" usually refers to the nuclear genome. (slidetodoc.com)
  • Each virion comprises a viral envelope and associated matrix enclosing a capsid, which itself encloses two copies of the single-stranded RNA genome and several enzymes. (wikipedia.org)
  • CMV shares many attributes with other herpes viruses, including genome, virion structure, and the ability to cause latent and persistent infections. (medscape.com)
  • We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. (elifesciences.org)
  • Understanding the scope and landscape of these interactions on a genome-wide scale is a vital step towards deciphering the genetic regulation of gene expression and, in turn, the mechanisms of non-coding variation on phenotypic outcomes. (elifesciences.org)
  • Sinorhizobium meliloti genomes showed high local (within-site) variation and little isolation by distance. (datadryad.org)
  • We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. (psu.edu)
  • Clinical genomics-genome structure and variation. (medlineplus.gov)
  • Daphnia is a versatile model system to investigate fundamental mechanisms of inheritance and development, cellular function, physiological systems, immunity response, disease, macromolecular structure/function relationships and the genetic basis of complex phenotypic traits. (biomedcentral.com)
  • In genome-wide association studies (GWAS) genetic loci that influence complex traits are localized by inspecting associations between genotypes of genetic markers and the values of the trait of interest. (lu.se)
  • Analyses of these interactions has previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. (elifesciences.org)
  • The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. (biomedcentral.com)
  • Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. (cdc.gov)
  • We used a genome-wide analysis which not only examined differential gene expression levels but could also detect differences in splice isoform usage. (jneurosci.org)
  • Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)
  • Analysis of the squid teeth showed nanotubular structure and strong polymers. (scienceblog.com)
  • Further analysis showed that Suckerin-39's structure allowed it to be reprocessed into a variety of shapes. (scienceblog.com)
  • A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. (bvsalud.org)
  • The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. (biomedcentral.com)
  • These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. (biomedcentral.com)
  • In order to explore into the genome structure it is necessary to assembly the complete genome. (koneensaatio.fi)
  • Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. (bvsalud.org)
  • We will genetically engineer the genome to surgically perturb or alter the way it is folded. (umassmed.edu)
  • Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization. (datadryad.org)
  • GRAF™ Germline Variant Detection Workflow - uses a Pan-Genome graph containing genetic information from many populations around the world. (sevenbridges.com)
  • We present the first annotated genome for A. esculenta and call variant positions in 54 individuals from populations in Atlantic Canada, Greenland, Faroe Islands, Norway and Ireland. (au.dk)
  • High numbers of repetitive DNA elements (RepMPs), designated RepMP1, RepMP2/3, RepMP4, and RepMP5, comprise ≈8% of the M. pneumoniae genome and play essential roles in survival niches of M. pneumoniae by engaging in recombination events to generate surface antigen diversity ( 5 ). (cdc.gov)
  • GRAF™ Construction Service - consists of bioinformatics methods and services that enable the construction of representative and accurate genome graph references. (sevenbridges.com)
  • William Scott and colleagues have used X-ray crystallography to measure the exact positions of individual ribonucleotides and the interactions between them in a small segment of the SARS virus genome called the s2m element. (sciencedaily.com)
  • With this method we have imaged ~50 different domains from the Drosophila genome, each enriched in a distinct class of transcription factor (TF) activity and carrying distinct epigenetic marks (shown in red blue and black in the image, left). (alistairboettiger.info)
  • Genome Structure l l l Distinct components of genomes Abundance and complexity of m. (slidetodoc.com)
  • From these, Dekker and colleagues hope to uncover similarities between the genomic structures that point to general rules that govern how and why genomes fold in all cells. (umassmed.edu)
  • Nucleome believes its high-resolution view into 3D genomic structures can pull actionable drug targets out of the "dark" non-coding regions that make up most of the genome. (biocentury.com)
  • Finally, the center will develop entirely new technology for locally mapping the spatial organization of the genome. (umassmed.edu)
  • The final model used jumbo squid sucker ring teeth (SRT), grappling-hook-like structures used for predatory attacks. (scienceblog.com)
  • This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. (psu.edu)
  • It is expected to improve confidence in and clarify scientific communication, data reporting, and data interpretation in the genome editing field. (nist.gov)
  • Modules provide IRMA with all the data and configuration necessary to assemble a particular virus genome. (cdc.gov)
  • By comparing the genomes of various species over different periods, we can trace the journey of our hominin ancestry and understand the intricate tapestry that forms our genetic heritage. (drfournier.com)
  • A modified version of the Bayesian information criterion is developed for building a multilocus model that accounts for the differential correlation structure due to linkage disequilibrium (LD) and admixture LD. (lu.se)
  • The goal is to understand how 3D genome structure influences gene expression, cellular function, development and disease. (umassmed.edu)
  • To properly understand how the genome works to coordinate gene expression, it's necessary to understand how and why the genome is organized in space. (umassmed.edu)
  • Professor Dekker's work is at the cutting edge of connecting the structure of DNA with its function, one of the final frontiers in understanding gene regulation," said Terence R. Flotte, MD, the Celia and Isaac Haidak Professor of Medical Education , executive deputy chancellor, provost and dean of the School of Medicine. (umassmed.edu)