• These data confirm that the mitochondrial genome originated from a eubacterial (specifically α-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome. (biomedcentral.com)
  • A number of specific and general insights into mitochondrial genome evolution follow from these data. (biomedcentral.com)
  • Our evaluation against the HG002 truth data has produced several metrics (such as f-score, recall and precision) across different variant types (such as SNP and indels), subtypes (such as insertions or deletions of specific size ranges) and genomic contexts (such as whole genome, coding regions, etc.), leading to thousands of computed numbers per challenge entry. (fda.gov)
  • Within the PC12 neuronal context, putative p53-occupied genomic loci spanned the entire Rattus norvegicus genome upon NGF treatment. (biomedcentral.com)
  • Combined evidence annotation of transposable elements in genome sequences. (genscript.com)
  • Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. (biomedcentral.com)
  • The biological sciences are undergoing an explosion in the amount of genome sequences. (biomedcentral.com)
  • The applications of this technology are quite varied, from assembling chromosome-scale genomes, linking non-coding disease-associated risk variants to target genes, understanding the mechanisms of gene regulation in a wide variety of diseases, and detecting gene fusions in tumor samples that were missed by other technologies, to name a few. (arimagenomics.com)
  • Using a genome-wide chromatin immunoprecipitation cloning technique, we identified and validated 14 novel p53-regulated genes following NGF treatment. (biomedcentral.com)
  • With roughly 30,000 genes in mammalian genomes, fection with a vector encoding MyoD (Tapscott et al. (lu.se)
  • explosion further, consider that a fictitious small genome with 2002) More recently and more dramatically, the potential for 260 genes would host the same number of combinations as cell state conversions is exemplified by the reprogramming of the number of atoms in the visible universe! (lu.se)
  • Here we determined genome-wide changes in DNA methylation in the nervous system in neuropathic pain. (jneurosci.org)
  • However, genome-wide changes in DNA methylation in the nervous system and their roles in neuropathic pain development remain unclear. (jneurosci.org)
  • Here we used digital restriction enzyme analysis of methylation to quantitatively determine genome-wide DNA methylation changes caused by nerve injury. (jneurosci.org)
  • So, as of today, that event happened approximately 1,021 years ago (2021 - 1000 = 1021). (millerfortexas.com)
  • Plant viruses contain single-stranded or double-stranded RNA or DNA genomes and vary substantially in their genome structure and organization. (encyclopedia.pub)
  • By studying the self-assembly of hundreds of communities in replicate, synthetic habitats, we show that the reproducibility of microbial community assembly reflects an emergent metabolic structure, which is quantitatively predictable from first-principles, genome-scale metabolic models. (biorxiv.org)
  • First, sequence: because the 3D genome is studied using next-generation sequencing, sequence information is retained and can be combined with chromatin conformation. (arimagenomics.com)
  • They exist in biological systems as different as promiscuous enzymes and genome-scale metabolic reaction networks, and can give rise to evolutionary adaptations and innovations. (biomedcentral.com)
  • Jensen A.B., Palmer K.A., Boomsma J.J., and Pedersen B.V. (2005) Varying degrees of Apis mellifera ligustica introgression in protected populations of the black honeybee, Apis mellifera mellifera , in northwest Europe, Mol. (apidologie.org)
  • We are now able to assess patterns of introgression on a genome-wide scale. (biomedcentral.com)
  • how the DNA is organized into the nucleus is critically important for coordination of gene expression and genome function. (arimagenomics.com)
  • Experimental [ 21 ] and theoretical [ 22 ] studies hint that gene regulatory circuits harbor latent phenotypes because their gene expression patterns often vary when a circuit is exposed to distinct external stimuli. (biomedcentral.com)
  • To varying degrees, these fates also extend to the Such state stability is required in stem and progenitor cells to immediate progeny of stem cells, known as progenitor or support self-renewal and maintenance of the uncommitted transit-amplifying cells. (lu.se)
  • Within any tumor, nuclear size may vary, but uniformly, these tumors are of a high Fuhrman nuclear grade. (medscape.com)
  • Structure: the 3D structure of the Genome can be used to identify structural variants such as gene fusions as potential drivers of disease. (arimagenomics.com)
  • Garnery L., Solignac M., Celebrano G., Cornuet J.-M. (1993) A simple test using restricted PCR-amplified mitochondrial DNA to study the genetic structure of Apis mellifera L, Experientia 49, 1016-1021. (apidologie.org)
  • The characters in Russula varied within and overlapped between my delimited species. (ubc.ca)
  • We find evidence of both recent and more ancient admixture, and that levels of admixture vary across species. (biomedcentral.com)
  • On the other hand, with high rates of gene flow and low levels of reproductive isolation (RI), introduced alleles could be transmitted in such a way that the genomes of locally adapted species with small population sizes (e.g. in alpine glacial refugia) could ultimately become extinct by being swamped by a different lineage [ 7 , 8 ]. (biomedcentral.com)
  • But, over time, each coronavirus has fashioned these proteins a little differently, and the evolutionary clues about these modifications are spelled out in their genomes. (nih.gov)
  • The development of experimental methods for genome scale analysis of molecular interaction networks offers new ways to infer protein function from protein-protein interaction (PPI) network data. (biomedcentral.com)
  • In recent years, the development of experimental methods for genome scale analysis of molecular interaction networks offers new ways to infer protein function in the context of protein-protein interaction (PPI) network, wherein proteins and detected PPIs are represented by nodes and edges, respectively. (biomedcentral.com)
  • Their analysis showed that the backbone of the new coronavirus's genome most closely resembles that of a bat coronavirus discovered after the COVID-19 pandemic began. (nih.gov)
  • To put this into a data storage context, storing all the DNA contained in the biosphere would require approximately 1021 supercomputers with the average storage capacity of the world's four most powerful supercomputers. (arimagenomics.com)
  • The utility of 3D genome data is quite varied. (arimagenomics.com)
  • This second precisionFDA challenge was conducted in collaboration with the Genome in a Bottle (GiaB) consortium, which provided the "truth" data, as well as with the Global Alliance for Genomics and Health (GA4GH), which provided best practices and software for conducting the comparison of participants' entries to the truth data. (fda.gov)
  • Ecologic, climatic, socioeconomic, and cultural aspects might all play a role in explaining these dynamics, but their relative importance might vary across TBE-endemic regions ( 4 - 6 ). (cdc.gov)
  • Sequencing has also shown that mitochondrial genomes have, to variable extents, undergone a streamlining process ("reductive evolution" [ 20 ]), leading to a marked loss of coding capacity compared to that of their closest eubacterial relatives. (biomedcentral.com)
  • We conducted the two-sample Mendelian randomization with the public genome-wide association studies (GWASs) summary statistics in European population to evaluate the causality between SS and nine types of cancers. (biomedcentral.com)
  • The metatranscriptomic approach showed that a) expression of several ARGs and MGEs increased upon adding ciprofloxacin for biofilms from hospital WW only and b) that the abundance and type of plasmids that carried individual or multiple ARGs varied depending on the WW origins of the biofilms. (bvsalud.org)
  • Moreover, limited viral genome sizes and coding capacities have resulted in evolution of multifunctional proteins that are involved in different steps in the virus life cycle, including replication, movement, encapsidation and transmission. (encyclopedia.pub)
  • The first is that ATP production, coupled to electron transport, and translation of mitochondrial proteins represent the essence of mitochondrial function: these functions are common to all mitochondrial genomes and can be traced unambiguously and directly to an α-proteobacterial ancestor. (biomedcentral.com)
  • The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. (lovd.nl)
  • Thus, the incorporation of new alleles into existing lineages through hybridization (i.e. admixture) has varying effects on speciation and local adaptation, either slowing or accelerating the evolution of RI between populations through gene flow and recombination. (biomedcentral.com)
  • Of course, this is just an estimate, and the actual number of years may vary slightly depending on the specific time period in question. (millerfortexas.com)
  • The 3D genome is organized at multiple levels into chromosome territories, compartments, domains including topologically associated domains (TADs), and looping structures. (arimagenomics.com)
  • The genus Boechera is an extraordinary example of admixture, with over 400 hybrid derivates of varying ploidy levels. (biomedcentral.com)
  • Protein expression is influenced by many factors that may vary between experiments or laboratories. (genscript.com)
  • Outcomes vary significantly based on a number of factors, including race/ethnicity, socioeconomic status, health insurance status, and geographic location. (canceradvocacy.org)
  • The researchers began by homing in on the parts of the coronavirus genomes that encode the spike proteins that give this family of viruses their distinctive crown-like appearance. (nih.gov)