• bacterium
  • A comparison with the proteome of the "minimal" synthetic bacterium JCVI-Syn3.0 allowed us to classify domains and proteins essential for minimal life. (frontiersin.org)
  • To uncover unannotated small genes in the model bacterium Salmonella enterica Typhimurium 14028s, we used the genomic technique ribosome profiling, which provides a snapshot of all mRNAs being translated (translatome) in a given growth condition. (g3journal.org)
  • In this lateral gene transfer, one particular insect parasite, a bacterium called Wolbachia, has a special relationship with the pests: Wolbachia provide something that blood meals do not - a vitamin B complex that helps bedbugs live and thrive. (eurekalert.org)
  • What is not known are the genes or the proteins that allow these bacteria to mediate the transformation," said ORNL's Steven Brown, who led a research team to sequence the genome of a bacterium in the Desulfovibrio genus that is capable of methylating mercury. (redorbit.com)
  • Jean R. Lobry was the first to illustrate the nucleotide composition asymmetry throughout the genome of three bacterium: E. coli, Bacillus subtilis, and haemophilus influenzae by using GC and AT bias. (wikipedia.org)
  • With the advent of next generation DNA sequencing it is now possible to sequence the complete genome of a bacterium (typically ~4 million bases) within a single day. (wikipedia.org)
  • coli
  • A plasmid with a mob site (like many found in Rhodococcus species) cannot be transferred via transfer genes which normally interact with the oriT site (which is common in E. coli) Each of the individual genes in the tra operon codes for a different protein product. (wikipedia.org)
  • Researcher Yoshizumi Ishino and colleagues published their findings on the sequence of a gene called "iap" and its relation to E. coli. (wikipedia.org)
  • organisms
  • My method for BLAST'ing large numbers of organisms was just construct a database from the SEED Network, download all the genomes of interest. (biology-online.org)
  • Analysis of the Z curve has also been shown to be able to predict if a gene contains introns, Experiments have shown that the Z curve can be used to identify the replication origin in various organisms. (wikipedia.org)
  • Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. (beds.ac.uk)
  • Protein family memberships reflected known metabolic characteristics of the organisms. (beds.ac.uk)
  • If we can identify the genes involved in mercury methylation, we hope to go to the local environment and understand more about the function and the ecology of the organisms and their gene products that mediate this transformation. (redorbit.com)
  • The general trends of bacterial evolution indicate that bacteria started as free-living organisms. (wikipedia.org)
  • These methods are most useful in organisms with straightforward methods for the introduction and selection of genes of interest, such as bacteria and yeast. (wikipedia.org)
  • H1 forms a complex family of related proteins with distinct specificity for tissues, developmental stages, and organisms in which they are expressed. (wikipedia.org)
  • distinct
  • Plant cells have two distinct types of vacuoles: the prototypical lytic vacuole (LV), which has high hydrolytic activity and shares functions with the yeast vacuole and mammalian lysosome, and the protein storage vacuole (PSV), a plant-specific organelle that is specialized in accumulating reserve proteins and is prevalent in seeds [ 6 ]. (hindawi.com)
  • Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. (beds.ac.uk)
  • For example, individual H1 variant knockout mice reveal specific phenotypes and distinct effects on gene expression and chromatin structure. (wikipedia.org)
  • Therefore a model has been proposed according to which H1 variants have two distinct roles, a common and a specific one: Individual H1 proteins are redundant in their ability to compact chromatin globally and to stabilize overall higher order chromatin structures. (wikipedia.org)
  • newly
  • Therefore prior assumptions about the properties of prokaryotic gene starts may cause suboptimal predictions for newly sequenced genomes with TIS signals differing from those of well-investigated genomes. (biomedcentral.com)
  • The endoplasmic reticulum (ER) is the first organelle in the secretory pathway, and this dynamic and highly specialized organelle contains enzymes and chaperones that mediate the folding and assembly of newly synthesized proteins [ 1 ]. (hindawi.com)
  • A newly sequenced bacterial genome from a team led by the Department of Energy's Oak Ridge National Laboratory (ORNL) could contain clues as to how microorganisms produce a highly toxic form of mercury. (redorbit.com)
  • However, a continuing challenge with microbial genomics is finding the resources or tools for annotating the large number of newly sequenced genomes. (wikipedia.org)
  • enzymes
  • Selective molecular communication between disulfide-generating enzymes and disulfide carrier proteins, which reflects the molecular and structural diversity of disulfide carrier proteins, is key to the efficient transfer of disulfides to specific sets of substrates. (hindawi.com)
  • pathogens
  • Recent studies have revealed that viruses and bacterial pathogens exploit the host ubiquitination pathways to gain entry and to aid their survival/replication inside host cells. (frontiersin.org)
  • covalently
  • A key step in oxidative protein folding is the formation of disulfide bonds, which covalently link the side chains of pairs of Cys residues, impart thermodynamic and mechanical stability to proteins, and control protein folding and activity [ 2 ]. (hindawi.com)
  • Ubiquitination is a post-translational modification in which one or more 76 amino acid polypeptide ubiquitin molecules are covalently linked to the lysine residues of target proteins. (frontiersin.org)
  • Others have linear genomes with covalently closed ends (Poxviridae and Phycodnaviridae). (wikipedia.org)
  • homologous
  • However, a homologous IIC protein from Listeria monocytogenes has been shown to be required for D-arabitol fermentation. (wikipedia.org)
  • A major addition to the understanding of CRISPR came with Jansen's observation that the prokaryote repeat cluster was accompanied by a set of homologous genes that make up CRISPR-associated systems or cas genes. (wikipedia.org)
  • residues
  • PDI directly transfers a disulfide to two Cys residues of a substrate protein by means of a thiol-disulfide exchange reaction. (hindawi.com)
  • BLAST
  • The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. (pubmedcentralcanada.ca)
  • I've tried a few things like doing a Blast search in the sequenced genomes in NCBI and get a taxonomy report. (biology-online.org)
  • Then to blast against this file the gene of interest. (biology-online.org)
  • Many of the tools on the net such as BLAST on NCBI will give you the result - if you perform a BLAST (I prefer psi BLAST), and then you set your level type your gene sequence into ncbi home page - this gives you the huige amount of refernces. (biology-online.org)
  • Each genome map in BacMap is searchable via BLAST and a gene name/synonym search. (wikipedia.org)
  • Salmonella
  • The well-annotated genome of Salmonella typhimurium LT2 is used as an example to demonstrate the applicability of the method. (biomedcentral.com)
  • For comprehensive identification of unannotated small genes, we obtained Salmonella translatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg 2+ (10 µM) and low pH (5.8). (g3journal.org)
  • double stranded
  • Several others have been described since: most have head-tail morphologies and linear double-stranded DNA genomes. (wikipedia.org)
  • A group known as the pleolipoviruses, although having a similar genome organisation, differ in having either single or double stranded DNA genomes. (wikipedia.org)
  • Fundamental to the use of nucleases in genome editing is the concept of DNA double stranded break (DSB) repair mechanics. (wikipedia.org)
  • degradation
  • Interaction of Bpa with the proteasome stimulates proteosomal peptidase and casein degradation activity, which suggests Bpa could play a role in the removal of non-native or damaged proteins by influencing the conformation of the proteasome complex upon interaction. (uniprot.org)
  • The story started with a search for a non-lysosomal pathway for protein degradation. (frontiersin.org)
  • pilin
  • A group of related bacteria makes these bendy, stretchy structures out of a protein called pilin, and an even smaller group uses these structures like electrical wires. (bio-medicine.org)
  • Many pilin proteins work together to form a fiber, and Reardon and Mueller only had one. (bio-medicine.org)
  • The tra locus includes the pilin gene and regulatory genes, which together form pili on the cell surface, polymeric proteins that can attach themselves to the surface of F-bacteria and initiate the conjugation. (wikipedia.org)
  • novel
  • Church says the technology will eventually lead to all manner of breakthroughs: we will be able to replace diseased tissues and organs by reprogramming cells to make new ones, create novel microbes that efficiently secrete fuels and other chemicals, and fashion DNA switches that turn on the right genes inside a patient's cells to prevent arteries from getting clogged. (technologyreview.com)
  • A virus with a novel method of genome packing infecting species of the genus Sulfolobus has been described. (wikipedia.org)
  • patterns
  • Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria. (wikipedia.org)
  • The use of other mutagenic techniques (such as P-element transgenesis in Drosophila) also has limitations, the major one being the randomness of incorporation and the possibility of affecting other genes and expression patterns. (wikipedia.org)
  • sufficiently
  • The results suggest that a 3.9-fold coverage of the bacterial genome could be sufficiently used for the in silico reconstruction of the metabolic network. (biomedcentral.com)
  • All identified genes in a BacMap chromosome map are colored according to coding directions and when sufficiently zoomed-in, gene labels are visible. (wikipedia.org)
  • comparative
  • The Z-curve method has been used in many different areas of genome research, such as replication origin identification,, ab initio gene prediction, isochore identification, genomic island identification and comparative genomics. (wikipedia.org)
  • Comparative genomic analyses have identified large numbers of signature proteins that are uniquely present in species from the genera Chlamydia and Chlamydophila, supporting the distinctness of these genera. (wikipedia.org)
  • ribosome
  • The ribosome, the molecular machine for protein biosynthesis, is the hallmark of cellular life forms . (pubmedcentralcanada.ca)
  • To facilitate the identification of small genes, ribosome profiling data were analyzed in combination with in silico predicted putative open reading frames and transcriptome profiles. (g3journal.org)
  • persistent
  • Many of those essential protein domains, essential Domains of Unknown Function (DUFs) and essential hypothetical proteins are not persistent across mycoplasma genomes suggesting that mycoplasma species support alternative domain configurations that bypass their essentiality. (frontiersin.org)
  • different
  • Functionally closely related mycoplasma species, which have a highly similar protein domain repertoire, but different hosts could not be separated. (frontiersin.org)
  • p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
  • A large section of its genome appears to have been acquired from a different species of bacteria. (nytimes.com)
  • How to get electrons from the inside of bacteria to the outside is important for many different things, such as bacterial fuel cells, how carbon cycles through the environment and how to make new nanomaterials for applications like biocomputers," said Reardon. (bio-medicine.org)
  • For example, oriT and bom are two origins of transfer which interact with different sets of transfer genes. (wikipedia.org)
  • The corresponding H1 variants in two different species, such as human and mouse H1.4 are orthologs - they had a common ancestor gene and were separated by speciation. (wikipedia.org)
  • analysis
  • The analysis revealed several genes with cell membrane-related functions. (wikipedia.org)
  • Lokiarchaeota was introduced in 2015 after the identification of a candidate genome in a metagenomic analysis of a mid-oceanic sediment sample. (wikipedia.org)
  • The metagenomic analysis determined the presence of an organism's genome in the sample. (wikipedia.org)
  • Resonance structure analysis of the complex reveals two similar helix-turn-helix hairpin structures formed by the individual proteins, which lie anti-parallel to each other and forms a four-helix bundle. (wikipedia.org)
  • Because of the growing interest in metagenomics and large-scale bacterial genome analysis, BacMap was extensively updated in 2012. (wikipedia.org)
  • parasitic
  • Mycoplasmas have evolved from a common gram-positive ancestor ( Razin and Yogev, 1998 ) and the evolutionary path of genome reduction has led to an obligatory parasitic lifestyle which presumably has selected for those bacteria that best manipulate their hosts and make optimal use of their specific niche with a minimal set of genes. (frontiersin.org)
  • membrane
  • Bacteriophages (viruses infecting bacteria) belonging to the families Tectiviridae and Corticoviridae have a lipid bilayer membrane inside the icosahedral protein capsid and the membrane surrounds the genome. (wikipedia.org)
  • Rv3871 then interacts with the CFP-10 C-terminal, and escorts the ESAT-6/CFP-10 complex to Rv3870 and Rv3877, a multi-transmembrane protein which makes up the pore that spans the cytosolic membrane of the virulent host cell. (wikipedia.org)
  • available
  • Few experimental approaches are available that can complement the insensitivity of current annotation pipelines in detecting small genes. (g3journal.org)
  • Our predicted protein interactions are freely available through PInt, an online resource on our website ( www.bahlerlab.info/PInt ). (g3journal.org)
  • Many additional protein interactions are known from various small-scale experiments, such as co-immunoprecipitations or affinity capture, which provide us with data for species in which large-scale studies are not yet available. (g3journal.org)
  • pathways
  • Disulfide transfer pathways that function in the endoplasmic reticulum (ER) and chloroplasts of plants play critical roles in the development of protein storage organelles and the biogenesis of chloroplasts, respectively. (hindawi.com)
  • Protein interactions not only hold together protein complexes, the operational units within cells, but also mediate cellular information flow along signaling pathways and networks. (g3journal.org)
  • The natural properties of these pathways form the very basis of nuclease-based genome editing. (wikipedia.org)
  • mammalian
  • Casein kinase members CK1ε and CK1δ were both found to be mammalian protein kinases involved in circadian regulation. (wikipedia.org)
  • The mammalian H1 isoforms are paralogs, which means their encoding genes originated from gene duplication events. (wikipedia.org)
  • Mutations
  • Mutations to the genes prevent the bacteria from reading their codes and making the corresponding proteins. (nytimes.com)
  • In 1923, Ingeborg Beling published her paper "Über das Zeitgedächtnis der Bienen" ("On the Time Memory of Bees") which extended oscillations to animals, specifically bees In 1971, Ronald Konopka and Seymour Benzer discovered that mutations of the PERIOD gene caused changes in the circadian rhythm of flies under constant conditions. (wikipedia.org)
  • Thus if one is able to create a DSB at a desired gene in multiple samples, it is very likely that mutations will be generated at that site in some of the treatments because of errors created by the NHEJ infidelity. (wikipedia.org)
  • Interactions
  • A systems-level understanding of biological processes and information flow requires the mapping of cellular component interactions, among which protein-protein interactions are particularly important. (g3journal.org)
  • We exploited gene and protein properties, global genome regulation datasets, and conservation of interactions between budding and fission yeast to predict fission yeast protein interactions in silico . (g3journal.org)
  • and third, by verifying predicted interactions of the Cbf11 transcription factor using mass spectrometry of TAP-purified protein complexes. (g3journal.org)
  • plasmid
  • The existence of the tra region of a plasmid genome was first discovered in 1979 by David H. Figurski and Donald R. Helinski In the course of their work, Figurski and Helinski also discovered a second key fact about the tra region - that it can act in trans to the mobilization marker which it affects. (wikipedia.org)
  • The transfer genes - Though a functioning set of tra genes is necessary for plasmid transfer, they may be located in a variety of places including the plasmid in question, another plasmid in the same host cell, or even in the bacterial genome. (wikipedia.org)