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Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans. (cdc.gov)
Open up in another window Physique 1 Phylogenetic romantic relationship of BIIE 0246 supplier human being SLC26 polypeptides generated with Jalview (http://www.jalview.org) using NCBI proteins sequences listed in Desk 1. (exposed-skin-care.net)
We've been more likely to make an error than to guess correctly when trying to predict which bacterial DNA sequences contain these very small genes," Bhatt said. (technologynetworks.com)
When they do this, occasionally mistakes in the DNA sequences get included (e.g. an A gets replaced with a C). These mistakes only happen very rarely, but the very large population sizes (billions and trillions) of bacteria, means that this happens frequently enough that occasionally these mutations are present in bacterial populations in the presence of antibiotics. (futurelearn.com)
Biochemists have long recognized that the nucleotide sequences comprising DNA molecules encode digital information. (reasons.org)
The nucleotide sequences represent a succession of discrete units (i.e., genetic letters), just like the 1's and 0's that encode the digital information on a CD or in an MP3 file. (reasons.org)
2 They note that the nucleotide sequences of DNA not only encode information to make proteins, these sequences also impact the higher order architecture of DNA, which houses the analog information. (reasons.org)
Mutation rates are tricky to measure directly because mutations are identified by examining the phenotypes or DNA sequences of bacterial cultures many generations after the mutations would have happened. (fieldofscience.com)
A bacterial artificial chromosome (BAC) is a vector system based on the E. coli F-plasmid, cos sites of the lambda phage and loxP of the P1 phage, used for cloning long (150-350 kbp) DNA sequences. (genomequebecplatforms.com)
After that, the read sequences are aligned in silico, resulting in the complete sequence of the organism's genome. (genomequebecplatforms.com)
Comparison of the complete genome sequences of Pseudomonas syringae pv. (nih.gov)
Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. (nih.gov)
Introns sequences account for about 30% of the genome. (blogspot.com)
By scanning the available genome sequences, Demuth et al. (blogspot.com)
The sequencing of the human genome revealed that at least 1% of the human genome consists of endogenous retroviral sequences, representing past encounters with retroviruses during the course of human evolution. (msdmanuals.com)

Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans. (wikipedia.org)
SSB protein domains in bacteria are important maintaining DNA metabolism, more specifically DNA replication, repair and recombination. (wikipedia.org)
Given the high number of virulence factors present in these bacteria, and the niche-specific role many of them play during different stages of the infectious process, gene expression must be finely tuned in order to efficiently coordinate their expression, and also continue to preserve energy pools. (biomedcentral.com)
These transport proteins appear to be unique to mitochondria, plant plastids, and obligate-intracellular bacteria. (usda.gov)
The proteins belong to more than 4,000 new biological families predicted to be involved in, among other processes, the warfare waged among different bacterial strains as they vie for primacy in coveted biological niches, the cell-to-cell communication between microbes and their unwitting hosts, and the critical day-to-day housekeeping duties that keep the bacteria happy and healthy. (technologynetworks.com)
This chemotactic signaling pathway is relatively conserved across bacteria, whereas chemoeffectors and chemoreceptors vary among bacterial species/strains. (nature.com)
As bacteria grow and replicate they copy their genetic material (the genome). (futurelearn.com)
The three-domain tree, containing Eukarya, Archea, and Bacteria, soon became too simplistic due to the realization that some bacteria possessed the ability to exchange genetic information by horizontal gene transfer (Koonin and Wolf, 2012). (bartleby.com)
Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. (darkenergybiosphere.org)
The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. (darkenergybiosphere.org)
RRResearch: Have bacteria evolved gene-specific rates of point mutations? (fieldofscience.com)
Among a number of processes, these proteins help decide the constant battle for space and nutrients in your body that bacteria wage against one another, the cell-to-cell communication between bacteria and the greater network they call home (your body), and assist the crucial daily housekeeping jobs that keep your body and the bacteria that lives inside it at tip-top shape. (probioticscouncil.org)
The researchers at Stanford believe that these proteins that were ultimately broken up into 4,000 related groups, or families, are likely to be involved in some key processes such as intercellular communication and warfare as well as jobs that are absolutely necessary to keep the probiotic bacteria healthy. (probioticscouncil.org)
The tools that bacteria and other microbes use to make natural products are enzymes, specialized proteins encoded by genes. (illinois.edu)

Due to an inability to genetically manipulate Las at the present time, the translocase (tlc) open reading frame was cloned and expressed in Escherichia coli to determine if this putative gene was in fact functional. (usda.gov)
L. agilis BKN88 contains five putative chemoreceptor genes ( mcp1 - mcp5 ). (nature.com)
The positive clones employing the largest halo size were sequenced and a gene encoding a putative lipase was found. (unina.it)
Proteins/genes with a putative catabolic role and bacterium adaptation mechanisms during OPP degradation were identified via genomic and proteomic analysis. (nature.com)
Transcription analysis of all putative catabolic genes established their role in the metabolism of OPP. (nature.com)
Then, we selected 48 genes that may encode uncharacterised effectors (e. g. no detectable amino acid identity to other proteins or with a particular putative biochemical activity) from the genome of C. trachomatis strain L2/434/Bu. (europa.eu)
In summary, we have identified 22 novel putative C. trachomatis T3S effectors, seven of which were also secreted as full-length proteins by Y. enterocolitica in different experimental conditions. (europa.eu)
Here, we describe B. pseudomallei genes encoding putative penicillin binding proteins (PBPs) and investigate their utility for determining phylogeography and differentiating closely related species. (cdc.gov)

Antimicrobial resistance in bacterial pathogens is a major impediment to successful therapy, and in sever- al instances, bacterial strains have arisen that are refracto- ry to most available antimicrobial treatments (1). (cdc.gov)
Although the bacterial translocase has been characterized in other intercellular pathogens such as Chlamydia trachomatis and Rickettsia prowazeki, this is the first characterization of an ATP/ADP translocases in an obligate-intracellular plant pathogen and, given the conservation of the ATP uptake mechanism, may represent an evolutionary link between plant and animal pathogens. (usda.gov)
Of the bacterial ATP/ADP translocases characterized thus far, all have been found in endosymbionts of protozoa or pathogens of higher order animals including humans. (usda.gov)
Home / Healthcare & Medicine / Antimicrobial & Antibiotic Resistance / Bacterial Genomes: Antimicrobial Resistance in Bacterial Pathogens / What are the Mechanisms of Antimicrobial Resistance? (futurelearn.com)
In addition to the intrinsic mechanisms of resistance, bacterial pathogens can acquire genes and mutations that mediate resistance to antibiotics. (futurelearn.com)
β-lactamases are a family of enzymes (there are thousands of different versions) found in many bacterial pathogens. (futurelearn.com)
New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. (biomedcentral.com)
Probiotics help reduce the risk of diarrhea and bloat, help protect the body against bacterial infection and pathogens, and much, much more. (probioticscouncil.org)
Chlamydia trachomatis are obligate intracellular bacterial pathogens that cause ocular and genital infections, which are a significant public health concern worldwide. (europa.eu)

The actual origins of acquired resistance genes are unknown, but environmental microbes, including the strains producing antimicrobial agents, are believed to be important sources (4,5). (cdc.gov)
As a single colony can be analyzed, colonies derived from multiple bacterial strains on the agar medium do not hinder analysis. (shimadzu.com)
2000), so that as the different parts of penicillin biosynthesis operons in and various other antibiotic-producing strains of includes three open up reading structures encoding SulP polypeptides. (exposed-skin-care.net)
Even though diverse strains of S. aureus have been extensively studied, and subjected to genome sequencing, the function of a large proportion of their genes remains unidentified. (biomedcentral.com)
Finally, we examine the conservation of 135 USA300 TFs amongst 11 other S. aureus strains, identifying a key group of regulators that display a high degree of conservation, including many that have previously been demonstrated to play a role in virulence gene regulation. (biomedcentral.com)
In addition to chemical damage in the form of crosslinks, structural proteins also suffer mechanical damage, resulting from the same kinds of stresses and strains that cause automobile and airplane parts to distort or to shear. (sens.org)
Isolated bacterial strains were identified on the basis of morphological and biochemical tests. (bvsalud.org)
The recent development of second generation sequencing platforms (reviewed by Mardis [ 7 , 8 ] and Shendure [ 7 , 8 ]) offers an opportunity to change the direction of microbial genomics, enabling the rapid genome sequencing of large numbers of strains of both pathogenic and non-pathogenic strains. (biomedcentral.com)
Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. (bvsalud.org)
Using BLASTn analyses of complete assembled genomes in the NCBI database, we determined genes encoding PBPs were conserved among B. pseudomallei (n = 101) and Burkholderia mallei (n = 26) strains. (cdc.gov)
Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. (cdc.gov)

In 1986 Nobel laureate Renato Dulbecco laid down the gauntlet to the scientific community to sequence the complete human genome. (learner.org)
Like the conquest of space, sequencing the human genome required the development of wholly new technologies. (learner.org)
The human genome, containing more than three billion nucleotides, is vast. (learner.org)
The capstone, of course, was the completion of the human genome sequence. (learner.org)
In 2001 two rival teams jointly announced the completion of a draft sequence of the entire human genome, consisting of more than three billion nucleotides. (learner.org)
One major surprise emerged from the sequencing of the human genome. (learner.org)
Although some scientists expected to find at least 100,000 genes coding for proteins, only about 30,000-35,000 of such genes appear to be in the human genome. (learner.org)
We should think of the human genome as a database of critical information that serves as a tool for exploring the workings of the cell and, ultimately, understanding how a complex living organism functions. (learner.org)
The human genome encodes only 19,000 proteins. (aithics.co)
Artificial bacterial chromosomes are often used to sequence the genomes of organisms in various projects, such as the Human Genome project. (genomequebecplatforms.com)

Search for antimicrobial resistance genes and replicon/plasmid sequence types run using Center for Genomic Epidemiology website ( https://genomicepidemiology.org ) and local BLAST. (cdc.gov)
One special type of plasmid used for genome sequencing is a bacterial artificial chromosome (BAC) , which can contain DNA fragments of about 150 kb. (learner.org)
However, unlike the bacteriophage, which, during a latent (lysogenic) state, integrates its chromosome into the chromosome of the host bacteriophage, the P1 phage maintains the chromosome in the cytoplasm of bacterial cells in the form of a circular covalently closed molecule resembling a plasmid, the size of which is 100 kbp. (genomequebecplatforms.com)
The F-plasmid encodes genes that regulate replication and control copy number (1-2 molecules per cell). (genomequebecplatforms.com)
At the loxP site, plasmid DNA can be cleaved by the Cre protein of the P1 phage, at the cos site by the corresponding enzyme of the lambda phage. (genomequebecplatforms.com)
A similar vector system called PAC (p1-derived artificial chromosome) was made on the basis of a bacterial P1 plasmid from the DNA of the P1 phage. (genomequebecplatforms.com)
The DNA may remain separate as a plasmid or be incorporated into the host genome. (pressbooks.pub)
The Pss B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. (nih.gov)
One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)

Measure using MALDI-TOF MS. The unique mass spectrum for the bacterial species is rapidly obtained. (shimadzu.com)
SuperSpectra TM contains peak groups that can act as markers to offer stable detection of commonly detected bacterial species under multiple conditions. (shimadzu.com)
Databases can be supplied even for rarely detected bacterial species. (shimadzu.com)
Focusing on the S10 -spc-alpha operon, for which about half the ribosomal proteins are coded, enables genetic information to be associated with molecular weight information from MALDI-TOF MS, even for non-genome sequenced bacterial species. (shimadzu.com)
By 2003 biologists had sequenced genomes from about one hundred different species. (learner.org)
Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. (darkenergybiosphere.org)
Using those techniques, Li has found that cells appear to strictly control the ratios of proteins that they produce, and that these ratios are consistent across cell types and across species. (techaiapp.com)
The deepest branching species in the genus, Y. ruckeri , causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. (biomedcentral.com)
In each species DNA has been 'added' by horizontal gene transfer in the form of plasmids and genomic islands. (biomedcentral.com)
The analysis revealed altered transcription levels of 12 E. coli genes in response to phage infection, and the observed regulation of phage genes correlated with the known in vivo pattern of M13 mRNA species. (lu.se)
HGT allows even distantly related species to share genes, influencing their phenotypes. (pressbooks.pub)
Of these, 3,114 were single genes confined to a single species. (blogspot.com)
To screen for novel T3S effectors of C. trachomatis, we used Yersinia enterocolitica as a genetically tractable surrogate bacterial species assembling a T3S apparatus, which has been shown to recognise heterologous T3S substrates. (europa.eu)
The team's long-term research goal is to learn to read through bacterial genomes and, based on the genes each species possesses, predict what compounds they are able to make. (illinois.edu)

The image below depicts the supercoiling of a typical bacterial genome. (reasons.org)
A typical bacterial genome contains more than 4,000 genes, which encode all of the proteins that the cells need to survive. (techaiapp.com)

Replication protein A is the functional equivalent of SSB in the nucleus of eukaryotic cells, though there is no sequence homology. (wikipedia.org)
Human mitochondrial SSB (mtSSB) binds to single-stranded mitochondrial DNA as a tetramer and has sequence similarity to bacterial SSB. (wikipedia.org)
It requires not only finding the nucleotide sequence of small pieces of the genome, but also ordering those small pieces together into the whole genome. (learner.org)
Using the amino acid sequence from the Las encoded translocase, a homologous protein was identified in Ca. Liberibacter solanacearum (Lso), the bacterium associated with zebra chip disease. (usda.gov)
This seemed a very doable number, and I have dedicated my career to building a complete and accurate classification of all proteins," says Bateman, who is Head of Protein Sequence Resources at EMBL-EBI in Hinxton, UK. (embo.org)
Our work can help scientists identify the proteins encoded in a genome sequence, learn how they interact, and understand their function. (embo.org)
Machine learning presents the opportunity to take a sequence and accurately predict a protein structure, which provides a powerful way of finding similarities," he says. (embo.org)
In this framework, a gene consists of an isolated piece of code specifying the digital information (i.e., amino acid sequence) used by the cell's machinery to build a particular protein . (reasons.org)
That is, the nucleotide sequence specifies the digital information of the gene and, at the same time, the higher order architectures of the genome, which in turn influence the expression of the digital information found in the gene. (reasons.org)
Sequence reads were assembled to the human reference genome using Burrows-Wheeler Aligner software (BWA) and the Genome Analysis Tool Kit (GATK) which identifies genomic variants. (umich.edu)
Genome Sequence of Mariprofundus sp. (darkenergybiosphere.org)
Genome Sequence of Hydrogenovibrio sp. (darkenergybiosphere.org)
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. (darkenergybiosphere.org)
however, as evidenced by genome sequence analysis, the organism lacks common enzymes required for the de novo synthesis of precursors of PGN, which rationalizes its MurNAc auxotrophy. (karger.com)
For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. (bvsalud.org)
Classification of viruses is principally according to their genome sequence taking into consideration nature and structure of their genome and their method of replication, but not according to the diseases they cause (see International Committee on Taxonomy of Viruses (ICTV), 2021 release ). (msdmanuals.com)
Positive-sense RNA viruses possess a single-stranded RNA genome that can serve as messenger RNA (mRNA) that can be directly translated to produce an amino acid sequence. (msdmanuals.com)

The mitochondria of eukaryotic cells contain their own single stranded DNA binding protein. (wikipedia.org)
Although they possess many valuable roles this does not explain the ubiquity of introns within eukaryotic genomes. (bartleby.com)
Hence, the proportion of introns in the LECA genome is considerably greater than in contemporary eukaryotic lineages, excluding some vertebrates (Figure.1). (bartleby.com)
In response, cells produce the interferon inducible RNA-dependent protein kinase (PKR) that, when bound to viral dsRNA, phosphorylates eukaryotic initiation factor 2αand attenuates viral protein translation. (uleth.ca)

This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus. (biomedcentral.com)
Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. (nih.gov)
To study the function of known effectors, we focused on the C. trachomatis Inc proteins, an important group of potential chlamydial virulence factors. (europa.eu)
Altogether, this work frames the relative importance of the P5 and Hap surface proteins in NTHi virulence. (qub.ac.uk)

Genomic analysis identified two orthologous operons encoding the ortho -cleavage of benzoic acid (BA) ( ben/cat ). (nature.com)
Bacterial DNA could be separated from host DNA based on genomic size. (bvsalud.org)
In this chapter, we describe a complete pipeline of analysis, starting from (i) the integration of information from a reference set of experimentally studied systems, (ii) the identification of conserved proteins and the construction of their HMM protein profiles, (iii) the definition and optimization of "macsy-models," and (iv) their use and online distribution as tools to search genomic data for secretion systems of interest. (bvsalud.org)
The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism. (nih.gov)
The Mining Microbial Genomes research team aims to accelerate the natural product hunt using the power of next-generation genomic technologies. (illinois.edu)
Some viruses have an outer envelope consisting of protein and lipid, surrounding a protein capsid complex with genomic RNA or DNA and sometimes enzymes needed for the first steps of viral replication. (msdmanuals.com)
Negative-sense RNA viruses possess a single-stranded negative-sense genome that first must synthesize a complementary positive-sense antigenome, which is then used to make genomic negative-sense RNA. (msdmanuals.com)
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland. (who.int)

Two general strategies have been used in the sequencing of large genomes: clone-based sequencing and whole genome sequencing (Fig. 1). (learner.org)
It turns out that the size of the nucleus is related to the size of the cell, such that large genomes give rise to large nuclei and large cells. (blogspot.com)

The proteins themselves belong to more than 4,000 new biological families. (probioticscouncil.org)

The herpes simplex virus (HSV-1) SSB, ICP8, is a nuclear protein that, along other replication proteins is required for viral DNA replication during lytic infection. (wikipedia.org)
Six herpes virus-group-common genes encode proteins that likely constitute the replication fork machinery, including a two-subunit DNA polymerase, a Helicase-primase complex and a single-stranded DNA-binding protein. (wikipedia.org)
The HHHV-1 UL5, UL8, and UL52 genes encode an essential heterotrimeric DNA helicase-primase that is responsible for concomitant DNA unwinding and primer synthesis at the viral DNA replication fork. (wikipedia.org)
DNA-binding protein Replication protein A Comparison of nucleic acid simulation software Mapelli M, Panjikar S, Tucker PA (2005). (wikipedia.org)
Throughout the cell cycle, the chromosome progressively goes from being fully methylated to hemimethylated during DNA replication - this results in differential binding of regulatory proteins to activate or repress transcription. (kenyon.edu)
The general stages to a viral life cycle are: infection, replication of the viral genome, assembly of new viral particles and then release of the progeny particles from the host. (bionity.com)
pII (aka p2) nicks the double stranded form of the genome to initiate replication of the + strand. (bionity.com)
Without p2, no replication of the phage genome can occur. (bionity.com)
The vectors of this series contain genes of the moderate bacteriophage P1, which ensure replication of the phage chromosome in infected bacterial cells. (genomequebecplatforms.com)
The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component contains the only virally-encoded function required for autonomous replication in infected plant cells. (ncsu.edu)

Mechanisms by which E. chaffeensis establishes intracellular infection, and avoids host defenses are not well understood, but involve functionally relevant host-pathogen interactions associated with tandem and ankyrin repeat effector proteins. (frontiersin.org)
Despite its small genome and limited number of effector proteins, Ehrlichia efficiently establishes an intracellular infection and avoids immune defenses in vertebrate and invertebrate hosts through complex molecular and cellular reprogramming strategies. (frontiersin.org)
100 effector proteins. (europa.eu)

In this study, we focused on the ompP5 and hap genes, present in all H. influenzae genome sequenced isolates, and encoding the P5 and Hap surface proteins, respectively. (qub.ac.uk)

M13 is a filamentous bacteriophage composed of circular single stranded DNA (ssDNA) which is 6407 nucleotides long encapsulated in approximately 2700 copies of the major coat protein P8, and capped with 5 copies of two different minor coat proteins (P9, P6, P3) on the ends. (bionity.com)
The coat's dimensions are flexible though and the number of p8 copies adjusts to accommodate the size of the single stranded genome it packages. (bionity.com)

These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. (darkenergybiosphere.org)

The papers are split about evenly on the subject, but I personally find the evidence in favor of (b) to be more compelling (particularly since we know of an actual example of a secretion system evolving from bacterial flagella, namely, the Buchnera homolog of the flagellar system). (evcforum.net)
Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane and sometimes through multiple other barriers. (bvsalud.org)
Here, we describe how to identify protein secretion systems in bacterial genomes using the MacSyFinder program. (bvsalud.org)
T3S assays performed with T3S-competent Y. enterocolitica or with an isogenic T3S-deficient strain individually expressing the TEM-1 fusions revealed a statistically significant higher level of secretion of 22 fusion proteins relative to RplJ20-TEM-1. (europa.eu)
Thirteen proteins showed a statistically significant higher level of secretion than full-length C. trachomatis RplJ. (europa.eu)
We also tested secretion of 11 out of these 13 proteins when expressed from an arabinose-inducible promoter in Y. enterocolitica, which revealed T3S-dependent secretion of 7 proteins. (europa.eu)

Other kinds of crosslinks are formed intentionally by enzymes whose proper job is to shape and reshape the functional properties of proteins in response to other age-related changes - but such crosslinks can sometimes serve short-term needs, while becoming dysfunctional as they accumulate excessively over time. (sens.org)
A full structural and functional protein characterization was carried on and in addition, the enzyme was able to form diamond crystals which diffracted at 1.7 Å. (unina.it)
A fosmid containing an ORF encoding a gene with potential esterase/lipase activity was detected by functional screening on tributyrin agar plates. (unina.it)
A biochemical approach highlighted protein features with a functional characterization methodology. (unina.it)
In functional analyses, these small genes are often overlooked. (cyanolab.de)

Create and customize bacterial strain databases. (shimadzu.com)
The software broadens the range of possible applications using the AXIMA-iD Plus Microorganism Identification System by enabling bacterial characterization down to the strain level. (shimadzu.com)
We employed isogenic single and double mutants of the ompP5 and hap genes generated in the pathogenic strain NTHi375 to evaluate P5 and Hap contribution to biofilm growth under continuous flow, to NTHi adhesion, and invasion/phagocytosis on nasal, pharyngeal, bronchial, alveolar cultured epithelial cells and alveolar macrophages, and to NTHi murine pulmonary infection. (qub.ac.uk)
By acquisition of the complete part or a large part of a novel ospC gene, an otherwise adapted strain would assume a new serotypic identity, thereby being comparatively fitter in an area with a high prevalence of immunity to existing OspC types. (cdc.gov)

Comparison of nuclear-encoded cytoplasmic ribosomal proteins and mitochondrial ribosomal proteins showed that intron positions were conserved (Yoshihama et al. (bartleby.com)
Nuclear and cytoplasmic mRNAs for several phytochrome-regulated genes were examined in Pisum seedlings in order to investigate possible light effects on mRNA partitioning between the nucleus and cytoplasm. (ncsu.edu)
Transcripts from each of five light-regulated genes exhibited different responses to a variety of light treatments, but for each transcript we observed a characteristic linear relationship between nuclear and cytoplasmic levels over a wide range of total transcript abundance. (ncsu.edu)

Temperate phages are capable of protecting their host from phage reinfection and may change the bacterial phenotype through the expression of viral genes, a process known as lysogenic conversion ( 1 ). (asm.org)
The phage coat is primarily assembled from a 50 amino acid protein called pVIII (or p8), which is encoded by gene VIII (or g8) in the phage genome . (bionity.com)
For example, when the phage genome was mutated to reduce its number of DNA bases (from 6.4 kb to 221 bp) [1] , then the number of p8 copies was decreased to less than 100, causing the p8 coat to shrink in order to fit the reduced genome. (bionity.com)
However, deletion of a phage protein (p3) prevents full escape from the host E. coli , and phage that are 10-20X the normal length with several copies of the phage genome can be seen shedding from the E. coli host. (bionity.com)
There are four other proteins on the phage surface, two of which have been extensively studied. (bionity.com)
At the other end of the phage particle are five copies of the surface exposed pIII (p3) and its less exposed accessory protein, pVI (p6). (bionity.com)
These form the rounded tip of the phage and are the first proteins to interact with the E. coli host during infection. (bionity.com)
p3 is also the last point of contact with the host as new phage bud from the bacterial surface. (bionity.com)
Filamentous phage use a bacterial structure known as the F pilus to infect E. coli , with the M13 p3 tip contacting the TolA protein on the bacterial pilus. (bionity.com)
This DNA then serves as a template for expression of the phage genes. (bionity.com)
Two phage gene products play critical roles in the next stage of the phage life cycle, namely amplification of the genome. (bionity.com)
pV (aka p5) competes with double stranded DNA formation by sequestering copies of the + stranded DNA into a protein/DNA complex destined for packaging into new phage particles. (bionity.com)
Interestingly there is one additional phage-encoded protein, pX (p10), that is important for regulating the number of double stranded genomes in the bacterial host. (bionity.com)
To identify Escherichia coli genes potentially regulated by filamentous phage infection, we used oligonucleotide microarrays. (lu.se)
Genome-wide comparison of phage M13-infected and uninfected E. coli, 2 and 20 min after infection, was performed. (lu.se)
The significantly upregulated genes encode proteins involved in reactions of the energy-generating phosphotransferase system and transcription processing, which could be related to phage transcription. (lu.se)

It was found that the C . crescentus genome encodes for more two-component signal transduction proteins that assist in cell cycle progression than any other bacterial genome sequenced so far. (kenyon.edu)
Several two-component signal transduction proteins are involved in the cell cycle progression by accumulating at one or both poles "in a spatial and temporal pattern that is reproduced during each cycle" (Jacobs-Wagner 2003). (kenyon.edu)

The genome of Caulobacter crescentus is structured in a circular chromosome and is comprised of 4,016,942 bp encoding for 3,767 genes. (kenyon.edu)
The genome of T. maritima consists of a single circular 1.8 megabase chromosome encoding for 1877 proteins. (eol.org)
Even in wild-type “Chinese Spring”, the NOR on chromosome 1B is partially dominant to that on chromosome 6B, since the 1B locus is more active in spite of having fewer genes. (ncsu.edu)
Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)

A cluster and humans coming into contact with the animals (farm that includes three genes, vanH , vanA , and vanX , is required for high-level resistance to glycopeptides. (cdc.gov)
In the vancomycin producer Amycolatopsis orientalis C329.2, homologs of these genes are present, suggesting an origin for the cluster. (cdc.gov)
The seven cyanobacterial core PSI genes identified in this study, psaA, B, C, D, E, K and a unique J and F fusion, form a cluster in cyanophage genomes, suggestive of selection for a distinct function in the virus life cycle. (nih.gov)
6 identified a gene cluster, hbpCAD , encoding the upper metabolic pathway of OPP which involves the transformation of OPP to 2-hydroxypenta-2,4-dienoateand benzoic acid (BA). (nature.com)
Yersinia genomes had a similar global partition of protein functions, as measured by the distribution of Cluster of Orthologous Groups families. (biomedcentral.com)
were able to cluster all genes into 15,389 groups called "gene families. (blogspot.com)

The bacterial genome is like a book with long strings of letters, only some of which encode the information necessary to make proteins," Bhatt said. (technologynetworks.com)

Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin, syringomycin, indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. (nih.gov)

Hierarchical clustering of distances between genomes calculated using 10 (HC10) or 20 (HC20) shared core genome MLST alleles and genomes linked on a single-linkage clustering criteria. (cdc.gov)
Because longer genes encode longer BPRPs, we investigated the possibility of exon sequencing BPRP alleles encoded by PRB1 and PRB2. (umich.edu)

In ICP8, the herpes simplex virus (HSV-1) single-strand DNA-binding protein (ssDNA-binding protein (SSB)), the head consists of the eight alpha helices. (wikipedia.org)
The encoded protein consists of an N-terminal death domain and a C-terminal Toll-interleukin1 receptor domain. (origene.com)

Chromatin structure and expression of plant ribosomal RNA genes. (ncsu.edu)
DNase I sensitivity of ribosomal RNA Genes in chromatin and nucleolar dominance in wheat. (ncsu.edu)
Ribosomal RNA genes at different nucleolar organizer (NOR) loci in hexaploid wheat are expressed at different levels. (ncsu.edu)

This was studied by using the CtrA gene, which encodes for an important cell cycle regulatory protein. (kenyon.edu)
Virulent or obligate lytic phages infect and quickly kill their bacterial host cell, whereas temperate or lysogenic phages may either stably integrate into their host's genome or enter into the lytic life cycle. (asm.org)
The quest to understand the workings of human cells will not be over until we understand how this genetic blueprint is used to produce a particular set of proteins - the proteome - for each type of cell and how these proteins control the physiology of the cell. (learner.org)
Bacterial ATP/ADP translocases transport ATP from the host cell cytosol, across the lipid bilayer, and into the bacterial cell. (usda.gov)
The Las gene encoding the translocase (tlc) was subsequently expressed in Escherichia coli and shown to enable E.coli to uptake ATP directly into the cell. (usda.gov)
These functions are likely to be found in very small proteins, which may be more likely than larger proteins to be secreted outside the cell. (technologynetworks.com)
Small proteins, they reasoned, are more likely than their larger cousins to slip through the cell membrane to ferry messages - or threats - to neighboring host or bacterial cells. (technologynetworks.com)
We will only be able to do experiments on a small fraction of genes and proteins: to understand the functions of those we don't do experiments on, we need to transfer knowledge from the ones we do," says Bateman, who also leads a research group that studies bacterial cell surface proteins that mediate host colonization. (embo.org)
Since the flagellar filament is external to the cell membrane, this poses an engineering problem: namely, how can we design the flagellum such that a large number of proteins assemble outside the cell? (evcforum.net)
The cell doesn't need every protein encoded in its genome all the time. (reasons.org)
For axenic growth under laboratory conditions, it specifically relies on the external supply of N -acetylmuramic acid (MurNAc), which is an essential constituent of the peptidoglycan (PGN) of bacterial cell walls. (karger.com)
Full length human recombinant protein of human MYD88 (NP_002459) produced in HEK293T cell. (origene.com)
Bhatt and other researchers at Stanford now believe that these proteins may be so small that they can actually come out of the microbes that create them and travel through human cell membrane in order to communicate with them. (probioticscouncil.org)
b) In transduction, a bacteriophage injects DNA that is a hybrid of viral DNA and DNA from a previously infected bacterial cell. (pressbooks.pub)
One of the things that Gregory works on is the correlation between cell size and genome size. (blogspot.com)
These effectors manipulate host cell processes to enable e. g. bacterial invasion, acquisition of nutrients, inhibition of apoptosis, or interference with immune signalling. (europa.eu)
The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. (ncsu.edu)
They later discovered that dncV encodes a molecular "switch" that activates the cell shrinking machinery of another VSP gene called capV . (beacon-center.org)
At the outset of the present study, they wanted to understand what gene products enable a cell to form a key feature of a particular phosphonate called fosfazinomycin, a compound with antifungal properties: a chemical bond between two nitrogen atoms. (illinois.edu)
Hap involvement in NTHi375-host interaction was shown to be limited, despite promoting bacterial cell adhesion when expressed in H. influenzae RdKW20. (qub.ac.uk)
[10] [11] A cell that switches to the biofilm mode of growth undergoes a phenotypic shift in behavior in which large suites of genes are differentially regulated . (wikipedia.org)
This points to a special role in dealing with the light-absorbing pigment-protein complexes, which are potentially dangerous for the cell during phycobilisome disassembly. (cyanolab.de)
Retroviruses use reverse transcription to create a double-stranded DNA copy (a provirus) of their RNA genome, which is inserted into the genome of their host cell. (msdmanuals.com)
Once the provirus is integrated into the host cell DNA, it is transcribed using typical cellular mechanisms to produce viral proteins and genetic material. (msdmanuals.com)

The S10 -GERMS method links ribosomal protein molecular weight information obtained using MALDI-TOF MS to genetic information to classify and identify microorganisms. (shimadzu.com)
The downstream transformation of BA involved a meta -cleavage pathway, although its genetic organization and function was not revealed and the overall network of genes driving the full metabolic pathway of OPP is still not known. (nature.com)
BACKGROUND: While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. (bvsalud.org)
Typically, when we consider genetic transfer, we think of vertical gene transfer, the transmission of genetic information from generation to generation. (pressbooks.pub)
Vertical gene transfer is by far the main mode of transmission of genetic information in all cells. (pressbooks.pub)
When prokaryotes and eukaryotes reproduce asexually, they transfer a nearly identical copy of their genetic material to their offspring through vertical gene transfer. (pressbooks.pub)
In prokaryotes, horizontal gene transfer (HGT), the introduction of genetic material from one organism to another organism within the same generation, is an important way to introduce genetic diversity. (pressbooks.pub)

Bacterial identification and phylogenetic analysis were carried out by 16S rRNA gene sequencing. (bvsalud.org)
It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene. (ncsu.edu)

In this context, DNA-binding transcription factors (TFs) play an important regulatory role by either repressing or activating genes in response to environmental and physiological conditions. (biomedcentral.com)
What's particularly interesting about p10 is that it's identical to the C-terminal portion of p2 since the gene for p10 is within the gene for p2 and the protein arises from transcription initiation within gene 2. (bionity.com)
Transcription of the wheat chloroplast gene that encodes the 32 kd polypeptide. (ncsu.edu)
One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. (ncsu.edu)
A transcription map of the pea chloroplast genome. (ncsu.edu)
A set of 53 cloned pea chloroplast DNA fragments representing approximately 90% of the chloroplast genome was used to probe Northern blots of total pea RNA, resulting in a nearly complete chloroplast transcription map. (ncsu.edu)
This study indicates that chloroplast genes are often grouped into multigene transcriptional units which can be cotranscribed, and that light-stimulated plastid development involves changes in the relative abundance of the overlapping RNAs of different length that result from transcription of these genes or gene clusters. (ncsu.edu)
Real-time quantitative PCR (RT-qPCR) analysis and sfGFP (superfolder green fluorescent protein) analysis reveal that AmtR directly and negatively regulates the transcription and expression of crn A, cre T, csh A, and hyu B. A growth test shows that C. glutamicum ATCC 14067 can use creatine or creatinine as a sole nitrogen source. (frontiersin.org)

Chemotaxis is triggered by the binding of ligands (chemoeffectors) to chemoreceptors called methyl-accepting chemotaxis proteins (MCPs) and transducer-like proteins (Tlps). (nature.com)

Resistance arises by mutation (influencing the target or efflux of the antimicrobial agent) or by the acquisition of resistance genes (encoding antimicrobial or target alter- ation, or alternate pathways) (2,3). (cdc.gov)
This protein functions as an essential signal transducer in the interleukin-1 and Toll-like receptor signaling pathways. (origene.com)
These pathways regulate that activation of numerous proinflammatory genes. (origene.com)
No genes belonging to any known E. coli stress response pathways were scored as upregulated. (lu.se)

This manageable size together with the current advances in nucleotide sequencing technology means that partial and whole virus genome sequencing will become an essential component in epidemiologic investigations of disease outbreaks. (msdmanuals.com)

Bacillus anthracis, the causative agent of anthrax, is a high-consequence bacterial pathogen that occurs naturally in many parts of the world and is considered an agent of biowarfare or bioterrorism. (cdc.gov)
Borrelia burgdorferi , an emerging bacterial pathogen, is maintained in nature by transmission from one vertebrate host to another by ticks. (cdc.gov)
By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)

Bacteriophages (phages) are viruses capable of infecting and replicating within bacterial cells. (asm.org)
Here we show evidence for the presence of photosystem I (PSI) genes in the genomes of viruses that infect these marine cyanobacteria, using pre-existing metagenomic data from the global ocean sampling expedition as well as from viral biomes. (nih.gov)
Viruses depend completely on cells (bacterial, plant, or animal) to reproduce. (msdmanuals.com)
the genome of RNA viruses ranges from 3.5 kilobases (some retroviruses) to 27 kilobases (some reoviruses), and the genome of DNA viruses ranges from 5 kilobases (some parvoviruses) to 280 kilobases (some poxviruses). (msdmanuals.com)

Crosslinks act like molecular "handcuffs," taking two previously independent neighboring proteins and binding them together, impairing their function similarly to how tying together participants' legs in a three-legged race makes it a struggle to get to the finish line. (sens.org)

The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. (ncsu.edu)
The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. (ncsu.edu)
For many regions of the genome, we have detected multiple overlapping transcripts including both small, gene-sized RNAs and large transcripts covering entire gene clusters. (ncsu.edu)
Light effects on the expression of nuclear genes for plastid proteins and for the 18S, 5.8S and 25S ribosomal RNAs are discussed, together with some recent information concerning the expression of chloroplast genes in developing plastids. (ncsu.edu)
Bacterial genomes are not only densely packed for the 'normal' protein-coding genes but harbor also hundreds of genes for non-coding RNAs and an unknown number of small genes encoding peptides and small proteins. (cyanolab.de)

Bhatt and her colleagues wondered if answers might be found in the small proteins they knew were likely to wiggle through the nets cast by other studies focusing on the microbiome. (technologynetworks.com)
We thank our colleagues for helpful discussions and the Deutsche Forschungsgemeinschaft for funding Vanessa through the priority program SPP 2002 " Small Proteins in Prokaryotes, an Unexplored World ", facilitating collaboration within the research group FOR2816 "SCyCode" and through the RTG MeInBio - 322977937/GRK2344. (cyanolab.de)

According to Shomron 7 (2010), this field of the clinical pharmacology studies the contribution of genomes, transcriptomes and proteomes in determining drug-response phenotypes (safety and efficacy). (bvsalud.org)

Proteins are the fundamental materials from which all organisms are built, and there are billions of genes coding for them. (embo.org)

Analyses of chlorophylls a and b and the chlorophyll a/b-binding protein suggest that accumulation of the protein and its mRNA are coordinated with chlorophyll abundance at several steps. (ncsu.edu)
analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)

These similarites include introns, histones, several types of RNA polymerase, and methionine as the first amino acid in protein synthesis. (bartleby.com)

This flexible computational tool uses the knowledge gathered from experimental studies to identify homologous systems in genome data. (bvsalud.org)

Photobleaching was found to affect the expression of the various genes in different ways. (ncsu.edu)

Because they are so small - fewer than 50 amino acids in length - it's likely the proteins fold into unique shapes that represent previously unidentified biological building blocks. (technologynetworks.com)
These proteins are very small, containing only 33 and 32 amino acids respectively, though some additional residues can be added to the N-terminal portion of each which are then presented on the outside of the coat. (bionity.com)
For this, we constructed translational fusions comprising the first 20 amino acids of the IncA or IncC effectors and a reporter protein (the mature form of TEM-1 beta-lactamase), expressed under the control of the Y. enterocolitica yopE effector gene promoter (PyopE). (europa.eu)
As negative control, we used a fusion between the first 20 amino acids of a C. trachomatis ribosomal protein and TEM-1 (RplJ20-TEM-1). (europa.eu)

In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)

concludes that E. coli genes have different mutation rates. (fieldofscience.com)

Such "extracellular matrix" (ECM) proteins are responsible for the elasticity of the artery wall, the transparency of the lens of the eye, and the high tensile strength of the ligaments, for example, as well as sustaining the function of our tissue stem cells and preventing cancerous cells from escaping their local environment to spread into far tissues. (sens.org)

Certainly, STAS domain-encoding SulP genes have already been found as the different parts of antibiotic operons, like the BLM bleomycin biosynthesis operon of (Du et al. (exposed-skin-care.net)
The second ben/cat operon was located in a 92-kb scaffold along with (i) an operon ( opp ) comprising genes for the transformation of OPP to BA and 2-hydroxypenta-2,4-dienoate (and genes for its transformation) and (ii) an incomplete biphenyl catabolic operon ( bph ). (nature.com)

The phylogenetically ancient SLC26 gene family encodes multifunctional anion exchangers and anion channels transporting a wide selection of substrates, including Cl? (exposed-skin-care.net)

Bhatt further explained what might be going on with these microscopic proteins. (probioticscouncil.org)

Three glycosylated serine-rich repeat proteins play a pivotal role in adhesion and colonization of the pioneer commensal bacterium, Streptococcus salivarius. (helmholtz-hzi.de)
The surface protein Srr-1 of Streptococcus agalactiae binds human keratin 4 and promotes adherence to epithelial HEp-2 cells. (helmholtz-hzi.de)
Surface proteins involved in the adhesion of Streptococcus salivarius to human intestinal epithelial cells. (helmholtz-hzi.de)
Serine-rich repeat proteins and pili promote Streptococcus agalactiae colonization of the vaginal tract. (helmholtz-hzi.de)

Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins. (nih.gov)
The minor coat protein P3 attaches to the receptor at the tip of the F pilus of the host Escherichia coli . (bionity.com)
Bacterial adhesion is a critical step for colonization of the host. (helmholtz-hzi.de)
Genome to genome variation in islands with genes encoding functions such as ureases, hydrogeneases and B-12 cofactor metabolite reactions may reflect adaptations to colonizing specific host habitats. (biomedcentral.com)
Here, we provide a step-by-step protocol to (1) identify whether host genome projects contain reads from associated Wolbachia and (2) isolate/retrieve the Wolbachia reads from the rest of the sequenced material. (bvsalud.org)
Ten of the 12 host genes affected could be grouped into 3 different categories based on cellular function, suggesting a coordinated response. (lu.se)
These downregulated genes are normally part of the host stress response mechanisms that protect the bacterium during conditions of acid stress and stationary phase transition. (lu.se)
PRRSV employs −1 PRF directed by RNA secondary and tertiary structures within its viral genome (canonical PRF), as well as a noncanonical −1 and −2 PRF that are stimulated by the interactions of PRRSV nonstructural protein 1β (nsp1β) and host protein poly(C)-binding protein (PCBP) 1 or 2 with the viral genome. (uleth.ca)
Acquisitions of OspC genes that are novel for the region confer to recipients unique identities to host immune systems and, presumably, selective advantage when immunity to existing types is widespread among hosts. (cdc.gov)

According to a recent report, the human microbiome in our gut also appears to be responsible for creating thousands of tiny, previously unidentified proteins. (probioticscouncil.org)

In this article, we explain the mechanisms of bacterial resistance to antibiotics. (futurelearn.com)
There are three prokaryote-specific mechanisms leading to horizontal gene transfer in prokaryotes. (pressbooks.pub)

Anatomy14

Organisms33

Diseases3

Chemicals and Drugs59

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Psychiatry and Psychology1

Phenomena and Processes122

Disciplines and Occupations3

Technology, Industry, Agriculture5

Information Science12

Health Care1

Sequences15

Bacteria14

Putative8

Pathogens9

Strains11

Human genome10

Plasmid9

Species14

Typical bacterial genome2

Sequence17

Eukaryotic4

Virulence4

Genomic8

Large genomes2

4,0001

Replication10

Effector proteins3

Isolates1

Single-stranded2

Transposons1

Secretion6

Functional5

Strain4

Cytoplasmic3

Phage16

Signal transduction2

Chromosome4

Cluster6

Make proteins1

Degradation1

Alleles2

Consists2

Ribosomal RNA3

Cell24

Genetic7

RRNA gene2

Transcription8

Chemotaxis1

Pathways4

Nucleotide1

Pathogen3

Viruses4

Molecular1

RNAs5

Small proteins2

Phenotypes1

Organisms1

Analyses2

Synthesis1

Homologous1

Various genes1

Amino acids4

Resistance genes1

Coli genes1

Extracellular matrix1

Operon2

Phylogenetically1

Bhatt1

Streptococcus4

Host9

Previously unidentified1

Mechanisms2