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Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. (chalmers.se)
Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains. (cdc.gov)
Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018. (cdc.gov)
In contrast to expectations, none of the major S-layer proteins of the IPEC-1 -adhering strains mediated bacterial adherence. (biomedcentral.com)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
Horizontal gene transfer between strains is mediated by mobile genetic elements (such as plasmids, integrons, phages, transposons, etc.) of various drug-resistant genes that can be passed between bacterial strains of the same and different species, thus allowing rapid transmission of bacterial resistance, with recipient bacteria exhibiting multi-drug resistance. (cd-genomics.com)
It was observed that plasmid exchange between the gram positive bacterial strains occurred in space flgiht more efficient than in the ground control experiment. (sckcen.be)
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)
The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. (biomedcentral.com)
We describe enterococci in raw-frozen dog food commercialized in Europe as a source of genes encoding resistance to the antibiotic drug linezolid and of strains and plasmids enriched in antibiotic-resistance and virulence genes in hospitalized patients. (escmid.org)
Three strains possess an 18.8 kb-long genomic island designated SbCIccr with a ccr gene complex designated ccrDE that had a conserved structure like a ccr gene complex from known SCC types. (muni.cz)
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)

All of these isolates, plus an additional 19 from clinical infections, were characterised through whole-genome sequencing. (bvsalud.org)
Findings: The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.3% of all isolates) that could be divided into 20 distinct clusters, defined through genome sequencing. (bvsalud.org)
Whole genome sequences of these isolates were determined and analysed to compute bacterial multilocus sequence types and plasmid replicon types, infer phylogenetic relationships, and identify antimicrobial resistance and virulence genes. (biomedcentral.com)
The most abundant carbapenemase gene family in the K. pneumoniae isolates (33/39) was bla OXA-232 , with bla NDM-1 additionally identified in 19 of them. (biomedcentral.com)
Objectives The whole genomes of two Acinetobacter baumannii isolates recovered from a single patient were sequenced to gain insight into the nature and extent of genomic plasticity in this important nosocomial pathogen over the course of a short infection. (uea.ac.uk)
Sequence analysis demonstrated the presence of plasmids pAB0057 and pACICU2 in both isolates. (uea.ac.uk)
Conclusions This study demonstrates that significant differences were detectable between two bacterial isolates recovered 1 week apart from the same patient, and reveals the potential of whole-genome sequencing as a tool for elucidating the processes responsible for changes in antibiotic susceptibility profiles. (uea.ac.uk)
Whole-genome sequencing was fundamental to linking isolates from dog food to human cases across Europe. (escmid.org)
Genomic analysis revealed a 16 amino acid deletion in the protease gene in isolates lacking protease activity, including strain B1. (usda.gov)
The same deletion was found in genomes of isolates from North Dakota and Iran. (usda.gov)
The mcr-1 gene was first reported in 2015 in food, animal, and patient isolates from China ( 1 ) and is notable for being the first plasmid-mediated colistin resistance mechanism to be identified. (cdc.gov)
Methods: We sequenced the genomes of 175 isolates longitudinally collected from 30 patients with MABC lung infection. (cdc.gov)

Long-read nanopore sequencing with the MinION device (Oxford Nanopore Technologies, https://nanoporetech.com ) can resolve repetitive sequences and structural genomic rearrangements and enables complete bacterial genome finishing ( 9 ). (cdc.gov)
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)
To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. (frontiersin.org)
The information on plasmid sequences in Pandoraea spp. (frontiersin.org)
is useful as the sequences did not match any known plasmid sequence deposited in public databases. (frontiersin.org)
With the recent flood of genome sequences, one of the greatest backlogs in dealing with these sequences is annotation. (uidaho.edu)
MTase methylates specific DNA sequences (recognition sites) in the host genome. (biomedcentral.com)
Within CRISPR sites, the repeats are separated by short spacer sequences that match phage or plasmid genomes and specify the targets of interference. (rockefeller.edu)
All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
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)
Results Automated gene prediction detected 3850 putative coding sequences (CDSs). (uea.ac.uk)
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)
The reported sequences are the first genome-scale plastid data available for these three poorly studied glaucophyte genera. (pacb.com)

the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. (jci.org)
While the genome sequence was already transformative at the time, the past 25 years of progress have substantially increased its impact on TB taxonomy, drug discovery, resistance mechanisms, epidemiology, vaccine development, and pathogenesis. (jci.org)
Because errors in sequence annotation are propagated by automated searches of gene sequence relatedness, the relatively simple job of studying gene function in plasmids has become increasingly difficult. (uidaho.edu)
Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. (rockefeller.edu)
Upon infection, CRISPR arrays can acquire new spacer units that match the sequence of the infecting phage or plasmid. (rockefeller.edu)
Using the cross-linking relationship, the sequence from the same cell is determined, and the genome of a single bacteria is constructed. (cd-genomics.com)
The whole genome sequence analysis revealed the presence of several variable genomic elements including staphylococcal chromosomal cassette (SCC), prophages, genomic islands, various full and partial IS elements, and plasmids conferring beta-lactam and macrolide resistance. (muni.cz)
Although initial phenotypic and 16S rRNA analysis identified this isolate as B. cereus, the rapid generation and analysis of a high-coverage draft genome sequence revealed the presence of a circular plasmid, named pBCXO1, with 99.6% similarity with the B. anthracis toxin-encoding plasmid, pXO1. (ox.ac.uk)
Moreover, it is not known whether IEs play an important role in the origin of ORFans (open reading frames without matches in current sequence databases), whose proportion remains stable despite the growing number of complete sequenced genomes. (pasteur.fr)
We developed an accurate in silico Markov model-based strategy to identify clusters of genes that show atypical sequence composition (clusters of atypical genes or CAGs) and are thus likely to be recently integrated foreign elements, including IEs. (pasteur.fr)
Analysis of the Campylobacter phage CP8 genome identified significant sequence identity of protein gp010 with the avian leukocyte receptor CD30 ligand. (nottingham.ac.uk)
In humans, knowledge of the entire genome sequence has facilitated searching for genes that produce hereditary diseases. (netlify.app)
Pairwise distances estimated from 19 different plastid genes revealed that the highest sequence divergence between glaucophyte genera is frequently higher than distances between species of different classes within red algae or viridiplants. (pacb.com)
Gene synteny and sequence similarity in the ptDNAs of the two Glaucocystis species analyzed is conserved. (pacb.com)
This is a specific sequence of DNA where the replication of the plasmid begins. (stemcelldaily.com)

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While many bacteria have intrinsic, chromosomally encoded ARDs and the capability of increasing resistance through mutation, they can also enrich their resistance capabilities through the acquisition of exogenous ARDs located on mobile genetic elements (MGEs) such as plasmids, transposons or phages. (nature.com)
In bacteria and archaea, CRISPRs-clustered, regularly interspaced, short palindromic repeats-constitutes a recently discovered genetic interference pathway that protects cells from phages and conjugative plasmids. (rockefeller.edu)
Hi-C not only clusters metagenomic results to species and strain levels, but also associates plasmids, phages and host bacteria in microbial communities. (cd-genomics.com)
Mobile genetic elements (MGEs) such as phages, plasmids and transposons, play a crucial role in bacterial adaptation and evolution. (sckcen.be)
Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. (biomedcentral.com)
Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. (biomedcentral.com)
Corollaries of this finding are that, even among closely related prokaryotes, the most commonly encountered phages and plasmids are different and/or that the dominant phages and plasmids turn over rapidly. (biomedcentral.com)
It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. (biomedcentral.com)
However, it appears that this inheritance is extremely unstable on the evolutionary scale such that the repertoires of unique psiRNAs are completely replaced even in closely related prokaryotes, presumably, in response to rapidly changing repertoires of dominant phages and plasmids. (biomedcentral.com)

Single-nucleotide mutations in chromosomal B. anthracis quinolone resistance-determining regions of gyrA , gyrB , parC , and parE genes can lead to ciprofloxacin resistance, and gene acquisition can lead to tetracycline and doxycycline resistance ( 3 , 4 , 6 ). (cdc.gov)
Detection of known antimicrobial resistance (AMR) mutations or other novel gene insertions and deletions (indels) in the clonal B. anthracis genome signals genetic anomalies and could influence treatment and postexposure prophylaxis strategies. (cdc.gov)
Whole-genome sequencing (WGS) can identify gene indels, mutations, or previously undescribed genetic elements, including extrachromosomal plasmid DNA. (cdc.gov)
The most frequent target of resistance mutations was the plasmid-encoded SpCas9 that was inactivated by bacterial genome rearrangements involving translocation of mobile genetic elements such as insertion elements. (dtu.dk)
In humans, one of the most significant potential applications is preventing and treating so-called monogenic diseases, heritable genetic conditions that are caused by mutations in a single gene. (lindau-nobel.org)
Once a gene is duplicated, the two copies can diverge in function through mutations, such as point mutations, deletions, and insertions. (tutorialspoint.com)
Introduction DNA microarrays are powerful tools for analysing gene expression patterns, detecting DNA mutations, and identifying genetic variations. (tutorialspoint.com)
RRResearch: Have bacteria evolved gene-specific rates of point mutations? (fieldofscience.com)
Aerotolerance was associated with mutations to genes involved in central and carbohydrate metabolism. (nottingham.ac.uk)
We further annotated nonrandom parallel mutations in 22 genes and demonstrated altered macrolide susceptibility co-occurring with a nonsynonymous whiB1 mutation. (cdc.gov)
Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)

AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. (mdpi.com)
It is designed to cross species barriers and to jump into genomes, and it has homologies to the DNA of many species and their genetic parasites (plasmids, transposons and viruses), thereby enhancing recombination with all of them [2]. (i-sis.org.uk)

This project will start with plasmids whose genomes have been annotated automatically. (uidaho.edu)
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)

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)
Similar to the principle of Hi-C technology applied to eukaryotic chromosome-level reference genome-assisted assembly, Hi-C/3C technology can be applied to the assembly of metagenomes to improve the results of metagenome assembly. (cd-genomics.com)
Introduction Bacterial Artificial Chromosome (BAC) is a powerful tool in Genetic Research Bacterial Artificial Chromosome (BAC) is a widely used tool in genetic research for the manipulation and study of DNA. (tutorialspoint.com)
By a PCR assay we showed that the SbCIccr could be mobilized from the bacterial chromosome. (muni.cz)
H13-3 possesses a linear chromosome (2.15Mb) that is related to its reference replicon and features chromosomal and plasmid-like properties. (uni-bielefeld.de)
The chromosome encodes a complete type VI secretion system and plasmid genes encode type IV secretion proteins. (nottingham.ac.uk)
They are not part of the main chromosome of the cell, but they can replicate independently and carry genes that may confer some advantages to the host organism. (stemcelldaily.com)
Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)

PGS was the first company (in 1985) to develop genetically engineered (tobacco) plants with insect tolerance by expressing genes encoding for insecticidal proteins from Bacillus thuringiensis (Bt). (wikipedia.org)
From the 178 plasmids sent, 167 were able to grow in bacterial culture and 92 of the ASFV proteins were expressed individually in mammalian cells. (intvetvaccnet.co.uk)
Proteins/genes with a putative catabolic role and bacterium adaptation mechanisms during OPP degradation were identified via genomic and proteomic analysis. (nature.com)
Vaccines with viral proteins produced by bacteria or yeast from recombined viral genes are considered safer Other Pharmaceutical Products. (netlify.app)
For example, plasmids can be used to produce recombinant proteins, such as insulin or human growth hormone, in bacteria or yeast cells. (stemcelldaily.com)

They also found a way to make plant cells resistant to the antibiotic kanamycin by transferring a bacterial neomycin phosphotransferase gene into the plant genome. (wikipedia.org)
Antibiotic resistance genes spreading to pathogenic bacteria. (i-sis.org.uk)
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. (nature.com)
The intestinal microbiota plays a pivotal role in this phenomenon as it harbours a vast diversity of bacterial species, some of them possessing antibiotic resistance determinants (ARDs) that may enable their survival under antibiotic exposure. (nature.com)
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)
Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. (frontiersin.org)
The impact is enhanced if coupled with the presence of functional genes for antibiotic resistance. (frontiersin.org)
Hence, the spread of virulence factors and antibiotic resistance properties caused by plasmids is possible, leading to a threat in public health. (frontiersin.org)
Dissecting host-plasmid and host-phage associations is critical to understanding the ecology of antibiotic resistance and the pathways of resistance gene transmission in the clinic, and is a prerequisite for designing and implementing interventions to reduce the threat of bacterial infection. (cd-genomics.com)
Diversity of metal and antibiotic resistance genes in Enterococcus spp. (escmid.org)
The mcr-1 gene confers resistance to the polymyxins, including the antibiotic colistin, a medication of last resort for multidrug-resistant infections. (cdc.gov)
Plasmids often carry genes that confer some advantage to the host cell, such as antibiotic resistance, virulence factors, or metabolic capabilities. (stemcelldaily.com)
This is a gene that confers resistance to a certain antibiotic or toxin, which helps in identifying and selecting the cells that contain the plasmid. (stemcelldaily.com)

It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. (biomedcentral.com)
Some general classes- plasmid vectors, bacteriophage vectors. (free-essays.us)
These three enzymes, often encoded in bacterial plasmids and bacteriophage genomes, are known to participate in the mobilization and replication of DNA mobile elements. (pacb.com)

The intestinal microbiota harbours thousands of bacterial species including well-known pathogens (for example, Enterobacteriaceae and Enterococcus spp. (nature.com)
S (surface) layers are the outermost cell envelope structures commonly found on the surface of lactobacilli and other bacterial species. (biomedcentral.com)
It hops between species via a plasmid - a small molecule of DNA that can transfer from one bacterial cell to another and slot into its new host's genome. (cosmosmagazine.com)
When they wiped samples on agar plates and monitored what grew, they found multiple species of bacteria carrying the bla IMP-27 gene in samples collected from the farrowing environment but failed to find it in slaughter-ready pigs. (cosmosmagazine.com)
In each species DNA has been 'added' by horizontal gene transfer in the form of plasmids and genomic islands. (biomedcentral.com)
All three human pathogens carry a 70-kb pYV virulence plasmid (also known as pCD), which carries the Ysc type III secretion system and Yops effectors [ 18 - 20 ], that is not detected in non-pathogenic species. (biomedcentral.com)
While transformation procedures have become routine for a growing number of plant species, the random introduction of complex transgenenic DNA into the plant genome by current methods generates unpredictable effects on both transgene and homologous native gene expression. (bioone.org)
Plasmids can be transferred between bacteria, potentially spreading the resistance gene to other bacterial species. (cdc.gov)
Plasmids can vary in size from 1 kb to 200 kb, and they can exist in different species and get transferred from one cell to another. (stemcelldaily.com)

We completed Bacillus anthracis nanopore whole-genome sequencing in our high-containment laboratory from a human anthrax isolate hours after receipt. (cdc.gov)
The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. (jci.org)
Whole-genome sequencing (WGS) of M. tuberculosis and related mycobacteria is now routine, allowing comparisons across time and space. (jci.org)

These data indicate that plasmid exchange between microorganisms is occuring during space flight conditions. (sckcen.be)
Plasmids are small circular DNA fragments that are found in many microorganisms, such as bacteria, archaea, and some eukaryotes. (stemcelldaily.com)

Penicillin resistance can result from a chromosomal mutation in the antisigma factor gene, rsiP ( 5 ). (cdc.gov)
concludes that E. coli genes have different mutation rates. (fieldofscience.com)
That phenomenon has been shown to not be due to changes in the mutation rate (considered per base pair), but to initially unsuspected cryptic growth on the sugar and changes in the number of copies of the gene under selection. (fieldofscience.com)

Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. (frontiersin.org)
The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. (frontiersin.org)
Generally, these genes are related to replication and maintaining copies of the plasmid across generations. (uidaho.edu)
Gene duplication occurs through several mechanisms, including chromosomal duplication, retro transposition, and DNA replication errors. (tutorialspoint.com)
The copy number is regulated by various factors, such as the size of the plasmid, the origin of replication, and the availability of nutrients and energy. (stemcelldaily.com)
Some plasmids are compatible with each other and can be maintained together in a stable state, while others are incompatible and compete for resources or interfere with each other`s replication or expression. (stemcelldaily.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)
Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. (nih.gov)
CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. (frontiersin.org)

Because plasmids are parasitic and rely upon their bacterial host for almost all of their functions, it should be straightforward to determine the functions of the few genes the plasmid encodes for itself. (uidaho.edu)
The MCS is usually located within a lacZ gene, which encodes for β-galactosidase enzyme. (stemcelldaily.com)

I-SIS submitted written questions to the upcoming 'Open Meeting' of the Advisory Committee for Novel Food Products (ACNFP) in which horizontal gene transfer is to be discussed. (i-sis.org.uk)
Horizontal gene transfer is one of the most serious, if not the most serious hazard of transgenic technology. (i-sis.org.uk)
Transgenic DNA is in many respects optimised for horizontal gene transfer. (i-sis.org.uk)
Since then, we have continued to warn our regulators that the CaMV 35S promoter will be extra prone to spread by horizontal gene transfer and recombination [7-9]. (i-sis.org.uk)
Archaeal and bacterial genomes contain a number of genes of foreign origin that arose from recent horizontal gene transfer, but the role of integrative elements (IEs), such as viruses, plasmids, and transposable elements, in this process has not been extensively quantified. (pasteur.fr)
Probabilistic analysis of gene content indicates that 56% of these new CAGs are likely IEs, whereas only 7% likely originated via horizontal gene transfer from distant cellular sources. (pasteur.fr)

It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by the presence of plasmids pXO1 and pXO2, which encode the lethal toxin complex and the poly-gamma-d-glutamic acid capsule, respectively. (ox.ac.uk)

This further leads to the hypothesis of host-plasmid interaction. (frontiersin.org)

However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. (osti.gov)
The vaccine is based on the plasmid DNA platform, which allows for the insertion of specific genes into a bacterial or viral genome. (zikeal.com)
Plasmids have been widely used in biotechnology and genetic engineering, as they can be manipulated to introduce, modify, or delete specific genes in the host cell. (stemcelldaily.com)

Plasmids are also known as extra-chromosomal elements or genetic tools. (stemcelldaily.com)
Plasmids are also known as sex factors , conjugants , extra chromosomal replicons , or transfer factors . (stemcelldaily.com)
Plasmids are small, circular, double-stranded DNA molecules that are distinct from the chromosomal DNA of the host cell. (stemcelldaily.com)
The virulence of this bacterium results from the 32 Y pestis chromosomal genes and two Y pestis -specific plasmids, constituting the only new genetic material acquired since its evolution from its predecessor. (medscape.com)

The clinical isolate S. epidermidis RP62a harbors a CRISPR spacer that matches the nickase gene ( nes ) that is present in nearly all staphylococcal conjugative plasmids and prevents their spread. (rockefeller.edu)

R-M systems are widely spread among prokaryotes: they have been found or predicted with computational methods in the vast majority of bacterial and archaeal genomes [ 13 ]. (biomedcentral.com)
The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)
We have performed a large-scale survey of potential recently acquired IEs in 119 archaeal and bacterial genomes. (pasteur.fr)
Thirty-four percent of CAGs remain unassigned, what may reflect a still poor sampling of IEs associated with bacterial and archaeal diversity. (pasteur.fr)

They developed a vector system for transferring foreign genes into the plant genome, by using the Ti plasmid of Agrobacterium tumefaciens. (wikipedia.org)

The risk of cancer is highlighted by the recent report that gene therapy - genetic modification of human cells - claimed its first cancer victim [4]. (i-sis.org.uk)
Advances in genome engineering are enabling researchers to achieve unprecedented breakthroughs, from curing genetic disorders to developing disease-resistant crops. (sigmaaldrich.com)
An excellent example of how mis-annotations cause problems is the automated annotation of bacterial plasmids, independently replicating mobile genetic elements that can transfer between bacteria, sometimes even between very different taxonomic groups. (uidaho.edu)
While they are highly specific, the use of gene editing systems can also lead to so-called off-target effects, i.e., unwanted changes to the genetic material. (lindau-nobel.org)
One of the earliest genetic tools developed on the path to gene editing was recombinant gene technology, that is, the ability to recombine DNA molecules from distinct organisms or to insert DNA from one (source) organism into the genome of another. (lindau-nobel.org)
The 3C technology, the predecessor of Hi-C technology, Meta 3C can also be used to associate mobile genetic elements (resistance genes, plasmids and integrons) with the host genome. (cd-genomics.com)
2. Associating mobile genetic elements (resistance genes, plasmids, and integrons) with the host genome. (cd-genomics.com)
Introduction Retrotransposons are genetic elements that are capable of replicating and inserting themselves into different parts of the genome. (tutorialspoint.com)
In this study, we combined a public health approach with genome analysis to provide insight into the correlation of phenotypic characteristics and their genetic basis. (ox.ac.uk)
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)
The term plasmid was coined by Joshua Lederberg in 1952, who discovered that some bacteria can exchange genetic material through a process called conjugation. (stemcelldaily.com)

First, we searched for T6SS genes across a curated dataset of over 20â 000 genomes representing the full phylogenetic diversity of E. coli. (bvsalud.org)
This revealed large, non-phylogenetic variation in the presence of T6SS genes. (bvsalud.org)
A polyphasic taxonomic approach based on whole genomic sequencing with expert annotation, extensive biotyping, DNA fingerprinting by rep-PCR, MALDI-TOF MS, and chemotaxonomy analyses was applied to establish their phylogenetic position and characterize virulence and drug-resistance genes. (muni.cz)
H13-3 has been established and the genome structure and phylogenetic assignment of the organism was analysed. (uni-bielefeld.de)

In this article, we present an application of our novel E. coli CRISPR/Cas-mediated Lambda-Red (λ-Red) homologous recombination (HR) vector system, which facilitates gene editing through the homology-directed repair (HDR) of double-stranded DNA breaks (DSBs) created by Cas9 endonuclease, using either ssDNA or dsDNA as an editing template. (sigmaaldrich.com)
Functional pangenomic analysis of 19,571 E. coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. (bvsalud.org)
BACs are circular DNA molecules that are derived from the F-factor plasmid found in the bacterium E. coli. (tutorialspoint.com)
The genome of C. coli OR12 was sequenced to identify factors which contribute to its fitness in colonizing chickens. (nottingham.ac.uk)
Since its discovery, the mcr-1 gene has been reported from Africa, Asia, Europe, South America, and North America ( 2 , 3 ), including the United States, where it has been identified in Escherichia coli isolated from three patients and from two intestinal samples from pigs ( 2 , 4 - 6 ). (cdc.gov)

The use of site-specific recombination to remove undesired DNA from the plant genome and concomitantly, via excision-mediated DNA rearrangement, switch-activate by choice transgenes of agronomical, food or feed quality traits provides a versatile "transgene maintenance and control" strategy that can significantly contribute to the transfer of transgenic laboratory developments into farming practice. (bioone.org)
This review focuses on recent reports demonstrating the elimination of undesirable transgenes (essentially selectable marker and recombinase genes) from the plant genome and concomitant activation of a silent transgene (e.g., a reporter gene) mediated by different site-specific recombinases driven by constitutive or chemically, environmentally or developmentally regulated promoters. (bioone.org)

We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones. (bvsalud.org)
Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. (cdc.gov)

Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens. (nature.com)
New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. (biomedcentral.com)

In the past ten years I have collaborated with Dr. Eva Top on the annotation and evolution of broad host range plasmids. (uidaho.edu)
This process is essential for evolution as it provides an opportunity for the duplicated gene to evolve new functions while the original gene remains intact. (tutorialspoint.com)
In this article, we will explore the concept of gene duplication and its role in evolution. (tutorialspoint.com)
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)

Marraffini investigates the molecular mechanisms that make CRISPR immunity possible, and also explores genome editing and other potential applications for CRISPR-Cas systems. (rockefeller.edu)
In this way, CRISPR-Cas systems provide adaptive and inheritable immunity to the bacterial cell. (rockefeller.edu)

Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. (biomedcentral.com)
We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. (biomedcentral.com)
The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. (biomedcentral.com)
There are now more than 8,000 fully sequenced and annotated prokaryotic genomes available. (ku.dk)

While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. (chalmers.se)

This work describes a non-B. anthracis isolate that possesses the anthrax toxin genes and is capable of causing a severe inhalation anthrax-like illness. (ox.ac.uk)

Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. (frontiersin.org)

Adopted 1990, TRS No 814, This track is designed to meet the needs of students with varied academic background who desire to develop significant experience in recombinant DNA This created a recombinant DNA molecule-- a plasmid containing recombined DNA from two different sources. (netlify.app)
The limitation enzyme of EcoRI doing a individual cut in a round Deoxyribonucleic acid molecule such as plasmid, the cut opens up the circle, and the ensuing additive molecule has sticky terminals. (free-essays.us)
He named this molecule plasmid, from the Greek word plasmos, meaning molded or formed. (stemcelldaily.com)

The siderophores yersiniabactin and aerobactin, considered to be important virulence factors, were only identified in the CPKP-ST231 genomes. (biomedcentral.com)

Prior to the availability of an effective vaccine, H influenzae type b (Hib) was the most common cause of pediatric bacterial meningitis in the United States. (medscape.com)
Surveillance on Pediatric Bacterial Meningitis has been set up by the World Health Organization to generate data on vaccine preventable causes of Meningitis in under-five children. (bvsalud.org)

These plasmids are of interest because they can confer resistance to many antibiotics in a diversity of pathogenic and non-pathogenic bacteria. (uidaho.edu)
Understanding the biology of these plasmids may help in combatting the growing problem of multi-drug resistant, pathogenic bacteria. (uidaho.edu)

Because the entire genome of a laboratory strain of H influenzae has been sequenced, additional insights into its molecular mechanisms of pathogenesis will undoubtedly be gained in the near future. (medscape.com)

A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3 indicating that it is a non-virulent isolate. (uni-bielefeld.de)
Virulence of strain B1 was significantly increased by introducing a functional copy of the protease gene on a plasmid. (usda.gov)
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)

Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. (ox.ac.uk)

In this article, we will focus on LTR retrotransposons, their structure, and their role in eukaryotic genomes. (tutorialspoint.com)
There are two major, distinct forms of regulatory small RNAs involved in eukaryotic gene silencing: small interfering (si) RNAs and micro (mi) RNAs. (biomedcentral.com)

To understand plasmid biology, as with understanding human biology, it is useful to understand the functions of genes that are encoded in the plasmid genome. (uidaho.edu)
This fellowship includes significant training in computational techniques, commonly known as bioinformatics, and a cursory background in molecular and plasmid biology. (uidaho.edu)

Conjugation genes were identified portraying the conjugation ability amongst Pandoraea plasmids. (frontiersin.org)
Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. (frontiersin.org)
The Mobilisatsia/Plasmida experiment was set up to invesitgate the impact of space flight on plasmid-mediated conjugation. (sckcen.be)
These names reflect their ability to transfer from one cell to another through a process called conjugation, which involves the formation of a pilus (a thin tube-like structure) between two cells and the transfer of a copy of the plasmid. (stemcelldaily.com)

We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)

Introduction Genes are the building blocks of life, and they determine everything from the color of our eyes to our susceptibility to diseases. (tutorialspoint.com)
Our research has demonstrated that the correlation of bacterial pigments on their susceptibility to antimicrobial agents. (biomedcentral.com)
Finally, we highlighted a 23-kb mercury -resistance plasmid whose loss during chronic infection conferred phenotypic susceptibility to organic and nonorganic mercury compounds. (cdc.gov)

BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies. (cdc.gov)
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)

CoNS serve as a reservoir of accessory genes, including virulence and antimicrobial resistance factors for the genus Staphylococcus. (muni.cz)

Next, they inserted the plasmid into bacteria and 1 Jun 2020 Recombinant DNA is the combination of DNA from two different sources. (netlify.app)

The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. (osti.gov)

However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis. (biomedcentral.com)
The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. (biomedcentral.com)

Because of their large, complex genomes, it was difficult to study one gene Steps for recombinant DNA technology. (netlify.app)

The comments, "it is extremely unlikely that genes from genetically modified (GM) food can end up in bacteria in the gut of people who eat them", and "the findings had been assessed by several Government experts who had ruled that humans were not at risk", are seriously misleading. (i-sis.org.uk)
Food-to-Humans Bacterial Transmission. (escmid.org)

Bacterial plasmids with a resistance gene present (usually ampicillin or kanamycin resistant) are used as vector DNA. (netlify.app)

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 cloning vector is then inserted into the genome of the organism. (netlify.app)

Our optimized, custom lentiviral vectors are fully compatible with Chromium Single Cell Gene Expression v3 and v3.1 (Next GEM) solution utilizing Feature Barcode technology. (sigmaaldrich.com)
1983): Expression of bacterial genes in plant cells. (elementedernaturwissenschaft.org)
These operons are involved in regulating the expression of genes in bacteria and play an essential role in the survival of these organisms. (tutorialspoint.com)
Plasmids can also be used to study gene expression and regulation, gene function and interaction, and gene therapy. (stemcelldaily.com)

These MGEs mobilise and reorganize genes within a given genome or between bacterial cells. (sckcen.be)

The genomic island harbours genes for the restriction-modification system commonly found on SCC elements, a putative transposon with IS6 family element similar to IS431mec, a putative transcriptional regulator and accessory genes, which have been found frequently on plasmids. (muni.cz)
Transcription analysis of all putative catabolic genes established their role in the metabolism of OPP. (nature.com)

We contextualized our cohort amidst the broader MABC phylogeny and investigated genes undergoing parallel adaptation across patients. (cdc.gov)

The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. (asm.org)

Plasmids have certain essential elements that enable them to replicate and maintain themselves in the host cell. (stemcelldaily.com)

In this excerpt from the panel discussion on gene editing at the 2021 Lindau Nobel Laureate Meeting, Alena Buyx, German bioethicist and President of the German Ethics Council, makes clear the important distinction between somatic and germline gene editing. (lindau-nobel.org)
In this excerpt from her lecture at the 2021 Lindau Meeting, Emmanuelle Charpentier talks about important milestones - all landmark discoveries in themselves - which paved the way for gene editing and the different tools that currently exist. (lindau-nobel.org)
In this study we described the epidemiological data on Bacterial meningitis in under-five children at Gondar University Hospital from 2012-2021. (bvsalud.org)
Results: In this study, a total of 4311 under-five admitted with suspected bacterial meningitis from 2012 to 2021 were enrolled. (bvsalud.org)

Complete genome sequencing of Agrobacterium sp. (uni-bielefeld.de)
Comparable to the genome of Agrobacterium tumefaciens C58, Agrobacterium sp. (uni-bielefeld.de)

Anatomy9

Organisms28

Diseases4

Chemicals and Drugs55

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes135

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science12

Health Care2

Strains12

Isolates12

Sequences14

Sequence15

Genomics6

Phages9

Mutations11

Transposons2

Whose genomes2

Chromosome8

Proteins5

Antibiotic13

Bacteriophage3

Species9

Whole-Genome Sequencing3

Microorganisms2

Mutation3

Replication6

Genomic islands3

Encodes2

Horizontal6

Presence of plasmids1

Leads to the hypothesis1

Specific genes3

Chromosomal4

Conjugative plasmids1

Archaeal4

Foreign genes1

Genetic11

Phylogenetic4

Coli5

Plant genome2

Recombination2

Pathogens2

Evolution4

CRISPR-Cas2

Prokaryotic4

Thousands of bacterial1

Possesses1

Protein-encod1

Molecule3

Virulence factors1

Pediatric bacterial meningitis2

Pathogenic bacteria2

Entire genome1

Strain3

Bacillus1

Eukaryotic2

Biology2

Conjugation4

Pestis1

Susceptibility3

Taxonomic2

Staphylococcus1

20201

Microbial1

Hypothesis2

Recombinant1

Humans2

Resistance gene1

Operon1

Organism1

Expression4

MGEs1

Putative2

Adaptation1

Encode1

Replicate1

20214

Agrobacterium2