Rrna genomes loci genes bacterial. Medical search. Frequent questions

Whole-genome sequencing used to investigate a nationwide outbreak of listeriosis caused by ready-to-eat delicatessen meat, Denmark, 2014. (cdc.gov)
Sub-objective 4.1: Analysis of ExPEC isolated from chickens and humans: biofilm assays, virulence gene profiles, antimicrobial resistance profiles, whole genome comparison of ExPEC strains isolated from chicken and human infections. (usda.gov)
Harmonization of whole-genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci. (applied-maths.com)
Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumericsTM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa. (applied-maths.com)
Retrospective Definition of Clostridioides difficile PCR Ribotypes on the Basis of Whole Genome Polymorphisms: A Proof of Principle Study. (applied-maths.com)
The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a National Reference Laboratory in a smaller country. (applied-maths.com)
In recent years, advances in sequencing technology have led to what is known as "next-generation sequencing" becoming much more affordable and available, paving the way to whole genome sequencing of bacterial isolates as a more cost-effective means than MLST for comparing isolates of the same species, and this is now our preferred approach, for a number of different reasons. (rapidmicrobiology.com)
When you are planning to submit or have submitted whole genome scale data obtained from the same samples. (nig.ac.jp)
For whole genome-scale sequence , it is optional to describe biological features except source and assembly_gap. (nig.ac.jp)
Conclusions The comparative whole-genome along with transcriptome analysis indicated that G. stearothermophilus B5 owned the ability of lignocellulose degradation and could be considered as a potential inoculant in composting efficiency, thus are also valuable for the lignocellulosic bioenergy industry. (researchsquare.com)
Whole Genome Shotgun Sequencing (WGS) WGS generally involves six steps, isolation of genomic DNA, random fragmentation of genomic DNA, size selection using electrophoresis, library construction, paired-end sequencing (PE sequencing), and genome assembly. (allclearmister.com)
What is whole-genome shotgun sequencing? (allclearmister.com)
Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development. (allclearmister.com)

Sequence analysis of the thymidylate synthase (TS) and superoxide dismutase (SODA) gene loci, the EPSP synthase domain of the multifunctional arom gene, and the mitochondrial small subunit ribosomal RNA (mt SSU rRNA) locus have been used to distinguish Pneumocystis species from diverse mammalian hosts ( 6 , 20 , 21 ). (cdc.gov)
Furthermore, we used 16S ribosomal RNA gene sequencing to detect associations with different abundances of the gut microbiota with dietary patterns. (uni-frankfurt.de)

Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira. (nih.gov)
In this study, we performed genome analyses of more than 1,000 bifidobacterial strains publicly available revealing that Bifidobacterium adolescentis taxon might represent a model GABA producer in human gastrointestinal tract. (nature.com)
Recently, the term "psychobiotic" has been introduced to designate live bacterial strains, including lactobacilli and bifidobacteria, which are able to influence the CNS function 8 . (nature.com)
Click "Sequence Details" to view all sequence information for this locus, including that for other strains. (yeastgenome.org)
We will use omic technologies to analyze a large variety of strains of each of the pathogens to identify genes and proteins necessary for pathogens to survive stresses encountered in food environments and cause human illness. (usda.gov)
Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. (frontiersin.org)
Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. (pacb.com)
We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. (peerj.com)
High levels of recombination could confound studies of the gonococcal populations, especially if the studies are based on few genetic loci within strains as compared to the entire genomes. (peerj.com)
Different strains of the same bacterial species show enough variation within each of these housekeeping genes i.e. at each of the seven loci, to create a vast number of distinct allelic profiles. (rapidmicrobiology.com)

Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes , as previously thought. (uibk.ac.at)
The presence of many "polysaccharide utilization loci" (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. (biomedcentral.com)

Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1-V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. (bvsalud.org)
The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. (mbl.edu)
We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)
We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. (frontiersin.org)
Thus, with its lack of genomic redundancy and contingenciesfor different environmental conditions, M. genitalium is already closeto being a minimal bacterial cell. (fullblog.com.ar)
In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. (umassmed.edu)

Because of the generally low sequence divergence among P. jirovecii isolates at these loci, they are not highly discriminative for P. jirovecii typing. (cdc.gov)
Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. (bvsalud.org)
This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. (nih.gov)
The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii, in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. (nih.gov)
Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. (biomedcentral.com)
10,200 protein-encoding genes were predicted based on the genome sequence. (springeropen.com)
The genes and proteins were predicted and annotated based on the genome sequence. (springeropen.com)
Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
The alignment of the gene orders was used to identify orthology relationships between the genes (since there are multiple copies of each type of rRNA and tRNA genes), instead of using traditional methods for identifying gene orthologies from sequence information. (biomedcentral.com)
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. (pacb.com)
Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. (pacb.com)
Draft genome sequence of Micromonospora sp. (pacb.com)
Complete genome sequence of Kosakonia oryzae type strain Ola 51(T). (pacb.com)
Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. (pacb.com)
The seven fragments sequenced are each approximately 450 - 500 base pairs long - so around the same length as the section of the 16S gene that we sequence for identification purposes. (rapidmicrobiology.com)
While Sanger technology is well suited to sequencing part, or all, of a single gene, when multiplied up to the requirement to sequence seven distinct loci, it does become a more expensive option. (rapidmicrobiology.com)
Hidden Markov Models are used to detect the conserved boundaries of the target region and to extract the interjacent sequence information (that is for example the hyper-variable regions of the rRNA gene or the internal transcribed spacer regions of the rRNA operon). (microbiome.ch)
Metaxa2 is an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets (e.g. shotgun metagenomes) and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. (microbiome.ch)
DNA sequence analysis of the O37 wb* region revealed that a novel approximately 23.4-kb gene cluster had replaced all but the approximately 4.2-kb right junction of the 22-kb O1 wbe region. (omicsdi.org)

By in silico analysis of 13â 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. (bvsalud.org)
The nucleotide sequences of maturaseK ( matK ) and ribulose-1, 5-bisphosphate carboxylase ( rbcL ) marker loci are commonly used in plant species identification. (biomedcentral.com)
The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. (biomedcentral.com)
The rationale for using this approach is that tRNA genes especially are very short (maximum length is around 90 nucleotides), and the sequences are highly conserved [ 12 ]. (biomedcentral.com)
0.5) selected from among all common variants discovered in genome sequences in this population. (biomedcentral.com)
MLST uses the sequences of internal fragments of seven essential, single-copy, housekeeping genes - i.e. genes required for processes that are essential for cell operation - to characterise isolates. (rapidmicrobiology.com)
Using data from reference databases and from full-length organelle and organism genomes, Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. (microbiome.ch)
The most functionally significant differences between the nucleotide sequences of CTX(calc)phi and CTX(ET)phi are located within the phages' repressor genes (rstR(calc) and rstR(ET), respectively) and their RstR operators. (omicsdi.org)
Since, in general, the sequences of the two alleles differ by about 1% genome wide17, we were able to identify many polymorphic sites that could be used to determine the histone acetylation pattern of each allele separately. (estme.org)

We introduce BOPAL , a new approach for the inference of evolutionary histories of rRNA and tRNA genes in bacteria, which is based on the identification of orthologous operons. (biomedcentral.com)
However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. (springer.com)
Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. (springer.com)
Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. (springer.com)
In fact, quantitative trait locus (QTL) approaches have successfully identified variation in candidate host genes that influence the RA of specific bacteria not only in Drosophila and mice but also in humans [ 22 ]. (biomedcentral.com)
The bacteria exhibit potent collagen-digesting properties, and genome sequencing has identified novel metalloprotease, collagenase and chitinase enzymes representing potential virulence factors. (biomedcentral.com)
Thisinvention relates, e.g., to the identification of non-essential genesof bacteria, and of a minimal set of genes required to supportviability of a free-living organism. (fullblog.com.ar)
It is only throughgene essentiality studies of bacteria that have near minimal genomesthat we bring empirical verification to the compositions ofhypothetical minimal gene sets. (fullblog.com.ar)
The Mollicutes, generically known as the mycoplasmas, are an excellentexperimental platform for experimentally defining a minimal gene set.These wall-less bacteria evolved from more conventional progenitors inthe Firmicutes taxon by a process of massive genome reduction.Mycoplasmas are obligate parasites that live in relatively unchangingniches requiring little adaptive capability. (fullblog.com.ar)
While more conventional bacteria withlarger genomes used in gene essentiality studies have on average 26% oftheir genes in paralogous gene families, M genitalium has only 6%(Table 1). (fullblog.com.ar)
Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca . Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. (uibk.ac.at)
The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. (uibk.ac.at)
At NCIMB, our microbial identification identifies bacteria by sequencing the first 500 bp of the 16S rRNA gene and searching for matches using the MicroSEQ database. (rapidmicrobiology.com)
However, phages mutate in an effort to bypass these defenses: a mutation in the region of the phage genome corresponding to, say, a blue spacer means that the phage can attack and escape the defense of bacteria with blue spacers (fuzzy green circle), but not bacteria with green, orange or pink spacers (red X inside a circle). (elifesciences.org)
Further experiments showed that compared to bacteria grown in liquid culture, bacterial cells in the resistant colonies had often acquired multiple spacers and were able to fight off phages with other mutations ( Figure 1 , right). (elifesciences.org)

Co-located quantitative trait loci for resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrid rootstock. (usda.gov)

Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. (biomedcentral.com)
Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. (biomedcentral.com)
Generally, uropathogenic E. coli (UPEC), newborn meningitis-associated E. coli (MNEC) as well as sepsis-associated E. coli (SEPEC) differ in their repertoire of virulence-associated genes from IPEC [ 1 ]. (biomedcentral.com)
To test this hypothesis, 300 V. cholerae isolates of non-O1 and non-O139 serogroups were screened for the presence of virulence genes and an epidemic genetic background by DNA dot blotting, IS1004 fingerprinting, and restriction fragment length polymorphism (RFLP) analysis. (omicsdi.org)

The cells are lysed and overlaid with a matrix, which forms protein complexes with the bacterial proteins. (wikipedia.org)
More than half of all human genes are alternatively spliced, so it is expected that alternative pre- mRNA splicing will be responsible for the identification of more than 90 percent of all human proteins. (genomicglossaries.com)
In the RT-qPCR, expression ratio demonstrated that the α-amylase gene of two different larval stages grown on both proteins treated leaves had significantly differentiated expression and was up-regulated in third instar larvae and down-regulated in fourth instar larvae compared to control. (potatobeetle.org)

The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. (biomedcentral.com)
Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach. (cdc.gov)
Most of thesestudies were done with human pathogens, often with the aim ofidentifying essential genes that might be used as antibiotic targets.Almost all of these organisms contain relatively large genomes thatinclude many paralogous gene families. (fullblog.com.ar)

In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit. (biomedcentral.com)
Comparing the rRNA and tRNA gene contents and organization in different species and inferring evolutionary scenarios allows to make predictions about core sets of tRNA genes, ancestral protein synthesis, ancestral codon usage and evolutionary rates. (biomedcentral.com)
In 2012, a new method was developed to infer evolutionary histories of rRNA and tRNA genes that was based on a gene order alignment approach and considered duplication and loss events [ 11 ]. (biomedcentral.com)

Now, in eLife, Nora Pyenson and Luciano Marraffini from the Rockefeller University report that the number of spacers each bacterial cell acquires depends on its local environment ( Pyenson and Marraffini, 2020 ). (elifesciences.org)

Since operons can move around in the genome but are rarely transformed (e.g. rarely broken into different parts), this approach allows for a better inference of orthologous genes in genomes that have been affected by many rearrangements, which in turn helps with the inference of more realistic evolutionary scenarios and ancestors. (biomedcentral.com)
In a comparisonof the first two bacterial genomes sequenced, Mushegian and Kooninprojected that the 256 orthologous genes shared by the Gram negativeHaemophilus influenzae and the Gram positive M. genitalium genomes area close approximation of a minimal gene set for bacterial life(2). (fullblog.com.ar)

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species. (usda.gov)
Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. (biomedcentral.com)

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies. (bornogastma.dk)
In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. (springer.com)
Moreover, these IBD-associated loci are mostly involved with immune system deregulation, a process which the gut microbiome has also been implicated in [ 18 ]. (springer.com)

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. (cdc.gov)

Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA-DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. (nih.gov)
Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark. (cdc.gov)
When it comes to isolates from pharmaceutical manufacturing environments, the focus is often on identifying unknown bacterial isolates at the species level. (rapidmicrobiology.com)
16S sequencing is quite a flexible approach and sequencing the full 16S gene, rather than just the first 500 bp, provides additional data that is sometimes required for accurate species-level identification, but can also be useful for highlighting differences between bacterial isolates. (rapidmicrobiology.com)

Nonetheless,some of the putatively disrupted genes, such as isoleucyl andtyrosyl-tRNA synthetases (MG345 & MG455), DNA replication gene dnaA(MG469), and DNA polymerase HI, subunit alpha (MG261) are thought toperform essential functions. (fullblog.com.ar)

Many genetic typing methods use DNA sequencing approaches, but others use specific gene probes, single-strand conformation polymorphism (SSCP), or restriction fragment length polymorphisms (RFLP). (cdc.gov)
Interestingly, a genome-wide association study has shown that noncoding polymorphisms in the de novo methyltransferase enzyme DNMT3A locus are associated with a higher risk for IBD, and for Crohn´s disease (CD) in particular 11 . (nature.com)
We first chose a single clone Rabbit polyclonal to MCAM (E9-3) and carried out anti-histone H3Ac ChIP, which was then assayed by PCR analysis of various V segments within the locus, using polymorphisms at restriction-enzyme binding sites to distinguish between the alleles (Fig. 1a). (estme.org)

Engineering the human genome: reflections on the beginning. (chop.edu)
See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)

The pipeline extends the R package ArchR for downstream analysis with added support to any eukaryotic species with an annotated reference genome. (umassmed.edu)

The gut microbiota, which has a complex community of a hundred trillion bacterial and archaeal cells comprising more than a thousand species, provides benefits to the host such as short-chain fatty acids (SCFA) and amino acids, metabolism of undigested carbohydrate, and stimulation of the immune system [ 19 , 20 ]. (springer.com)

Using methods such as differential media or genome sequencing, physicians and scientists can observe novel functions in organisms for more effective and accurate diagnosis of organisms. (wikipedia.org)
Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. (springer.com)
Shotgun metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. (allclearmister.com)
Metagenomics is the study of a collection of genetic material (genomes) from a mixed community of organisms. (allclearmister.com)

0.05) and were enriched for genes in mucosal immunity pathways. (biomedcentral.com)
An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota . (biomedcentral.com)

We focus on the methods and genes that have been most widely used for molecular epidemiologic analyses or have the greatest potential application. (cdc.gov)
However, the two loci ribulose-1,5-bisphosphate Carboxylase ( rbcL ) and maturase K ( matK ) gene regions are widely used in plant barcoding studies for phylogenetic analyses or species identification [ 10 , 11 ]. (biomedcentral.com)
OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. (umassmed.edu)
Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. (umassmed.edu)
analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)

Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. (biomedcentral.com)

In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. (biomedcentral.com)

A biological process that is crucial for gene expression in most animal life, including humans. (genomicglossaries.com)
Our findings provide evidence of host genetic influences on upper airway microbial composition in humans and implicate mucosal immunity genes in this relationship. (biomedcentral.com)
B. burgdorferi is transmitted to humans disequilibrium among genetic loci can result from several during the blood meal of an infected Ixodes tick, predomi- evolutionary and ecologic forces in addition to small popu- nantly Ixodes scapularis in North America ( 2 ). (cdc.gov)

Analyzing how these genes and operons evolve can help us understand what are the most common evolutionary events affecting them and give us a better picture of ancestral codon usage and protein synthesis. (biomedcentral.com)
There are several reasons for the interest in these operons, since those genes are fundamental for protein synthesis, and their numbers and organization can be used to better understand codon usage [ 10 ]. (biomedcentral.com)
q = 0.002), a long non-coding RNA that binds to peptidoglycan recognition protein 3 ( PGLYRP3 ) mRNA , a gene encoding a known antimicrobial protein. (biomedcentral.com)
proposed a 206 protein-coding gene core of aminimal bacterial gene set based on analysis of several free-living andendosymbiotic bacterial genomes (3). (fullblog.com.ar)
M. genitalium, a humanurogenital pathogen, is the extreme manifestation of this genomicparsimony, having only 482 protein-coding genes and the smallest genomeat -580 kb of any known free-living organism capable of being grown inpure culture(13). (fullblog.com.ar)
The1999 report by some of the present inventors on the essential microbialgene for M. genitalium and its closest relative, Mycoplasma pneumoniae,mapped ~2200 transposon insertion sites in these two species, andidentified 130 putatively non-essential M. genitalium protein-codinggenes or M. pneumoniae orthologs of M. genitalium genes. (fullblog.com.ar)
1999) Science 286, 2165-9), those authors estimatedthat 265 to 3,50 of the protein-coding genes of M. genitalium areessential under laboratory growth conditions(4). (fullblog.com.ar)
A higher protein intake correlated with a lower Bacteroides abundance and an altered abundance of several other bacterial taxa. (uni-frankfurt.de)
Considering the relevance of insect α-amylases and natural α-amylase inhibitors present in plants to protect against insect damage, we investigated the effect of white bean and rapeseed protein extracts on digestive α-amylase gene expression of the Colorado potato beetle, Leptinotarsa decemlineata (Say). (potatobeetle.org)

We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. (biomedcentral.com)

In order to clarify the biological and pharmacological mechanisms of O. sinensis , we carried out the genome sequencing of H. sinensis, anamorph of O. sinensis , for the first time, described the annotation and gene expression, and analyzed the complete sequencing data (Li et al. (springeropen.com)
For the prokaryote genome, you can create the files by using DFAST(DDBJ Fast Annotation and Submission Tool) . (nig.ac.jp)
For prokaryote genome, we strongly recommend that you should use DFAST (DDBJ Fast Annotation and Submission Tool) . (nig.ac.jp)
However, in case of a novel species that have not been reported so far, it is required to describe feature annotation against at least one genome as a representative. (nig.ac.jp)
When you submit a genome with annotation, it is required to reserve locus_tag prefix at the registration of BioSample . (nig.ac.jp)

This system protects the bacterial cell by taking a short length of DNA from the phage and inserting this 'spacer' into its own genome. (elifesciences.org)
If the bacterial cell becomes re-infected, the spacer allows the cell to recognize the phage and stop it from replicating by cutting and destroying its DNA. (elifesciences.org)
Phage populations, however, can also adapt and evade bacterial CRISPR-Cas systems. (elifesciences.org)
When growing in a liquid environment (left), individual bacterial cells usually acquire a single spacer that targets just one region of the wild-type (WT) phage (shown in grey). (elifesciences.org)

Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. (mbl.edu)

This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. (pacb.com)
We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. (uibk.ac.at)
These findings highlight a new level of Shikimic acid (Shikimate) immune system regulation that optimizes gene diversity. (estme.org)
The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. (allclearmister.com)

Neisseria gonorrhoeae , a Gram-negative bacterium, causes gonorrhea, the most common bacterial sexually transmitted infection (STIs), causing more than 106 million cases per year globally ( World Health Organization (WHO), 2012 ). (peerj.com)
Lyme disease, caused by the bacterium Borrelia burg- Genetic loci are found in perfect or near-perfect association dorferi , is the most common vector-borne disease in the in B. burgdorferi in the Northeast ( 9-12 ). (cdc.gov)

Seven chloroplast loci have been tested for plant species identification by The Consortium for the Barcode of Life (CBOL) Plant Working Group, where the suitability of matK and rbcL loci as a barcode was showed [ 12 ]. (biomedcentral.com)

A variety of typing methods have been used for Pneumocystis genetic analysis, and a large number of gene loci have been examined. (cdc.gov)
An analysis of 12 Bacillus genomes also showed that BOPAL performs just as well as other programs at building ancestral histories in a minimal amount of events. (biomedcentral.com)
Analysis of the ~7.1-Mb genome provides insight into this strain's biosynthetic potential, means of regulation, and response to coculturing conditions. (pacb.com)
Botting SK, Trzeciakowski JP, Benoit MF, Pritelivir research buy Salama SA, Diaz-Arrastia CR: Sample entropy analysis of cervical neoplasia gene-expression signatures. (bcl2signaling.com)
Fu LM, Fu-Liu CS: Multi-class cancer subtype classification based on gene expression signatures with reliability analysis. (bcl2signaling.com)
Tai F, Pan W: Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data. (bcl2signaling.com)
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. (umassmed.edu)
Metagenomics is defined as the direct genetic analysis of genomes contained with an environmental sample. (allclearmister.com)

High- fidelity mRNA amplification for gene profiling. (genomicglossaries.com)
An operon is basically a cluster of closely located genes (also called polycistronic genes) that share a single promoter and are transcribed simultaneously into a single polycistronic messenger RNA (mRNA). (biomedcentral.com)

They sequencedamplicons from inverse PCRs using that DNA as a template to identifythe transposon insertion sites in the mycoplasma genomes. (fullblog.com.ar)

Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. (yeastgenome.org)
Metagenomic shotgun sequencing Having reads of 400-500 base pairs length is sufficient to determine the species or strain of the organism where the DNA comes from, provided its genome is already known, by using for example a k-mer based taxonomic classifier software. (allclearmister.com)

Gordon GJ, Jensen RV, Hsiao LL, Gullans SR, Blumenstock JE, Ramaswamy S, Richards WG, Sugarbaker DJ, Bueno R: Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma. (bcl2signaling.com)

Imbalances or changes in the composition of bacterial communities can shift this relationship from symbiotic to pathogenic, a condition known as dysbiosis, which has been implicated in a variety of diseases [ 3 ]. (biomedcentral.com)

13 ] studied a total of 20 species belonging to the family Zingiberaceae from India by using nine plastids and two nuclear loci and reported that matK and rbcL aids in the determination of 15 species (75%) into monophyletic groups. (biomedcentral.com)

Ten peaks were obtained in the C. glutamicum ATCC 14067 genome including two new peaks related to three operons (RS_01910-RS_01915, RS_15995, and RS_16000). (frontiersin.org)

We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing. (bvsalud.org)
However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. (uibk.ac.at)
The density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. (biomedcentral.com)

Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. (springer.com)

It pores optimal that the Kaplan-Meier genes from empirical enzymes is the Kaplan-Meier materials transcribed on the applied administrator in the improved biglycan of Figure 4. (naturheilpraxis-gisbert-fussek.de)

V-RevComp is a Perl-based, high-throughput software tools that uses hidden Markov models to detect the conserved loci of rRNA genes in order to determine its orientation. (microbiome.ch)

To gain deeper insight into the biological and pharmacological mechanisms, we sequenced the genome of H. sinensis . (springeropen.com)
It has been reported that a large percentage (~ 30%) of these loci are common between CD and UC, showing involvement of common biological processes in both conditions [ 14 , 17 ]. (springer.com)
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies ( Molecular Function , Biological Process , and Cellular Component ), a reference, and an evidence code. (yeastgenome.org)
Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes. (yeastgenome.org)
This bacterial pathogen represents a prospective biological control agent for important nematode parasites. (biomedcentral.com)
Integrating biological knowledge with gene expression profiles for survival prediction of cancer. (bcl2signaling.com)

From our comparisons of BOPAL with other gene order alignment programs using simulated data, we have found that BOPAL infers evolutionary events and ancestral gene orders more accurately than other methods based on alignments. (biomedcentral.com)
This wealth of genetic information provides a great opportunity to study bacterial genome evolution, compare evolutionary rates between different genera, and study the prevalence, frequencies and average size of different evolutionary events. (biomedcentral.com)
Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. (cdc.gov)

In1999 some of the present inventors reported the first use of globaltransposon mutagenesis to experimentally determine the genes notessential for laboratory growth of M. genitalium{A). Since then therehave been numerous other experimental determinations of bacterialessential gene sets using our approach and other methods such as sitedirected gene knockouts and antisense RNA (5- 12). (fullblog.com.ar)
Methods: The individual taxonomic microbiota composition of fecal samples from 90 NAFLD patients and 21 healthy controls was analyzed using 16S rRNA gene sequencing. (uni-frankfurt.de)
He regulates more than 160 E22The methods( in both baseline and same numerous genes of methods, effects and prokaryotes, at free index zu das christlich koptische agypten in arabischer zeit tavo b 41 1 6 tubinger atlas des vorderen orients vigorously fully as to-date fuse) and more than 700 Basic measurements. (naturheilpraxis-gisbert-fussek.de)

Rearrangement of immune receptor loci in B and T lymphocytes takes place in an ordered developmental manner using transcription factors and regulatory elements to open up and turn on the rearrangement process at each individual cluster during its specific stage of differentiation1,2,3,4,5. (estme.org)

Organisms2

Chemicals and Drugs7

Analytical, Diagnostic and Therapeutic Techniques and Equipment6

Phenomena and Processes31

Disciplines and Occupations1

Technology, Industry, Agriculture1

Information Science4

Whole genome13

Ribosomal2

Strains10

Polysaccharide utilization loci2

Genomic6

Sequence20

Sequences9

Bacteria15

Quantitative trai1

Virulence4

Proteins3

Pathogens3

TRNA genes3

20201

Orthologous2

High-quality genome2

Microbiome3

Hypervariable regions1

Isolates4

Subunit1

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Human genome2

Reference Genome1

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Bacteroidetes1

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Protein9

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