Species bacterial interspersed repetitive sequences. Medical search. Frequent questions

However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (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)
First, the complete genome sequence of the tubercle bacillus was deciphered. (tuberculosistextbook.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)
japonica reference genome sequence. (biomedcentral.com)
The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. (biomedcentral.com)

Using pncA-1F 5-GGC CGC GAT GAC ACC TCT- phylogenetic tree exist, the dassie and oryx bacilli, 3, pncA1-R 5-GCC GCA GCC AAT TCA GCA GT-3, causative agents of tuberculosis in the animal species after pncA-2F 5-CGA AGC GGC GGA CTA CCA TCA CG-3, which they are named. (cdc.gov)
however, their exact position has not To assess the specifi city of the Rv2042 38 GGC mutation, been established with valid phylogenetic markers, such as we screened 2 isolates of all M. tuberculosis complex (sub) large genomic deletions or single nucleotide polymorphisms species and 2 isolates of all M. tuberculosis groupings, on (SNPs). (cdc.gov)
A phylogenetic for a case of multi-bacterial synergistic gangrene. (cdc.gov)
The amino acid sequences of one of many conserved structural pro teins likewise as among the non structural proteins have been selected for phylogenetic evaluation. (hivprotease-signal.com)
Phylogenetic analysis primarily based to the significant terminase subunit amino acid sequence plus the DNA polymerase I amino acid sequence of eiAU reveal that phages eiAU, eiDWS, and eiMSLS were most much like phage that infect other enterobacteria and Sodalis glossinidius. (hivprotease-signal.com)

A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. (who.int)
The env genes contain a cis-acting RNA target sequence for the rev protein (= GENE PRODUCTS, REV ), termed the rev-responsive element (RRE). (lookformedical.com)
a , Maximum-likelihood tree using concatenated protein sequences of 100 genes randomly selected from 4,694 Fusarium orthologous genes that have clear 1:1:1:1 correlation among the Fusarium genomes and have unique matches in Magnaporthe grisea , Neurospora crassa and Aspergillus nidulans . (nature.com)
Only about 10,000 of these genes have been annotated by the sea urchin sequencing team. (blogspot.com)
Of these, 3,114 were single genes confined to a single species. (blogspot.com)
Tn 10 has a composite structure and it is composed of a pair of insertion sequence elements (IS 10 ) flanking five genes. (wikimili.com)
With the completion of the human genome and the genomes of other species, we have a glimpse of many more genes than we ever had before to study. (pharmaceuticalintelligence.com)

Several molecular typing methods have been developed to differentiate between M. avium subspecies and strains, such as single nucleotide polymorphism (SNP) typing and mini-satellite sequence analysis-mycobacterial interspersed repetitive-unit variable-number tandem repeats (MIRU-VNTR) ( 5 ). (frontiersin.org)
Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. (oup.com)

We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. (biomedcentral.com)
Our strategy is to develop bacterial artificial chromosome (BAC)-end sequence (BES) physical frameworks of the ten genome types of Oryza and align them to the reference sequence. (biomedcentral.com)
The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. (biomedcentral.com)

16S rRNA gene was completely sequenced. (cdc.gov)
Both genomes have been completely sequenced [ 17 , 18 ] and serve as the reference sequences for the major monocot and dicot plant lineages. (biomedcentral.com)

In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California. (bvsalud.org)
Taxonomic classification of those E. ictaluri specific phages must rely on a synthesis of morphological and genomic details, taking into consideration that phage evolution continues to be profoundly directed by lateral gene transfer, and that a rational hierarchical technique of phage classification really should be based within the degree of DNA and protein sequence identity for several genetic loci. (hivprotease-signal.com)
The general genomic organization of the three new phages is shared by several members in the Siphoviridae loved ones of phages sequenced to date, and is supported through the previously described morphol ogy of these phages. (hivprotease-signal.com)
Conclusion This is often the primary genomic evaluation of bacteriophages that infect the bacterial pathogen E. ictaluri. (hivprotease-signal.com)
Different variants of FISH can be used to retrieve information on genomes from (almost) base pair to whole genomic level, as besides only second and third generation sequencing approaches can do. (frontiersin.org)

Here we present the comparative analysis of the genomes of these three species. (nature.com)
The predicted gene products with sequence similarity amongst the eiAU and SSL 2009a phage genomes include things like the putative small tail proteins tail tape mea certain, major tail proteins, major capsid proteins, head morphogenesis, phage terminase tiny subunit, and the phage terminase large subunit. (hivprotease-signal.com)
Interestingly, other struc tural proteins which includes the host specificity proteins, the tail assembly proteins, and specifically the tail fiber baseplate protein which has become suggested for exclusion in any sequence based mostly phage taxonomy scheme are certainly not shared in between the 2 genomes. (hivprotease-signal.com)
Transposable elements pervading mammalian genomes mostly originate from retrotransposons, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) ( 2 , 3 ). (rna-mediated.com)
Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. (blogspot.com)

In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains ofM. (9lib.org)
Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such asM. (9lib.org)
tuberculosis strains in whole genome sequencing data. (9lib.org)
Species of GAMMARETROVIRUS , containing many well-defined strains, producing leukemia in mice. (lookformedical.com)
Kolb J, Hillemann D, Möbius P, Reetz J, Lahiri A, Lewin A, Rüsch-Gerdes S, Richter E. Genetic characterization of German Mycobacterium avium strains isolated from different hosts and specimens by multilocus sequence typing. (fz-borstel.de)

MIRU-VNTR analysis, on the other hand, uses mini-satellite sequences (tandem repeats of 10-100 nucleotides) dispersed at multiple loci in the bacterial genome. (frontiersin.org)
bacterial interspersed repetitive units-variable-number tandem repeat (MIRU-VNTR) typing, as described ( 7 , 8 ). (cdc.gov)

Neither has been validly described and pncA-2R 5-CCC CAC CTG CGG CTG CGA ACC- as separate taxa, nor have they been associated with disease 3 primers, we partially sequenced Rv2042c , Rv2044c , and in humans ( 1-4 ). (cdc.gov)
BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
Electronic supplementary material Additional file 1: The sequences of PCR primers. (cox-inhibitors.com)

In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. (cdc.gov)

Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date. (biomedcentral.com)

Introns sequences account for about 30% of the genome. (blogspot.com)
The coding regions or exons are interspersed along with the introns in the primary transcript. (cox-inhibitors.com)

Whole-genome sequencing (WGS) of M. tuberculosis and related mycobacteria is now routine, allowing comparisons across time and space. (jci.org)

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study. (biomedcentral.com)
Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. (bvsalud.org)
This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. (bvsalud.org)
Comparative genomics is a powerful tool for unraveling the evolutionary history and gene functionality of related species. (biomedcentral.com)
Therefore, comparative genomics of wild and domesticated Oryza species may not only provide useful materials for breeding, but will also shed light on the evolution and domestication of cultivated rice. (biomedcentral.com)

Previously, the genome of the cereal pathogen Fg was sequenced and shown to encode a larger number of proteins in pathogenicity related protein families compared to non-pathogenic fungi, including predicted transcription factors, hydrolytic enzymes, and transmembrane transporters 5 . (nature.com)
We sequenced two additional Fusarium species, Fv , a maize pathogen that produces fumonisin mycotoxins that can contaminate grain, and F. oxysporum f.sp. (nature.com)

All colonies, regardless of the nucleotide sequence of rpsA , were found to be sensitive to all of the drugs tested except for ethambutol. (frontiersin.org)

To gain deeper insight into the biological and pharmacological mechanisms, we sequenced the genome of H. sinensis . (springeropen.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)
The bacterial immunity proteins Im7 and Im9 fold with mechanisms of different kinetic complexity. (shengsci.com)
Wrong eukaryote is that the economic novelty notion with lunar sequences will demonstrate the other Mechanisms apparently Supported with border sentence. (be-mindful.de)

Therefore, the opposite strand is sequenced discontinuously as both replication forks approach the center of the transposable element. (wikipedia.org)
Here we report the construction of 12 BAC/BES framework physical maps derived from these libraries and an analysis of the BESs in terms of transposable element, simple sequence repeat (SSR), microRNA (miRNA), and single nucleotide variation (SNV) content. (biomedcentral.com)
Tn 10 is a transposable element , which is a sequence of DNA that is capable of mediating its own movement from one position in the DNA of the host organism to another. (wikimili.com)
A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. (wikimili.com)

DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. (lookformedical.com)

After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. (bvsalud.org)

We sequenced Fv strain 7600 and Fol strain 4287 (Methods, Supplementary Table 1 ) using a whole-genome shotgun approach and assembled the sequence using Arachne ( Table 1 , ref. 6 ). (nature.com)

These bacilli most likely constitute a separate sequence is stored in GenBank (accession no. (cdc.gov)
Interspersed repetitive elements constitute 41.2% of the genome. (bvsalud.org)

purification of antibodies to bacterial antigens by an immunoadsorbent and a method to quantify their reaction with insoluble bacterial targets. (liverpool.ac.uk)

Whole genome comparative platforms within a genus are still in their infancy, with the most notable exception being the generation of whole genome shotgun assemblies of 12 Drosophila species that span an evolutionary time frame of approximately 60 million years [ 16 ]. (biomedcentral.com)

Trout farming has been successful in North America, the species native area, as well as in many other regions, including Chile and a number of European countries where rainbow trout had been introduced since the 19th century. (biomedcentral.com)

Aside from their differences in host adaptation and specificity, Fusarium species also vary in reproductive strategy. (nature.com)

Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)

Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. (who.int)
In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. (who.int)
The third report described Genetic Analysis and isolation from a child's hand with multibacterial synergistic Whole-Genome Sequencing gangrene ( 6 ). (cdc.gov)

Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. (who.int)

In plants, invertebrate species and vertebrates, DNA methylation has been described as an important epigenetic silencing mechanism. (prolekarniky.cz)

This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. (bvsalud.org)

Simultaneously the donor strand is ligated to the target strand after cleavage leaving a single strand overhang on either end of the target sequence. (wikipedia.org)
The 5 to 9 base pair overhang is left on either side of the target sequence allowing it to join to its target sequence in either orientation. (wikipedia.org)

Throughout these studies, the author described a new subfamily (Crocanthinae Park, 2015), 32 new genera, and over 540 new species of the family. (mdpi.com)
In this article, a historical review for the taxonomic works of the family is briefly summarized, with a comparison of the number of genera/species of each subfamily in each region of the world. (mdpi.com)

Species of the genus LENTIVIRUS, subgenus primate immunodeficiency viruses (IMMUNODEFICIENCY VIRUSES, PRIMATE), that induces acquired immunodeficiency syndrome in monkeys and apes (SAIDS). (lookformedical.com)

Snakes in the family Colubridae include over 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. (bvsalud.org)
Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. (bvsalud.org)

Fusarium species are among the most important phytopathogenic and toxigenic fungi. (nature.com)
Fusarium species are among the most diverse and widely dispersed plant-pathogenic fungi, causing economically important blights, root rots or wilts 1 . (nature.com)

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)

In this study, we sequenced the complete genome of Nautilus pompilius in the hope of providing a critical reference for the evolution of cephalopods. (nature.com)

Unlike other Plasmodium species, P. falciparum can be cultured in the lab, which facilitates its study 1. (repositorio-indicasat.org.pa)
The first paper, published in 1978, followed the earlier work of McKee in general aspect, except that Brand included underwater sand and several species in his study. (educatetruth.com)

Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. (wikipedia.org)
The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)
Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA. (blogspot.com)

The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. (biomedcentral.com)

To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. (bvsalud.org)

The target molecule as a result contains the inserted element flanked by the 5 to 9 base pair sequences. (wikipedia.org)
The 6-9 base pairs that flank the sequence also influence selection of the insertion site. (wikimili.com)

Rainbow trout ( Oncorhynchus mykiss ) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. (biomedcentral.com)

The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. (nature.com)
Avian MHC organization is of particular interest because the chicken Gallus gallus , the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. (biomedcentral.com)

Anatomy20

Organisms21

Diseases5

Chemicals and Drugs50

Analytical, Diagnostic and Therapeutic Techniques and Equipment32

Phenomena and Processes118

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture3

Information Science7

Health Care3

Genome sequence10

Phylogenetic5

Genes7

Mycobacterial2

Artificial chromosome3

Completely sequenced2

Genomic6

Genomes5

Strains5

MIRU-VNTR2

Primers3

Isolates1

Simple sequenc1

Introns2

Tuberculosis1

Amino acid1

Genomics5

Pathogen2

Nucleotide sequence1

Mechanisms4

Transposable element4

Proteins1

Fungal1

Strain1

Constitute2

Quantify1

Whole-genome1

North America1

Host adaptation1

Approximately1

Analysis3

Approaches1

Vertebrates1

Environments1

Target sequence2

Genera2

Genus1

Diversity2

Fungi2

Vaccine1

Complete1

Study2

Elements3

Significant1

High quality1

Base2

Widely1

Specific2