Whole-genomeRegularly interspersed short palindromicGenome sequencePhylogeneticCompletely sequencedRepeatsStrainsAmino acidNucleic acidsCRISPRRetrotransposonsArtificialLociPhagesGenomesTRANSPOSABLE ELEMENTSIntronsCopiesMechanismsGeneGenomicPrimersBase pairsInsertion sequenceGeneticReadsTranscriptionPolymeraseTarget sequenceMolecularElementsDrugsAnalysisSpecificCompleteDataDirectlyDegree
Whole-genome7
- Bacterial DNA was subjected to macroarray-based spoligotyping ( 8 ) and whole-genome sequencing on the MiSeq platform (Illumina, San Diego, CA, USA). (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)
- In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains ofM. (9lib.org)
- tuberculosis strains in whole genome sequencing data. (9lib.org)
- The third report described Genetic Analysis and isolation from a child's hand with multibacterial synergistic Whole-Genome Sequencing gangrene ( 6 ). (cdc.gov)
- Using whole-genome sequencing of OS, we found features of TP53 intron 1 rearrangements suggesting a unique mechanism correlated with transcription. (oncotarget.com)
Regularly interspersed short palindromic3
- To generate healthy patient-derived cells, mutations might be repaired with new gene-editing technology based on the bacterial system of clustered regularly interspersed short palindromic repeats (CRISPR)/Cas9, thereby yielding grafts that require no patient immunosuppression. (nature.com)
- Although the original disease-causing mutation would still be present in patient iPSCs, precise mutation correction is possible through gene editing techniques adapted from the bacterial clustered regularly interspersed short palindromic repeats (CRISPR)/Cas9 system 3 . (nature.com)
- Three types of endonucleases , namely ZFNs (zinc finger nucleases), TALENs (transcription activator-like effector nucleases ), and the CRISPR (clustered regularly interspersed short palindromic regions) associated (Cas9) system have been predominantly utilized for gene editing. (ac.ir)
Genome sequence9
- 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)
- 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)
- 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)
- 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)
Phylogenetic4
- On the basis of 24 mycobacterial interspersed repetitive unit variable number tandem repeats clustering and robust phylogenetic single-nucleotide polymorphisms, SIT264 and SIT266 isolates are assigned to the Latin American-Mediterranean lineage of M. tuberculosis ( 2 ). (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)
Completely sequenced2
- 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)
Repeats7
- 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)
- 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)
- BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
- TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (lookformedical.com)
- Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats). (lookformedical.com)
- 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)
- Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. (oup.com)
Strains1
- 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)
Amino acid1
- 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)
Nucleic acids1
- The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)
CRISPR1
- CRISPR gRNAs were selected to minimize the off-target profile and to maximize the degree of homology with a target sequence directly centered on the mutation site. (nature.com)
Retrotransposons3
- Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. (edu.au)
- Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. (bvsalud.org)
- Here we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at long interspersed nuclear element (LINE) retrotransposons (also known as LINE-1s or L1s) that are theoretically transcribed in the head-on direction with replication fork movement. (bvsalud.org)
Artificial5
- Development of comparative physical gene maps for cattle, sheep, goat and deer by fluorescence in situ hybridisation (FISH) using ovine bacterial artificial chromosome (BAC) clones. (edu.au)
- 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)
- 10. Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF. Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors. (ac.ir)
Loci2
- SNP typing takes advantage of nucleotide changes in specific single-copy genes-i.e., gyrA, gyrB, groEL1, sodA, rpsA , and hsp65 -( 10 - 12 ) or chromosomal loci-i.e., 16S−23S rDNA internal transcribed spacer (ITS)-( 13 ) to use them as biomarkers for subspecies differentiation. (frontiersin.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)
Phages2
- The substantial terminase subunit which is a structural protein is together with the portal protein viewed as essentially the most universally conserved gene sequence in phages, consequently they are good possibilities to assist in phage classification. (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)
Genomes4
- Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. (bvsalud.org)
- 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)
- 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 ELEMENTS2
- There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (lookformedical.com)
- DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (lookformedical.com)
Introns1
- The coding regions or exons are interspersed along with the introns in the primary transcript. (cox-inhibitors.com)
Copies4
- Despite the gene's repetitive and GC-rich sequences, 13% of RPGR gene copies showed mutation correction and conversion to the wild-type allele. (nature.com)
- The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (lookformedical.com)
- Sequences of DNA or RNA that occur in multiple copies. (lookformedical.com)
- TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (lookformedical.com)
Mechanisms4
- 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)
Gene2
- Sequence homology is an indication of the genetic relatedness of different organisms and gene function. (lookformedical.com)
- Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)
Genomic2
- 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)
- Conclusion This is often the primary genomic evaluation of bacteriophages that infect the bacterial pathogen E. ictaluri. (hivprotease-signal.com)
Primers1
- Electronic supplementary material Additional file 1: The sequences of PCR primers. (cox-inhibitors.com)
Base pairs4
- 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)
- Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)
- Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. (lookformedical.com)
- The 6-9 base pairs that flank the sequence also influence selection of the insertion site. (wikimili.com)
Insertion sequence1
- Tn 10 has a composite structure and it is composed of a pair of insertion sequence elements (IS 10 ) flanking five genes. (wikimili.com)
Genetic1
- 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)
Reads2
- The short sequencing reads were subjected to analysis by using the SpoTyping program ( https://github.com/xiaeryu/SpoTyping ) ( 9 ) and the TGS-TB online tool ( https://gph.niid.go.jp/tgs-tb/ ) ( 10 ) to deduce their spoligoprofile. (cdc.gov)
- 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)
Transcription2
- The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
- 6. Miller J, Mc Lachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. (ac.ir)
Polymerase1
- Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (lookformedical.com)
Target sequence1
- This insertion would disrupt a target sequence for biotin-labeled DRa primer, thus preventing spacer 8 from amplification. (cdc.gov)
Molecular1
- Next-generation sequencing (NGS) technology is becoming more affordable and is increasingly being widely used for high-resolution molecular epidemiology of tuberculosis. (cdc.gov)
Elements1
- There are two classes of interspersed repetitive elements. (edu.au)
Drugs1
- 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)
Analysis3
- A detailed secondary metabolism analysis and structure verification of the main ingredients were performed, and the biosynthesis pathways of seven ingredients (mannitol, cordycepin, purine nucleotides, pyrimidine nucleotides, unsaturated fatty acid, cordyceps polysaccharide and sphingolipid) were predicted and drawn. (springeropen.com)
- Development of PCR and sequencing techniques for DNA and RNA diagnostics, RFLP analysis and direct carrier testing. (edu.au)
- 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)
Specific1
- The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. (nature.com)
Complete1
- 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)
Data1
- M. tuberculosis NGS data were deposited in the National Center for Biotechnology Information Sequence Read Archive (project no. (cdc.gov)
Directly1
- Long-read RNA sequencing technologies, including Oxford Nanopore and PacBio, can directly sequence relatively long transcripts, thus providing the opportunity to examine full-length LINE transcripts. (bvsalud.org)
Degree1
- 1% identical with the nucleotide degree. (hivprotease-signal.com)