• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. (ox.ac.uk)
  • Gene drives can be used to bias genetic inheritance in favor of rapidly spreading, self-destructive genes - such as those that disrupt fertility - and could be an environmentally friendly and cost-effective way to suppress populations of disease-spreading insects. (universityofcalifornia.edu)
  • a CRISPR is a small length of DNA with a repeating and reversing sequence of base pairs (the pieces that make up genetic code). (reverserett.org)
  • Yeast genetic manipulation is far more precise than can be achieved in crop plants, and the genes in yeast have been precisely altered by mutations. (i-sis.org.uk)
  • Although genes can be altered precisely to avoid collateral genetic damage, changing a metabolic network will still result in unexpected metabolic effects. (i-sis.org.uk)
  • For example, instead of breeding for many years to move a disease resistance gene from a wild strawberry into a modern strawberry, gene editing allows a direct introduction of the genetic information. (ufl.edu)
  • By using CRISPR technology, these genes or gene variants can be moved into desirable genetic backgrounds that can be further moved via conventional crossing in later generations. (ufl.edu)
  • This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
  • Gene duplication is long recognized as a potential source of genetic innovation ( Ohno, 1970 ). (elifesciences.org)
  • 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)
  • We have developed a powerful computational framework for revealing the genetic basis of bacterial traits by correlating the inheritance patterns of genes and phenotypes across all the sequenced bacterial genomes (Jim et al. (columbia.edu)
  • From an experimental perspective, we have developed a whole-genome fitness profiling method using microarray-based genetic footprinting (Girgis et al. (columbia.edu)
  • To do this, we have developed an experimental system that quantifies the degree to which every genetic locus contributes to antibiotic sensitivity. (columbia.edu)
  • By applying this framework to mild resistance, we have identified a large number of loci whose genetic perturbations significantly affect antibiotic sensitivity. (columbia.edu)
  • 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)
  • Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. (asm.org)
  • The identification of loci for agronomic traits and their genetic characterisation are crucial for breeding new varieties. (mdpi.com)
  • These Cas9 strains can be used to develop split-gene drives which are a form of gene-drive by which the Cas9 and the guide RNA's are inserted at separate genomic loci and depend on each other for spread. (universityofcalifornia.edu)
  • The simplicity of programming the CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on a genome-wide scale. (ewha.ac.kr)
  • We describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. (cdc.gov)
  • Libraries of large fragments, mainly bacterial artificial chromosome libraries, are mostly used in genomic projects. (wikipedia.org)
  • To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. (ox.ac.uk)
  • Introduction of a 1.1 Mb fragmented yeast artificial chromosome (YAC) mapping to this region completely suppresses the tumorigenic properties of a human NSCLC cell line, A549. (elsevierpure.com)
  • To further localize the gene(s) responsible for this partial suppression, a bacterial artificial chromosome (BAC) and P1-based artificial chromosome (PAC) contig was constructed, completely spanning the candidate region. (elsevierpure.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)
  • We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). (peerj.com)
  • The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. (biomedcentral.com)
  • Our understanding of the ecology of oral microbes surged thanks to the Human Microbiome Project (HMP) [ 20 ], which generated extensive sequencing data from 9 oral sites sampled from 200 healthy individuals and over 300 reference genomes for bacteria isolated from the human oral cavity. (biomedcentral.com)
  • or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
  • 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)
  • 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)
  • This study also identified 43 growth-impairing inserts carrying multiple loci targeting 105 genes, of which 25 have homologs reported as essential in other bacteria. (biomedcentral.com)
  • In both Gram-positive and Gram-negative bacteria, 'competence' for DNA uptake requires the coordinated action of rough-ly two dozen genes ( including some with regulatory func-tions ) organized within several operons. (asmblog.org)
  • The bacteria exhibit potent collagen-digesting properties, and genome sequencing has identified novel metalloprotease, collagenase and chitinase enzymes representing potential virulence factors. (biomedcentral.com)
  • The bacteria is gram negative, rod shaped and aerobic belongs to the bacterial family of pseudomonadanceae. (ukessays.com)
  • Next steps should be undertaken to identify the regulatory sequences that can be used to express the guide RNAs from the genome, and once these sequences are identified developing gene drives in the species should be turnkey," Akbari said. (universityofcalifornia.edu)
  • In parallel, multiple technologies and manual finishing were used to produce an 85-Mb reference genome assembly from the more readily available mouse parasite species T. muris (Online Methods and Supplementary Note ). (nature.com)
  • Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species. (peerj.com)
  • Comparative genomics is a powerful tool for unraveling the evolutionary history and gene functionality of related species. (biomedcentral.com)
  • 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)
  • 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)
  • and 16 were "novel" essential genes with no homologs reported to have an essential role in other bacterial species. (biomedcentral.com)
  • The picture is si-milar in Vibrio - 'similar' refers to a great deal of protein homology among the numerous components in various species, despite vastly different regulatory circuits - for which the present model for competence involves 19+ genes, and, as core components: 1. (asmblog.org)
  • This would result in many many mutations as plant genomes are easily in the range of 1,000,000,000 Bases (Gbases) Name some sources of mistakes which could eventually lead to mutations: tautomeric structures of DNA bases cell internal metabolites, e.g. reactive oxygen species external chemicals e.g. alkylation agents radiation e.g. (usadellab.org)
  • DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. (biomedcentral.com)
  • The nucleotide sequences of maturaseK ( matK ) and ribulose-1, 5-bisphosphate carboxylase ( rbcL ) marker loci are commonly used in plant species identification. (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)
  • 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)
  • It mainly involves discrimination of species through standardized molecular marker gene and is gaining support from the taxonomists as well. (biomedcentral.com)
  • 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)
  • 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)
  • 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)
  • Using an innovative DNA hybridisation capture protocol, the DNA barcode of the lectotype of (Fabricius, 1794) was partially recovered for comparison with the 229 DNA barcode sequences of specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. (unige.ch)
  • CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is one form of gene editing that can be used to precisely modify a gene of interest without otherwise compromising the favorable traits of an elite variety (Rani et al. (ufl.edu)
  • Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. (asm.org)
  • All isolates contained a closely related plasmid (pKPC2) harboring bla KPC-2 , a K. pneumoniae carbapenemase gene, and had a hypervirulent background of capsular serotypes K1, K2, and K20. (cdc.gov)
  • Intrapatient isolates were also able to acquire additional antimicrobial drug resistance genes when inside human bodies. (cdc.gov)
  • 2,200 K. pneumoniae genomes, distinct evolutionary patterns of horizontal gene transfer were observed in MDR isolates versus hypervirulent isolates ( 17 ). (cdc.gov)
  • The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. (uni-wuerzburg.de)
  • 26.2% of isolates in the collection contained either a TEM-1 or ROB-1 -lactamase gene, including 88.8% of ampicillin-resistant isolates. (cdc.gov)
  • Meningococcal isolates (N = 1,514) obtained from these evaluations were characterized for capsule biosynthesis by whole-genome sequencing (WGS). (cdc.gov)
  • Approximately half [732 (48.4%)] of isolates could not be genogrouped because of the lack of any serogroup-specific genes. (cdc.gov)
  • The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. (asm.org)
  • The mutant oligonucleotide is annealed to the wild type gene in the plasmid, which is amplified to produce plasmids carrying the gene with the specific mutations. (i-sis.org.uk)
  • Genomes were sequenced to identify genes and mutations known to be associated with reduced susceptibility to clinically relevant drugs. (cdc.gov)
  • among these, 79% contained mosaic penA gene mutations. (cdc.gov)
  • Strikingly, we find dozens of loci in which null mutations dramatically increase resistance (Girgis et al. (columbia.edu)
  • Via positional cloning, we show that mutations in a zebrafish LTCC encoding gene, cav1.3a , underlie the auditory-vestibular defects of gemini ( gem ) circler mutants. (jneurosci.org)
  • First, we used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells. (ewha.ac.kr)
  • Therefore comparative genomic analysis of T . equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T . equi relative to sequenced apicomplexan parasites. (biomedcentral.com)
  • Certain coding sequences vary significantly between different haplotypes, making them candidates for functional and disease-association studies. (ox.ac.uk)
  • These rapid adaptations in fungi provide excellent models for studying general processes of eukaryotic genome evolution, including the functional and ecological impact of horizontal gene transfer 1 and changes in metabolism 2 . (nature.com)
  • Together, these genomes and associated functional data elucidate key aspects of the molecular host-parasite interactions that define chronic whipworm infection. (nature.com)
  • The reason is that because genes are connected in a complex functional network, one gene cannot be altered without affecting many others [3] ( Living with the Fluid Genome , I-SIS Publications). (i-sis.org.uk)
  • The fact is that whenever hemoglobin is found in the living world, it's always fully functional and completely optimized to the needs of the specific creature in which it resides. (icr.org)
  • Improved methods are needed for the knockout of individual genes in genome-scale functional screens. (ewha.ac.kr)
  • Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. (uibk.ac.at)
  • Such datasets can be analysed using the same phylogenetic inference tools as single loci datasets. (biomedcentral.com)
  • CRISPR/Cas9-mediated disruption of genes associated with eye pigment caused eye color to change from black to white. (universityofcalifornia.edu)
  • The addition of Cas9 will enable the use of the CRISPR gene editing tool to make efficient, targeted changes to the mosquitoes' DNA. (universityofcalifornia.edu)
  • Their long-term goal is to use Cas9-expressing mosquitoes together with another technology - called gene drives - to insert and spread genes that suppress the insects while avoiding the resistance that evolution would typically favor. (universityofcalifornia.edu)
  • Akbari and colleagues developed transgenic mosquitoes that stably express a bacterial Cas9 enzyme in the germline, enabling highly efficient genome editing using the CRISPR system. (universityofcalifornia.edu)
  • We show that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells. (ewha.ac.kr)
  • We observe a high level of consistency between independent guide RNAs targeting the same gene and a high rate of hit confirmation, demonstrating the promise of genome-scale screening with Cas9. (ewha.ac.kr)
  • p. 84 , published online 12 December) used the bacterial CRISPR/Cas9 system to power-screen protocols that avoid several of the pitfalls associated with small interfering RNA (siRNA) screens. (ewha.ac.kr)
  • We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)
  • To date, various genome-scale loss-of-function screening methods have been developed, including approaches employing RNA interference 1 , 2 and the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) adaptive immune system 3 , 4 . (cdc.gov)
  • Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.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)
  • Difficulties with this approach may arise if orthologous genes cannot be identified with certainty or if the combined sequence length is still too small to give well-resolved trees. (biomedcentral.com)
  • CRISPR works like a pair of molecular scissors, cutting out and replacing specific DNA sequences based on a ribonucleic acid (RNA) guide. (universityofcalifornia.edu)
  • Preceding a CRISPR sequence are cas genes which make enzymes that copy the foreign DNA sequence and insert it as small fragments into the bacterial genome as new spacers. (reverserett.org)
  • This approach is known as 'CRISPR' gene editing. (ufl.edu)
  • We anticipate that, over the next decade, CRISPR and other gene editing techniques will be used to rapidly develop elite strawberry varieties with improved disease resistance, fruit quality, and other valuable attributes. (ufl.edu)
  • What is CRISPR gene editing? (ufl.edu)
  • Does CRISPR gene editing = transgenic technology? (ufl.edu)
  • CRISPR, on the other hand, can be used to precisely change DNA sequence, switching it from one naturally occurring variant to another naturally occurring variant. (ufl.edu)
  • We published another article about CRISPR gene editing in crop improvement ( https://edis.ifas.ufl.edu/publication/HS1334 ). (ufl.edu)
  • Right here, we display that the CRISPR-MAD7 system can be utilized for genome enhancing and acknowledges T-rich PAM sequences (YTTN) in crops. (trancheproject.org)
  • Furthermore, we present that MAD7 can be utilized for multiplex gene enhancing and that it's efficient in producing indels when mixed with different CRISPR RNA orthologs. (trancheproject.org)
  • Furthermore, gene targeting by the CRISPR system is more precise and appears to produce substantially fewer off-target effects than existing methods. (ewha.ac.kr)
  • Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
  • Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. (biomedcentral.com)
  • On the basis of whole-transcriptome analyses, we identify many genes that are expressed in a sex- or life stage-specific manner and characterize the transcriptional landscape of a morphological region with unique biological adaptations, namely, bacillary band and stichosome, found only in whipworms and related parasites. (nature.com)
  • 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)
  • Therefore, we performed de novo transcriptome sequencing of A. maculatum appendix and male floret tissue collected during- and post-anthesis, from ten natural populations across Europe. (unige.ch)
  • Despite these examples, the lack of specific evolutionary trends in reported cases of lateral gene transfer in eukaryotes has led to the view of ancient, sporadic and isolated events with relatively little global impact on eukaryotic kingdoms, rather than a more frequently and widely occurring phenomenon. (nature.com)
  • The main problem here is the reliability of evolutionary reconstructions based on sequence data. (icr.org)
  • The fatal outbreak that occurred in a hospital in China in 2016 was caused by a carbapenem-resistant hypervirulent K. pneumoniae strain that had acquired a virulence plasmid by a classic sequence type (ST) 11 strain ( 16 ). (cdc.gov)
  • This technique, also known as "directed sequencing," employs a series of Sanger sequencing reactions to either confirm the reference sequence of a known plasmid or PCR product based on the reference sequence (sequence confirmation service) or to discover the unknown sequence of a full plasmid or PCR product by designing primers to sequence overlapping sections (sequence discovery service). (wikipedia.org)
  • The DNA of interest may be a plasmid insert, a PCR product or a fragment representing a gap when sequencing a genome. (wikipedia.org)
  • The quick change kit provides the tools for changing the wild type gene carried on a bacterial plasmid. (i-sis.org.uk)
  • 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)
  • We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. (frontiersin.org)
  • To achieve this goal, the plant biology community is engaged in a concerted effort to functionally characterize all plant genes in both model plants using approaches including genetics, transgenetics, and comparative genomics. (biomedcentral.com)
  • Comparative genomic analysis of T . equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp . (biomedcentral.com)
  • Akbari said these strains represent the first step toward using gene drive systems to control mosquito populations and reduce the diseases they spread. (universityofcalifornia.edu)
  • Highly duplicated and polymorphic regions of the human genome such as the MHC are, however, somewhat refractory to some whole-genome analysis methods. (ox.ac.uk)
  • End sequence generated in the construction of the BAC/PAC contig identified a previously unmapped EST and served to order genomic sequence contigs from the publicly available Celera Genomics (CG) and Human Genome Project (HGP) efforts. (elsevierpure.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)
  • Thus, new chromosomal regions present in the vicinity of a gene could be identified. (wikipedia.org)
  • We resolve chromosomal sequences and infer sex chromosome-specific parasite genes and new potential drug targets. (nature.com)
  • Fluorescence microscopy of chitin bead-co-lo-nizing cells of V. cholerae engineered to carry trans-lational fusions for the competen-ce protein ComEA-mCherry (red) and the T6SS sheath pro-tein VipA-sfGFP (green), both encod-ed at their native chromosomal locus. (asmblog.org)
  • Translated partial amino acid sequence of pln A gene in MCC4246 displayed 48 amino acid sequences showing 100% similarity with plantaricin A of Lactobacillus plantarum (WP_0036419). (researchsquare.com)
  • Moreover, we show that PNPase affects mRNA levels of the master regulator of virulence PrfA and PrfA-regulated genes, and these results could help to explain the reduced bacterial internalization in human cells of the ΔpnpA mutant. (bvsalud.org)
  • Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. (peerj.com)
  • These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. (peerj.com)
  • Compared to the domesticates, the wild relatives of rice are phenotypically inferior grass-like plants, but are a virtually untapped reservoir of agriculturally important genes and allelic variants that can be used to improve cultivated rice [ 21 , 29 ]. (biomedcentral.com)
  • Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. (elifesciences.org)
  • In order to expand our understanding of how recombination might influence virus variation during the course of adaptation, we focused on large DNA viruses, in which rapidly evolving populations can simultaneously harbor both adaptive gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus. (elifesciences.org)
  • 0.5) selected from among all common variants discovered in genome sequences in this population. (biomedcentral.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)
  • BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. (biomedcentral.com)
  • Recent technology has been developed to precisely engineer genes for traits of interest. (ufl.edu)
  • The UF/IFAS strawberry breeding program has identified several important gene regions controlling disease resistance traits that are directly relevant to Florida growers. (ufl.edu)
  • However, just as each cultivar has different traits and qualities, they also behave differently with respect to introduction of new genes. (ufl.edu)
  • Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae. (biomedcentral.com)
  • Antibiotic susceptibility is one of the most important yet poorly characterized bacterial phenotypes. (columbia.edu)
  • We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). (ox.ac.uk)
  • 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)
  • 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)
  • However, over the last 20 years or so, a number of cases of gene transfer in eukaryotes have been described. (nature.com)
  • Methylation of Adenine e.g. for the bacterial restriction system Why is DNA methylation (in eukaryotes) risky? (usadellab.org)
  • It has been shown in past that secretory proteins of eukaryotes have signal sequence at N-terminus, which can be used to predict its secretory nature. (biomedcentral.com)
  • The problematic microbial resistance to antibiotics has led to an increasing interest in bacterial persistence and its impact on infection. (bvsalud.org)
  • Gene expression data from mice with low-dose whipworm infection provide a detailed description of a regulated T H 1-like immune response to the infected cecum that is not limited to the immediate site of infection. (nature.com)
  • Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. (peerj.com)
  • Whole-genome transposon-mutagenesis (TM) followed by identification of insertion sites is one of the most practical and frequently used experimental approaches to screen for essential bacterial genes [ 6 - 8 ]. (biomedcentral.com)
  • Genome-scale GOF screening approaches have largely remained limited to the use of cDNA library overexpression systems. (cdc.gov)
  • Furthermore, length and, hence, information content of individual genes is limited, sometimes causing a lack of resolution in the inferred trees. (biomedcentral.com)
  • Transfers of a single gene, a complete metabolic pathway 10 , whole chromosomes 11 or even cases of the integration of almost complete genomes from bacterial endosymbionts into their eukaryotic hosts 12 have been described. (nature.com)
  • Published Nov. 14 in the Proceedings of the National Academy of Sciences (PNAS), the study was led by Omar Akbari , an assistant professor of entomology in UC Riverside's College of Natural and Agricultural Sciences and a member of the university's Institute for Integrative Genome Biology. (universityofcalifornia.edu)
  • Too long fragments cannot be sequenced in a single sequence read using the chain termination method. (wikipedia.org)
  • Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti , and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti -called Wallaby -present as identical fragments at non-homologous loci in P. camemberti and P. rubens . (nature.com)
  • Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)
  • With the completion of Plasmodium genome sequence, the challenge is to combine experimental and bioinformatics tools in order to develop algorithm with high predictive value for secretory proteins of malaria parasite. (biomedcentral.com)
  • Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
  • This effect is independent of the antibiotics' mechanisms of action or the locus of cat. (bvsalud.org)
  • Resistance mechanisms were characterized using whole genome sequencing. (cdc.gov)
  • The availability of these two important whipworm genomes and the integration of parasite and host data presented here will underpin future efforts to control these parasites and exploit their immunological interplay for human benefit. (nature.com)
  • This bacterial pathogen represents a prospective biological control agent for important nematode parasites. (biomedcentral.com)
  • The exopolysaccharide genes such as pilB, pslA, lecA, ureB and alginate genes are responsible for the formation of pseudomonas biofilms. (ukessays.com)
  • Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. (biomedcentral.com)
  • Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
  • A relatively obvious approach to phylogenetic analysis of whole genomes is to extract as many genes as possible from the genome sequences, create a multiple sequence alignment from each of the genes and to concatenate all alignments. (biomedcentral.com)
  • Furthermore, the use of concatenated multiple sequence alignments discards information that can be utilised by other methods of phylogenetic inference. (biomedcentral.com)
  • Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T . equi and closely related organisms. (biomedcentral.com)
  • The underlying method for sequencing is the Sanger chain termination method which can have read lengths between 100 and 1000 basepairs (depending on the instruments used). (wikipedia.org)
  • In the case of the regulatory protein gene targeted to the uracil locus, the transformed yeast colonies would be identified using replica plating on growth medium lacking uracil. (i-sis.org.uk)
  • 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)
  • lyrata (Lyre-leaved rock-cress) hypothetical protein (at5g25770) , arath-C7A10.830 Arabidopsis thaliana DNA chromosome 4,gene C7A10.830 No. 2 AT4G36530 , arath-F1N18.12 Arabidopsis thaliana (Mouse-ear cress) f1n18.12 AT1G29840 protein , arath-F1P2.110 Arabidopsis thaliana (Mouse-ear cress). (inrae.fr)
  • Transcriptomic analysis of wild-type and PNPase mutant biofilms reveals that PNPase impacts many regulatory pathways associated with biofilm formation, particularly by affecting the expression of genes involved in the metabolism of carbohydrates (e.g., lmo0096 and lmo0783, encoding PTS components), of amino acids (e.g., lmo1984 and lmo2006, encoding biosynthetic enzymes) and in the Agr quorum sensing-like system (lmo0048-49). (bvsalud.org)
  • Furthermore, we have developed a genome-wide epistasis analysis framework that efficiently reveals the organization of these genes within signaling and regulatory networks such as the Rcs phosphorelay pathway and the cyclic-di-GMP second-messenger system. (columbia.edu)
  • IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. (uibk.ac.at)
  • Molecular phylogenies of many taxonomic groups are based on analyses of single loci. (biomedcentral.com)
  • This work shows evidence that the insertion of the resistance gene Chloramphenicol Acetyl Transferase (cat) together with its cognate antibiotic chloramphenicol (CAM), is capable to modulate Salmonella Typhimurium persistence to several antibiotics and decrease its survival. (bvsalud.org)
  • Biofilms provide an environment that protects microorganisms from external stresses such as nutrient deprivation, antibiotic treatments, and immune defences, thereby creating favorable conditions for bacterial survival and pathogenesis. (bvsalud.org)
  • A new antibiotic cures superbugs without bacterial resistance. (universityofcalifornia.edu)
  • Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. (biomedcentral.com)
  • The locus of the psl polysacchide genes encode the cells to adhere to a surface and thus maintaining the biofilm structure. (ukessays.com)
  • Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II-related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. (ox.ac.uk)
  • Our analysis uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. (elifesciences.org)
  • Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. (biomedcentral.com)
  • Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica , which while found in porpoises without associated pathology can also cause severe opportunistic infections. (biomedcentral.com)
  • Homologous recombination inserts the DNA and disrupts the target gene, allowing rapid selection of cells with the inserted gene. (i-sis.org.uk)
  • Genome editing by these methods completely disrupts target genes, thus avoiding weak signals that can occur when transcript abundance is partially decreased by siRNA. (ewha.ac.kr)
  • The convergence of carbapenem-resistance and hypervirulence genes in Klebsiella pneumoniae has led to the emergence of highly drug-resistant superbugs capable of causing invasive disease. (cdc.gov)
  • Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)
  • Thus performance of method based on PSSM profile is more accurate than method based on sequence composition. (biomedcentral.com)
  • The genes responsible for the biofilm formation are quantified by comparing the planktonic and biofilm samples. (ukessays.com)
  • This sort of out-of-the-blue brain blast is exactly what happened in 2012 when a study about bacteria's adaptive immunity opened up the possibility for a new approach to gene therapy. (reverserett.org)
  • It was not until a series of studies between 2005 and 2007, however, that their role in the bacterial adaptive immunity was revealed. (reverserett.org)
  • The authors of that study postulated that hypervirulent clones might be subject to some sort of constraint against horizontal gene transfer and show more conserved pangenomic diversity than MDR clones. (cdc.gov)
  • bored to see yet another post on horizontal gene transfer (HGT). (asmblog.org)
  • Previous efforts to use genome editing to prevent mosquitoes from spreading pathogens have been hampered by low mutation rates, poor survival of edited mosquitoes, and inefficient transmission of disrupted genes to offspring. (universityofcalifornia.edu)
  • Cas enzymes and base repair templates would be delivered via gene therapy vectors. (reverserett.org)
  • 2008 ). All of these prebiotics are also hydrolyzed by brush border enzymes, but not completely (Ferreira-Lazarte et al. (springer.com)
  • There are over 300 alleles (one of two or more forms of a gene that produce variations in a given trait) for the hemoglobin gene, part of the globin gene superfamily. (icr.org)
  • When two alleles at the same locus interact, and where one allels causes a heritable change in the other allele. (usadellab.org)
  • This method necessitates the discovery of a marker that is firmly related to the mutant locus. (wikipedia.org)
  • Next, the mutant gene is inserted into the yeast at a specific locus, a step that involves legitimate recombination. (i-sis.org.uk)
  • As the yeast is not intended for making very strong beer for consumption but ethanol biofuel, toxin production may seem less of a problem, provided the yeast strain can be completely contained, which is well nigh impossible. (i-sis.org.uk)
  • The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)
  • Twelve years ago, Japanese scientists reported that a transgenic yeast engineered for increased rate of fermentation with multiple copies of one of its own genes ended up accumulating the metabolite methylglyoxal at toxic, mutagenic levels [4]. (i-sis.org.uk)
  • T . equi has lost the putative genes for host cell transformation, or the genes were acquired by T . parva and T . annulata after divergence from T . equi . (biomedcentral.com)
  • Advancement in identification of MHC genes that confer susceptibility to disease requires greater knowledge of sequence variation across the complex. (ox.ac.uk)