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plasmids, etc ; Markov chain; metagenomics; molecular biology; Show all 4 Subjects
Abstract:
... Machine learning or deep learning models have been widely used for taxonomic classification of metagenomic sequences and many studies reported high classification accuracy. Such models are usually trained based on sequences in several training classes in hope of accurately classifying unknown sequences into these classes. However, when deploying the classification models on real testing data sets, ...
plasmids, etc ; Acinetobacter baumannii; bioinformatics; host range; Show all 4 Subjects
Abstract:
... The bioinformatic analysis that we made of 492 Acinetobacter baumannii plasmid sequences identified 418 genes encoding Replication Initiator (Rep) proteins that fell into at least fourteen groups according to the protein domains that they contained. The most abundant group of Rep proteins contained a Rep_3 superfamily domain, followed by Rep proteins containing Replicase/PriCT_1 superfamily domain ...
plasmids, etc ; drugs; dyes; genes; humans; toxicity; yeasts; Show all 7 Subjects
Abstract:
... AIMS: This study aimed to establish a yeast‐based screening system for potential compounds that can alleviate the toxicity of α‐synuclein (α‐syn), a neuropathological hallmark of Parkinson’s disease, either inhibition of α‐syn aggregation or promotion of ubiquitin‐mediated degradation of α‐syn. METHODS AND RESULTS: A powerful yeast‐based screening assay using the rsp5ᴬ⁴⁰¹ᴱ‐mutant strain, which is ...
plasmids, etc ; biotechnology; methyltransferases; prokaryotic cells; restriction endonucleases; Show all 5 Subjects
Abstract:
... Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methyl ...
plasmids, etc ; Yersinia enterocolitica; cold; rapid methods; virulence; yersiniosis; Show all 6 Subjects
Abstract:
... Yersinia enterocolitica and Y. pseudotuberculosis are important causes of enteric illness worldwide. Rapid response to suspected foodborne outbreaks is hampered by the widespread use of cold enrichment methods that require incubation periods of 10–21 days. Although these species grow faster at elevated temperatures, part of the rationale for cold enrichment is that a key pathogenicity marker (pYV ...
Sriram KK; Elina Ekedahl; Ngoc Thi Bich Hoang; Tsegaye Sewunet; Björn Berglund; Ludwig Lundberg; Shoeib Nematzadeh; Maud Nilsson; Lennart E Nilsson; Ngai Kien Le; Dien Minh Tran; Håkan Hanberger; Linus Olson; Mattias Larsson; Christian G. Giske; Fredrik Westerlund
plasmids, etc ; Klebsiella pneumoniae; antibiotic resistance; hospitals; society; Vietnam; Show all 6 Subjects
Abstract:
... The carbapenemase-encoding gene blaNDM₋₁ has been reported in Vietnam during the last 10 years, and blaNDM-producing Enterobacteriaceae are now silently and rapidly spreading. A key factor behind dissemination of blaNDM₋₁ is plasmids, mobile genetic elements that commonly carry antibiotic resistance genes and spread via conjugation. The diversity of blaNDM₋₁-encoding plasmids from neonates at a la ...
plasmids, etc ; RNA replication; luciferase; mutants; reporter genes; viruses; Show all 6 Subjects
Abstract:
... To investigate the role of PRRSV nonstructural proteins (nsps) in viral RNA replication and transcription, we generated a cDNA clone of PRRSV strain NCV1 carrying the nanoluciferase (nluc) gene under the control of the transcription regulatory sequence 6 (TRS6) designated as pNCV1-Nluc. Cells transfected with the pNCV1-Nluc DNA plasmid produced an infectious virus and high levels of luciferase act ...
plasmids, etc ; biotechnology; cell viability; mammals; manufacturing; polyethyleneimine; transfection; Show all 7 Subjects
Abstract:
... The transient transfection of mammalian cells is a rapid and versatile platform for the manufacture of recombinant proteins, but industrial processes depend on reliable scalability and efficient conversion from adherent to suspension cell cultures. Here we describe the optimized transfection of HEK 293T cells in both culture formats. DMEM was the best transfection medium for adherent HEK 293T cell ...
plasmids, etc ; Influenza A virus; human influenza; humans; poultry; swine; Show all 6 Subjects
Abstract:
... The H1N1 subtype influenza viruses (H1N1) have been causing persistent epidemics in human, swine and poultry populations since 1918. This subtype has evolved into four relatively stable genetic lineages, including classical swine influenza virus lineage, seasonal human influenza virus lineage, avian influenza virus lineage and Eurasian avian-like swine influenza virus lineage. In this study, four ...
plasmids, etc ; Bradyrhizobium japonicum; bacteriocins; enzymes; inoculum; mutants; rhizosphere; soybeans; Show all 8 Subjects
Abstract:
... Bacteriocins are narrow-spectrum antibiotics of bacterial origin that can affect competition in resource-limited environments, such as the rhizosphere. Therefore, bacteriocins may be good candidates for manipulation to generate more competitive inocula for soybean. In this study, Bradyrhizobium japonicum FN1, along with other Bradyrhizobia in our culture collection, was screened for bacteriocin-li ...
plasmids, etc ; biosynthesis; chromosomes; food chemistry; plantaricins; transcription (genetics); transcriptome; Show all 7 Subjects
Abstract:
... Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plant ...
plasmids, etc ; Pseudomonas aeruginosa; beta-lactamase; evolution; genomics; transposons; China; Show all 7 Subjects
Abstract:
... To investigate a detailed genomic characterization of the blaIMP₋₁₀-carrying plasmid p12NE515 from a Pseudomonas aeruginosa isolate in China. Plasmid p12NE515 was subjected to whole-genome sequencing and the complete sequence was compared with related plasmid sequences. Transferability of plasmid, carbapenemase activity and bacterial susceptibility profiles were determined to assess p12NE515-media ...
plasmids, etc ; Acidithiobacillus ferrooxidans; bioleaching; biotechnology; gene overexpression; genes; iron; sulfur; Show all 8 Subjects
Abstract:
... There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their ...
plasmids, etc ; biosynthesis; gene expression; genes; p-coumaric acid; transcription (genetics); Show all 6 Subjects
Abstract:
... Dynamic regulation has been proved efficient in controlling gene expression at transcriptional, translational, and post-translational level. However, the dynamic regulation at gene replication level has been rarely explored so far. In this study, we established dynamic regulation at gene copy level through engineering controllable plasmid replication to dynamically control the gene expression. Pro ...
plasmids, etc ; Escherichia coli; ambient temperature; electric potential difference; electrophoresis; electroporation; Show all 6 Subjects
Abstract:
... A frequent limitation of electroporation (EP) and chemical transformation (CT) are the need of tedious and time‐consuming procedures for inducing transformation competence, the substantial number of cells required, and the low transformation yields typically achieved. Here, we show a new and rapid electrokinetic method for transformation of small number of noncompetent Escherichia coli TOP10 cells ...
plasmids, etc ; Escherichia coli; cephalosporins; chromosomes; genes; growth curves; hybridization; China; Show all 8 Subjects
Abstract:
... The use of antimicrobials in food animals is the major determinant for the propagation of resistant bacteria in the animal reservoir. The objective of this study was to investigate the presence and distribution of third-generation cephalosporin (3GC) -resistant and plasmid-mediated AmpC (pAmpC)-producing Escherichia coli isolated from food animals in Southern China. In total, 744 3GC-resistant and ...
plasmids, etc ; RNA; Rhodobacteraceae; bacteria; chromosomes; cold; genomics; lifestyle; nucleotide sequences; seawater; Show all 10 Subjects
Abstract:
... Parasedimentitalea marina W43ᵀ is a novel psychrotolerant and piezotolerant Rhodobacteraceae bacterium isolated from deep-sea water (4000 m) of the New Britain Trench. Here we present the first complete genome sequence of the bacterial genus Parasedimentitalea, which contains a circular chromosome and four plasmids. The 5,080,916 bp long genome exhibits a G + C content of 55.9 mol% and contains 50 ...
plasmids, etc ; Pseudomonas aeruginosa; beta-lactamase; carbapenems; evolution; genome; infection; public health; Show all 8 Subjects
Abstract:
... The high rates of carbapenem resistance among Brazilian Pseudomonas aeruginosa isolates are mainly associated with the clone ST277 producing the carbapenemase SPM-1. Here, the complete genetic composition of a IncP plasmid harboring blaKPC₋₂ in isolates of this endemic clone carrying chromosomal blaSPM₋₁ was described using whole genome sequencing. These results confirm the association of these tw ...
plasmids, etc ; Enterococcus; Neottia; antibiotic resistance; biofilm; horizontal gene transfer; hospitals; pollution; Show all 8 Subjects
Abstract:
... Enterococci, which are on the WHO list of priority pathogens, are commonly encountered in hospital acquired infection and are becoming increasing significant due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment, and their presence is frequently used as an indicator of faecal pollution. Their success is related to thei ...
plasmids, etc ; Enterobacter; beta-lactamase; colistin; hospitals; multiple drug resistance; therapeutics; China; Show all 8 Subjects
Abstract:
... Enterobacter spp. are members of the ‘ESKAPE’ group of pathogens, which which are recognised as the leading cause of multidrug-resistant (MDR) hospital-acquired infections. Colistin is usually regarded as a last-line therapeutic option for MDR Gram-negative bacilli infections. However, colistin-resistant Enterobacter spp. have emerged in the last decade. Here we investigated the prevalence of coli ...