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1. MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences

Author:
Xin Bai; Jie Ren; Fengzhu Sun
Source:
Journal of molecular biology 2022 pp. 167586
ISSN:
0022-2836
Subject:
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, ...
DOI:
10.1016/j.jmb.2022.167586

2. Replication initiator proteins of Acinetobacter baumannii plasmids: An update note

Author:
Semiramis Castro-Jaimes; Gabriela Guerrero; Elena Bello-López; Miguel A. Cevallos
Source:
Plasmid 2022 v.119-120 pp. 102616
ISSN:
0147-619X
Subject:
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 ...
DOI:
10.1016/j.plasmid.2021.102616

3. A novel yeast‐based screening system for potential compounds that can alleviate human α‐synuclein toxicity

Author:
Anyaporn Sangkaew; Thanaporn Kojornna; Ryoya Tanahashi; Hiroshi Takagi; Chulee Yompakdee
Source:
Journal of applied microbiology 2022 v.132 no.2 pp. 1409-1421
ISSN:
1364-5072
Subject:
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 ...
DOI:
10.1111/jam.15256

4. Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review

Author:
Jun Ren; Hyang-Mi Lee; JunHao Shen; Dokyun Na
Source:
Biotechnology letters 2022 v.44 no.1 pp. 33-44
ISSN:
0141-5492
Subject:
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 ...
DOI:
10.1007/s10529-021-03208-9

5. Cold Enrichment Methods for the Detection of Foodborne Yersiniosis: Friend or Foe?

Author:
Yuwei Zhang; Stephen L. W. On
Source:
Pathogens 2022 v.11 no.2 pp. -
ISSN:
2076-0817
Subject:
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 ...
DOI:
10.3390/pathogens11020278

6. High diversity of blaNDM-1-encoding plasmids in Klebsiella pneumoniae isolated from neonates in a Vietnamese hospital

Author:
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
Source:
International journal of antimicrobial agents 2022 v.59 no.2 pp. 106496
ISSN:
0924-8579
Subject:
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 ...
DOI:
10.1016/j.ijantimicag.2021.106496

7. Identification of Cryptic Promoter Activity in cDNA Sequences Corresponding to PRRSV 5′ Untranslated Region and Transcription Regulatory Sequences

Author:
Jayeshbhai Chaudhari; The Nhu Nguyen; Hiep L. X. Vu
Source:
Viruses 2022 v.14 no.2 pp. -
ISSN:
1999-4915
Subject:
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 ...
DOI:
10.3390/v14020400

8. Statistical experimental designs to optimize the transient transfection of HEK 293T cells and determine a transfer criterion from adherent cells to larger-scale cell suspension cultures

Author:
Gregor Dekevic; Lars Tasto; Peter Czermak; Denise Salzig
Source:
Journal of biotechnology 2022 v.346 pp. 23-34
ISSN:
0168-1656
Subject:
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 ...
DOI:
10.1016/j.jbiotec.2022.01.004

9. A SYBR Green-based real-time RT-PCR assay to differentiate the H1N1 influenza virus lineages

Author:
Yulin Cong; Yixue Sun; Xiaoyu Deng; Haiying Yu; Xiaohuan Lian; Yanlong Cong
Source:
Journal of virological methods 2022 v.300 pp. 114387
ISSN:
0166-0934
Subject:
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 ...
DOI:
10.1016/j.jviromet.2021.114387

10. Bradyrhizobium japonicum FN1 produces an inhibitory substance that affects competition for nodule occupancy

Author:
MacLean G. Kohlmeier; Harry Yudistira; Amanat Ali; Ivan J. Oresnik
Source:
Canadian journal of microbiology 2022 v.68 no.4 pp. 227-236
ISSN:
1480-3275
Subject:
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 ...
DOI:
10.1139/cjm-2021-0355

11. TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163

Author:
Deyin Zhao; Qian Wang; Fanqiang Meng; Fengxia Lu; Xiaomei Bie; Zhaoxin Lu; Yingjian Lu
Source:
Journal of agricultural and food chemistry 2022 v.70 no.14 pp. 4362-4372
ISSN:
1520-5118
Subject:
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 ...
DOI:
10.1021/acs.jafc.2c00206

12. The first report of the blaIMP-10 gene and complete sequence of the IMP-10-encoding plasmid p12NE515 from Pseudomonas aeruginosa in China

Author:
Wei Feng; Jun Lv; Hongping Wang; Pu Yao; Lirong Xiong; Peiyuan Xia; Qian Yuan; Fengjun Sun
Source:
Acta tropica 2022 v.228 pp. 106326
ISSN:
0001-706X
Subject:
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 ...
DOI:
10.1016/j.actatropica.2022.106326

13. Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans

Author:
Heejung Jung; Yuta Inaba; Scott Banta
Source:
Trends in biotechnology 2022 v.40 no.6 pp. 677-692
ISSN:
0167-7799
Subject:
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 ...
DOI:
10.1016/j.tibtech.2021.10.004

14. Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria

Author:
Chenyi Li; Yusong Zou; Tian Jiang; Jianli Zhang; Yajun Yan
Source:
Metabolic engineering 2022 v.70 pp. 67-78
ISSN:
1096-7176
Subject:
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 ...
DOI:
10.1016/j.ymben.2022.01.003

15. Isotachophoresis for rapid transformation of Escherichia coli

Author:
Monica N. Alves; Yi Heng Nai; Shane M. Powell; Mirek Macka; Michael C. Breadmore
Source:
Electrophoresis 2022 v.43 no.4 pp. 543-547
ISSN:
0173-0835
Subject:
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 ...
DOI:
10.1002/elps.202100095

16. Plasmid and chromosomal copies of blaCMY-2 mediate resistance to third-generation cephalosporins in Escherichia coli from food animals in China

Author:
Xing-Run Zheng; Yin-Huan Sun; Man-Xia Chang; Hong-Xia Jiang
Source:
Veterinary microbiology 2022 v.271 pp. 109493
ISSN:
0378-1135
Subject:
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 ...
DOI:
10.1016/j.vetmic.2022.109493

17. Complete genome sequence of a psychrotolerant and piezotolerant bacterium Parasedimentitalea marina W43T, isolated from deep sea water of the New Britain trench

Author:
Hongge Zhang; Jiasong Fang; Hongcai Zhang; Junwei Cao
Source:
Marine genomics 2022 v.61 pp. 100915
ISSN:
1874-7787
Subject:
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 ...
DOI:
10.1016/j.margen.2021.100915

18. Description of a novel IncP plasmid harboring blaKPC-2 recovered from a SPM-1-producing Pseudomonas aeruginosa from ST277

Author:
Melise Chaves Silveira; Rodolpho Mattos Albano; Cláudio Marcos Rocha-de-Souza; Robson Souza Leão; Elizabeth Andrade Marques; Renata Cristina Picão; Gabriela Bergiante Kraychete; Ivson Cassiano de Oliveira Santos; Thamirys Rachel Tavares e Oliveira; Camila Bastos Tavares-Teixeira; Ana Paula D'Alincourt Carvalho-Assef
Source:
Infection, genetics, and evolution 2022 v.102 pp. 105302
ISSN:
1567-1348
Subject:
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 ...
DOI:
10.1016/j.meegid.2022.105302

19. Enterococcal biofilm—A nidus for antibiotic resistance transfer?

Author:
Michael Conwell; James S. G. Dooley; Patrick J. Naughton
Source:
Journal of applied microbiology 2022 v.132 no.5 pp. 3444-3460
ISSN:
1364-5072
Subject:
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 ...
DOI:
10.1111/jam.15441

20. High prevalence of colistin resistance and mcr-9/10 genes in Enterobacter spp. in a tertiary hospital over a decade

Author:
Weichao Liao; Yushan Cui; Jingjing Quan; Dongdong Zhao; Xinhong Han; Qiucheng Shi; Qian Wang; Yan Jiang; Xiaoxing Du; Xi Li; Yunsong Yu
Source:
International journal of antimicrobial agents 2022 v.59 no.5 pp. 106573
ISSN:
0924-8579
Subject:
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 ...
DOI:
10.1016/j.ijantimicag.2022.106573