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1. An ultra-sensitive test strip combining with RPA and CRISPR/Cas12a system for the rapid detection of GM crops

Author:
Jinbin Wang; Yu Wang; Hua Liu; Xiuwen Hu; Minghao Zhang; Xiaofeng Liu; Hailong Ye; Haijuan Zeng
Source:
Food control 2023 v.144 pp. 109383
ISSN:
0956-7135
Subject:
plasmids,   etc   ; biotechnology; detection limit; food safety; genetically modified organisms; immunoassays; markets; rapid methods;     Show all 8 Subjects
Abstract:
... Advanced molecular biotechnology has been developed to provide favorable technical support for genetically modified (GM) crop detection. For sensitive on-site detection, a Cas12a-based immunoassay strip was self-prepared and evaluated in this study. The strip was applied to analyze transgenic screening elements P-CaMV 35S and T-NOS by combination with RPA and Cas12a cleavage reaction. The assay ca ...
DOI:
10.1016/j.foodcont.2022.109383

2. Effective CRISPR/Cas9-based genome editing in large yellow croaker (Larimichthys crocea)

Author:
Qiuhua Li; Guangming Shao; Yangyang Ding; Libing Xu; Jianchun Shao; Jingqun Ao; Xinhua Chen
Source:
Aquaculture and fisheries 2023 v.8 no.1 pp. 26-32
ISSN:
2468-550X
Subject:
plasmids,   etc   ; CRISPR-Cas systems; Larimichthys crocea; aquaculture; chorion; disease resistance; genes; genetic improvement; genomics; green fluorescent protein; meat quality; mutants; survival rate; China;     Show all 14 Subjects
Abstract:
... The large yellow croaker (Larimichthys crocea) is an economically important marine species with the highest annual production among the farmed marine fishes in China. However, the aquaculture industry of this species is suffering from severe problems that include weakened disease resistance, decreased growth rate, and reduced meat quality due to frequent inbreeding. Genome editing, which has a hug ...
DOI:
10.1016/j.aaf.2021.04.008

3. Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action

Author:
Xiaojing Yan; Wenwen Liu; Shengfang Wen; Lanjun Wang; Lusheng Zhu; Jun Wang; Young Mo Kim; Jinhua Wang
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 399-409
ISSN:
1001-0742
Subject:
plasmids,   etc   ; Escherichia coli; antibacterial properties; antibiotic resistance; cell membranes; gene expression; horizontal gene transfer; mechanism of action; outer membrane proteins; oxidative stress; permeability; pollutants; sulfamethazine; China;     Show all 14 Subjects
Abstract:
... As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to st ...
DOI:
10.1016/j.jes.2022.06.014

4. Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

Author:
Yanchu Ke; Wenjun Sun; Zibo Jing; Zhinan Zhao; Shuguang Xie
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 714-725
ISSN:
1001-0742
Subject:
plasmids,   etc   ; Achromobacter; Mycobacterium; Stenotrophomonas; ammonia; antibiotic resistance; antibiotic resistance genes; antibiotics; autumn; biofilm; community structure; hardness; metagenomics; microbial communities; plate count; seasonal variation; spring; suburban areas; summer; temperature; total organic carbon; water distribution; water treatment; winter; China;     Show all 25 Subjects
Abstract:
... Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial commun ...
DOI:
10.1016/j.jes.2022.07.001

5. Plasmids Carrying Antimicrobial Resistance Genes in Gram-Negative Bacteria

Author:
Nadezhda K. Fursova; Angelina A. Kislichkina; Olga E. Khokhlova
Source:
Microorganisms 2022 v.10 no.8 pp. -
ISSN:
2076-2607
Subject:
plasmids,   etc   ; antibiotic resistance; patients;     Show all 3 Subjects
Abstract:
... Gram-negative bacteria are prevalent pathogens associated with hospital-acquired infections (HAI) that are a major challenge for patient safety, especially in intensive care units [...] ...
DOI:
10.3390/microorganisms10081678

6. A selection marker-free method for gene deletion and editing in baculovirus genomes

Author:
Wujie Su; Wentao Ye; Wanwan Wang; Piao Feng; Xiqian Guo; Wenbing Wang; Fanchi Li; Wei Liu; Bing Li
Source:
Journal of virological methods 2022 v.310 pp. 114624
ISSN:
0166-0934
Subject:
plasmids,   etc   ; gene deletion; genes; loci;     Show all 4 Subjects
Abstract:
... Here, we develop a simple, efficient, bacmid-based, selection marker-free method for gene deletion and editing in baculovirus genomes. Specifically, based on pFastbac1, a donor plasmid with long left and right homology arms but without a reporter was constructed for disrupting ie1, an essential baculovirus gene. Instead of ligating with a plasmid, the homology arms were introduced to the polyhedri ...
DOI:
10.1016/j.jviromet.2022.114624

7. 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 v.434 no.15 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

8. 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

9. A facile biosynthesis strategy of plasmid DNA-derived nanowires for readable microRNA logic operations

Author:
Xue Yin; Dongbao Yao; Michael Hon-Wah Lam; Haojun Liang
Source:
Journal of materials chemistry B 2022 v.10 no.16 pp. 3055-3063
ISSN:
2050-7518
Subject:
plasmids,   etc   ; agarose; biosynthesis; gels; microRNA; nanowires;     Show all 6 Subjects
Abstract:
... Multiple microRNA (miRNA) logical assays have attracted wide attention recently, which can be applied to mimic and reveal cellular events at the molecular level. However, it remains challenging to develop labeling- and amplification-free approaches to perform logical functions with low levels of miRNA molecules. Herein, we proposed a strategy for miRNA logic operations using plasmid DNA-derived na ...
DOI:
10.1039/d1tb02699b

10. 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

11. Effect of the array of amines on the transfection efficiency of cationic peptidomimetic lipid molecules into neural cells

Author:
Xiang Yu; Hai Xiao; Muqier Muqier; Shuqin Han; Huricha Baigude
Source:
RSC advances 2022 v.12 no.33 pp. 21567-21573
ISSN:
2046-2069
Subject:
plasmids,   etc   ; flow cytometry; glucose; lipids; oxygen; transfection;     Show all 6 Subjects
Abstract:
... The amino groups in the head group of a cationic lipid play a determinative role regarding the nucleic acid delivery efficiency of the LNP formulated from lipids. Herein, we designed four types of lipid bearing different amine-containing branched head groups to investigate the influence of type and number of amines on the neural cell targeted nuclei acid delivery. Conjugation of an ethylamino grou ...
DOI:
10.1039/d2ra03347j

12. Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions

Author:
Nesrine Nabi; Ahmed Ben Hafsa; Vincent Gaillard; Xavier Nesme; Maher Chaouachi; Ludovic Vial
Source:
Molecular phylogenetics and evolution 2022 v.169 pp. 107388
ISSN:
1055-7903
Subject:
plasmids,   etc   ; Agrobacterium; crown galls; oncogenes; phylogeny; virulence;     Show all 6 Subjects
Abstract:
... Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types ...
DOI:
10.1016/j.ympev.2022.107388

13. 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

14. Lentiviral mediated delivery of shrnas to hescs and npcs using low-cost cationic polymer polyethylenimine (pei)

Author:
Sheikh Muhammad Abid; Ansari Suraiya Anjum
Source:
Journal of visualized experiments 2022 no.183 pp. e63953
ISSN:
1940-087X
Subject:
plasmids,   etc   ; Western blotting; humans; polyethyleneimine; puromycin; ultracentrifugation;     Show all 6 Subjects
Abstract:
... The current protocol describes the use of lentiviral particles for the delivery of short hairpin RNAs (shRNAs) to both human embryonic stem cells (hESCs) as well as neural progenitor cells (NPCs) derived from hESCs at high efficiency. Lentiviral particles were generated by co-transfecting HEK293T cells using entry vectors (carrying shRNAs) along with packaging plasmids (pAX and pMD2.G) using the l ...
DOI:
10.3791/63953

15. Within-Household Transmission and Bacterial Diversity of Staphylococcus pseudintermedius

Author:
Alice Wegener; Birgitta Duim; Linda van der Graaf-van Bloois; Aldert L. Zomer; Caroline E. Visser; Mirlin Spaninks; Arjen J. Timmerman; Jaap A. Wagenaar; Els M. Broens
Source:
Pathogens 2022 v.11 no.8 pp. -
ISSN:
2076-0817
Subject:
plasmids,   etc   ; Staphylococcus pseudintermedius; antibiotic resistance; genome; humans;     Show all 5 Subjects
Abstract:
... Staphylococcus pseudintermedius can be transmitted between dogs and their owners and can cause opportunistic infections in humans. Whole genome sequencing was applied to identify the relatedness between isolates from human infections and isolates from dogs in the same households. Genome SNP diversity and distribution of plasmids and antimicrobial resistance genes identified related and unrelated i ...
DOI:
10.3390/pathogens11080850

16. An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants

Author:
Federica Sacco; Giammarco Raponi; Alessandra Oliva; Giulia Bibbolino; Vera Mauro; Federica Maria Di Lella; Lorenzo Volpicelli; Guido Antonelli; Mario Venditti; Alessandra Carattoli; Gabriele Arcari
Source:
International journal of antimicrobial agents 2022 v.60 no.2 pp. 106615
ISSN:
0924-8579
Subject:
plasmids,   etc   ; Klebsiella pneumoniae; aminoglycosides; genes; genomics; methyltransferases;     Show all 6 Subjects
Abstract:
... The spread of extremely-drug-resistant Klebsiella pneumoniae has become a major health threat worldwide. This is largely mediated by certain lineages, recognized as high-risk clones dispersed throughout the world. Analysis of an outbreak of nine ST15, NDM-1 metallo-β-lactamase-producing K. pneumoniae was performed. An IncC plasmid carrying the blaNDM₋₁ gene also carried the rare rmtC gene, encodin ...
DOI:
10.1016/j.ijantimicag.2022.106615

17. 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

18. Establishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus

Author:
Haiyan Ren; Anqi Yin; Pingping Wu; Huanyu Zhou; Jungang Zhou; Yao Yu; Hong Lu
Source:
Microorganisms 2022 v.10 no.6 pp. -
ISSN:
2076-2607
Subject:
plasmids,   etc   ; Kluyveromyces marxianus; centromeres; cytotoxicity; recombinases; reporter genes;     Show all 6 Subjects
Abstract:
... The Cre-loxP system produces structural variations, such as deletion, duplication, inversion and translocation, at specific loci and induces chromosomal rearrangements in the genome. To achieve chromosomal rearrangements in Kluyveromyces marxianus, the positions and sequences of centromeres were identified in this species for the first time. Next, a Cre-loxP system was established in K. marxianus. ...
DOI:
10.3390/microorganisms10061240

19. Characterization of a Novel Carbapenem-Resistant Klebsiella michiganensis Strain Coharboring the blaSIM-1, blaOXA-1, blaCTX-M-14, qnrS, and aac(6′)-Ib-cr Genes

Author:
Jianfen Xu; Hui Ding; Yunan Zhao; Jiaoli Chen; Zhigang Zhao; Jiansheng Huang; Rongzhen Wu
Source:
Current microbiology 2022 v.79 no.8 pp. 228
ISSN:
0343-8651
Subject:
plasmids,   etc   ; Klebsiella oxytoca; drug resistance; hospitals; microbiology; China;     Show all 6 Subjects
Abstract:
... Carbapenem-resistant Klebsiella michiganensis (CRKM) and Klebsiella oxytoca (CRKO) strains have occasionally been reported to cause severe infections. However, SIM-producing K. michiganensis strains have never been described. In this study, we phenotypically and genetically characterized 6 CRKM and CRKO strains isolated over the past 10 years at a Chinese tertiary hospital. All six strains were po ...
DOI:
10.1007/s00284-022-02920-7

20. Excision and integration of unconventional circularizable structures involving the erm(B) gene in enterococci

Author:
Xinxin Shan; Hong Yao; Stefan Schwarz; Dexi Li; Xin-Sheng Li; Xiang-Dang Du
Source:
Veterinary microbiology 2022 v.273 pp. 109542
ISSN:
0378-1135
Subject:
plasmids,   etc   ; antibiotic resistance; databases; excision; multigene family; transposases;     Show all 6 Subjects
Abstract:
... Traditionally, insertion sequences (ISs) play a major role in disseminating antimicrobial resistance genes (ARGs) in bacteria through transposition and translocation, forming regions that contain multiple ARGs flanked by single or multiple copies of IS. In addition, unconventional circularizable structures (UCSs), lacking recombinase genes but being surrounded by directly repeated sequences (DRs) ...
DOI:
10.1016/j.vetmic.2022.109542