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1. Rapid assembly of multi-gene constructs using modular golden gate cloning

Author:
Mukherjee, Minakshi; Caroll, Emily; Wang, Zhen Q.
Source:
Journal of visualized experiments 2021 no.168 pp. e61993
ISSN:
1940-087X
Subject:
plasmids,   etc   ; fluorescent proteins; yeasts;     Show all 3 Subjects
Abstract:
... The Golden Gate cloning method enables the rapid assembly of multiple genes in any user-defined arrangement. It utilizes type IIS restriction enzymes that cut outside of their recognition sites and create a short overhang. This modular cloning (MoClo) system uses a hierarchical workflow in which different DNA parts, such as promoters, coding sequences (CDS), and terminators, are first cloned into ...
DOI:
10.3791/61993

2. AUF1, an mRNA decay factor, has a discordant role in Cpeb1 expression

Author:
Oe, Souichi; Koike, Taro; Hirahara, Yukie; Tanaka, Susumu; Hayashi, Shinichi; Nakano, Yosuke; Kase, Masahiko; Noda, Yasuko; Yamada, Hisao; Kitada, Masaaki
Source:
Biochemical and biophysical research communications 2021 v.534 pp. 491-497
ISSN:
0006-291X
Subject:
plasmids,   etc   ; gene expression; research;     Show all 3 Subjects
Abstract:
... Cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates polyadenylation and subsequent translation of CPE-containing mRNAs involved in various physiological and pathological phenomena. Although the significance of CPEB1-mediated translational regulation has recently been reported, the detailed regulatory mechanism of Cpeb1 expression remains unclear. To elucidate the post-transcrip ...
DOI:
10.1016/j.bbrc.2020.11.054

3. Dilemma on plasmid DNA purification: binding capacity vs selectivity

Author:
Valente, J.F.A.; Queiroz, J.A.; Sousa, F.
Source:
Journal of chromatography 2021 v.1637 pp. 461848
ISSN:
0021-9673
Subject:
plasmids,   etc   ; chromatography; evolution; gene therapy; ligands; scientists;     Show all 6 Subjects
Abstract:
... Plasmid DNA chromatography is a powerful field in constant development and evolution. The use of this technique is considered mandatory in the production of an efficient and safe formulation to be applied for plasmid-mediated gene therapy. Concerning this, the search for an ideal chromatographic support/ligand combination motivated scientist to pursue a continuous improvement on the plasmid chroma ...
DOI:
10.1016/j.chroma.2020.461848

4. Stability of plasmid and viral banks supporting the cGMP manufacture of Q-Griffithsin from a TMV-based viral vector

Author:
Corman, Julia M.; Hamorsky, Krystal T.; Shepherd, John W.; Hiatt, Ernie; Fuqua, Joshua L.; Palmer, Kenneth E.
Source:
Journal of biotechnology 2020 v.320 pp. 74-76
ISSN:
0168-1656
Subject:
plasmids,   etc   ; biotechnology; manufacturing; virion;     Show all 4 Subjects
Abstract:
... The “whole genome” TMV-based expression system, Geneware®, was used in the cGMP production of the plant-made pharmaceutical Q-Griffithsin and demonstrates stable expression for up to a two-year period. Virion and plasmid banks which contained viral cDNA and a Q-Griffithsin sequence were able to produce >200 g of Q-Griffithsin. Data assessing the quality and stability of the product banks were meas ...
DOI:
10.1016/j.jbiotec.2020.06.009

5. Analysis of CRISPR systems of types II-A, I-E and I-C in strains of Lacticaseibacillus

Author:
Pujato, Silvina; Galliani, Valentina; Irazoqui, José Matías; Amadío, Ariel; Quiberoni, Andrea; Mercanti, Diego
Source:
International dairy journal 2021 v.118 pp. 105027
ISSN:
0958-6946
Subject:
plasmids,   etc   ; CRISPR sequences; CRISPR-Cas systems; bacteriophages; economic impact; morphogenesis;     Show all 6 Subjects
Abstract:
... A total of 49 strains of Lacticaseibacillus were screened for the presence of CRISPR-Cas systems. Type II-A CRISPR-Cas loci were sequenced for 8 Lacticaseibacillus paracasei and 3 Lacticaseibacillus rhamnosus strains. They contained 21 to 49 spacers, a few of them with similarity to plasmids. Cas9 identity was well correlated with spacer content of the strains. Only strain L. paracasei 85 containe ...
DOI:
10.1016/j.idairyj.2021.105027

6. Potential dissemination mechanism of the tetC gene in Aeromonas media from the aerobic biofilm reactor under oxytetracycline stresses

Author:
Shi, Yanhong; Zhang, Yu; Wu, Xiangyang; Zhang, Hong; Yang, Min; Tian, Zhe
Source:
Journal of environmental sciences (China) 2021 v.105 pp. 90-99
ISSN:
1001-0742
Subject:
plasmids,   etc   ; ; biofilm; databases; genes; oxytetracycline; tetracycline; transposons; China;     Show all 9 Subjects
Abstract:
... The tetC gene has been found to be one of the most widely distributed tetracycline resistance (tet) genes in various environmental niches, but the detailed dissemination mechanisms are still largely unknown. In the present study, 11 tetC-containing Aeromonas media strains were isolated from an aerobic biofilm reactor under oxytetracycline stresses, and the genome of one strain was sequenced using ...
DOI:
10.1016/j.jes.2020.12.038

7. Thermophilic rather than mesophilic sludge anaerobic digesters possess lower antibiotic resistant genes abundance

Author:
Zhang, Yan; Mao, Qiuyan; Su, Yu-ao; Zhang, Huimin; Liu, He; Fu, Bo; Su, Zhiguo; Wen, Donghui
Source:
Bioresource technology 2021 v.329 pp. 124924
ISSN:
0960-8524
Subject:
plasmids,   etc   ; Firmicutes; anaerobic digestion; antibiotic resistance; microbial communities; sludge; temperature;     Show all 7 Subjects
Abstract:
... For exploring the impact of temperature on antibiotic resistant genes (ARGs) during sludge anaerobic digestion (AD), the dynamic variations of sludge ARGs, plasmid ARGs, and cell-free ARGs in mesophilic (25 °C and 35 °C) and thermophilic (55 °C) digesters were investigated. The study revealed that the abundance of sludge ARGs and plasmid ARGs in thermophilic sludge AD was significantly lower than ...
DOI:
10.1016/j.biortech.2021.124924

8. Maximization of saturated fatty acids through the production of P450BM3 monooxygenase in the engineered Escherichia coli

Author:
Awad, Gamal; Garnier, Alain
Source:
Food and bioproducts processing 2021 v.126 pp. 130-142
ISSN:
0960-3085
Subject:
plasmids,   etc   ; Escherichia coli; biobased products; bioreactors; biosynthesis; genes; glycerol; iron;     Show all 8 Subjects
Abstract:
... The microbial fatty acid biosynthesis, which can be utilized as precursors for diverse chemical production has recently attracted important attention. Saturated fatty acids (SFAs) occur rarely in nature but are more significant due to their higher industrial applications. They can be improved by engineered Escherichia coli; although, the previous production was low. In this work, improvements of b ...
DOI:
10.1016/j.fbp.2021.01.001

9. Cell-cycle-dependent EBNA1-DNA crosslinking promotes replication termination at oriP and viral episome maintenance

Author:
Dheekollu, Jayaraju; Wiedmer, Andreas; Ayyanathan, Kasirajan; Deakyne, Julianna S.; Messick, Troy E.; Lieberman, Paul M.
Source:
Cell 2021 v.184 no.3 pp. 643-654.e13
ISSN:
0092-8674
Subject:
plasmids,   etc   ; ; DNA-binding proteins; Human gammaherpesvirus 4; crosslinking; humans; tyrosine;     Show all 7 Subjects
Abstract:
... Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that persists as a multicopy episome in proliferating host cells. Episome maintenance is strictly dependent on EBNA1, a sequence-specific DNA-binding protein with no known enzymatic activities. Here, we show that EBNA1 forms a cell cycle-dependent DNA crosslink with the EBV origin of plasmid replication oriP. EBNA1 tyrosine 518 (Y518) is e ...
DOI:
10.1016/j.cell.2020.12.022

10. Distribution of Virulence Factors and Resistance Determinants in Three Genotypes of Staphylococcus argenteus Clinical Isolates in Japan

Author:
Aung, Meiji Soe; Urushibara, Noriko; Kawaguchiya, Mitsuyo; Hirose, Mina; Ike, Miyo; Ito, Masahiko; Kobayashi, Nobumichi
Source:
Pathogens 2021 v.10 no.2
ISSN:
2076-0817
Subject:
plasmids,   etc   ; ; Japan; aminoglycosides; enterotoxins; genotype; macrolides; multigene family; oxacillin; virulence;     Show all 10 Subjects
Abstract:
... Staphylococcus argenteus, a novel staphylococcal species independent of S. aureus, causes a wide spectrum of infectious diseases. As detection of this species from humans and animals has been increasingly reported worldwide, its growing virulence and drug resistance via external genetic determinants has become concerning. In this study, the prevalence and genetic characteristics of virulence facto ...
DOI:
10.3390/pathogens10020163

11. A cell line development strategy to improve a bispecific antibody expression purity in CHO cells

Author:
Ding, Mingjian; Shen, Li; Xiao, Liang; Liu, Xiaohui; Hu, Jianzhong
Source:
Biochemical engineering journal 2021 v.166 pp. 107857
ISSN:
1369-703X
Subject:
plasmids,   etc   ; T-lymphocytes; antibodies; cell lines; polypeptides; therapeutics; transfection;     Show all 7 Subjects
Abstract:
... Among antibody-based therapies, bispecific antibodies (BsAbs) have gained momentum in preclinical and clinical investigations following the regulatory approvals of the T-cell engaging BsAb blinatunomab and the FVIII cofactor mimicking BsAb emicizumab. Production of BsAbs with high purity is one of the challenges in commercializing BsAb therapeutics. Therefore, several protein engineering approache ...
DOI:
10.1016/j.bej.2020.107857

12. NanoString Technology for Human Papillomavirus Typing

Author:
Rajeevan, Mangalathu S.; Patel, Sonya; Li, Tengguo; Unger, Elizabeth R.
Source:
Viruses 2021 v.13 no.2
ISSN:
1999-4915
Subject:
plasmids,   etc   ; Papillomaviridae; automation; computer software; detection limit; genes; humans; vaccination;     Show all 8 Subjects
Abstract:
... High-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter® platform for detection and digital readout of 48 HPV types in a single reaction. NanoString (NS) used proprietary software to design CodeSets: type-specific probe pairs targeting 48 ...
DOI:
10.3390/v13020188

13. Molecular characterization for food safety assessment of a genetically modified late blight resistant potato: an unusual case

Author:
Zarka, Kelly A.; Hokanson, Karen; Douches, David S.
Source:
Transgenic research 2021 v.30 no.2 pp. 169-183
ISSN:
0962-8819
Subject:
plasmid vectors; plasmids,   etc   ; Phytophthora infestans; commercialization; food safety; genetic engineering; genetic markers; potatoes; safety assessment; Bangladesh; Indonesia;     Show all 11 Subjects
Abstract:
... Standard food safety assessments of genetically modified crops require a thorough molecular characterization of the novel DNA as inserted into the plant that is intended for commercialization, as well as a comparison of agronomic and nutritional characteristics of the genetically modified to the non-modified counterpart. These characterization data are used to identify any unintended changes in th ...
DOI:
10.1007/s11248-021-00241-2

14. Click Synthesis of Size- and Shape-Tunable Star Polymers with Functional Macrocyclic Cores for Synergistic DNA Complexation and Delivery

Author:
Carbajo-Gordillo, Ana I.; Jiménez Blanco, José L.; Benito, Juan M.; Lana, Hugo; Marcelo, Gema; Di Giorgio, Christophe; Przybylski, Cédric; Hinou, Hiroshi; Ceña, Valentín; Ortiz Mellet, Carmen; Mendicuti, Francisco; Tros de Ilarduya, Conchita; García Fernández, José M.
Source:
Biomacromolecules 2020 v.21 no.12 pp. 5173-5188
ISSN:
1526-4602
Subject:
plasmids,   etc   ; cyclodextrins; cytotoxicity; dendrimers; transfection;     Show all 5 Subjects
Abstract:
... The architectural perfection and multivalency of dendrimers have made them useful for biodelivery via peripheral functionalization and the adjustment of dendrimer generations. Modulation of the core-forming and internal matrix-forming structures offers virtually unlimited opportunities for further optimization, but only in a few cases this has been made compatible with strict diastereomeric purity ...
DOI:
10.1021/acs.biomac.0c01283

15. In situ analysis of antibiotic resistance genes in anaerobically digested dairy manure and its subsequent disposal facilities

Author:
Lu, Yi; Sun, Renhua; Zhang, Changai; Ding, Shaohua; Ying, Mengfei; Shan, Shengdao
Source:
Bioresource technology 2021 v.333 pp. 124988
ISSN:
0960-8524
Subject:
plasmids,   etc   ; Clostridium difficile; anaerobic digestion; antibiotic resistance; dairy manure; metagenomics; quantitative polymerase chain reaction; slurries; soil;     Show all 9 Subjects
Abstract:
... The metagenomic and quantitative polymerase chain reaction approaches were combined to evaluate the profiles of ARGs and plasmids in anaerobically digested dairy manure in situ and reveal the persistence and elevation of typical ARGs and plasmids in its subsequent disposal facilities in CAFOs, respectively. Our results indicated that the typical ARGs and plasimd were mainly sul2, mefa, tetm-01, te ...
DOI:
10.1016/j.biortech.2021.124988

16. Acute hepatopancreatic necrosis disease (AHPND) toxin degradation by Bacillus subtilis DSM33018

Author:
Nguyen, Ngoc Diem; Pande, Gde Sasmita Julyantoro; Kashem, Md Abul; Baruah, Kartik; Bossier, Peter
Source:
Aquaculture 2021 v.540 pp. 736634
ISSN:
0044-8486
Subject:
plasmids,   etc   ; Artemia franciscana; Bacillus subtilis; Penaeidae; Vibrio parahaemolyticus; mortality; necrotizing hepatopancreatitis; shrimp; shrimp culture; toxicity; toxins;     Show all 11 Subjects
Abstract:
... Early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND), results in significant mortality in penaeid shrimp aquaculture. AHPND is caused by toxins secreted by pathogenic strains of Vibrio parahaemolyticus, that have acquired a unique 63–70 kb AHPND-associated plasmid (pVA1). This plasmid encodes the binary PirA/Bⱽᴾ toxins that consist of two subunits PirAⱽᴾ and PirBⱽᴾ. Co ...
DOI:
10.1016/j.aquaculture.2021.736634

17. Comparative genomics provides new insights into pathogenesis of spotting disease causative bacteria in farmed Strongylocentrotus intermedius

Author:
Sun, Jingxian; Liu, Li; Zhan, Yaoyao; Song, Jian; Zhang, Weijie; Wang, Bin; Chang, Yaqing
Source:
Aquaculture 2021 v.539 pp. 736564
ISSN:
0044-8486
Subject:
plasmids,   etc   ; Strongylocentrotus intermedius; Vibrio; aquaculture; biomarkers; genomics; pathogenesis; phylogeny; virulence; China;     Show all 10 Subjects
Abstract:
... The bacterial genus Vibrio includes major pathogens of spotting disease in sea urchins. However, information concerning spotting disease causative Vibrio species is still lacking in regard to genetic features, classification biomarkers, and evolutionary relationships. The current study provides complete genome descriptions of two Vibrio strains (named HD-1 and HD-2) isolated from diseased Strongyl ...
DOI:
10.1016/j.aquaculture.2021.736564

18. Zn2+-dependent enhancement of Atrazine biodegradation by Klebsiella variicola FH-1

Author:
Zhang, Jinpeng; Wu, Xian; Zhang, Xianghui; Pan, Hongyu; Shearer, Julia E.S.; Zhang, Hao; Sun, Fengjie
Source:
Journal of hazardous materials 2021 v.411 pp. 125112
ISSN:
0304-3894
Subject:
plasmids,   etc   ; Klebsiella variicola; atrazine; biodegradation; chromosomes; flow cytometry; fluorescence; hydrolases; membrane permeability; mutants;     Show all 10 Subjects
Abstract:
... Degradation efficiency of Atrazine by Klebsiella variicola FH-1 is improved by the addition of Zn²⁺. Both the chromosome and plasmid genomes of strain FH-1 were sequenced and annotated to identify genes involved in the degradation of Atrazine. Four open reading frames (ORFs) 1040, 2582, 3597, and 4043 encoding Zn²⁺-dependent hydrolases were knocked out to verify their predicted functions in the de ...
DOI:
10.1016/j.jhazmat.2021.125112

19. Development of multiplexing gene silencing system using conditionally induced polycistronic synthetic antisense RNAs in Escherichia coli

Author:
Fujita, Shouta; Tsumori, Yutaka; Makino, Yuko; Saito, Mineki; Kawano, Mitsuoki
Source:
Biochemical and biophysical research communications 2021 v.556 pp. 163-170
ISSN:
0006-291X
Subject:
plasmids,   etc   ; Escherichia coli; alkaline phosphatase; antisense RNA; eukaryotic cells; genes; models; promoter regions; research;     Show all 9 Subjects
Abstract:
... Although efficient methods of gene silencing have been established in eukaryotes, many different techniques are still used in bacteria due to the lack of a standardized tool. Here, we developed a convenient and efficient method to downregulate the expression of a specific gene using ∼140 nucleotide RNA with a 24-nucleotide antisense region from an arabinose-inducible expression plasmid by taking E ...
DOI:
10.1016/j.bbrc.2021.03.152

20. A novel plasmid from Aerococcus urinaeequi of porcine origin co-harboring the tetracycline resistance genes tet(58) and tet(61)

Author:
Yang, Qin; Zhu, Yao; Schwarz, Stefan; Wang, Lingli; Liu, Wenyu; Yang, Wenlin; Luan, Tian; Liu, Siguo; Zhang, Wanjiang
Source:
Veterinary microbiology 2021 v.257 pp. 109065
ISSN:
0378-1135
Subject:
plasmids,   etc   ; Aerococcus; Escherichia coli; animal production; doxycycline; ribosomes; swine; tetracycline; veterinary medicine;     Show all 9 Subjects
Abstract:
... Tetracyclines are the broad-spectrum agents used in veterinary medicine and food animal production. Known mechanisms of tetracycline resistance include ribosome protection, active efflux and enzymatic inactivation. However, the presence of two different tet genes conferring different resistance mechanisms on the same plasmid has rarely been reported. In this study, we identified the tandem tetracy ...
DOI:
10.1016/j.vetmic.2021.109065