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1. Loop assembly: a simple and open system for recursive fabrication of DNA circuits

Author:
Pollak, Bernardo; Cerda, Ariel; Delmans, Mihails; Álamos, Simón; Moyano, Tomás; West, Anthony; Gutiérrez, Rodrigo A.; Patron, Nicola J.; Federici, Fernán; Haseloff, Jim
Source:
Thenew phytologist 2019 v.222 no.1 pp. 628-640
ISSN:
0028-646X
Subject:
plasmids,   etc   ; DNA assembly; genes; restriction endonucleases;     Show all 4 Subjects
Abstract:
... High‐efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucle ...
DOI:
10.1111/nph.15625

2. An improved plasmid size standard, 39R861+

Author:
Moran, Robert A.; Anantham, Sashindran; Hall, Ruth M.
Source:
Plasmid 2019 v.102 pp. 6-9
ISSN:
0147-619X
Subject:
plasmids,   etc   ; Escherichia coli; genetic conjugation; nucleotide sequences;     Show all 4 Subjects
Abstract:
... The four plasmids in E. coli 39R861 have been used as size standards for closed-circular plasmid DNA since the 1980s. However, their sizes had only been estimated. Here, the complete sequence of the 61.3 kb cryptic FII plasmid p39R861–3 is reported, and the sizes of p39R861–4, pSa and NTP168 were determined to be 155.8, 40.1 and 6.8 kb, respectively. An improved size standard, 39R861+, was created ...
DOI:
10.1016/j.plasmid.2019.01.002

3. A modified method for plasmid extraction from Lactobacillus plantarum contained lysozyme removal step

Author:
Yao, F.; Xu, X.Y.; Pan, Q.
Source:
Analytical biochemistry 2019 v.566 pp. 37-39
ISSN:
0003-2697
Subject:
plasmids,   etc   ; Lactobacillus plantarum; Weissella cibaria; lysozyme; protocols;     Show all 5 Subjects
Abstract:
... Plasmids of Lactobacillus plantarum PC518 cannot be effectively extracted by existing methods. It was studied that the effect of lysozyme treatment and removal on plasmid extraction by 7 protocols. The modified method was compared with a commercial kit using L. plantarum PC518, 410, 9L15, and JS193 and Weissella cibaria M2 as the tested strains. The results suggested that the step of lysozyme remo ...
DOI:
10.1016/j.ab.2018.11.005

4. Correction to: Rational design of engineered microbial cell surface multi-enzyme co-display system for sustainable NADH regeneration from low-cost biomass

Author:
Han, Lei; Liang, Bo; Song, Jianxia; Liu, Aihua
Source:
Journal of industrial microbiology & biotechnology 2018 v.45 no.9 pp. 855
ISSN:
1367-5435
Subject:
plasmids,   etc   ; NAD (coenzyme); biomass;     Show all 3 Subjects
Abstract:
... In the original publication, the author group has been published incorrectly. All authors have agreed to add Aihua Liu as co-author of this article, since the original idea for the experiments, the experimental expertise and some of the plasmids originated from him. ...
DOI:
10.1007/s10295-018-2065-x

5. Assembly of TALE-based DNA scaffold for the enhancement of exogenous multi-enzymatic pathway

Author:
Xie, Si-si; Qiu, Xin-yuan; Zhu, Lv-yun; Zhu, Chu-shu; Liu, Chuan-yang; Wu, Xiao-min; Zhu, Lingyun; Zhang, Dong-yi
Source:
Journal of biotechnology 2019 v.296 pp. 69-74
ISSN:
0168-1656
Subject:
plasmids,   etc   ; Escherichia coli; biochemical pathways; enzymes; transcription (genetics);     Show all 5 Subjects
Abstract:
... Synthetic scaffold systems, which exhibit enzyme clustering effect, have been considered as an important parallel approach for metabolic flux control and pathway enhancement. Here, we described an improved DNA-based scaffold system for synthetic tri-enzymatic pathway in Escherichia coli. With plasmid DNA serving as scaffold and exogenous enzymes fused with rationally designed transcription activat ...
DOI:
10.1016/j.jbiotec.2019.03.008

6. Pif1-Family Helicases Support Fork Convergence during DNA Replication Termination in Eukaryotes

Author:
Deegan, Tom D.; Baxter, Jonathan; Ortiz Bazán, María Ángeles; Yeeles, Joseph T.P.; Labib, Karim P.M.
Source:
Molecular cell 2019 v.74 no.2 pp. 231-244.e9
ISSN:
1097-2765
Subject:
plasmids,   etc   ; DNA helicases; DNA replication; Escherichia coli; eukaryotic cells; yeasts;     Show all 6 Subjects
Abstract:
... The convergence of two DNA replication forks creates unique problems during DNA replication termination. In E. coli and SV40, the release of torsional strain by type II topoisomerases is critical for converging replisomes to complete DNA synthesis, but the pathways that mediate fork convergence in eukaryotes are unknown. We studied the convergence of reconstituted yeast replication forks that incl ...
DOI:
10.1016/j.molcel.2019.01.040

7. Immobilization of plasmids in bacterial nanocellulose as gene activated matrix

Author:
Pötzinger, Yvette; Rahnfeld, Lisa; Kralisch, Dana; Fischer, Dagmar
Source:
Carbohydrate polymers 2019 v.209 pp. 62-73
ISSN:
0144-8617
Subject:
plasmids,   etc   ; bacteria; biocompatibility; cellulose; genes; scanning electron microscopy; staining; transfection;     Show all 8 Subjects
Abstract:
... The synergy of the local delivery of nucleic acids using a hydrogel-based gene activated matrix (GAM) might support regenerative processes on a genetic level by concurrently providing a cell-friendly microenvironment. To investigate bacterial nanocellulose (BNC) as GAM, two plasmids (pSV-β-Gal and pGL3) were incorporated by reswelling and injection techniques forming matrix and core-shell systems ...
DOI:
10.1016/j.carbpol.2019.01.009

8. A rapid bioanalytical tool for detection of sequence-specific circular DNA and mitochondrial DNA point mutations

Author:
Zhang, Yuqian; Kaynak, Ahmet; Huang, Taosheng; Esfandiari, Leyla
Source:
Analytical and bioanalytical chemistry 2019 v.411 no.10 pp. 1935-1941
ISSN:
1618-2642
Subject:
plasmids,   etc   ; denaturation; mitochondrial DNA; point mutation; polymerase chain reaction; screening;     Show all 6 Subjects
Abstract:
... Mutations in mitochondrial DNA (mtDNA) have been an essential cause of numerous diseases, making their identification critically important. The majority of mtDNA screening techniques require polymerase chain reaction (PCR) amplification, enzymatic digestion, and denaturation procedures, which are laborious and costly. Herein, we developed a sensitive PCR-free electrokinetic-based sensor combined w ...
DOI:
10.1007/s00216-019-01683-8

9. Naturally-occurring right terminal hairpin mutations in three genotypes of canine parvovirus (CPV-2a, CPV-2b and CPV-2c) have no effect on their growth characteristics

Author:
Yu, Yongle; Zhang, Jianlou; Wang, Jigui; Xi, Ji; Zhang, Xiaomei; Li, Peiran; Liu, Ying; Liu, Weiquan
Source:
Virus research 2019 v.261 pp. 31-36
ISSN:
0168-1702
Subject:
plasmids,   etc   ; Carnivore protoparvovirus 1; genotype; mutation; nucleotide sequences; China;     Show all 6 Subjects
Abstract:
... We have isolated 4 naturally-occurring strains of CPV in mainland China and have identified them as CPV-2, 2a, 2b and 2c genotypes according to their VP2 sequences which also revealed substitutions within their right terminal regions. To determine if these substitutions affected the growth characteristics of the 4 strains, we constructed plasmids based on their genomic sequences minus their right ...
DOI:
10.1016/j.virusres.2018.12.007

10. Overexpression system for recombinant RNA in Corynebacterium glutamicum using a strong promoter derived from corynephage BFK20

Author:
Hashiro, Shuhei; Mitsuhashi, Mayu; Yasueda, Hisashi
Source:
Journal of bioscience and bioengineering 2019
ISSN:
1389-1723
Subject:
plasmid vectors; plasmids,   etc   ; Corynebacterium glutamicum; fermenters; gene overexpression; messenger RNA; models; nucleotides; pesticides; ribonucleases; small nuclear RNA; therapeutics;     Show all 12 Subjects
Abstract:
... In recent years, it has been shown that recombinant RNA molecules have a great potential in mRNA therapy and as novel agricultural pesticides. We developed a fundamental system for efficient production of target RNA molecules in Corynebacterium glutamicum, composed of a strong promoter named F1 and a terminator derived from corynephage BFK20 in a high-copy number plasmid vector. As a target model ...
DOI:
10.1016/j.jbiosc.2019.03.003

11. Dendritic targeted mRNA expression via a cis-acting RNA UTR element

Author:
Lu, Liangsheng; Zhang, Fan; Li, Yuting; Yang, AnYong; Guan, Chenguang; Ding, Xin; Liu, Yuan; Liu, Yuyan; Zhang, Chen-Yu; Li, Liang; Zhang, Qipeng
Source:
Biochemical and biophysical research communications 2019 v.509 no.2 pp. 402-406
ISSN:
0006-291X
Subject:
plasmid vectors; plasmids,   etc   ; Tick-borne encephalitis virus; cytotoxicity; gene expression; genes; messenger RNA; neurites; neuroplasticity; proteins; virion;     Show all 11 Subjects
Abstract:
... Local translation in neurites is considered as an important mechanism to modulate synaptic plasticity of neurons. However, it is hard to specifically express a protein-coding gene in neurites. Recently, the 5′-UTR of Tick-borne encephalitis virus (TBEV) is reported to be able to drive its RNA to the dendrites of infected neurons, as a cis-acting RNA element. To construct a neurite specific gene ex ...
DOI:
10.1016/j.bbrc.2018.12.137

12. Genetic control of ColE1 plasmid stability that is independent of plasmid copy number regulation

Author:
Standley, Melissa S.; Million-Weaver, Samuel; Alexander, David L.; Hu, Shuai; Camps, Manel
Source:
Current genetics 2019 v.65 no.1 pp. 179-192
ISSN:
0172-8083
Subject:
plasmid vectors; plasmids,   etc   ; Escherichia coli; bioremediation; cell division; fluorescence microscopy; gene expression; genes; genetic engineering; models; point mutation; replication origin;     Show all 12 Subjects
Abstract:
... ColE1-like plasmid vectors are widely used for expression of recombinant genes in E. coli. For these vectors, segregation of individual plasmids into daughter cells during cell division appears to be random, making them susceptible to loss over time when no mechanisms ensuring their maintenance are present. Here we use the plasmid pGFPuv in a recA relA strain as a sensitized model to study factors ...
DOI:
10.1007/s00294-018-0858-0

13. Triple deletion of clpC, porB, and mepA enhances production of small ubiquitin-like modifier-N-terminal pro-brain natriuretic peptide in Corynebacterium glutamicum

Author:
Peng, Feng; Liu, Xiuxia; Wang, Xinyue; Chen, Jing; Liu, Meng; Yang, Yankun; Bai, Zhonghu
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.1 pp. 67-79
ISSN:
1367-5435
Subject:
plasmid curing; plasmids,   etc   ; Corynebacterium glutamicum; gene editing; genes; heart failure; hosts; mutants; natriuretic peptides; protein synthesis; proteinases; proteolysis; recombinant proteins;     Show all 13 Subjects
Abstract:
... In our previous work, a two-plasmid CRISPR/Cas9 system was constructed for genome editing in Corynebacterium glutamicum. To increase the transformation efficiency and simplify the plasmid curing steps, an all-in-one CRISPR/Cas9 system was constructed for efficient genome editing. In addition, to research proteolysis during the production of recombinant proteins and generate a host for enhanced exp ...
DOI:
10.1007/s10295-018-2091-8

14. Plasmid curing resulted in improved heterologous gene expression in Leuconostoc citreum EFEL2700

Author:
Jang, Y.‐J.; Kim, S.‐A.; Seo, S.‐O.; Li, L.; Han, N.S.
Source:
Letters in applied microbiology 2019 v.68 no.5 pp. 430-436
ISSN:
0266-8254
Subject:
plasmid curing; plasmids,   etc   ; Leuconostoc citreum; enzyme activity; gene editing; gene expression; genes; heterologous gene expression; kimchi; metabolic engineering; phenotype; protein synthesis;     Show all 12 Subjects
Abstract:
... Leuconostoc citreum EFEL2700 isolated from kimchi was used as a host strain for genetic and metabolic engineering in our previous studies, but the cells of EFEL2700 contained a cryptic plasmid (P‐cells). Thus, we created plasmid‐free cells (F‐cells) using the CRISPR/Cas9 system. In this study, we compared the microbial characteristics of P‐ and F‐cells in terms of growth rate, biochemical properti ...
DOI:
10.1111/lam.13118

15. Biodegradation of dinitrotoluene sulfonates and other nitro-aromatic compounds by Pseudomonas sp. X5 isolated from TNT red water contaminated soil

Author:
Xu, Wenjie; Zhao, Quanlin; Li, Zhilin; Lu, Xinyue; Han, Shiqun; Ye, Zhengfang
Source:
Journal of cleaner production 2019 v.214 pp. 782-790
ISSN:
0959-6526
Subject:
plasmid curing; plasmids,   etc   ; Pseudomonas; bacteria; biodegradation; genes; liquid chromatography; mass spectrometry; nitroaromatic compounds; pH; pollutants; polluted soils; salinity; sulfonates; trinitrotoluene; water pollution; China;     Show all 17 Subjects
Abstract:
... A dinitrotoluene sulfonates degrading bacterium strain Pseudomonas sp. X5 was isolated from 2, 4, 6-trinitrotoluene red water contaminated soil in Gansu, China, which was used for biodegradation of dinitrotoluene sulfonates. The growth experiments were carried out to optimize the growth condition of X5. Effect of inoculation amount was investigated. Plasmid curing tests were conducted to determine ...
DOI:
10.1016/j.jclepro.2019.01.025

16. Oxacillin-susceptible mecA-positive Staphylococcus aureus associated with processed food in Europe

Author:
Quijada, Narciso M.; Hernández, Marta; Oniciuc, Elena-Alexandra; Eiros, José María; Fernández-Natal, Isabel; Wagner, Martin; Rodríguez-Lázaro, David
Source:
Food microbiology 2019 v.82 pp. 107-110
ISSN:
0740-0020
Subject:
plasmids,   etc   ; air; airports; cheeses; gene expression; genes; methicillin-resistant Staphylococcus aureus; processed foods; Austria;     Show all 9 Subjects
Abstract:
... We report for the first time an oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) associated with a processed food product in Europe. One isolate (MRSA-ST5-type V SCCmec) was found in cheese among 600 food samples confiscated from air passengers from international flights in Vienna Airport (Austria). Type V SCCmec strains do not harbor functional mecI-mecR1 genes and in such stra ...
DOI:
10.1016/j.fm.2019.01.021

17. Construction, expression and antiviral activity analysis of recombinant adenovirus expressing human IFITM3 in vitro

Author:
Du, Shouwen; Jiang, Yinyue; Xu, Wang; Bai, Jieying; Tian, Mingyao; Wang, Maopeng; Wang, Yuhang; Cao, Tingting; Song, Lina; Jiang, Yuhang; Chen, Jing; Fu, Tingting; Hao, Penfeng; Li, Tiyuan; Wu, Shipin; Ren, Linzhu; Jin, Ningyi; Li, Chang
Source:
International journal of biological macromolecules 2019 v.131 pp. 925-932
ISSN:
0141-8130
Subject:
plasmids,   etc   ; Adenoviridae; Influenza A virus; antiviral properties; genes; humans; morphogenesis; progeny; transcription (genetics); transmembrane proteins;     Show all 10 Subjects
Abstract:
... Interferon-inducible transmembrane protein 3 (IFITM3) inhibits the replication of multiple pathogenic viruses by blocking their entry. In this study, we constructed a shuttle plasmid, harboring human IFITM3. Thereafter, recombinant adenovirus rAd5-IFITM3 was obtained by co-transfection of the linearized viral backbone vector pAd5 and the shuttle plasmid. The results showed that human IFITM3 did no ...
DOI:
10.1016/j.ijbiomac.2019.03.161

18. TLR2 promotes development and progression of human glioma via enhancing autophagy

Author:
Li, Chenglong; Ma, Lixin; Liu, Yongliang; Li, Zhenzhu; Wang, Qingbo; Chen, Zheng; Geng, Xin; Han, Xinyu; Sun, Jingdong; Li, Zefu
Source:
Gene 2019 v.700 pp. 52-59
ISSN:
0378-1119
Subject:
plasmids,   etc   ; Toll-like receptor 2; Western blotting; autophagy; cell cycle; genome; glioma; humans; patients; prognosis;     Show all 10 Subjects
Abstract:
... In this study, we aim to evaluate Toll-like receptor 2 (TLR2) expression in human glioma tumors and the correlation between its expression with degrees of malignancy and autophagy, development of tumors.Immunohistochemistry and Western blot were carried out to determine the expression of LC3, Beclin1 and TLR2 in 74 glioma specimens. We analyzed the prognosis of 551 glioma patients through the Canc ...
DOI:
10.1016/j.gene.2019.02.084

19. A co-delivery platform based on plasmid DNA peptide-surfactant complexes: formation, characterization and release behavior

Author:
Costa, Diana; Albuquerque, Tânia; Queiroz, João A.; Valente, Artur J.M.
Source:
Colloids and surfaces 2019 v.178 pp. 430-438
ISSN:
0927-7765
Subject:
plasmids,   etc   ; cationic surfactants; cytotoxicity; doxorubicin; encapsulation; nanoparticles; nitrogen; paclitaxel; peptides; phosphates; therapeutics;     Show all 11 Subjects
Abstract:
... The development of delivery systems based on cell penetrating peptides represents an incredible asset and may deeply contribute for the evolution of therapies efficacy. In this context, we explore the plasmid DNA (pDNA) condensation ability of TAT peptide to produce a suitable intracellular delivery platform. The nanoparticles were formed at various ratios of nitrogen to phosphate groups (N/P) and ...
DOI:
10.1016/j.colsurfb.2019.03.029

20. Agroinfiltration is a key factor to improve the efficiency of apple and pear transformation

Author:
Chevreau, Elisabeth; Dousset, Nicolas; Joffrion, Clément; Richer, Andréa; Charrier, Aurélie; Vergne, Emilie
Source:
Scientia horticulturae 2019 v.251 pp. 150-154
ISSN:
0304-4238
Subject:
plasmids,   etc   ; Agrobacterium radiobacter; agroinfiltration; apples; crushing; explants; genetic transformation; inoculum; pears; surfactants; transgenic plants;     Show all 11 Subjects
Abstract:
... Genetic transformation of apple and pear is mainly performed via Agrobacterium tumefaciens. The average efficiency of transformation remains low in most laboratories and the success of the transformation experiments is very variable. Improving the efficiency and the reproducibility of apple and pear transformation is thus highly desirable. Adventitious regeneration ability of the explants is not a ...
DOI:
10.1016/j.scienta.2019.03.003