Plasmids - Science topic

In this work, Oxford Nanopore sequencing is tested as an accessible method for quantifying heterogeneity of amplified DNA. This method enables rapid quantification of deletions, insertions, and substitutions, the probability of each mutation error, and their locations in the replicated sequences. Amplification techniques tested were conventional po...

Carbapenems are the last-resort antibiotics used to treat infections caused by bacterial pathogens. Many bacterial pathogens have evolved to produce NDM carbapenemases to hydrolyze carbapenems, posing a great challenge to public health. In this study, we report a multidrug resistant clinical E. coli strain 673. Strain 673 belongs to sequence type (...

Autonomously replicating sequences (ARSs) are important accessories in episomal vectors that allow them to be replicated and stably maintained within transformants. Despite their importance, no information on ARSs in diatoms has been reported. Therefore, we attempted to identify ARS candidates in the model diatom, Phaeodactylum tricornutum, via chr...

Untreated chicken manure causes a large amount of antibiotics and heavy metals to enter the soil environment. Currently, there is limited research on antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in soil profile. In this study, we conducted a preliminary investigation on the soil profile of vegetable field contaminated...

Background: Introducing unnatural base pairs into a natural, double-stranded DNA construct is a powerful tool within synthetic biology. Accordingly, the ability to detect these unnatural base pairs has many applications, including the study and detection of semisynthetic organisms. Objective and Methods: The work described here aimed to select huma...

Duck Tembusu virus (DTMUV) is an emerging flavivirus that has inflicted significant economic losses on China’s poultry industry. Rapid and accurate detection of DTMUV is crucial for effective prevention and control measures. In this study, we developed a novel, rapid visual detection assay that combines reverse transcriptase loop-mediated isotherma...

Background Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to...

The non-structural protein 1 (nsp1) of SARS-CoV-2 plays a key role in host innate immune evasion. We identified two deletion variants (Δ82-85 and Δ 83-86) in the N-terminal region of the nsp1 of a SARS-CoV-2 BA.5.2.1 variant recovered from a human patient. Analysis of the sequence databases revealed a frequency of 0.5% of these mutations amongst av...

Tuberculosis ( TB ), the disease caused by Mycobacterium tuberculosis ( Mtb ), remains a major health problem with 10.6 million cases of the disease and 1.6 million deaths in 2021. It is well understood that pulmonary TB is due to Mtb growth in the lung but quantitative estimates of rates of Mtb replication and death in lungs of patients or animals...

We have developed a cell-based relocalization (ReLo) assay for the detection of direct protein-protein interactions. In the assay, one protein is anchored to a membrane, causing the other protein to relocalize upon interaction. The assay can be used to study the influence of protein domains, post-translational modifications, protein conformations,...

The first-generation pCMViR-TSC, implemented through the promoter sandwich rule, yields 10- to 100-fold higher gene expression than the standard plasmid used with the CMV (cytomegalovirus) or CAG promoter. However, the vector’s shortcomings limit its utility to transient expression only, as it is not suitable for establishing stable transformants i...

Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compared 38,912 bacterial genomes and 6,073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-ass...

A laser-plasma source emitting photons with energies in the water window spectral range has been used to reveal the radiation chemical yields of single-strand breaks in plasmid DNA as a function of ·OH radical scavenger concentration. Direct and indirect effects were investigated separately using DNA samples with various levels of hydration. We exp...

Tibial dyschondroplasia (TD) is a kind of metabolic bone disease in fast-growing broilers, which seriously restricts the development of poultry industry. Our previous studies have revealed a significant upregulation of miR-205a in TD cartilage tissue, suggesting its potential role as a regulatory factor in the pathogenesis of TD. However, the preci...

The virulence plasmid of the obligate intracellular bacterium Chlamydia encodes eight proteins. Among these, Pgp3 is crucial for pathogenicity, and Pgp4 functions as a transcriptional regulator of both plasmid and chromosomal genes. The remaining proteins, Pgp1, Pgp5, Pgp6, Pgp7, and Pgp8, are predicted to play various roles in plasmid replication...

Background and Objectives Tripartite motif-containing protein 50 (TRIM50) is a recently discovered E3 ubiquitin ligase that participates in tumor progression. TRIM50 is overexpressed in many cancers, although few studies focused on TRIM50‘s role in breast cancer. Methods We overexpressed TRIM50 in triple-negative breast cancer cell lines using pla...

The transformation of DNA into cells is the basis of molecular biology. Commonly employed techniques include heat shock transformation, electro-transformation, conjugation, transduction, and protoplast fusion. Recently, ultrasonic transformation technology has been developed to transfer DNA into competent cells. The transformation conditions, such...

Numerous studies have reported in the past that the use of protein‐encoding DNA hydrogels as templates for cell‐free protein synthesis (CFPS) leads to better yields than the use of conventional templates such as plasmids or PCR fragments. Systematic investigation of different types of bulk materials from pure DNA hydrogels and DNA hydrogel composit...

This study aims to explore the inhibitory effects of combined metformin and simvastatin therapy on the malignant progression of glioma. The research specifically examines how the maturation of SREBP2 as a transcription factor affects the expression of GLUT1 and GLUT6 in glioma cells. Additionally, it investigates the impact of this combination ther...

Conjugative plasmids are important drivers of bacterial evolution. Most plasmids lack genes for conjugation and characterized origins of transfer (oriT), which has hampered our understanding of plasmid mobility. Here we used bioinformatic analyses to characterize occurrences of known oriT families across 38,057 plasmids, confirming that most conjug...

The plasmid encoded mobile colistin resistance (MCRs) enzyme poses a significant challenge to the clinical efficacy of colistin, which is frequently employed as a last resort antibiotic for treating infections caused by multidrug resistant bacteria. This transferase catalyzes the addition of positively charged phosphoethanolamine to lipid A of the...

Chromopyrrolic acid (CPA) and its congeners are important intermediates for the biosynthesis and synthesis of various dimeric tryptophan natural products. We have constructed two E. coli strains (CPA001/CPA002) harboring a single plasmid carrying genes coding for a combination of two enzymes (LaStaO/LzrO and VioB) that are able to convert L‐tryptop...

In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discover...

Staphylococcus aureus can cause outbreaks and becomes multi-drug resistant through gene mutations and acquiring resistance genes. However, why S. aureus easily adapts to hospital environments, promoting resistance and recurrent infections, remains unknown. Here we show that a specific S. aureus lineage evolved from a clone that expresses the access...

Background WHIM syndrome is a rare, autosomal dominant inborn error of immunity characterized by warts, hypogammaglobulinemia, infection, and myelokathexis. It is caused mainly by heterozygous mutations at the C-terminus of the C-X-C chemokine receptor type 4 (CXCR4) gene. Methods We described the detailed clinical, genetic, immunological and trea...

The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that infl...

The balance between chromosomal and plasmid DNAs determines the genomic plasticity of prokaryotes. Natural selections, acting on the level of organisms or plasmids, shape the abundances of plasmid DNAs in prokaryotic genomes. Despite the importance of plasmids in health and engineering, there have been rare systematic attempts to quantitatively mod...

The transferable genetic elements are associated with the dissemination of virulence determinants amongst Klebsiella pneumoniae. Thus, we assessed the correlated antimicrobial resistance in carbapenem-resistant Klebsiella pneumoniae clinical isolates. Each isolate’s ability to biosynthesize biofilm, carbapenemase, and extended-spectrum β-lactamase...

Plasmids include genes that code for precise functions, like resistance to antibiotic and virulence factors, which allow microorganisms to survive treatment and flourish in the hostile host environment. Organized with other genetic components like integrating genes and transposons, plasmids help transmit these traits through a variety of mechanisms...

Recent advancements in bacterial two-component systems (TCS) have spurred research into TCS-based biosensors, notably for their signal amplification and broad input responsiveness. The CusRS system in Escherichia coli (E. coli), comprising cusS and cusR genes, is a copper-sensing module in E. coli. However, due to insufficient sensing performance,...

The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed...

The rapid rise of multidrug resistance (MDR) among Gram-negative bacteria has accelerated the development of novel therapies. Ceftazidime-avibactam (CZA) is a novel β-lactam/β-lactamase inhibitor recently approved for the treatment of limited infectious diseases. Here, we describe a novel CMY variant, CMY-192, that confers high-level resistance to...

The Lyme disease agent Borrelia burgdorferi is a polyploid bacterium with a segmented genome in which both the chromosome and over 20 distinct plasmids are present in multiple copies per cell. This pathogen can survive at least nine months in its tick vector in an apparent dormant state between blood meals, without losing cell proliferative capabil...

In this study, a highly levansucrase-producing strain was isolated, identified as Bacillus lichniformans MJ8, and registered with the accession number OM672244.1 in the NCBI database. The SacB gene responsible for levansucrase production was transferred from this bacterium into Escherichia coli. It was found that the gene contains 1449 bp nucleotid...

Background Transcription factor 7-like 2 (TCF7L2) variants seem to affect diabetes susceptibility through β-cell dysfunction, underlying basis of which has been considered to be β-cell dedifferentiation rather than apoptotic β-cell death. The Extracellular regulated protein kinases/Mitogen-activated protein kinase signaling pathway (ERK/MAPK signal...

Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation in prokaryotes. Shufflon invertase (SI) Rci from plasmid R64, recognizing asymmetric sfx sites, has been adopted as a tool for synthetic biology. However, the availability of a single enzyme with moderate rates of recombination has...

High-copy-number plasmids are indispensable tools for gene overexpression studies in prokaryotes to engineer pathways or probe phenotypes of interest. The development of genetic tools for the industrially relevant Actinobacteria is of special interest, given their utility in producing keratolytic enzymes and biologically active natural products. Wi...

Background Senecavirus A (SVA) is a newly pathogenic virus correlated with the acute death of piglets and vesicular lesions in pigs. The further prevalence of SVA will cause considerable economic damage to the global pig farming industry. Therefore, rapid and accurate diagnostic tools for SVA are crucial for preventing and controlling the disease....

Here, we report the genetic features and evolutionary mechanisms of two tet (M)-bearing plasmids (pTA2 and pTA7) recovered from swine Escherichia coli isolates. The genetic profiles of pTA2 and pTA7 and corresponding transconjugants were accessed by S1 nuclease pulsed-field gel electrophoresis and Southern hybridization, followed by whole genome se...

We announce the complete genome sequence of Sagittula stellata strain E-37. The hybrid assembly of long and short reads revealed one chromosome and four plasmids. Furthermore, the genome analysis showed that the plasmid-encoded type six secretion system is linked to plasmid replication genes that may be common to Roseobacters.

Species of the Karenia genus are widely distributed in global waters and frequently cause harmful algal blooms (HABs), posing significant threats to coastal ecosystems, aquaculture, and human safety. Among them, Karenia brevis is one of the most extensively studied species due to its production of brevetoxins, which are highly toxic to marine life...

Site-directed mutagenesis is a fundamental tool indispensable for protein and plasmid engineering. An important technological question is how to achieve the efficiency at the ideal level of 100%. Based on complementary primer pairs, the QuickChange method has been widely used, but it requires significant improvements due to its low efficiency and f...

This study presented a novel breast cancer therapy model that uses magnetic field-controlled heating to trigger gene expression in cancer cells. We created silica- and amine-modified superparamagnetic nanoparticles (MSNP-NH2) to carry genes and release heat under an alternating current (AC) magnetic field. The heat-inducible expression plasmid (pHS...

Tracking the localization and proximal interaction partners of endogenous proteins provides valuable functional insight. Here, we present a protocol for CRISPR-based endogenous protein tagging in mammalian cells. We describe steps for endogenously tagging human TSC22D2 and MAP4, including designing Cas9 and Cas12a guides for knockin, modularized re...

Promoters for artificial control of gene expression are central tools in genetic engineering. In the budding yeast S. cerevisiae, a variety of constitutive and controllable promoters with different strengths have been constructed using endogenous gene promoters, synthetic transcription factors and their binding sequences, and artificial sequences....

Background Achieving cost-competitiveness remains challenging for industrial biomanufacturing. With whole-cell biocatalysis, inefficiency presents when individual cells vary in their production levels. The problem exacerbates when the basis for such production heterogeneity is heritable. Here, evolution selects for the low- and non-producers, as th...

Bacterial and bacteriophage genomes contain genomic regions of hyper-variability (diversity hotspots) caused by insertions of mobile genetic elements (MGEs), non-homologous recombination events and non-horizontal hypermutation. Accessory genes encoded in the diversity hotspots are involved in anti-MGE defence and counter-defence, virulence and anti...

DNA extraction technology continues to evolve along with the need for a fast and simple process. The DNA extraction with magnetic nanoparticles accommodates these demands by providing a method that is safe, simple, and yet able to give good purity. The purity parameter of the extracted DNA is based on the A260/280 value. This meta-analysis aims to...

The diarrhoeal disease, shigellosis, can be sustained as a sexually transmissible enteric illness among gay, bisexual, and other men who have sex with men (GBMSM). Multiple extensively drug-resistant strains of Shigella have been detected through genomic surveillance, which have typically been associated with plasmids carrying the gene variant bla...

Klebsiella pneumoniae is among the most important Gram-negative pathogens that can cause serious nosocomial infections. The emergence and prevalence of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP) pose a significant challenge to public health. In this study, we characterized thirty carbapenem-resistant K. pneumoniae (CRKP) strains fro...

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin-antitoxin (TA) systems serve as ubiquitous and diverse...

Transfer ribonucleic acids (tRNAs) are essential for protein synthesis, decoding mRNA sequences into amino acids. In E. coli K-12 MG1655, 86 tRNA genes are organized in 43 transcription units (TUs) and the essentiality of individual tRNA TUs in bacterial physiology remains unclear. To address this, we systematically generated 43 E. coli tRNA deleti...

Clostridium perfringens is a causative agent of various human and animal enteric diseases including food poisoning. In this study, we describe an interesting case of a persistent food poisoning outbreak among Finnish peacekeepers in Eritrea, possibly caused by Clostridium perfringens carrying a new variant of the chromosomally encoded enterotoxin g...

Fed-batch processes are prevalent in biotechnological industries, but design of experiments often results in sub-optimal conditions due to incomplete solution space characterization. We employ a single-level dynamic control (DC) algorithm for dynamic flux balance analysis (dFBA), enhancing efficiency by reducing Karush-Kuhn-Tucker (KKT) condition c...

Pseudomonas aeruginosa, a versatile bacterium, relies on several TonB-dependent transporters (TBDTs) for nutrient acquisition (such as iron-siderophore complexes) and adaptation to various environments. While some TBDTs are well characterized, a significant number remain unexplored despite their potential role in pathogenicity. In this study, we de...

Streptomyces clavuligerus is a species used worldwide to industrially produce clavulanic acid (CA), a molecule that enhances antibiotic effectiveness against β-lactamase-producing bacterial strains. Despite its low inherent CA production, hyper-producing strains have been developed. However, genomic analyses specific to S. clavuligerus and CA biosy...

Changes in intracellular concentrations of Na ⁺ and K ⁺ are shown to alter Fos gene expression. Here, we obtained a genetic construct encoding TurboGFP-dest1 gene under control of the human Fos promoter (-549; +155) and studied its expression in HEK293T. Amplification of the Fos promoter sequence from genomic DNA was only efficient in the presence...

Transfection of mammalian and human cell lines in medical research both are key technologies in molecular biology and genetic engineering. A vast variety of techniques to facilitate transfection exists including different chemical and nanoparticle-based agents as mediators of nucleic acid uptake, with nanoparticles composed of the lipids DOSPA/DOPE...