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Academic literature on the topic 'Plasmids'

Author: Grafiati

Published: 4 June 2021

Last updated: 31 July 2024

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Journal articles on the topic "Plasmids"

Lopez, Jaime G., Mohamed S. Donia, and Ned S. Wingreen. "Modeling the ecology of parasitic plasmids." ISME Journal 15, no. 10 (April 8, 2021): 2843–52. http://dx.doi.org/10.1038/s41396-021-00954-6.

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AbstractPlasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids’ natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid’s population dynamics and optimal infection strategy are strongly determined by the plasmid’s HGT mechanism. We then analyze models of co-infecting plasmids and show that parasitic plasmids are prone to a “tragedy of the commons” in which runaway plasmid invasion severely reduces host fitness. We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. We derive predicted distributions of unique plasmid types in genomes—comparison to the distribution of plasmids in a collection of 17,725 genomes supports a model of parasitic plasmids with positive plasmid–plasmid interactions that ameliorate plasmid fitness costs or promote the invasion of new plasmids.

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Lopez-Diaz, Maria, Nicholas Ellaby, Jane Turton, Neil Woodford, Maria Tomas, and Matthew J. Ellington. "NDM-1 carbapenemase resistance gene vehicles emergent on distinct plasmid backbones from the IncL/M family." Journal of Antimicrobial Chemotherapy 77, no. 3 (January 5, 2022): 620–24. http://dx.doi.org/10.1093/jac/dkab466.

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Abstract Objectives To assess the genetic contexts surrounding blaNDM-1 genes carried on IncM plasmids harboured by six carbapenemase-producing Enterobacterales (CPE) isolates referred to the UK Health Security Agency’s Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. Methods Between 2014 and 2018, the AMRHAI Reference Unit undertook WGS of CPE isolates using Illumina NGS. Nanopore sequencing was used for selected isolates and publicly available plasmid references were downloaded. Analysis of incRNA, which encodes the antisense RNA regulating plasmidic repA gene expression, was performed and bioinformatics tools were used to analyse whole plasmid sequences. Results Of 894 NDM-positive isolates of Enterobacterales, 44 NDM-1-positive isolates of five different species (Citrobacter spp., Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca) encoded the IncRNA locus of IncM2 plasmids. Long-read sequencing of six diverse isolates revealed related IncM2, NDM-1-encoding plasmids. Plasmid ‘backbone’ areas were conserved and contrasted with highly variable resistance regions. Sub-groupings of IncM2 plasmids encoding blaNDM-1 were detected; one sub-group occurred in five different health regions of England in every year. The diversity of NDM-1-encoding resistance gene integrons and transposons and their insertions sites in the plasmids indicated that NDM-1 has been acquired repeatedly by IncM2 variants. Conclusions The use of sequencing helped inform: (i) a wide geographical distribution of isolates encoding NDM-1 on emergent IncM2 plasmids; (ii) variant plasmids have acquired NDM-1 separately; and (iii) dynamic arrangements and evolution of the resistance elements in this plasmid group. The geographical and temporal distribution of IncM2 plasmids that encode NDM-1 highlights them as a public health threat that requires ongoing monitoring.

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Li, Feifeng, Jiong Wang, Ying Jiang, Yingyi Guo, Ningjing Liu, Shunian Xiao, Likang Yao, et al. "Adaptive Evolution Compensated for the Plasmid Fitness Costs Brought by Specific Genetic Conflicts." Pathogens 12, no. 1 (January 13, 2023): 137. http://dx.doi.org/10.3390/pathogens12010137.

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New Delhi metallo-β-lactamase (NDM)-carrying IncX3 plasmids is important in the transmission of carbapenem resistance in Escherichia coli. Fitness costs related to plasmid carriage are expected to limit gene exchange; however, the causes of these fitness costs are poorly understood. Compensatory mutations are believed to ameliorate plasmid fitness costs and enable the plasmid’s wide spread, suggesting that such costs are caused by specific plasmid–host genetic conflicts. By combining conjugation tests and experimental evolution with comparative genetic analysis, we showed here that the fitness costs related to ndm/IncX3 plasmids in E. coli C600 are caused by co-mutations of multiple host chromosomal genes related to sugar metabolism and cell membrane function. Adaptive evolution revealed that mutations in genes associated with oxidative stress, nucleotide and short-chain fatty acid metabolism, and cell membranes ameliorated the costs associated with plasmid carriage. Specific genetic conflicts associated with the ndm/IncX3 plasmid in E. coli C600 involve metabolism and cell-membrane-related genes, which could be ameliorated by compensatory mutations. Collectively, our findings could explain the wide spread of IncX3 plasmids in bacterial genomes, despite their potential cost.

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Bahl, Martin Iain, Lars Hestbjerg Hansen, Tine Rask Licht, and Søren J. Sørensen. "Conjugative Transfer Facilitates Stable Maintenance of IncP-1 Plasmid pKJK5 in Escherichia coli Cells Colonizing the Gastrointestinal Tract of the Germfree Rat." Applied and Environmental Microbiology 73, no. 1 (November 3, 2006): 341–43. http://dx.doi.org/10.1128/aem.01971-06.

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ABSTRACT Quantitative determination of IncP-1 plasmid loss from Escherichia coli cells colonizing the gastrointestinal tracts of germfree rats was achieved by flow cytometry. Results show that the plasmid's ability to conjugate counteracts plasmid loss and is thus an important mechanism for the stable maintenance of IncP-1 plasmids within the gastrointestinal environment.

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Longtine, M. S., S. Enomoto, S. L. Finstad, and J. Berman. "Yeast telomere repeat sequence (TRS) improves circular plasmid segregation, and TRS plasmid segregation involves the RAP1 gene product." Molecular and Cellular Biology 12, no. 5 (May 1992): 1997–2009. http://dx.doi.org/10.1128/mcb.12.5.1997-2009.1992.

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Telomere repeat sequences (TRSs) can dramatically improve the segregation of unstable circular autonomously replicating sequence (ARS) plasmids in Saccharomyces cerevisiae. Deletion analysis demonstrated that yeast TRSs, which conform to the general sequence (C(1-3)A)n, are able to stabilize circular ARS plasmids. A number of TRS clones of different primary sequence and C(1-3)A tract length confer the plasmid stabilization phenotype. TRS sequences do not appear to improve plasmid replication efficiency, as determined by plasmid copy number analysis and functional assays for ARS activity. Pedigree analysis confirms that TRS-containing plasmids are missegregated at low frequency and that missegregated TRS-containing plasmids, like ARS plasmids, are preferentially retained by the mother cell. Plasmids stabilized by TRSs have properties that distinguish them from centromere-containing plasmids and 2 microns-based recombinant plasmids. Linear ARS plasmids, which include two TRS tracts at their termini, segregate inefficiently, while circular plasmids with one or two TRS tracts segregate efficiently, suggesting that plasmid topology or TRS accessibility interferes with TRS segregation function on linear plasmids. In strains carrying the temperature-sensitive mutant alleles rap1grc4 and rap1-5, TRS plasmids are not stable at the semipermissive temperature, suggesting that RAP1 protein is involved in TRS plasmid stability. In Schizosaccharomyces pombe, an ARS plasmid was stabilized by the addition of S. pombe telomere sequence, suggesting that the ability to improve the segregation of ARS plasmids is a general property of telomere repeats.

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Pollet, Rebecca M., James D. Ingle, Jeff P. Hymes, Thomas C. Eakes, Karina Yui Eto, Stephen M. Kwong, Joshua P. Ramsay, Neville Firth, and Matthew R. Redinbo. "Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci." Journal of Bacteriology 198, no. 6 (January 4, 2016): 888–97. http://dx.doi.org/10.1128/jb.00832-15.

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ABSTRACTAntimicrobial resistance inStaphylococcus aureuspresents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at theoriTregion of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES proteinin vitro. Second, pSK156 and pCA347 are nonconjugativeStaphylococcus aureusplasmids that contain sequences similar to theoriTregion of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate theoriTsequences of these nonconjugative plasmidsin vitro. Although pSK41 could mobilize a coresident plasmid harboring its cognateoriT, it was unable to mobilize plasmids containing the pSK156 and pCA347 variantoriTmimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-likeoriT. These data indicate that the conjugative relaxase intransmechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids.IMPORTANCEUnderstanding the mechanism of antimicrobial resistance transfer in bacteria such asStaphylococcus aureusis an important step toward potentially slowing the spread of antimicrobial-resistant infections. This work establishes protein-DNA interactions essential for the transfer of theStaphylococcus aureusmultiresistance plasmid pSK41 by its relaxase, NES. This enzyme also processed variantoriT-like sequences found on numerous plasmids previously considered nontransmissible, suggesting that in conjunction with an uncharacterized accessory protein, these plasmids may be transferred horizontally via a relaxase intransmechanism. These findings have important implications for our understanding of staphylococcal resistance plasmid evolution.

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Brown, Celeste J., Diya Sen, Hirokazu Yano, Matthew L. Bauer, Linda M. Rogers, Geraldine A. Van der Auwera, and Eva M. Top. "Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes." Applied and Environmental Microbiology 79, no. 24 (October 4, 2013): 7684–95. http://dx.doi.org/10.1128/aem.02252-13.

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ABSTRACTBroad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.

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Wu, Shang Wei, Kathrine Dornbusch, Göran Kronvall, and Mari Norgren. "Characterization and Nucleotide Sequence of a Klebsiella oxytoca Cryptic Plasmid Encoding a CMY-Type β-Lactamase: Confirmation that the Plasmid-Mediated Cephamycinase Originated from the Citrobacter freundii AmpC β-Lactamase." Antimicrobial Agents and Chemotherapy 43, no. 6 (June 1, 1999): 1350–57. http://dx.doi.org/10.1128/aac.43.6.1350.

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ABSTRACT Plasmid pTKH11, originally obtained by electroporation of aKlebsiella oxytoca plasmid preparation intoEscherichia coli XAC, expressed a high level of an AmpC-like β-lactamase. The enzyme, designated CMY-5, conferred resistance to extended-spectrum β-lactams in E. coli; nevertheless, the phenotype was cryptic in the K. oxytocadonor. Determination of the complete nucleotide sequence of pTKH11 revealed that the 8,193-bp plasmid encoded seven open reading frames, including that for the CMY-5 β-lactamase (bla CMY-5). Thebla CMY-5 product was similar to the plasmidic CMY-2 β-lactamase of K. pneumoniae and the chromosomal AmpC of Citrobacter freundii, with 99.7 and 97.0% identities, respectively; there was a substitution of phenylalanine in CMY-5 for isoleucine 105 in CMY-2. bla CMY-5 was followed by the Blc and SugE genes of C. freundii, and this cluster exhibited a genetic organization identical to that of the ampC region on the chromosome ofC. freundii; these results confirmed that C. freundii AmpC was the evolutionary origin of the plasmidic cephamycinases. In the K. oxytoca host, the copy number of pTKH11 was very low and the plasmid coexisted with plasmid pNBL63. Analysis of the replication regions of the two plasmids revealed 97% sequence similarity in the RNA I transcripts; this result implied that the two plasmids might be incompatible. Incompatibility of the two plasmids might explain the cryptic phenotype ofbla CMY-5 in K. oxytoca through an exclusion effect on pTKH11 by resident plasmid pNBL63.

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Paganini, Julian A., Nienke L. Plantinga, Sergio Arredondo-Alonso, Rob J. L. Willems, and Anita C. Schürch. "Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data." Microorganisms 9, no. 8 (July 28, 2021): 1613. http://dx.doi.org/10.3390/microorganisms9081613.

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The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

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Dissertations / Theses on the topic "Plasmids"

Jansen, Yvette. "Characterisation of a high copy number mutant pAL5000 origin of replication." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52159.

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Thesis (MScMedSc)--Stellenbosch University, 2001.
ENGLISH ABSTRACT: The plasmid pAL5000 is a mycobacterial plasmid isolated from Mycobacterium fortuitum. It is a low copy number plasmid, which replicates in both fast growing (e.g. M. smegmatis) and slow growing (e.g. M. bovis BCG) mycobacteria. Most mycobacterial-E. coli shuttle vectors utilise the pAL5000 origin of replication. The minimum replicon consists of ORF1 (RepA), ORF2 (RepB) and the origin of replication. Dr W.R. Bourn created an E. coli-mycobacterial vector based on the pAL5000 origin of replication (pORI) and then subjected it to semi-random mutagenesis. A high copy number mutant was identified (pHIGH) and the causative mutation was tentatively identified as a 3bp deletion situated just upstream of repB. This work describes the further characterisation of the mutant plasmid. Firstly, it was shown by retransforming M. smegmatis with both the original and mutant plasmids (pORI and pHIGH), that the mutation causing the increased copy number was plasmid-encoded and not on the chromosome. Following this, it was demonstrated by simple subcloning of the region that carries the 3 bp deletion, that other pAL5000-based vectors could be converted to high copy number. In addition to this, the subcloned region was sequenced and the nature of the mutations was confirmed. The subcloning experiment confirmed that the 3bp deletion caused the high copy number phenotype. Following this, the exact copy number of pHIGH and the relative increase in copy number was determined. From this, the copy number of pORI could also be determined. The plasmid pHIGH has a copy number of approximately 54, compared to the 8 of pORI (a relative increase by a factor of 7). Because it is important for researchers to know the characteristics of the vectors that they use, especially the influence it will have on its host, stability tests and growth curves were also performed. It was seen that the higher copy number did not markedly increase the stability, however, this is because pORI is already extremely, and unexpectedly, stable in the host M. smegmatis. According to the growth curves, the increased copy number has little effect on the growth of the host M. smegmatis. Possible mechanisms for the increased copy number were then investigated. By using a promoter probe vector, the possible existence of a promoter situated between the two open reading frames of pAL5000 (repA and repB) was investigated. It was thought that the mutation might have created, or changed an existing promoter, situated between repA and repB. The results showed, however, that in both pORI and pHIGH there might be a very weak promoter upstream of repB, but the mutation did not cause any change that was measurable by the method that was used. A further possibility was that the mutation caused a change in the RNA secondary structure, which might then have an effect on the translational efficiency of RepB. It was found that the 3bp deletion in pHIGH causes a change in the local RNA secondary structure around the ribosomal binding site and the start codon, when compared to pORI (wild type). This change may cause the translation initiation rate of RepB to be different between pHIGH and pORI. Ultimately it would lead to a different ratio of RepA and RepB in the cell.
AFRIKAANSE OPSOMMING: Die plasmied pAL5000 is ‘n mikobakteriele plasmied wat vanuit Mycobacterium fortuitum gei'soleer is. Dit is ‘n lae kopie-getal plasmied wat in beide vinnig groeiende (bv. M. smegmatis) en stadig groeiende (bv. M. bovis BCG) mikobakteriee kan repliseer. Die meeste mikobakteriele-E. coli shuttle vektore gebruik die pAL5000 oorsprong van replisering. Die minimum replikon bestaan uit ORF1 (RepA), ORF2 (RepB) en die oorsprong van replisering. Dr. W.R. Bourn het ‘n E. coli-mikobakteriele vektor gemaak wat gebaseer is op die pAL5000 oorsprong van replisering (pORI), en dit onderwerp aan semi-random mutagenese. ‘n Hoë kopie-getal mutant is gei'dentifiseer (pHIGH) en die mutasie hiervoor verantwoordelik was tentatief gei'dentifiseer as ‘n 3bp delesie, net stroomop van repB. Die projek beskryf die verdere karakterisering van die mutante plasmied. Eerstens, deur M. smegmatis te hertransformeer met die plasmied DNA (pORI en pHIGH), is dit bewys dat dit mutasie wat die toename in kopie-getal veroorsaak, deur die plasmied gekodeer word, en dat dit nie ‘n mutasie op die chromosoom is nie. Hierna is dit deur eenvoudige subklonering bewys dat die gedeelte wat die 3bp delesie dra, ander pAL5000-gebaseerde vektore ook kan verander in ‘n hoër kopie-getal. Die sub-klonerings eksperiment het ook bewys dat die 3 bp delesie die oorsaak is vir die hoë kopie-getal fenotipe. Volgende is die presiese kopie-getal van pHIGH en die relatiewe toename in kopiegetal bepaal. Die kopie-getal van pORI kon vanaf hierdie data bepaal word. Die plasmied pHIGH het ‘n kopie-getal van ongeveer 54 in M. smegmatis, in vergelyking met die 8 van pORI (‘n relatiewe toename met ‘n faktor van 7). Aangesien dit vir navorsers belangrik is om die eienskappe van die vektore wat hulle gebruik, te ken, en veral die invloed wat dit op die gasheer sal hê, is stabiliteits toetse, en groeikurwes gedoen. Die hoër kopie-getal het nie die stabiliteit werklik verbeter nie, maar dit is omdat pORI alreeds uiters stabiel is in die gasheer M. smegmatis. Volgens die groeikurwes het die toename in kopie-getal ‘n minimale effek op die groei van die gasheer M. smegmatis. Moontlike meganismes vir die hoër kopie-getal is ook ondersoek. Die moontlike bestaan van ‘n promoter tussen die twee oop-leesrame van pAL5000 (repA en repB) is ondersoek deur gebruik te maak van ‘n “promoter probe” vektor. Die mutasie kon moontlik ‘n promoter geskep het, of ‘n bestaande een tussen repA en repB verander het. Die resultate het gewys dat daar in beide pORI en pHIGH moontlik ‘n baie swak promoter stroomop van repB is, maar die mutasie het nie enige veranderinge veroorsaak wat meetbaar was met die metode wat gebruik is nie. ‘n Verdere moontlikheid was dat die mutasie ‘n verandering in die RNA sekondere struktuur kon veroorsaak het, en dit mag ‘n effek hê op die translasie effektiwiteit van RepB. Daar is gevind dat, in vergelyking met pORI, het die 3bp delesie in pHIGH ‘n verandering in die lokale RNA sekondere struktuur rondom die ribosomale bindings posisie en die begin-kodon veroorsaak. Die verandering mag veroorsaak dat die translasie inisiasie tempo van RepB verskillend is vir pORI en pHIGH. Uiteindelik sal dit lei tot ‘n heeltemal ander verhouding van RepA en RepB in die sel.

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Udo, Edet Ekpenyong. "Characterisation and molecular studies of plasmids from Nigerian staphylococci." Thesis, Curtin University, 1991. http://hdl.handle.net/20.500.11937/1845.

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Fifty three Staphylococcus aureus isolates were obtained from three centres, two hospitals and a private pathology laboratory, and studied for susceptibility to bacteriophages, resistance to antimicrobial agents and plasmid contents.Results of bacteriophage typing revealed that they belonged to a variety of phage types. Eighteen were untypable by any of the International Set of Phages, 16 belonged to phage group 111, nine to group I, four to group 11, two to group IV and two to the miscellaneous group.The isolates were resistant to one or more of methicillin (Mc), benzyl penicillin (Pc), gentamicin (Gm) , kanamycin (Km) , neomycin (Nm) , streptomycin (Sm) , trimethoprim (Tp), sulphonamides (Su), tetracycline (Tc), minocycline (Mn), chloramphenicol (Cm), novobiocin (Nb) and fusidic acid (Fa). Resistance to Pc was due to the production of beta-lactamase (Bla). No resistance to vancomycin, spectinomycin and erythromycin was detected. Resistance was also found to heavy metals such as cadmium (Cd), mercury (Hg), phenyl mercuric acetate (Pma), arsenate (Asa) and to the nucleic-acid binding compounds propamidine isethionate (Pi) and ethidium bromide (Eb).All but one of the isolates harboured plasmids. The number of plasmids the isolates carried varied from one to six and their sizes ranged from < 1.0 kb to c.48 kb.Location of the resistance determinants was ascertained by curing and transfer experiments. Loss of resistance was tested after growth at 43.5°C and transfer of resistance determinants was attempted by transduction, mixed-culture transfer and conjugation. The results revealed that resistance to Mc, Gm, Tp, Mn and Fa was chromosomal in all the resistant isolates and in some isolates Bla and resistance to Sm and Cd were chromosomal as well as plasmid encoded. In the majority of cases Bla and resistance to Km, Nm, Sm, Tc, Cin, Cd, Hg, Asa, Pma, Pi and Eb was encoded by plasmids.Conjugation experiments led to the isolation of three unique conjugative plasmids which have not been found to confer resistance to antimicrobials or to produce haemolysins or diffusible pigment (Dip). The three plasmids, pWBG620, pWBG637 and pWBG661, were indistinguishable by restriction endonuclease analysis and DNA-DNA hybridisation. However pWBG620, unlike pWBG637 and pWBG661, was not detected in the cytoplasm of its host and was only detected in transconjugants after it mobilised a non-conjugative Sm-resistance (SmR) plasmid. Further analysis indicated that it is integrated into the chromosome of its host, excises during conjugation and mobilises the SmR plasmid.These plasmids were studied further using pWBG637 as a representative. It was compared with representatives of the two groups of conjugative plasmids which have been reported in the staphylococci. These are the plasmids which encode resistance to Gm, Km and Nm and those which code for the production of diffusible pigment. The three types of conjugative plasmids were compared by restriction endonuclease analysis and DNA- DNA hybridisation and were found to be different. A preliminary restriction map of pWBG637 has also been constructed.However since pWBG637 has no resistance phenotype direct selection for it was not possible in transfer experiments and for incompatibility (Inc.). To study it further it was necessary to construct resistant derivatives which could be selected for in transfer experiments. This was achieved by labelling pWBG637 with resistance transposons to generate two conjugative plasmids, pWBG636 carrying an insert of Tn3851 (Gm- resistance) and pWBG642 carrying an insert of Tn551 (hn- resistance). It was found that transposon labelling had not changed the incompatibility of pWBG637 and therefore pWBG636 and pWBG642 were used in further experiments in place of pWBG637. Inc. tests with the pWBG637 derivatives revealed that the pWBG637 type of plasmid is not only different from the other two types of conjugative plasmids but is different from any of the described staphylococcal Inc. groups and therefore the pWBG637 type of plasmids represent a new Inc. group 15. The pWBG637 type of plasmids were studied further using plasmids pWBG636 and pWBG642. They were able to transfer conjugatively to a capsulated S.aureus strain either by the polyethylene glycol method or on filter membranes. They also transferred by conjugation to S. epidermidis and Streptococcus faecalis and were able to transfer back from these strains to S.aureus indicating that they also replicate in these hosts. Consequently they have been used to mobilise non-conjugative plasmids from S.epidermidis and non phage typable S.aureus. Both plasmids failed to transfer conjugatively to Bacillus subtilis and Escherichia coli.pWBG637 transferred non-conjugative plasmids by mobilising them in a manner similar to mobilisation (donation) in E.coli or by recombining with them to form new resistance plasmids. In one case, pWBG628 which encodes Bla and resistance to Cd, Km, Nm and Sm and has no homology with pWBG637 recombined with it during conjugation to produce three new conjugative plasmids pWBG629, pWBG630 and pWBG631 carrying resistance determinants from pWBG628. One of these plasmids, pWBG629, was found to be pWBG637 which had acquired a 4.5 kb element encoding resistance to Km, Nm and Sm. This element was shown to be transposable in both rec+ and rec- backgrounds and has been designated Tn3854. It expressed Sm resistance in E.coli and differs on this account from the Gram-negative transposon Tn5 which expresses resistance to Km, Nm and Sm in non-enteric bacteria but only resistance to Km and Nm in E. coli.Where possible the non-conjugative plasmids encoding resistance to antimicrobial agents were compared with phenotypically similar plasmids isolated from other parts of the world. It was found that the Tc and Sm resistance plasmids were closely related to other plasmids with the same phenotype whereas the Cm resistance plasmids were different.Although the majority of the Bla plasmids belonged to Inc. group 1 they demonstrated significant restriction enzyme fragment length polymorphism when compared with other Bla plasmids.This study has provided the first data on the genetics of antimicrobial resistance in Nigerian S.aureus. Although many of the plasmids studied were found to be similar to those previously described the isolates also contained some unique and previously undescribed plasmids.

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Seyler, Richard W. "Plasmid stability of pUB110 and pUB110-derived plasmids in Bacillus sphaericus 2362." Thesis, This resource online, 1991. http://scholar.lib.vt.edu/theses/available/etd-03022010-020139/.

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Hirst, Jonathan Michael. "Plasmids in thermoactinomyces." Thesis, Heriot-Watt University, 1991. http://hdl.handle.net/10399/826.

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Udo, Edet Ekpenyong. "Characterisation and molecular studies of plasmids from Nigerian staphylococci." Curtin University of Technology, School of Biomedical Sciences, 1991. http://espace.library.curtin.edu.au:80/R/?func=dbin-jump-full&object_id=15648.

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Fifty three Staphylococcus aureus isolates were obtained from three centres, two hospitals and a private pathology laboratory, and studied for susceptibility to bacteriophages, resistance to antimicrobial agents and plasmid contents.Results of bacteriophage typing revealed that they belonged to a variety of phage types. Eighteen were untypable by any of the International Set of Phages, 16 belonged to phage group 111, nine to group I, four to group 11, two to group IV and two to the miscellaneous group.The isolates were resistant to one or more of methicillin (Mc), benzyl penicillin (Pc), gentamicin (Gm) , kanamycin (Km) , neomycin (Nm) , streptomycin (Sm) , trimethoprim (Tp), sulphonamides (Su), tetracycline (Tc), minocycline (Mn), chloramphenicol (Cm), novobiocin (Nb) and fusidic acid (Fa). Resistance to Pc was due to the production of beta-lactamase (Bla). No resistance to vancomycin, spectinomycin and erythromycin was detected. Resistance was also found to heavy metals such as cadmium (Cd), mercury (Hg), phenyl mercuric acetate (Pma), arsenate (Asa) and to the nucleic-acid binding compounds propamidine isethionate (Pi) and ethidium bromide (Eb).All but one of the isolates harboured plasmids. The number of plasmids the isolates carried varied from one to six and their sizes ranged from < 1.0 kb to c.48 kb.Location of the resistance determinants was ascertained by curing and transfer experiments. Loss of resistance was tested after growth at 43.5°C and transfer of resistance determinants was attempted by transduction, mixed-culture transfer and conjugation. The results revealed that resistance to Mc, Gm, Tp, Mn and Fa was chromosomal in all the resistant isolates and in some isolates Bla and resistance to Sm and Cd were chromosomal as well as plasmid encoded. In the majority of cases Bla and resistance to Km, Nm, Sm, Tc, Cin, Cd, Hg, Asa, Pma, Pi and Eb was encoded ++
by plasmids.Conjugation experiments led to the isolation of three unique conjugative plasmids which have not been found to confer resistance to antimicrobials or to produce haemolysins or diffusible pigment (Dip). The three plasmids, pWBG620, pWBG637 and pWBG661, were indistinguishable by restriction endonuclease analysis and DNA-DNA hybridisation. However pWBG620, unlike pWBG637 and pWBG661, was not detected in the cytoplasm of its host and was only detected in transconjugants after it mobilised a non-conjugative Sm-resistance (SmR) plasmid. Further analysis indicated that it is integrated into the chromosome of its host, excises during conjugation and mobilises the SmR plasmid.These plasmids were studied further using pWBG637 as a representative. It was compared with representatives of the two groups of conjugative plasmids which have been reported in the staphylococci. These are the plasmids which encode resistance to Gm, Km and Nm and those which code for the production of diffusible pigment. The three types of conjugative plasmids were compared by restriction endonuclease analysis and DNA- DNA hybridisation and were found to be different. A preliminary restriction map of pWBG637 has also been constructed.However since pWBG637 has no resistance phenotype direct selection for it was not possible in transfer experiments and for incompatibility (Inc.). To study it further it was necessary to construct resistant derivatives which could be selected for in transfer experiments. This was achieved by labelling pWBG637 with resistance transposons to generate two conjugative plasmids, pWBG636 carrying an insert of Tn3851 (Gm- resistance) and pWBG642 carrying an insert of Tn551 (hn- resistance). It was found that transposon labelling had not changed the incompatibility of pWBG637 and therefore pWBG636 and pWBG642 were used in further experiments in place of pWBG637. Inc. ++
tests with the pWBG637 derivatives revealed that the pWBG637 type of plasmid is not only different from the other two types of conjugative plasmids but is different from any of the described staphylococcal Inc. groups and therefore the pWBG637 type of plasmids represent a new Inc. group 15. The pWBG637 type of plasmids were studied further using plasmids pWBG636 and pWBG642. They were able to transfer conjugatively to a capsulated S.aureus strain either by the polyethylene glycol method or on filter membranes. They also transferred by conjugation to S. epidermidis and Streptococcus faecalis and were able to transfer back from these strains to S.aureus indicating that they also replicate in these hosts. Consequently they have been used to mobilise non-conjugative plasmids from S.epidermidis and non phage typable S.aureus. Both plasmids failed to transfer conjugatively to Bacillus subtilis and Escherichia coli.pWBG637 transferred non-conjugative plasmids by mobilising them in a manner similar to mobilisation (donation) in E.coli or by recombining with them to form new resistance plasmids. In one case, pWBG628 which encodes Bla and resistance to Cd, Km, Nm and Sm and has no homology with pWBG637 recombined with it during conjugation to produce three new conjugative plasmids pWBG629, pWBG630 and pWBG631 carrying resistance determinants from pWBG628. One of these plasmids, pWBG629, was found to be pWBG637 which had acquired a 4.5 kb element encoding resistance to Km, Nm and Sm. This element was shown to be transposable in both rec+ and rec- backgrounds and has been designated Tn3854. It expressed Sm resistance in E.coli and differs on this account from the Gram-negative transposon Tn5 which expresses resistance to Km, Nm and Sm in non-enteric bacteria but only resistance to Km and Nm in E. coli.Where possible the non-conjugative plasmids encoding resistance to ++
antimicrobial agents were compared with phenotypically similar plasmids isolated from other parts of the world. It was found that the Tc and Sm resistance plasmids were closely related to other plasmids with the same phenotype whereas the Cm resistance plasmids were different.Although the majority of the Bla plasmids belonged to Inc. group 1 they demonstrated significant restriction enzyme fragment length polymorphism when compared with other Bla plasmids.This study has provided the first data on the genetics of antimicrobial resistance in Nigerian S.aureus. Although many of the plasmids studied were found to be similar to those previously described the isolates also contained some unique and previously undescribed plasmids.

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Ophel, Kathleen Margaret. ""Agrobacterium" : plasmids and biovars /." Title page, contents and summary only, 1987. http://web4.library.adelaide.edu.au/theses/09PH/09pho61.pdf.

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Pinder, David. "Illegitimate recombination in plasmids." Thesis, University of Edinburgh, 1996. http://hdl.handle.net/1842/11260.

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Illegitimate recombination mechanisms are important for genetic change within an organism. They are also the cause of many instability problems in biotechnology and have been associated with certain human genetic disorders and cancers. The original aim of this work was to construct a deletion (illegitimate recombination) resistant cosmid based, cloning system, for the cloning of unstable human DNA. Two 'mutant plasmids' pMS5 and pMS7 were isolated. The plasmids were derived from pUC18 and appeared to stabilise the propagation of a long DNA palindrome. The basic concept was to construct a new cosmid using pMS7 as part of the backbone. The construction of two new cosmids cDRII (Deletion Resistant) and cDRIII is described. However, they are unlikely to contain a mutation which stabilises unstable sequences. This thesis also describes the search for the 'mutation' in pMS7 by, single-strand conformation polymorphism and fragment swap analysis. This work led to the isolation of a novel mutation composed of both direct and inverted repeats, which I have called DIR. The presence of DIR in pAC2 (a derivative of pUC18, with the same DNA palindrome as pMS7), supports the absence of a stabilising 'mutation in pMS7. The structure of the DIR mutation is analysed in detail and a hypothesis for its formation is proposed. Finally, the behaviour of four long DNA palindromes (other than that cloned in pMS7), is investigated when ligated into pM^* (a derivative of pMS7).

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Maia, Mauricio Silva. "Plasmids of Azotobacter vinelandii." Thesis, North Texas State University, 1986. https://digital.library.unt.edu/ark:/67531/metadc798298/.

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Nineteen laboratory strains of Azotobacter vinelandii and two organisms of the same species isolated from water samples were screened for the presence of plasmid deoxyribonucleic acid (DNA). Three laboratory strains and both organisms isolated from water samples contained one plasmid each. The migration distances of the plasmids in agarose gel electrophoresis were different molecular weights. The plasmids were cured by SDS or ethidium bromide treatment of the cultures.

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Chilley, Paul Morris. "Leading regions of enterobacterial plasmids." Thesis, University of Leicester, 1995. http://hdl.handle.net/2381/34394.

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Gram-negative bacterial conjugation is a specialised replicative event that increases the population size of a plasmid during its horizontal transfer between organisms. Work reported in this thesis has focused on the genetic structure of the leading regions of enterobacterial plasmids. A leading region is the first segment of a plasmid to enter the recipient cell during conjugation. Some leading regions carry conserved loci. Examples are ssb encoding a single-stranded DNA binding protein; psiB which functions to inhibit induction of the bacterial SOS response; ardA which encodes antirestriction activity, and hok, a gene that contributes to plasmid maintenance. The objective of this work was to determine the distribution of these genes on enterobacterial plasmids and their arrangement relative to the origin of conjugative transfer (oriT). Sequences homologous to ardA were found on plasmid representatives of five (FV, B, I, K and N) out of 23 incompatibility groups tested. Mapping data shows that the ardA homologues are leading region genes, and subcloning experiments coupled with phenotypic assays provide evidence that the IncB and IncFV ardA homologues are functional antirestriction genes. Sequence data reveal that the ardA gene family has diverged by at least 60% at the nucleotide sequence level when compared to the prototype ardA gene of ColIb-F9. A non-homologous antirestriction gene, ardB, was only detected on IncN plasmids. Conserved ssb and psiB genes are known to be present on a number of enterobacterial plasmids representing nine different incompatibility groups (B, com9, I1, FI, FII, FIV, K and Y). It is reported that the leading region of an IncFV plasmid, F0lac, also carries conserved ssb-psiB genes. In common with previous findings, the genes are separated by a spacer of ~2.5kb, indicating their presence in a conserved module. Genes of the hok family of killer genes are found on the leading region of FI and FII plasmids. Southern hybridisation experiments revealed that IncI1 plasmids lack a member of the hok subfamily but contain a member of the pnd subfamily. Functional and hybridisation tests localised pnd to the trailing region, defined as the last segment of a plasmid to enter the recipient during conjugation. Hybridisation data also localised the pnd genes of B and K plasmids to be outside of the leading region. The finding that the killer genes are scattered is consistent with the concept that the ecological role of the hok gene family is in plasmid maintenance rather than in conjugation. The results show that while enterobacterial plasmid leading regions collectively contain some conserved genes, there is considerable heterogeneity in their combination and arrangement on different plasmids with respect to oriT. It is postulated that the difference reflects independent acquisition of modules during the evolution of the different plasmid types. An important finding is that leading region genes are each orientated such that the transcribed strand is the same as the transferred strand. This arrangement holds for plasmids ColIb (IncI1), F (IncFI), pKM101 (IncN) and F0lac (IncFV) and could be important for the expression of these genes. One possibility is that the genes are expressed from the incoming plasmid strand before it is converted into duplex DNA.

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McKibben, Ann Laura. "Characterization of plasmids in Gluconobacter." Thesis, Virginia Tech, 1992. http://hdl.handle.net/10919/44232.

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Books on the topic "Plasmids"

Tolmasky, Marcelo E., and Juan C. Alonso, eds. Plasmids. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818982.

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Helinski, Donald R., Stanley N. Cohen, Don B. Clewell, David A. Jackson, and Alexander Hollaender, eds. Plasmids in Bacteria. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4613-2447-8.

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Meinhardt, Friedhelm, and Roland Klassen, eds. Microbial Linear Plasmids. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-72025-6.

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Esser, Karl, Ulrich Kück, Christine Lang-Hinrichs, Paul Lemke, Heinz Dieter Osiewacz, Ulf Stahl, and Paul Tudzynski. Plasmids of Eukaryotes. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-82585-9.

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Friedhelm, Meinhardt, and Klassen Roland, eds. Microbial linear plasmids. New York: Berlin, 2007.

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R, Helinski Donald, ed. Plasmids in bacteria. New York: Plenum Press, 1985.

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B, Clewell Don, ed. Bacterial conjugation. New York: Plenum Press, 1993.

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G, Hardy K., ed. Plasmids: A practical approach. Oxford: IRL, 1986.

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G, Hardy K., ed. Plasmids: A practical approach. Oxford, England: IRL Press, 1987.

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G, Hardy K., ed. Plasmids: A practical approach. 2nd ed. Oxford: IRL Press at Oxford University Press, 1993.

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Book chapters on the topic "Plasmids"

Inouye, Sachiye. "Plasmids." In Pseudomonas, 1–33. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4899-0120-0_1.

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Gooch, Jan W. "Plasmids." In Encyclopedic Dictionary of Polymers, 915. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14515.

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Falkinham, Joseph O., and Jack T. Crawford. "Plasmids." In Tuberculosis, 185–98. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818357.ch13.

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Jannière, Laurent, Alexandra Gruss, and S. Dusko Ehrlich. "Plasmids." In Bacillus subtilis and Other Gram-Positive Bacteria, 625–44. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818388.ch43.

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Tolmasky, Marcelo E., Luis A. Actis, Timothy J. Welch, and Jorge H. Crosa. "Plasmids." In Methods for General and Molecular Microbiology, 709–34. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555817497.ch30.

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Kado, Clarence I. "Historical Events That Spawned the Field of Plasmid Biology." In Plasmids, 1–11. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818982.ch1.

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Hernández-Arriaga, Ana María, Wai Ting Chan, Manuel Espinosa, and Ramón Díaz-Orejas. "Conditional Activation of Toxin-Antitoxin Systems: Postsegregational Killing and Beyond." In Plasmids, 175–92. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818982.ch10.

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Volante, Andrea, Nora E. Soberón, Silvia Ayora, and Juan C. Alonso. "The Interplay between Different Stability Systems Contributes to Faithful Segregation: Streptococcus pyogenes pSM19035 as a Model." In Plasmids, 193–207. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818982.ch11.

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Samson, Julie E., Alfonso H. Magadan, and Sylvain Moineau. "The CRISPR-Cas Immune System and Genetic Transfers: Reaching an Equilibrium." In Plasmids, 209–18. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818982.ch12.

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de Toro, María, M. Pilar Garcillán-Barcia, and Fernando de la Cruz. "Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Escherichia coli Plasmids." In Plasmids, 219–35. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818982.ch13.

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Conference papers on the topic "Plasmids"

Saksaganskaia, Alla S., Victoria S. Muntyan, Alexey N. Muntyan, Boris V. Simarov, and Marina L. Roumiantseva. "ABUNDANCE OF PHAGE-RELATED SEQUENCES ON NON-SYMBIOTIC PLASMIDS OF SINORHIZOBIUM MELILOTI FROM CENTERS OF LEGUME PLANTS DIVERSITY." In 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022/6.1/s25.06.

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Genomes of alfalfa root nodule bacteria, Sinorhizobium meliloti, symbionts of alfalfa are enriched in non-symbiotic (cryptic) plasmids, which gene pool is remained weakly studied. S. meliloti strains are significantly varied in number and size of these plasmids. The goal of the study was to assess the occurrence of phage-related sequences (PRS) on cryptic plasmids. Whole genome sequences of 12 S. meliloti strains native to Caucasian and Kazakhstan centers of alfalfa diversity (NCG and PAG, correspondingly) were studied and 20 cryptic plasmids, which sizes varied from 17.2 to 453.8 kb, were assembled. In total 55 PRS were identified on cryptic plasmids, and these sequences were represented by intact, questionable and incomplete sequences according to PHASTER. Significant differences in the occurrence of above-mentioned types of PRS on cryptic plasmids was detected between strains native to NCG and PAG (X2 = 6.73, p = 0.03). The sizes of the desired PRS varied from 5.1 to 33 kb, and their number was from 1 to 11 per replicon in tested strains. It was revealed that PRS on plasmids of strains from NCG were predominantly related to Siphoviridae family (p smaller than 0.05), while PRS homologous to phages of Siphoviridae and Podoviridae families prevailed with equal frequencies on plasmids of strains from PAG. For 40% of tested PRS the attL/attR sequences were detected and that is proving their site-specific integration type. ORFs of PRS as it was revealed are encoded integrases, fiber protein and tail shaft, and nearly all PRS are contained ORFs encoded transposases. Summarizing, S. meliloti strains native to origins of alfalfa diversity are enriched in cryptic plasmids, and the latest are attractive for soil bacteriophages, that is strongly evident the participation of small size plasmids in horizontal gene transfer process.

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Paulsson, Johan. "Plasmids as stochastic model systems." In SPIE's First International Symposium on Fluctuations and Noise, edited by Sergey M. Bezrukov, Hans Frauenfelder, and Frank Moss. SPIE, 2003. http://dx.doi.org/10.1117/12.500143.

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Ezerskii, V. A., E. M. Koloskova, and T. P. Trubitsina. "Green fluorescent protein gene for site-specific integration into the locus of the rabbit whey acidic protein gene." In CURRENT STATE, PROBLEMS AND PROSPECTS OF THE DEVELOPMENT OF AGRARIAN SCIENCE. Federal State Budget Scientific Institution “Research Institute of Agriculture of Crimea”, 2020. http://dx.doi.org/10.33952/2542-0720-2020-5-9-10-129.

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The high content of whey acidic protein in rabbit milk makes the gene of this protein a promising candidate for its replacement by the gene of pharmacologically active protein using the CRISPR/Cas9 system. The plasmid that contains 5’ and 3’ arms of homology to the rabbit WAP gene was created. A fragment containing a green fluorescent protein gene under the CMV promoter has been integrated into this site. A strategy of making double-stranded cuts in the gene WAP and receiving four pX330 plasmids encoding the endonuclease Cas9 and guide RNAs was developed. The plasmid containing a fragment cmvEGFP was designed for site-specific integration by homologous recombination into the gene WAP to assess the effectiveness of site-specificity of components of the CRISPR/Саѕ9 in vitro.

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Vladimirova, Mariia, Maria Vladimirova, Alexey Afonin, Boris Simarov, and Marina Roumiantseva. "CRYPTIC PLASMIDS ESSENTIAL FOR SINORHIZOBIUM MELILOTI FITNESS." In 20th International Multidisciplinary Scientific GeoConference Proceedings SGEM 2020. STEF92 Technology, 2020. http://dx.doi.org/10.5593/sgem2020/6.1/s25.029.

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Alwa, Amira, and Samir Jaoua. "Investigation of Bacillus Thuringiensis Plasmid Instability and its Effect on the Synthesis of Crystals." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0107.

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In order to explore plasmid instability in Bt, four Bt strains belonging to two Bt subspecies were cultured at 42°C for 9 days. HD1 and QBT376 belong to subspecies kurstaki, while H14 and QBT218 belong to subspecies israelensis. Results showed 100% crystal loss for H14 and QBT218, while 76% and 90% crystal loss for HD1 and QBT376, respectively, showing that cry-carrying plasmids are more stable in Bt kurs. than in Bt isr.. HD1, QBT376, and QBT218 cured clones showed significant protease activity compared to their non-cured counterparts. Microscopic observation revealed the delay of sporulation for high number of HD1 and QBT376 cry- clones, while the absence of spores in several H14 and QBT218 cry- clones. Spo-cry- clones of Bti strains had irregular elongated cell shape. Kinetics/day of plasmid curing for H14 and QBT218 showed H14 to have higher pBtoxis plasmid stability. The number of vegetative cells in Bti strains increased with the increase of curing period. As an attempt to create hybrid Bt strains, cry1Aa gene was extracted to transform cured and non-cured strains.

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Ratnadewi, Anak Agung Istri, Sabella Muyasyaroh, Fatih Harum, Wuryanti Handayani, and Sudarko Sudarko. "Expression and Characterization of Recombinant Endo-β-1,4-D-xylanases XynBTN63D from Soil Termite Abdomen in <i>Escherichia coli</i> BL21 (DE3)." In International Conference on Chemistry and Material Sciences 2023 (IC2MS). Switzerland: Trans Tech Publications Ltd, 2024. http://dx.doi.org/10.4028/p-5cqsmp.

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The xynBTN63D gene sub-cloned on the plasmid shuttle vector pESC and pYHM1 in the host Escherichia coli BL21 (DE3) was successfully expressed and characterized. The xynBTN63D gene in the soluble fraction of each plasmid is expressed at induction temperatures of 25, 30, 35, 37, and 40 °C with a molecular weight of ±30 kDa. The soluble fraction of the xynBTN63D gene in both plasmids was expressed at induction temperatures of 25, 30, 35, 37, and 40°C with a molecular weight of ±30 kDa. The recombinant XynBTN63D, purified using the fast protein liquid chromatography (FPLC) method also has a molecular weight of ±30 kDa, observed using the sodium dodecyl polyacrylamide sodium electrophoresis (SDS-PAGE) method. The recombinant XynBTN63D has a temperature of 40 °C and an optimum pH of 5.5. It shows stability from 4 to 40 °C after preincubation for 1 hour with relative activity on the pCES and pMH1 plasmid of more than 50%. Recombinant XynBT63D also showed pH stability after being preincubated for 24 hours by showing relative activity of 86-100% at pH 5.0 to 6.0 for each plasmid

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Ibragimov, A., An Baymiev, and O. Lastochkina. "Development of fluorescent protein-marked strains of Bacillus subtilis." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.104.

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Bergeron, Nadia, F. Daigle, Ann Letellier, and Sylvain Quessy. "Identification of plasmids in a Salmonella Typhimurium septicemic isolate without the classical 95 kb virulence plasmid." In Ninth International Conference on the Epidemiology and Control of Biological, Chemical and Physical Hazards in Pigs and Pork. Iowa State University, Digital Press, 2011. http://dx.doi.org/10.31274/safepork-180809-649.

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Connelly, Brian D., Luis Zaman, Philip K. McKinley, and Charles Ofria. "Modeling the evolutionary dynamics of plasmids in spatial populations." In the 13th annual conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2001576.2001608.

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Sona, S., M. Aswathy, Biya Bellermin, Jaya Vinny Eapen, Anu Yamuna Joseph, R. Sajith, and P. Vidya. "PCR based replicon typing of plasmids of MDROs: A review." In INTERNATIONAL CONFERENCE ON SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS: STAM 20. AIP Publishing, 2020. http://dx.doi.org/10.1063/5.0017785.

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Reports on the topic "Plasmids"

Top, Eva M., and Ben Ridenhour. Persistence of Antibiotic Resistance Plasmids in Biofilms. Fort Belvoir, VA: Defense Technical Information Center, October 2014. http://dx.doi.org/10.21236/ada614277.

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Plumley, F. G. Marine Diatom Plasmids and their Biotechnological Applications. Fort Belvoir, VA: Defense Technical Information Center, February 1992. http://dx.doi.org/10.21236/ada264407.

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Top, Eva M., and Silvia E. Smith. Persistence of Antibiotic Resistance Plasmids in Biofilms. Fort Belvoir, VA: Defense Technical Information Center, October 2013. http://dx.doi.org/10.21236/ada615372.

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Coons, Terry. Restriction mapping and expression of recombinant plasmids containing the arsenic resistance genes of the plasmid R45. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.5481.

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Eisen, Jonathan. Shotgun Sequencing of Plasmids from Marine Sediment Bacteria - Genetic Exploration. Fort Belvoir, VA: Defense Technical Information Center, September 2001. http://dx.doi.org/10.21236/ada398735.

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Hamilton, Nicklas. Use of Two-replisome Plasmids to Characterize how Chromosome Replication Completes. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.6940.

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Clark, Joshua. Determination of homology between the arsenic resistance plasmids R45 and R773 in Escherichia coli. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.5644.

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Lindow, Steven, Isaac Barash, and Shulamit Manulis. Relationship of Genes Conferring Epiphytic Fitness and Internal Multiplication in Plants in Erwinia herbicola. United States Department of Agriculture, July 2000. http://dx.doi.org/10.32747/2000.7573065.bard.

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Most bacterial plant pathogens colonize the surface of healthy plants as epiphytes before colonizing internally and initiating disease. The epiphytic phase of these pathogens is thus an important aspect of their epidemiology and a stage at which chemical and biological control is aimed. However, little is known of the genes and phenotypes that contribute to the ability of bacteria to grow on leaves and survive the variable physical environment in this habitat. In addition, while genes such as hrp awr and others which confer pathogenicity and in planta growth ability have been described, their contribution to other aspects of bacterial epidemiology such as epiphytic fitness have not been addressed. We hypothesized that bacterial genes conferring virulence or pathogenicity to plants also contribute to the epiphytic fitness of these bacteria and that many of these genes are preferentially located on plasmids. We addressed these hypotheses by independently identifying genes that contribute to epiphytic fitness, in planta growth, virulence and pathogenicity in the phytopathogenic bacterium Erwinia herbicola pv gypsophilae which causes gall formation on gypsophila. This species is highly epiphytically fit and has acquired a plasmid (pPATH) that contains numerous pathogenicity and virulence determinants, which we have found to also contribute to epiphytic fitness. We performed saturation transposon mutagenesis on pPATH as well as of the chromosome of E.h. gypsophilae, and identified mutants with reduced ability to grow in plants and/or cause disease symptoms, and through a novel competition assay, identified mutants less able to grow or survive on leaves. The number and identity of plasmid-borne hrp genes required for virulence was determined from an analysis of pPATH mutants, and the functional role of these genes in virulence was demonstrated. Likewise, other pPATH-encoded genes involved in IAA and cytokinin biosynthesis were characterized and their pattern of transcriptional activity was determined in planta. In both cases these genes involved in virulence were found to be induced in plant apoplasts. About half of avirulent mutants in pPATH were also epiphytically unfit whereas only about 10% of chromosomal mutants that were avirulent also had reduced epiphytic fitness. About 18% of random mutants in pPATH were avirulent in contrast to only 2.5% of random chromosomal mutants. Importantly, as many as 28% of pPATH mutants had lower epiphytic fitness while only about 10% of random chromosomal mutants had lower epiphytic fitness. These results support both of our original hypotheses, and indicate that genes important in a variety of interactions with plant have been enriched on mobile plasmids such as pPATH. The results also suggest that the ability of bacteria to colonize the surface of plants and to initiate infections in the interior of plants involves many of the same traits. These traits also appear to be under strong regulatory control, being expressed in response to the plant environment in many cases. It may be possible to alter the pattern of expression of such genes by altering the chemical environment of plants either by genetic means or by additional or chemical antagonists of the plant signals. The many novel bacterial genes identified in this study that are involved in plant interactions should be useful in further understanding of bacterial plant interactions.

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Singh, Anjali. What Is Optogenetics and How Does It Work? ConductScience, July 2022. http://dx.doi.org/10.55157/cs20220704.

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Optogenetics is a biotechnological method that combines optical systems and genetic engineering to control and monitor the functions of cells, tissues, and organisms. It involves using light-sensitive proteins called opsins to manipulate specific cells or regions with precision. This technique has revolutionized neuroscience, allowing researchers to study neural circuits and behavior by turning cells on and off. Opsins are categorized into microbial and animal types, each with specific functions. Optogenetic experiments require opsins, suitable plasmids or viral vectors, and a light source. This method has broad applications in neurology, animal behavior, and physiology, providing insights into various biological processes. It is used to map neural circuits, study diseases, and understand behaviors.

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Weil, Clifford F., Anne B. Britt, and Avraham Levy. Nonhomologous DNA End-Joining in Plants: Genes and Mechanisms. United States Department of Agriculture, July 2001. http://dx.doi.org/10.32747/2001.7585194.bard.

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Repair of DNA breaks is an essential function in plant cells as well as a crucial step in addition of modified DNA to plant cells. In addition, our inability to introduce modified DNA to its appropriate locus in the plant genome remains an important hurdle in genetically engineering crop species.We have taken a combined forward and reverse genetics approach to examining DNA double strand break repair in plants, focusing primarily on nonhomologous DNA end-joining. The forward approach utilizes a gamma-plantlet assay (miniature plants that are metabolically active but do not undergo cell division, due to cell cycle arrest) and has resulted in identification of five Arabidopsis mutants, including a new one defective in the homolog of the yeast RAD10 gene. The reverse genetics approach has identified knockouts of the Arabidopsis homologs for Ku80, DNA ligase 4 and Rad54 (one gene in what proves to be a gene family involved in DNA repair as well as chromatin remodeling and gene silencing)). All these mutants have phenotypic defects in DNA repair but are otherwise healthy and fertile. Additional PCR based screens are in progress to find knockouts of Ku70, Rad50, and Mre11, among others. Two DNA end-joining assays have been developed to further our screens and our ability to test candidate genes. One of these involves recovering linearized plasmids that have been added to and then rejoined in plant cells; plasmids are either recovered directly or transformed into E. coli and recovered. The products recovered from various mutant lines are then compared. The other assay involves using plant transposon excision to create DNA breaks in yeast cells and then uses the yeast cell as a system to examine those genes involved in the repair and to screen plant genes that might be involved as well. This award supported three graduate students, one in Israel and two in the U.S., as well as a technician in the U.S., and is ultimately expected to result directly in five publications and one Masters thesis.

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