Collections libraries plasmids. Medical search. Frequent questions

The BCCM/GeneCorner Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance. (go.jp)
The consortium comprises more than 269,000 publicly available strains of bacteria including mycobacteria and cyanobacteria, filamentous fungi, yeasts, diatoms and plasmids. (wikipedia.org)
These well-documented and authenticated strains of bacteria, filamentous and yeasts fungi (including the most important test and control strains), diatoms, plasmids and DNA libraries are made publicly available and are distributed worldwide. (wikipedia.org)
Sometimes particular E. coli strains are sub-optimal for plasmid extraction. (zymoresearch.com)
When possible, stick to tried and tested strains like E. coli DH5α which contain mutations to lack certain endonucleases and increase plasmid stability. (zymoresearch.com)
Thus, these modified E. coli strains are used as workhorses for molecular cloning and plasmid production. (zymoresearch.com)
The second method uses chloramphenicol, an antibiotic that halts protein synthesis and decouples it from plasmid replication, when culturing strains containing a plasmid with a relaxed origin of replication. (zymoresearch.com)

Today in this short video we are going to show you the basic steps that you need to follow to do a plasmid purification using our Monarch Plasmid Miniprep Kit. (neb.com)
Sometimes, plasmid purification just doesn't go according to plan. (zymoresearch.com)
Whether a vector is kept at low copy number, low culture density, or culture overgrowth, this guide will help you navigate your purification woes and determine the best way to boost your plasmid yields from E. coli cultures. (zymoresearch.com)
The efficacy of column-based plasmid purification doesn't just depend on how much plasmid is loaded onto the column, but also the total amount of biomass being loaded as well. (zymoresearch.com)
If you want to scale up your plasmid purification, try using a kit designed for high inputs of culture, such the ZymoPURE II Midipreps and Maxipreps , which can process more culture. (zymoresearch.com)
Purification from cultures grown in highly enriched media such as Terrific Broth (TB) yield higher amounts of plasmid DNA per ml of culture than standard Luria-Bertani Broth (LB). (zymoresearch.com)
Chloramphenicol treatment can stop protein production but allow the E. coli to continue to "amplify" the plasmids, resulting in increased yields during plasmid purification 1 . (zymoresearch.com)
One method for plasmid amplification uses an inhibitory amount of chloramphenicol (170 µg/ml) added to a culture, which is then incubated further until plasmid purification (typically the next day) 2 . (zymoresearch.com)
A variation of this method that reports higher plasmid yield uses lower amounts of chloramphenicol (10-20 µg/ml) added to exponentially growing cells that are subsequently incubated overnight prior to plasmid purification 3 . (zymoresearch.com)

AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. (mdpi.com)
One of the hallmarks of the emergence of M. ulcerans as a more severe pathogen is the acquisition of a 174-kb plasmid that bears a cluster of genes necessary for the synthesis of the polyketide toxin mycolactone. (cdc.gov)
To do this, a fragment carrying tra genes and oriT of wild-type F plasmid, which are essential for conjugation and transfer, were combined with oriRg replicon. (cam.ac.uk)
Plasmids and Lentivirus Creation gRNAs targeting specific genes had been synthesized from IDT (Integrated DNA Systems), annealed as previously referred to (15) and cloned in to the BsmBI limitation sites from the LentiGuide-Puro vector (Addgene, 52963). (campaignfornonviolentschools.org)
RESULTS: All carbapenemase-producing K. pneumoniae isolates (carrying either bla(NDM-1), or/and bla(OXA-48)) carried multiple AMR plasmids encoding 34 antimicrobial resistance genes (ARGs) conferring resistance to antimicrobials from 6 different classes. (cdc.gov)

The focus is on the collection of recombinant plasmids that can replicate in a microbial host strain. (go.jp)
This recombinant DNA plasmid was then inserted into bacteria. (pressbooks.pub)
This recombinant plasmid can then be used to transform bacteria, which gain the ability to produce the insulin protein. (pressbooks.pub)
Recombinant clones were constructed in the plasmid vector pBluescript II KS(+) (Stratagene, La Jolla, Calif.). Chemicals, media, and growth conditions. (careersfromscience.org)
A recombinant phage library was constructed in the phage vector gt11 (Promega) using partially digested strain R expressing the 55-kDa product of PvpA (49). (careersfromscience.org)

Resuspend the bacterial pellet in 200 μl of Plasmid Resuspension Buffer [B1]. (neb.com)
From the 178 plasmids sent, 167 were able to grow in bacterial culture and 92 of the ASFV proteins were expressed individually in mammalian cells. (intvetvaccnet.co.uk)
In this example, the human insulin gene is inserted into a bacterial plasmid. (pressbooks.pub)
Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. (bvsalud.org)
The ability to sequence large bacterial collections means that the molecular epidemiology and gene content of epidemic and sporadic lineages can now be defined systematically. (nature.com)
This study emphasizes the need for characterization of MDR plasmids to determine their complete molecular background and monitor AMR through plasmid transmission between multi-resistant bacterial pathogens. (cdc.gov)

Gain even greater insights into complex biological networks using Sigma-Aldrich ® Advanced Genomics CRISPR activation and CRISPR inhibition libraries for gene knockdown and overexpression experiments. (sigmaaldrich.com)
GeCKO V2 human Gefarnate being CRISPR knockout collection (Addgene) was transduced into Endura? (campaignfornonviolentschools.org)
Extended CRISPR plasmid libraries had been purified by Maxi-Prep (Qiagen) and useful for lentivirus creation (3, 16). (campaignfornonviolentschools.org)

Addgene is a nonprofit plasmid repository. (addgene.org)

and reintroduced into the bacterium, which will replicate, thus making multiple copies of the hybrid plasmid. (pharmacy180.com)
This plasmid can replicate in cells supplying pir gene product. (cam.ac.uk)

A DNA library is a collection of cloned restriction fragments of the DNA of an organism. (pharmacy180.com)
A genomic library is a collection of fragments of dsDNA obtained by digestion of the total DNA of the organism with a restriction endonuclease and subsequent ligation to an appropriate vector. (pharmacy180.com)
PCR-amplified ORFs of the target organism are cloned into our plasmid expression vector via a high-throughput homologous recombination method. (antigendiscovery.com)

Interestingly, 10 of these markers are carried by a replicon of 11.2 kbp that contains sequences highly similar to those of a plasmid detected in Vibrio shilonii, a coral pathogen. (pasteur.fr)
Workflows have been developed for the expansion of pathogen-specific CD4 or CD8 T cells expressing CD137, which can then be used in screens against pathogen protein libraries to identify those that specifically activate T cells (e.g. proliferation or cytokine secretion). (antigendiscovery.com)
We underscore the advantages of our approach by analysing a population-wide plasmid data set obtained from the opportunistic pathogen Escherichia coli, studying the prevalence of the colistin resistance gene mcr-1.1 within the plasmid population, and describing an instance of resistance plasmid transmission within a hospital environment. (bvsalud.org)

However, by using a prototype plasmid-based microarray that covered 10% of the genome, we found multiple genomic DNA deletions among 30 M. ulcerans clinical isolates of diverse geographic origins. (cdc.gov)
When this information is not available, an alternative is a PCR product-based shotgun DNA microarray ( 11 ), which we developed further into a plasmid-based microarray. (cdc.gov)

These MGEs, most typically plasmids and integrative and conjugative elements (ICEs), are therefore important constituents of the accessory genome that imbue K . pneumoniae organisms with their distinct HA or CA clinical profiles. (biomedcentral.com)

In this project we propose a comprehensive approach where we will compare the pattern of antibody recognition of domestic pig and wild pig sera using a DNA library encoding the complete ASFV Kenya 1033 genome individually and test their neutralizing capacity. (intvetvaccnet.co.uk)
ORF expression clone libraries can be constructed from any genome sequence and corresponding source of genomic DNA using our high-throughput polymerase chain reaction ("PCR")/recombination cloning method. (antigendiscovery.com)
Genome comparison with a global collection identified that L1 and L3 were also present in the USA, but were genetically distinct. (nature.com)
Nowadays, molecular biology researchs are featured a wide range of antimicrobial peptides (AMP)-related topics such as AMP genome library construction, development of antimicrobial peptides and their mimetics as therapeutic agents, structure/function analysis, cloning and expression, regulation, mechanisms of action, microbial escaping strategies and human disease associations. (ukessays.com)

These dominant types also carry hypermucoidy ( rmpA ) determinants and include all previously described virulence plasmids of K . pneumoniae . (biomedcentral.com)
OBJECTIVES: The study aim was to investigate multidrug-resistant (MDR) plasmids from a collection of 10 carbapenemase-producing Klebsiella pneumoniae clinical isolates identified within the same healthcare institution in Pakistan. (cdc.gov)
METHODS: Plasmids were isolated from 10 clinical isolates of Klebsiella pneumoniae, and from a corresponding set of Escherichia coli transconjugants, then sequenced using Nanopore/Illumina technology to generate plasmid hybrid assemblies. (cdc.gov)
Most bla(NDM-1-)plasmids shared identical AMR regions suggesting potential genetic material/plasmid exchange between K. pneumoniae isolates of this collection. (cdc.gov)

To amplify the library 10 ng of plasmid library was transferred into E.coli DH5α (Invitrogen catalog no. 18258-012) with heat shock method. (nih.gov)

Prokaryotic organisms normally contain small, circular, extrachromosomal DNA molecules called plasmids that can serve as vectors. (pharmacy180.com)

cDNAs from the Mammalian Gene Collection, cloned into pCMV-Sprot 6 plasmid, were collected from three 384-well plates (total of human 1062 transcripts) as follows: 10 µl sterile dH2O was added to each well and incubated at 37oC for 10 min to resuspend plasmid DNA in water. (nih.gov)

Sigma-Aldrich ® Advanced Genomics offers multiple Cas9 variants (wild-type, enhanced specificity, nickase, GFP-fused, catalytically inactive) and in several formats (plasmid, lentivirus, lyophilized protein). (sigmaaldrich.com)
Cas9-expressing K562 cells had been transduced with GeCKO V2 lentivirus libraries at a minimal MOI of 0.3 and decided on in puromycin for seven days. (campaignfornonviolentschools.org)

This library was enriched for full-length clones and was constructed by Clontech Laboratories (Palo Alto, CA). Note: this is a Xenopus Gene Collection library. (xenbase.org)

55 of these were detected in all virulent isolates from our collection (n = 32), and 13 were detected only in the isolates demonstrating the highest pathogenicity (n = 19), suggesting that they could be used as genetic markers for high virulence capacity. (pasteur.fr)
The major burden of iuc and iro amongst the genomes analysed was due to two linked lineages ( iuc1 / iro1 74% and iuc2 / iro2 14%), each carried by a distinct non-self-transmissible IncFIB K virulence plasmid type that we designate KpVP-1 and KpVP-2. (biomedcentral.com)

Both workflows are rooted in the development of a clone library using microbial genomic DNA, shown in the salmon-colored box. (antigendiscovery.com)
Genomic library building. (careersfromscience.org)

As described in Materials and Methods, we constructed a cDNA library from fat body tissues of E. coli - challenged A. mylitta larvae and randomly sequenced a large number of inserts from the library. (biomedcentral.com)
In contrast, complementary DNA (cDNA) libraries contain only those DNA sequences that are complementary to messenger RNA (mRNA) molecules present in a cell and differ from one cell type to another. (pharmacy180.com)
ATCC staff) Vector useful for constructing cDNA libraries. (addgene.org)
Probe collections were at first PCR amplification products from cDNA templates, but now can include PCR products from BACs, 60-70mer oligonucleotides, or shorter derivitized oligomers that specifically attach to coated surfaces. (upenn.edu)

Capacity of Aquatic Bacteria to Act as Recipients for Plasmid DNA. (epa.gov)

In 1983 the Belgian Council of Ministers decided to bring the microbial resources and the expertise available in different Belgian institutes together in a network of culture collections: with this the consortium of Belgian Co-ordinated Collections of Microorganisms (BCCM) saw the light of day. (wikipedia.org)
In the last twelve years, we have built a large collection of expressible open reading frame (ORF) libraries from over 50 medically-important infectious microorganisms and we are constantly expanding our collection. (antigendiscovery.com)

A plasmid vector was constructed that allowed the expression of biotinylated scFvs in Escherichia coli. (usda.gov)
An expressed sequence tag (EST) library was constructed from mRNA obtained from fat bodies of A. mylitta larvae that had been challenged by infection with Escherichia coli cells. (biomedcentral.com)
1] To enable the positive selection of inserts, the library should be plated on a P2 lysogen such as Escherichia coli Q359 (ATCC 47019). (addgene.org)
Title : Changing plasmid types responsible for extended spectrum cephalosporin resistance in Escherichia coli O157:H7 in the United States, 1996-2009 Personal Author(s) : Folster, J. P.;Pecic, G.;Stroika, S.;Rickert, R.;Whichard, J. (cdc.gov)

Single chain antibody fragments (scFvs) of desired specificity are selected from a large collection of bacteriophage expressing unique scFvs through the binding of the phage displayed scFv with the target of interest. (usda.gov)
ethnicities for plasmid and bacteriophage isolation were produced with shaking at 37C in Luria-Bertani broth (34). (careersfromscience.org)

Full characterization of the MDR plasmids including structure, typing characteristics, and AMR content as well as determination of their plasmid-based antimicrobial susceptibility profiles were carried out. (cdc.gov)

The resultant pseudo F plasmid is transferred by conjugation to the newly established single gene deletion mutant and selected Hfr strain integrated F plasmid by antibiotic resistance selection. (cam.ac.uk)

In 2011, 3 additional dedicated collections were included in the BCCM consortium: the diatom collection of the Laboratory for Protistology & Aquatic Ecology of Ghent University (BCCM/DCG) the mycobacteria collection of the Institute of Tropical Medicine in Antwerp (BCCM/ITM) the cyanobacteria collection of the Centre for Protein Engineering of the University of Liège (BCCM/ULC). (wikipedia.org)

In 1990 the plasmid collection of the Laboratory of Molecular Biology of Ghent University was added to the consortium (BCCM/GeneCorner). (wikipedia.org)
We, therefore, searched a collection of 442 histone mutants [24] for ones that failed to respond to rapamycin in an attempt to identify molecular pathways critical for rapamycin response at the level of chromatin. (researchsquare.com)
This molecular biology workflow authorized streamlined collection and constitutional stability. (licenseapp.org)

We screened the Nebraska Transposon Mutant Library of 1920 single-gene inactivations in S. aureus strain JE2, for increased susceptibility to the anti-staphylococcal antimicrobials (ciprofloxacin, oxacillin, linezolid, fosfomycin, daptomycin, mupirocin, vancomycin, and gentamicin). (frontiersin.org)
If you are experiencing low yields for your plasmid prep, double check that the strain you're using is best for plasmid propagation. (zymoresearch.com)
Strain ts-11, a vaccine strain originally from Kevin Whithear (46), and strain K2101 were from the Georgia laboratory collection. (careersfromscience.org)

It's imperative to ensure the correct amount of antibiotic is present in your culture, otherwise the lack of selection pressure will cause your culture to start to dilute out the plasmid during cell division. (zymoresearch.com)

Plasmids were purified using Qiagen maxiperep kit (catalog no. 12163), according to the manufacturer's protocol. (nih.gov)

The detection of this plasmid was correlated with the highest pathogenicity status of the isolates from our collection. (pasteur.fr)
CONCLUSION: This study highlights the complexity and diversity of the plasmid-based genetic background of carbapenemase-producing clinical isolates from Pakistan. (cdc.gov)

A collection of ca. 1,200 Arabidopsis thaliana TF open reading frames (ORFs) was arrayed in a 96-well format (RR library) and a convenient mating based yeast one hybrid (Y1H) screening procedure was established. (upm.es)
A plasmid DNA library encoding all the ASFV Kenya-1033 ORFs was designed and generated in collaboration with GeneMill (Liverpool, UK). (intvetvaccnet.co.uk)

You will need to add 4 volumes of ethanol to one volume of Plasmid Wash Buffer 2 according to the instructions on the bottle's label. (neb.com)
To lyse the cells you will add 200 μl of Plasmid Lysis Buffer [B2] to the cell suspension. (neb.com)
To neutralize the lysate add 400 μl of Plasmid Neutralization Buffer [B3], and again gently invert the tube until the color is uniformly yellow and a precipitate forms. (neb.com)
Re-insert the column into the collection tube, and add 200 μl of Plasmid Wash Buffer 1. (neb.com)
Add 400 μl of Plasmid Wash Buffer 2, and centrifuge for 1 minute. (neb.com)
Reaction composed of 1 µg of library plasmid, 1X transcription buffer, 0.5 mM of NTPs (GTP,ATP, CTP, and UTP), 40 U of SP6 RNA polymerase and 10 µl of RNase-free water. (nih.gov)

Plasmid DNAs were collected and combined in 1.5 mL tube with aid of multichannel pipette and concentrated by ethanol precipitation. (nih.gov)

There are a couple ways to ensure high yield plasmid preparations from E. coli cultures by using antibiotics for selective pressure. (zymoresearch.com)

Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. (bvsalud.org)

For IVT RNA: Plasmids were linearized by NotI-HF enzyme so that the SP6 polymerase promoter site will be upstream of the sequences to be transcribed. (nih.gov)
R3189L), 5 µg library plasmid DNA, 1 X NEBuffer 4 (supplied with enzyme) and 90 µl of dH2O. (nih.gov)

Additionally, total plasmid yield can vary depending on the type of culture broth used, typically Luria-Bertani broth (LB) or Terrific Broth (TB). (zymoresearch.com)

The complete digestion of plasmid DNA was assessed by DNA gel electrophoresis. (nih.gov)

Luciferase-containing plasmids are commonly used to investigate the effect of regulatory elements, such as promoters, enhancers and untranslated regions, or the effect of mutations of these regulatory elements on gene expression. (addgene.org)

The origin and consequence of this plasmid acquisition are discussed. (pasteur.fr)

The Belgian Co-ordinated Collections of Micro-organisms (BCCM) is a Belgian government funded consortium of seven scientific institutions, who manage and exploit a collection of microbial and genetic resources. (wikipedia.org)

BCCM/GeneCorner also accepts natural and genetically modified animal or human cell lines, including hybridomas, as well as other genetic material, in the safe deposit and patent deposit collections. (go.jp)

Increasing the amount of culture processed leads to higher total yield of plasmid DNA if kit parameters are adjusted accordingly to accommodate higher biomass. (zymoresearch.com)
Don't be afraid to experiment with your growth conditions to see which gives you the best plasmid yield. (zymoresearch.com)
Alternatively, another study demonstrated increased plasmid yield by growth in the presence of sub-inhibitory concentrations of chloramphenicol (3-5 µg/ml) from the time of culture inoculation until plasmid was harvested the next day 4 . (zymoresearch.com)

In addition, PCR was carried out with in vitro transcribed RNA to confirm total depletion of plasmid DNA as well. (nih.gov)
Proteins encoded by the cloned ORF plasmids are expressed using a cell free in vitro transcription/ translation ("IVTT") system. (antigendiscovery.com)

RZHM11106) and converted into Illumina RNA-seq libraries with the TruSeq RNA sample prep kit (Ilumina catalog no. (nih.gov)

There are also ways to combine both approaches by starting with an open-ended functional enrichment of transcribed sequences and using them to create probe collections for further profiling before determining their identities. (upenn.edu)

Cells were incubated with plasmid library for 5 min on ice and were subjected to 42oC for 30 sec. (nih.gov)
Plates were incubated for 16h at 37oC to grow the colonies and 3500 (approx 3-fold of library size) colonies were collected with liquid LB. Cells were transferred into 100 mL liquid LB and incubated at 37oC for 2 h. (nih.gov)

DNA microarrays have become an established method for generating transcript profiles using probe collections. (upenn.edu)

Probes can be used to identify which clone of a library or which band on a gel contains the target DNA. (pharmacy180.com)

In addition to discussing the current and historical significance of these organisms, the collection includes concepts and methodology relating to how they are maintained and reproduce in the laboratory. (mtsu.edu)

Safe deposits Resources in the safe deposit collection are not catalogued, and are only available to the depositor, or to third parties with the written authorisation of the depositor. (wikipedia.org)
Have questions about your order, deposit, or a plasmid? (addgene.org)

However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. (bvsalud.org)

Herein, we screened a histone mutant collection and report that one of the mutants, H2B R95A, is strikingly resistant to rapamycin due to a defective cell cycle arrest. (researchsquare.com)

Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. (addgene.org)

None of the bla(NDM-1) and bla(ESBL)-plasmids identified in this study were previously described. (cdc.gov)

Mge-cluster platform for plasmid analysis can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. (bvsalud.org)
The structure of MDR plasmids was analyzed using the Galileo AMR platform. (cdc.gov)

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