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An assay is an investigative (analytic) procedure in laboratory medicine, mining, pharmacology, environmental biology and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of a target entity. The measured entity is often called the analyte, the measurand, or the target of the assay. The analyte can be a drug, biochemical substance, chemical element or compound, or cell in an organism or organic sample. An assay usually aims to measure an analyte's intensive property and express it in the relevant measurement unit.
Transfection is the process of deliberately introducing naked or purified nucleic acids into eukaryotic cells. It may also refer to other methods and cell types, although other terms are often preferred: "transformation" is typically used to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. In animal cells, transfection is the preferred term as transformation is also used to refer to progression to a cancerous state (carcinogenesis) in these cells. Transduction is often used to describe virus-mediated gene transfer into eukaryotic cells.
The MTT assay is a colorimetric assay for assessing cell metabolic activity. NAD(P)H-dependent cellular oxidoreductase enzymes may, under defined conditions, reflect the number of viable cells present. These enzymes are capable of reducing the tetrazolium dye MTT, which is chemically 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, to its insoluble formazan, which has a purple color. Other closely related tetrazolium dyes including XTT, MTS and the WSTs, are used in conjunction with the intermediate electron acceptor, 1-methoxy phenazine methosulfate (PMS). With WST-1, which is cell-impermeable, reduction occurs outside the cell via plasma membrane electron transport. However, this traditionally assumed explanation is currently contended as proof has also been found of MTT reduction to formazan in lipidic cellular structures without apparent involvement of oxidoreductases.
Half maximal inhibitory concentration (IC50) is a measure of the potency of a substance in inhibiting a specific biological or biochemical function. IC50 is a quantitative measure that indicates how much of a particular inhibitory substance (e.g. drug) is needed to inhibit, in vitro, a given biological process or biological component by 50%. The biological component could be an enzyme, cell, cell receptor or microorganism. IC50 values are typically expressed as molar concentration.
In biology, a marker gene may have several meanings. In nuclear biology and molecular biology, a marker gene is a gene used to determine if a nucleic acid sequence has been successfully inserted into an organism's DNA. In particular, there are two sub-types of these marker genes: a selectable marker and a marker for screening. In metagenomics and phylogenetics, a marker gene is an orthologous gene group which can be used to delineate between taxonomic lineages.
Antibiotic sensitivity testing or antibiotic susceptibility testing is the measurement of the susceptibility of bacteria to antibiotics. It is used because bacteria may have resistance to some antibiotics. Sensitivity testing results can allow a clinician to change the choice of antibiotics from empiric therapy, which is when an antibiotic is selected based on clinical suspicion about the site of an infection and common causative bacteria, to directed therapy, in which the choice of antibiotic is based on knowledge of the organism and its sensitivities.
A selectable marker is a gene introduced into a cell, especially a bacterium or to cells in culture, that confers a trait suitable for artificial selection. They are a type of reporter gene used in laboratory microbiology, molecular biology, and genetic engineering to indicate the success of a transfection or other procedure meant to introduce foreign DNA into a cell. Selectable markers are often antibiotic resistance genes. Bacteria that have been subjected to a procedure to introduce foreign DNA are grown on a medium containing an antibiotic, and those bacterial colonies that can grow have successfully taken up and expressed the introduced genetic material. Normally the genes encoding resistance to antibiotics such as ampicillin, chloramphenicol, tetracycline or kanamycin, etc., are considered useful selectable markers for E. coli.
In microbiology, the minimum inhibitory concentration (MIC) is the lowest concentration of a chemical, usually a drug, which prevents visible in vitro growth of bacteria or fungi. MIC testing is performed in both diagnostic and drug discovery laboratories.
The disk diffusion test is a culture-based microbiology assay used in diagnostic and drug discovery laboratories. In diagnostic labs, the assay is used to determine the susceptibility of bacteria isolated from a patient's infection to clinically approved antibiotics. This allows physicians to prescribe the most appropriate antibiotic treatment. In drug discovery labs, especially bioprospecting labs, the assay is used to screen biological material and drug candidates for antibacterial activity. When bioprospecting, the assay can be performed with paired strains of bacteria to achieve dereplication and provisionally identify antibacterial mechanism of action.
Biotechnology is the use of living organisms to develop useful products. Biotechnology is often used in pharmaceutical manufacturing. Notable examples include the use of bacteria to produce things such as insulin or human growth hormone. Other examples include the use of transgenic pigs for the creation of hemoglobin in use of humans.
G418 (Geneticin) is an aminoglycoside antibiotic similar in structure to gentamicin B1. It is produced by Micromonospora rhodorangea. G418 blocks polypeptide synthesis by inhibiting the elongation step in both prokaryotic and eukaryotic cells. Resistance to G418 is conferred by the neo gene from Tn5 encoding an aminoglycoside 3'-phosphotransferase, APT 3' II. G418 is an analog of neomycin sulfate, and has similar mechanism as neomycin. G418 is commonly used in laboratory research to select genetically engineered cells. In general for bacteria and algae concentrations of 5 μg/mL or less are used, for mammalian cells concentrations of approximately 400 μg/mL are used for selection and 200 μg/mL for maintenance. However, optimal concentration for resistant clones selection in mammalian cells depends on the cell line used as well as on the plasmid carrying the resistance gene, therefore antibiotic titration should be done to find the best condition for every experimental system. Titration should be done using antibiotic concentrations ranging from 100 μg/mL up to 1400 μg/mL. Resistant clones selection could require from 1 to up to 3 weeks.
Transformation efficiency refers to the ability of a cell to take up and incorporate exogenous DNA, such as plasmids, during a process called transformation. The efficiency of transformation is typically measured as the number of transformants per microgram of DNA added to the cells. A higher transformation efficiency means that more cells are able to take up the DNA, and a lower efficiency means that fewer cells are able to do so.
The term host cell reactivation or HCR was first used to describe the survival of UV-irradiated bacteriophages, that were transfected to UV-pretreated cells. This phenomenon was first thought to be the result of homologous recombination between both bacteria and phage, but later recognized as enzymatic repair. Modifications of the assay were later developed, using transient expression plasmid DNA vectors on immortalized fibroblasts, and lately on human lymphocytes.
Magnet-assisted transfection is a transfection method which uses magnetic interactions to deliver DNA into target cells. Nucleic acids are associated with magnetic nanoparticles, and magnetic fields drive the nucleic acid-particle complexes into target cells, where the nucleic acids are released.
QMCF Technology is an episomal protein production system that uses genetically modified mammalian cells and specially designed plasmids. QMCF plasmids carry a combination of regulatory sequences from mouse polyomavirus (Py) DNA replication origin which in combination with Epstein-Barr virus (EBV) EBNA-1 protein binding site as nuclear retention elements ensure stable propagation of plasmids in mammalian cells. In addition the vectors carry the selection marker operational for selection of plasmid carrying bacteria and QMCF cells, bacterial ColE1 origin of replication, and cassette for expression of protein of interest. QMCF cell lines express Large-T antigen and EBNA-1 proteins which bind the viral sequences on the QMCF plasmid and hence support plasmid replication and maintenance in the cells. QMCF Technology has several important differences compared to commonly known transient expression and stable cell line expression systems. Unlike in transient expression system, QMCF Technology enables to maintain episomally replicating QMCF plasmids inside the cells for up to 50 days thus providing an option for production phase of 2–3 weeks. Therefore, the production levels of QMCF Technology are higher. Another difference is the option of establishing expression cell banks within one week, which is not feasible with transient system. Compared to usage of stable cell line, QMCF technology is a rapid method leaving out time-consuming clone selection step during cell line development.
A viability assay is an assay that is created to determine the ability of organs, cells or tissues to maintain or recover a state of survival. Viability can be distinguished from the all-or-nothing states of life and death by the use of a quantifiable index that ranges between the integers of 0 and 1 or, if more easily understood, the range of 0% and 100%. Viability can be observed through the physical properties of cells, tissues, and organs. Some of these include mechanical activity, motility, such as with spermatozoa and granulocytes, the contraction of muscle tissue or cells, mitotic activity in cellular functions, and more. Viability assays provide a more precise basis for measurement of an organism's level of vitality.
Crenolanib besylate is an investigational inhibitor being developed by AROG Pharmaceuticals, LLC. The compound is currently being evaluated for safety and efficacy in clinical trials for various types of cancer, including acute myeloid leukemia (AML), gastrointestinal stromal tumor (GIST), and glioma. Crenolanib is an orally bioavailable benzimidazole that selectively and potently inhibits signaling of wild-type and mutant isoforms of class III receptor tyrosine kinases (RTK) FLT3, PDGFR α, and PDGFR β. Unlike most RTK inhibitors, crenolanib is a type I mutant-specific inhibitor that preferentially binds to phosphorylated active kinases with the ‘DFG in’ conformation motif.
Ligand efficiency is a measurement of the binding energy per atom of a ligand to its binding partner, such as a receptor or enzyme.
3-MeO-PCMo is a dissociative anesthetic drug which is similar in structure to phencyclidine and been sold online as a designer drug. The inhibitory effect of 3-MeO-PCMo on the reduction in the density of the drebrin clusters by NMDAR stimulation with glutamic acid is lower than that of PCP or 3-MeO-PCP, with half maximal inhibitory concentration (IC50) values of 26.67 μM (3-MeO-PCMo), 2.02 μM (PCP) and 1.51 μM (3-MeO-PCP).
No-SCAR genome editing is an editing method that is able to manipulate the Escherichia coli genome. The system relies on recombineering whereby DNA sequences are combined and manipulated through homologous recombination. No-SCAR is able to manipulate the E. coli genome without the use of the chromosomal markers detailed in previous recombineering methods. Instead, the λ-Red recombination system facilitates donor DNA integration while Cas9 cleaves double-stranded DNA to counter-select against wild-type cells. Although λ-Red and Cas9 genome editing are widely used technologies, the no-SCAR method is novel in combining the two functions; this technique is able to establish point mutations, gene deletions, and short sequence insertions in several genomic loci with increased efficiency and time sensitivity.
References
- ↑ Delrue, I; Pan, Q; Baczmanska, AK; Callens, BW; Verdoodt, LLM (August 2018). "Determination of the Selection Capacity of Antibiotics for Gene Selection". Biotechnology Journal. 13 (8): e1700747. doi: 10.1002/biot.201700747 . PMID 29436782.
- ↑ Berridge, MV; Tan, AS (June 1993). "Characterization of the cellular reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT): subcellular localization, substrate dependence, and involvement of mitochondrial electron transport in MTT reduction". Archives of Biochemistry and Biophysics. 303 (2): 474–82. doi:10.1006/abbi.1993.1311. PMID 8390225.
- ↑ Grootjans, S; Hassannia, B; Delrue, I; Goossens, V; Wiernicki, B; Dondelinger, Y; Bertrand, MJ; Krysko, DV; Vuylsteke, M; Vandenabeele, P; Vanden Berghe, T (August 2016). "A real-time fluorometric method for the simultaneous detection of cell death type and rate". Nature Protocols. 11 (8): 1444–54. doi:10.1038/nprot.2016.085. PMID 27414760. S2CID 30945080.
- ↑ Brielmeier, M; Béchet, JM; Falk, MH; Pawlita, M; Polack, A; Bornkamm, GW (1 May 1998). "Improving stable transfection efficiency: antioxidants dramatically improve the outgrowth of clones under dominant marker selection". Nucleic Acids Research. 26 (9): 2082–5. doi:10.1093/nar/26.9.2082. PMC 147536 . PMID 9547263.