contamination Protocols

Category: Protein Protocols: Protein Quantitation Concentration Protocols

Absorbance assay at 280 nm.  This method is just as convenient as for absorbance at 280 nm.  It may be preferred if there is excessive contamination by nucleic acids, since nucleic acids absorb very little radiation at 205 nm.  Setting the wavelength is a bit tricky since 205 nm is right on the shoulder of the protein peak. - [Read Absorbance Assay 205 nm]

Category: Cell Culture Protocols: Sterile Technique Protocols

This unit describes some of the ways that a laboratory can deal with the constant threat of microbial contamination in cell cultures. A protocol on aseptic technique is described first. This catch-all term universally appears in any set of instructions pertaining to procedures in which noncontaminating conditions must be maintained. - [Read Aseptic Technique for Cell Culture Protocol]

Category: Cell Culture Protocols: Cell Culture Contamination Prevention and Removal Protocols

This unit describes how to detect and recognize bacterial, fungal, or mycoplasma contamination and how to verify the presence of mycoplasma. Strategies are described for dealing with culture contamination, if necessary. - [Read Assessing and Controlling Microbial Contamination in Cell Cultures Protocol]

Category: RNA Protocols: RT-PCR and cDNA synthesis

Avoiding DNA Contamination in RT-PCR Ambion - [Read Avoiding DNA Contamination in RT-PCR Ambion]

Category: PCR Protocols

Protocol for dealing with carryover contamination in PCR- enzymatic strategy. Repeated use of PCR and manipulation of its products cause aerosols that can contaminate neighboring samples and work areas.  Such "carryover contamination" can be prevented by including dUTP in place of dTTP for all amplification reactions. - [Read Dealing with Carryover Contamination in PCR: An Enzymatic Strategy Protocol]

Category: RNA Protocols: RT-PCR and cDNA synthesis

Detecting DNA Contamination in RT-PCR Qiagen. - [Read Detecting DNA Contamination in RT-PCR Qiagen.]

Category: Cell Culture Protocols: Cell Culture Contamination Prevention and Removal Protocols

Protocol describes a method for mycoplasma detection using Hoechst 33258, a fluorescent dye that stains DNA. Staining of particulate DNA matter around the cell nucleus (on the cell surface or in the cytoplasm) is indicative of mycoplasma contamination. - [Read Detection of Mycoplasma in Mammalian Cell Cultures Using Fluorescence Microscopy Protocol]

Category: PCR Protocols: cDNA Synthesis Protocols

This cDNA synthesis system simplifies your work dramatically.  All reaction components are premixed and lyophylised.  You have to add your RNA and (for Your-Prime beads) the primer.  Another advantage of the system is a little number of pipetting steps required, and therefore reduced risk of Rnase contamination and RNA degradation. - [Read First strand cDNA synthesis with Ready-To-Go Beads Protocol]

Category: PCR Protocols

Method describes how to modify the termini of PCR products by introducing restriction sites and other features.  To reduce the chance of contamination with exogenous DNAs, prepare and use a special set of reagents and solutions for PCR only.  Bake all glassware for 6 hours at 150°C and autoclave all plasticware. - [Read Genetic Engineering with PCR Protocol]

Category: PCR Protocols: PCR Optimization

Method describes how to modify the termini of PCR products by introducing restriction sites and other features.  To reduce the chance of contamination with exogenous DNAs, prepare and use a special set of reagents and solutions for PCR only.  Bake all glassware for 6 hours at 150°C and autoclave all plasticware. - [Read Genetic Engineering with PCR Protocol]

Category: RNA Protocols: RT-PCR and cDNA synthesis: RT-PCR and cDNA Synthesis FAQ

How can I eliminate DNA contamination from my RNA prior to RT-PCR? Invitrogen - [Read How can I eliminate DNA contamination from my RNA prior to RT-PCR?]

Category: Fungi Protocols: Neurospora Protocols

Information and tips on How to avoid contamination by airborne conidia. - [Read How to Avoid Contamination by Airborne Conidia]

Category: PCR Protocols: Standard PCR Protocol

Protocol can be used to amplify DNA up to 25 kb in length.  To reduce the chance of contamination with exogenous DNAs, prepare and use a special set of reagents and solutions for PCR only.  Bake all glassware for 6 hours at 150°C and autoclave all plasticware. - [Read Long PCR Protocol]

Category: Bacterial Protocols

Ice tea has a complex composition, which leads to reduced filterability, and a decrease in sample throughput. Its composition can generate background or false positive signals. It is also well known that ice tea contains molecules that can inhibit the bioluminescence reaction, which can generate false negative results. The aim of this study was to develop a protocol that was able to neutralize these affects and enable faster detection of contamination. - [Read Microbial Detection in Ice Tea Using the Millipore Milliflex Rapid Microbiology Detection System]

Category: Cell Culture Protocols: Cell Culture Contamination Prevention and Removal Protocols

One of the most important, but frequently overlooked, cell culture procedures is testing cultures for microbial contamination, especially mycoplasma. It is critical for every cell culture laboratory to only use cell lines that have been carefully screened for mycoplasma. Fortunately, there is a simple fluorochrome DNA staining test that can detect both mycoplasma and virtually any other prokaryote contaminants. - [Read Mycoplasma Detection Using DNA Staining Protocol]

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols: Standard PCR Protocol

Avoiding Contamination, Preparation of Reaction Mixture, and Cycling Conditions of a PCR Protocol - Fermentas - [Read Protocol for PCR with Taq DNA Polymerase - Fermentas]

Category: PCR Protocols: Standard PCR Protocol

Avoiding Contamination, Preparation of Reaction Mixture, and Cycling Conditions of a PCR Protocol - Fermentas - [Read Protocol for PCR with Taq DNA Polymerase - Fermentas]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols: Peroxisome Isolation Protocols

Peroxisomes can be purified in self-generated iodixanol gradients in high yield (80-90%) with no detectable contamination from any other organelle. In iodixanol peroxisomes are the densest of the major subcellular organelles (ρ = 1.18-1.20 g/ml) present in the light mitochondrial fraction from mammalian tissues and cells. - [Read Purification of Peroxisomes in a Self-Generated Gradient]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols: Peroxisome Isolation Protocols

Peroxisomes can be purified in iodixanol gradients in high yield (80-90%) with no detectable contamination from any other organelle. This is a property unique to iodixanol because the densities of other organelles, particularly that of mitochondria (approx ρ = 1.14 g/ml) and endoplasmic reticulum (approx ρ = 1.13 g/ml) are much lower than that of peroxisomes (approx ρ = 1.18 g/ml). - [Read Purification of Peroxisomes using a Density Barrier in a Swinging-Bucket Rotor]

Category: Cell Culture Protocols: Cell Culture Contamination Prevention and Removal Protocols

Quality is important in all aspects of tissue culture since the quality of materials used i.e. media and other reagents) will affect the quality of the cultures and products derived from them. The main areas of quality control that are of concern for tissue culture are: The quality of the reagents and materials; The provenance and integrity of the cell lines; The avoidance of microbial contamination. - [Read Quality Control Considerations for Cell Culture]

Category: Primary Cell Isolation and Culture Protocols: Mammalian Cell Culture Protocols

Quality control considerations for cell culture. Includes: Provenance and Integrity of Cell Lines; Avoidance of Microbial Contamination; Environmental Monitoring; What to do in the event of contamination; - [Read Quality Control Considerations for Cell Culture]

Category: Radioactivity: Radioaction Safety

Radiation Safety Manual EHS Princeton. Survey Instrumentation, Performing a Meter Survey, Defining Contamination, When to Survey, Where to Survey, When to Document Surveys, How to Document Surveys, When to Report Contamination, Purchase, Repair and Calibration of Survey Meters. - [Read Radiation Safety Manual EHS Princeton]

Category: PCR Protocols: Real-Time PCR Protocols

Protocol uses FAM-(6-carboxy-fluorescein) or JOE-(6-carboxy-4', 5' -dichloro-2',7' -dimethoxy-fluorescein) labeled LUX (Light Upon eXtension) primers, which can quantify 100 or fewer copies of the target DNA in a background of nonspecific templates, over a broad dynamic range of less than 100-107 copies.  It uses uracil deglycosylase (UDG) to minimize the risk of carryover contamination, and includes a melting curve analysis of the product. - [Read Real-Time PCR Protocol]

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: DNA Plasmid Preps Protocols

Contamination of plasmid DNA by fragments of DNA and RNA is reduced to an acceptable level by centrifugation through 1 M sodium chloride.  This method was devised by Brian Seed when he was a graduate student at Harvard University. - [Read Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Centrifugation]

Category: Cell Culture Protocols: Cell Culture Contamination Prevention and Removal Protocols

This method is advantageous for saving the occasional cultures that become contaminated. Yeast contaminated cultures will appear cloudy when slightly shaken and lymphocytes will not cluster together as much as normal. If cultures are suspect, a drop of culture can be streaked on a YPD media plate to check for growth of yeast colonies, or a 5 ml sample can be taken to Barnes Diagnostic Center for identification of yeast strain. - [Read Removal of Yeast Contamination from Lymphoblast Cultures Protocol]