screening Protocols

Category: Bioinformatics

Using AFPredictor, it was demonstrated that ‘ordered surface carbons’ (OSCs) are a distinguishing feature of AFPs and, more specifically, their ice-binding surfaces. AFPredictor identified AFPs from within a large set of structures with greater than 99% specificity. Furthermore, it was used to identify a novel ice-binding protein by screening a library of homology modeled structures based on cDNA sequences obtained from cold-acclimated winter rye (Secale cereale). - [Read A Computational Screening protocol for Antifreeze/Ice-Structuring Proteins]

Category: PCR Protocols: AFLP PCR

Ulrich G. Mueller and L. LaReesa Wolfenbarger. Amplified fragment length polymorphisms (AFLPs) are polymerase chain reaction (PCR)-based markers for the rapid screening of genetic diversity. AFLP. TREE October 1999 - [Read AFLP genotyping and fingerprinting Review PDF]

Category: Pharmacology and Toxicology Protocols: Cytotoxicity Protocols

The Allium test provides a rapid screening procedure for chemicals, pollutants contaminants, etc. which may represent environmental hazards.  Root growth inhibition and adverse effects upon chromosomes provide an indication of likely toxicity. - [Read Allium Test]

Category: Plant Biology Protocols

The Allium test provides a rapid screening procedure for chemicals, pollutants contaminants, etc. which may represent environmental hazards.  Root growth inhibition and adverse effects upon chromosomes provide an indication of likely toxicity. - [Read Allium Test]

Category: Cell Biology and Cell Culture: Endothelial Cell Protocols

Traditional animal models to quantify the degree of blood vessel formation are being replaced by cell culture assays that are easier to set up, statistically reliable and can be automated in a drug screening laboratory. These assays rely on the endothelial cells’ ability to form distinct blood-vessel-like tubules in an extracellular matrix where they can subsequently be visualized by fluorescence microscopy. - [Read An Image-Based Assay of Endothelial Cell Tube Formation as a Model of Angiogenesis]

Category: Yeast Protocols: Yeast Genetics Protocols: B-Galactosidase Assay Protocols

This assay is used when working with phage vectors carrying the beta-galactosidase gene (often used for immunological screening). If the cloning event disrupts a normally functional copy of the gene in the vector the resulting plaques would appear clear in the assay. If the phages contain a functional beta-galactosidase gene they will form blue rings around their plaques. Any strain which is not an overproducer of beta- galactosidase will work as indicator host bacteria. - [Read Assay for Phage Containing the Beta-galactosidase Gene Protocol]

Category: Cell Biology and Cell Culture

Protocol for automated imaging-based high-throughput screening for small molecules that reverse cellular senescence. - [Read Automated Imaging-Based High-Throughput Screening: Small Molecules that Reverse Cellular Senescence]

Category: RNA Protocols: cDNA Libraries Library

Includes procedures for cDNA screens using secondary and tertiary screening. Dr. Bart Frank Lab. - [Read Benton Davis Blots for cDNA Libraries]

Category: C. elegans Protocols: C. elegans Genetics Protocols

Protocol for C. elegans RNAi. Includes: Transformation of competent cells; Blunt-end ligation; Preparation of competent cells; Dephosphorylation of linear plasmid DNA; Restriction Digest: EcoRV; Insert amplification from gDNA; Gel purification: QiaQuick gel purification kit; Mini-prep; Transformant Screening; Bacterial preparation and induction; Preparation of worms for RNAi feeding. - [Read C. elegans RNAi Protocol]

Category: Cell Biology and Cell Culture: Cell Transfection Protocol

Protocol for cell transfection, clone screening and picking cell clones. Bjorkman Group. California I.T - [Read Calcium phosphate Tranfection for MDCK cells]

Category: RNA Protocols: cDNA Libraries Library

cDNA Library Screening Protocol - ZAPII Detailed Protocol. XLI-Blue MRF' and cDNA phage library screening. Dr. Laurie. University of Virginia Health Science Center - [Read cDNA Library Screening Protocol - ZAPII]

Category: Cell Biology and Cell Culture: Cell Viability Protocols

Choosing a cell viability or cytotoxicity assay from among the many different options available can be a challenging task. Includes information on: Establishing an In Vitro Model System; Choosing an Endpoint to Measure; Characterizing Assay Responsiveness; Determining Dose and Duration of Exposure; Homogeneous Assays for Multiwell Formats and Automated Screening; Additional Factors to Consider When Choosing a Cell Viability Assay; Cell Viability Assays that Measure ATP Protocol; etc.. - [Read Cell Viability Information For Protocols and Applications]

Category: DNA Protocols: cDNA Library Protocols: cDNA Library Construction Protocols

Protocol for cloning genes from a phage library. Includes: Titer and plate out phage; Lift plaques onto filters and prepare them for screening; Make a probe; Hybridize the probe to the filters; Wash the filters and expose to film; Purify putative plaques; Excise plasmid from the desired phage. - [Read Clone Genes From a Phage Library Protocol]

Category: DNA Protocols: Genomic DNA Library Protocols

This stage summarizes how to construct a cDNA library in a mammalian vector, using commercial kits. These kits are available from several manufacturers and generally include all the required reagents. - [Read Construction of cDNA Libraries in Eukaryotic Expression Vectors for Construction and Screening]

Category: Microscopy Protocols: Fluorescence Microscopy Protocols

Certain fluorescent dyes such as Blankophor have a high affinity for the b -glycosidically linked polysaccharides such as glucan and chitin, which are main the constituents of the fungal cell wall. Therefore, these fluorescent dyes can be used for screening clinical samples for the presence of fungal elements. This procedure can be performed using the following specimens: Nail, Skin, Bronchial alveolar lavage fluid, Sputum and Biopsies. - [Read Detection of Fungi by Fluorescence Microscopy Using Fluorescent Brighteners]

Category: RNA Protocols: cDNA Libraries Library

Differential cDNA Screening Procedures. The protocols listed refer to cDNA library construction and preliminary differential screening procedures. Nick Talbot lab - [Read Differential cDNA Screening Procedures]

Category: Yeast Protocols: Yeast Two-Hybrid Systems Protocols

Protocol utilizes the Y190 yeast strain, that characteristically turns from white to red during growth due to ademutation. Baits were subcloned into the pAS1cyh2 vector, and Preys subcloned into pACT2. - [Read Directed Yeast Two Hybrid Screening for MEKK1 Interaction Partners Protocol]

Category: siRNA and RNAi Protocols

dsRNA From Clones, Primer Designed dsRNA. Drosophila RNAi Screening Center at Harvard Medical School - [Read dsRNA Synthesis Protocol]

Category: ELISA Protocols

Qualitative ELISA (Enzyme-Linked Immunosorbent Assay) used for screening detection of anti-platelet antibodies or for detection of platelet-associated Ig (PAIg). Andrei Musaji Viral immunity and pathogenesis group, Universite Catholique de Louvain. - [Read ELISA for detection of platelet-associated Ig (PAIg)]

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

EMS is used at concentrations that induce multiple point mutations in each plant, such that mutant alleles of a specific locus are found at a rate of ~1 in 2000-5000 M2 plants. This high rate of mutagenesis makes possible the screening of relatively few plants to find those with the phenotype of interest, a particular advantage if the screen is laborious or if only a small number of genes mutate to the required phenotype. - [Read EMS Mutagenesis of Arabidopsis Seed Protocol]

Category: Molecular Model Organisms: Yeast Two-Hybrid Screen Protocol

Interactor Hunt Protocol. Testing whether a bait activates transcription. Screening a library for interactors. Finley Lab. 1997. - [Read EXAMINING THE FUNCTION OF PROTEINS AND PROTEIN NETWORKS WITH THE YEAST TWO-HYBRID SYSTEM]

Category: Pharmacology and Toxicology Protocols: Drug Discovery

To determine the selectivity of the inhibitors identified during screening efforts we developed gel-elongation assay using crude bacterial lysate directly to determine the target specificities of fatty acid synthesis inhibitors. - [Read Gel Elongation Assay for Type II Fatty Acid Synthesis Protocol]

Category: Lipid Protocols

New screening efforts and chemical modifications of existing compounds have been attempted to identify more selective and potent inhibitors. To determine the selectivity of the inhibitors identified during screening efforts we developed gel-elongation assay using crude bacterial lysate directly to determine the target specificities of fatty acid synthesis inhibitors. - [Read Gel-elongation Assay for Type II Fatty Acid Synthesis Protocol]

Category: Pharmacology and Toxicology Protocols: Drug Discovery

High-throughput and sensitive assay to measure yeast cell growth: a bench protocol for testing genotoxic agents. Method is highly sensitive, provides quantifiable data and offers high-throughput screening capability.  Starting with the treatment of cells with different doses of damaging agents, pre-prepared growing media containing 96-well plates are inoculated and cell population is automatically monitored every 10 min for 48 hours.  - [Read High Throughput and Sensitive Assay Measure Yeast Cell Growth Protocol]

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

Protocol describes how to identify cloned cDNAs encoding proteins that bind to specific DNA sequences. The methods used are very similar to those used for immunological screening of expression libraries except that the nitrocellulose filters carrying immobilized proteins are screened with 32P-labeled double-stranded DNA rather than with antibodies. - [Read Identifying DNA-binding Proteins in Bacteriophage ambda Expression Libraries Protocol]