identified 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: Plant Biology Protocols: Plant Genetics Protocols

AFLP was designed as a highly sensitive method for DNA fingerprinting to be used in a variety of fields. We are using this technology to generate DNA based markers for cloning genes involved in phototropic responses in higher plants that have only been identified genetically by mutant phenotype. Protocol includes: Generate polymorphic recombinant F2 (or F3) population; Isolate genomic DNA; Restriction of DNA; Ligation of adapters; Pre-amplification of template DNA; AFLP-PCR; etc. - [Read AFLP For Positional Cloning]

Category: Mouse Protocols

Mice fed with the cytohesin inhibitor SecinH3 for two days develop hepatic insulin resistance that can be identified by reduced liver glycogen levels, increased serum insulin and ketone body levels and decreased serum non-esterified fatty acid. To confirm the presence and identity of SecinH3 in mouse liver, we extracted the compound from liver homogenates with chloroform and identified it by LC/MS. - [Read Extraction of the SecinH3 from Mouse Liver Protocol]

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

Forward genetics is used to identify genes that are involved in particular biological processes. For example, genes required for disease resistance can be found by identifying mutants with reduced or increased disease resistance, genes that control flower development can be identified by searching for mutants with altered flower morphology, and genes encoding enzymes for tryptophan biosynthesis can be identified by searching for mutants that require exogenous tryptophan for growth. - [Read Forward Genetics in Arabidopsis: Finding Mutations that Cause Particular Phenotypes Protocol]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols

Acidocalcisomes, the dense acidic calcium-storing organelles, which were originally identified in Trypanosoma cruzi, have no parallels in mammalian cells. They thus represent a unique functional characteristic, not shared by the host and hence offer an important potential target for chemotherapy of Chagas disease. - [Read Fractionation of Acidocalcisomes and Other Organelles from Trypanosoma, Leishmania, Chlamydomonas]

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: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast PCR Protocols

To identify the YAC subclones containing both a human insert and a portion of either the left or right arm of the pYAC4 vector. Identification of these clones is necessary in order to do YAC chromosome walking, and is also useful in the determination of whether a particular YAC clone has a contiguous human insert or whether a co-cloning event has occurred. Vector arm sequences are identified using pBR322 fragments from a BamHI-PvuII double digest. - [Read Identification of End Clones in YAC Subclone Libraries Protocol]

Category: Western Blot Protocols: Antigen Detection Methods Protocols

The blot is blocked to prevent nonspecific adsorption of the immunological reagents.  Antibodies are then bound to the proteins immobilized on the membrane, and the antigen is detected by labeling the antibodies with conveniently identified tags.  Common labeling methods for chemiluminescent detection include anti-immunoglobulin antibody-coupled enzymes such as horseradish peroxidase, which catalyzes the oxidation of luminol and in turn releases light. - [Read Immunoblotting: Antigen Detection Using Chemiluminescence Protocol]

Category: Western Blot Protocols: Antigen Detection Methods Protocols

The blot is blocked to prevent nonspecific adsorption of the immunological reagents.  Antibodies are then bound to the proteins immobilized on the membrane, and the antigen is detected by labeling the antibodies with conveniently identified tags. - [Read Immunoblotting: Antigen Detection Using Chromogenic Methods Protocol]

Category: Yeast Cell Culture Protocols: Yeast Sporulation Protocols

Zygotes can be identified by their unique morphology. They can be easily separated away from nonmated cells using a micromanipulator. This method provides an alternative to the selection of diploid cells on a medium that prevents the growth of haploid parent cells. - [Read Picking Zygotes Protocol]

Category: Cell Culture Protocols

Protocol describes a method for plating cells for microinjection onto etched coverslips. The coverslips for microinjection must be marked so that microinjected cells can be identified at time points after injection. - [Read Plating Cells for Microinjection Protocol]

Category: Developmental Biology: Embryology Protocols

This protocol describes a method for visualizing early embryo implantation sites using Chicago Sky Blue 6B dye. Once implantation and interimplantation sites are identified and separated, they can be used for cellular, biochemical, and molecular biology analyses. - [Read Visualizing Early Embryo Implantation Sites by Dye Injection Protocol]