Late last year, while watching a news report that examined the challenges of annotating the human genome sequence, Bill Long had an epiphany. A programmer at Seattle-based Cray Inc., Long realized that many bioinformatics complexities are basically problems of pattern matching--a Cray specialty. So, Long phoned the National Cancer Institute's (NCI) Advanced Biomedical Computing Center (ABCC) and suggested a collaboration. He was well received. Says ABCC director Stan Burt, facility researchers "

The use of high-throughput gene expression analysis technologies, such as microarrays, yields reams of data. Unfortunately, data stemming from competing and alternate technologies is often stored in a variety of formats, making comprehensive analyses difficult. Kirkland, Wash.-based Rosetta Inpharmatics Inc. offers a product that now enables scientists to join all of their gene expression data in a single location, and to mine that data for nuggets of gold unimaginable when the experiments were

Click to view the PDF file: Proteomic Mass Spectrometry Equipment Courtesy of CiphergenCiphergen's SELDI process, a MALDI variant that includes a surface-based enrichment step Early in the twentieth century, scientists puzzled over the observation that certain elements that were otherwise physically indistinguishable from each other nevertheless exhibited different radioactive decay characteristics. These elements would ultimately come to be known as isotopes, but at the time this concept was

Pathologists and research scientists spend a great deal of time poring over histological samples on microscope slides. In a field containing tens of thousands of cells, these researchers might find a small section of the sample that warrants further study. For example, a pathologist examining a tissue biopsy might find a small colony of abnormal cells in a field of otherwise normal cells. Fortunately, these scientists can retrieve such a small colony of cells, or even a single cell, from the tis

Let's face it: Life scientists need computers. They need word processors to write grants and manuscripts; spreadsheets and statistical software to crunch numbers; image manipulation software to put the data into publication-ready formats; and sequence analysis software to, well, analyze sequence information. The Scientist recently conducted a survey in which readers were asked what software is used in their laboratories, and to what tasks they think the software manufacturers need to pay greater

The fundamental question of how cells sense oxygen has implications for embryogenesis, cancer, stroke, diabetes, and other ischemic diseases.

Researchers routinely prepare proteins in test tubes using the in vitro translation (IVT) reaction.1 These reactions are fast, efficient, and reasonably cost-effective. They are also highly flexible. Proteins can be synthesized either from RNA transcribed in vitro (uncoupled), or from plasmid DNA via a coupled transcription/translation system. In addition, the proteins are easily labeled with [35S]-methionine or biotinylated lysine simply by addition of the labeling reagent to the reaction. Unfo

Reagents That Distinguish Th1 and Th2 cells Courtesy of R&D SystemsSchematic representation of cytokines influencing the development of antigen-activated naive CD4+ T cells into Th1 and Th2 cells. Editor's note: Although individual techniques are associated with specific researchers in this article, it should be noted that these investigators commonly use several different techniques to analyze T lymphocyte populations. The human body is constantly under siege. It must defend itself fr

Antigen-specific T lymphocytes must be quantified in order to gauge the quality of an immune response. Typically this is accomplished using cytotoxicity assays or limiting dilution analysis (LDA), but these techniques are lengthy and provide indirect quantitation. Also, LDA cannot count nonproliferative cells. In 1996, Stanford University's Mark Davis developed an alternative strategy that overcomes these problems.1 Davis generated phycoerythrin-conjugated tetramers of human lymphocyte antigen (

Suppliers of in vitro Site-directed Mutagenesis Kits Biological research greatly benefits from the ability to introduce specific mutations into a DNA sequence. Researchers use site-directed mutagenesis procedures to precisely analyze individual amino acid residues in a protein sequence and in specific protein-nucleic acid interactions. Likewise, serial deletion and random insertion protocols can ease protein structural studies and promoter analyses. In their original incarnations, site-directe

Invitrogen's Gene Racer Kit Expressed sequence tags are powerful tools for gene expression studies, but when there is simply no substitute for a full-length cDNA, researchers turn to protocols for the Rapid Amplification of cDNA Ends (RACE). RACE techniques couple cDNA synthesis with a method that attaches a "known" sequence to the end of the gene to enable PCR amplification. Knowing the 5' end of a transcript can aid promoter, gene mapping, and alternate exon usage analyses. Unfortunately, 5' R

PCR has fundamentally changed molecular biology, offering a rapid means to amplify minute quantities of DNA. Real-time quantitative PCR (Q-PCR) techniques are designed to facilitate accurate measurement of target sequences by correlating amplification with the fluorescence of specially labeled probes in the reaction. Q-PCR methodologies using fluorescence resonance energy transfer (FRET) employ an oligonucleotide probe designed to hybridize to the center of the desired PCR product. This probe is