Torrey Pines Institute for Molecular Studies

About: Torrey Pines Institute for Molecular Studies is a nonprofit organization based out in San Diego, California, United States. It is known for research contribution in the topics: T cell & Antigen. The organization has 2323 authors who have published 2217 publications receiving 112618 citations.

Design and performance of a microcantilever-based hydrogen sensor

Abstract: This paper describes the design of, and the effects of basic environmental parameters on, a microelectromechanical (MEMS) hydrogen sensor. The sensor contains an array of 10 micromachined cantilever beams. Each cantilever is 500 μm wide×267 μm long×2 μm thick and has a capacitance readout capable of measuring cantilever deflection to within 1 nm. A 20-nm-thick coating of 90% palladium–10% nickel bends some of the cantilevers in the presence of hydrogen. The palladium–nickel coatings are deposited in ultra-high-vacuum (UHV) to ensure freedom from a “relaxation” artifact apparently caused by oxidation of the coatings. The sensor consumes 84 mW of power in continuous operation, and can detect hydrogen concentrations between 0.1 and 100% with a roughly linear response between 10 and 90% hydrogen. The response magnitude decreases with increasing temperature, humidity, and oxygen concentration, and the response time decreases with increasing temperature and hydrogen concentration. The 0–90% response time of an unheated cantilever to 1% hydrogen in air is about 90 s at 25 °C and 0% humidity.

Genomic fingerprints produced by PCR with consensus tRNA gene primers

Abstract: The polymerase chain reaction using only a single 'consensus' tRNA gene primer, or a pair of primers facing outward from tRNA genes, amplifies a set of DNA fragments in bacterial, plant and animal genomic DNAs. Presumably, these PCR fingerprints are mainly derived from the regions between closely linked tRNA genes. The pattern of the PCR products is determined by which genomes and which primer(s) are used. Genomic fingerprints are largely conserved within a species and, in bacteria, most products in the fingerprint are conserved between closely related species. Thus, PCR with tRNA gene consensus primers helps to identify species and genera.

Tandem orthogonal proteolysis-activity-based protein profiling (TOP-ABPP)—a general method for mapping sites of probe modification in proteomes

Abstract: Activity-based protein profiling (ABPP) utilizes active site-directed chemical probes to monitor the functional state of enzymes directly in native biological systems. Identification of the specific sites of probe labeling on enzymes remains a major challenge in ABPP experiments. In this protocol, we describe an advanced ABPP platform that utilizes a tandem orthogonal proteolysis (TOP) strategy coupled with mass spectrometric analysis to simultaneously identify probe-labeled proteins together with their exact sites of probe modification. Elucidation of probe modification sites reveals fundamental insights into the molecular basis of specific probe-protein interactions. The TOP-ABPP method can be applied to any type of proteomic sample, including those derived from in vitro or in vivo labeling experiments, and is compatible with a variety of chemical probe structures. Completion of the entire protocol, including chemical synthesis of key reagents, requires approximately 8-10 days.