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: Antigen & T cell. The organization has 2323 authors who have published 2217 publications receiving 112618 citations.

High output genetic mapping of polyploids using PCR-generated markers.

Abstract: The polymerase chain reaction (PCR) with arbitrarily selected primers has been established as an efficient method to generate fingerprints that are useful in genetic mapping and genomic fingerprinting. To further increase the productivity of mapping and fingerprinting efforts, we have altered existing protocols to include the use of the Stoffel fragment, which is derived from genetically engineered Taq polymerase. We also optimized the thermal profile of the reaction to increase the number of useful primers. In mapping of the genome of Saccharum spontaneum 'SES 208', a polyploid wild relative of sugarcane, these modifications allowed for an increase of 30% in the number of loci screened per primer, and an 80% increase in the number of polymorphisms per primer. Furthermore, the enzyme cost per reaction was decreased approximately 1.6-fold. Finally, there was an increase from about 70% to about 97% in the number of primers that were useful (i.e., gave a reproducible fingerprint) using our protocol. We have placed some of these markers into linkage groups.

High-resolution functional proteomics by active-site peptide profiling

Abstract: Characterization and functional annotation of the large number of proteins predicted from genome sequencing projects poses a major scientific challenge. Whereas several proteomics techniques have been developed to quantify the abundance of proteins, these methods provide little information regarding protein function. Here, we present a gel-free platform that permits ultrasensitive, quantitative, and high-resolution analyses of protein activities in proteomes, including highly problematic samples such as undiluted plasma. We demonstrate the value of this platform for the discovery of both disease-related enzyme activities and specific inhibitors that target these proteins.

Plasma Clearance of Bacteriophage Qβ Particles as a Function of Surface Charge

Abstract: Self-assembled protein capsids have gained attention as a promising class of nanoparticles for biomedical applications due to their monodisperse nature and versatile genetic and chemical tailorability. To determine the plasma clearance and tissue distribution in mice of the versatile capsid of bacteriophage Qβ, the particles were decorated with gadolinium complexes using the CuI-mediated azide-alkyne cycloaddition reaction. Interior surface labeling was engineered by the introduction of an azide-containing unnatural amino acid into the coat protein for the first time. Clearance rates were conveniently monitored by quantitative detection of Gd using inductively coupled plasma-optical emission spectroscopy, and were found to be inversely proportional to the number of complexes attached to the exterior surface of the particle. This phenomenon was correlated to changes in exterior surface charge brought about by acylation of surface exposed amine groups in the initial step of the bioconjugation protocol. When primary amine groups were reintroduced by azide-alkyne coupling, the circulation time increased accordingly. These results show that nanoparticle trafficking may be tailored in predictable ways by chemical and genetic modifications that modulate surface charge.

On the Pathogenicity of Autoantigen-Specific T-Cell Receptors

Abstract: Objective: Type 1 diabetes is mediated by T cell entry into pancreatic islets and destruction of insulin-producing β cells. The relative contribution of T cells specific for different autoantigens is largely unknown as relatively few have been assessed in vivo . Research Design and Methods: We generated mice possessing a monoclonal population of T cells expressing one of 17 T cell receptors (TCR) specific for either known autoantigens (GAD65, IA2, IA2β/phogrin and insulin), unknown islet antigens or control antigens on a NOD. scid background using retroviral-mediated stem cell gene transfer and 2A-linked multicistronic retroviral vectors [referred to herein as retrogenic mice (Rg)]. The TCR Rg approach provides a mechanism by which T cells with broad phenotypic differences can be directly compared. Results: Neither GAD- nor IA2-specific TCRs mediated T cell islet infiltration or diabetes even though T cells developed in these Rg mice and responded to their cognate epitope. IA2β/phogrin and insulin-specific Rg T cells produced variable levels of insulitis, with one TCR producing delayed diabetes. Three TCRs specific for unknown islet antigens produced a hierarchy of insulitogenic and diabetogenic potential (BDC-2.5>NY4.1>BDC-6.9), while a fourth (BDC-10.1) mediated dramatically accelerated disease with all mice diabetic by day 33, well before full T cell reconstitution (days 42-56). Remarkably as few as 1000 BDC-10.1 Rg T cells caused rapid diabetes following adoptive transfer into NOD. scid mice. Conclusions: Our data show that relatively few autoantigen-specific TCR can mediate islet infiltration and β cell destruction on their own, and that autoreactivity does not necessarily imply pathogenicity.