Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria

We have used a bioinformatics approach for the identification and reconstruction of metabolic pathways associated with amino acid metabolism in human mitochon- dria. Human mitochondrial proteins determined by experimental and computa- tional methods have been superposed on the reference pathways from the KEGG database to identify mitochondrial pathways. Enzymes at the entry and exit points for each reconstructed pathway were identified, and mitochondrial solute carrier proteins were determined where applicable. Intermediate enzymes in the mito- chondrial pathways were identified based on the annotations available from public databases, evidence in current literature, or our MITOPRED program, which pre- dicts the mitochondrial localization of proteins. Through integration of the data derived from experimental, bibliographical, and computational sources, we recon- structed the amino acid metabolic pathways in human mitochondria, which could help better understand the mitochondrial metabolism and its role in human health.     

Targeting the single-strand G-rich overhang of telomeres with PNA inhibits cell growth and induces apoptosis of human immortal cells

Telomeres are believed to stabilize chromosomes through several mechanisms that are dependent upon specific DNA-DNA and protein-DNA interactions. Telomeres are maintained by the enzyme telomerase. Telomerase activity, which is below detectable level in almost all types of diploid cells, is re-activated in most immortal and cancer cells. For this study, we designed peptide nucleic acid (PNA) oligonucleotides targeted to the telomeric G-rich strand, and tested their efficacy to reverse the immortality of transformed human fibroblasts. Anti-telomere PNAs, transfected into human fibroblasts along with a selectable marker, resulted in a significant reduction in colony size and elicited cell death by apoptosis. This PNA inhibitor does not inhibit telomerase activity in vitro, suggesting a distinct cellular mechanism from known PNA inhibitors. A combination of this class of PNA inhibitor with a PNA that does block telomerase activity resulted in nearly complete inhibition of colony growth, induction of apoptosis, and an apparent reduction in telomere length. Each effect was greater than that evoked by either agent alone, indicating enhanced efficacy for therapeutic approaches that target multiple, distinct mechanism of telomere maintenance.     

Evolution of bioengineering at UCSD: opening new vistas

Before this, the field of bioengineering refers to biomedical engineering of prosthetic devices in physiology. In addition to exciting applications of engineering principles, UCSD Department of Bioengineering began to extend the notion of engineering models of physiological systems to physiological processes. This led to a conceptual shift in the discipline and contributed to the areas of tissue and physiological process engineering. In 1988, Dr. Shu Chien and Richard Skalak joined UCSD to begin research and education on cellular and molecular bioengineering, especially, mechanobiology. Dr. Fung and Dr. Skalak initiated the new field of tissue engineering. These two decades of evolution of bioengineering and its growth across the country was spearheaded by the Whitaker Foundation, whose leitmotif was the building of bioand biomedical engineering across the country. We have garnered other accomplishments in the following fields: regenerative medicine; bioinspired artificial extracellular matrices; flexible bioelectronics and tatoos; cells show how to synchronize biological clocks; and systems medicine.     

Purification and characterization of a motility initiating protein from caprine epididymal plasma

Numerous reports have appeared on the occurrence of undefined protein factors in male reproductive fluids that promote motility of mature sperm and initiate forward motility in the immature (immotile) caput‐epididymal sperm. This study reports for the first time purification to apparent homogeneity of a motility initiating protein (MIP) from epididymal plasma and its characterization using the caprine sperm model. It is a 125 kDa (approximately) dimeric protein made up of two subunits: 70 and 54 kDa. MIP is an acidic protein with an isoelectric point of 4.75. The motility protein at 30 µg/ml (240 nM) level showed nearly maximal motility‐promoting activity. MIP is heat stable and it is maximally active at pH 8. It is a glycoprotein that binds with high affinity to concanavalin A and it contains mannose, galactose, and N‐acetyl glucosamine approximately in the ratios of 6:1:6. It is sensitive to the actions of α‐mannosidase and β‐N‐acetylglucoseaminidase thereby demonstrating that the sugar side chain of the glycoprotein is essential for its biological activity. Epididymal plasma is its richest source. It is also capable of enhancing forward motility of mature cauda‐sperm. Its antibody markedly inhibits sperm motility. MIP antibody is highly immunospecific and it recognizes both the subunits. MIP causes significant increase of the intrasperm level of cyclic AMP. MIP: the physiological motility‐activating protein has potential for use as a contraceptive vaccine and for solving some of the problems of human infertility and animal breeding. J. Cell. Physiol. 222:254–263, 2010. © 2009 Wiley‐Liss, Inc.     

Topsoil Stockpiling Versus Exposure to Traffic: A Case Study on In situ Uranium Wellfields

Management of soils on areas subjected to planned disturbance, such as surface mine sites, is crucial to post‐disturbance restoration. We conducted a study to determine which of the following two topsoil management strategies resulted in less of a negative impact to the soil and vegetation resources and better promoted site restoration on in situ uranium wellfields: (1) removal of topsoil from an entire wellfield and stockpiling until mining activity is complete; or (2) leaving the majority of topsoil on the wellfield and allowing it to be exposed to disturbance associated with wellfield development activity (primarily heavy vehicle traffic). Our study compared selected soil properties from areas on in situ uranium wellfields managed by the two strategies stated above and with adjacent, relatively undisturbed sites. Vegetation reestablishment was assessed on sites where topsoil was left in place. Results indicated that levels of vehicular traffic on wellfields did not cause significant soil compaction and that removal and stockpiling of topsoil results in more negative impacts than disturbance inflicted when topsoil is left in place.