News
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Cancer Genomics Browser gives cancer researchers a powerful new tool
By Tim Stephens, UCSC Public Information Office A Cancer Genomics Browser developed by researchers at the University of California, Santa Cruz, provides a new way to visualize and analyze data from studies aimed at improving cancer treatment by unraveling the complex genetic roots of the disease. The browser consists of a suite of web-based tools…
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Stem cell symposium showcases new facilities and research
By Tim Stephens, UCSC Public Information OfficeWhere do blood cells come from? How do neurons develop to create the complex wiring of the brain? Can we build a better microscope to study living cells?These are among the questions UCSC stem cell researchers are investigating with funding from the California Institute for Regenerative Medicine (CIRM). Their work could…
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New data suggest “jumping genes” play a significant role in gene regulatory networks
By Tim Stephens, UCSC Public Information Office David Haussler, CBSE director and distinguished professor of biomolecular engineering at UCSC’s Jack Baskin School of Engineering, said CBSE research teams are finding evidence that the early theories of Nobel Prize winner Barbara McClintock, later modeled by Roy Britten and Eric Davidson, are correct. Haussler discussed these findings…
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UCSC student business plan competition
UC Santa Cruz challenges any student who has a good idea for a business to participate in the campus’s first ever Business Plan Competition. This competition is open to students of any major, year, and experience. By participating in this competition, students can generate exposure to potential employers, gain important experience, place an impressive point…
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The ontogeny of aerobic and diving capacity in the skeletal muscles of Weddell seals
Our objective was to determine the ontogenetic changes in the skeletal muscles of Weddell seals that transform a non-diving pup into an elite diving adult. Muscle biopsies were collected from pups, juveniles and adults and analyzed for changes in fiber type, mitochondrial density, myoglobin concentrations and aerobic, lipolytic and anaerobic enzyme activities. The fiber type…
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A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the…
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Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
The human and mouse genomes share a number of long, perfectly conserved nucleotide sequences, termed ultraconserved elements1. Whereas these regions can act as transcriptional enhancers when upstream of genes, those within genes are less well understood. In particular, the function of ultraconserved elements that overlap alternatively spliced exons of genes encoding RNA-binding proteins is unknown.…
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Single-molecule analysis of DNA-protein complexes using nanopores
We present a method for rapid measurement of DNA-protein interactions using voltage-driven threading of single DNA molecules through a protein nanopore. Electrical force applied to individual ssDNA-exonuclease I complexes pulls the two molecules apart, while ion current probes the dissociation rate of the complex. Nanopore force spectroscopy (NFS) reveals energy barriers affecting complex dissociation. This…
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The cost of foraging by a marine predator, the Weddell seal Leptonychotes weddellii: pricing by the stroke
Foraging by mammals is a complex suite of behaviors that can entail high energetic costs associated with supporting basal metabolism, locomotion and the digestion of prey. To determine the contribution of these various costs in a free-ranging marine mammal, we measured the post-dive oxygen consumption of adult Weddell seals (N=9) performing foraging and non-foraging dives…
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The diving paradox: new insights into the role of the dive response in air-breathing vertebrates
When aquatic reptiles, birds and mammals submerge, they typically exhibit a dive response in which breathing ceases, heart rate slows, and blood flow to peripheral tissues is reduced. The profound dive response that occurs during forced submergence sequesters blood oxygen for the brain and heart while allowing peripheral tissues to become anaerobic, thus protecting the…
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Nanopore sensors for nucleic acid analysis
Abstract: In the past decade, nanometre-scale pores have been explored as the basis for technologies to analyze and sequence single nucleic acid molecules. Most approaches involve using such a pore to localize single macromolecules and interact with them to garner some information on their composition. Though nanopore sensors cannot yet claim success at deoxyribonucleic acid…
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Highly Accurate Classification of Watson-Crick Basepairs on Termini of Single DNA Molecules
Abstract: We introduce a computational method for classification of individual DNA molecules measured by an α-hemolysin channel detector. We show classification with better than 99% accuracy for DNA hairpin molecules that differ only in their terminal Watson-Crick basepairs. Signal classification was done in silico to establish performance metrics (i.e., where train and test data were…