Statistical Mechanics of Integral Membrane Protein Assembly

During the synthesis of integral membrane proteins (IMPs), the hydrophobic amino acids of the polypeptide sequence are partitioned mostly into the membrane interior and hydrophilic amino acids mostly into the aqueous exterior. We analyze the minimum free energy state of polypeptide sequences partitioned into alpha-helical transmembrane (TM) segments and the role of thermal fluctuations using a many-body statistical mechanics model. Results suggest that IMP TM segment partitioning shares important features with general theories of protein folding. For random polypeptide sequences, the minimum free energy state at room temperature is characterized by fluctuations in the number of TM segments with very long relaxation times. Simple assembly scenarios do not produce a unique number of TM segments and jamming phenomena interfere with segment placement. For sequences corresponding to IMPs, the minimum free energy structure with the wildtype number of segments is free of number fluctuations due to an anomalous gap in the energy spectrum, and simple assembly scenarios produce this structure. There is a threshold number of random point mutations beyond which the size of this gap is reduced so that the wildtype groundstate is destabilized and number fluctuations reappear

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

Motivation: High-throughput data is providing a comprehensive view of the molecular changes in cancer tissues. New technologies allow for the simultaneous genome-wide assay of the state of genome copy number variation, gene expression, DNA methylation and epigenetics of tumor samples and cancer cell lines

Hidden Voices of Black Men

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66982/2/10.1177_002193479402500102.pd

Computational solutions for omics data

High-throughput experimental technologies are generating increasingly massive and complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to make the arising problems computationally infeasible. Fortunately, powerful algorithmic techniques lead to software that can answer important biomedical questions in practice. In this Review, we sample the algorithmic landscape, focusing on state-of-the-art techniques, the understanding of which will aid the bench biologist in analysing omics data. We spotlight specific examples that have facilitated and enriched analyses of sequence, transcriptomic and network data sets.National Institutes of Health (U.S.) (Grant GM081871

MICROGEOGRAPHIC VARIATION AS THERMAL ACCLIMATION IN AN INTERTIDAL MOLLUSC

Volume: 111Start Page: 129End Page: 15

THE GORGONIAN-OVULID ASSOCIATIONS OF AN INTERTIDAL CORAL COMMUNITY ON PENANG ISLAND, WEST MALAYSIA

Over parts of the rocky north shore of Penang Island, West Malaysia, and Pulau Tikus, a small island one mile offshore from Penang, coral communities (Gorgonacea, Alcyonacea, Scleractinia) may be found in the turbid inshore waters. These corals are bathed by the waters of the Muda River system on the mainland and by the waters fluxing through extensive mangal along the mainland and around Penang Island. The diverse components of the coral community are truly intertidal being exposed during spring low tides throughout the year. It appears as though the gorgonians of the coral community are unusual in their diversity and intertidal distributions. So, too, does it appear, are the ovulid gastropods associated with the gorgonians. I will, both orally and visually, described the Penang-Pulau Tikus intertidal coral community, elaborate on the gorgonians and their associated ovulid snails, and discuss the stresses placed upon the complex by man

ACCLIMATION OF OXYGEN CONSUMPTION TO TEMPERATURE IN THE AMERICAN COCKROACH (PERIPLANETA AMERICANA)

Volume: 111Start Page: 53End Page: 6

ACCLIMATION OF OXYGEN CONSUMPTION TO TEMPERATURE IN THE AMERICAN COCKROACH (PERIPLANETA AMERICANA)

Volume: 111Start Page: 53End Page: 6