The rockefeller university

BENCHMRK-1 and -2 are ongoing double-blind phase III studies of raltegravir in patients experiencing failure of antiretroviral therapy with triple-class drug-resistant human immunodeficiency virus infection. At week 96 (combined data), raltegravir (400 mg twice daily) plus optimized background therapy was generally well tolerated, with superior and durable antiretroviral and immunological efficacy, compared with optimized background therapy alone.

We present measurements of the top quark mass using m(T2), a variable related to the transverse mass in events with two missing particles. We use the template method applied to t (t) over bar dilepton events produced in p (p) over bar collisions at Fermilab's Tevatron Collider and collected by the CDF detector. From a data sample corresponding to an integrated luminosity of 3.4 fb(-1), we select 236 t (t) over bar candidate events. Using the m(T2) distribution, we measure the top quark mass to be M-top = 168.0(-4.0)(4.8)(stat) +/- 2.9(syst) GeV/c(2). By combining m(T2) with the reconstructed top quark mass distributions based on a neutrino weighting method, we measure M-top = 169.3 +/- 2.7(stat) +/- 3.2(syst) GeV/c(2). This is the first application of the m(T2) variable in a mass measurement at a hadron collider.

We combine searches by the CDF and D0 Collaborations for a Higgs boson decaying to W+W-. The data correspond to an integrated total luminosity of 4.8 (CDF) and 5.4 (D0) fb(-1) of p (p) over bar collisions at root s = 1.96 TeV at the Fermilab Tevatron collider. No excess is observed above background expectation, and resulting limits on Higgs boson production exclude a standard model Higgs boson in the mass range 162-166 GeV at the 95% C.L.

Ubiquitination plays an important role in many cellular processes and is implicated in many diseases. Experimental identification of ubiquitination sites is challenging due to rapid turnover of ubiquitinated proteins and the large size of the ubiquitin modifier. We identified 141 new ubiquitination sites using a combination of liquid chromatography, mass spectrometry, and mutant yeast strains. Investigation of the sequence biases and structural preferences around known ubiquitination sites indicated that their properties were similar to those of intrinsically disordered protein regions. Using a combined set of new and previously known ubiquitination sites, we developed a random forest predictor of ubiquitination sites, UbPred. The class-balanced accuracy of UbPred reached 72%, with the area under the ROC curve at 80%. The application of UbPred showed that high confidence Rsp5 ubiquitin ligase substrates and protein with very short half-lives were significantly enriched in the number of predicted ubiquitination sites. Proteome-wide prediction of ubiquitination sites in Saccharomyces cerevisiae indicated that highly ubiquitinated substrates were prevalent among transcription/enzyme regulators and proteins involved in cell cycle control. In the human proteome, cytoskeletal, cell cycle, regulatory, and cancer-associated proteins display higher extent of ubiquitination than proteins from other functional categories. We show that gain and loss of predicted ubiquitination sites may likely represent a molecular mechanism behind a number of disease-associated mutations. UbPred is available at http:// www.ubpred.org. Proteins 2010; 78:365-380. (C) 2009 Wiley-Liss, Inc.

Hepatitis C virus (HCV), which infects 2-3% of the world population, is a causative agent of chronic hepatitis and the leading indication for liver transplantation(1). The ability to propagate HCV in cell culture (HCVcc) is a relatively recent breakthrough and a key tool in the quest for specific antiviral therapeutics. Monitoring HCV infection in culture generally involves bulk population assays, use of genetically modified viruses and/or terminal processing of potentially precious samples. Here we develop a cell-based fluorescent reporter system that allows sensitive distinction of individual HCV-infected cells in live or fixed samples. We demonstrate use of this technology for several previously intractable applications, including live-cell imaging of viral propagation and host response, as well as visualizing infection of primary hepatocyte cultures. Integration of this reporter with modern image-based analysis methods could open new doors for HCV research.

The zebrafish provides a useful experimental system for investigations of aural development. To permit the controlled expression of transgenes in developing hair cells, we isolated the genomic control regions of the parvalbumin 3a (pvalb3a) and parvalbumin 3b (pvalb3b) genes. Deletion analysis and somatic-cell transgenesis restricted the cis-acting control regions for hair cells to as little as 484 base pairs for pvalb3a and 650 base pairs for pvalb3b. Using both meganuclease-mediated and standard methods, we produced transgenic animals that transmit transgenes through their germ lines. These fish express GFP in hair cells in the inner ear and lateral line. Two stable transgenic lines express GFP prior to hair-bundle formation, so the associated promoter constructs are suitable for manipulating gene expression during bundle development. We additionally identified a transgenic line that offers variable labeling of supporting cells. (c) 2010 Elsevier B.V. All rights reserved.

Chemokines are small secreted proteins that act as chemoattractants, and their role as neuromodulators in the brain has recently been appreciated. CXCL12 is one of the few chemokines found in neurons and expressed constitutively in the central nervous system. Previous data from our laboratory demonstrate the ability of CXCL12 to modulate the behavioral effects of cocaine, and this modulation is dependent on the central site of administration of CXCL12. The present study used single-staining immunohistochemical and dual-staining immunofluorescent methods to deter-mine the localization of the CXCL12 receptor, CXCR4, in the caudate putamen and nucleus accumbens of the adult rat brain. Results demonstrated that individual neurons in both the caudate putamen and lateral shell of the nucleus accumbens express both CXCR4 and D1 dopamine receptors. Immunofluorescent studies showed that CXCR4 was co-expressed with ChAT, a marker for cholinergic neurons, and with GAD C38, a marker for GABAergic neurons, in the caudate putamen and lateral shell of the accumbens. No evidence of CXCR4 was found in the medial shell or core regions of the nucleus accumbens. These data demonstrate that CXCR4 is expressed by subpopulations of cholinergic and GABAergic neurons in the striatum and suggest that CXCR4 is well-positioned to modulate striatal function. (C) 2009 Elsevier B.V. All rights reserved.

The stress phytohormone ABA inhibits the developmental transition taking the mature embryo in the dry seed towards a young seedling. ABA also induces the accumulation of the basic leucine zipper (bZIP) transcription factor ABA-insensitive 5 (ABI5) which, apart from blocking endosperm rupture, also protects the embryo by stimulating the expression of late embryogenesis abundant (LEA) genes that conferred osmotolerance during seed maturation. It is unknown whether ABA recruits additional embryonic pathways to control early seedling growth and fitness. Here we identify gia3 (growth insensitive to ABA3), a recessive locus in Arabidopsis mediating cotyledon cellular maturation and ABA-dependent repression of cotyledon expansion and greening. Microarray studies showed that expression of the essential mid-embryogenesis gene Maternal Embryo Effect 26 (MEE26) is induced by ABA during early seedling growth in wild-type (WT) or abi5 plants but not in gia3 mutants. However, we also show that the GIA3 locus controls ABA-dependent gene expression responses that partially overlap with those controlled by ABI5. Thus, the gia3 locus identifies an additional arm of ABA signaling, distinct from that controlled by ABI5, which recruits MEE26 expression and maintains cotyledon embryonic identity. Fine mapping localized the gia3 locus within a 1Mb interval of chromosome 3, containing a large DNA insertion of a duplicated region of chromosome 2. It remains unknown at present whether gia3 phenotypes are the result of single or multiple genetic alterations.

Hepatitis C virus (HCV) is a liver-tropic pathogen with severe health consequences for infected individuals. Chronic HCV infection can progress to cirrhosis and hepatocellular carcinoma and is a leading indicator for liver transplantation. The HCV core protein is an essential component of the infectious virus particle, but many aspects of its role remain undefined. The C-terminal region of the core protein acts as a signal sequence for the E1 glycoprotein and undergoes dual processing events during infectious virus assembly. The exact C terminus of the mature, virion-associated core protein is not known. Here, we performed genetic analyses to map the essential determinants of the HCV core C-terminal region, as well as to define the minimal length of the protein that can function for infectious virus production in trans.