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871.
The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structure of all protein-coding genes in one or more of the sequences. Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem. N-SCAN can model the phylogenetic relationships between the aligned genome sequences, context dependent substitution rates, and insertions and deletions. An implementation of N-SCAN was created and used to generate predictions for the entire human genome and the genome of the fruit fly Drosophila melanogaster. Analyses of the predictions reveal that N-SCAN's accuracy in both human and fly exceeds that of all previously published whole-genome de novo gene predictors. 相似文献
872.
Programmed death 1 expression on HIV-specific CD4+ T cells is driven by viral replication and associated with T cell dysfunction 总被引:2,自引:0,他引:2
D'Souza M Fontenot AP Mack DG Lozupone C Dillon S Meditz A Wilson CC Connick E Palmer BE 《Journal of immunology (Baltimore, Md. : 1950)》2007,179(3):1979-1987
Functional impairment of HIV-specific CD4(+) T cells during chronic HIV infection is closely linked to viral replication and thought to be due to T cell exhaustion. Programmed death 1 (PD-1) has been linked to T cell dysfunction in chronic viral infections, and blockade of the PD-1 pathway restores HIV-specific CD4(+) and CD8(+) T cell function in HIV infection. This study extends those findings by directly examining PD-1 expression on virus-specific CD4(+) T cells. To investigate the role of PD-1 in HIV-associated CD4(+) T cell dysfunction, we measured PD-1 expression on blood and lymph node T cells from HIV-infected subjects with chronic disease. PD-1 expression was significantly higher on IFN-gamma-producing HIV-specific CD4(+) T cells compared with total or CMV-specific CD4(+) T cells in untreated HIV-infected subjects (p = 0.0001 and p < 0.0001, respectively). PD-1 expression on HIV-specific CD4(+) T cells from subjects receiving antiretroviral therapy was significantly reduced (p = 0.007), and there was a direct correlation between PD-1 expression on HIV-specific CD4(+) T cells and plasma viral load (r = 0.71; p = 0.005). PD-1 expression was significantly higher on HIV-specific T cells in the lymph node, the main site of HIV replication, compared with those in the blood (p = 0.0078). Thus, PD-1 expression on HIV-specific CD4(+) T cells is driven by persistent HIV replication, providing a potential target for enhancing the functional capacity of HIV-specific CD4(+) T cells. 相似文献
873.
874.
Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database 总被引:3,自引:0,他引:3
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Buckner B Beck J Browning K Fritz A Grantham L Hoxha E Kamvar Z Lough A Nikolova O Schnable PS Scanlon MJ Janick-Buckner D 《Genetics》2007,176(2):741-747
Through a multi-university and interdisciplinary project we have involved undergraduate biology and computer science research students in the functional annotation of maize genes and the analysis of their microarray expression patterns. We have created a database to house the results of our functional annotation of >4400 genes identified as being differentially regulated in the maize shoot apical meristem (SAM). This database is located at http://sam.truman.edu and is now available for public use. The undergraduate students involved in constructing this unique SAM database received hands-on training in an intellectually challenging environment, which has prepared them for graduate and professional careers in biological sciences. We describe our experiences with this project as a model for effective research-based teaching of undergraduate biology and computer science students, as well as for a rich professional development experience for faculty at predominantly undergraduate institutions. 相似文献
875.
Eva C. Enders Karen E. Smokorowski Curtis J. Pennell Keith D. Clarke Brent Sellars David A. Scruton 《Hydrobiologia》2007,582(1):133-142
Degradation and destruction of valuable spawning and rearing habitat due to anthropogenic changes (e.g., flow modification
and channelisation) is known to have dramatic impacts on fish populations. To compensate for habitat losses due to hydropower
development, an artificial fluvial habitat channel (‘Compensation Creek’) was constructed in south-central Newfoundland, Canada.
The creek was designed to include appropriate habitat features for the two dominant salmonid fish species, landlocked Atlantic
salmon (Salmo salar L.) and brook charr (Salvenius fontinalis Mitchell). The study examines the habitat use of landlocked Atlantic salmon and brook charr in the Compensation Creek using
electromyogram (EMG) radio telemetry. Ten landlocked Atlantic salmon and eight brook charr were captured and tagged with EMG
transmitters. In laboratory swimming experiments, the EMG values were calibrated against swimming speed. Fish were then released
in the Compensation Creek and tracked on a daily basis. The results show that (1) during residence in the creek, both species
used preferentially the habitat features designed to match their rearing habitat preferences, and (2) swimming speed did not
vary among habitat types for either species. 相似文献
876.
Amiel E Nicholson-Dykstra S Walters JJ Higgs H Berwin B 《Experimental cell research》2007,313(7):1438-1448
Class-A scavenger receptors (SR-A) are cellular pattern recognition receptors that bind and traffic a variety of endogenous and microbial ligands. However, despite an emerging role for SR-A as a contributor to the innate immune system, little is known of the regulation or function of SR-A on dendritic cells (DCs). Here we show that SR-A expression is upregulated during murine DC differentiation and that SR-A expression levels correlate with the expression of the murine DC marker CD11c. Using bone marrow-derived DCs (BMDCs) from SR-A knockout (SR-A(-/-)) mice, we investigated the contribution of SR-A to BMDC particulate phagocytosis. Functional analyses demonstrated that SR-A is a critical phagocytic receptor for BMDC internalization of the gram-negative bacteria E. coli. SR-A(-/-) BMDCs were impaired in their ability to phagocytose bacteria, and this deficit varied with the bacteria:BMDC cell ratio. Microscopic and biochemical analyses revealed that SR-A is broadly distributed on the surface of BMDCs and is not physically associated with lipid rafts. However, cholesterol depletion demonstrated dependence of SR-A-mediated phagocytosis upon lipid rafts. These data demonstrate a functional contribution for SR-A in the BMDC phagocytic pathway. 相似文献
877.
878.
Geoghegan JC Valdes PA Orem NR Deleault NR Williamson RA Harris BT Supattapone S 《The Journal of biological chemistry》2007,282(50):36341-36353
The central pathogenic event of prion disease is the conformational conversion of a host protein, PrPC, into a pathogenic isoform, PrPSc. We previously showed that the protein misfolding cyclic amplification (PMCA) technique can be used to form infectious prion molecules de novo from purified native PrPC molecules in an autocatalytic process requiring accessory polyanions (Deleault, N. R., Harris, B. T., Rees, J. R., and Supattapone, S. (2007) Proc. Natl. Acad. Sci. U. S. A. 104, 9741-9746). Here we investigated the molecular mechanism by which polyanionic molecules facilitate infectious prion formation in vitro.Ina PMCA reaction lacking PrPSc template seed, synthetic polyA RNA molecules induce hamster HaPrPC to adopt a protease-sensitive, detergent-insoluble conformation reactive against antibodies specific for PrPSc. During PMCA, labeled nucleic acids form nuclease-resistant complexes with HaPrP molecules. Strikingly, purified HaPrPC molecules subjected to PMCA selectively incorporate an approximately 1-2.5-kb subset of [32P]polyA RNA molecules from a heterogeneous mixture ranging in size from approximately 0.1 to >6 kb. Neuropathological analysis of scrapie-infected hamsters using the fluorescent dye acridine orange revealed that RNA molecules co-localize with large extracellular HaPrP aggregates. These findings suggest that polyanionic molecules such as RNA may become selectively incorporated into stable complexes with PrP molecules during the formation of native hamster prions. 相似文献
879.
Robotic devices hold much promise for use as rehabilitation aids but their success depends on identifying effective strategies for controlling human-robot interaction forces. We developed a robotic device to test a novel method of controlling interaction forces with the intent of improving force symmetry in the limbs. Users perform lower limb extensions against a computer-controlled resistive load. The control software increases resistance above baseline in proportion to lower limb force asymmetry (balance between left and right limb forces). As a preliminary trial to test the device and controller, we conducted two experiments on neurologically intact subjects. In experiment 1, one group of subjects received symmetry-based resistance while performing lower limb extensions (n=10). A control group performed the same movements with constant resistance (n=10). The symmetry-based resistance group improved lower limb symmetry during training (ANOVA, p<0.05), whereas the control subjects did not. In experiment 2, subjects (n=10) successfully used symmetry-based resistance to alter their lower limb force production towards a target asymmetry (ANOVA, p<0.05). These studies suggest that symmetry-based resistance may hold rehabilitation benefits after orthopedic or neurological injury. Specifically, performing strength training therapy with this controller may allow hemiparetic individuals to focus better on increasing strength and neuromuscular recruitment in their paretic limb while experiencing symmetric limb forces. 相似文献
880.
In a study of wolf pup survival, intraperitoneal radio transmitters were surgically implanted in 53 (27 male and 26 female) 3.5- to 8-wk-old Eastern wolf (Canis lycaon) pups at den sites in Algonquin Provincial Park, Ontario, Canada, over two whelping seasons (2004 and 2005). Pups were manually removed from dens and initially injected with butorphanol at a dosage of 0.1 mg/kg for sedation and intra-operative analgesia. Anesthesia was induced and maintained with 3% sevoflurane in oxygen via a face mask. Meloxicam (0.3 mg/kg intramuscularly) was given to provide additional analgesia. All surgeries were completed without complications, and pups were readily accepted back into the packs. No postoperative complications were identified, but two pups from a single litter drowned as a result of being moved by the pack to a flooded den following the surgery. In five pups necropsied following natural deaths, transmitters were found lying free within the peritoneal cavity, and there was no evidence of infection at the surgical site or peritonitis. Inhalation anesthesia provided extremely rapid induction (1 min) and recovery (<3 min) and was completely controllable with no residual anesthetic effects. The equipment for inhalation anesthesia was readily portable in field packs, and it has considerable advantages over injectable drugs for small and very young animals such as wolf pups. The utility of the procedure is demonstrated by the minimal effect it had on subsequent pup survival, the rapid recovery of pups following surgery, and the lack of long-term complications as determined by necropsies of pups following natural deaths. 相似文献