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A set of grid type knowledge‐based energy functions is introduced for ?–χ1, ψ–χ1, ?–ψ, and χ1–χ2 torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X‐ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement. Proteins 2013. Proteins 2013; 81:1156–1165. © 2013 Wiley Periodicals, Inc. 相似文献
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Dror Kolodkin-Gal Sandrine L. Hulot Birgit Korioth-Schmitz Randi B. Gombos Yi Zheng Joshua Owuor Michelle A. Lifton Christian Ayeni Robert M. Najarian Wendy W. Yeh Mohammed Asmal Gideon Zamir Norman L. Letvin 《Journal of virology》2013,87(24):13589-13597
Effective strategies are needed to block mucosal transmission of human immunodeficiency virus type 1 (HIV-1). Here, we address a crucial question in HIV-1 pathogenesis: whether infected donor mononuclear cells or cell-free virus plays the more important role in initiating mucosal infection by HIV-1. This distinction is critical, as effective strategies for blocking cell-free and cell-associated virus transmission may be different. We describe a novel ex vivo model system that utilizes sealed human colonic mucosa explants and demonstrate in both the ex vivo model and in vivo using the rectal challenge model in rhesus monkeys that HIV-1-infected lymphocytes can transmit infection across the mucosa more efficiently than cell-free virus. These findings may have significant implications for our understanding of the pathogenesis of mucosal transmission of HIV-1 and for the development of strategies to prevent HIV-1 transmission. 相似文献
105.
Pablo Penaloza-MacMaster Nicholas M. Provine Joshua Ra Erica N. Borducchi Anna McNally Nathaniel L. Simmons Mark J. Iampietro Dan H. Barouch 《Journal of virology》2013,87(3):1373-1384
The failure of the adenovirus serotype 5 (Ad5) vector-based human immunodeficiency virus type 1 (HIV-1) vaccine in the STEP study has led to the development of adenovirus vectors derived from alternative serotypes, such as Ad26, Ad35, and Ad48. We have recently demonstrated that vaccines using alternative-serotype Ad vectors confer partial protection against stringent simian immunodeficiency virus (SIV) challenges in rhesus monkeys. However, phenotypic differences between the T cell responses elicited by Ad5 and those of alternative-serotype Ad vectors remain unexplored. Here, we report the magnitude, phenotype, functionality, and recall capacity of memory T cell responses elicited in mice by Ad5, Ad26, Ad35, and Ad48 vectors expressing lymphocytic choriomeningitis virus (LCMV) glycoprotein (GP). Our data demonstrate that memory T cells elicited by Ad5 vectors were high in magnitude but exhibited functional exhaustion and decreased anamnestic potential following secondary antigen challenge compared to Ad26, Ad35, and Ad48 vectors. These data suggest that vaccination with alternative-serotype Ad vectors offers substantial immunological advantages over Ad5 vectors, in addition to circumventing high baseline Ad5-specific neutralizing antibody titers. 相似文献
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Johann Walker Jay J. Rotella Joshua H. Schmidt Charles R. Loesch Ronald E. Reynolds Mark S. Lindberg James K. Ringelman Scott E. Stephens 《The Journal of wildlife management》2013,77(2):392-404
Conservation programs for breeding ducks in the Prairie Pothole Region (PPR) of the United States and Canada require effective means of evaluating and characterizing breeding habitat across large landscapes. Extensive surveys of the distribution of duck broods in late-summer could help identify wetland basins with greater probabilities of occupancy. Broods are difficult to detect, however, rendering presence–absence data from single-visit surveys difficult to interpret, particularly when probability of detection is related to habitat features. Multiple-visit occupancy surveys offer a potential solution. From 20 July to 5 August 2007–2009, we conducted a 3-visit survey of wetland basins located on 167 10.4-km2 study plots in the PPR. Our survey focused on broods of the 5 most common breeding duck species (Anas spp.). Our main objectives were to investigate ecological relationships between occupancy of wetland basins by broods and habitat characteristics and to examine if habitat-specific detection was of enough concern to warrant multi-survey approaches in the future. We surveyed 3,226 wetland basins during the study. Probability of occupancy of a wetland basin by a brood was positively related to the log of wet area for all 5 study species and was greater on wetlands located on plots with a greater proportion of herbaceous perennial cover for 4 of 5 species. For example, the median probability of occupancy for gadwall (Anas strepera) increased from 0.08 (90% Credible Interval [CrI]: 0.07, 0.10) to 0.28 (90% CrI: 0.23, 0.33) as wet area increased from 0.19 ha to 2.12 ha, and increased from 0.12 (90% CrI: 0.09, 0.16) to 0.20 (90% CrI: 0.16, 0.25) as proportion of perennial grass cover on the study plot increased from 0.03 to 0.99. Because occupancy and detection were both related to attributes of wetland basins, we concluded that the multiple-visit survey was a useful approach for identifying habitat relationships of duck broods. Our results indicated that most broods of the study species were found in 10.4-km2 landscapes with greater densities of small- to mid-sized wetland basins and a greater proportion of herbaceous perennial vegetation. Our study provided new empirical support that could be used to help target conservation actions to the most productive landscapes for breeding ducks. © 2012 The Wildlife Society. 相似文献
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Genevieve G. A. Fouda Joshua D. Amos Andrew B. Wilks Justin Pollara Caroline A. Ray Anjali Chand Erika L. Kunz Brooke E. Liebl Kaylan Whitaker Angela Carville Shannon Smith Lisa Colvin David J. Pickup Herman F. Staats Glenn Overman Krissey Eutsey-Lloyd Robert Parks Haiyan Chen Celia LaBranche Susan Barnett Georgia D. Tomaras Guido Ferrari David C. Montefiori Hua-Xin Liao Norman L. Letvin Barton F. Haynes Sallie R. Permar 《Journal of virology》2013,87(12):6986-6999
We previously demonstrated that vaccination of lactating rhesus monkeys with a DNA prime/vector boost strategy induces strong T-cell responses but limited envelope (Env)-specific humoral responses in breast milk. To improve vaccine-elicited antibody responses in milk, hormone-induced lactating rhesus monkeys were vaccinated with a transmitted/founder (T/F) HIV Env immunogen in a prime-boost strategy modeled after the moderately protective RV144 HIV vaccine. Lactating rhesus monkeys were intramuscularly primed with either recombinant DNA (n = 4) or modified vaccinia virus Ankara (MVA) poxvirus vector (n = 4) expressing the T/F HIV Env C.1086 and then boosted twice intramuscularly with C.1086 gp120 and the adjuvant MF59. The vaccines induced Env-binding IgG and IgA as well as neutralizing and antibody-dependent cellular cytotoxicity (ADCC) responses in plasma and milk of most vaccinated animals. Importantly, plasma neutralization titers against clade C HIV variants MW965 (P = 0.03) and CAP45 (P = 0.04) were significantly higher in MVA-primed than in DNA-primed animals. The superior systemic prime-boost regimen was then compared to a mucosal-boost regimen, in which animals were boosted twice intranasally with C.1086 gp120 and the TLR 7/8 agonist R848 following the same systemic prime. While the systemic and mucosal vaccine regimens elicited comparable levels of Env-binding IgG antibodies, mucosal immunization induced significantly stronger Env-binding IgA responses in milk (P = 0.03). However, the mucosal regimen was not as potent at inducing functional IgG responses. This study shows that systemic MVA prime followed by either intranasal or systemic protein boosts can elicit strong humoral responses in breast milk and may be a useful strategy to interrupt postnatal HIV-1 transmission. 相似文献
108.
Royd Vinya Yadvinder Malhi Joshua B. Fisher Nick Brown Timothy J. Brodribb Luiz E. Aragao 《Oecologia》2013,173(3):711-720
Although precipitation plays a central role in structuring Africa’s miombo woodlands, remarkably little is known about plant-water relations in this seasonally dry tropical forest. Therefore, in this study, we investigated xylem vulnerability to cavitation for nine principal tree species of miombo woodlands, which differ in habitat preference and leaf phenology. We measured cavitation vulnerability (Ψ50), stem-area specific hydraulic conductivity (K S), leaf specific conductivity (K L), seasonal variation in predawn water potential (ΨPD) and xylem anatomical properties [mean vessel diameter, mean hydraulic diameter, mean hydraulic diameter accounting for 95 % flow, and maximum vessel length (V L)]. Results show that tree species with a narrow habitat range (mesic specialists) were more vulnerable to cavitation than species with a wide habitat range (generalists). Ψ50 for mesic specialists ranged between ?1.5 and ?2.2 MPa and that for generalists between ?2.5 and ?3.6 MPa. While mesic specialists exhibited the lowest seasonal variation in ΨPD, generalists displayed significant seasonal variations in ΨPD suggesting that the two miombo habitat groups differ in their rooting depth. We observed a strong trade-off between K S and Ψ50 suggesting that tree hydraulic architecture is one of the decisive factors setting ecological boundaries for principal miombo species. While vessel diameters correlated weakly (P > 0.05) with Ψ50, V L was positively and significantly correlated with Ψ50. ΨPD was significantly correlated with Ψ50 further reinforcing the conclusion that tree hydraulic architecture plays a significant role in species’ habitat preference in miombo woodlands. 相似文献
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Raul A. Dulce Omer Yiginer Daniel R. Gonzalez Garrett Goss Ning Feng Meizi Zheng Joshua M. Hare 《The Journal of biological chemistry》2013,288(9):6522-6533
Although the combined use of hydralazine and isosorbide dinitrate confers important clinical benefits in patients with heart failure, the underlying mechanism of action is still controversial. We used two models of nitroso-redox imbalance, neuronal NO synthase-deficient (NOS1−/−) mice and spontaneously hypertensive heart failure rats, to test the hypothesis that hydralazine (HYD) alone or in combination with nitroglycerin (NTG) or isosorbide dinitrate restores Ca2+ cycling and contractile performance and controls superoxide production in isolated cardiomyocytes. The response to increased pacing frequency was depressed in NOS1−/− compared with wild type myocytes. Both sarcomere length shortening and intracellular Ca2+ transient (Δ[Ca2+]i) responses in NOS1−/− cardiomyocytes were augmented by HYD in a dose-dependent manner. NTG alone did not affect myocyte shortening but reduced Δ[Ca2+]i across the range of pacing frequencies and increased myofilament Ca2+ sensitivity thereby enhancing contractile efficiency. Similar results were seen in failing myocytes from the heart failure rat model. HYD alone or in combination with NTG reduced sarcoplasmic reticulum (SR) leak, improved SR Ca2+ reuptake, and restored SR Ca2+ content. HYD and NTG at low concentrations (1 μm), scavenged superoxide in isolated cardiomyocytes, whereas in cardiac homogenates, NTG inhibited xanthine oxidoreductase activity and scavenged NADPH oxidase-dependent superoxide more efficiently than HYD. Together, these results revealed that by reducing SR Ca2+ leak, HYD improves Ca2+ cycling and contractility impaired by nitroso-redox imbalance, and NTG enhanced contractile efficiency, restoring cardiac excitation-contraction coupling. 相似文献