UV and X‐ray structural studies of a 101‐residue long Tat protein from a HIV‐1 primary isolate and of its mutated,detoxified, vaccine candidate

The 101‐residue long Tat protein of primary isolate 133 of the human immunodeficiency virus type 1 (HIV‐1), wt‐Tat₁₃₃ displays a high transactivation activity in vitro, whereas the mutant thereof, STLA‐Tat₁₃₃, a vaccine candidate for HIV‐1, has none. These two proteins were chemically synthesized and their biological activity was validated. Their structural properties were characterized using circular dichroism (CD), fluorescence emission, gel filtration, dynamic light scattering, and small angle X‐ray scattering (SAXS) techniques. SAXS studies revealed that both proteins were extended and belong to the family of intrinsically unstructured proteins. CD measurements showed that wt‐Tat₁₃₃ or STLA‐Tat₁₃₃ underwent limited structural rearrangements when complexed with specific fragments of antibodies. Crystallization trials have been performed on the two forms, assuming that the Tat₁₃₃ proteins might have a better propensity to fold in supersaturated conditions, and small crystals have been obtained. These results suggest that biologically active Tat protein is natively unfolded and requires only a limited gain of structure for its function. Proteins 2010. © 2009 Wiley‐Liss, Inc     

Likelihood-based inference for stochastic models of sexual network formation

Sexually-transmitted diseases (STDs) constitute a major public health concern. Mathematical models for the transmission dynamics of STDs indicate that heterogeneity in sexual activity level allow them to persist even when the typical behavior of the population would not support endemicity. This insight focuses attention on the distribution of sexual activity level in a population. In this paper, we develop several stochastic process models for the formation of sexual partnership networks. Using likelihood-based model selection procedures, we assess the fit of the different models to three large distributions of sexual partner counts: (1) Rakai, Uganda, (2) Sweden, and (3) the USA. Five of the six single-sex networks were fit best by the negative binomial model. The American women's network was best fit by a power-law model, the Yule. For most networks, several competing models fit approximately equally well. These results suggest three conclusions: (1) no single unitary process clearly underlies the formation of these sexual networks, (2) behavioral heterogeneity plays an essential role in network structure, (3) substantial model uncertainty exists for sexual network degree distributions. Behavioral research focused on the mechanisms of partnership formation will play an essential role in specifying the best model for empirical degree distributions. We discuss the limitations of inferences from such data, and the utility of degree-based epidemiological models more generally.     

Evolutionary dynamics of human retroviruses investigated through full-genome scanning

To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the human immunodeficiency virus type 1 (HIV-1) group M and the primate T-cell lymphotropic virus (PTLV) using a full-genome analysis. Evolutionary rates and nonsynonymous/synonymous substitution rate ratios were estimated across the genome using a maximum likelihood sliding window approach, and molecular clock properties were investigated. We confirm a remarkable difference in genetic stability and selective pressure at the interhost level. While there is evidence for adaptive evolution in HIV-1, the evolution of PTLV is almost exclusively characterized by negative selection or nearly neutral processes. For both retroviruses, evolutionary rate estimates across the genome reflect the differential selective constraints. However, based on the relationship between evolutionary rate and selective pressure and based on the comparison of synonymous substitution rates, the differences in rate between HIV-1 and PTLV cannot be explained by selective forces only. Several evolutionary and statistical assumptions, examined using a Bayesian coalescent method, were shown to have little influence on our inference.     

Hepatitis A virus and hepatitis E virus prevalence relates to human immunodeficiency virus infection in Japanese male blood donors

Hepatitis A virus (HAV) has begun to spread globally among men who have sex with men (MSM). Hepatitis E virus (HEV) also may be transmitted through sexual contact among MSM. To assess the current status of these viruses among MSM in Japan, the seroprevalence of both viruses using 503 plasma samples collected between 2009 and 2018 from human immunodeficiency virus (HIV)-positive male donors who were presumed to be mainly MSM was investigated. Our results suggested that HAV may be spreading within this population, as reported elsewhere. By contrast, the spread of HEV was confirmed only among younger HIV-positive donors.     

A potential prognostic marker and therapeutic target: SPOCK1 promotes the proliferation,metastasis, and apoptosis of pancreatic ductal adenocarcinoma cells

Pancreatic ductal adenocarcinoma (PDAC), a common malignancy originated from the digestive system worldwide, has a poor clinical outcome. SPOCK1 is a widely investigated member of the Ca²⁺-binding proteoglycan family and functions as an essential driver in several cancers. However, the complex regulatory role of SPOCK1 in PDAC is unclear. Bioinformatics analysis predicted an interrelationship between increased SPOCK1 expression and the clinical characteristics of patients with PDAC. The SPOCK1 expression levels in fresh tissue samples were confirmed, and SPOCK1 expression was then knocked down by lentivirus-mediated short hairpin RNA. Cell proliferation, metastasis, and apoptosis were detected through Cell Counting Kit-8, colony formation assays, invasion and migration assays, flow cytometric analysis, quantitative real-time polymerase chain reaction, and Western blot experiment. On the basis of the Cancer Genome Atlas database, we found a significantly higher level of SPOCK1 in PDAC than in adjacent nontumor tissues. Patients with PDAC with high SPOCK1 expression exhibited shorter overall survival time, as well as disease-free survival time. The knockdown of SPOCK1 significantly decreased the proliferation and metastasis of PCNA-1 and MIA PaCa-2 cells. Moreover, the knockdown of SPOCK1 led to cell cycle arrest in G0/G1 phase and increased the proportion of apoptotic PDAC cells by regulating members of the caspase and Bcl-2 families. Our data proved that SPOCK1 is a critical regulator of tumor proliferation and metastasis in PDAC cells. Therefore, SPOCK1 might be a potential prognostic and therapeutic target molecule in PDAC.     

A Look at Uganda's Early HIV Prevention Strategies Through a Moderate ‘African’ Communitarian Lens

This paper seeks to highlight the benefits of prioritizing moderate African communitarian principles as partly demonstrated in the HIV prevention strategies implemented in Uganda in the late 1980s. Pertinent lessons could be drawn so as to achieve the HIV prevention targets envisioned in the post‐2015 development era. Communitarianism emphasizes the importance of communities as part of healthy human existence. Its core ethical values include the virtues of generosity, compassion, and solidarity. Persuasion through communication, consensus through dialogue, and the awareness and commitment to responsibilities towards other members of the community, are chief practices relied upon to achieve appropriate social behaviour. All these elements signify individual rootedness in communities and contribute to the healthy existence of its members. Communitarianism is usually classified as either authoritarian/radical or responsive/moderate, depending on the primacy given to either community interests or the individual will and rights. Moderate communitarianism recognizes the individual's capacity for moral reasoning, virtue and free choice. The ensuing form of society is deemed more ethical as it relies on education in the virtues, moral persuasion and informal social controls, without stifling individual identity, agency, and capacity for self‐determination. If moderate African communitarianism, in particular, can to a certain extent be associated with the significant aspects of Uganda's HIV prevention strategies in the stated period, then its present‐day relevance for HIV prevention and other public health interventions may be emphasized accordingly. This applies especially in view of the ongoing efforts to achieve a balance between individual and collective interests in bioethics.     

Molecular heterogeneity in diffuse large B-cell lymphoma and its implications in clinical diagnosis and treatment

Over half of patients with diffuse large B-cell lymphoma (DLBCL) can be cured by standard R-CHOP treatment (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone). However, the remaining patients are refractory and ultimately succumb to progressive or relapsed disease. During the past decade, there has been significant progress in the understanding of molecular mechanisms in DLBCL, largely owing to collaborative efforts in large-scale gene expression profiling and deep sequencing, which have identified genetic alterations critical in lymphomagenesis through activation of key signaling transduction pathways in DLBCL. These discoveries have not only led to the development of targeted therapies, including several currently in clinical trials, but also laid a solid foundation for the future identification of more effective therapies for patients not curable by R-CHOP. This review summarizes the recent advances in our understanding of the molecular characterization and pathogenesis of DLBCL and new treatment directions.     

Predicting events in clinical trials using two time‐to‐event outcomes

In clinical trials with time‐to‐event outcomes, it is of interest to predict when a prespecified number of events can be reached. Interim analysis is conducted to estimate the underlying survival function. When another correlated time‐to‐event endpoint is available, both outcome variables can be used to improve estimation efficiency. In this paper, we propose to use the convolution of two time‐to‐event variables to estimate the survival function of interest. Propositions and examples are provided based on exponential models that accommodate possible change points. We further propose a new estimation equation about the expected time that exploits the relationship of two endpoints. Simulations and the analysis of real data show that the proposed methods with bivariate information yield significant improvement in prediction over that of the univariate method.     

Isoform-selective Inhibition of Facilitative Glucose Transporters: ELUCIDATION OF THE MOLECULAR MECHANISM OF HIV PROTEASE INHIBITOR BINDING*

Pharmacologic HIV protease inhibitors (PIs) and structurally related oligopeptides are known to reversibly bind and inactivate the insulin-responsive facilitative glucose transporter 4 (GLUT4). Several PIs exhibit isoform selectivity with little effect on GLUT1. The ability to target individual GLUT isoforms in an acute and reversible manner provides novel means both to investigate the contribution of individual GLUTs to health and disease and to develop targeted treatment of glucose-dependent diseases. To determine the molecular basis of transport inhibition, a series of chimeric proteins containing transmembrane and cytosolic domains from GLUT1 and GLUT4 and/or point mutations were generated and expressed in HEK293 cells. Structural integrity was confirmed via measurement of N-[2-[2-[2-[(N-biotinylcaproylamino)ethoxy)ethoxyl]-4-[2-(trifluoromethyl)-3H-diazirin-3-yl]benzoyl]-1,3-bis(mannopyranosyl-4-yloxy)-2-propylamine (ATB-BMPA) labeling of the chimeric proteins in low density microsome fractions isolated from stably transfected 293 cells. Functional integrity was assessed via measurement of zero-trans 2-deoxyglucose (2-DOG) uptake. ATB-BMPA labeling studies and 2-DOG uptake revealed that transmembrane helices 1 and 5 contain amino acid residues that influence inhibitor access to the transporter binding domain. Substitution of Thr-30 and His-160 in GLUT1 to the corresponding positions in GLUT4 is sufficient to completely transform GLUT1 into GLUT4 with respect to indinavir inhibition of 2-DOG uptake and ATB-BMPA binding. These data provide a structural basis for the selectivity of PIs toward GLUT4 over GLUT1 that can be used in ongoing novel drug design.