Recombination rate and selection strength in HIV intra-patient evolution

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.Comment: to appear in PLoS Computational Biolog

Drug Repurposing: Far Beyond New Targets for Old Drugs

Repurposing drugs requires finding novel therapeutic indications compared to the ones for which they were already approved. This is an increasingly utilized strategy for finding novel medicines, one that capitalizes on previous investments while derisking clinical activities. This approach is of interest primarily because we continue to face significant gaps in the drug–target interactions matrix and to accumulate safety and efficacy data during clinical studies. Collecting and making publicly available as much data as possible on the target profile of drugs offer opportunities for drug repurposing, but may limit the commercial applications by patent applications. Certain clinical applications may be more feasible for repurposing than others because of marked differences in side effect tolerance. Other factors that ought to be considered when assessing drug repurposing opportunities include relevance to the disease in question and the intellectual property landscape. These activities go far beyond the identification of new targets for old drugs

Structure, chemistry, and charge transfer resistance of the interface between Li7La3Zr2O12 electrolyte and LiCoO2 cathode

All-solid-state batteries promise significant safety and energy density advantages over liquid-electrolyte batteries. The interface between the cathode and the solid electrolyte is an important contributor to charge transfer resistance. Strong bonding of solid oxide electrolytes and cathodes requires sintering at elevated temperatures. Knowledge of the temperature dependence of the composition and charge transfer properties of this interface is important for determining the ideal sintering conditions. To understand the interfacial decomposition processes and their onset temperatures, model systems of LiCoO2 (LCO) thin films deposited on cubic Al-doped Li7La3Zr2O12 (LLZO) pellets were studied as a function of temperature using interface-sensitive techniques. X-ray photoelectron spectroscopy (XPS), secondary ion mass spectroscopy (SIMS), and energy-dispersive X-ray spectroscopy (EDS) data indicated significant cation interdiffusion and structural changes starting at temperatures as low as 300°C. La2Zr2O7 and Li2CO3 were identified as decomposition products after annealing at 500°C by synchrotron X-ray diffraction (XRD). X-ray absorption spectroscopy (XAS) results indicate the presence of also LaCoO3, in addition to La2Zr2O7 and Li2CO3. Based on electrochemical impedance spectroscopy, and depth profiling of the Li distribution upon potentiostatic hold experiments on symmetric LCO|LLZO|LCO cells, the interfaces exhibited significantly increased impedance, up to 8 times that of the as-deposited samples after annealing at 500°C. Our results indicate that lower-temperature processing conditions, shorter annealing time scales, and CO2-free environments are desirable for obtaining ceramic cathode-electrolyte interfaces that enable fast Li transfer and high capacity

Lysozyme M deficiency leads to an increased susceptibility to Streptococcus pneumoniae-induced otitis media

<p>Abstract</p> <p>Background</p> <p>Lysozyme is an antimicrobial innate immune molecule degrading peptidoglycan of the bacterial cell wall. Lysozyme shows the ubiquitous expression in wide varieties of species and tissues including the tubotympanum of mammals. We aim to investigate the effects of lysozyme depletion on pneumococcal clearance from the middle ear cavity.</p> <p>Methods</p> <p>Immunohistochemistry was performed to localize lysozyme in the Eustachian tube. Lysozyme expression was compared between the wild type and the lysozyme M^-/-mice using real time quantitative RT-PCR and western blotting. Muramidase activity and bactericidal activity of lysozyme was measured using a lysoplate radial diffusion assay and a liquid broth assay, respectively. To determine if depletion of lysozyme M increases a susceptibility to pneumococal otitis media, 50 CFU of <it>S. pneumoniae </it>6B were transtympanically inoculated to the middle ear and viable bacteria were counted at day 3 and 7 with clinical grading of middle ear inflammation.</p> <p>Results</p> <p>Immunolabeling revealed that localization of lysozyme M and lysozyme P is specific to some/particular cell types of the Eustachian tube. Lysozyme P of lysozyme M^-/-mice was mainly expressed in the submucosal gland but not in the tubal epithelium. Although lysozyme M^-/-mice showed compensatory up-regulation of lysozyme P, lysozyme M depletion resulted in a decrease in both muramidase and antimicrobial activities. Deficiency in lysozyme M led to an increased susceptibility to middle ear infection with <it>S. pneumoniae </it>6B and resulted in severe middle ear inflammation, compared to wild type mice.</p> <p>Conclusion</p> <p>The results suggest that lysozyme M plays an important role in protecting the middle ear from invading pathogens, particularly in the early phase. We suggest a possibility of the exogenous lysozyme as an adjuvant therapeutic agent for otitis media, but further studies are necessary.</p

Effects of job rotation and role stress among nurses on job satisfaction and organizational commitment

<p>Abstract</p> <p>Background</p> <p>The motivation for this study was to investigate how role stress among nurses could affect their job satisfaction and organizational commitment, and whether the job rotation system might encourage nurses to understand, relate to and share the vision of the organization, consequently increasing their job satisfaction and stimulating them to willingly remain in their jobs and commit themselves to the organization. Despite the fact that there have been plenty of studies on job satisfaction, none was specifically addressed to integrate the relational model of job rotation, role stress, job satisfaction, and organizational commitment among nurses.</p> <p>Methods</p> <p>With top managerial hospital administration's consent, questionnaires were only distributed to those nurses who had had job rotation experience. 650 copies of the questionnaire in two large and influential hospitals in southern Taiwan were distributed, among which 532 valid copies were retrieved with a response rate of 81.8%. Finally, the SPSS 11.0 and LISREL 8.54 (Linear Structural Relationship Model) statistical software packages were used for data analysis and processing.</p> <p>Results</p> <p>According to the nurses' views, the findings are as follows: (1) job rotation among nurses could have an effect on their job satisfaction; (2) job rotation could have an effect on organizational commitment; (3) job satisfaction could have a positive effect on organizational commitment; (4) role stress among nurses could have a negative effect on their job satisfaction; and (5) role stress could have a negative effect on their organizational commitment.</p> <p>Conclusion</p> <p>As a practical and excellent strategy for manpower utilization, a hospital could promote the benefits of job rotation to both individuals and the hospital while implementing job rotation periodically and fairly. And when a medical organization attempts to enhance nurses' commitment to the organization, the findings suggest that reduction of role ambiguity in role stress has the best effect on enhancing nurses' organizational commitment. The ultimate goal is to increase nurses' job satisfaction and encourage them to stay in their career. This would avoid the vicious circle of high turnover, which is wasteful of the organization's valuable human resources.</p

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence–structure–function relationships