Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection.

Recombination has been shown to contribute to human immunodeficiency virus-1 (HIV-1) evolution in vivo, but the underlying dynamics are extremely complex, depending on the nature of the fitness landscapes and of epistatic interactions. A less well-studied determinant of recombinant evolution is the mode of virus transmission in the cell population. HIV-1 can spread by free virus transmission, resulting largely in singly infected cells, and also by direct cell-to-cell transmission, resulting in the simultaneous infection of cells with multiple viruses. We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models to in vitro experimental data on the growth of fluorescent reporter viruses under static conditions (where both transmission pathways operate), and under gentle shaking conditions, where cell-to-cell transmission is largely inhibited. The parameterized mathematical models are then used to extrapolate the viral evolutionary dynamics beyond the experimental settings. Assuming a fixed basic reproductive ratio of the virus (independent of transmission pathway), we find that recombinant evolution is fastest if virus spread is driven only by cell-to-cell transmission and slows down if both transmission pathways operate. Recombinant evolution is slowest if all virus spread occurs through free virus transmission. This is due to cell-to-cell transmission 1, increasing infection multiplicity; 2, promoting the co-transmission of different virus strains from cell to cell; and 3, increasing the rate at which point mutations are generated as a result of more reverse transcription events. This study further resulted in the estimation of various parameters that characterize these evolutionary processes. For example, we estimate that during cell-to-cell transmission, an average of three viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to free virus transmission. In general, our study points towards the importance of infection multiplicity and cell-to-cell transmission for HIV evolution.

Building institutional resilience in the context of climate change in Aurora, Philippines.

The role of local government units (LGUs) in disaster resilience is crucial for a hazard-prone country such as the Philippines. Although the country has its own institutional framework on disaster risk reduction, a number of issues limit LGUs' potential to perform its role. This study focused on building institutional resilience of LGUs towards building climate risk resilience in Aurora, Philippines by engaging key actors in the formulation of Local Climate Change Action Plans (LCCAP). The study adopted the shared learning process from the Climate Resilience Framework (CRF) to strengthen partnership and implement capacity building activities, aimed at developing the Climate and Disaster Risk Assessment (CDRA) and LCCAP beyond compliance. An institutional capacity assessment was administered through a survey involving 87 members of the Technical Working Group (TWG) from eight municipalities and provincial government. Institutional capacity was measured using 70 indicators representing access rights and entitlements, information flows, decision-making processes, application of new knowledge, capacity to anticipate risk, capacity to respond, as well as capacity to recover and change. Data were analyzed using descriptive statistics. Both Spearman Correlation and Cramer's V determined the interrelationship between socio-demographic variables and institutional characteristics. Results revealed that the LGUs performed better in risk response and management. A strong correlation between expertise and position vis-à-vis all resilient institution metrics was also observed, while gender is moderately correlated with all parameters except access rights and entitlements. Three key areas, not adequately articulated in current literature, need to be improved to enhance institutional resilience towards climate and disaster risks, namely: staffing and human resource; access to financial support from other sources; and development of knowledge management systems.

Secreted frizzled related protein is a target of PaxB and plays a role in aquiferous system development in the freshwater sponge, Ephydatia muelleri.

Canonical and non-canonical Wnt signaling, as well as the Pax/Six gene network, are involved in patterning the freshwater sponge aquiferous system. Using computational approaches to identify transcription factor binding motifs in a freshwater sponge genome, we located putative PaxB binding sites near a Secreted Frizzled Related Protein (SFRP) gene in Ephydatia muelleri. EmSFRP is expressed throughout development, but with highest levels in juvenile sponges. In situ hybridization and antibody staining show EmSFRP expression throughout the pinacoderm and choanoderm in a subpopulation of amoeboid cells that may be differentiating archeocytes. Knockdown of EmSFRP leads to ectopic oscula formation during development, suggesting that EmSFRP acts as an antagonist of Wnt signaling in E. muelleri. Our findings support a hypothesis that regulation of the Wnt pathway by the Pax/Six network as well as the role of Wnt signaling in body plan morphogenesis was established before sponges diverged from the rest of the metazoans.

Intense focused ultrasound stimulation can safely stimulate inflamed subcutaneous tissue and assess allodynia.

BACKGROUND: Potential peripheral sources of deep pain can require invasive evocative tests for their assessment. Here we perform research whose ultimate goal is development of a non-invasive evocative test for deep painful tissue. METHODS: We used a rat model of inflammation to show that intense focused ultrasound (iFU) differentially stimulates inflamed versus control tissue and can identify allodynia. To do so we applied iFU to inflamed and normal tissue below the skin of rats' hind paws and measured the amount of ultrasound necessary to induce paw withdrawal. RESULTS: iFU of sufficient strength (spatial and temporal average intensities ranged from 100-350 W/cm(2)) caused the rat to withdraw its inflamed paw, while the same iFU applied to the contralateral paw failed to induce withdrawal, with sensitivity and specificity generally greater than 90%. iFU stimulation of normal tissue required twice the amount of ultrasound to generate a withdrawal than did inflamed tissue, thereby assessing allodynia. Finally, we verified in a preliminary way the safety of iFU stimulation with acute histological studies coupled with mathematical simulations. CONCLUSIONS: Given that there exist systems to guide iFU deep to the skin, image-guided iFU may one day allow assessment of patient's deep, peripheral pain generators.

Intense focused ultrasound as a potential research tool for the quantification of diurnal inflammatory pain.

Quantifying pain through assay of a human's or animal's response to a known stimulus as a function of time of day is a critical means of advancing chronotherapeutic pain management. Current methods for quantifying pain, even in the context of etiologies involving deep tissue, generally involve stimulation by quantifiable means of either cutaneous (heat-lamp tests, electrical stimuli) or both cutaneous and subcutaneous tissue (von Frey hairs, tourniquets, etc.) or study of proxies for pain (such as stress, via assay of cortisol levels). In this study, we evaluate the usefulness of intense focused ultrasound (iFU), already shown to generate sensations and other biological effects deep to the skin, as a means of quantifying deep diurnal pain using a standard animal model of inflammation. Beginning 5 days after injection of Complete Freund's Adjuvant into the plantar surface of the rat's right hind paw to induce inflammation, the rats were divided into two groups, the light-phase test group (09:00-18:00h) and the dark-phase test group (23:00-06:00h), both of which underwent iFU application deep to the skin. We used two classes of iFU protocol, motivated by the extant literature. One consisted of a single pulse (SP) lasting 0.375s. The other, a multiple pulse (MP) protocol, consisted of multiple iFU pulses each of length 0.075s spaced 0.075s apart. We found the night group's threshold for reliable paw withdrawal to be significantly higher than that of the day group as assayed by each iFU protocol. These results are consistent with the observation that the response to mechanical stimuli by humans and rodents display diurnal variations, as well as the ability of iFU to generate sensations via mechanical stimulation. Since iFU can provide a consistent method to quantify pain from deep, inflamed tissue, it may represent a useful adjunct to those studying diurnal pain associated with deep tissue as well as chronotherapeutics targeting that pain.