Two-site exchange revisited: a new method for extracting exchange parameters in biological systems.

A new analysis is presented which links real volume fractions, relaxation rates, and intracompartmental exchange rates directly with apparent volume fractions and relaxation rates obtained from biexponential fits of transverse magnetization decay curves. The analysis differs from previous methods in that measurements from two paramagnetic doping levels are used to close the two-site exchange equations. Both the new method and one previously described by Herbst and Goldstein (HG) have been applied to paramagnetically doped whole-blood data sets. Significant differences in the calculated exchange parameters are found between the two methods. A small dependence of the intracellular relaxation rate on extracellular paramagnetic agent concentration, assumed nonexistent with the HG method, is inferred from the new analysis. The analysis was also applied to published data on perfused rat hearts, and we obtained a limited assessment of two-site exchange in this system.     

Neutral complexes as oxidants for the reduced form of parsley (Petroselinum crispum) [2Fe--2S] ferredoxin. Evidence for partial blocking by redox-inactive Cr(III) complexes.

The 1 : 1 reactions of three neutral Co(III) oxidants, Co(acac)3, Co(NH3)3(NO2)3 and Co(acac)2(NH3)(NO2), with reduced parsley (Petroselinum crispum) [2Fe--2S] ferredoxin (which carries a substantial negative charge), have been studied at 25 degrees C, pH 8.0 (Tris/HCl), I0.10 (NaCl). Whereas it has previously been demonstrated that with Co(NH3)6+ as oxidant the reaction if completely blocked by redox-inactive Cr(NH3)63+, the neutral oxidants are only partially blocked by this same complex. The effects of three Cr(III) complexes, Cr(NH3)63+%, Cr(en)33+ and (en)2Cr . mu(OH,O2CCH3) . CR(en)24+ have been investigated. Kinetic data for the response of 3+, neutral, as well as 1--oxidants to the presence of 3+ (and 4+) Cr(III) complexes can now be rationalized in terms of a single functional site on the protein for electron transfer. Electrostatics have a significant influence on association at this site.     

Genetic relationships of cichlid fishes from Lake Malawi based on mitochondrial DNA sequences

Limnology - The purpose of this study was to estimate the genetic distance, diversity and relationship of two large groups of Malawian cichlid, ‘mbuna’ living in rocky area and feeding...     

SAVVY? (C31G) Gel for Prevention of HIV infection in Women: A Phase 3, Double-Blind,Randomized, Placebo-Controlled Trial in Ghana

Objective

The objective of this trial was to determine the effectiveness of 1.0% C31G (SAVVY) in preventing male-to-female vaginal transmission of HIV infection among women at high risk.

Methodology/Principal Findings

This was a Phase 3, double-blind, randomized, placebo-controlled trial. Participants made up to 12 monthly visits for HIV testing, adverse event reporting, and study product supply. The study was conducted between March 2004 and February 2006 in Accra and Kumasi, Ghana. We enrolled 2142 HIV-negative women at high risk of HIV infection, and randomized them to SAVVY or placebo gel. Main outcome measures were the incidence of HIV-1 and HIV-2 infection as determined by detection of HIV antibodies from oral mucosal transudate specimens and adverse events. We accrued 790 person-years of follow-up in the SAVVY group and 772 person-years in the placebo group. No clinically significant differences in the overall frequency of adverse events, abnormal pelvic examination findings, or abnormal laboratory results were seen between treatment groups. However, more participants in the SAVVY group reported reproductive tract adverse events than in the placebo group (13.0% versus 9.4%). Seventeen HIV seroconversions occurred; eight in participants randomized to SAVVY and nine in participants receiving placebo. The Kaplan-Meier estimates of the cumulative probability of HIV infection through 12 months were 0.010 in the SAVVY group and 0.011 in the placebo group (p = 0.731), with a hazard ratio (SAVVY versus placebo) of 0.88 (95% confidence interval 0.33, 2.27). Because of a lower-than-expected HIV incidence, we were unable to achieve the required number of HIV infections (66) to obtain the desired study power.

Conclusions/Significance

SAVVY was not associated with increased adverse events overall, but was associated with higher reporting of reproductive adverse events. Our data are insufficient to conclude whether SAVVY is effective at preventing HIV infection relative to placebo.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00129532","term_id":"NCT00129532"}}NCT00129532     

Data exploration tools for the Gene Ontology database

MOTIVATION: To improve the ability of biologists (both researchers and students) to ask biologically interesting questions of the Gene Ontology (GO) database and to explore the ontologies by seeing large portions of the ontology graphs in context, along with details of individual terms in the ontologies. RESULTS: GoGet and GoView are two new tools built as part of an extensible web application system based on Java 2 Enterprise Edition technology. GoGet has a user interface that enables users to ask biologically interesting questions, such as (1) What are the DNA binding proteins involved in DNA repair, but not in DNA replication? and (2) Of the terms containing the word triphosphatase, which have associated gene products from mouse, but not fruit fly? The results of such queries can be viewed in a collapsed tabular format that eases the burden of getting through large tables of data. GoView enables users to explore the large directed acyclic graph structure of the ontologies in the GO database. The two tools are coordinated, so that results from queries in GoGet can be visualized in GoView in the ontology in which they appear, and explorations started from GoView can request details of gene product associations to appear in a result table in GoGet. AVAILABILITY: Free access to the GoGet query tool and free download of the GoView ontology viewer are provided to all users at http://db.math.macalester.edu/goproject. In addition, source code for the GoView tool is also available from this site, along with a user manual for both tools.     

Discovery of novel conformationally restricted diazocan peptidomimetics as inhibitors of interleukin-1beta synthesis

A novel diazocan containing dipeptide mimetic was synthesized via reductive N-N bond cleavage of a pyrazolidino-pyrazolidine using Raney-Ni and evaluated as an ICE inhibitor. This versatile 8-membered ring containing scaffold possesses an N-5 ring nitrogen that was used to explore structure-activity relationships in a cell-based assay measuring inhibition of interleukin-1beta.     

A model-based study of passive joint properties on muscle effort during static stance

This study examined the impact of lower extremity joint stiffnesses and simulated joint contractures on the muscle effort required to maintain static standing postures after a spinal cord injury (SCI). Static inverse computer simulations were performed with a three-dimensional 15 degree of freedom musculoskeletal model placed in 1600 different standing postures. The required lower extremity muscle forces were calculated through an optimization routine that minimized the sum of the muscle stresses squared, which was used as an index of the muscle effort required for each standing posture. Joint stiffnesses were increased and decreased by 100 percent of their nominal values, and contractures were simulated to determine their effects on the muscle effort for each posture. Nominal muscle and passive properties for an individual with a SCI determined the baseline muscle effort for comparisons. Stiffness changes for the ankle plantar flexion/dorsiflexion, hip flexion/extension, and hip abduction/adduction directions had the largest effect on reducing muscle effort by more than 5 percent, while changes in ankle inversion/eversion and knee flexion/extension had the least effect. For erect standing, muscle effort was reduced by more than 5 percent when stiffness was decreased at the ankle plantar flexion/dorsiflexion joint or hip flexion/extension joint. With simulated joint contractures, the postural workspace area decreased and muscle effort was not reduced by more than 5 percent for any posture. Using this knowledge, methods can be developed through the use of orthoses, physical therapy, surgery or other means to appropriately augment or diminish these passive moments during standing with a neuroprosthesis.     

Risk Factors for Buruli Ulcer in Ghana—A Case Control Study in the Suhum-Kraboa-Coaltar and Akuapem South Districts of the Eastern Region

Background

Buruli ulcer (BU) is a skin disease caused by Mycobacterium ulcerans. Its exact mode of transmission is not known. Previous studies have identified demographic, socio-economic, health and hygiene as well as environment related risk factors. We investigated whether the same factors pertain in Suhum-Kraboa-Coaltar (SKC) and Akuapem South (AS) Districts in Ghana which previously were not endemic for BU.

Methods

We conducted a case control study. A case of BU was defined as any person aged 2 years or more who resided in study area (SKC or AS District) diagnosed according to the WHO clinical case definition for BU and matched with age- (+/−5 years), gender-, and community controls. A structured questionnaire on host, demographic, environmental, and behavioural factors was administered to participants.

Results

A total of 113 cases and 113 community controls were interviewed. Multivariate conditional logistic regression analysis identified presence of wetland in the neighborhood (OR = 3.9, 95% CI = 1.9–8.2), insect bites in water/mud (OR = 5.7, 95% CI = 2.5–13.1), use of adhesive when injured (OR = 2.7, 95% CI = 1.1–6.8), and washing in the Densu river (OR = 2.3, 95% CI = 1.1–4.96) as risk factors associated with BU. Rubbing an injured area with alcohol (OR = 0.21, 95% CI = 0.008–0.57) and wearing long sleeves for farming (OR = 0.29, 95% CI = 0.14–0.62) showed protection against BU.

Conclusion

This study identified the presence of wetland, insect bites in water, use of adhesive when injured, and washing in the river as risk factors for BU; and covering limbs during farming as well as use of alcohol after insect bites as protective factors against BU in Ghana. Until paths of transmission are unraveled, control strategies in BU endemic areas should focus on these known risk factors.