HIVToolbox, an Integrated Web Application for Investigating HIV

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com

Potential new tool for anemia screening: An evaluation of the performance and usability of the TrueHb Hemometer.

In low- and middle-income countries, many women experience anemia during pregnancy due to insufficient dietary intake of key micronutrients, parasitic infections, hemoglobinopathies, and chronic infections. Maternal anemia increases perinatal risks for both mothers and infants, and slow progress to reduce the prevalence may be due in part to the lack of affordable tools to quantify hemoglobin levels in antenatal care (ANC) clinics. A simple, inexpensive, accurate, and robust diagnostic is needed to measure hemoglobin in ANC. This study evaluated the performance and usability of the TrueHb Hemometer. A cross-sectional diagnostic accuracy study was conducted to compare the accuracy of the TrueHb and the HemoCue® 201+ using capillary samples. Next, analytical performance (precision, coefficient of variation, R2) of the TrueHb was evaluated in varying environmental conditions using linearity panels with serial dilutions of venous blood samples. Lastly, the usability of the TrueHb Hemometer was assessed across three domains (effectiveness, efficiency, and satisfaction) by 20 ANC providers in Ghana. Capillary blood test results were not well correlated (R2 = 0.35) between the TrueHB and HemoCue201+, but 80% of TrueHb measurements were within +/-1.0 g/dl of the HemoCue® 201+ hemoglobin values. Precision tests indicated similar mean values across the three environmental conditions (CV 0.90) but begins to underestimate the hemoglobin concentration below 7.0 g/dl. The usability study identified potential failure modes due to inadequate instructions and device feedback. With some modifications, both to the product and to the instructions for use, the TrueHb may be suitable for use in ANC settings to help fill the diagnostic gap for anemia screening during pregnancy. Further testing is required with anemic populations in LMIC settings

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal

Spontaneously fermented food products contain a complex, natural microbial community with potential probiotic activity. The addition of a health-promoting, probiotic bacterium to these products ensures the delivery of that probiotic activity to consumers. Here, we assess the microbial community of a traditional Senegalese milk product produced by spontaneous fermentation, called lait caillé. We produced the lait caillé in a traditional way and added a probiotic starter containing Lactobacillus rhamnosus yoba 2012 to the traditional process. We found various species that are known for their ability to ferment milk, including species from the genera Lactobacillus, Acetobacter, Lactococcus, and Streptococcus. Our results show that the addition of L. rhamnosus to the inoculum, can result in detectable levels of this strain in the final product, ranging between 0.2 and 1 percent of the total bacterial population. Subsequent rounds of fermentation using passive back-slopping without the addition of new L. rhamnosus led to a loss of this strain from the community of fermenting bacteria. Our results suggest that the addition of probiotic strains at every fermentation cycle can enrich the existing complex communities of traditionally fermented lait caillé while traditional bacterial strains remain dominant in the bacterial communitie

Naturally Fermented Milk From Northern Senegal: Bacterial Community Composition and Probiotic Enrichment With Lactobacillus rhamnosus

A variety of foods fermented with lactic acid bacteria serve as dietary staples in many African communities; yet, their bacterial profiles are poorly characterized. The integration of health-promoting probiotics into naturally fermented milk products could make a profound impact on human health. Here, we characterize the bacterial community composition of a naturally fermented milk product (lait caillé) from northern Senegal, prepared in wooden bowls (lahals) with a bacterial biofilm to steer the fermentation process. We incorporated a probiotic starter culture containing the most documented probiotic strain Lactobacillus rhamnosus GG (generic strain name yoba 2012) into the local fermentation process. Bar-coded 16S rRNA amplicon sequencing of lait caillé samples indicated that the bacterial community of lait caillé has high species richness with over 100 bacterial genera; however, few have high abundance. In contrast to the diverse bacterial compositions of other characterized naturally fermented milk products, the composition of lait caillé predominantly consists of the lactic acid bacteria Streptococcus and Lactobacillus, resembling the bacterial composition in regular yogurt. The bacterial community composition of lait caillé varies geographically based on the presence of some genera, including Lactoccoccus, Enterococcus, Bifidobacterium, and Bacillus, but this trend is not consistent within production communities. The diversity of bacterial communities is much higher in the lahal biofilm than in the naturally fermented milk products, which is in turn greater than in commercial yogurts. Addition of a starter culture with L. Rhamnosus yoba 2012 to milk in lahals led to substantial growth of this probiotic bacterium during the fermentation process. Two independent quantitative PCR-analyses specific for L. Rhamnosus yoba 2012 indicated a 20-to 60-fold increase in the total number of probiotic bacteria in the first batch after inoculation. A similar increase of the probiotic was observed in a variation of lait caillé prepared with carbohydrate-rich millet granules (thiakry) added prior to fermentation. This study shows the feasibility of integrating health-promoting probiotic strains into naturally fermented foods produced in regions with a high prevalence of malnutrition

Cultured proteins: An analysis of the policy and regulatory environment in selected geographies

The global burden of malnutrition is unacceptably high. Animal-source foods are important components of diverse diets and provide high-quality proteins and other essential nutrients that promote optimal growth and development. The global demand for animal-source foods is projected to increase substantially, particularly in many low- and lower-middle income countries (LMICs). However, cost is a significant barrier to access and meeting this growing demand through livestock production will be highly resource intensive. As such, sustainable, high-quality alternatives to protein from livestock have the potential for significant transformative impact for both people and the planet. Through a process known as fermentation-based cellular agriculture, animal proteins found in milk and eggs can be produced without animals. According to this method, a gene encoded with an animal protein is introduced into a starter culture of microflora (e.g., fungi or yeast). This culture is grown in controlled fermentation tanks, where it expresses the desired protein. Finally, the protein is separated from the microflora, generally producing a purified protein powder. These resulting “cultured” proteins are designed to be identical to the corresponding animal-source proteins produced through traditional livestock farming and can be used as ingredients in existing or new food products. Although there are many potential sustainability and nutritionrelated benefits of these nnovations, they also face several challenges to commercialization and market uptake

Naturally Fermented Milk From Northern Senegal: Bacterial Community Composition and Probiotic Enrichment With Lactobacillus rhamnosus

A variety of foods fermented with lactic acid bacteria serve as dietary staples in many African communities; yet, their bacterial profiles are poorly characterized. The integration of health-promoting probiotics into naturally fermented milk products could make a profound impact on human health. Here, we characterize the bacterial community composition of a naturally fermented milk product (lait caillé) from northern Senegal, prepared in wooden bowls (lahals) with a bacterial biofilm to steer the fermentation process. We incorporated a probiotic starter culture containing the most documented probiotic strain Lactobacillus rhamnosus GG (generic strain name yoba 2012) into the local fermentation process. Bar-coded 16S rRNA amplicon sequencing of lait caillé samples indicated that the bacterial community of lait caillé has high species richness with over 100 bacterial genera; however, few have high abundance. In contrast to the diverse bacterial compositions of other characterized naturally fermented milk products, the composition of lait caillé predominantly consists of the lactic acid bacteria Streptococcus and Lactobacillus, resembling the bacterial composition in regular yogurt. The bacterial community composition of lait caillé varies geographically based on the presence of some genera, including Lactoccoccus, Enterococcus, Bifidobacterium, and Bacillus, but this trend is not consistent within production communities. The diversity of bacterial communities is much higher in the lahal biofilm than in the naturally fermented milk products, which is in turn greater than in commercial yogurts. Addition of a starter culture with L. rhamnosus yoba 2012 to milk in lahals led to substantial growth of this probiotic bacterium during the fermentation process. Two independent quantitative PCR-analyses specific for L. rhamnosus yoba 2012 indicated a 20- to 60-fold increase in the total number of probiotic bacteria in the first batch after inoculation. A similar increase of the probiotic was observed in a variation of lait caillé prepared with carbohydrate-rich millet granules (thiakry) added prior to fermentation. This study shows the feasibility of integrating health-promoting probiotic strains into naturally fermented foods produced in regions with a high prevalence of malnutrition

Interactive protein display page for Tat in HIVToolbox.

<p>Sequence window, Structure windows, Log windows, and Sequence Alignment section of HIVToolbox are shown. The interactive results page for HIV-1 tat is shown. The scrollable sequence window shows the protein sequence, domains (with colored fonts), functional residues (highlighted), protein-protein interaction sites (thin lines under sequence), mapped protein structures (thin colored lines over sequence) and minimotifs (figures under sequence). The synchronized interactive structural displays show domains and selected minimotifs (left panel), functional sites and selected protein-protein interaction sites (center panel), and residues conserved at or above a sequence conservation threshold selected with a slider or text box (right panel). The Sequence Alignment section shows alignment of a representative set of 20 sequences with the RefSeq sequence and the structure sequence. A second tab reveals a position specific-scoring matrix of amino acid frequencies at each position in the protein. More details about the features and use of HIVToolbox are in the supplement, and video tutorials are at Bio-Toolkit [<a href="http://www.bio-toolkit.com" target="_blank">http://www.bio-toolkit.com</a>].</p

A model of IN:LEDGF:viral DNA based on the PFV IN structure.

<p>(<b>A</b>) A model of HIV-1 IN complex with 4 IN subunits, 4 LEDGF subunits (light gray), and two viral DNA strands (dark gray); (<b>A, B</b>) Left panels (IN NTD = green, CCD = blue, CTD = red. (<b>A, B</b>) Right panels show functional sites (green = DNA binding), red = dimerization interface in 1EX4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Chen1" target="_blank">[10]</a>, cyan = dimerization interface in 1WJA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Cai1" target="_blank">[11]</a>; blue = tetramerization interface in 1K6Y <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Wang1" target="_blank">[8]</a>; purple = zinc binding site <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Cai1" target="_blank">[11]</a>; brown = reverse transcriptase binding site <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Wilkinson1" target="_blank">[31]</a>, light brown = tetramerization residues <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Lutzke2" target="_blank">[16]</a>. (<b>B</b>) A 90° rotation about the Y-axis of <b>A</b>. Orange arrowhead indicated channel proposed to bind target DNA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020122#pone.0020122-Hare1" target="_blank">[36]</a>.</p