Automatic step-detection algorithm for analysis of sarcomere dynamics

Motile systems exhibit a stepwise nature, seen most prominently in muscle contraction. A novel algorithm has been developed that detects steps automatically in sarcomere-length change data and computes their size. The method is based on a nonlinear filter and a step detection protocol that detects local slope values in comparison to a threshold. The algorithm was first evaluated using artificial data with various degrees of Gaussian noise. Steps were faithfully detected even with significant noise. With actual data, the algorithm detected 2.7 nm steps and integer multiples thereof. The results confirm a quantal 2.7 nm step-size reported earlier. As stepwise phenomena become increasingly evident, automatic step-detection algorithms become increasingly useful since the limiting factor is almost always noise. The algorithm presented here offers a versatile and accurate tool that should be useful not only within muscle contraction and motility fields, but in fields which quantal phenomena play a role.     

A study of the microbial quality of grey water and an evaluation of treatment technologies for reuse

The reuse of grey water for non-potable water applications is a potential solution for water-deprived regions worldwide. Adequate treatment of grey water prior to reuse is important to reduce the risks of pathogen transmission and to improve the efficacy of subsequent disinfection. This study investigated the presence of common pathogens in grey water and compared the pathogen removal performance of leading contender treatment technologies. The opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus were detected in the grey water tested. Three configurations of constructed wetland, a membrane bioreactor (MBR), and a membrane chemical reactor (MCR) were evaluated for indicator bacteria (total coliforms, Escherichia coli, Enterococci, Clostridia, and heterotrophs) removal over a period of 2 years under conditions of low and high strength grey water influent. Total coliforms were found to be good indicators for P. aeruginosa, showing strong and significant Spearman's rank correlations in the influent grey water (r_s = 0.77, P = 0.005) and treated effluents (r_s = 0.81, P ≤ 0.001). The MBR provided the highest quality treated effluent and was the most robust treatment technology, remaining unaffected by an increase in influent grey water strength. Of the three constructed wetlands, the VFRB was the most reliable performer under low and high strength influent conditions, indicating aerobic unsaturated wetland to be the most suitable form of the technology for pathogen removal.     

Low-dose Ad26.COV2.S protection against SARS-CoV-2 challenge in rhesus macaques

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Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

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Twenty-five years of international exchanges of plant genetic resources facilitated by the CGIAR genebanks: a case study on global interdependence

This article analyses 25 years of data about international movements of plant genetic resources for food and agriculture (PGRFA), facilitated by the gene banks hosted by seven centres of the Consultative Group on International Agricultural Research. It identifies trends in the movements of PGRFA for use in research and development, and describes the diversity of those resources transferred over time. The paper also presents data on the number of countries involved in the global exchanges, analyses their development status and describes their role as providers and/or recipients, providing a picture of the breadth of these global exchanges. We highlight that it is primarily developing and transition economies that have participated in the flows, and that the transferred germplasm has been largely used within their public agricultural research and development programmes. We conclude that, when provided the opportunity of facilitated access, countries will use a wide diversity of germplasm from many other countries, sub-regions and continents as inputs into their agricultural research and development programmes. We highlight the importance of enabling the continuation of the non-monetary benefits from international access to germplasm. We discuss the implications for the process of development and reform of the multilateral system of access and benefit sharing under International Treaty on Plant Genetic Resources for Food and Agriculture.     

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.Subject terms: Water microbiology, Microbial ecology, Microbiome, Biogeochemistry, Biogeochemistry     

Determinants of physical activity among a convenience sample of Puerto Rican women residing in the Northeastern United States

The research examining determinants of physical activity among Hispanics focuses on Mexican Americans, although Puerto Ricans are the second largest Hispanic subgroup in the United States. The purpose of this study was to explore factors influencing physical activity among Puerto Rican women in the urban northeastern United States. Two bilingual female investigators administered the Women and Physical Activity Survey by telephone to a convenience sample of Puerto Rican women (n = 28). Women were categorized as physically active if they performed moderate-intensity physical activity for at least 30 minutes a day at least 5 days a week or vigorous-intensity physical activity for at least 20 minutes a day at least 3 days a week. Women not meeting these criteria were classified as physically inactive. Chi-squared testing revealed whether the physically active and inactive women differed among physical activity determinants. Respondents had a mean age of 36 years and were predominately college-educated (64%) and physically active (68%). More physically active women (90%) had an annual income of more than $35,000 than did the inactive women (10%) (p < 0.05). More physically active women belonged to community groups (42% versus 0%), lived in communities where people exercise (95% versus 11%), and felt their community was good for their family (100% versus 67%) than did the inactive women, respectively (p < 0.05). The physically active women reported the presence of exercise facilities (p = 0.084) and well-maintained sidewalks (p = 0.087) to be more important for exercise accessibility than did the inactive women. Annual income, sense of community, and exercise accessibility were the most important physical activity determinants in this convenience sample of Puerto Rican women. Factors influencing the physical activity levels of Puerto Rican women should continue to be explored so that targeted, culturally appropriate strategies can be developed to promote physically activity in this population.     

Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification

Custom-made zinc-finger nucleases (ZFNs) can induce targeted genome modifications with high efficiency in cell types including Drosophila, C. elegans, plants, and humans. A bottleneck in the application of ZFN technology has been the generation of highly specific engineered zinc-finger arrays. Here we describe OPEN (Oligomerized Pool ENgineering), a rapid, publicly available strategy for constructing multifinger arrays, which we show is more effective than the previously published modular assembly method. We used OPEN to construct 37 highly active ZFN pairs which induced targeted alterations with high efficiencies (1%-50%) at 11 different target sites located within three endogenous human genes (VEGF-A, HoxB13, and CFTR), an endogenous plant gene (tobacco SuRA), and a chromosomally integrated EGFP reporter gene. In summary, OPEN provides an "open-source" method for rapidly engineering highly active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN technology for biological research and gene therapy.