Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

Evidence-based urology in practice : heterogeneity in a systematic review meta-analysis

The definitive version is available at www3.interscience.wiley.com.Peer reviewedPreprin

The Swift-BAT hard X-ray sky monitoring unveils the orbital period of the HMXB IGR J16493-4348

IGR J16493-4348 is a supergiant high mass X-ray binary discovered by INTEGRAL in 2004. The source is detected at a significance level of $\sim21$ standard deviations in the Swift-BAT survey data collected during the first 54 months of the Swift mission. The timing analysis reveals an orbital period of $\sim$6.78 days and the presence of a full eclipse of the compact ob\ ject. The dynamical range (variability up to a factor $\sim$20) observed during the BAT monitoring suggests that IGR J16493-4348 is a wind-fed system. The derived semi-major axis of the binary system is \sim55 R_{\sun} with an orbit eccentr\ icity lower than 0.15.Comment: 4 pages, 6 figures. Accepted for publication in MNRA

Long distance electron transfer through the aqueous solution between redox partner proteins

Despite the importance of electron transfer between redox proteins in photosynthesis and respiration, the inter-protein electron transfer rate between redox partner proteins has never been measured as a function of their separation in aqueous solution. Here, we use electrochemical tunneling spectroscopy to show that the current between two protein partners decays along more than 10 nm in the solution. Molecular dynamics simulations reveal a reduced ionic density and extended electric field in the volume confined between the proteins. The distance-decay factor and the calculated local barrier for electron transfer are regulated by the electrochemical potential applied to the proteins. Redox partners could use electrochemically gated, long distance electron transfer through the solution in order to conciliate high specificity with weak binding, thus keeping high turnover rates in the crowded environment of cells.España, MINECO BFU2015-71017-P/España, Gobierno de Andalucía (BIO198)Comisión de Universidades e Investigación del Departamento de Innovación, Universidades y Empresa de la Generalitat de Catalunya.(2017 SGR 1442, 2014 SGR 1442, and 2017 SGR 1189

Elastic lever arm model for myosin V

We present a mechanochemical model for myosin V, a two-headed processive motor protein. We derive the properties of a dimer from those of an individual head, which we model both with a 4-state cycle (detached, attached with ADP.Pi, attached with ADP and attached without nucleotide) and alternatively with a 5-state cycle (where the power stroke is not tightly coupled to the phosphate release). In each state the lever arm leaves the head at a different, but fixed, angle. The lever arm itself is described as an elastic rod. The chemical cycles of both heads are coordinated exclusively by the mechanical connection between the two lever arms. The model explains head coordination by showing that the lead head only binds to actin after the power stroke in the trail head and that it only undergoes its power stroke after the trail head unbinds from actin. Both models (4- and 5-state) reproduce the observed hand-over-hand motion and fit the measured force-velocity relations. The main difference between the two models concerns the load dependence of the run length, which is much weaker in the 5-state model. We show how systematic processivity measurement under varying conditions could be used to distinguish between both models and to determine the kinetic parameters.Comment: 15 pages, 15 figures, to appear in Biophys.

Strategies to Improve Employee Ethical Conduct in Health Care Organizations

Organizational leaders face challenges related to implementing ethical standards, which influence performance, organization sustainability, and culture. The purpose of this single case study was to explore ethics strategies that health care business leaders used to improve employees\u27 ethical conduct. Data were collected through face-to-face, semistructured interviews with a purposive sample of 7 business leaders of a health care organization located in central Georgia and a review of organization documents. The conceptual framework was Brady\u27s Janus-headed model of ethical theory. Using a priori coding during the data analysis process provided 3 thematic categories: policy strategies for the improvement of employee ethical conduct, ethics strategies used to address employee unethical conduct, and strategies to overcome barriers of strategy implementation. Themes that emerged from the data were accountability and responsibility, leadership development, escalating behaviors, and adapting to change. The findings from this study might contribute to social change by providing information about ethical strategies leaders used to improve employee ethical conduct, which can be used to influence individuals\u27 livelihood, stakeholders\u27 comfort level, and the well-being of the community

Double Field Inflation

We present an inflationary universe model which utilizes two coupled real scalar fields. The inflation field $\phi$ experiences a first order phase transition and its potential dominates the energy density of the Universe during the inflationary epoch. This field $\phi$ is initially trapped in its metastable minimum and must tunnel through a potential barrier to reach the true vacuum. The second auxiliary field $\psi$ couples to the inflaton field and serves as a catalyst to provide an abrupt end to the inflationary epoch; i.e., the $\psi$ field produces a time-dependent nucleation rate for bubbles of true $\phi$ vacuum. In this model, we find that bubbles of true vacuum can indeed percolate and we argue that thermalization of the interiors can more easily take place. The required degree of flatness (i.e., the fine tuning) in the potential of the $\psi$ field is comparable to that of other models which invoke slowly rolling fields. Pseudo Nambu-Goldstone bosons may naturally provide the flat potential for the rolling field.Comment: 18 pages, 2 figures, This early paper is being placed on the archive to make it more easily accessible in light of recent interest in reviving tunneling inflationary models and as its results are used in an accompanying submissio

Paper : explorando la técnica del stop motion

Realització d'un curt d'animació mitjançant la tècnica del stop motion, documentant el procés des de els plantejaments inicials fins la postproducció. L'objectiu es explorar la tècnica cinematogràfica del stop motion i aproximar aquesta al públic.Realización de un corto de animación mediante la técnica del stop motion, documentando el proceso desde los planteamientos iniciales hasta la postproducción. El objetivo es explorar la técnica cinematográfica del stop motion y aproximar el público a ella.Production of a stop motion animated short film and documentation of the process, from its initial planning stages to its postproduction. The aim is to explore the stop motion animating technique and bring it closer to the audience

Project Frozo: A Solution to the Cold-Chain Problem

Project Frozo has designed an ultra-low temperature portable freezer capable of storing 500 COVID-19 vaccine vials for global distribution. The device does not require external power, and utilizes a combination of vacuum insulation panels, aerogel, and phase change material to maintain a storage volume temperature of -70°C for over 10 days. This duration of time was determined by running a one-dimensional transient heat transfer simulation with a constant ambient temperature of 48.89°C (120°F). Construction of a prototype is underway which will be used to perform physical testing and validate the simulation results. The design will enable cost effective distribution of the COVID-19 vaccine on a global scale. The design follows guidelines set by The Setty Family Foundation: 2022 Applied Engineering Challenge as well as the American Society of Heating, Refrigerating, and Air-Conditioning Engineers (ASHRAE) standards. Vaccine storage requirements were determined using public information provided by Pfizer. Project Frozo’s design will function as the final storage system for vaccines prior to doses being administered to recipients

Optical and X-ray observations of candidate isolated neutron stars in the G315.4-2.3 SNR

G315.4-2.3 is a young Galactic supernova remnant (SNR), whose identification as the remains of a Type-II supernova (SN) explosion has been debated for a long time. In particular, recent multi-wavelength observations suggest that it is the result of a Type Ia SN, based on spectroscopy of the SNR shell and the lack of a compact stellar remnant.However, two X-ray sources, one detected by Einstein and ROSAT (Source V) and the other by Chandra (Source N) have been proposed as possible isolated neutron star candidates. In both cases, no clear optical identification was available and, therefore, we performed an optical and X-ray study to determine the nature of these two sources. Based on Chandra astrometry, Source V is associated with a bright V~14 star, which had been suggested based on the less accurate ROSAT position. Similarly, from VLT archival observations, we found that Source N is associated with a relatively bright star ($V=20.14$). These likely identifications suggest that both X-ray sources cannot be isolated neutron stars.Comment: 4 pages, 4 figures, accepted for publication in MNRA