Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq.

Background: Deer antlers are bony structures that re-grow at very high rates, making them an attractive model for studying rapid bone regeneration.

Methods: To identify the genes that are involved in this fast pace of bone growth, an in vitro RNA-seq model that paralleled the sharp differences in bone growth between deer antlers and humans was established. Subsequently, RNA-seq (> 60 million reads per library) was used to compare transcriptomic profiles.

Infant skull fracture risk for low height falls.

Skull fractures are common injuries in young children, typically caused by accidental falls and child abuse. The paucity of detailed biomechanical data from real-world trauma in children has hampered development of biomechanical thresholds for skull fracture in infants. The objectives of this study were to identify biomechanical metrics to predict skull fracture, determine threshold values associated with fracture, and develop skull fracture risk curves for low-height falls in infants.

Marine Mammal Microbiota Yields Novel Antibiotic with Potent Activity Against Clostridium difficile.

The recent explosion of research on the microbiota has highlighted the important interplay between commensal microorganisms and the health of their cognate hosts. Metabolites isolated from commensal bacteria have been demonstrated to possess a range of antimicrobial activities, and it is widely believed that some of these metabolites modulate host behavior, affecting predisposition to disease and pathogen invasion. Our access to the local marine mammal stranding network and previous successes in mining the fish microbiota poised us to test the hypothesis that the marine mammal microbiota is a novel source of commensal bacteria-produced bioactive metabolites.

Highly Stable Molybdenum Disulfide Protected Silicon Photocathodes for Photoelectrochemical Water Splitting.

Developing materials, interfaces, and devices with improved stability remains one of the key challenges in the field of photoelectrochemical water splitting. As a barrier to corrosion, molybdenum disulfide is a particularly attractive protection layer for photocathodes due to its inherent stability in acid, the low permeability of its basal planes, and the excellent hydrogen evolution reaction (HER) activity the MoS edge. Here, we demonstrate a stable silicon photocathode containing a protecting layer consisting of molybdenum disulfide, molybdenum silicide, and silicon oxide which operates continuously for two months.

Physical Limits on the Precision of Mitotic Spindle Positioning by Microtubule Pushing forces: Mechanics of mitotic spindle positioning.

Tissues are shaped and patterned by mechanical and chemical processes. A key mechanical process is the positioning of the mitotic spindle, which determines the size and location of the daughter cells within the tissue. Recent force and position-fluctuation measurements indicate that pushing forces, mediated by the polymerization of astral microtubules against- the cell cortex, maintain the mitotic spindle at the cell center in Caenorhabditis elegans embryos.

Propagation of errors from skull kinematic measurements to finite element tissue responses.

Real-time quantification of head impacts using wearable sensors is an appealing approach to assess concussion risk. Traditionally, sensors were evaluated for accurately measuring peak resultant skull accelerations and velocities. With growing interest in utilizing model-estimated tissue responses for injury prediction, it is important to evaluate sensor accuracy in estimating tissue response as well.

Latiglutenase Improves Symptoms in Seropositive Celiac Disease Patients While on a Gluten-Free Diet.

Background And Aims: Celiac disease (CD) is a widespread condition triggered by dietary gluten and treated with a lifelong gluten-free diet (GFD); however, inadvertent exposure to gluten can result in episodic symptoms. A previous trial of latiglutenase (clinicaltrials.gov; NCT01917630), an orally administered mixture of two recombinant gluten-specific proteases, was undertaken in symptomatic subjects with persistent injury.

Shallow Representation Learning via Kernel PCA Improves QSAR Modelability.

Linear models offer a robust, flexible, and computationally efficient set of tools for modeling quantitative structure-activity relationships (QSARs) but have been eclipsed in performance by nonlinear methods. Support vector machines (SVMs) and neural networks are currently among the most popular and accurate QSAR methods because they learn new representations of the data that greatly improve modelability. In this work, we use shallow representation learning to improve the accuracy of L1 regularized logistic regression (LASSO) and meet the performance of Tanimoto SVM.

Electrochemical CO reduction on Au surfaces: mechanistic aspects regarding the formation of major and minor products.

In the future, industrial CO electroreduction using renewable energy sources could be a sustainable means to convert CO and water into commodity chemicals at room temperature and atmospheric pressure. This study focuses on the electrocatalytic reduction of CO on polycrystalline Au surfaces, which have high activity and selectivity for CO evolution. We explore the catalytic behavior of polycrystalline Au surfaces by coupling potentiostatic CO electrolysis experiments in an aqueous bicarbonate solution with high sensitivity product detection methods.

Validation of Protein-Ligand Crystal Structure Models: Small Molecule and Peptide Ligands.

Models of target proteins in complex with small molecule ligands or peptide ligands are of significant interest to the biomedical research community. Structure-guided lead discovery and structure-based drug design make extensive use of such models. The bound ligands comprise only a small fraction of the total X-ray scattering mass, and therefore particular care must be taken to properly validate the atomic model of the ligand as experimental data can often be scarce.

Flexible Analog Search with Kernel PCA Embedded Molecule Vectors.

Studying analog series to find structural transformations that enhance the activity and ADME properties of lead compounds is an important part of drug development. Matched molecular pair (MMP) search is a powerful tool for analog analysis that imitates researchers' ability to select pairs of compounds that differ only by small well-defined transformations. Abstraction is a challenge for existing MMP search algorithms, which can result in the omission of relevant, inexact MMPs, and inclusion of irrelevant, contextually dissimilar MMPs.

Origins of chemoreceptor curvature sorting in Escherichia coli.

Bacterial chemoreceptors organize into large clusters at the cell poles. Despite a wealth of structural and biochemical information on the system's components, it is not clear how chemoreceptor clusters are reliably targeted to the cell pole. Here, we quantify the curvature-dependent localization of chemoreceptors in live cells by artificially deforming growing cells of Escherichia coli in curved agar microchambers, and find that chemoreceptor cluster localization is highly sensitive to membrane curvature.

Materials for solar fuels and chemicals.

The conversion of sunlight into fuels and chemicals is an attractive prospect for the storage of renewable energy, and photoelectrocatalytic technologies represent a pathway by which solar fuels might be realized. However, there are numerous scientific challenges in developing these technologies. These include finding suitable materials for the absorption of incident photons, developing more efficient catalysts for both water splitting and the production of fuels, and understanding how interfaces between catalysts, photoabsorbers and electrolytes can be designed to minimize losses and resist degradation.

In Situ Polymer Graphenization Ingrained with Nanoporosity in a Nitrogenous Electrocatalyst Boosting the Performance of Polymer-Electrolyte-Membrane Fuel Cells.

Rich, porous graphene frameworks decorated with uniformly dispersed active sites are prepared by using polyaniline as a graphene precursor and introducing phenanthroline as a pore-forming agent. The unprecedented fuel-cell performance of this electrocatalyst is linked to the graphene frameworks with vast distribution of pore sizes, which maximizes the active-sites accessibility, facilitates mass-transport properties, and improves the carbon corrosion resistance.

Solar water splitting by photovoltaic-electrolysis with a solar-to-hydrogen efficiency over 30.

Hydrogen production via electrochemical water splitting is a promising approach for storing solar energy. For this technology to be economically competitive, it is critical to develop water splitting systems with high solar-to-hydrogen (STH) efficiencies. Here we report a photovoltaic-electrolysis system with the highest STH efficiency for any water splitting technology to date, to the best of our knowledge.

The Mitotic Spindle in the One-Cell C. elegans Embryo Is Positioned with High Precision and Stability.

Precise positioning of the mitotic spindle is important for specifying the plane of cell division, which in turn determines how the cytoplasmic contents of the mother cell are partitioned into the daughter cells, and how the daughters are positioned within the tissue. During metaphase in the early Caenorhabditis elegans embryo, the spindle is aligned and centered on the anterior-posterior axis by a microtubule-dependent machinery that exerts restoring forces when the spindle is displaced from the center. To investigate the accuracy and stability of centering, we tracked the position and orientation of the mitotic spindle during the first cell division with high temporal and spatial resolution.

A highly active and stable IrOx/SrIrO3 catalyst for the oxygen evolution reaction.

Oxygen electrochemistry plays a key role in renewable energy technologies such as fuel cells and electrolyzers, but the slow kinetics of the oxygen evolution reaction (OER) limit the performance and commercialization of such devices. Here we report an iridium oxide/strontium iridium oxide (IrO/SrIrO) catalyst formed during electrochemical testing by strontium leaching from surface layers of thin films of SrIrO This catalyst has demonstrated specific activity at 10 milliamps per square centimeter of oxide catalyst (OER current normalized to catalyst surface area), with only 270 to 290 millivolts of overpotential for 30 hours of continuous testing in acidic electrolyte. Density functional theory calculations suggest the formation of highly active surface layers during strontium leaching with IrO or anatase IrO motifs.

Engineering biosynthesis of the anticancer alkaloid noscapine in yeast.

Noscapine is a potential anticancer drug isolated from the opium poppy Papaver somniferum, and genes encoding enzymes responsible for the synthesis of noscapine have been recently discovered to be clustered on the genome of P. somniferum. Here, we reconstitute the noscapine gene cluster in Saccharomyces cerevisiae to achieve the microbial production of noscapine and related pathway intermediates, complementing and extending previous in planta and in vitro investigations.

Molybdenum Disulfide as a Protection Layer and Catalyst for Gallium Indium Phosphide Solar Water Splitting Photocathodes.

Gallium indium phosphide (GaInP2) is a semiconductor with promising optical and electronic properties for solar water splitting, but its surface stability is problematic as it undergoes significant chemical and electrochemical corrosion in aqueous electrolytes. Molybdenum disulfide (MoS2) nanomaterials are promising to both protect GaInP2 and to improve catalysis because MoS2 is resistant to corrosion and also possesses high activity for the hydrogen evolution reaction (HER). In this work, we demonstrate that GaInP2 photocathodes coated with thin MoS2 surface protecting layers exhibit excellent activity and stability for solar hydrogen production, with no loss in performance (photocurrent onset potential, fill factor, and light-limited current density) after 60 h of operation.

Protein stability: a crystallographer's perspective.

Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer.

Tuning the Range of Polyacrylamide Gel Stiffness for Mechanobiology Applications.

Adjusting the acrylamide monomer and cross-linker content in polyacrylamide gels controls the hydrogel stiffness, yet the reported elastic modulus for the same formulations varies widely and these discrepancies are frequently attributed to different measurement methods. Few studies exist that examine stiffness trends across monomer and cross-linker concentrations using the same characterization platform. In this work, we use Atomic Force Microscopy and analyze force-distance curves to derive the elastic modulus of polyacrylamide hydrogels.

A Sensitive and Biodegradable Pressure Sensor Array for Cardiovascular Monitoring.

An array of highly sensitive pressure sensors entirely made of biodegradable materials is presented, designed as a single-use flexible patch for application in cardiovascular monitoring. The high sensitivity in combination with fast response time is unprecedented when compared to recent reports on biodegradable pressure sensors (sensitivity three orders of magnitude higher), as illustrated by pulse wave velocity measurements, toward hypertension detection.

Toward Controlled Growth of Helicity-Specific Carbon Nanotubes.

The underlying mechanisms for the nucleation of carbon nanotubes as well as their helicity, remain elusive. Here, using van der Waals dispersion force calculations implemented within density functional theory, we study the cap formation, believed to be responsible for the chirality of surface-catalyzed carbon nanotubes. We find the energetics associated with growth along different facets to be independent of the surface orientation and that the growth across an edge along the axis of the metal particle leads to a perfect honeycomb lattice in a curved geometry.

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation.

Unlabelled: The CRISPR/Cas9 system was recently developed as a powerful and flexible technology for targeted genome engineering, including genome editing (altering the genetic sequence) and gene regulation (without altering the genetic sequence). These applications require the design of single guide RNAs (sgRNAs) that are efficient and specific. However, this remains challenging, as it requires the consideration of many criteria.

A twentieth anniversary tribute to PSB.

PSB brings together top researchers from around the world to exchange research results and address open issues in all aspects of computational biology. PSB 2015 marks the twentieth anniversary of PSB. Reaching a milestone year is an accomplishment well worth celebrating.