Stress accumulation versus shape flattening in frustrated, warped-jigsaw particle assemblies

Geometrically frustrated assembly has emerged as an attractive paradigm for understanding and engineering assemblies with self-limiting, finite equilibrium dimensions. We propose and study a novel 2D particle based on a so-called "warped jigsaw" (WJ) shape design: directional bonds in a tapered particle favor curvature along multi-particle rows that frustrate 2D lattice order. We investigate how large-scale intra-assembly stress gradients emerge from the microscopic properties of the particles using a combination of numerical simulation and continuum elasticity. WJ particles can favor anisotropic ribbon assemblies, whose lateral width may be self-limiting depending on the relative strength of cohesive to elastic forces in the assembly, which we show to be controlled by the range of interactions and degree of shape misfit. The upper limits of self-limited size are controlled by the crossover between two elastic modes in assembly: the accumulation of shear with increasing width at small widths giving way to unbending of preferred row curvature, permitting assembly to grow to unlimited sizes. We show that the stiffness controlling distinct elastic modes is governed by combination and placement of repulsive and attractive binding regions, providing a means to extend the range of accumulating stress to sizes that are far in excess of the single particle size, which we corroborate via numerical studies of discrete particles of variable interactions. Lastly, we relate the ground-state energetics of the model to lower and upper limits on equilibrium assembly size control set by the fluctuations of width along the ribbon boundary.Comment: 18 pages, 9 figures, 2 appendice

Isotopic constraints on nitrogen transformation rates in the deep sedimentary marine biosphere

Author Posting. © American Geophysical Union,2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Isotopic constraints on nitrogen transformation rates in the deep sedimentary marine biosphere. Global Biogeochemical Cycles, 32, (2018):1688–1702., doi: 10.1029/2018GB005948.Little is known about the nature of microbial community activity contributing to the cycling of nitrogen in organic-poor sediments underlying the expansive oligotrophic ocean gyres. Here we use pore water concentrations and stable N and O isotope measurements of nitrate and nitrite to constrain rates of nitrogen cycling processes over a 34-m profile from the deep North Atlantic spanning fully oxic to anoxic conditions. Using a 1-D reaction-diffusion model to predict the distribution of nitrogen cycling rates, results converge on two distinct scenarios: (1) an exceptionally high degree of coupling between nitrite oxidation and nitrate reduction near the top of the anoxic zone or (2) an unusually large N isotope effect (~60‰) for nitrate reduction that is decoupled from the corresponding O isotope effect, which is possibly explained by enzyme-level interconversion between nitrite and nitrate.Samples analyzed for this study were collected during the final expedition of the RV Knorr, KN223. The expedition would not have been possible without the captain and crew of the RV Knorr and the efforts of the shipboard science party. We would like to acknowledge Robert Pockalny for planning and facilitating the expedition. Inorganic geochemistry sample collection, processing, and analysis were performed shipboard by Arthur Spivack,Dennis Graham, Chloe Anderson, Emily Estes, Kira Homola, Claire McKinley, Theodore Present, and Justine Sauvage. Coring capabilities were provided by the Oregon State University and Woods Hole Oceanographic Institute Coring Facilities, directed and funded by the U. S. National Science Foundation (NSF) Ship Facilities Program. The cored materials and discrete samples from the expedition are curated and stored by the Marine Geological Samples Laboratory at the University of Rhode Island, codirected by Rebecca Robinson and Katherine Kelly and funded by the NSF Ocean Sciences Division. The nutrient and isotope data from pore waters in this study will be available at The Biological and Chemical Data Management Office (https://www.bcodmo.org/project/567401). This project was partially funded by an NSF CDEBI postdoctoral fellowship to C. Buchwald. Portions of this material are based upon work supported while R. W. M. was serving at the National Science Foundation.2019-04-1

Hydrogen Utilization Potential in Subsurface Sediments

Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones

Archaea dominate oxic subseafloor communities over multimillion-year time scales

Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years

Examining smoking-induced differential gene expression changes in buccal mucosa

<p>Abstract</p> <p>Background</p> <p>Gene expression changes resulting from conditions such as disease, environmental stimuli, and drug use, can be monitored in the blood. However, a less invasive method of sample collection is of interest because of the discomfort and specialized personnel necessary for blood sampling especially if multiple samples are being collected. Buccal mucosa cells are easily collected and may be an alternative sample material for biomarker testing. A limited number of studies, primarily in the smoker/oral cancer literature, address this tissue's efficacy as an RNA source for expression analysis. The current study was undertaken to determine if total RNA isolated from buccal mucosa could be used as an alternative tissue source to assay relative gene expression.</p> <p>Methods</p> <p>Total RNA was isolated from swabs, reverse transcribed and amplified. The amplified cDNA was used in RT-qPCR and microarray analyses to evaluate gene expression in buccal cells. Initially, RT-qPCR was used to assess relative transcript levels of four genes from whole blood and buccal cells collected from the same seven individuals, concurrently. Second, buccal cell RNA was used for microarray-based differential gene expression studies by comparing gene expression between a group of female smokers and nonsmokers.</p> <p>Results</p> <p>An amplification protocol allowed use of less buccal cell total RNA (50 ng) than had been reported previously with human microarrays. Total RNA isolated from buccal cells was degraded but was of sufficient quality to be used with RT-qPCR to detect expression of specific genes. We report here the finding of a small number of statistically significant differentially expressed genes between smokers and nonsmokers, using buccal cells as starting material. Gene Set Enrichment Analysis confirmed that these genes had a similar expression pattern to results from another study.</p> <p>Conclusions</p> <p>Our results suggest that despite a high degree of degradation, RNA from buccal cells from cheek mucosa could be used to detect differential gene expression between smokers and nonsmokers. However the RNA degradation, increase in sample variability and microarray failure rate show that buccal samples should be used with caution as source material in expression studies.</p

In situ detection of boron by ChemCam on Mars

We report the first in situ detection of boron on Mars. Boron has been detected in Gale crater at levels Curiosity rover ChemCam instrument in calcium-sulfate-filled fractures, which formed in a late-stage groundwater circulating mainly in phyllosilicate-rich bedrock interpreted as lacustrine in origin. We consider two main groundwater-driven hypotheses to explain the presence of boron in the veins: leaching of borates out of bedrock or the redistribution of borate by dissolution of borate-bearing evaporite deposits. Our results suggest that an evaporation mechanism is most likely, implying that Gale groundwaters were mildly alkaline. On Earth, boron may be a necessary component for the origin of life; on Mars, its presence suggests that subsurface groundwater conditions could have supported prebiotic chemical reactions if organics were also present and provides additional support for the past habitability of Gale crater

Familial aggregation of lung cancer in a high incidence area in China

To investigate whether lung cancer clusters in families in a high incidence county of China, an analysis was conducted using data on domestic fuel history and tobacco use for family members of 740 deceased lung cancer probands and 740 controls (probands' spouses). Lung cancer prevalence was compared among first-degree relatives of probands and of controls, taking into account various factors using logistic regression and generalised estimating equations. First-degree relatives of probands, compared with those of controls, showed an excess risk of lung cancer (odds ratio (OR)=2.05, 95% confidence interval (CI): 1.68–2.53). Overall, female relatives of probands had a greater risk than did their male counterparts, and the risk was 2.90-fold for parents of probands as compared with parents of spouses. Female relatives of probands had 2.67-fold greater risk than female controls. Lung cancer risk was particularly marked among mothers (OR=3.78, 95% CI: 2.03–7.12). Having two or more affected relatives was associated with a 2.69–5.40-fold risk increase. The risk elevation was also found for other cancers overall. Results confirm previous findings of a genetic predisposition to lung cancer, and also imply that lung cancer may share a genetic background with other cancers

Educational paper: Abusive Head Trauma Part I. Clinical aspects

Abusive Head Trauma (AHT) refers to the combination of findings formerly described as shaken baby syndrome. Although these findings can be caused by shaking, it has become clear that in many cases there may have been impact trauma as well. Therefore a less specific term has been adopted by the American Academy of Pediatrics. AHT is a relatively common cause of childhood neurotrauma with an estimated incidence of 14–40 cases per 100,000 children under the age of 1 year. About 15–23% of these children die within hours or days after the incident. Studies among AHT survivors demonstrate that approximately one-third of the children are severely disabled, one-third of them are moderately disabled and one-third have no or only mild symptoms. Other publications suggest that neurological problems can occur after a symptom-free interval and that half of these children have IQs below the 10th percentile. Clinical findings are depending on the definitions used, but AHT should be considered in all children with neurological signs and symptoms especially if no or only mild trauma is described. Subdural haematomas are the most reported finding. The only feature that has been identified discriminating AHT from accidental injury is apnoea. Conclusion: AHT should be approached with a structured approach, as in any other (potentially lethal) disease. The clinician can only establish this diagnosis if he/she has knowledge of the signs and symptoms of AHT, risk factors, the differential diagnosis and which additional investigations to perform, the more so since parents seldom will describe the true state of affairs spontaneously