Threshold logic implementation of a modular computer system design

Threshold logic implementation for LSI design of modular computer syste

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host–symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts’ metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts’ interaction with regional-scale differences in geochemistry.National Science Foundation (U.S.) (OCE-0732369)National Science Foundation (U.S.) (GRF grant no. DGE-1144152)Gordon and Betty Moore Foundation (Investigator)Agouron Institut

The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content

Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning

Thermodynamics and Kinetics of Sulfide Oxidation by Oxygen: A Look at Inorganically Controlled Reactions and Biologically Mediated Processes in the Environment

The thermodynamics for the first electron transfer step for sulfide and oxygen indicates that the reaction is unfavorable as unstable superoxide and bisulfide radical ions would need to be produced. However, a two-electron transfer is favorable as stable S(0) and peroxide would be formed, but the partially filled orbitals in oxygen that accept electrons prevent rapid kinetics. Abiotic sulfide oxidation kinetics improve when reduced iron and/or manganese are oxidized by oxygen to form oxidized metals which in turn oxidize sulfide. Biological sulfur oxidation relies on enzymes that have evolved to overcome these kinetic constraints to affect rapid sulfide oxidation. Here we review the available thermodynamic and kinetic data for H2S and HS• as well as O2, reactive oxygen species, nitrate, nitrite, and NOx species. We also present new kinetic data for abiotic sulfide oxidation with oxygen in trace metal clean solutions that constrain abiotic rates of sulfide oxidation in metal free solution and agree with the kinetic and thermodynamic calculations. Moreover, we present experimental data that give insight on rates of chemolithotrophic and photolithotrophic sulfide oxidation in the environment. We demonstrate that both anaerobic photolithotrophic and aerobic chemolithotrophic sulfide oxidation rates are three or more orders of magnitude higher than abiotic rates suggesting that in most environments biotic sulfide oxidation rates will far exceed abiotic rates due to the thermodynamic and kinetic constraints discussed in the first section of the paper. Such data reshape our thinking about the biotic and abiotic contributions to sulfide oxidation in the environment

Links from mantle to microbe at the Lau Integrated Study Site : insights from a back-arc spreading center

Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 1 (2012): 62–77, doi:10.5670/oceanog.2012.04.The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna.Support was provided by National Science Foundation grants OCE-1038135 to MKT, OCE-0732369 and OCE-0240985 to CRF, OCE-0732369 and OCE-0838107 to PRG, OCE-0242618 to CHL, OCE-0242902 and OCE-0752256 to PJM, OCE-0728391 and OCE-0937404 to A-LR, and a GRFP to RB

Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB)

Recommendations for exercise adherence measures in musculoskeletal settings : a systematic review and consensus meeting (protocol)

Background: Exercise programmes are frequently advocated for the management of musculoskeletal disorders; however, adherence is an important pre-requisite for their success. The assessment of exercise adherence requires the use of relevant and appropriate measures, but guidance for appropriate assessment does not exist. This research will identify and evaluate the quality and acceptability of all measures used to assess exercise adherence within a musculoskeletal setting, seeking to reach consensus for the most relevant and appropriate measures for application in research and/or clinical practice settings. Methods/design: There are two key stages to the proposed research. First, a systematic review of the quality and acceptability of measures used to assess exercise adherence in musculoskeletal disorders; second, a consensus meeting. The systematic review will be conducted in two phases and reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to ensure a robust methodology. Phase one will identify all measures that have been used to assess exercise adherence in a musculoskeletal setting. Phase two will seek to identify published and unpublished evidence of the measurement and practical properties of identified measures. Study quality will be assessed against the COnsensus-based Standards for the selection of health Measurement Instruments (COSMIN) guidelines. A shortlist of best quality measures will be produced for consideration during stage two: a meeting of relevant stakeholders in the United Kingdom during which consensus on the most relevant and appropriate measures of exercise adherence for application in research and/or clinical practice settings will be sought. Discussion: This study will benefit clinicians who seek to evaluate patients’ levels of exercise adherence and those intending to undertake research, service evaluation, or audit relating to exercise adherence in the musculoskeletal field. The findings will impact upon new research studies which aim to understand the factors that predict adherence with exercise and which test different adherence-enhancing interventions. PROSPERO reference: CRD4201300621

Clinical supervision for clinical psychology students in Uganda: an initial qualitative exploration

Background Burn out in clinical psychologists working in low income countries has been reported. Clinical supervisory structures do not yet exist in Uganda. A way to decrease levels of burn out and increase quality of care for people with mental illness is through clinical supervision. The aim of this study was to explore the initial experiences of supervision for clinical psychology students in Uganda to ascertain whether or not clinical supervision is culturally appropriate, and what aspects of supervision had been helpful and unhelpful. Methods A qualitative design with thematic analysis was utilized. A focus group was held with 12 second year clinical psychology students to ask their experiences of receiving supervision. Results Data analysis created five themes. Firstly, the negative emotions that resulted from the training processed were discussed, and how supervision helped and did not help the students to manage these. Secondly, the students voiced that supervision helped them to learn through observational experiences, co-therapist roles and parallel processes within the supervisory relationship. Thirdly, supervision had taught the clinical psychology students their role as a clinical psychology student, how to act within the Ugandan mental health system and skills to conduct therapy. Fourthly, suggestions for the future of supervision were given, with the students requesting for it to start earlier in the training, for supervisors who can meet with the students on a regular basis to be selected and for the training the students receive at university to match the skills required on their placements, with a request for more practical techniques rather than theory. The final theme related to left over miscellaneous data, such as the students agreeing with each other. Conclusions The students stated that supervision was helpful overall, implying that clinical supervision is culturally appropriate for clinical psychology students in Uganda. Suggestions for future supervision were given. In order to decrease high levels of staff burn out in the mental health systems in Uganda, supervisory structures with an emphasis on self care need to be established

Showing Israel the red card. Activists engaged in pro-Palestinian sport-related campaigns

© 2017 Informa UK Limited, trading as Taylor & Francis Group. This article explores the motivations of activists involved in pro-Palestinian sports-based campaigns. The activists’ intention is to bring pressure to bear upon Israel until it complies with international law and supports the rights of Palestinian people under the universal principles of human rights. In response to expressions of pro-Palestinian solidarity, the Israeli state and its supporters are interpreting such activity as a ‘new’ manifestation of ‘old’ antisemitism. In seeking to assess whether such activity is informed by antisemitism, 10 semi-structured interviews were conducted with activists to examine their motives. Their political biographies were explored as were their views on the use of sport as platform to express support for the Palestinian people and/or their displeasure at Israeli participation in international sport. One central theme was the activists’ responses to the suggestion that they were motivated by antisemitism. A qualitative content analysis of the interview transcripts revealed a shared observation that the accusation of antisemitism was a ‘shameless tactic’ employed by those seeking to cover up the ongoing injustices experienced by the Palestinian people. Sport was seen as a legitimate platform for political activity, to raise public awareness and to put pressure on the Israeli state. The findings contribute to a better understanding of activist motivations, the use of sport as a political platform and the challenges facing sport and its governing bodies

Degradation of communal rangelands in South Africa: towards an improved understanding to inform policy

In South Africa, the relative extent of range degradation under freehold compared to communal tenure has been strongly debated. We present a perspective on the processes that drive rangeland degradation on land under communal tenure. Our findings are based on literature as well as extensive field work on both old communal lands and ‘released’ areas, where freehold farms have been transferred to communal ownership. We discuss the patterns of degradation that have accompanied communal stewardship and make recommendations on the direction policy should follow to prevent further degradation and mediate rehabilitation of existing degraded land.Keywords: communal rangelands, land degradation, rehabilitation, social systemsAfrican Journal of Range & Forage Science 2013, 30(1&2): 57–6