Genome assembly of the chemosynthetic endosymbiont of the hydrothermal vent snail Alviniconcha adamantis from the Mariana Arc

Chemosynthetic animal-microbe symbioses sustain hydrothermal vent communities in the global deep sea. In the Indo-Pacific Ocean, hydrothermal ecosystems are often dominated by gastropod species of the genus Alviniconcha, which live in association with chemosynthetic Gammaproteobacteria or Campylobacteria. While the symbiont genomes of most extant Alviniconcha species have been sequenced, no genome information is currently available for the gammaproteobacterial endosymbiont of Alviniconcha adamantis—a comparatively shallow living species that is thought to be the ancestor to all other present Alviniconcha lineages. Here, we report the first genome sequence for the symbiont of A. adamantis from the Chamorro Seamount at the Mariana Arc. Our phylogenomic analyses show that the A. adamantis symbiont is most closely related to Chromatiaceae endosymbionts of the hydrothermal vent snails Alviniconcha strummeri and Chrysomallon squamiferum, but represents a distinct bacterial species or possibly genus. Overall, the functional capacity of the A. adamantis symbiont appeared to be similar to other chemosynthetic Gammaproteobacteria, though several flagella and chemotaxis genes were detected, which are absent in other gammaproteobacterial Alviniconcha symbionts. These differences might suggest potential contrasts in symbiont transmission dynamics, host recognition, or nutrient transfer. Furthermore, an abundance of genes for ammonia transport and urea usage could indicate adaptations to the oligotrophic waters of the Mariana region, possibly via recycling of host- and environment-derived nitrogenous waste products. This genome assembly adds to the growing genomic resources for chemosynthetic bacteria from hydrothermal vents and will be valuable for future comparative genomic analyses assessing gene content evolution in relation to environment and symbiotic lifestyles

A Preliminary Study of Soundscape Analysis as a Measurement of Ecosystem Health

In this study, acoustic ecology, the analysis of soundscapes -- composed of geophony, biophony, and anthrophony -- is applied as a potential measurement of ecosystem health. Recordings were taken from four locations in the greater Chicago area. By combining traditional ecological assessments including soil analysis, worm density surveys, and vegetation surveys, and correlating the results with acoustic data we highlight the value of soundscape analysis and suggest lines of future inquiry

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts

Background: Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snail Alviniconcha hessleri from two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. Results: Our phylogenomic analyses show that the free-living and host-associated symbionts of A. hessleri from both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. Conclusion: Together, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition

SUBSEA 2019 Expedition to the Gorda Ridge

The SUBSEA (Systematic Underwater Biogeochemical Science and Exploration Analog) program blends ocean exploration with “ocean worlds” research, along with NASA analog and work studies research, to address science, science operations, and technology knowledge gaps related to the exploration of our solar system. The science group researches venting fluids at isolated seamounts and spreading ridges in the Pacific Ocean as analog environments to putative volcanically hosted hydrothermal systems on other “ocean worlds” (defined as places in the outer solar system that could possess subsurface oceans). The science operations research group studies E/V Nautilus architecture, distributed teams, communication, and lowlatency telerobotics. The technology research group provided Exploration Ground Data Systems (xGDS) software to the shore team to support the integration and visualization of diverse data products during the cruise

Individual nutrition therapy and exercise regime: A controlled trial of injured, vulnerable elderly (INTERACTIVE trial)

© 2008 Thomas et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background Proximal femoral fractures are amongst the most devastating consequences of osteoporosis and injurious accidental falls with 25–35% of patients dying in the first year post-fracture. Effective rehabilitation strategies are evolving however, despite established associations between nutrition, mobility, strength and strength-related functional outcomes; there has been only one small study with older adults immediately following fragility fracture where a combination of both exercise and nutrition have been provided. The aim of the INTERACTIVE trial is to establish whether a six month, individualised exercise and nutrition program commencing within fourteen days of surgery for proximal femur fracture, results in clinically and statistically significant improvements in physical function, body composition and quality of life at an acceptable level of cost and resource use and without increasing the burden of caregivers. Methods and Design This randomised controlled trial will be performed across two sites, a 500 bed acute hospital in Adelaide, South Australia and a 250 bed acute hospital in Sydney, New South Wales. Four hundred and sixty community-dwelling older adults aged > 70 will be recruited after suffering a proximal femoral fracture and followed into the community over a 12-month period. Participants allocated to the intervention group will receive a six month individualised care plan combining resistance training and nutrition therapy commencing within 14 days post-surgery. Outcomes will be assessed by an individual masked to treatment allocation at six and 12 months. To determine differences between the groups at the primary end-point (six months), ANCOVA or logistic regression will be used with models adjusted according to potential confounders. Discussion The INTERACTIVE trial is among the first to combine nutrition and exercise therapy as an early intervention to address the serious consequence of rapid deconditioning and weight loss and subsequent ability to regain pre-morbid function in older patients post proximal femoral fracture. The results of this trial will guide the development of more effective rehabilitation programs, which may ultimately lead to reduced health care costs, and improvements in mobility, independence and quality of life for proximal femoral fracture sufferers. Trial registration Australian Clinical Trials Registry: ACTRN12607000017426

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Forgetting of prior remembering in persons reporting recovered memories of childhood sexual abuse

Case studies of individuals reporting recovered memories of childhood sexual abuse suggest that some overestimate their prior forgetting of the abuse. People reporting recovered or continuous memories of childhood sexual abuse and control subjects reporting no history of abuse participated in two experiments examining this 'forgot it all along" phenomenon. Participants in Experiment 1 were more likely to forget that they had previously recalled a studied item if they were cited to think of it differently on two recall tests than if they were cued to think of it in the same way on. the two tests. This effect was stronger for recovered-memory participants than for continuous-memory and control participants. In Experiment 2, participants recalled autobiographical events three times over a period of 4 months. Much as in Experiment 1, they underestimated prior remembering when. the events had been recalled in a different emotional frame (Positive vs. negative) on the previous occasion. This underestimation was more pronounced for recovered-memory participants than, for continuous-memory and control participants.</p

The Optimal Timing of Step 1 in Medical Education Following the Transition to Pass/Fail: A Unique Perspective from Post-clerkship Step 1 Schools

The National Board of Medical Examiners' decision to change Step 1 of the United States Medical Licensing Examination (USMLE) from a three-digit score to Pass/Fail (P/F) represents a disruptive change for students, faculty, and leaders in the academic community. In the context of this change, some schools may re-consider the optimal timing of Step 1 as they strive to align their assessment practices with sound educational principles. Currently, over 20 schools administer USMLE Step 1 after the core clerkships. In this commentary, we review the educational rationale for a post-clerkship Step 1, highlighting how adult learning theories support this placement. We discuss some short-term challenges post-clerkship Step 1 schools may encounter due to the proposed timing of the change in scoring, which creates three unique scenarios for learners that can introduce inequity in the system and provoke anxiety. We review outcomes of potentially heightened importance when Step 1 is P/F, including lower clinical subject exam scores in some clerkships, lower failure rates on Step 1 and stable Step 2 Clinical Knowledge scores with implications for the residency match. We outline the future potential for performance-based time-variable Step 1 study periods that are facilitated by post-clerkship placement of the exam. Finally, we discuss opportunities to achieve the goal of enhancing student well-being, which was a major rationale for eliminating the three-digit score

Forgetting of prior remembering in people reporting recovered memories of childhood sexual abuse

Case studies of individuals reporting recovered memories of childhood sexual abuse suggest that some overestimate their prior forgetting of the abuse. People reporting recovered or continuous memories of childhood sexual abuse and control subjects reporting no history of abuse participated in two experiments examining this "forgot it all along" phenomenon. Participants in Experiment 1 were more likely to forget that they had previously recalled a studied item if they were cued to think of it differently on two recall tests than if they were cued to think of it in the same way on the two tests. This effect was stronger for recovered-memory participants than for continuous-memory and control participants. In Experiment 2, participants recalled autobiographical events three times over a period of 4 months. Much as in Experiment 1, they underestimated prior remembering when the events had been recalled in a different emotional frame (positive vs. negative) on the previous occasion. This underestimation was more pronounced for recovered-memory participants than for continuous-memory and control participant