Physiological responses of coccolithophores to abrupt exposure of naturally low pH deep seawater

Upwelling is the process by which deep, cold, relatively high-CO2, nutrient-rich seawater rises to the sunlit surface of the ocean. This seasonal process has fueled geoengineering initiatives to fertilize the surface ocean with deep seawater to enhance productivity and thus promote the drawdown of CO2. Coccolithophores, which inhabit many upwelling regions naturally ‘fertilized’ by deep seawater, have been investigated in the laboratory in the context of ocean acidification to determine the extent to which nutrients and CO2 impact their physiology, but few data exist in the field except from mesocosms. Here, we used the Porcupine Abyssal Plain (north Atlantic Ocean) Observatory to retrieve seawater from depths with elevated CO2 and nutrients, mimicking geoengineering approaches. We tested the effects of abrupt natural deep seawater fertilization on the physiology and biogeochemistry of two strains of Emiliania huxleyi of known physiology. None of the strains tested underwent cell divisions when incubated in waters obtained from 1,000 m, artificial upwelling using shallower waters may not be a suitable approach for promoting carbon sequestration for some locations and assemblages, and should therefore be investigated on a site-by-site basis

Telomere dysfunction accurately predicts clinical outcome in chronic lymphocytic leukaemia, even in patients with early stage disease

© 2014 John Wiley & Sons Ltd. Defining the prognosis of individual cancer sufferers remains a significant clinical challenge. Here we assessed the ability of high-resolution single telomere length analysis (STELA), combined with an experimentally derived definition of telomere dysfunction, to predict the clinical outcome of patients with chronic lymphocytic leukaemia (CLL). We defined the upper telomere length threshold at which telomere fusions occur and then used the mean of the telomere 'fusogenic' range as a prognostic tool. Patients with telomeres within the fusogenic range had a significantly shorter overall survival (P  <  0·0001; Hazard ratio [HR] = 13·2, 95% confidence interval [CI]  = 11·6-106·4) and this was preserved in early-stage disease patients (P  <  0·0001, HR=19·3, 95% CI = 17·8-802·5). Indeed, our assay allowed the accurate stratification of Binet stage A patients into those with indolent disease (91% survival at 10 years) and those with poor prognosis (13% survival at 10 years). Furthermore, patients with telomeres above the fusogenic mean showed superior prognosis regardless of their IGHV mutation status or cytogenetic risk group. In keeping with this finding, telomere dysfunction was the dominant variable in multivariate analysis. Taken together, this study provides compelling evidence for the use of high-resolution telomere length analysis coupled with a definition of telomere dysfunction in the prognostic assessment of CLL

Jelly biomass sinking speed reveals a fast carbon export mechanism

Sinking of gelatinous zooplankton biomass is an important component of the biological pump removing carbon from the upper ocean. The export efficiency, e.g., how much biomass reaches the ocean interior sequestering carbon, is poorly known because of the absence of reliable sinking speed data. We measured sinking rates of gelatinous particulate organic matter (jelly-POM) from different species of scyphozoans, ctenophores, thaliaceans, and pteropods, both in the field and in the laboratory in vertical columns filled with seawater using high-quality video. Using these data, we determined taxon-specific jelly-POM export efficiencies using equations that integrate biomass decay rate, seawater temperature, and sinking speed. Two depth scenarios in several environments were considered, with jelly-POM sinking from 200 and 600 m in temperate, tropical, and polar regions. Jelly-POM sank on average between 850 and 1500 m d−1 (salps: 800–1200 m d−1; ctenophores: 1200–1500 m d−1; scyphozoans: 1000–1100 m d−1; pyrosomes: 1300 m d−1). High latitudes represent a fast-sinking and low-remineralization corridor, regardless of species. In tropical and temperate regions, significant decomposition takes place above 1500 m unless jelly-POM sinks below the permanent thermocline. Sinking jelly-POM sequesters carbon to the deep ocean faster than anticipated, and should be incorporated into biogeochemical and modeling studies to provide more realistic quantification of export via the biological carbon pump worldwide

A mixed methods systematic review of digital interventions to support the psychological health and well-being of people living with dermatological conditions

Background: Dermatological conditions can have a substantial impact on psychological as well as physical health yet dedicated face-to-face psychological support for patients is lacking. Thus, individuals may require additional support to self-manage dermatological conditions effectively. Digital technology can contribute to long-term condition management, but knowledge of the effectiveness of digital interventions addressing psychological (cognitive, emotional, and behavioural) aspects of dermatological conditions is limited. Objectives: To identify, determine the effectiveness, and explore people’s views and experiences of digital interventions supporting the psychological health of people with dermatological conditions. Methods: A mixed methods systematic review informed by JBI methodology. The protocol was registered on PROSPERO. Eight electronic databases were searched for papers written between January 2002 and October 2021. Data screening and extraction were conducted in Covidence. The methodological quality of studies were scrutinised against JBI critical appraisal tools. Intervention characteristics were captured using the Template for Intervention Description and Replication checklist and guide. Data were synthesised using a convergent segregated approach. The results were reported in a narrative summary. Results: Twenty-three papers were identified from 4,883 references, including 15 randomised controlled trials. Nineteen interventions were condition-specific, 13 were delivered online, 16 involved an educational component, and 7 endorsed established, evidence-based therapeutic approaches. Improvements in knowledge, mood, quality of life, the therapeutic relationship, and reduced disease severity in the short to medium term, were reported, although there was substantial heterogeneity within the literature. Thirteen studies captured feedback from users, who considered various digital interventions as convenient and helpful for improving knowledge, emotion regulation, and personal control, but technical and individual barriers to use were reported. Use of established qualitative methodologies was limited and, in some cases, poorly reported. Conclusion: Some web-based digital psychological interventions seem to be acceptable to people living with mainly psoriasis and eczema. Whilst some digital interventions benefitted cognitive and emotional factors, heterogeneity and inconsistencies in the literature meant definitive statements about their effectiveness could not be drawn. Interdisciplinary and patient-centred approaches to research are needed to develop and test quality digital interventions supporting the psychological health of adults living with common and rare dermatological conditions

Dignity and respect during pregnancy and childbirth: a survey of the experience of disabled women

Background: Despite the increasing number of women with disability globally becoming pregnant, there is currently limited research about their experiences. A national survey of women’s experience of dignity and respect during pregnancy and childbirth raised concerns about the possibility of women with disability having unequal care with overall less choice and control. To address this further we conducted a study to explore the experiences of dignity and respect in childbirth of women with disability. Methods: The study involved a self-selecting, convenience sample of 37 women who had given birth in the United Kingdom and Ireland and had completed an internet-based survey. Women were identified through online networks and groups of and for disabled parents and for people with specific medical conditions. Data were collected using an online survey tool. Survey data were analysed using descriptive statistics. Thematic analysis was used for open questions. Results: Despite generally positive responses, just over half of the group of women expressed dissatisfaction with care provision. Only 19% thought that reasonable adjustments or accommodations had been made for them (7/37). When reasonable adjustments were not in place, participants’ independence and dignity were undermined. More than a quarter of women felt they were treated less favourably because of their disability (10/37, 27%). At all points in the pregnancy continuum more than a quarter of women felt their rights were either poorly or very poorly respected; however this was greatest in the postnatal period (11/35, 31%). In addition, more than half of the women (20/36, 56%) felt that maternity care providers did not have appropriate awareness of or attitudes to disability. Conclusions: Women’s experiences of dignity and respect in childbirth revealed that a significant proportion of women felt their rights were poorly respected and that they were treated less favourably because of their disability. This suggests that there is a need to look more closely at individualised care. It was also evident that more consideration is required to improve attitudes of maternity care providers to disability and services need to adapt to provide reasonable adjustments to accommodate disability, including improving continuity of carer

The Quest for Orthologs orthology benchmark service in 2022

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.European Molecular Biology Laboratory (EMBL) (core funds to D.J. and M.J.M.); National Institutes of Health [U24HG007822 to D.J. and M.J.M., 75N93019C00077 to D.S.R.]; National Human Genome Research Institute (NHGRI) [U24HG003345 to T.E.M.J, B.Y., E.A.B.]; JSPS KAKENHI [16H06279, 19H05688 to W.I.]; JST CREST [JPMJCR19S2 to W.I.]; MEXT [JPMXD1521474594 to W.I.]; Horizon 2020 [676559 to S.C.-G., 637765] (to D.M.E.), ELIXIR (to S.C.-G.); Wellcome Grant [208349/Z/17/Z to E.A.B.]; National Science Foundation (USA) [1917302 to P.D.T.]; Wellcome Trust [WT-218288, WT-212929 to D.S.R.]; Service and Infrastructure grant from the Swiss Institute of Bioinformatics, Swiss National Science Foundation [186397, 205085 to C.D.]. Funding for open access charge: Swiss National Science Foundation [205085].Peer Reviewed"Article signat per 31 autors/es: Yannis Nevers, Tamsin E M Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, the OpenEBench team the Quest for Orthologs Consortium , Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S Roos, Toni Gabaldón, David Thybert, Paul D Thomas, Yanhui Hu, David M Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J Martin, Christophe Dessimoz, Adrian Altenhoff"Postprint (published version

The effect of the COVID-19 pandemic on mental health in individuals with pre-existing mental illness

BACKGROUND: There is evidence that the COVID-19 pandemic has negatively affected mental health, but most studies have been conducted in the general population. AIMS: To identify factors associated with mental health during the COVID-19 pandemic in individuals with pre-existing mental illness. METHOD: Participants (N = 2869, 78% women, ages 18–94 years) from a UK cohort (the National Centre for Mental Health) with a history of mental illness completed a cross-sectional online survey in June to August 2020. Mental health assessments were the GAD-7 (anxiety), PHQ-9 (depression) and WHO-5 (well-being) questionnaires, and a self-report question on whether their mental health had changed during the pandemic. Regressions examined associations between mental health outcomes and hypothesised risk factors. Secondary analyses examined associations between specific mental health diagnoses and mental health. RESULTS: A total of 60% of participants reported that mental health had worsened during the pandemic. Younger age, difficulty accessing mental health services, low income, income affected by COVID-19, worry about COVID-19, reduced sleep and increased alcohol/drug use were associated with increased depression and anxiety symptoms and reduced well-being. Feeling socially supported by friends/family/services was associated with better mental health and well-being. Participants with a history of anxiety, depression, post-traumatic stress disorder or eating disorder were more likely to report that mental health had worsened during the pandemic than individuals without a history of these diagnoses. CONCLUSIONS: We identified factors associated with worse mental health during the COVID-19 pandemic in individuals with pre-existing mental illness, in addition to specific groups potentially at elevated risk of poor mental health during the pandemic

Linkage and association of haplotypes at the APOA1/C3/A4/A5 genecluster to familial combined hyperlipidemia

Combined hyperlipidemia (CHL) is a common disorder of lipidmetabolism that leads to an increased risk of cardiovascular disease. Thelipid profile of CHL is characterised by high levels of atherogeniclipoproteins and low levels of high-density-lipoprotein-cholesterol.Apolipoprotein (APO) A5 is a newly discovered gene involved in lipidmetabolism located within 30kbp of the APOA1/C3/A4 gene cluster. Previousstudies have indicated that sequence variants in this cluster areassociated with increased plasma lipid levels. To establish whethervariation at the APOA5 gene contributes to the transmission of CHL, weperformed linkage and linkage disequilibrium (LD) tests on a large cohortof families (n=128) with familial CHL (FCHL). The linkage data producedevidence for linkage of the APOA1/C3/A4/A5 genomic interval to FCHL (NPL= 1.7, P = 0.042). The LD studies substantiated these data. Twoindependent rare alleles, APOA5c.56G and APOC3c.386G of this gene clusterwere over-transmitted in FCHL (P = 0.004 and 0.007, respectively), andthis was associated with a reduced transmission of the most commonAPOA1/C3/A4/A5 haplotype (frequency 0.4425) to affected subjects (P =0.013). The APOA5c.56G allele was associated with increased plasmatriglyceride levels in FCHL probands, whereas the second, andindependent, APOC3c.386G allele was associated with increased plasmatriglyceride levels in FCHL pedigree founders. Thus, this allele (or anallele in LD) may mark a quantitative trait associated with FCHL, as wellas representing a disease susceptibility locus for the condition. Thisstudy establishes that sequence variation in the APOA1/C3/A4/A5 genecluster contributes to the transmission of FCHL in a substantialproportion of affected families, and that these sequence variants mayalso contribute to the lipid abnormalities of the metabolic syndrome,which is present in up to 40 percent of persons with cardiovasculardisease

Mre11 modulates the fidelity of fusion between short telomeres in human cells

The loss of telomere function can result in the fusion of telomeres with other telomeric loci, or non-telomeric double-stranded DNA breaks. Sequence analysis of fusion events between short dysfunctional telomeres in human cells has revealed that fusion is characterized by a distinct molecular signature consisting of extensive deletions and micro-homology at the fusion points. This signature is consistent with alternative error-prone end-joining processes. We have examined the role that Mre11 may play in the fusion of short telomeres in human cells; to do this, we have analysed telomere fusion events in cells derived from ataxia-telangiectasia-like disorder (ATLD) patients that exhibit hypomorphic mutations in MRE11. The telomere dynamics of ATLD fibroblasts were indistinguishable from wild-type fibroblasts and they were proficient in the fusion of short telomeres. However, we observed a high frequency of insertion of DNA sequences at the fusion points that created localized sequence duplications. These data indicate that Mre11 plays a role in the fusion of short dysfunctional telomeres in human cells and are consistent with the hypothesis that as part of the MRN complex it serves to stabilize the joining complex, thereby controlling the fidelity of the fusion reaction