Horizontal and Vertical Distributions of Transparent Exopolymer Particles (TEP) in the NW Mediterranean Sea Are Linked to Chlorophyll a and O2 Variability

12 pages, 6 figures, 3 tables, supplementary material http://journal.frontiersin.org/article/10.3389/fmicb.2016.02159/full#supplementary-materialTransparent Exopolymer Particles (TEP) are relevant in particle and carbon fluxes in the ocean, and have economic impact in the desalination industry affecting reverse osmosis membrane fouling. However, general models of their occurrence and dynamics are not yet possible because of the poorly known co-variations with other physical and biological variables. Here, we describe TEP distributions in the NW Mediterranean Sea during late spring 2012, along perpendicular and parallel transects to the Catalan coast. The stations in the parallel transect were sampled at the surface, while the stations in the perpendicular transect were sampled from the surface to the bathypelagic, including the bottom nepheloid layers. We also followed the short-term TEP dynamics along a 2-day cycle in offshore waters. TEP concentrations in the area ranged from 4.9 to 122.8 and averaged 31.4 ± 12.0 μg XG eq L−1. The distribution of TEP measured in transects parallel to the Catalan Coast correlated those of chlorophyll a (Chla) in May but not in June, when higher TEP-values with respect to Chla were observed. TEP horizontal variability in epipelagic waters from the coast to the open sea also correlated to that of Chla, O2 (that we interpret as a proxy of primary production) and bacterial production (BP). In contrast, the TEP vertical distributions in epipelagic waters were uncoupled from those of Chla, as TEP maxima were located above the deep chlorophyll maxima. The vertical distribution of TEP in the epipelagic zone was correlated with O2 and BP, suggesting combined phytoplankton (through primary production) and bacterial (through carbon reprocessing) TEP sources. However, no clear temporal patterns arose during the 2-day cycle. In meso- and bathypelagic waters, where phytoplanktonic sources are minor, TEP concentrations (10.1 ± 4.3 μg XG eq l−1) were half those in the epipelagic, but we observed relative TEP increments coinciding with the presence of nepheloid layers. These TEP increases were not paralleled by increases in particulate organic carbon, indicating that TEP are likely to act as aggregating agents of the mostly inorganic particles present in these bottom nepheloid layersThis work was funded by projects funded by the Spanish Ministry of Science STORM (CTM2009-09352/MAR), SUMMER (CTM2008-03309/MAR), DOREMI (CTM2012-34294), REMEI (CTM2015-70340-R), ANIMA (CTM2015-65720-R), PEGASO (CTM2012-37615), and Grup consolidat de Recerca de la Generalitat de Catalunya (2014SGR/1179)Peer Reviewe

New genetic drivers in hemorrhagic hereditary telangiectasia.

Background: Hereditary hemorrhagic telangiectasia (HHT) is a rare vascular disease inherited in an autosomal dominant manner. Disease-causing variants in endoglin (ENG) and activin A receptor type II-like 1 (ACVRL1) genes are detected in around 90% of the patients; also 2% of patients harbor pathogenic variants at SMAD4 and GDF2. Importantly, the genetic cause of 8% of patients with clinical HHT remains unknown. Here, we present new putative genetic drivers of HHT. Methods: To identify new HHT genetic drivers, we performed exome sequencing of 19 HHT patients and relatives with unknown HHT genetic etiology. We applied a multistep filtration strategy to catalog deleterious variants and prioritize gene candidates based on their known relevance in endothelial cell biology. Additionally, we performed in vitro validation of one of the identified variants. Results: We identified variants in the INHA, HIF1A, JAK2, DNM2, POSTN, ANGPTL4, FOXO1 and SMAD6 genes as putative drivers in HHT. We have identified the SMAD6 p.(Glu407Lys) variant in one of the families; this is a loss-of-function variant leading to the activation of the BMP/TGFβ signaling in endothelial cells. Conclusions: Variants in these genes should be considered for genetic testing in patients with HHT phenotype and negative for ACVRL1/ENG mutations

A Molecular Epidemiological and Genetic Diversity Study of Tuberculosis in Ibadan, Nnewi and Abuja, Nigeria

Background Nigeria has the tenth highest burden of tuberculosis (TB) among the 22 TB high-burden countries in the world. This study describes the biodiversity and epidemiology of drug-susceptible and drug-resistant TB in Ibadan, Nnewi and Abuja, using 409 DNAs extracted from culture positive TB isolates. Methodology/Principal Findings DNAs extracted from clinical isolates of Mycobacterium tuberculosis complex were studied by spoligotyping and 24 VNTR typing. The Cameroon clade (CAM) was predominant followed by the M. africanum (West African 1) and T (mainly T2) clades. By using a smooth definition of clusters, 32 likely epi-linked clusters related to the Cameroon genotype family and 15 likely epi-linked clusters related to other “modern” genotypes were detected. Eight clusters concerned M. africanum West African 1. The recent transmission rate of TB was 38%. This large study shows that the recent transmission of TB in Nigeria is high, without major regional differences, with MDR-TB clusters. Improvement in the TB control programme is imperative to address the TB control problem in Nigeria

Pharmaceutical cost and multimorbidity with type 2 diabetes mellitus using electronic health record data

© 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.[EN] Background: The objective of the study is to estimate the frequency of multimorbidity in type 2 diabetes patients classified by health statuses in a European region and to determine the impact on pharmaceutical expenditure. Methods: Cross-sectional study of the inhabitants of a southeastern European region with a population of 5,150,054, using data extracted from Electronic Health Records for 2012. 491,854 diabetic individuals were identified and selected through clinical codes, Clinical Risk Groups and diabetes treatment and/or blood glucose reagent strips. Patients with type 1 diabetes and gestational diabetes were excluded. All measurements were obtained at individual level. The prevalence of common chronic diseases and co-occurrence of diseases was established using factorial analysis. Results: The estimated prevalence of diabetes was 9.6 %, with nearly 70 % of diabetic patients suffering from more than two comorbidities. The most frequent of these was hypertension, which for the groups of patients in Clinical Risk Groups (CRG) 6 and 7 was 84.3 % and 97.1 % respectively. Regarding age, elderly patients have more probability of suffering complications than younger people. Moreover, women suffer complications more frequently than men, except for retinopathy, which is more common in males. The highest use of insulins, oral antidiabetics (OAD) and combinations was found in diabetic patients who also suffered cardiovascular disease and neoplasms. The average cost for insulin was 153€ and that of OADs 306€. Regarding total pharmaceutical cost, the greatest consumers were patients with comorbidities of respiratory illness and neoplasms, with respective average costs of 2,034.2€ and 1,886.9€. Conclusions: Diabetes is characterized by the co-occurrence of other diseases, which has implications for disease management and leads to a considerable increase in consumption of medicines for this pathology and, as such, pharmaceutical expenditure.This study was financed by a grant from the Fondo de Investigaciones de la Seguridad Social Instituto de Salud Carlos III, the Spanish Ministry of Health (FIS PI12/0037).Sancho Mestre, C.; Vivas Consuelo, DJJ.; Alvis, L.; Romero, M.; Usó Talamantes, R.; Caballer Tarazona, V. (2016). Pharmaceutical cost and multimorbidity with type 2 diabetes mellitus using electronic health record data. BMC Health Services Research. 16(394):1-8. https://doi.org/10.1186/s12913-016-1649-2S1816394Whiting DR, Guariguata L, Weil C, Shaw J. 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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

The Variant rs1867277 in FOXE1 Gene Confers Thyroid Cancer Susceptibility through the Recruitment of USF1/USF2 Transcription Factors

In order to identify genetic factors related to thyroid cancer susceptibility, we adopted a candidate gene approach. We studied tag- and putative functional SNPs in genes involved in thyroid cell differentiation and proliferation, and in genes found to be differentially expressed in thyroid carcinoma. A total of 768 SNPs in 97 genes were genotyped in a Spanish series of 615 cases and 525 controls, the former comprising the largest collection of patients with this pathology from a single population studied to date. SNPs in an LD block spanning the entire FOXE1 gene showed the strongest evidence of association with papillary thyroid carcinoma susceptibility. This association was validated in a second stage of the study that included an independent Italian series of 482 patients and 532 controls. The strongest association results were observed for rs1867277 (OR[per-allele] = 1.49; 95%CI = 1.30–1.70; P = 5.9×10−9). Functional assays of rs1867277 (NM_004473.3:c.−283G>A) within the FOXE1 5′ UTR suggested that this variant affects FOXE1 transcription. DNA-binding assays demonstrated that, exclusively, the sequence containing the A allele recruited the USF1/USF2 transcription factors, while both alleles formed a complex in which DREAM/CREB/αCREM participated. Transfection studies showed an allele-dependent transcriptional regulation of FOXE1. We propose a FOXE1 regulation model dependent on the rs1867277 genotype, indicating that this SNP is a causal variant in thyroid cancer susceptibility. Our results constitute the first functional explanation for an association identified by a GWAS and thereby elucidate a mechanism of thyroid cancer susceptibility. They also attest to the efficacy of candidate gene approaches in the GWAS era

Groundwater abstraction has caused extensive ecological damage to the Doñana World Heritage Site, Spain

Se incluye información suplementaria.Acreman et al. (2022) reviewed evidence for ecological damage to the Doñana wetlands (UNESCO World Heritage Site [WHS] and Ramsar site), Spain, associated with intensification of groundwater use, particularly for agriculture. Acreman et al. presented a multistep methodology for evidence-based risk assessment that involves identification of conservation issues, and a systematic review of scientific evidence for ecological damage and its causes. However, they involved few local scientists, used a questionable methodology in stakeholder selection and involvement, used a flawed conceptual framework, and an incomplete literature review. We propose improvements to their methodology. They overlooked or misinterpreted key evidence, and underestimated the impacts that abstraction for irrigation for red fruits (mainly strawberries), rice and other crops has had on Doñana and its biodiversity. They reported groundwater level depletion of up to 10 m in the deep aquifer, but wrongly concluded that there is no evidence for impacts on the natural marsh ecosystem, the dune ponds or the ecotone. Groundwater drawdowns are actually up to 20 m, and have inverted the formerly ascending vertical hydraulic gradient in discharge areas. Phreatic levels have been lowered from 0.5 to 2 m in some areas. Groundwater abstraction has caused multiple ecological impacts to temporary ponds and marshes in the WHS, as well as to terrestrial vegetation, and should be urgently reduced. Furthermore, Acreman et al. focused on groundwater quantity while overlooking the importance of severe impacts on quality of both surface and groundwater, intimately connected to the use of agrochemicals for irrigated crops.Part of this work (marsh hydroperiod and water depth) has been funded by eLTER Plus project (INFRAIA, Horizon 2020, Agreement No 871128) and FEDER actions [SUMHAL, LIFEWATCH-2019-09-CSIC-13, POPE 2014-2020] by the Ministry of Science, Innovation and Universities, Subtask LWE2103022: Integration into VRE in the framework of the CSIC Interdisciplinary Thematic Platforms (PTI) PTI EcoBioDiv and Teledetect. PMRG was funded by the Portuguese Foundation for Science and Technology (FCT), through the Individual Stimulus to Scientific Employment Programme with the 2020.03356.CEECIND grant, and Forest Research Centre by the FCT (UIDB/00239/2020) grant.N