Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

Diatoms (Bacillariophyceae) are characterized by silicified cell walls that favor their long-term preservation in sediments, therefore widely used as bioindicators of present and past water conditions. Alongside with traditional morphological analyses, metabarcoding has become a valuable tool to study the community structures of various organisms, including diatoms. Here, we test whether the quantity of sediment sample used for DNA extraction affects the results obtained from high-throughput sequencing (metabarcoding) of the diatom rbcL region by isolating DNA from 10 g and 0.5 g (wet weight) of lake surface sediment samples. Because bioinformatics processing of metabarcoding data may affect the outcome, we also tested the consistency of the results from three different pipelines: 1) ESVs (exact sequence variants) pipeline; 2) clustering sequences at 95% sequence identity to form OTUs (operational taxonomic units; 95% OTUs); and 3) 97% OTUs pipeline. Additionally, the agreement between metabarcoding data and morphological inventories of corresponding samples were compared. Our results demonstrate highly uniform patterns between the diatom rbcL amplicons from 10 g and 0.5 g of sedimentary DNA (sedDNA) extracts (HTS 10 and HTS 0.5, respectively). Furthermore, after the careful curation of the sequencing data, metabarcoding results were highly consistent among the data sets produced by different bioinformatics pipelines. Comparing results from metabarcoding and microscopy, we identified some taxonomic mismatches: morphological analyses identified 59 diatom genera, whereas metabarcoding 49 to 54 genera. These mismatches are related to incompleteness of the sequence databases, but also to inconsistencies in diatom taxonomy in general and potential dissolution effects of diatom valves caused by high alkalinity of the investigated lake waters. Nevertheless, multivariate community analysis revealed consistent results between data sets identified by microscopy and metabarcoding – water depth and conductivity as the most significant variables in driving diatom communities in Lake Nam Co – further confirming that metabarcoding is a viable method for identifying diatom-environment relationships

pSESYNTH project: Community mobilization for a multi-disciplinary paleo database of the Global South

How to enhance paleoscientific research, collaboration and application in the Global South? The INQUA-funded multi-year pSESYNTH project envisions the first multi-disciplinary Holocene paleo database through a collaborative vision for past human-environmental systems in the Global South, and their future sustainability

The TRPV4 channel links calcium influx to DDX3X activity and viral infectivity

Ion channels are well placed to transduce environmental cues into signals used by cells to generate a wide range of responses, but little is known about their role in the regulation of RNA metabolism. Here we show that the TRPV4 cation channel binds the DEAD-box RNA helicase DDX3X and regulates its function. TRPV4-mediated Ca2+ influx releases DDX3X from the channel and drives DDX3X nuclear translocation, a process that involves calmodulin (CaM) and the CaM-dependent kinase II. Genetic depletion or pharmacological inhibition of TRPV4 diminishes DDX3X-dependent functions, including nuclear viral export and translation. Furthermore, TRPV4 mediates Ca2+ influx and nuclear accumulation of DDX3X in cells exposed to the Zika virus or the purified viral envelope protein. Consequently, targeting of TRPV4 reduces infectivity of dengue, hepatitis C and Zika viruses. Together, our results highlight the role of TRPV4 in the regulation of DDX3X-dependent control of RNA metabolism and viral infectivity.This work was supported by the Spanish Ministry of Economy and Competitiveness through grants SAF2015-69762R, BFU2016-80039-R, BFU2017-87843-R, an institutional “Maria de Maeztu” Programme for Units of Excellence in R&D (MDM-2014-0370) and FEDER funds; Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme (PIOF-GA-2009-237120) and the Generalitat de Catalunya research program (AGAUR, 2014-SGR-1628 and FI-2013FIB00251)

Biodiversity 2016. Status and Trends of Colombian Continental Biodiversity

This third volume of the annual report on biodiversity in Colombia continues the editorial line that begun in 2014. Using novel analytical and graphic proposals, these reports have the goal of communicating the contents to a broad public, making it available for discussion without sacrificing the quality of information. The challenge of communication continues to be a major part of the institutional project, and the new languages with which we are learning to communicate with society and other institutions are an experiment that we expect to be increasingly gratifying. The report for 2017 is already under construction and it counts on new digital technologies so the power of a colombian vital connection may be entirely expressed. The included content evidences that we are still far away from having a systematic follow-up about most of the topics related to the management of biodiversity and ecosystem services, which is the only way to evaluate the effectiveness of policies and investments made by society. In fact, a limitation that is recognized is that of identifying positive or negative changes that affect different levels of organization of life on this planet; therefore, our global navigation route of the Aichi targets is still to be verified. An additional purpose of this process includes the invitation of all Colombians to contribute in constructing and maintaining basic monitoring indicators for management since it is impossible to identify long-term trends of flora and fauna in the country without the support of institutions, researchers, and citizens. This challenge is immense in a megadiverse country such as Colombia. For this reason, the report will continue to open its pages to experts, and even indigenous peoples or local communities, for them to present their perspectives about environmental change and its effects on biodiversity in a systematic and documented manner. This has the objective of stimulating the commitment of everyone in the management of biodiversity and ecosystem services. The only way of overcoming the risk of extinction is through the active process of social learning in which all sectors assume a part of the complex responsibility in protecting the forms of life of the country, a roughly counted tenth of all creatures on Earth. I thank all the people that contributed in this Report, those who have supported us in the phases of production, and all readers and users, who are the ultimate judges of its utility.Bogotá, D. C

Biodiversidad 2016. Estado y Tendencias de la Biodiversidad Continental de Colombia

Esta tercera entrega del reporte anual de la biodiversidad en Colombia profundiza en la línea editorial iniciada el año 2014 mediante nuevas propuestas analíticas y gráficas, con la intención de garantizar que la información llegue a todos los públicos y pueda ser discutida de manera amena sin sacrificio de calidad. La apuesta comunicativa sigue siendo central en el proyecto institucional y los nuevos lenguajes con los que estamos aprendiendo a conversar con la sociedad y las instituciones son un experimento que esperamos sea cada vez más satisfactorio: ya estamos construyendo la versión 2017 con el apoyo de las nuevas tecnologías digitales de manera que la potencia de la conexión vital colombiana se exprese en toda su capacidad. Por los contenidos es evidente que aún distamos mucho de tener una capacidad de seguimiento sistemático para la mayoría de temas relativos a la gestión de la biodiversidad y los servicios ecosistémicos, la única manera de evaluar si las medidas de política y las inversiones que realiza la sociedad están teniendo los efectos deseados. De hecho, parte de las limitaciones reconocidas por robustamente los cambios positivos o negativos que afectan los diferentes niveles de organización de la vida planetaria, por lo cual las mismas metas de Aichi, nuestra carta de navegación global, están pendientes de verificación. Un propósito adicional de este proceso es la invitación a todos los colombianos para contribuir con la construcción y alimentación de los indicadores básicos de seguimiento a la gestión, ya que es imposible identificar las tendencias de largo plazo en que están inmersas la flora y fauna colombianas sin el apoyo de las instituciones, los investigadores y los ciudadanos: en el país de la megadiversidad, el reto es inmenso. Por este motivo, este reporte irá abriendo sus páginas a expertos, incluso indígenas o de comunidades locales, para que presenten de manera sistemática y documentada sus perspectivas del cambio ambiental y sus efectos en la biodiversidad, con el ánimo de promover el compromiso de todos en su gestión. La única manera de superar el riesgo de extinción es mediante un activo proceso de aprendizajes sociales que haga que todos los sectores asuman una parte de la compleja responsabilidad que significa proteger todas las formas de vida del país, una décima parte mal contada de las planetarias. Agradezco a las decenas de personas que contribuyeron con este reporte, a quienes nos han apoyado en todas las etapas de producción y a sus lectores y usuarios, quienes son en último término los jueces de su utilidad.Bogotá, D. C