Dinoflagellate cysts production, excystment and transport in the upwelling off Cape Blanc (NW Africa)

To extend the understanding of dinoflagellate cysts production, excystment and vertical/lateral transport in the water column, we compared upper water cyst export production with cysts associations and concentrations in the subsurface nepheloid layer, bottom nepheloid layer and deeper water column during active upwelling off Cape Blanc (NW Africa) in August 2020. Export production was collected by two drifting trap surveys; DTS1 in an active upwelling cell for 4 days and DTS2 in an offshore drifting upwelling filament for 2 days. Subsurface, bottom nepheloid layers and deeper waters were sampled by in-situ pumps along two transects perpendicular to the shelf break. During DTS1, light limitation hampered phytoplankton production which might have influenced cyst production negatively due to up- and downward movement of water masses. Cyst export production increased at the rim of the upwelling cell. For DTS2, upwelling filament cyst export production was up to 3 times lower than that of DTS1. Echinidinium delicatum had highest relative and absolute abundances in the active upwelling, Echinidinium zonneveldiae and Bitectatodinium spongium in the upwelling filament, and Impagidinium spp. and cysts of Gymnodinium microreticulatum/nolleri at the most distal stations. Comparison of concentrations of cysts with and without cell contents showed that the majority of cysts hatched before reaching deeper waters and displayed a dormancy period of less than 6 days. About 5% of the living cysts reached deeper waters and/or the ocean floor. Living cysts were transported offshore in the upwelling filament. In case ships exchange ballast waters in the studied region, they will take up laterally transported living cysts. Upon release of the ballast waters in the port of arrival, these cysts have the potential to become “invader species” that can threaten economy and/or health. Lateral transport of cysts was observed in the bottom nepheloid layer and in deeper waters (800 - 1200m depth) with a maximal extension of about 130km off the shelf break. Therefore, sediments in the region will contain a mixture of regionally and locally produced dinoflagellate cysts. This insight contributes to the improvement of environmental reconstructions of the Cape blanc upwelling system based on downcore cyst associations

Climate change, society, and pandemic disease in Roman Italy between 200 BCE and 600 CE

Records of past societies confronted with natural climate change can illuminate social responses to environmental stress and environment-disease connections, especially when locally constrained high-temporal resolution paleoclimate reconstructions are available. We present a temperature and precipitation reconstruction for ~200 BCE to ~600 CE, from a southern Italian marine sedimentary archive-the first high-resolution (~3 years) climate record from the heartland of the Roman Empire, stretching from the so-called Roman Climate Optimum to the Late Antique Little Ice Age. We document phases of instability and cooling from ~100 CE onward but more notably after ~130 CE. Pronounced cold phases between ~160 to 180 CE, ~245 to 275 CE, and after ~530 CE associate with pandemic disease, suggesting that climate stress interacted with social and biological variables. The importance of environment-disease dynamics in past civilizations underscores the need to incorporate health in risk assessments of climate change

Study on inflammation-related genes and microRNAs, with special emphasis on the vascular repair factor HGF and miR-574-3p, in monocytes and serum of patients with T2D

Background: Recently, we reported signs of inflammation (raised IL-8, reduced miR-146a) and signs of vascular repair (raised HGF) in the serum of Ecuadorian patients with type 2 diabetes (T2

Type 2 diabetes monocyte microrna and mrna expression

There is increasing evidence that inflammatory macrophages in adipose tissue are involved in insulin resistance of type 2 diabetes (T2D). Due to a relative paucity of data on circulating monocytes in T2D, it is unclear whether the inflammatory changes of adipose tissue macrophages are reflected in these easily accessible cells. Objective To study the expression pattern of microRNAs and mRNAs related to inflammation in T2D monocytes. Design A microRNA finding study on monocytes of T2D patients and controls using array profiling was followed by a quantitative Real Time PCR (qPCR) study on monocytes of an Ecuadorian validation cohort testing the top over/under-expressed microRNAs. In addition, monocytes of the validation cohort were tested for 24 inflammation-related mRNAs and 2 microRNAs previously found deregulated in (auto)-inflammatory monocytes. Results In the finding study, 142 significantly differentially expressed microRNAs were identified, 15 having the strongest power to discriminate T2D patients from controls (sensitivity 66%, specificity 90%). However, differences in expression of these microRNAs between patients and controls were small. On the basis of >1.4 or <0.6-fold change expression 5 microRNAs were selected for further validation. One microRNA (miR-34c-5p) was validated as significantly over-expressed in T2D monocytes. In addition, we found over expression of 3 mRNAs (CD9, DHRS3 and PTPN7) in the validation cohort. These mRNAs are important for cell morphology, adhesion, shape change, and cell differentiation. Classical inflammatory genes (e.g. TNFAIP3) were only over-expressed in monocytes of patients with normal serum lipids. Remarkably, in dyslipidemia, there was a reduction in the expression of inflammatory genes (e.g. ATF3, DUSP2 and PTGS2). Conclusions The expression profile of microRNAs/mRNAs in monocytes of T2D patients indicates an altered adhesion, differentiation, and shape change potential. Monocyte inflammatory activation was only found in patients with normal serum lipids. Abnormal lipid values coincided with a reduced monocyte inflammatory state. Copyright

New physical and biological evidence of lateral transport affecting dinoflagellate cyst distribution in the benthic nepheloid layer along a land-sea transect off Figueira da Foz (Atlantic Iberian margin)

30 pages, 12 figures, 3 tables.-- This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)[Introduction] The production of resting cysts is a key dispersal and survival strategy of many dinoflagellate species. However, little is known about the role of suspended cysts in the benthic nepheloid layer (BNL) in the initiation and decline of planktonic populations. [Method] In September 2019, sampling of the dinoflagellate cyst community at different water depths in the water column and in the bottom sediments, and studies of spatio-temporal changes in physical properties (temperature, salinity, density and suspended sediment concentration), were carried out along a land-sea transect off Figueira da Foz (NW Portugal) to investigate the dinoflagellate cyst distribution and the factors (physical and biological) affecting it. A clustering analysis was used to compare the BNL and sediment cyst records with the cyst rain recorded by a sediment trap at a fixed station. Furthermore, Lagrangian particle experiments enabled simulating cyst trajectories in the BNL 5 and 10 days before sampling and assessing cross-shore, vertical and alongshore transport within the studied region. [Results] A well-developed BNL was present during the survey, which covered a change from active (14th of September) to relaxed (19th of September) upwelling conditions. Organic-walled dinoflagellate cysts were dominant in all samples, although calcareous dinoflagellate cysts consistently occurred (at low abundances). High proportions of full cysts were observed in the BNL, of which a significant portion was viable as shown by excystment experiments. Moreover, BNL cyst records collected on the 19th of September along the land-sea transect were similar to the sediment trap cyst record but greatly differed from sediment cyst records. The heterotrophic small spiny brown cysts (SBC) and cysts of the autotrophic yessotoxin-producer Protoceratium reticulatum notably increased during the survey, in the BNL and in the water column above. [Discussion] The comparison of the BNL, surface sediment and sediment trap cyst records supported that the main origin of cysts in the BNL was the recent production in the water column. The spatial coincidences in the distribution of cysts and vegetative cells of Protoceratium reticulatum also supported that full cysts in the water column were being produced in surface waters. New data evidenced the presence of a significant reservoir of viable cysts in the BNL that have the potential to seed new planktonic blooms. Furthermore, back-track particle modelling evidenced that alongshore advection was the main physical mechanism controlling cyst dynamics in the BNL during most part of the survey period, being particularly intense in coastal stations (<100 m depth). Consequently, the sediment cyst signal is a mixture of locally and regionally produced cysts. We provide multi-disciplinary data evidencing that cysts recently formed in the photic zone can be laterally advected within the studied region through the BNL, contributing to a better understanding of the role of the BNL in cyst dynamics and tracing the seed sources of the new bloomsThis work is a contribution to HABWAVE project LISBOA-01-0145-FEDER-031265, co-funded by EU ERDF funds, within the PT2020 Partnership Agreement and Compete 2020, and national funds through Fundação para a Ciência e Tecnologia, I.P.(FCT, I.P.) also to AQUIMAR project MAR2020; MAR-02.01.01-FEAMP-017. This study had the support of FCT through the strategic projects UIDB/04292/2020 and UIDP/04292/2020 awarded to MARE and through project LA/P/0069/2020 granted to the Associate Laboratory ARNET, the strategic project UIDB/04326/2020 awarded to CCMAR. Thanks are also due for the financial support to CESAM by FCT/MCTES (UIDP/50017/2020+UIDB/50017/2020+LA/P/0094/2020), Partnership Agreement and Compete 2020. IG-M was supported by a postdoctoral fellowship from Xunta de Galicia, Spain (ref. ED481B-2019-074, 2019). JM gratefully acknowledges the Fundação para a Ciência e Tecnologia and its support via strategic funding UIDB/04423/2020 and UIDP/04423/2020, and project MIWAVES (PTDC/2022.01215.PTDC)Peer reviewe

Cohesin complex-associated holoprosencephaly

Marked by incomplete division of the embryonic forebrain, holoprosencephaly is one of the most common human developmental disorders. Despite decades of phenotype-driven research, 80–90% of aneuploidy-negative holoprosencephaly individuals with a probable genetic aetiology do not have a genetic diagnosis. Here we report holoprosencephaly associated with variants in the two X-linked cohesin complex genes, STAG2 and SMC1A, with loss-of-function variants in 10 individuals and a missense variant in one. Additionally, we report four individuals with variants in the cohesin complex genes that are not X-linked, SMC3 and RAD21. Using whole mount in situ hybridization, we show that STAG2 and SMC1A are expressed in the prosencephalic neural folds during primary neurulation in the mouse, consistent with forebrain morphogenesis and holoprosencephaly pathogenesis. Finally, we found that shRNA knockdown of STAG2 and SMC1A causes aberrant expression of HPE-associated genes ZIC2, GLI2, SMAD3 and FGFR1 in human neural stem cells. These findings show the cohesin complex as an important regulator of median forebrain development and X-linked inheritance patterns in holoprosencephaly

The dinoflagellate cyst genera Achomosphaera Evitt 1963 and Spiniferites Mantell 1850 in Pliocene to modern sediments: a summary of round table discussions

Source at https://doi.org/10.1080/01916122.2018.1465739. We present a summary of two round-table discussions held during two subsequent workshops in Montreal (Canada) on 16 April 2014 and Ostend (Belgium) on 8 July 2015. Five species of the genus Achomosphaera Evitt 1963 and 33 of the genus Spiniferites Mantell 1850 emend. Sarjeant 1970 occuring in Pliocene to modern sediments are listed and briefly described along with remarks made by workshop participants. In addition, several holotypes and topotypes are reillustrated. Three species previously assigned to Spiniferites are here considered/accepted as belonging to other genera: Impagidinium inaequalis (Wall and Dale in Wall et al.1973) Londeix et al. 2009, Spiniferites? rubinus (Rossignol 1962 ex Rossignol 1964) Sarjeant 1970, and Thalassiphora balcanica Baltes ̧ 1971. This summary forms the basis for a set of papers that follows, where points raised during the workshops are explored in greater detail

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock