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

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

Stable oxygen isotope data of Thoracosphaera heimii in surface sediment samples of the equatorial Atlantic and South Atlantic

To investigate the potential use of the stable isotope composition of the vegetative cysts of the photosynthetic dinoflagellate Thoracosphaera heimii for quantitative palaeotemperature reconstructions a method has been developed to purify T. heimii cysts from sediment samples. Stable oxygen and carbon isotopes have been measured on T. heimii cysts from 21 surface sediment samples from the equatorial Atlantic and South Atlantic Oceans. Calculated temperatures based on the palaeotemperature equation for inorganic calcite precipitation generally reflect mean annual temperatures of the upper water column, notably of thermocline depths. Although the present results suggest that the isotopic composition of T. heimii shells might be formed in equilibrium with the seawater in which the shells are being formed, future investigations are required to determine possible effects of metabolic and kinetic processes on the fractionation process. This pilot study therefore forms the basis for future investigations on the development of this tool and the determination of a species-specific palaeotemperature equation. The wide geographic and stratigraphic distribution of T. heimii cysts in sediments, the stable position of T. heimii within the water column and the high resistance of its cysts against calcite dissolution underline its potential for a wide usability in palaeotemperature reconstructions