Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment

Targeted next generation sequencing as a reliable diagnostic assay for the detection of somatic mutations in tumours using minimal DNA amounts from formalin fixed paraffin embedded material

Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5%concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detectio

The UCSC genome browser database: 2023 update.

The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations

Movimentação de partículas de calcário no perfil de um Cambissolo em plantio direto Movement of lime particles in the profile of an Inceptisol under no-tillage

A aplicação superficial de calcário tem-se mostrado eficiente na correção da acidez do solo no sistema plantio direto. Ao contrário do esperado, os efeitos da aplicação de calcário têm ocorrido em profundidade e em períodos de tempo relativamente curtos, apesar da sua baixa solubilidade no solo. Os objetivos deste trabalho foram: (a) detectar a presença dos minerais calcita e dolomita do calcário no solo; (b) verificar as alterações químicas relacionadas com a acidez no perfil do solo, decorrentes da aplicação de calcário na superfície, e (c) verificar a movimentação de partículas de calcário e a sua participação na correção da acidez do solo no sistema plantio direto. Foi realizado um experimento em casa de vegetação, utilizando colunas de PVC com amostras indeformadas de um Cambissolo Húmico alumínico léptico argiloso, manejado há cinco anos em sistema plantio direto. A dose de calcário comercial (PRNT 76 %) aplicada no topo da coluna correspondeu a 12 Mg ha-1. Aos sete dias da aplicação do calcário, já foi possível verificar o transporte de partículas finas (< 0,105 mm) do calcário aplicado na superfície do solo até à profundidade de 20 cm, visto que foram detectados os minerais calcita e dolomita nesta profundidade. Os efeitos nos atributos químicos do solo, decorrentes da aplicação de calcário na superfície, ocorreram em todo o perfil, sendo mais expressivos até 10 cm e aos 20 cm de profundidade, onde houve acúmulo de calcário. O transporte de calcário através da água da chuva pode ser um mecanismo importante na correção da acidez do solo em profundidade no sistema plantio direto.<br>Surface lime application has shown to be efficient for correcting soil acidity in no-tillage systems. Contrary to the expected, this effect has occurred in deeper soil layers and in a relatively short time, in spite of the low solubility of liming materials. The objectives of this research were: (a) to detect the presence of calcite and dolomite minerals originated from lime in the soil; (b) to verify chemical alterations related to soil acidity in the soil profile due to surface lime application, and (c) to verify the movement of lime particles and its effects in correcting the soil acidity in no-tillage system. A greenhouse experiment was conducted with undisturbed columns of an Inceptisol (Haplumbrept), which has been under no-tillage for five years. A commercial lime rate of 12 Mg ha-1 was applied on top of the columns. Seven days after the application of lime it was possible to verify a transfer of fine lime particles (< 0.105 mm) from the soil surface down to 20 cm soil depth as substantiated by the presence of calcite and dolomite minerals at this depth. The effects of surface lime application on chemical soil attributes were observed throughout the soil profile, but were more evident up to 10 cm and also at a depth of 20 cm, where there was accumulation of lime. The movement of lime particles with rain water may be an important mechanism of correction of soil subsurface soil acidity in no-tillage systems

On a stochastic Trotter formula with application to spontaneous localization models

We consider the relation between so called continuous localization models—i.e. non-linear stochastic Schrödinger evolutions—and the discrete GRW-model of wave function collapse. The former can be understood as scaling limit of the GRW process. The proof relies on a stochastic Trotter formula, which is of interest in its own right. Our Trotter formula also allows to complement results on existence theory of stochastic Schrödinger evolutions by Holevo and Mora/Rebolledo