Effects of Episodic Turbulence on Diatoms: with Comments on the use of Evans Blue Stain for Live-Dead Determinations

Episodic turbulence is a short-lived, high-intensity phenomenon in marine environments produced by both anthropogenic and natural causes, such as boat propellers, strong winds, and breaking waves. Episodic turbulence has been shown to cause mortality in zooplankton, but its effects on marine phytoplankton have rarely been investigated. This study focused on two diatoms: Thalassiosira weissflogii and Skeletonema costatum. I found that exposure for 45 s to turbulence intensities above 2.5 cm2 s-3 caused 24-32% reduction in diatom abundance and increased the amount of intact dead cells to 22%. Turbulence also caused extracellular release of optically reactive DOM. At a turbulence level of 4.0 cm2 s-3, photosynthetic efficiency (Fv/Fm) decreased from 0.51 to 0.38 and 0.55 to 0.50 in T. weissflogii and S. costatum respectively. These turbulence levels are comparable to those under breaking surface waves and are much smaller than those generated by boat propellers. Despite its relatively short duration, episodic turbulence has the potential to affect phytoplankton via lethal and sublethal effects. An improved technique using the Evans Blue stain was developed to enable visual live/dead plankton cell determinations. When used in conjunction with preservation and flow cytometry, this staining method allows the study of phytoplankton mortality due to turbulence and other environmental stresses

Guidelines and Safety Practices for Improving Patient Safety

AbstractThis chapter explains why clinical practice guidelines are needed to improve patient safety and how further research into safety practices can successfully influence the guideline development process. There is a description of the structured process by which guidelines that aim to increase the likelihood of a higher score are created. Proposals are made relating to (a) the live updating of individual guideline recommendations and (b) tackling challenges related to the improvement of guidelines

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

An Open Interview and Lunch : Fuse Magazine - 16 Beaver Group

This unbound document contains the results of an unconventional conference in which at least 87 identified artists/writers participated from different locations. A series of questions and answers pertaining to collaborative work, artist’s organisations, possible models for the future, and the relationship between art/politics are presented

Gaps and complex structurally variant loci in phased genome assemblies

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation