The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity

Differential gene expression and coding sequence evolution play complementary roles in the adaptive diversification of cichlid sensory systems

Vitenskapelig (u)redelighet

Since the 1980’s, there has been a marked increase in disclosures of fraud in research. Cases of scientific fraud and misconduct do not only damage society’s confidence in research, they also contribute to reduce the trustworthiness in research in itself. Research ethics, however, involve much more than investigations of misconduct. How can we encourage good scientific practice? What does honest research entail? Which gray areas exist, and when is the limit to misconduct crossed? How should allegations of misconduct be handled? What are the consequences of fraud, and what sanctions should follow? In this anthology, Norwegian researches contribute to the discussion of various perspectives on scientific integrity and misconduct. The purpose of this book is not to give unequivocal or definitive answers to what scientific misconduct is, but to convey a diversity of positions and perspectives. Some of these are overlapping, others contradictory - which also reflects the field internationally. This anthology is an important resource for students and researchers, particularly in education and training. In addition, it will also provide insights for others involved in the prevention of misconduct and the promotion of good scientific practice

Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity.

BACKGROUND: Antivirals are needed to combat the COVID-19 pandemic, which is caused by SARS-CoV-2. The clinically-proven protease inhibitor Camostat mesylate inhibits SARS-CoV-2 infection by blocking the virus-activating host cell protease TMPRSS2. However, antiviral activity of Camostat mesylate metabolites and potential viral resistance have not been analyzed. Moreover, antiviral activity of Camostat mesylate in human lung tissue remains to be demonstrated. METHODS: We used recombinant TMPRSS2, reporter particles bearing the spike protein of SARS-CoV-2 or authentic SARS-CoV-2 to assess inhibition of TMPRSS2 and viral entry, respectively, by Camostat mesylate and its metabolite GBPA. FINDINGS: We show that several TMPRSS2-related proteases activate SARS-CoV-2 and that two, TMPRSS11D and TMPRSS13, are robustly expressed in the upper respiratory tract. However, entry mediated by these proteases was blocked by Camostat mesylate. The Camostat metabolite GBPA inhibited recombinant TMPRSS2 with reduced efficiency as compared to Camostat mesylate. In contrast, both inhibitors exhibited similar antiviral activity and this correlated with the rapid conversion of Camostat mesylate into GBPA in the presence of serum. Finally, Camostat mesylate and GBPA blocked SARS-CoV-2 spread in human lung tissue ex vivo and the related protease inhibitor Nafamostat mesylate exerted augmented antiviral activity. INTERPRETATION: Our results suggest that SARS-CoV-2 can use TMPRSS2 and closely related proteases for spread in the upper respiratory tract and that spread in the human lung can be blocked by Camostat mesylate and its metabolite GBPA. FUNDING: NIH, Damon Runyon Foundation, ACS, NYCT, DFG, EU, Berlin Mathematics center MATH+, BMBF, Lower Saxony, Lundbeck Foundation, Novo Nordisk Foundation

The genomic substrate for adaptive radiation in African cichlid fish

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Reference cases for verification of operation and maintenance simulation models for offshore wind farms

Due to lack of operating experience in the field of offshore wind energy and large costs associated with maintaining offshore wind farms, there is a need to develop accurate operation and maintenance models for strategic planning purposes. This paper provides an approach for verifying such simulation models and demonstrates it by describing the verification process for four models. A reference offshore wind farm is defined and simulated using these models to provide test cases and benchmark results for verification for wind farm availability and O&M costs. This paper also identifies key modelling assumptions that impact the results. The calculated availabilities for the four models show good agreement apart from cases where maintenance resources are heavily constrained. There are also larger discrepancies between the cost results. All the differences in the results can be explained by different modelling assumptions. Therefore, the models can be regarded as verified based on the presented approach