Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Clayton, S., Alexander, H., Graff, J. R., Poulton, N. J., Thompson, L. R., Benway, H., Boss, E., & Martiny, A. Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology. Frontiers in Marine Science, 8, (2022): 767443, https://doi.org/10.3389/fmars.2021.767443.In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.The Bio-GO-SHIP pilot program was funded under the National Oceanographic Partnership Program as an inter-agency partnership between NOAA and NASA, with the US Integrated Ocean Observing System and NOAA's Global Ocean Monitoring and Observing program (HA, SC, JG, AM, and NP). HA was supported by a WHOI Independent Research and Development award. AM was supported by funding from NSF OCE-1848576 and 1948842 and NASA 80NSSC21K1654. JG was funded by NASA from grants 80NSSC17K0568 and NNX15AAF30G. LT was supported by award NA06OAR4320264 06111039 to the Northern Gulf Institute by NOAA's Office of Oceanic and Atmospheric Research, U.S. Department of Commerce

Risk Prediction Models for Colorectal Cancer Incorporating Common Genetic Variants: A Systematic Review.

Colorectal cancer screening reduces colorectal cancer incidence and mortality. Risk models based on phenotypic variables have relatively good discrimination in external validation and may improve efficiency of screening. Models incorporating genetic variables may perform better. In this review, we updated our previous review by searching Medline and EMBASE from the end date of that review (January 2014) to February 2019 to identify models incorporating at least one SNP and applicable to asymptomatic individuals in the general population. We identified 23 new models, giving a total of 29. Of those in which the SNP selection was on the basis of published genome-wide association studies, in external or split-sample validation the AUROC was 0.56 to 0.57 for models that included SNPs alone, 0.61 to 0.63 for SNPs in combination with other risk factors, and 0.56 to 0.70 when age was included. Calibration was only reported for four. The addition of SNPs to other risk factors increases discrimination by 0.01 to 0.06. Public health modeling studies suggest that, if determined by risk models, the range of starting ages for screening would be several years greater than using family history alone. Further validation and calibration studies are needed alongside modeling studies to assess the population-level impact of introducing genetic risk-based screening programs

Novos catalisadores a base de argilas para a produção do biodiesel.

Nas últimas décadas uma quantidade substancial de pesquisas foi realizada a fim de encontrar novas fontes de energia renovável e sustentável para substituir o diesel de petróleo. Uma fonte alternativa promissora de energia é o biodiesel, que é um combustível renovável que pode ser produzido a partir dos óleos e gorduras animais/vegetais ou mesmo ácidos graxos reciclados da indústria de alimentos. Os catalisadores heterogêneos podem melhorar os métodos de síntese eliminando os custos adicionais associados aos catalisadores homogêneos e minimizando a produção de poluentes. As argilas ativadas têm atraído atenção como catalisadores para uma variedade de reações ácidas. O comportamento físico-químico dos minerais argilosos tem sido estudado devido a sua relação como adsorvente e/ou propriedades catalíticas. Diante do exposto verifica-se a necessidade de desenvolver estudos sobre a utilização de argilas como catalisador na produção do biodiesel, tornando-se, portanto, fundamental conhecer a estabilidade e propriedades do biodiesel produzido a partir desses catalisadores. Visando avaliar a eficiência das argilas como catalisadores no processo de transesterificação deste combustível, foram estudados nesse trabalho 27 tipos de argilas, fornecidas pela empresa BENTONISA- Bentonita do Nordeste S.A, para produção do biodiesel na rota etílica e metílica, utilizando óleo de soja. Inicialmente foi realizada uma pré-seleção das argilas, utilizando as análises de umidade e pH, onde foram escolhidos 15 tipos de amostras, as mesmas foram submetidas a ensaios nos sistemas reacionais S1 e S2 e utilizando as técnicas de cor do óleo (aspecto visual) e viscosidade, optou-se pelos dois melhores catalisadores argilosos (A23 e A24) a serem testados no sistema padrão para produção do biodiesel, denominado S3. Os catalisadores A23 e A24 foram caracterizados por : fluorescência de raios-X (FRX); difração de raios-X (DRX); espectroscopia de absorção no infravermelho (IV); microscopia eletrônica de varredura (MEV); energia dispersiva de raios-X (EDS) e área específica pelo método BET. O óleo de soja e o biodiesel formado foram caracterizados através das seguintes técnicas: composição química, umidade, acidez, densidade 20ºC, glicerol total e viscosidade 40ºC, teor de éster, teor de álcool e cromatografia gasosa. Os resultados mostraram que é possível obter o biodiesel a partir de catalisadores argilosos.In the last decades a substantial amount of research has been undertaken to find new sources of renewable and sustainable energy to replace Diesel. A promising alternative energy source is biodiesel, which is a renewable fuel produced from vegetable oils and animal fats or even from recycled fat from the food industry. Heterogeneous catalysts can improve the synthesis methods eliminating additional costs associated with the homogeneous catalysts and minimizing the production of pollutants. Activated clays have attracted attention as catalysts for a variety of acid reactions. The physical and chemical behavior of clay minerals has been studied because of their property as adsorbent and / or catalysts. Therefore the need to develop studies on the use of clays as a catalyst in the production of biodiesel, making it, therefore, necessary to know the stability and properties of biodiesel produced by these catalysts. To evaluate the efficiency of clays as catalysts in the transesterification process of this fuel, 27 types of clay supplied by the company BENTONISA- Bentonite Nordeste SA, were studied in this work. The biodiesel was produced on the ethyl and methyl route, using soybean oil as raw material. The initial preselection for the clays was carried out on moisture and pH analysis, whereby 15 samples were selected. These were submitted to the testing systems in the S1 and S2, using the techniques of oil color (visual aspect) and viscosity. The two best clay catalysts (A23 and A24) were chosen to be tested in the standard system for production of biodiesel called S3. The catalysts A23 and A24 were characterized by: FRX; XRD; IR, SEM, EDS and BET. The soybean oil and biodiesel were characterized by the following techniques: chemical composition, moisture, acidity, density 20ºC, viscosity 40ºC, total glycerol, ester content, alcohol content and gas chromatography. The results showed that it is possible to get biodiesel from clay catalysts

Physiology and evolution of nitrate acquisition in Prochlorococcus

Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ~17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.Gordon and Betty Moore Foundation (Grant GBMF495)National Science Foundation (U.S.) (Grant OCE-1153588)National Science Foundation (U.S.) (Grant DBI-0424599

Three-dimensional CFD simulations with large displacement of the geometries using a connectivity-change moving mesh approach

This paper deals with three-dimensional (3D) numerical simulations involving 3D moving geometries with large displacements on unstructured meshes. Such simulations are of great value to industry, but remain very time-consuming. A robust moving mesh algorithm coupling an elasticity-like mesh deformation solution and mesh optimizations was proposed in previous works, which removes the need for global remeshing when performing large displacements. The optimizations, and in particular generalized edge/face swapping, preserve the initial quality of the mesh throughout the simulation. We propose to integrate an Arbitrary Lagrangian Eulerian compressible flow solver into this process to demonstrate its capabilities in a full CFD computation context. This solver relies on a local enforcement of the discrete geometric conservation law to preserve the order of accuracy of the time integration. The displacement of the geometries is either imposed, or driven by fluid–structure interaction (FSI). In the latter case, the six degrees of freedom approach for rigid bodies is considered. Finally, several 3D imposed-motion and FSI examples are given to validate the proposed approach, both in academic and industrial configurations

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

External Validation of Risk Prediction Models Incorporating Common Genetic Variants for Incident Colorectal Cancer Using UK Biobank.

The aim of this study was to compare and externally validate risk scores developed to predict incident colorectal cancer that include common genetic variants (SNPs), with or without established lifestyle/environmental (questionnaire-based/classical/phenotypic) risk factors. We externally validated 23 risk models from a previous systematic review in 443,888 participants ages 37 to 73 from the UK Biobank cohort who had 6-year prospective follow-up, no prior history of colorectal cancer, and data for incidence of colorectal cancer through linkage to national cancer registries. There were 2,679 (0.6%) cases of incident colorectal cancer. We assessed model discrimination using the area under the operating characteristic curve (AUC) and relative risk calibration. The AUC of models including only SNPs increased with the number of included SNPs and was similar in men and women: the model by Huyghe with 120 SNPs had the highest AUC of 0.62 [95% confidence interval (CI), 0.59-0.64] in women and 0.64 (95% CI, 0.61-0.66) in men. Adding phenotypic risk factors without age improved discrimination in men but not in women. Adding phenotypic risk factors and age increased discrimination in all cases (P < 0.05), with the best performing models including SNPs, phenotypic risk factors, and age having AUCs between 0.64 and 0.67 in women and 0.67 and 0.71 in men. Relative risk calibration varied substantially across the models. Among middle-aged people in the UK, existing polygenic risk scores discriminate moderately well between those who do and do not develop colorectal cancer over 6 years. Consideration should be given to exploring the feasibility of incorporating genetic and lifestyle/environmental information in any future stratified colorectal cancer screening program

Managing toxicities associated with immune checkpoint inhibitors: consensus recommendations from the Society for Immunotherapy of Cancer (SITC) Toxicity Management Working Group.

Cancer immunotherapy has transformed the treatment of cancer. However, increasing use of immune-based therapies, including the widely used class of agents known as immune checkpoint inhibitors, has exposed a discrete group of immune-related adverse events (irAEs). Many of these are driven by the same immunologic mechanisms responsible for the drugs\u27 therapeutic effects, namely blockade of inhibitory mechanisms that suppress the immune system and protect body tissues from an unconstrained acute or chronic immune response. Skin, gut, endocrine, lung and musculoskeletal irAEs are relatively common, whereas cardiovascular, hematologic, renal, neurologic and ophthalmologic irAEs occur much less frequently. The majority of irAEs are mild to moderate in severity; however, serious and occasionally life-threatening irAEs are reported in the literature, and treatment-related deaths occur in up to 2% of patients, varying by ICI. Immunotherapy-related irAEs typically have a delayed onset and prolonged duration compared to adverse events from chemotherapy, and effective management depends on early recognition and prompt intervention with immune suppression and/or immunomodulatory strategies. There is an urgent need for multidisciplinary guidance reflecting broad-based perspectives on how to recognize, report and manage organ-specific toxicities until evidence-based data are available to inform clinical decision-making. The Society for Immunotherapy of Cancer (SITC) established a multidisciplinary Toxicity Management Working Group, which met for a full-day workshop to develop recommendations to standardize management of irAEs. Here we present their consensus recommendations on managing toxicities associated with immune checkpoint inhibitor therapy