Phenotypic effects of knocking out the pigmentation related genes, abcg2, bco1, and bco1-like in Atlantic salmon

The red muscle color is one of the main quality parameters of Atlantic salmon (Salmo salar). Unique to salmonids, the color comes from the accumulation of astaxanthin in the muscle, which is strictly obtained from the diet since salmon cannot synthesize it de novo. Despite increasingly higher dietary levels of astaxanthin, this quality trait has been slowly abating over the last decade. The diet plays a central role in the coloration together with the farming environment and genetic background which also affects muscle redness. To help understand the enigma, it is important to know how astaxanthin metabolism works in Atlantic salmon and what may affect it. Previous studies have identified that this trait to be of medium-high heritability (h2 = 0.3-0.5), identified two QTLs (quantitative trait loci) and potential causative genes which may explain differences in astaxanthin metabolism in intestine and liver. The candidate genes included abcg2, bco1, and bco1-like, all of which have been knocked out in individual lines using CRISPR/CAS9. In this thesis the different phenotypes have been characterized in order to prove causality. Analysis of specimens (200g) of each line revealed that some individuals of abcg2KO and bco1KO described modest increase in muscle color compared to the wild type controls, the latter line also revealed some specimens with a very pale muscle color. Knockout of bco1-like, however, had a large positive impact on muscle redness. These results are inline with the effect of the QTLs except for the pale bco1KO individuals. However, it is important to keep in mind that all these are mosaic founder fish with variable degree of knockout efficacy. Hence the KO efficiency was calculated using getPCR and specimens of each line with the highest KO percentage were chosen for further analysis. Formalin fixed mid intestine and liver samples were analyzed for lipid droplet content using fluorescence microscopy. Image analysis of liver showed that there was a statistically significant increase in lipid accumulation for all the KO lines, and that lipid droplet size was also affected. For liver, only abcg2KO fish described steatosis, with an increase in lipid load and droplet size. RNA sequencing and differential gene expression (DEG) analysis was carried out in the intestine and liver samples of the KO fish. In addition, corresponding samples from salmon genetically selected to be either red or pale was included in the analysis. The most important findings from DEG came from abcg2KO mid intestine and bco1KO liver. While the other KO fish showed no changes in gene expression. The abcg2KO mid intestine had 1726 genes showing differential expression with several regulated networks involving cholesterol and steroid biosynthetic processes. In addition, four genes involved in carotenoid metabolism were found moderately upregulated (logFold2 change 1.0-1.3; 1-apoA1, carm1, jun and rdh12). In the liver of the bco1KO, there was upregulation of lipid metabolic processes and metabolism with genes involving hypoxia were regulated both ways. In summary, phenotyping the abcg2, bco1, and bco1-like CRISPR/CAS9 knockouts showed that bco1-like affects the muscle redness, with a considerable increase in color intensity. Furthermore, all investigated genes are influencing in lipid metabolism and KO of abcg2 had the greatest effect.M-A

Decolonizing Risk Communication: Indigenous Responses to COVID-19 using Social Media

In this exploratory study, we examine how American Indian and Alaska Native (AIAN) governments and organizations are using social media to share critical health information about coronavirus disease 2019 (COVID-19) with their citizens.  Through a thematic analysis of 119 public Facebook posts made by Tribal governments and organizations, we identified three broad categories and 13 subthemes. Tribal governments and organizations created risk communication material for their respective communities that fell under (1) risk reduction, (2) meeting community members’ needs, and (3) staying connected to community and culture.  Our findings suggest that through social media AIAN communities and organizations played a crucial role in disseminating reliable culturally adapted risk communication and vital community information to Tribal citizens during the COVID-19 pandemic. Such communication included clear illustrations, posts and messages about the importance of masking up, social distancing and washing one’s hands; mandated border closures; and suggestions for maintaining a sense of connectedness with community.  By doing so they are filling a gap that ensures their communities receive the relevant information they need to mitigate and manage risks.  In order to understand how to better meet community needs, more work is needed to improve the wellbeing and visibility of AIAN people in the areas of health disparities, technology, social media, and the many impacts of COVID-19.&nbsp

Coordinating vector field equations and diagrams with a serious game in introductory physics

Mathematical reasoning with algebraic and graphical representations is essential for success in physics courses. Many problems require students to fluently move between algebraic and graphical representations. We developed a freely available serious game to challenge the representational fluency of introductory students regarding vector fields. Within the game, interactive puzzles are solved using different types of vector fields that must be configured with the correct mathematical parameters. A reward system implemented in the game prevents from using trial-and-error approaches and instead encourages the player to establish a mental connection between the graphical representation of the vector field and the (algebraic) equation before taking any action. For correct solutions, the player receives points and can unlock further levels. We report about the aim of the game from an educational perspective, describe potential learning scenarios and reflect about a first attempt to use the game in the classroom

CMAS Reactive Coatings for TBCs

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Etna International Training School of Geochemistry. Science meets Practice

Also this year, the \u201cEtna International Training School of Geochemistry. Science meets practice\u201d took place at Mt. Etna, now in its fourth edition. The school was hosted in the historical Volcanological Observatory \u201cPizzi Deneri\u201d, one of the most important sites of the INGV - Osservatorio Etneo for geochemical and geophysical monitoring. Mount Etna, located in eastern Sicily, is the largest active volcano in Europe and one of the most intensely degassing volcanoes of the world [Allard et al., 1991; Gerlach, 1991]. Mt Etna emits about 1.6 % of global H2O fluxes from arc volcanism [Aiuppa et al., 2008] and 10 % of global average volcanic emission of CO2 and SO2 [D\u2019Alessandro et al., 1997; Caltabiano et al., 2004; Aiuppa et al., 2008; Carn et al., 2017]. Furthermore, Gauthier and Le Cloarec, [1998] underscored that Mt. Etna is an important source of volcanic particles, having a mass flux of particle passively released from the volcano during non-eruptive period estimated between 7 to 23 tons/day [Martin et al., 2008; Calabrese et al., 2011]. In general, Etna is considered to be still under evolution and rather \u2018friendly\u2019, which, along with the above, makes it a favorable natural laboratory to study volcanic geochemistry. The Observatory Pizzi Deneri was sponsored by Haroun Tazieff, and it was built in 1978 by the CNR - International Institute of Volcanology under the direction of Prof. Letterio Villari. It is located at the base of the North-East crater (2,850 m a.s.l.), near the Valle del Leone and it was built on the rim of the Ellittico caldera. A picturesque building, consisting of two characteristics domes in front of the breath-taking panorama of the summit craters. Even though it is quite spartan as an accommodation facility, the dormitories, kitchen, seminar room and laboratory are well equipped. In other words, the Pizzi Deneri observatory is a unique place close to the top of the most active volcano of Europe. The observatory lies in a strategic location making it one of the most important sites for monitoring, research and dissemination of the scientific culture. After six field multidisciplinary campaigns (2010-2015) organized by a group of researchers of several institutions (INGV of Palermo, Catania, Naples, Bologna; Universities of Palermo, Florence, Mainz, Heidelberg), the idea of sharing and passing on the experience to the new generation of students has materialized, and the \u201cEtna International Training School of Geochemistry. Science meets practice\u201d was born in 2016. The four editions of the school were partially funded by INGV of Palermo and Catania, European Geoscience Union (EGU), Societ\ue0 Geochimica Italiana (SoGeI) and Associazione Naturalistica Geode. The conceptual idea of the school is to share scientific knowledge and experiences in the geochemical community, using local resources with a low-cost organization in order to allow as many students as possible access to the school. The \u201cEtna International Training School of Geochemistry. Science meets practice\u201d is addressed to senior graduate students, postdoctoral researchers, fellows, and newly appointed assistant professors, aiming to bring together the next generation of researchers active in studies concerning the geochemistry and the budget of volcanic gases. Introduce the participants with innovative direct sampling and remote sensing techniques. Furthermore, it gives young scientists an opportunity to experiment and evaluate new protocols and techniques to be used on volcanic fluid emissions covering a broad variety of methods. The teaching approach includes theoretical sessions (lectures), practical demonstrations and field applications, conducted by international recognized geochemists. We thank all the teachers who helped to make the school possible, among these: Tobias Fischer (University of New Mexico Albuquerque), Jens Fiebig (Institut f\ufcr Geowissenschaften Goethe-Universit\ue4t Frankfurt am Main), Andri Stefansson (University of Iceland, Institute of Earth Sciences), Mike Burton (University of Manchester), Nicole Bobrowski (Universit\ue4t Heidelberg Institute of Environmental Physics and Max Planck Institute for Chemistry), Alessandro Aiuppa (Universit\ue0 di Palermo), Franco Tassi (Universit\ue0 di Firenze), Walter D\u2019Alessandro (INGV of Palermo), Fatima Viveiros (University of the Azores). Direct sampling of high-to-low temperature fumaroles, plume measurement techniques (using CO2/SO2 sensors such as Multi-GAS instruments, MAX-DOAS instruments and UV SO2 cameras, alkaline traps and particle filters), measurement of diffuse soil gas fluxes of endogenous gases (CO2, Hg0, CH4 and light hydrocarbons), sampling of mud volcanoes, groundwaters and bubbling gases. Sampling sites include the active summit craters, eruptive fractures and peripheral areas. The students have shown an active participation both to the lessons and the fieldworks. Most of them describe the school as formative and useful experience for their future researches. Their enthusiasm is the real engine of this school

Etna International Training School of Geochemistry. Science meets Practice

Also this year, the “Etna International Training School of Geochemistry. Science meets practice” took place at Mt. Etna, now in its fourth edition. The school was hosted in the historical Volcanological Observatory “Pizzi Deneri”, one of the most important sites of the INGV - Osservatorio Etneo for geochemical and geophysical monitoring. Mount Etna, located in eastern Sicily, is the largest active volcano in Europe and one of the most intensely degassing volcanoes of the world [Allard et al., 1991; Gerlach, 1991]. Mt Etna emits about 1.6 % of global H2O fluxes from arc volcanism [Aiuppa et al., 2008] and 10 % of global average volcanic emission of CO2 and SO2 [D’Alessandro et al., 1997; Caltabiano et al., 2004; Aiuppa et al., 2008; Carn et al., 2017]. Furthermore, Gauthier and Le Cloarec, [1998] underscored that Mt. Etna is an important source of volcanic particles, having a mass flux of particle passively released from the volcano during non-eruptive period estimated between 7 to 23 tons/day [Martin et al., 2008; Calabrese et al., 2011]. In general, Etna is considered to be still under evolution and rather ‘friendly’, which, along with the above, makes it a favorable natural laboratory to study volcanic geochemistry. The Observatory Pizzi Deneri was sponsored by Haroun Tazieff, and it was built in 1978 by the CNR - International Institute of Volcanology under the direction of Prof. Letterio Villari. It is located at the base of the North-East crater (2,850 m a.s.l.), near the Valle del Leone and it was built on the rim of the Ellittico caldera. A picturesque building, consisting of two characteristics domes in front of the breath-taking panorama of the summit craters. Even though it is quite spartan as an accommodation facility, the dormitories, kitchen, seminar room and laboratory are well equipped. In other words, the Pizzi Deneri observatory is a unique place close to the top of the most active volcano of Europe. The observatory lies in a strategic location making it one of the most important sites for monitoring, research and dissemination of the scientific culture. After six field multidisciplinary campaigns (2010-2015) organized by a group of researchers of several institutions (INGV of Palermo, Catania, Naples, Bologna; Universities of Palermo, Florence, Mainz, Heidelberg), the idea of sharing and passing on the experience to the new generation of students has materialized, and the “Etna International Training School of Geochemistry. Science meets practice” was born in 2016. The four editions of the school were partially funded by INGV of Palermo and Catania, European Geoscience Union (EGU), Società Geochimica Italiana (SoGeI) and Associazione Naturalistica Geode. The conceptual idea of the school is to share scientific knowledge and experiences in the geochemical community, using local resources with a low-cost organization in order to allow as many students as possible access to the school. The “Etna International Training School of Geochemistry. Science meets practice” is addressed to senior graduate students, postdoctoral researchers, fellows, and newly appointed assistant professors, aiming to bring together the next generation of researchers active in studies concerning the geochemistry and the budget of volcanic gases. Introduce the participants with innovative direct sampling and remote sensing techniques. Furthermore, it gives young scientists an opportunity to experiment and evaluate new protocols and techniques to be used on volcanic fluid emissions covering a broad variety of methods. The teaching approach includes theoretical sessions (lectures), practical demonstrations and field applications, conducted by international recognized geochemists. We thank all the teachers who helped to make the school possible, among these: Tobias Fischer (University of New Mexico Albuquerque), Jens Fiebig (Institut für Geowissenschaften Goethe-Universität Frankfurt am Main), Andri Stefansson (University of Iceland, Institute of Earth Sciences), Mike Burton (University of Manchester), Nicole Bobrowski (Universität Heidelberg Institute of Environmental Physics and Max Planck Institute for Chemistry), Alessandro Aiuppa (Università di Palermo), Franco Tassi (Università di Firenze), Walter D’Alessandro (INGV of Palermo), Fatima Viveiros (University of the Azores). Direct sampling of high-to-low temperature fumaroles, plume measurement techniques (using CO2/SO2 sensors such as Multi-GAS instruments, MAX-DOAS instruments and UV SO2 cameras, alkaline traps and particle filters), measurement of diffuse soil gas fluxes of endogenous gases (CO2, Hg0, CH4 and light hydrocarbons), sampling of mud volcanoes, groundwaters and bubbling gases. Sampling sites include the active summit craters, eruptive fractures and peripheral areas. The students have shown an active participation both to the lessons and the fieldworks. Most of them describe the school as formative and useful experience for their future researches. Their enthusiasm is the real engine of this school

Functional analysis and transcriptional output of the Göttingen minipig genome

In the past decade the Göttingen minipig has gained increasing recognition as animal model in pharmaceutical and safety research because it recapitulates many aspects of human physiology and metabolism. Genome-based comparison of drug targets together with quantitative tissue expression analysis allows rational prediction of pharmacology and cross-reactivity of human drugs in animal models thereby improving drug attrition which is an important challenge in the process of drug development.; Here we present a new chromosome level based version of the Göttingen minipig genome together with a comparative transcriptional analysis of tissues with pharmaceutical relevance as basis for translational research. We relied on mapping and assembly of WGS (whole-genome-shotgun sequencing) derived reads to the reference genome of the Duroc pig and predict 19,228 human orthologous protein-coding genes. Genome-based prediction of the sequence of human drug targets enables the prediction of drug cross-reactivity based on conservation of binding sites. We further support the finding that the genome of Sus scrofa contains about ten-times less pseudogenized genes compared to other vertebrates. Among the functional human orthologs of these minipig pseudogenes we found HEPN1, a putative tumor suppressor gene. The genomes of Sus scrofa, the Tibetan boar, the African Bushpig, and the Warthog show sequence conservation of all inactivating HEPN1 mutations suggesting disruption before the evolutionary split of these pig species. We identify 133 Sus scrofa specific, conserved long non-coding RNAs (lncRNAs) in the minipig genome and show that these transcripts are highly conserved in the African pigs and the Tibetan boar suggesting functional significance. Using a new minipig specific microarray we show high conservation of gene expression signatures in 13 tissues with biomedical relevance between humans and adult minipigs. We underline this relationship for minipig and human liver where we could demonstrate similar expression levels for most phase I drug-metabolizing enzymes. Higher expression levels and metabolic activities were found for FMO1, AKR/CRs and for phase II drug metabolizing enzymes in minipig as compared to human. The variability of gene expression in equivalent human and minipig tissues is considerably higher in minipig organs, which is important for study design in case a human target belongs to this variable category in the minipig. The first analysis of gene expression in multiple tissues during development from young to adult shows that the majority of transcriptional programs are concluded four weeks after birth. This finding is in line with the advanced state of human postnatal organ development at comparative age categories and further supports the minipig as model for pediatric drug safety studies.; Genome based assessment of sequence conservation combined with gene expression data in several tissues improves the translational value of the minipig for human drug development. The genome and gene expression data presented here are important resources for researchers using the minipig as model for biomedical research or commercial breeding. Potential impact of our data for comparative genomics, translational research, and experimental medicine are discussed

The uniqueome: a mappability resource for short-tag sequencing

Summary: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the ‘uniqueome’, a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data