Eukaryotic genome size databases

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs

Applications of graphics to support a testbed for autonomous space vehicle operations

Researchers describe their experience using graphics tools and utilities while building an application, AUTOPS, that uses a graphical Machintosh (TM)-like interface for the input and display of data, and animation graphics to enhance the presentation of results of autonomous space vehicle operations simulations. AUTOPS is a test bed for evaluating decisions for intelligent control systems for autonomous vehicles. Decisions made by an intelligent control system, e.g., a revised mission plan, might be displayed to the user in textual format or he can witness the effects of those decisions via out of window graphics animations. Although a textual description conveys essentials, a graphics animation conveys the replanning results in a more convincing way. Similarily, iconic and menu-driven screen interfaces provide the user with more meaningful options and displays. Presented here are experiences with the SunView and TAE Plus graphics tools used for interface design, and the Johnson Space Center Interactive Graphics Laboratory animation graphics tools used for generating out out of the window graphics

The evolution of farnesoid X, vitamin D, and pregnane X receptors: insights from the green-spotted pufferfish (Tetraodon nigriviridis) and other non-mammalian species

<p>Abstract</p> <p>Background</p> <p>The farnesoid X receptor (FXR), pregnane X receptor (PXR), and vitamin D receptor (VDR) are three closely related nuclear hormone receptors in the NR1H and 1I subfamilies that share the property of being activated by bile salts. Bile salts vary significantly in structure across vertebrate species, suggesting that receptors binding these molecules may show adaptive evolutionary changes in response. We have previously shown that FXRs from the sea lamprey (<it>Petromyzon marinus</it>) and zebrafish (<it>Danio rerio</it>) are activated by planar bile alcohols found in these two species. In this report, we characterize FXR, PXR, and VDR from the green-spotted pufferfish (<it>Tetraodon nigriviridis</it>), an actinopterygian fish that unlike the zebrafish has a bile salt profile similar to humans. We utilize homology modelling, docking, and pharmacophore studies to understand the structural features of the <it>Tetraodon </it>receptors.</p> <p>Results</p> <p><it>Tetraodon </it>FXR has a ligand selectivity profile very similar to human FXR, with strong activation by the synthetic ligand GW4064 and by the primary bile acid chenodeoxycholic acid. Homology modelling and docking studies suggest a ligand-binding pocket architecture more similar to human and rat FXRs than to lamprey or zebrafish FXRs. <it>Tetraodon </it>PXR was activated by a variety of bile acids and steroids, although not by the larger synthetic ligands that activate human PXR such as rifampicin. Homology modelling predicts a larger ligand-binding cavity than zebrafish PXR. We also demonstrate that VDRs from the pufferfish and Japanese medaka were activated by small secondary bile acids such as lithocholic acid, whereas the African clawed frog VDR was not.</p> <p>Conclusions</p> <p>Our studies provide further evidence of the relationship between both FXR, PXR, and VDR ligand selectivity and cross-species variation in bile salt profiles. Zebrafish and green-spotted pufferfish provide a clear contrast in having markedly different primary bile salt profiles (planar bile alcohols for zebrafish and sterically bent bile acids for the pufferfish) and receptor selectivity that matches these differences in endogenous ligands. Our observations to date present an integrated picture of the co-evolution of bile salt structure and changes in the binding pockets of three nuclear hormone receptors across the species studied.</p

Anchoring Hepatic Gene Expression with Development of Fibrosis and Neoplasia in a Toxicant-induced Fish Model of Liver Injury

ABSTRACT Fish have been used as laboratory models to study hepatic development and carcinogenesis but not for pathogenesis of hepatic fibrosis. In this study, a dimethylnitrosamine-induced fish model of hepatic injury was developed in Japanese medaka (Oryzias latipes) and gene expression was anchored with the development of hepatic fibrosis and neoplasia. Exposed livers exhibited mild hepatocellular degenerative changes 2 weeks&apos; postexposure. Within 6 weeks, hepatic fibrosis/cirrhosis was evident with development of neoplasia by 10 weeks. Stellate cell activation and development of fibrosis was associated with upregulation of transforming growth factor beta 1 (tgfb1), tgfb receptor 2, mothers against decapentaplegic homolog 3 (smad3a), smad3b, beta-catenin (ctnnb1), myc, matrix metalloproteinase (mmp2), mmp14a, mmp14b, tissue inhibitors of metalloproteinase (timp) 2a, timp2b, timp3, collagen type I alpha 1a (col1a1a), and col1a1b and a less pronounced increase in mmp13 and col4a1 expression. Tgfb receptor I expression was unchanged. Immunohistochemistry suggested that biliary epithelial cells and stellate cells were the main producers of TGF-b1. This study identified a group of candidate genes likely to be involved in the development of hepatic fibrosis and demonstrated that the TGF-b pathway likely plays a major role in the pathogenesis. These results support the medaka as a viable fish model of hepatic fibrosis

A 3D mixed reality visualization of network topology and activity results in better dyadic cyber team communication and cyber situational awareness

BackgroundCyber defense decision-making during cyber threat situations is based on human-to-human communication aiming to establish a shared cyber situational awareness. Previous studies suggested that communication inefficiencies were among the biggest problems facing security operation center teams. There is a need for tools that allow for more efficient communication of cyber threat information between individuals both in education and during cyber threat situations.MethodsIn the present study, we compared how the visual representation of network topology and traffic in 3D mixed reality vs. 2D affected team performance in a sample of cyber cadets (N = 22) cooperating in dyads. Performance outcomes included network topology recognition, cyber situational awareness, confidence in judgements, experienced communication demands, observed verbal communication, and forced choice decision-making. The study utilized network data from the NATO CCDCOE 2022 Locked Shields cyber defense exercise.ResultsWe found that participants using the 3D mixed reality visualization had better cyber situational awareness than participants in the 2D group. The 3D mixed reality group was generally more confident in their judgments except when performing worse than the 2D group on the topology recognition task (which favored the 2D condition). Participants in the 3D mixed reality group experienced less communication demands, and performed more verbal communication aimed at establishing a shared mental model and less communications discussing task resolution. Better communication was associated with better cyber situational awareness. There were no differences in decision-making between the groups. This could be due to cohort effects such as formal training or the modest sample size.ConclusionThis is the first study comparing the effect of 3D mixed reality and 2D visualizations of network topology on dyadic cyber team communication and cyber situational awareness. Using 3D mixed reality visualizations resulted in better cyber situational awareness and team communication. The experiment should be repeated in a larger and more diverse sample to determine its potential effect on decision-making

Filmic geographies: audio-visual, embodied-material

Although conventionally described as a ‘visual’ method, film-making is also increasingly used within research on embodiment. However, much remains to be said about the ability of filmic methods to enhance researchers’ capacity to think and research through the body. Drawing on my experience of making four research films, in this paper, I attempt to advance this agenda in three steps. First, I introduce anthropological work on the filming body to shed light on the technologically-mediated encounters that enfold around a camera and discuss how they might inform geographical thinking. Second, I describe the corporeally-mediated object ecologies that take shape within the filming setting and highlight how a camera might make objects ‘speak’. Finally, I discuss the affective dimension of screening research films to research participants and the contribution of such intense events to the articulation of collective matters of concerns. Through these three themes, I make the case for understanding knowledge production as located not merely in encounters with filmed audio-visual content, but also in the embodied-material encounters of bodies and objects around the filming and screening apparatus. I finally discuss the implications of these reflections for conceptualising the ‘body’ within embodied methods in social and cultural geography