Genome sequences of 10 new carnation mottle virus variants

Here, we report the genome sequences of 10 Carnation mottle virus variants. Six variants originated from a single proprietary carnation cultivar, and four were derived from four different proprietary cultivars. All variants showed nucleotide differences, but the last four did not show any variation at the amino acid level

Expression of of distinct maternal and somatic 5.8S, 18S and 28S rRNA types during zebrafish development

Animal science

A systems biology approach to understand gut microbiota and host metabolism in morbid obesity: design of the BARIA Longitudinal Cohort Study

Introduction: Prevalence of obesity and associated diseases, including type 2 diabetes mellitus, dyslipidaemia and non-alcoholic fatty liver disease (NAFLD), are increasing. Underlying mechanisms, especially in humans, are unclear. Bariatric surgery provides the unique opportunity to obtain biopsies and portal vein blood-samples. Methods: The BARIA Study aims to assess how microbiota and their metabolites affect transcription in key tissues and clinical outcome in obese subjects and how baseline anthropometric and metabolic characteristics determine weight loss and glucose homeostasis after bariatric surgery. We phenotype patients undergoing bariatric surgery (predominantly laparoscopic Roux-en-Y gastric bypass), before weight loss, with biometrics, dietary and psychological questionnaires, mixed meal test (MMT) and collect fecal-samples and intra-operative biopsies from liver, adipose tissues and jejunum. We aim to include 1500 patients. A subset (approximately 25%) will undergo intra-operative portal vein blood-sampling. Fecal-samples are analyzed with shotgun metagenomics and targeted metabolomics, fasted and postprandial plasma-samples are subjected to metabolomics, and RNA is extracted from the tissues for RNAseq-analyses. Data will be integrated using state-of-the-art neuronal networks and metabolic modeling. Patient follow-up will be ten years. Results: Preoperative MMT of 170 patients were analysed and clear differences were observed in glucose homeostasis between individuals. Repeated MMT in 10 patients showed satisfactory intra-individual reproducibility, with differences in plasma glucose, insulin and triglycerides within 20% of the mean difference. Conclusion: The BARIA study can add more understanding in how gut-microbiota affect metabolism, especially with regard to obesity, glucose metabolism and NAFLD. Identification of key factors may provide diagnostic and therapeutic leads to control the obesity-associated disease epidemic

Fibronectin is a stress responsive gene regulated by HSF1 in response to geldanamycin

Fibronectin is an extracellular matrix glycoprotein with key roles in cell adhesion and migration. Hsp90 binds directly to fibronectin and Hsp90 depletion regulates fibronectin matrix stability. Where inhibition of Hsp90 with a C-terminal inhibitor, novobiocin, reduced the fibronectin matrix, treatment with an N-terminal inhibitor, geldanamycin, increased fibronectin levels. Geldanamycin treatment induced a stress response and a strong dose and time dependent increase in fibronectin mRNA via activation of the fibronectin promoter. Three putative heat shock elements (HSEs) were identified in the fibronectin promoter. Loss of two of these HSEs reduced both basal and geldanamycin-induced promoter activity, as did inhibition of the stress-responsive transcription factor HSF1. Binding of HSF1 to one of the putative HSE was confirmed by ChIP under basal conditions, and occupancy shown to increase with geldanamycin treatment. These data support the hypothesis that fibronectin is stress-responsive and a functional HSF1 target gene. COLA42 and LAMB3 mRNA levels were also increased with geldanamycin indicating that regulation of extracellular matrix (ECM) genes by HSF1 may be a wider phenomenon. Taken together, these data have implications for our understanding of ECM dynamics in stress-related diseases in which HSF1 is activated, and where the clinical application of N-terminal Hsp90 inhibitors is intended

A multimodal cell census and atlas of the mammalian primary motor cortex

ABSTRACT We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties

Methods for culturing the american lobster (Homarus americanus)

The objectives of this research are to evaluate the usefulness of waste heat from steam electric generating stations as an inexpensive and suitable source of warmed seawater for use in aquaculture of American lobsters and to develop the techniques and systems necessary for the commercially viable culture of this species. Growth rates of larval and juvenile stage lobsters are significantly greater in effluent of elevated temperature than at ambient ocean temperature. Water quality analyses suggest that concentrations of heavy metals and chlorinated hydrocarbons are similar in each water source. 1 Culture techniques have been developed for the larval and juvenile stages and current research efforts are directed toward controlling reproduction, reducing cannibalism, refinement of artificial diets, developing methods of disease prevention, and in engineering culture systems to rear large numbers juveniles to market size. Criteria essential to the development of culture systems for the intensive rearing of lobsters and other cannibalistic crustacean species in individual holding compartments are considered. Latest cost projections indicate that lobster culture utilizing these systems may be economically feasible.Cette recherche a pour objectif l’évaluation des possibilités d’utilisation de la chaleur perdue dans des centrales électriques thermiques, comme source d’eau réchauffée convenable et économique, dans l'aquaculture du homard américain, et de développer des techniques et des systèmes permettant des élevages commercialement viables de cette espèce. Les taux de croissance des stades larvaires et juvéniles des homards sont significativement plus élevés dans les effluents à température élevée que dans une eau océanique normale. Les analyses de qualité de l'eau suggèrent que les concentrations de métaux lourds et d’hydrocarbures halogénés sont similaires dans chacune de ces sources. Des méthodes d’élevage ont été développées pour les stades larvaires et juvéniles, et l'effort de recherche actuel est dirigé vers le contrôle de la reproduction, la prévention des maladies, la limitation du cannibalisme, le perfectionnement des aliments composés, et la conception de systèmes de production à grande échelle d animaux conmercialisables. Les critères de base du développement de systèmes de culture adaptés à l’élevage intensif du homard et d’autres espèces cannibales dans des compartiments individuels sont envisagés. Les plus récentes études de coût indiquent que l'élevage du homard dans de tels systèmes pourrait être économiquement rentable

World Cup 2010 traffic simulation

Paper presented at the 26th Annual Southern African Transport Conference 9 - 12 July 2007 "The challenges of implementing policy?", CSIR International Convention Centre, Pretoria, South Africa. ABSTRACT:The purpose of the paper is to describe how the use of tools like Geospatial Information technology and a traffic simulator, can determine the most efficient way to transport ticket holders from their accommodation to the match venue. The major focus is to determine the optimum number of Park ‘n Ride facilities to provide for the spectators from the Northern Suburbs of Johannesburg. Success is defined by providing a service, which alleviates congestion on the roads but still ensures less than two hours of travel. The simulations were designed with the aid of a Geographic Information System (ArcGIS). It is preliminarily concluded that the existing City of Joburg plan is inadequate as it does not cater for the key regions of Sandton and Midrand. It is recommended that additional Park ‘n Ride facilities, namely Innesfree Park and Megawatt Park should be added and further investigation is required into the amalgamation of other underutilised facilities.This paper was transferred from the original CD ROM created for this conference. The material on the CD ROM was published using Adobe Acrobat technology. The original CD ROM was produced by Document Transformation Technologies Postal Address: PO Box 560 Irene 0062 South Africa. Tel.: +27 12 667 2074 Fax: +27 12 667 2766 E-mail: [email protected] URL: http://www.doctech.co.z

Practical system for realtime on-plant flotation froth visual parameter extraction

In plants where froth flotation is utilized to extract minerals from mined ore, the visual interpretation of the froth surface can be used to optimize the flotation process, thus yielding a more efficient extraction. We present a computer-based system that is able to extract a wide range of on-line static and dynamic visual parameters from the froth surface. The system has been installed in several refineries and performs well in both laboratory and industrial environments.Articl