Beam profile and beam time structure monitors for the extracted beams from the GANIL cyclotrons

International audienc

Evolutionarily Successful Asian 1 Dengue Virus 2 Lineages Contain One Substitution in Envelope That Increases Sensitivity to Polyclonal Antibody Neutralization.

This is the author accepted manuscript. The final version is available from Oxford University Press via http://dx.doi.org/10.1093/infdis/jiv536The 4 dengue virus serotypes (DENV-1-4) cause the most prevalent mosquito-borne viral disease of humans worldwide. DENV-2 Asian 1 (A1) genotype viruses replaced the Asian-American (AA) genotype in Vietnam and Cambodia, after which A1 viruses containing Q or M at envelope (E) residue 160 became more prevalent than those with residue 160K in both countries (2008-2011). We investigated whether these substitutions conferred a fitness advantage by measuring neutralizing antibody titer against reporter virus particles (RVPs) representing AA, A1-160K, A1-160Q, and A1-160M, using patient sera from Vietnam and a well-characterized Nicaraguan cohort. Surprisingly, we found that A1-160Q and A1-160M RVPs were better neutralized by heterologous antisera than A1-160K. Despite this, Vietnamese patients infected with A1-160Q or A1-160M viruses had higher viremia levels than those infected with A1-160K. We thus found that independent lineages in Vietnam and Cambodia acquired a substitution in E that significantly increased polyclonal neutralization but nonetheless were successful in disseminating and infecting human hosts.This work was supported by the Bill and Melinda Gates Foundation and the Instituto Carlos Slim de la Salud (FIRST Program); the Nicaraguan Pediatric Dengue Cohort Study was supported by the Pediatric Dengue Vaccine Initiative (grant VE-1 to E. H.) and the National Institutes of Health (NIH) R01 AI099631 (to Dr Angel Balmaseda); and L. C. K. was supported by a Gates Cambridge Scholarship and the NIH Oxford-Cambridge Scholars Program

Topological Analysis of Metabolic Networks Integrating Co-Segregating Transcriptomes and Metabolomes in Type 2 Diabetic Rat Congenic Series

Background: The genetic regulation of metabolic phenotypes (i.e., metabotypes) in type 2 diabetes mellitus is caused by complex organ-specific cellular mechanisms contributing to impaired insulin secretion and insulin resistance. Methods: We used systematic metabotyping by 1H NMR spectroscopy and genome-wide gene expression in white adipose tissue to map molecular phenotypes to genomic blocks associated with obesity and insulin secretion in a series of rat congenic strains derived from spontaneously diabetic Goto-Kakizaki (GK) and normoglycemic Brown-Norway (BN) rats. We implemented a network biology strategy approach to visualise shortest paths between metabolites and genes significantly associated with each genomic block. Results: Despite strong genomic similarities (95-99%) among congenics, each strain exhibited specific patterns of gene expression and metabotypes, reflecting metabolic consequences of series of linked genetic polymorphisms in the congenic intervals. We subsequently used the congenic panel to map quantitative trait loci underlying specific metabotypes (mQTL) and genome-wide expression traits (eQTL). Variation in key metabolites like glucose, succinate, lactate or 3-hydroxybutyrate, and second messenger precursors like inositol was associated with several independent genomic intervals, indicating functional redundancy in these regions. To navigate through the complexity of these association networks we mapped candidate genes and metabolites onto metabolic pathways and implemented a shortest path strategy to highlight potential mechanistic links between metabolites and transcripts at colocalized mQTLs and eQTLs. Minimizing shortest path length drove prioritization of biological validations by gene silencing. Conclusions: These results underline the importance of network-based integration of multilevel systems genetics datasets to improve understanding of the genetic architecture of metabotype and transcriptomic regulations and to characterize novel functional roles for genes determining tissue-specific metabolism

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

<p>Abstract</p> <p>Background</p> <p>The Solanaceae family contains a number of important crop species including potato (<it>Solanum tuberosum</it>) which is grown for its underground storage organ known as a tuber. Albeit the 4^thmost important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses.</p> <p>Results</p> <p>In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to <it>Solanum lycopersicon </it>(tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, <it>Oryza sativa</it>. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two <it>Solanum </it>species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed.</p> <p>Conclusion</p> <p>Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported.</p

‘It Brings Light to What You Really Put into Your Body’: A Focus Group Study of Reactions to Messages about Nicotine Reduction in Cigarettes

Objective: In 2017, the U.S. Food and Drug Administration (FDA) announced a proposed regulation to lower nicotine in cigarettes to minimally addictive levels to help smokers quit. We sought to explore effective message strategies communicating about nicotine reduction in cigarettes across the different key audiences that the regulation is most likely to influence. Methods: We designed four types of messages: efficacy messages, risk messages, a message about alternative sources of nicotine, and a compensation message. Sixteen virtual focus groups were conducted in Atlanta and San Francisco in April-May 2020. Data were analyzed in NVivo 12.0 using a thematic analysis approach. Findings: Exclusive smokers were receptive to both efficacy messages and risk messages. Dual users were the only group that was open to resorting to alternative sources of nicotine. Former smokers were critical of these messages as promoting the new kinds of cigarettes and potentially encouraging initiation and relapse of smoking. Nonsmokers felt that efficacy messages downplayed the risks of smoking and did not scare people away from smoking. Presenting information that very low nicotine cigarettes (VLNCs) still contain harmful chemicals made smokers question continued smoking in the absence of nicotine and view VLNCs as harmful. Conclusions: Messages communicating about nicotine reduction in cigarettes might help to motivate smokers to quit and can correct the misperceptions that VLNCs are less harmful. The FDA should consider specific target audiences and use different messages that complement each other in communicating about this regulation