Project description:ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
Project description:BackgroundIn 2009, a novel influenza virus (2009 pandemic influenza A (H1N1) virus (pH1N1)) caused significant disease in the United States. Most states, including Florida, experienced a large fall wave of disease from September through November, after which disease activity decreased substantially. We determined the prevalence of antibodies due to the pH1N1 virus in Florida after influenza activity had peaked and estimated the proportion of the population infected with pH1N1 virus during the pandemic.MethodsDuring November-December 2009, we collected leftover serum from a blood bank, a pediatric children's hospital and a pediatric outpatient clinic in Tampa Bay Florida. Serum was tested for pH1N1 virus antibodies using the hemagglutination-inhibition (HI) assay. HI titers ≥40 were considered seropositive. We adjusted seroprevalence results to account for previously established HI assay specificity and sensitivity and employed a simple statistical model to estimate the proportion of seropositivity due to pH1N1 virus infection and vaccination.ResultsDuring the study time period, the overall seroprevalence in Tampa Bay, Florida was 25%, increasing to 30% after adjusting for HI assay sensitivity and specificity. We estimated that 5.9% of the population had vaccine-induced seropositivity while 25% had seropositivity secondary to pH1N1 virus infection. The highest cumulative incidence of pH1N1 virus infection was among children aged 5-17 years (53%) and young adults aged 18-24 years (47%), while adults aged ≥50 years had the lowest cumulative incidence (11-13%) of pH1N1 virus infection.ConclusionsAfter the peak of the fall wave of the pandemic, an estimated one quarter of the Tampa Bay population had been infected with the pH1N1 virus. Consistent with epidemiologic trends observed during the pandemic, the highest burdens of disease were among school-aged children and young adults.
Project description:Why is agreeing on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression, gene-gene and gene-product interactions and evolutionary relatedness across species. To agree on a particular gene name not only makes one's own research easier, but will also be helpful to the present generation, as well as future generations, of graduate students and postdoctoral fellows who are about to enter genomics research.
Project description:BackgroundThe main objective of this study was to describe the patients who were hospitalised at Oslo University Hospital Aker during the first wave of pandemic Influenza A (H1N1) in Norway.MethodsClinical data on all patients hospitalised with influenza-like illness from July to the end of November 2009 were collected prospectively. Patients with confirmed H1N1 Influenza A were compared to patients with negative H1N1 tests.Results182 patients were hospitalised with suspected H1N1 Influenza A and 64 (35%) tested positive. Seventeen patients with positive tests (27%) were admitted to an intensive care unit and four patients died (6%). The H1N1 positive patients were younger, consisted of a higher proportion of non-ethnic Norwegians, had a higher heart rate on admission, and fewer had pre-existing hypertension, compared to the H1N1 negative patients. However, hypertension was the only medical condition that was significantly associated with a more serious outcome defined as ICU admission or death, with a univariate odds ratio of the composite endpoint in H1N1 positive and negative patients of 6.1 (95% CI 1.3-29.3) and 3.2 (95% CI 1.2-8.7), respectively. Chest radiography revealed pneumonia in 24/59 H1N1 positive patients. 63 of 64 H1N1 positive patients received oseltamivir.ConclusionsThe extra burden of hospitalisations was relatively small and we managed to admit all the patients with suspected H1N1 influenza without opening new pandemic isolation wards. The morbidity and mortality were similar to reports from comparable countries. Established hypertension was associated with more severe morbidity and patients with hypertension should be considered candidates for vaccination programs in future pandemics.
Project description:In grapevine, serine peptidases from the subtilase family were recently associated to Plasmopara viticola resistance. This family in grapevine, first characterized in 2014, was re-analyzed last year and 82 subtilase genes were identified. However, in November of 2016, the National Center for Biotechnology Information database (NCBI) made a new public release of the grapevine genome annotation based on new sequencing data and better prediction algorithms. As a consequence, some gene annotations and lengths changed. Here we present an update to the grapevine subtilase gene family sequences (SBT), namely sequence identifiers, bioinformatic predictions and recommend a nomenclature for the grapevine SBT genes. Our results show that grapevine subtilase gene family is now constituted by 87 subtilase genes encoding for 109 subtilase proteins and, despite the reported alterations, expression data on subtilases associated to grapevine resistance to P. viticola pathosystem did not suffer any alteration.
Project description:BackgroundNo information is available on the viral etiology of upper respiratory tract infections in Cameroon.MethodsWe prospectively enrolled outpatients with influenza-like illness (ILI) presenting at 14 sentinel clinics located across the country from January through December 2009. The specimens were tested using real-time and multiplex reverse-transcription polymerase chain reaction methods for the detection of 15 RNA respiratory viruses.ResultsWe detected at least 1 respiratory virus in 365 of 561 specimens (65.1%). Overall, influenza virus was the most commonly detected virus (28.2% of specimens), followed by human rhinovirus (17.8%); parainfluenza virus (PIV) types 1-4 (7.5%); enterovirus (5.9%); respiratory syncytial virus (RSV; 5.7%); human coronavirus (HCoV) OC43, 229E, NL63, and HKU1 (5.3%); and human metapneumovirus (HMPV; 5.0%). RSV (26 of 31 specimens [83.9%]), PIV (30 of 39 [76.9%]), and HRV (64 of 99 [64.6%]) were most common among children <5 years of age. Coinfections were found in 53 of 365 positive specimens (14.5%), and most (71.7%) were in children <5 years of age. While influenza virus, enterovirus, RSV, and HMPV had a defined period of circulation, the other viruses were detected throughout the year.ConclusionsWe found that respiratory viruses play an important role in the etiology of ILI in Cameroon, particularly in children <5 years of age.
Project description:The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.