Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

BackgroundThe recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics.DesignThe Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.ResultsTo demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks.ConclusionsThe IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics

Effects of Feeding a Novel Alfalfa Leaf Pellet Product (ProLEAF MAX) and Alfalfa Stems (ProFiber Plus) on Performance in the Feedlot and Carcass Quality of Beef Steers

Alfalfa is often included in the diets of beef animals; however, the nutrient content of alfalfa is variable depending on the region in which it is grown, climate, soil, and many other factors. The leaf portion of alfalfa has a less variable nutrient composition than the stem portion of the plant. The variability that is present in the alfalfa plant can make the development of total mixed rations of consistent nutrient content difficult. As such, the purpose of this study was to determine how the inclusion of fractionated alfalfa leaves and alfalfa stems impacts performance and carcass quality of finishing beef steers. Twenty-four steers were allocated to one of three treatments: a control group fed a typical finishing diet with alfalfa as the forage (CON; n = 8), a typical diet that replaced alfalfa with fractionated alfalfa leaf pellets and alfalfa stems (ProLEAF MAX™ + ProFiber Plus™; PLM+PFP; n = 8), or a typical diet that replaced alfalfa with alfalfa stems (PFP; n = 8) for 63 days. Steers were fed individually once daily, weighed every 14 days and ultrasound images were collected every 28 days. At the end of the feeding trial, steers were harvested at a commercial facility and carcass data was obtained. Analysis of dry matter intake demonstrated that steers receiving the PFP and CON diets consumed more feed (P \u3c 0.001) than steers consuming the PLM+PFP diet. Steers receiving the PLM+PFP diet gained less (P \u3c 0.001) weight than the steers receiving the other two dietary treatments. No differences (P \u3e 0.10) in feed efficiency or carcass characteristics were observed. Steers receiving the PFP diet had improved (P = 0.016) cost of gain ($0.93 per kg) when compared with steers receiving PLM+PFP ($1.08 per kg) diet. Overall, our findings demonstrate that the inclusion of PFP in place of alfalfa hay in a finishing diet has the potential to improve cost of gain, without negatively affecting growth, performance, or carcass characteristics of finishing feedlot steers

Structural basis for phosphorylation and lysine acetylation cross-talk in a kinase motif associated with myocardial ischemia and cardioprotection

Myocardial ischemia and cardioprotection by ischemic pre-conditioning induce signal networks aimed at survival or cell death if the ischemic period is prolonged. These pathways are mediated by protein post-translational modifications that are hypothesized to cross-talk with and regulate each other. Phosphopeptides and lysine-acetylated peptides were quantified in isolated rat hearts subjected to ischemia or ischemic pre-conditioning, with and without splitomicin inhibition of lysine deacetylation. We show lysine acetylation (acetyl-Lys)-dependent activation of AMP-activated protein kinase, AKT, and PKA kinases during ischemia. Phosphorylation and acetyl-Lys sites mapped onto tertiary structures were proximal in >50% of proteins investigated, yet they were mutually exclusive in 50 ischemic pre-conditioning- and/or ischemia-associated peptides containing the KXXS basophilic protein kinase consensus motif. Modifications in this motif were modeled in the C terminus of muscle-type creatine kinase. Acetyl-Lys increased proximal dephosphorylation by 10-fold. Structural analysis of modified muscle-type creatine kinase peptide variants by two-dimensional NMR revealed stabilization via a lysine-phosphate salt bridge, which was disrupted by acetyl-Lys resulting in backbone flexibility and increased phosphatase accessibility

A novel role for NUAK1 in promoting ovarian cancer metastasis through regulation of fibronectin production in Spheroids

Epithelial ovarian cancer (EOC) has a unique mode of metastasis, where cells shed from the primary tumour, form aggregates called spheroids to evade anoikis, spread through the peritoneal cavity, and adhere to secondary sites. We previously showed that the master kinase Liver kinase B1 (LKB1) is required for EOC spheroid viability and metastasis. We have identified novel (nua) kinase 1 (NUAK1) as a top candidate LKB1 substrate in EOC cells and spheroids using a multiplex inhibitor beads-mass spectrometry approach. We confirmed that LKB1 maintains NUAK1 phosphorylation and promotes its stabilization. We next investigated NUAK1 function in EOC cells. Ectopic NUAK1-overexpressing EOC cell lines had increased adhesion, whereas the reverse was seen in OVCAR8-NUAK1KO cells. In fact, cells with NUAK1 loss generate spheroids with reduced integrity, leading to increased cell death after long-term culture. Following transcriptome analysis, we identified reduced enrichment for cell interaction gene expression pathways in OVCAR8-NUAK1KO spheroids. In fact, the FN1 gene, encoding fibronectin, exhibited a 745-fold decreased expression in NUAK1KO spheroids. Fibronectin expression was induced during native spheroid formation, yet this was completely lost in NUAK1KO spheroids. Co-incubation with soluble fibronectin restored the compact spheroid phenotype to OVCAR8-NUAK1KO cells. In a xenograft model of intraperitoneal metastasis, NUAK1 loss extended survival and reduced fibronectin expression in tumours. Thus, we have identified a new mechanism controlling EOC metastasis, through which LKB1-NUAK1 activity promotes spheroid formation and secondary tumours via fibronectin production

Communication aid requirements of intensive care unit patients with transient speech loss

Alert and transiently nonvocal intensive care unit (ICU) patients are dependent on augmentative and alternative communication (AAC). Unfortunately, the literature demonstrates that existent AAC devices have not been widely adopted, and unaided methods are often the primary modalities used despite being insufficient, and frustrating. We present the results of a qualitative semi-structured interview study with 8 ex-ICU patients, 4 ICU patient relatives, and 6 ICU staff, exploring their AAC needs and requirements. Participants identified important AAC hardware, software, and content requirements. Salient factors impacting on AAC adoption in the ICU setting were also highlighted and included the need for staff training and bedside patient assessment. Based on the study results, we propose a series of recommendations regarding the design and implementation of future AAC tools specifically targeted at this group

Quintessential Maldacena-Maoz Cosmologies

Maldacena and Maoz have proposed a new approach to holographic cosmology based on Euclidean manifolds with disconnected boundaries. This approach appears, however, to be in conflict with the known geometric results [the Witten-Yau theorem and its extensions] on spaces with boundaries of non-negative scalar curvature. We show precisely how the Maldacena-Maoz approach evades these theorems. We also exhibit Maldacena-Maoz cosmologies with [cosmologically] more natural matter content, namely quintessence instead of Yang-Mills fields, thereby demonstrating that these cosmologies do not depend on a special choice of matter to split the Euclidean boundary. We conclude that if our Universe is fundamentally anti-de Sitter-like [with the current acceleration being only temporary], then this may force us to confront the holography of spaces with a connected bulk but a disconnected boundary.Comment: Much improved exposition, exponent in Cai-Galloway theorem fixed, axionic interpretation of scalar explained, JHEP version. 33 pages, 3 eps figure

BDNF signaling in the VTA links the drug-dependent state to drug withdrawal aversions

Drug administration to avoid unpleasant drug withdrawal symptoms has been hypothesized to be a crucial factor that leads to compulsive drug-taking behavior. However, the neural relationship between the aversive motivational state produced by drug withdrawal and the development of the drug-dependent state still remains elusive. It has been observed that chronic exposure to drugs of abuse increases brain-derived neurotrophic factor (BDNF) levels in ventral tegmental area (VTA) neurons. In particular, BDNF expression is dramatically increased during drug withdrawal, which would suggest a direct connection between the aversive state of withdrawal and BDNF-induced neuronal plasticity. Using lentivirus-mediated gene transfer to locally knock down the expression of the BDNF receptor tropomyosin-receptor-kinase type B in rats and mice, we observed that chronic opiate administration activates BDNF-related neuronal plasticity in the VTA that is necessary for both the establishment of an opiate-dependent state and aversive withdrawal motivation. Our findings highlight the importance of a bivalent, plastic mechanism that drives the negative reinforcement underlying addiction

Exercise and pregnancy in recreational and elite athletes: 2016 evidence summary from the IOC expert group meeting, Lausanne. Part 2 - The effect of exercise on the fetus, labour and birth

This is Part 2 of 5 in the series of evidence statements from the IOC expert committee on exercise and pregnancy in recreational and elite athletes. Part 1 focused on the effects of training during pregnancy and on the management of common pregnancy-related symptoms experienced by athletes. In Part 2, we focus on maternal and fetal perinatal outcomes

ViPR: an open bioinformatics database and analysis resource for virology research

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal ‘Workbenches’ for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses

Efficiency of Peptide Nucleic Acid-Directed PCR Clamping and Its Application in the Investigation of Natural Diets of the Japanese Eel Leptocephali

Polymerase chain reaction (PCR)-clamping using blocking primer and DNA-analogs, such as peptide nucleotide acid (PNA), may be used to selectively amplify target DNA for molecular diet analysis. We investigated PCR-clamping efficiency by studying PNA position and mismatch with complementary DNA by designing PNAs at five different positions on the nuclear rDNA internal transcribed spacer 1 of the Japanese eel Anguilla japonica in association with intra-specific nucleotide substitutions. All five PNAs were observed to efficiently inhibit amplification of a fully complementary DNA template. One mismatch between PNA and template DNA inhibited amplification of the template DNA, while two or more mismatches did not. DNA samples extracted from dorsal muscle and intestine of eight wild-caught leptochephalus larvae were subjected to this analysis, followed by cloning, nucleotide sequence analysis, and database homology search. Among 12 sequence types obtained from the intestine sample, six were identified as fungi. No sequence similarities were found in the database for the remaining six types, which were not related to one another. These results, in conjunction with our laboratory observations on larval feeding, suggest that eel leptocephali may not be dependent upon living plankton for their food source