Characterizing Fishing Effort and Spatial Extent of Coastal Fisheries

Biodiverse coastal zones are often areas of intense fishing pressure due to the high relative density of fishing capacity in these nearshore regions. Although overcapacity is one of the central challenges to fisheries sustainability in coastal zones, accurate estimates of fishing pressure in coastal zones are limited, hampering the assessment of the direct and collateral impacts (e.g., habitat degradation, bycatch) of fishing. We compiled a comprehensive database of fishing effort metrics and the corresponding spatial limits of fisheries and used a spatial analysis program (FEET) to map fishing effort density (measured as boat-meters per km2) in the coastal zones of six ocean regions. We also considered the utility of a number of socioeconomic variables as indicators of fishing pressure at the national level; fishing density increased as a function of population size and decreased as a function of coastline length. Our mapping exercise points to intra and interregional ‘hotspots’ of coastal fishing pressure. The significant and intuitive relationships we found between fishing density and population size and coastline length may help with coarse regional characterizations of fishing pressure. However, spatially-delimited fishing effort data are needed to accurately map fishing hotspots, i.e., areas of intense fishing activity. We suggest that estimates of fishing effort, not just target catch or yield, serve as a necessary measure of fishing activity, which is a key link to evaluating sustainability and environmental impacts of coastal fisheries

Mesofluidic Devices for DNA-Programmed Combinatorial Chemistry

Hybrid combinatorial chemistry strategies that use DNA as an information-carrying medium are proving to be powerful tools for molecular discovery. In order to extend these efforts, we present a highly parallel format for DNA-programmed chemical library synthesis. The new format uses a standard microwell plate footprint and is compatible with commercially available automation technology. It can accommodate a wide variety of combinatorial synthetic schemes with up to 384 different building blocks per chemical step. We demonstrate that fluidic routing of DNA populations in the highly parallel format occurs with excellent specificity, and that chemistry on DNA arrayed into 384 well plates proceeds robustly, two requirements for the high-fidelity translation and efficient in vitro evolution of small molecules

Decreased Serologic Response in Vaccinated Military Recruits during 2011 Correspond to Genetic Drift in Concurrent Circulating Pandemic A/H1N1 Viruses

Population-based febrile respiratory illness surveillance conducted by the Department of Defense contributes to an estimate of vaccine effectiveness. Between January and March 2011, 64 cases of 2009 A/H1N1 (pH1N1), including one fatality, were confirmed in immunized recruits at Fort Jackson, South Carolina, suggesting insufficient efficacy for the pH1N1 component of the live attenuated influenza vaccine (LAIV).To test serologic protection, serum samples were collected at least 30 days post-vaccination from recruits at Fort Jackson (LAIV), Parris Island (LAIV and trivalent inactivated vaccine [TIV]) at Cape May, New Jersey (TIV) and responses measured against pre-vaccination sera. A subset of 78 LAIV and 64 TIV sera pairs from recruits who reported neither influenza vaccination in the prior year nor fever during training were tested by microneutralization (MN) and hemagglutination inhibition (HI) assays. MN results demonstrated that seroconversion in paired sera was greater in those who received TIV versus LAIV (74% and 37%). Additionally, the fold change associated with TIV vaccination was significantly different between circulating (2011) versus the vaccine strain (2009) of pH1N1 viruses (ANOVA p value = 0.0006). HI analyses revealed similar trends. Surface plasmon resonance (SPR) analysis revealed that the quantity, IgG/IgM ratios, and affinity of anti-HA antibodies were significantly greater in TIV vaccinees. Finally, sequence analysis of the HA1 gene in concurrent circulating 2011 pH1N1 isolates from Fort Jackson exhibited modest amino acid divergence from the vaccine strain.Among military recruits in 2011, serum antibody response differed by vaccine type (LAIV vs. TIV) and pH1N1 virus year (2009 vs. 2011). We hypothesize that antigen drift in circulating pH1N1 viruses contributed to reduce vaccine effectiveness at Fort Jackson. Our findings have wider implications regarding vaccine protection from circulating pH1N1 viruses in 2011-2012

Spike Protein Fusion Peptide and Feline Coronavirus Virulence

Mutations can occur erratically and accompany tropism changes, resulting in unpredictable new diseases

Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential

Despite evidence for avian influenza A virus (AIV) transmission between wild and domestic ecosystems, the roles of bird migration and poultry trade in the spread of viruses remain enigmatic. In this study, we integrate ecosystem interactions into a phylogeographic model to assess the contribution of wild and domestic hosts to AIV distribution and persistence. Analysis of globally sampled AIV datasets shows frequent two-way transmission between wild and domestic ecosystems. In general, viral flow from domestic to wild bird populations was restricted to within a geographic region. In contrast, spillover from wild to domestic populations occurred both within and between regions. Wild birds mediated long-distance dispersal at intercontinental scales whereas viral spread among poultry populations was a major driver of regional spread. Viral spread between poultry flocks frequently originated from persistent lineages circulating in regions of intensive poultry production. Our analysis of long-term surveillance data demonstrates that meaningful insights can be inferred from integrating ecosystem into phylogeographic reconstructions that may be consequential for pandemic preparedness and livestock protection.National Institutes of Health (U.S.) (NIH Centers for Excellence in Influenza Research and Surveillance (CEIRS, contract # HHSN266200700010C))National Institutes of Health (U.S.) (NIH Centers for Excellence in Influenza Research and Surveillance (CEIRS, contract # HHSN272201400008C))National Institutes of Health (U.S.) (NIH Centers for Excellence in Influenza Research and Surveillance (CEIRS, contract # HHSN272201400006C)

Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data.

Low pathogenic avian influenza A viruses (IAVs) have a natural host reservoir in wild waterbirds and the potential to spread to other host species. Here, we investigated the evolutionary, spatial and temporal dynamics of avian IAVs in Eurasian wild birds. We used whole-genome sequences collected as part of an intensive long-term Eurasian wild bird surveillance study, and combined this genetic data with temporal and spatial information to explore the virus evolutionary dynamics. Frequent reassortment and co-circulating lineages were observed for all eight genomic RNA segments over time. There was no apparent species-specific effect on the diversity of the avian IAVs. There was a spatial and temporal relationship between the Eurasian sequences and significant viral migration of avian IAVs from West Eurasia towards Central Eurasia. The observed viral migration patterns differed between segments. Furthermore, we discuss the challenges faced when analysing these surveillance and sequence data, and the caveats to be borne in mind when drawing conclusions from the apparent results of such analyses.We thank all ornithologists and other collaborators for their continuous support. We thank V. Munster, E. Skepner, O. Vuong, C. Baas, J. Guldemeester, M. Schutten, G. van der Water, D. Smith and E. Bortz for technical support and stimulating discussions. This manuscript was prepared while D.E. Wentworth was employed at the JCVI. The opinions expressed in this article are the author’s own and do not reflect the view of the Centers for Disease Control, the Department of Health and Human Services, or the United States government. This work was supported by NIAID/NIH contract HHSN266200700010C, HHSN272201400008C, HHSN272201400006C and HHSN272200900007C, a Wellcome Trust Fellowship Strategic Travel Award under contract WT089235MF, a DTRA FRCWMD Broad Agency Announcement under contract HDTRA1-09-14-FRCWMD GRANT11177182, by the EU Framework six program NewFluBird (044490) by contracts with the Dutch Ministry of Economic Affairs and a NIAID/NIH CEIRS travel grant under contract HHSN266200700010C. The Swedish sampling and analysis was supported by the Swedish Research Councils VR and FORMAS.This is the final version of the article. It first appeared from the Society for General Microbiology via http://dx.doi.org/10.1099/vir.0.00015

Work-family life courses and metabolic markers in mid-life: evidence from the British National Child Development Study

Background Previous studies have found generally better health among those who combine employment and family responsibilities; however, most research excludes men, and relies on subjective measures of health and information on work and family activities from only 1 or 2 time points in the life course. This study investigated associations between work-family life course types (LCTs) and markers of metabolic risk in a British birth cohort study. Methods Multichannel sequence analysis was used to generate work-family LCTs, combining annual information on work, partnership and parenthood between 16 and 42 years for men and women in the British National Child Development Study (NCDS, followed since their birth in 1958). Associations between work-family LCTs and metabolic risk factors in mid-life (age 44-45) were tested using multivariate linear regression in multiply imputed data. Results Life courses characterised by earlier transitions into parenthood were associated with significantly increased metabolic risk, regardless of attachment to paid work or marital stability over the life course. These associations were only partially attenuated by educational qualifications, early life circumstances and adult mediators. The positive association between weak labour markets ties and metabolic risk was weaker than might be expected from previous studies. Associations between work-family LCTs and metabolic risk factors did not differ significantly by gender. Conclusions Earlier transitions to parenthood are linked to metabolic risk in mid-life

Highly Parallel Translation of DNA Sequences into Small Molecules

A large body of in vitro evolution work establishes the utility of biopolymer libraries comprising 1010 to 1015 distinct molecules for the discovery of nanomolar-affinity ligands to proteins.[1], [2], [3], [4], [5] Small-molecule libraries of comparable complexity will likely provide nanomolar-affinity small-molecule ligands.[6], [7] Unlike biopolymers, small molecules can offer the advantages of cell permeability, low immunogenicity, metabolic stability, rapid diffusion and inexpensive mass production. It is thought that such desirable in vivo behavior is correlated with the physical properties of small molecules, specifically a limited number of hydrogen bond donors and acceptors, a defined range of hydrophobicity, and most importantly, molecular weights less than 500 Daltons.[8] Creating a collection of 1010 to 1015 small molecules that meet these criteria requires the use of hundreds to thousands of diversity elements per step in a combinatorial synthesis of three to five steps. With this goal in mind, we have reported a set of mesofluidic devices that enable DNA-programmed combinatorial chemistry in a highly parallel 384-well plate format. Here, we demonstrate that these devices can translate DNA genes encoding 384 diversity elements per coding position into corresponding small-molecule gene products. This robust and efficient procedure yields small molecule-DNA conjugates suitable for in vitro evolution experiments

Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem.

Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter, or stage. The Republic of Georgia is located at the intersection of three migratory flyways: the Central Asian flyway, the East Africa/West Asia flyway, and the Black Sea/Mediterranean flyway. For six complete study years (2010 to 2016), we collected AIV samples from various duck and gull species that breed, migrate, and overwinter in Georgia. We found a substantial subtype diversity of viruses that varied in prevalence from year to year. Low-pathogenic AIV (LPAIV) subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, and H16N3, and two highly pathogenic AIVs (HPAIVs) belonging to clade 2.3.4.4, H5N5 and H5N8, were found. Whole-genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide sequence diversity for LPAIVs among different host species. Hemagglutinin clade 2.3.4.4 H5N8 viruses, which circulated in Eurasia during 2014 and 2015, did not reassort, but analysis after their subsequent dissemination during 2016 and 2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions, with maintenance of local AIVs in Georgia, whereas other lineages showed considerable genetic interrelationships with viruses circulating in other parts of Eurasia and Africa, despite relative undersampling in the area.IMPORTANCE Waterbirds (e.g., gulls and ducks) are natural reservoirs of avian influenza viruses (AIVs) and have been shown to mediate the dispersal of AIVs at intercontinental scales during seasonal migration. The segmented genome of influenza viruses enables viral RNA from different lineages to mix or reassort when two viruses infect the same host. Such reassortant viruses have been identified in most major human influenza pandemics and several poultry outbreaks. Despite their importance, we have only recently begun to understand AIV evolution and reassortment in their natural host reservoirs. This comprehensive study illustrates AIV evolutionary dynamics within a multihost ecosystem at a stopover site where three major migratory flyways intersect. Our analysis of this ecosystem over a 6-year period provides a snapshot of how these viruses are linked to global AIV populations. Understanding the evolution of AIVs in the natural host is imperative to mitigating both the risk of incursion into domestic poultry and the potential risk to mammalian hosts, including humans