Addressing the land loss-fish production paradox

Saltmarsh loss is occurring at high rates in Louisiana (LA), but understanding the impacts that marsh degradation has had on historical abundance of estuarine nekton in Barataria Bay, LA is lacking. I first examined the differences between fishery independent and fishery dependent data as indices of relative abundance. Previous studies used landings data to evaluate the importance of marsh habitat (e.g. distance of marsh edge and area of intertidal marsh) to fisheries production, but for most species, landings and survey data showed differing patterns of abundance through time. These findings emphasize the importance of using survey data (not landings data) to conduct habitat-related analyses in Louisiana and elsewhere. Next, I investigated the influence of a suite of environmental and fishery related predictors on fishery independent catch-per-unit-effort (CPUE) and developed descriptive models for these relationships. The descriptive models show that abundance of estuarine nekton varied only marginally with marsh habitat related predictors. Using both parametric and non-parametric statistical analyses, I then tested previous hypotheses that explained the relationship between marsh habitat and fish abundance, in addition to exploring community level effects. Results indicated that marsh and marsh edge distance do not appear to be driving nekton abundance. However, differences were found when comparing the community structure of Barataria Bay from different time periods over the last 44 years. Finally, I developed an ecosystem model to test the influence of marsh loss on nekton abundance, while accounting for changes in salinity and trophic interactions. Results indicate that marsh edge accounted for only a small portion of historical variation in nekton abundance. While this study suggests the influence of marsh loss on fisheries may be less significant than once thought, the importance of protecting coastal saltmarshes remains vital to the health and prosperity of Louisiana’s deltaic ecosystem

End-To-End Modeling Reveals Species-Specific Effects of Large-Scale Coastal Restoration On Living Resources Facing Climate Change

Coastal erosion and wetland loss are affecting Louisiana to such an extent that the loss of land between 1932 and 2016 was close to 5,000 km2. To mitigate this decline, coastal protection and restoration projects are being planned and implemented by the State of Louisiana, United States. The Louisiana Coastal Master Plan (CMP) is an adaptive management approach that provides a suite of projects that are predicted to build or maintain land and protect coastal communities. Restoring the coast with this 50-year large-scale restoration and risk reduction plan has the potential to change the biomass and distribution of economically and ecologically important fisheries species in this region. However, not restoring the coast may have negative impacts on these species due to the loss of habitat. This research uses an ecosystem model to evaluate the effects of plan implementation versus a future without action (FWOA) on the biomass and distribution of fisheries species in the estuaries over 50 years of model simulations. By simulating effects using a spatially-explicit ecosystem model, not only can the changes in biomass in response to plan implementation be evaluated, but also the distribution of species in response to the planned restoration and risk reducation projects. Simulations are performed under two relative sea level rise (SLR) scenarios to understand the effects of climate change on project performance and subsequent fisheries species biomass and distribution. Simulation output of eight economically important fisheries species shows that the plan mostly results in increases in species biomass, but that the outcomes are species-specific and basin-specific. The SLR scenarios highly affects the amount of wetland habitat maintained after 50 years (with higher levels of wetland loss under increased SLR) and, subsequently, the biomass of species depending on that habitat. Species distribution results can be used to identify expected changes for specific species on a regional basis. By making this type of information available to resource managers, precautionary measures of ecosystem management and adaptation can be implemented

Observer-reported skate bycatch in the commercial groundfish fisheries of Alaska

We analyzed skate catch data collected by observers in the North Pacific Groundfish Observer Program (NPGOP) from 1998 through 2008 to document recent changes in the identification of skates by observers and to examine the species composition of observed skate catch in Alaska’s groundfish fisheries as well as recent trends in skate retention by commercial fishermen. Historically, almost all skate bycatch has been reported by NPGOP observers as “skate unidentified.” However, since 2004 observers have been trained to identify skates to the genus and species level. In 2008 over 95% of all skates were identified at least to the genus level, and over 50% were identified to species. The most common species of skates identified by observers in groundfish fisheries are Bathyraja parmifera (Alaska skate), Raja binoculata (big skate), and Bathyraja aleutica (Aleutian skate). Species composition of reported skate catch generally reflects recent survey-derived biomass estimates, with B. parmifera dominating the catches in the Bering Sea and, to a lesser extent, in the Aleutian Islands region, and species of the genus Raja dominating catches in the Gulf of Alaska. A relatively high percentage of the skate catch on longline vessels is still reported at the family or genus level because of difficulties in the identification of skates not brought onboard the vessel. For the larger skate species, the proportion retained for processing has increased in recent years as the market price for skate product has increased. Although observed skate catch does not give a complete account of skate bycatch in the fisheries of the region, observer data provide critical information for the appropriate management of skate populations in Alaska

Simulated climate change impacts on striped bass, blue crab and Eastern oyster in oyster sanctuary habitats of Chesapeake Bay

Oyster reefs and the species that inhabit them will likely be impacted by shifts in environmental conditions due to climate change. This study examined the potential impact of long-term shifts in water temperature and salinity as a result of climate change on the biomasses of important fisheries species within oyster sanctuary sites in the Choptank and Little Choptank river complex (CLC) in Chesapeake Bay using an Ecopath with Ecosim food web model. The model was used to evaluate changes in the oyster reef food web, with particular emphasis on impacts to striped bass (Morone saxatilis), blue crab (Callinectes sapidus), and Eastern oysters (Crassostrea virginica). Eight different climate change scenarios were used to vary water temperature and salinity within Chesapeake Bay up to the year 2100 based on projections given by previous studies. Simulations used a 4 °C increase in temperature along with an increase (+12 or +10) or decrease (−2) in salinity at annual time steps. The rate of change in species biomasses across scenarios ranged from −0.0052 to 0.0008 t/km2/month for striped bass, −0.0021 to 0.0026 t/km2/month for blue crab and −0.0018 to 0.0026 t/km2/month for oysters. Across the majority of scenarios, the biomasses of striped bass and blue crab decreased, while oyster biomass increased. These results begin to offer insight on the interaction between oyster reef restoration benefits and climate change. The modeling framework utilized by this study may be adapted to other systems to assess the effects of climate change on other coastal restoration habitats

Linking physical activity to breast cancer:text mining results and a protocol for systematically reviewing three potential mechanistic pathways

Epidemiological research suggests that physical activity is associated with a reduced risk of breast cancer, but the causal nature of this link is not clear. Investigating mechanistic pathways can provide evidence of biological plausibility and improve causal inference. This project will examine three putative pathways (sex steroid hormones, insulin signalling, and inflammation) in a series of two-stage systematic reviews. Stage 1 used Text Mining for Mechanism Prioritisation (TeMMPo) to identify and prioritise relevant biological intermediates. Stage 2 will systematically review the findings from studies of (i) physical activity and intermediates; and (ii) intermediates and breast cancer. Ovid MEDLINE, EMBASE, and SPORTDiscus will be searched using a combination of subject headings and free-text terms. Human intervention and prospective, observational studies will be eligible for inclusion. Meta-analysis will be performed where possible. Risk of bias will be assessed using the Cochrane Collaboration tool, the ROBINS-I or ROBINS-E tool, depending on study type. Strength of evidence will be assessed using the GRADE system. In addition to synthesising the mechanistic evidence that links physical activity with breast cancer risk, this project may also identify priority areas for future research and help inform the design and implementation of physical activity interventions

Linking Physical Activity to Breast Cancer via Sex Steroid Hormones, Part 2:The Effect of Sex Steroid Hormones on Breast Cancer Risk

We undertook a systematic review and appraised the evidence for an effect of circulating sex steroid hormones and sex hormone–binding globulin (SHBG) on breast cancer risk in pre- and postmenopausal women. Systematic searches identified prospective studies relevant to this review. Meta-analyses estimated breast cancer risk for women with the highest compared with the lowest level of sex hormones, and the DRMETA Stata package was used to graphically represent the shape of these associations. The ROBINS-E tool assessed risk of bias, and the GRADE system appraised the strength of evidence. In premenopausal women, there was little evidence that estrogens, progesterone, or SHBG were associated with breast cancer risk, whereas androgens showed a positive association. In postmenopausal women, higher estrogens and androgens were associated with an increase in breast cancer risk, whereas higher SHBG was inversely associated with risk. The strength of the evidence quality ranged from low to high for each hormone. Dose–response relationships between sex steroid hormone concentrations and breast cancer risk were most notable for post-menopausal women. These data support the plausibility of a role for sex steroid hormones in mediating the causal relationship between physical activity and the risk of breast cancer. See related reviews by Lynch et al., p. 11 and Swain et al., p. 1

Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism

Recurrent venous thromboembolism (VTE) occurs infrequently following a provoked event but occurs in up to 30% of individuals following an initial unprovoked event. There is limited understanding of the biological mechanisms that predispose patients to recurrent VTE

Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi.

Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder