Soft-Shell Clam (Mya Arenaria) Distribution & Abundance at Selected Sites in the Great Bay Estuary

Previous surveys (1996 to 2002) provided distribution and abundance data for soft-shell clam (Mya arenaria) populations in ten areas of the Great Bay and Piscataqua River estuaries identified as potentially good clam habitat. The present study was designed to complete the overall survey by sampling six remaining areas: Weeks Point, Brackett\u27s Point, Squamscott River mouth, Moody Point, Herods Cove, and Upper Little Bay (western shore). The objectives of the present project were to: (1) visually inspect the six study areas for the general distribution of sediment types and soft-shell clams, (2) quantitatively sample the six areas to determine densities of soft-shell clams, (3) produce GIS maps based on the survey data, and (4) assess clam distributions considering data from the present study and previous research. At each of the six sampling areas, the approximate boundary of potential clam habitat (=intertidal soft sediments) was determined by visual inspection at low tide. Notes were made on changes in major sediment types, the presence of clam siphon holes, and empty clam shells. At each site, nine to fourteen 0.125 m2 quadrats were haphazardly tossed onto the sediment surface, excavated to at least 20 cm depth using clam rakes, and all excavated sediments washed through a 5 mm mesh sieve. All clams retained on the sieve were measured (shell length to nearest mm with calipers), counted, and returned to the general area. A sample of the upper 5 cm of sediment was collected from each quadrat and stored at Jackson Estuarine Laboratory. Quadrat locations were geo-referenced using DGPS.The general environmental conditions in all six areas appeared suitable as soft-shell clam habitat. However, very few live clams were collected and very few empty shells were observed. From a total of 65 excavated quadrats, only 8 live clams were collected with mean densities ranging from 0.0 to 3.1/m2 at the six sites. It was concluded that none of the six areas were productive clam flats at the time of sampling, and they probably had not been in the recent past. Previous research and the present study indicate that many of the expansive intertidal flats in the Great Bay/Piscataqua River system have not been productive clam habitat for decades, probably since at least the 1940s in some areas. However, moderate to high densities of clams have been reported in some areas, particularly in sandy sediments. Previous research also showed high densities of early post-set clams in some areas, suggesting that spat mortality (probably predation effects) may be an important cause of low densities of larger clams in these areas. Future research should focus on sandy sediments and mixed soft sediments with cobble to better characterize the distribution and abundance of clams in the Great Bay/Piscataqua River system. Future research also should assess the role of predation on newly set spat in controlling clam populations

Effects of a Large Fishing Closure on Benthic Communitites in the Western Gulf of Maine: Recovery from the Effects of Gillnets and Otter Trawls

The recovery of benthic communities inside the western Gulf of Maine fishing closure area was evaluated by comparing invertebrate assemblages at sites inside and outside of the closure four to six years after the closure was established. The major restriction imposed by the closure was a year-round prohibition of bottom gillnets and otter trawls. A total of 163 seafloor sites (~half inside and half outside the closure) within a 515-km2 study area were sampled with some combination of Shipek grab, Wildco box corer, or underwater video. Bottom types ranged from mud (silt and clay) to boulders, and the effects of the closure on univariate measures (total density, biomass, taxonomic richness) of benthos varied widely among sediment types. For sites with predominantly mud sediments, there were mixed effects on inside and outside infauna and no effect on epifauna. For sites with mainly sand sediments, there were higher density, biomass, and taxonomic richness for infauna inside the closure, but no significant effects on epifauna. For sites dominated by gravel (which included boulders in some areas), there were no effects on infauna but strong effects on epifaunal density and taxonomic richness. For fishing gear, the data indicated that infauna recovered in sand from the impacts of otter trawls operated inside the closure but that they did not recover in mud, and that epifauna recovered on gravel bottoms from the impact of gillnets used inside the closure. The magnitudes of impact and recovery, however, cannot be inferred directly from our data because of a confounding factor of different fishing intensities outside the closure for a direct comparison of preclosure and postclosure data. The overall negative impact of trawls is likely underestimated by our data, whereas the negative impact of gillnets is likely overestimated

Breaking it Down: Defining the Framework & Evaluating the Impact of a Peer Education Program

Evaluation in the field of youth development continues to evolve.  Youth development programs vary significantly in their focus, setting and outcomes.  Community-based programs seeking to create or strengthen their evaluation methods and tools may have difficulty identifying what to measure and how to capture anticipated outcomes.  This article focuses on a youth development program combining service learning and peer education, serving urban adolescents ages 14 to 19.  The purposes of this study are: 1) to illustrate a strategy used to clarify and align core activities, anticipated outcomes and evaluation tools, and 2) to provide an overview of the updated data collection instruments created by the program

Assessment of the dining environment on and near the campuses of fifteen post-secondary institutions

Objective: The present study evaluated the restaurant and dining venues on and near post-secondary campuses varying in institution size. Design: The Nutrition Environment Measures Survey for Restaurants (NEMS-R) was modified to evaluate restaurants as fast food, sit down and fast casual; and campus dining venues as dining halls, student unions and snack bar/cafe ́s. ANOVA with post hoc Tukey’s B and T tests were used to distinguish differences between dining venues and associated institutions by size. Setting: The study was conducted at fifteen US post-secondary institutions, 2009–2011. Subjects: Data presented are from a sample of 175 restaurants and sixty-eight on-campus dining venues. Results: There were minimal differences in dining halls by institution size, although medium-sized institutions as compared with small-sized institutions offered significantly more healthful side dish/salad bar items. Dining halls scored significantly higher than student unions or snack bar/cafe ́s on healthful entre ́es, side dish/salad bar and beverages offerings, but they also had the most barriers to healthful dietary habits (i.e. all-you-can-eat). No differences were found by restaurant type for NEMS-R scores for total restaurant dining environment or healthful entre ́es and barriers. Snack bars had more healthful side dishes (P 5 0?002) and fast-food restaurants had the highest level of facilitators (i.e. nutrition information; P 5 0?002). Conclusions: Based on this evaluation in fifteen institutions, the full campus dining environment provides limited support for healthy eating and obesity prevention. The quality of campus dining environments can be improved via healthful offerings, providing nutrition information and other supports to facilitate healthy eating and prevent unwanted weight gain

Effect of dietary protein restriction on nutritional status in the Modification of Diet in Renal Disease Study

Effect of dietary protein restriction on nutritional status in the Modification of Diet in Renal Disease Study. The safety of dietary protein and phosphorous restriction was evaluated in the Modification of Diet in Renal Disease (MDRD) Study. In Study A, 585 patients with a glomerular filtration rate (GFR) of 25 to 55 ml/min/1.73m2 were randomly assigned to a usual-protein diet (1.3 g/kg/day) or a low-protein diet (0.58 g/kg/day). In Study B, 255 patients with a GFR of 13 to 24 ml/min/1.73m2 were randomly assigned to the low-protein diet or a very-low-protein diet (0.28 g/kg/day), supplemented with a ketoacid-amino acid mixture (0.28 g/kg/day). The low-protein and very-low-protein diets were also low in phosphorus. Mean duration of follow-up was 2.2 years in both studies. Protein and energy intakes were lower in the low-protein and very-low-protein diet groups than in the usual-protein group. Two patients in Study B reached a “stop point” for malnutrition. There was no difference between randomized groups in the rates of death, first hospitalizations, or other “stop points” in either study. Mean values for various indices of nutritional status remained within the normal range during follow-up in each diet group. However, there were small but significant changes from baseline in some nutritional indices, and differences between the randomized groups in some of these changes. In the low-protein and very-low-protein diet groups, serum albumin rose, while serum transferrin, body wt, percent body fat, arm muscle area and urine creatinine excretion declined. Combining patients in both diet groups in each study, a lower achieved protein intake (from food and supplement) was not correlated with a higher rate of death, hospitalization or stop points, or with a progressive decline in any of the indices of nutritional status after controlling for baseline nutritional status and follow-up energy intake. These analyses suggest that the low-protein and very-low-protein diets used in the MDRD Study are safe for periods of two to three years. Nonetheless, both protein and energy intake declined and there were small but significant declines in various indices of nutritional status. These declines are of concern because of the adverse effect of protein calorie malnutrition in patients with end-stage renal disease. Physicians who prescribe low-protein diets must carefully monitor patients' protein and energy intake and nutritional status

Human Impacts on Forest Biodiversity in Protected Walnut-Fruit Forests in Kyrgyzstan

We used a spatially explicit model of forest dynamics, supported by empirical field data and socioeconomic data, to examine the impacts of human disturbances on a protected forest landscape in Kyrgyzstan. Local use of 27 fruit and nut species was recorded and modeled. Results indicated that in the presence of fuelwood cutting with or without grazing, species of high socioeconomic impor- tance such as Juglans regia, Malus spp., and Armeniaca vulgaris were largely eliminated from the landscape after 50–150 yr. In the absence of disturbance or in the presence of grazing only, decline of these species occurred at a much lower rate, owing to competi- tive interactions between tree species. This suggests that the current intensity of fuelwood harvesting is not sustainable. Conversely, cur- rent grazing intensities were found to have relatively little impact on forest structure and composition, and could potentially play a positive role in supporting regeneration of tree species. These results indicate that both positive and negative impacts on biodiversity can arise from human populations living within a protected area. Potentially, these could be reconciled through the development of participatory approaches to conservation management within this reserve, to ensure the maintenance of its high conservation value while meeting human needs

Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor

<p>Abstract</p> <p>Background</p> <p>In candidate-gene association studies of single nucleotide polymorphisms (SNPs), multilocus analyses are frequently of high dimensionality when considering haplotypes or haplotype pairs (diplotypes) and differing modes of expression. Often, while candidate genes are selected based on their biological involvement in a given pathway, little is known about the functionality of SNPs to guide association studies. Investigators face the challenge of exploring multiple SNP models to elucidate which variants, independently or in combination, might be associated with a disease of interest. A data mining module, hapConstructor (freely-available in Genie software) performs systematic construction and association testing of multilocus genotype data in a Monte Carlo framework. Our objective was to assess its utility to guide statistical analyses of haplotypes within a candidate region (or combined genotypes across candidate genes) beyond that offered by a standard logistic regression approach.</p> <p>Methods</p> <p>We applied the hapConstructor method to a multilocus investigation of candidate genes involved in pro-inflammatory cytokine IL6 production, <it>IKBKB</it>, <it>IL6</it>, and <it>NFKB1 </it>(16 SNPs total) hypothesized to operate together to alter colorectal cancer risk. Data come from two U.S. multicenter studies, one of colon cancer (1,556 cases and 1,956 matched controls) and one of rectal cancer (754 cases and 959 matched controls).</p> <p>Results</p> <p>HapConstrcutor enabled us to identify important associations that were further analyzed in logistic regression models to simultaneously adjust for confounders. The most significant finding (nominal <it>P </it>= 0.0004; false discovery rate <it>q </it>= 0.037) was a combined genotype association across <it>IKBKB </it>SNP rs5029748 (1 or 2 variant alleles), <it>IL6 </it>rs1800797 (1 or 2 variant alleles), and <it>NFKB1 </it>rs4648110 (2 variant alleles) which conferred an ~80% decreased risk of colon cancer.</p> <p>Conclusions</p> <p>Strengths of hapConstructor were: systematic identification of multiple loci within and across genes important in CRC risk; false discovery rate assessment; and efficient guidance of subsequent logistic regression analyses.</p

Toll-like receptor polymorphisms and cerebral malaria: <it>TLR2 </it>Δ22 polymorphism is associated with protection from cerebral malaria in a case control study

<p>Abstract</p> <p>Background</p> <p>In malaria endemic areas, host genetics influence whether a <it>Plasmodium falciparum</it>-infected child develops uncomplicated or severe malaria. TLR2 has been identified as a receptor for <it>P. falciparum</it>-derived glycosylphosphatidylinositol (GPI), and polymorphisms within the TLR2 gene may affect disease pathogenesis. There are two common polymorphisms in the 5' un-translated region (UTR) of TLR2, a 22 base pair deletion in the first unstranslated exon (Δ22), and a GT dinucleotide repeat in the second intron (GTn).</p> <p>Methods</p> <p>These polymorphisms were examined in a Ugandan case control study on children with either cerebral malaria or uncomplicated malaria. Serum cytokine levels were analysed by ELISA, according to genotype and disease status. In vitro TLR2 expression was measured according to genotype.</p> <p>Results</p> <p>Both Δ22 and GTn polymorphisms were highly frequent, but only Δ22 heterozygosity was associated with protection from cerebral malaria (OR 0.34, 95% confidence intervals 0.16, 0.73). In vitro, heterozygosity for Δ22 was associated with reduced pam3cys inducible TLR2 expression in human monocyte derived macrophages. In uncomplicated malaria patients, Δ22 homozygosity was associated with elevated serum IL-6 (<it>p </it>= 0.04), and long GT repeat alleles were associated with elevated TNF (<it>p </it>= 0.007).</p> <p>Conclusion</p> <p>Reduced inducible TLR2 expression may lead to attenuated pro-inflammatory responses, a potential mechanism of protection from cerebral malaria present in individuals heterozygous for the TLR2 Δ22 polymorphism.</p

A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community

BACKGROUND:Gray wolves (Canis lupus) were reintroduced into Yellowstone National Park (YNP) after a >70 year absence, and as part of recovery efforts, the population has been closely monitored. In 1999 and 2005, pup survival was significantly reduced, suggestive of disease outbreaks. METHODOLOGY/PRINCIPAL FINDINGS:We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991-2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. We found high, constant exposure to canine parvovirus (wolf seroprevalence: 100%; coyote: 94%), canine adenovirus-1 (wolf pups [0.5-0.9 yr]: 91%, adults [>or=1 yr]: 96%; coyote juveniles [0.5-1.5 yrs]: 18%, adults [>or=1.6 yrs]: 83%), and canine herpesvirus (wolf: 87%; coyote juveniles: 23%, young adults [1.6-4.9 yrs]: 51%, old adults [>or=5 yrs]: 87%) suggesting that these pathogens were enzootic within YNP wolves and coyotes. An average of 50% of wolves exhibited exposure to the protozoan parasite, Neospora caninum, although individuals' odds of exposure tended to increase with age and was temporally variable. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. The years of high wolf-pup mortality in 1999 and 2005 in the northern region of the park were correlated with peaks in CDV seroprevalence, suggesting that CDV contributed to the observed mortality. CONCLUSIONS/SIGNIFICANCE:Of the pathogens we examined, none appear to jeopardize the long-term population of canids in YNP. However, CDV appears capable of causing short-term population declines. Additional information on how and where CDV is maintained and the frequency with which future epizootics might be expected might be useful for future management of the Northern Rocky Mountain wolf population

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A&gt;T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations