PIT tag antennae arrays as fishery monitoring tools in tropical environments

ABSTRACT Long-term monitoring of marine and estuarine fishes is labor intensive and subject to varying environmental conditions and spatio-temporal constraints. To better understand fish populations and increase predictive capabilities, scientists and managers need reliable long-term monitoring systems that collect data on populations through all environmental conditions and reduce the labor required for data collection. To collect long-term data on fish survival and movements, we adapted autonomous passive integrated transponder (PIT) tag antennae for use in tropical environments. These antennae function through all environmental conditions, accurately recording the unique identification number of each PIT tagged individual passing over an antenna, and only require labor for construction, data download, maintenance, and the marking of fish. Antennae have long life spans and function continuously, and PIT tags have a lifespan measured in decades, making this system ideal for long-term studies. The utility of this recapture system was demonstrated during a nursery habitat study in Charlotte Harbor, Florida USA. From November 2008 to February 2010, we marked 1,446 juvenile common snook (Centropomus undecimalis) with PIT tags (and a total of 3,810 snook since 2004). Between August 2008 and August 2010, the 11 antennae we constructed throughout four mangrove creeks recorded 362,880 PIT tag detections of 1,594 individual fish. The antenna array recaptured 83.7% of fish marked after antenna construction was complete. The detailed recapture information allowed for highly precise calculation of apparent survival and examination of long-term habitat use. In addition to discussing the data we have collected, this paper details how to design and construct customized PIT tag antenna systems and covers the issues and limitations associated with adapting these systems to tropical marine and estuarine environments. These systems may be especially useful in the tropics for monitoring juveniles of other species that use near shore nursery habitats such as mangroves

Hostos Online Learning Assessment: A Survey of Student Perceptions

The Office of Education Technology (EdTech) at Hostos Community College and faculty members from various departments created the Hostos Online Learning Assessment (HOLA) Task Force to design a survey for gathering and assessing data about students’ perceptions of their online learning experiences. The task force wanted to utilize the survey results to identify strengths and weaknesses in online instruction and student preparedness for the online learning environment. Student perceptions of online learning are integral to building upon current best practices and also gauging the preparedness of the students for the online learning environment, particularly in an urban, Hispanic-serving community college. The survey and results will be discussed within the broader context of best practices and online learning assessments as well as the way the HOLA Task Force is utilizing the data to make meaningful changes in the survey instrument, in addition planning for continuous improvement in online learning

A strong association between non-musculoskeletal symptoms and musculoskeletal pain symptoms: results from a population study

<p>Abstract</p> <p>Background</p> <p>There is a lack of knowledge about the pattern of symptom reporting in the general population as most research focuses on specific diseases or symptoms. The number of musculoskeletal pain sites is a strong predictor for disability pensioning and, hence, is considered to be an important dimension in symptom reporting. The simple method of counting symptoms might also be applicable to non-musculoskeletal symptoms, rendering further dimensions in describing individual and public health. In a general population, we aimed to explore the association between self-reported non-musculoskeletal symptoms and the number of pain sites.</p> <p>Methods</p> <p>With a cross-sectional design, the Standardised Nordic Questionnaire and the Subjective Health Complaints Inventory were used to record pain at ten different body sites and 13 non-musculoskeletal symptoms, respectively, among seven age groups in Ullensaker, Norway (n = 3,227).</p> <p>Results</p> <p>Results showed a strong, almost linear relationship between the number of non-musculoskeletal symptoms and the number of pain sites (r = 0.55). The <it>number </it>and <it>type </it>of non-musculoskeletal symptoms had an almost equal explanatory power in the number of pain sites reported (27.1% vs. 28.2%).</p> <p>Conclusion</p> <p>The linear association between the number of non-musculoskeletal and musculoskeletal symptoms might indicate that the symptoms share common characteristics and even common underlying causal factors. The total burden of symptoms as determined by the number of symptoms reported might be an interesting generic indicator of health and well-being, as well as present and future functioning. Research on symptom reporting might also be an alternative pathway to describe and, possibly, understand the medically unexplained multisymptom conditions.</p

Major depression, fibromyalgia and labour force participation: A population-based cross-sectional study

BACKGROUND: Previous studies have documented an elevated frequency of depressive symptoms and disorders in fibromyalgia, but have not examined the association between this comorbidity and occupational status. The purpose of this study was to describe these epidemiological associations using a national probability sample. METHODS: Data from iteration 1.1 of the Canadian Community Health Survey (CCHS) were used. The CCHS 1.1 was a large-scale national general health survey. The prevalence of major depression in subjects reporting that they had been diagnosed with fibromyalgia by a health professional was estimated, and then stratified by demographic variables. Logistic regression models predicting labour force participation were also examined. RESULTS: The annual prevalence of major depression was three times higher in subjects with fibromyalgia: 22.2% (95% CI 19.4 – 24.9), than in those without this condition: 7.2% (95% CI 7.0 – 7.4). The association persisted despite stratification for demographic variables. Logistic regression models predicting labour force participation indicated that both conditions had an independent (negative) effect on labour force participation. CONCLUSION: Fibromyalgia and major depression commonly co-occur and may be related to each other at a pathophysiological level. However, each syndrome is independently and negatively associated with labour force participation. A strength of this study is that it was conducted in a large probability sample from the general population. The main limitations are its cross-sectional nature, and its reliance on self-reported diagnoses of fibromyalgia

A case control study of premorbid and currently reported physical activity levels in chronic fatigue syndrome

BACKGROUND: Patients with chronic fatigue syndrome typically report high levels of physical activity before becoming ill. Few studies have examined premorbid and current activity levels in chronically fatigued patients. METHODS: In a case-control study, 33 patients with chronic, unexplained, disabling fatigue attending a university-based clinic specializing in fatigue were compared to 33 healthy, age- and sex-matched controls. Patients rated their activity levels before their illness and currently, using scales designed for this purpose. Controls reported their level of activity of 2 years previously and currently. Chi-square analyses, Student's t tests, and Wilcoxon signed rank tests were used in pair matched analyses. RESULTS: Compared to healthy controls, patients with chronic, unexplained fatigue rated themselves as more active before their illness (p ≤ 0.001) and less active currently (p ≤ 0.001). The patients also reported they currently stood or walked less than the controls (median [inter-quartile range] = 4 [2-5] versus 9 [7.5–12] hours, p ≤ 0.001), and spent more time reclining (median [inter-quartile range] = 12 [10-16] versus 8 [8–9.5] hours, p ≤ 0.001). These differences remained significant for the subset of patients who met strict criteria for chronic fatigue syndrome or fibromyalgia. CONCLUSION: Patients with chronic, unexplained, disabling fatigue reported being more active before becoming ill than healthy controls. This finding could be explained by greater premorbid activity levels that could predispose to illness, or by an overestimation of previous activity. Either possibility could influence patients' perceptions of their current activity levels and their judgments of recovery. Perceived activity should be addressed as part of management of the illness

The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs

Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at similar to 24.5 degrees C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk

The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs

This work was supported by grants from the National Institutes of Health R01AI091595, R01AI120810, R01AI050529, and P30AI045008 (B.H.H.); R01HL139337 (M.T.D.), the National Geographic Society (E.J.S.), the International Primatological Society (E.J.S.), and the American Society of Primatologists (E.J.S.), as well as fellowships from Harvard University (E.J.S.) and the National Science Foundation (E.J.S.).Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at ~24.5 °C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk.Publisher PDFPeer reviewe

Limited release of previously-frozen C and increased new peat formation after thaw in permafrost peatlands

Permafrost stores globally significant amounts of carbon (C) which may start to decompose and be released to the atmosphere in form of carbon dioxide (CO 2 ) and methane (CH 4 ) as global warming promotes extensive thaw. This permafrost carbon feedback to climate is currently considered to be the most important carbon-cycle feedback missing from climate models. Predicting the magnitude of the feedback requires a better understanding of how differences in environmental conditions post-thaw, particularly hydrological conditions, control the rate at which C is released to the atmosphere. In the sporadic and discontinuous permafrost regions of north-west Canada, we measured the rates and sources of C released from relatively undisturbed ecosystems, and compared these with forests experiencing thaw following wildfire (well-drained, oxic conditions) and collapsing peat plateau sites (water-logged, anoxic conditions). Using radiocarbon analyses, we detected substantial contributions of deep soil layers and/or previously-frozen sources in our well-drained sites. In contrast, no loss of previously-frozen C as CO 2 was detected on average from collapsed peat plateaus regardless of time since thaw and despite the much larger stores of available C that were exposed. Furthermore, greater rates of new peat formation resulted in these soils becoming stronger C sinks and this greater rate of uptake appeared to compensate for a large proportion of the increase in CH 4 emissions from the collapse wetlands. We conclude that in the ecosystems we studied, changes in soil moisture and oxygen availability may be even more important than previously predicted in determining the effect of permafrost thaw on ecosystem C balance and, thus, it is essential to monitor, and simulate accurately, regional changes in surface wetness

Dynamics of Genome Rearrangement in Bacterial Populations

Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of “symmetric inversions”—inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes