How many is enough? Determining optimal count totals for ecological and palaeoecological studies of testate amoebae

Testate amoebae are increasingly used in ecological and palaeoecological studies of wetlands. To characterise the amoeba community a certain number of individuals need to be counted under the microscope. To date, most studies have aimed for 150 individuals, but that sample size is not based on adequate evidence. When testate amoeba concentrations are low, it can be difficult or impossible to reach this total. The impacts of lower count totals have never been seriously scrutinised. We investigated the impact of count size on number of taxa identified, quantitative inferences of environmental variables and the strength of the links between amoebae and environmental data in the context of predicting depth to water table. Low counts were simulated by random selection of individuals from four existing datasets. Results show progressively diminishing returns by all criteria as count size increases from low numbers to counts of 150. A higher count is required to identify all taxa than to adequately characterise the community for transfer function inference. We suggest that in most cases, it will be a more efficient use of time to count a greater number of samples to a lower count. While a count of 50 individuals may be sufficient for some samples from some sites we recommend that counts of 100 individuals should be sufficient for most samples. Counts need only be increased to 150 or more where the aim is to identify relatively minor, but still potentially ecologically relevant community changes. This approach will help reduce lack of replication and low resolution, which are common limitations in testate amoeba-based palaeoecological and ecological studies

Relative validity of a semiquantitative food frequency questionnaire designed for schoolchildren in western Greece

<p>Abstract</p> <p>Background</p> <p>The use of food frequency questionnaires (FFQs) has become increasingly important in epidemiologic studies. During the past few decades, a wide variety of nutritional studies have used the semiquantitative FFQ as a tool for assessing and evaluating dietary intake. One of the main concerns in a dietary analysis is the validity of the collected dietary data.</p> <p>Methods</p> <p>This paper discusses several methodological and statistical issues related to the validation of a semiquantitative FFQ. This questionnaire was used to assess the nutritional habits of schoolchildren in western Greece. For validation purposes, we selected 200 schoolchildren and contacted their respective parents. We evaluated the relative validity of 400 FFQs (200 children's FFQs and 200 parents' FFQs).</p> <p>Results</p> <p>The correlations between the children's and the parents' questionnaire responses showed that the questionnaire we designed was appropriate for fulfilling the purposes of our study and in ranking subjects according to food group intake.</p> <p>Conclusion</p> <p>Our study shows that the semiquantitative FFQ provides a reasonably reliable measure of dietary intake and corroborates the relative validity of our questionnaire.</p

High Brain Ammonia Tolerance and Down-Regulation of Na+:K+:2Cl- Cotransporter 1b mRNA and Protein Expression in the Brain of the Swamp Eel, Monopterus albus, Exposed to Environmental Ammonia or Terrestrial Conditions

10.1371/journal.pone.0069512PLoS ONE89-POLN

Analyzing the Impacts of Dams on Riparian Ecosystems: A Review of Research Strategies and Their Relevance to the Snake River Through Hells Canyon

River damming provides a dominant human impact on river environments worldwide, and while local impacts of reservoir flooding are immediate, subsequent ecological impacts downstream can be extensive. In this article, we assess seven research strategies for analyzing the impacts of dams and river flow regulation on riparian ecosystems. These include spatial comparisons of (1) upstream versus downstream reaches, (2) progressive downstream patterns, or (3) the dammed river versus an adjacent free-flowing or differently regulated river(s). Temporal comparisons consider (4) pre- versus post-dam, or (5) sequential post-dam conditions. However, spatial comparisons are complicated by the fact that dams are not randomly located, and temporal comparisons are commonly limited by sparse historic information. As a result, comparative approaches are often correlative and vulnerable to confounding factors. To complement these analyses, (6) flow or sediment modifications can be implemented to test causal associations. Finally, (7) process-based modeling represents a predictive approach incorporating hydrogeomorphic processes and their biological consequences. In a case study of Hells Canyon, the upstream versus downstream comparison is confounded by a dramatic geomorphic transition. Comparison of the multiple reaches below the dams should be useful, and the comparison of Snake River with the adjacent free-flowing Salmon River may provide the strongest spatial comparison. A pre- versus post-dam comparison would provide the most direct study approach, but pre-dam information is limited to historic reports and archival photographs. We conclude that multiple study approaches are essential to provide confident interpretations of ecological impacts downstream from dams, and propose a comprehensive study for Hells Canyon that integrates multiple research strategies

Micro-spectroscopic investigation of selenium-bearing minerals from the Western US Phosphate Resource Area

Mining activities in the US Western Phosphate Resource Area (WPRA) have released Se into the environment. Selenium has several different oxidation states and species, each having varying degrees of solubility, reactivity, and bioavailability. In this study we are investigating the speciation of Se in mine-waste rocks. Selenium speciation was determined using bulk and micro-x-ray absorption spectroscopy (XAS), as well as micro-x-ray fluorescence mapping. Rocks used for bulk-XAS were ground into fine powders. Shale used for micro-XAS was broken along depositional planes to expose unweathered surfaces. The near edge region of the XAS spectra (XANES) for the bulk rock samples revealed multiple oxidation states, with peaks indicative of Se(-II), Se(IV), and Se(+VI) species. Micro-XANES analysis of the shale indicated that three unique Se-bearing species were present. Using the XANES data together with ab initio fitting of the extended x-ray absorption fine structure region of the micro-XAS data (micro-EXAFS) the three Se-bearing species were identified as dzharkenite, a di-selenide carbon compound, and Se-substituted pyrite. Results from this research will allow for a better understanding of the biogeochemical cycling of Se in the WPRA

The Role of T cell PPAR γ in mice with experimental inflammatory bowel disease

<p>Abstract</p> <p>Background</p> <p>Peroxisome proliferator-activated receptor γ (PPAR γ) is a nuclear receptor whose activation has been shown to modulate macrophage and T cell-mediated inflammation. The objective of this study was to investigate the mechanisms by which the deletion of PPAR γ in T cells modulates immune cell distribution and colonic gene expression and the severity of experimental IBD.</p> <p>Methods</p> <p>PPAR γ flfl; CD4 Cre⁺(CD4cre) or Cre- (WT) mice were challenged with 2.5% dextran sodium sulfate in their drinking water for 0, 2, or 7 days. Mice were scored on disease severity both clinically and histopathologically. Flow cytometry was used to assess lymphocyte and macrophage populations in the blood, spleen, and mesenteric lymph nodes (MLN). Global gene expression in colonic mucosa was profiled using Affymetrix microarrays.</p> <p>Results</p> <p>The deficiency of PPAR γ in T cells accelerated the onset of disease and body weight loss. Examination of colon histopathology revealed significantly greater epithelial erosion, leukocyte infiltration, and mucosal thickening in the CD4cre mice on day 7. CD4cre mice had more CD8⁺T cells than WT mice and fewer CD4⁺FoxP3⁺regulatory T cells (Treg) and IL10⁺CD4⁺T cells in blood and MLN, respectively. Transcriptomic profiling revealed around 3000 genes being transcriptionally altered as a result of DSS challenge in CD4cre mice. These included up-regulated mRNA expression of adhesion molecules, proinflammatory cytokines interleukin-6 (IL-6) and IL-1β, and suppressor of cytokine signaling 3 (SOCS-3) on day 7. Gene set enrichment analysis (GSEA) showed that the ribosome and Krebs cycle pathways were downregulated while the apoptosis pathway was upregulated in colons of mice lacking PPAR γ in T cells.</p> <p>Conclusions</p> <p>The expression of PPAR γ in T cells is involved in preventing gut inflammation by regulating colonic expression of adhesion molecules and inflammatory mediators at later stages of disease while favoring the recruitment of Treg to the mucosal inductive sites.</p

Predicting River Macroinvertebrate Communities Distributional Shifts under Future Global Change Scenarios in the Spanish Mediterranean Area

Several studies on global change over the next century predict increases in mean air temperatures of between 1°C to 5°C that would affect not only water temperature but also river flow. Climate is the predominant environmental driver of thermal and flow regimes of freshwater ecosystems, determining survival, growth, metabolism, phenology and behaviour as well as biotic interactions of aquatic fauna. Thus, these changes would also have consequences for species phenology, their distribution range, and the composition and dynamics of communities. These effects are expected to be especially severe in the Mediterranean basin due its particular climate conditions, seriously threatening Southern European ecosystems. In addition, species with restricted distributions and narrow ecological requirements, such as those living in the headwaters of rivers, will be severely affected. The study area corresponds to the Spanish Mediterranean and Balearic Islands, delimited by the Köppen climate boundary. With the application of the MEDPACS (MEDiterranean Prediction And Classification System) predictive approach, the macroinvertebrate community was predicted for current conditions and compared with three posible scenarios of watertemperature increase and its associated water flow reductions. The results indicate that the aquatic macroinvertebrate communities will undergo a drastic impact, with reductions in taxa richness for each scenario in relation to simulated current conditions, accompanied by changes in the taxa distribution pattern. Accordingly, the distribution area of most of the taxa (65.96%) inhabiting the mid-high elevations would contract and rise in altitude. Thus, families containing a great number of generalist species will move upstream to colonize new zones with lower water temperatures. By contrast, more vulnerable taxa will undergo reductions in their distribution area.This work was funded by GUADALMED-II (REN2001-3438-C07-06/HID), a project of excellence from “Junta de Andalucía” (RNM-02654/FEDER), the Spanish “Ministerio de Ciencia e Innovación” (CGL2007-61856/BOS), projects and a collaboration agreement between the “Spanish Ministerio de Medio Ambiente, Medio Rural y Marino” and the University of Granada (21.812-0062/8511)

The Effect of Recurrent Floods on Genetic Composition of Marble Trout Populations

A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global FST of 0.716), which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3–4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change

Tumor necrosis factor superfamily member APRIL contributes to fibrotic scar formation after spinal cord injury

BACKGROUND: Fibrotic scar formation contributes to the axon growth-inhibitory environment that forms following spinal cord injury (SCI). We recently demonstrated that depletion of hematogenous macrophages led to a reduction in fibrotic scar formation and increased axon growth after SCI. These changes were associated with decreased TNFSF13 (a proliferation inducing ligand (APRIL)) expression, but the role of APRIL in fibrotic scar formation after SCI has not been directly investigated. Thus, the goal of this study was to determine the role of APRIL in fibrotic scar formation after SCI. METHODS: APRIL knockout and wild-type mice received contusive SCI and were assessed for inflammatory cytokine/chemokine expression, leukocyte infiltration, fibrotic scar formation, axon growth, and cell proliferation. RESULTS: Expression of APRIL and its receptor BCMA is increased following SCI, and genetic deletion of APRIL led to reduced fibrotic scar formation and increased axon growth. However, the fibrotic scar reduction in APRIL KO mice was not a result of changes in fibroblast or astrocyte proliferation. Rather, APRIL knockout mice displayed reduced TNFα and CCL2 expression and less macrophage and B cell infiltration at the injury site. CONCLUSIONS: Our data indicate that APRIL contributes to fibrotic scar formation after SCI by mediating the inflammatory response