What's the relative humidity in tropical caves?

Relative humidity (RH) was measured at hourly intervals for approximately one year in two caves at seven stations near Playa del Carmen in Quintana Roo, Mexico. Sistema Muévelo Rico is a 1.1 km long cave with 12 entrances and almost no dark zone. Río Secreto (Tuch) is a large river cave with more than 40 km of passages, and an extensive dark zone. Given the need for cave specialists to adapt to saturated humidity, presumably by cuticular thinning, the major stress of RH would be its deviation from saturation. RH in Río Secreto (Tuch) was invariant at three sites and displayed short deviations from 100% RH at the other four sites. These deviations were concentrated at the end of the nortes and beginning of the rainy season. Three of the sites in Sistema Muévelo Rico showed a similar pattern although the timing of the deviations from 100% RH was somewhat displaced. Four sites in Sistema Muévelo Rico were more variable, and were analyzed using a measure of amount of time of deviation from 100% RH for each 24 hour period. Strong seasonality was evident but, remarkably, periods of constant high humidity were not the same at all sites. In most Sistema Muévelo Rico sites, there was a detectable 24 hour cycle in RH, although it was quite weak in about half of them. For Río Secreto (Tuch) only one site showed any sign of a 24 hour cycle. The troglomorphic fauna was more or less uniformly spread throughout the caves and did not concentrate in any one area or set of RH conditions. Compared to temperature, RH is much more constant, perhaps even more constant than the amount of light. However, changes in RH as a result of global warming may have a major negative effect on the subterranean fauna.

Macroinfauna responses and recovery trajectories after an oil spill differ from those following saltmarsh restoration

Given the severity of injuries to biota in coastal wetlands from the Deepwater Horizon oil spill (DWH) and the resulting availability of funding for restoration, information on impacted salt marshes and biotic development of restored marshes may both help inform marsh restoration planning in the near term and for future spills. Accordingly, we performed a meta-analysis to model a restoration trajectory of total macroinfauna density in constructed marshes (studied for ~30 y), and with a previously published restoration trajectory for amphipods, we compared these to recovery curves for total macroinfauna and amphipods from DWH impacted marshes (over 8.5 y). Total macroinfauna and amphipod densities in constructed marshes did not consistently reach equivalency with reference sites before 20 y, yet in heavily oiled marshes recovery occurred by 4.5 y post spill (although it is unlikely that macroinfaunal community composition fully recovered). These differences were probably due to initial conditions (e.g., higher initial levels of belowground organic matter in oiled marshes) that were more conducive to recovery as compared to constructed marshes. Furthermore, we found that amphipod trajectories were distinctly different in constructed and oiled marshes as densities at oiled sites exceeded that of reference sites by as much as 20x during much of the recovery period. Amphipods may have responded to the rapid increase and high biomass of benthic microalgae following the spill. These results indicate that biotic responses after an oil spill may be quantitatively different than those following restoration, even for heavily oiled marshes that were initially denuded of vegetation. Our dual trajectories for oil spill recovery and restoration development for macroinfauna should help guide restoration planning and assessment following the DWH as well as for restoration scaling for future spills.

The Effect of Weather and Location of Fruit within the Tree on the Incidence and Severity of Citrus Black Spot on Fruit

Citrus black spot (CBS) caused by the fungus Phyllosticta citricarpa occurs in tropical and sub-tropical citrus production regions and affects all varieties of citrus. In Florida, the disease cycle is unique, having only the asexual spore. This work examines incidence and severity of CBS (hard spot symptoms) on fruit in two citrus groves during 2013-2014, 2014-2015 (Grove III) and 2015-2016 (Grove II) citrus seasons. Disease incidence and severity on fruit were analyzed based on citrus season, side of tree evaluated, height within the canopy, tree health, and tree age. Results indicate an increase in CBS incidence in Grove III between 2013-2014 and 2014-2015 seasons, with more infected or symptomatic fruit on the road side of the canopy and a higher incidence above 2 meters. Tree health status affected incidence but not severity and tree age had a significant effect on severity of CBS in Grove II. Analysis of weather data conducive for infection, between 2010 and 2017, indicated an average of 172 days per year (range: 104-261 days) when the temperature (15-35 °C) and relative humidity (RH ≥ 90% for 8 consecutive hours) were conducive for infection of fruit and an average of 98 days per year (range: 72-123 days) when the fruit were susceptible to infection.

Probiotic Medilac-S® for the induction of clinical remission in a Chinese population with ulcerative colitis: A systematic review and meta-analysis

AIM

To assess the effects of probiotic Medilac-S® as adjunctive therapy for the induction of remission of ulcerative colitis (UC) in a Chinese population through a systematic review and meta-analysis.

METHODS

A systematic literature search was conducted to find randomized, controlled trials in a Chinese population with at least two study arms - a control arm which receives a conventional, oral aminosalicylate drug, and a treatment arm, which administers the same conventional drug in conjunction with the probiotic Medilac-S® per os. Both English and Chinese databases were searched, including PubMed, EMBASE, Google Scholar, Chinese National Knowledge Infrastructure, Wanfang Data, and VIP Search, and study data was extracted onto standardized abstraction sheets. Meta-analyses were conducted for primary and secondary outcomes of interest using a fixed or random effects model. The primary outcome was the induction of clinical remission and the secondary outcomes included changes in Sutherland index, endoscopic and histological scores, proportion of reported clinical symptoms and adverse events (AEs). For outcomes with sufficient data, the type of conventional drug therapy was also assessed to determine if the effects of combination therapy with Medilac-S® was influenced by drug type. All tests were conducted using a type I error rate of 0.05 and all confidence intervals (CI) were based on a 95% confidence level. Review protocol was uploaded to PROSPERO (CRD42018085658 upon completion).

RESULTS

Fifty-three clinical trials with a total of 3984 participants were identified and included in the review. Medilac-S® adjunctive therapy significantly improved induction of clinical remission (RR = 1.21; 95%CI: 1.18-1.24; P < 0.0001) with the estimated likelihood of effective treatment, on average, 21% higher for those consuming the probiotic. Sutherland index scores showed the control mean was on average 3.10 (CI: 2.41-3.78; P = 0.0428) units greater than the treatment mean, thereby demonstrating significant improvement in participants taking the probiotic. Similarly, a significant difference was seen between the overall reduction of endoscopic and histological scores of control and treatment arm participants, with score decreases in the control groups 0.71 (CI: 0.3537-1.0742) and 1.1 (CI: 0.9189-1.2300) units smaller than treatment group score decreases. The proportion of participants reporting clinical symptoms, (abdominal pain, tenesmus, blood and mucous in stool, and diarrhea) was significantly reduced after combination therapy with Medilac-S® (P < 0.0001) and estimated to be on average 44% (RR = 0.44, CI: 0.32-0.59), 53% (RR = 0.53, CI: 0.38-74), 40% (RR = 0.40, CI: 0.28-0.58) and 47% (RR = 0.47 CI: 0.36-0.42) respectively, of the proportion of individuals reporting the aforementioned symptoms after conventional therapy alone. The risk of AEs was also significantly reduced with adjunctive Medilac-S® therapy. The proportion of individuals in the treatment groups reporting AEs was an estimated 72% of the proportion of individuals in the control groups reporting AEs (RR = 0.72, CI: 0.55-0.94, P = 0.0175). Upon comparing effect means for different drug types in conjunction with Medilac-S®, evidence of significant variability (P < 0.0001) was observed, and sulfasalazine was found to be the most effective drug in both primary and secondary outcomes.

CONCLUSION

Evidence suggests Medilac-S® adjunctive therapy should be considered standard care for UC in a Chinese population because it aids in the induction of clinical remission, improves symptoms of the gastrointestinal tract and reduces risk of AEs.

In healthy adults, resistant maltodextrin produces a greater change in fecal bifidobacteria counts and increases stool wet weight: a double-blind, randomized, controlled crossover study

Dietary fiber stimulates the growth of potentially beneficial bacteria (eg, bifidobacteria), yet most Americans do not meet daily fiber recommendations. Resistant maltodextrin (RMD), a fermentable functional fiber, may help individuals meet total fiber recommendations and potentially increase bifidobacteria. It was hypothesized that fecal bifidobacteria counts/ng fecal DNA would increase after adding 25 g RMD to inadequate fiber diets of healthy adults. In this double-blind, controlled crossover study, 51 participants (26.3 ± 6.8 years, mean ± SD) were randomized to consume 0, 15, and 25 g RMD daily for 3 weeks followed by a 2-week washout. Participants collected all stools for 2 days at weeks 0 and 3 of each intervention for stool wet weight (WW) measurements and fecal bifidobacteria counts. Weekly 24-hour dietary recalls assessed total fiber intake. Only 25 g RMD resulted in a change (final minus baseline) in bifidobacteria that was significant compared with 0 g (0.17 ± 0.09 vs -0.17 ± 0.09 log₁₀[counts], respectively, mean ± SEM, P = .008). Stool WW increased only with 25 g (150 ± 11 vs baseline 121±11 g/d; P = .011). Mean daily total fiber intake (including RMD) was significantly higher (both P< .001) with 15 g (17.8 ± 0.6 g/1000 kcal or 4184 kJ) and 25 g (25.3 ± 1.1 g/1000 kcal) compared with 0 g RMD (8.4±0.4 g/1000 kcal). Mean daily total fiber intakes exceeded recommendations (14 g/1000 kcal) with 15 and 25 g of RMD, and 25 g RMD increased fecal bifidobacteria counts and stool WW, suggesting health benefits from increasing total fiber intake.

The influence of herbivory and weather on the vital rates of two closely related cactus species

Herbivory has long been recognized as a significant driver of plant population dynamics, yet its effects along environmental gradients are unclear. Understanding how weather modulates plant-insect interactions can be particularly important for predicting the consequences of exotic insect invasions, and an explicit consideration of weather may help explain why the impact can vary greatly across space and time. We surveyed two native prickly pear cactus species (genus Opuntia) in the Florida panhandle, USA, and their specialist insect herbivores (the invasive South American cactus moth, Cactoblastis cactorum, and three native insect species) for five years across six sites. We used generalized linear mixed models to assess the impact of herbivory and weather on plant relative growth rate (RGR) and sexual reproduction, and we used Fisher's exact test to estimate the impact of herbivory on survival. Weather variables (precipitation and temperature) were consistently significant predictors of vital rate variation for both cactus species, in contrast to the limited and varied impacts of insect herbivory. Weather only significantly influenced the impact of herbivory on Opuntia humifusa fruit production. The relationships of RGR and fruit production with precipitation suggest that precipitation serves as a cue in determining the trade-off in the allocation of resources to growth or fruit production. The presence of the native bug explained vital rate variation for both cactus species, whereas the invasive moth explained variation only for O. stricta. Despite the inconsistent effect of herbivory across vital rates and cactus species, almost half of O. stricta plants declined in size, and the invasive insect negatively affected RGR and fruit production. Given that fruit production was strongly size-dependent, this suggests that O. stricta populations at the locations surveyed are transitioning to a size distribution of predominantly smaller sizes and with reduced sexual reproduction potential.

Probiotics (Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2) improve rhinoconjunctivitis-specific quality of life in individuals with seasonal allergies: a double-blind, placebo-controlled, randomized trial

Background: Rhinoconjunctivitis-specific quality of life is often reduced during seasonal allergies. The Mini Rhinoconjunctivitis Quality of Life Questionnaire (MRQLQ) is a validated tool used to measure quality of life in people experiencing allergies (0 = not troubled to 6 = extremely troubled). Probiotics may improve quality of life during allergy season by increasing the percentage of regulatory T cells (Tregs) and inducing tolerance.Objective: The objective of this study was to determine whether consuming Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and B. longum MM-2 compared with placebo would result in beneficial effects on MRQLQ scores throughout allergy season in individuals who typically experience seasonal allergies. Secondary outcomes included changes in immune markers as part of a potential mechanism for changes in MRQLQ scores.Design: In this double-blind, placebo-controlled, parallel, randomized clinical trial, 173 participants (mean ± SEM: age 27 ± 1 y) who self-identified as having seasonal allergies received either a probiotic (2 capsules/d, 1.5 billion colony-forming units/capsule) or placebo during spring allergy season for 8 wk. MRQLQ scores were collected weekly throughout the study. Fasting blood samples were taken from a subgroup (placebo, n = 37; probiotic, n = 35) at baseline and week 6 (predicted peak of pollen) to determine serum immunoglobulin (Ig) E concentrations and Treg percentages.Results: The probiotic group reported an improvement in the MRQLQ global score from baseline to pollen peak (-0.68 ± 0.13) when compared with the placebo group (-0.19 ± 0.14; P = 0.0092). Both serum total IgE and the percentage of Tregs increased from baseline to week 6, but changes were not different between groups.Conclusions: This combination probiotic improved rhinoconjunctivitis-specific quality of life during allergy season for healthy individuals with self-reported seasonal allergies; however, the associated mechanism is still unclear. This trial was registered at clinicaltrials.gov as NCT02349711.

A Statistical Evaluation of Methods of In-Vitro Growth Assessment for Phyllosticta citricarpa: Average Colony Diameter vs. Area

Fungal growth inhibition on solid media has been historically measured and calculated based on the average of perpendicular diameter measurements of growth on fungicide amended media. We investigated the sensitivity of the calculated area (DA) and the measured area (MA) for assessing fungicide growth inhibition of the ascomycete, Phyllosticta citricarpa on solid media. Both the calculated, DA and the actual measured area, MA were adequate for distinguishing significant treatment effects of fungicide on fungal growth, however MA was more sensitive at identifying significant differences between the controls and fungicide concentrations below 5 ppm.

Predicting the Occurrence of Cave-Inhabiting Fauna Based on Features of the Earth Surface Environment

One of the most challenging fauna to study in situ is the obligate cave fauna because of the difficulty of sampling. Cave-limited species display patchy and restricted distributions, but it is often unclear whether the observed distribution is a sampling artifact or a true restriction in range. Further, the drivers of the distribution could be local environmental conditions, such as cave humidity, or they could be associated with surface features that are surrogates for cave conditions. If surface features can be used to predict the distribution of important cave taxa, then conservation management is more easily obtained. We examined the hypothesis that the presence of major faunal groups of cave obligate species could be predicted based on features of the earth surface. Georeferenced records of cave obligate amphipods, crayfish, fish, isopods, beetles, millipedes, pseudoscorpions, spiders, and springtails within the area of Appalachian Landscape Conservation Cooperative in the eastern United States (Illinois to Virginia and New York to Alabama) were assigned to 20 x 20 km grid cells. Habitat suitability for these faunal groups was modeled using logistic regression with twenty predictor variables within each grid cell, such as percent karst, soil features, temperature, precipitation, and elevation. Models successfully predicted the presence of a group greater than 65% of the time (mean = 88%) for the presence of single grid cell endemics, and for all faunal groups except pseudoscorpions. The most common predictor variables were latitude, percent karst, and the standard deviation of the Topographic Position Index (TPI), a measure of landscape rugosity within each grid cell. The overall success of these models points to a number of important connections between the surface and cave environments, and some of these, especially soil features and topographic variability, suggest new research directions. These models should prove to be useful tools in predicting the presence of species in understudied areas.

Bifidobacterium bifidum R0071 decreases stress-associated diarrhoea-related symptoms and self-reported stress: a secondary analysis of a randomised trial

Psychological stress is associated with gastrointestinal (GI) distress. This secondary analysis from a randomised, double-blind, placebo-controlled study examined whether three different probiotics could normalise self-reported stress-associated GI discomfort and reduce overall self-reported stress. Undergraduate students (n=581) received Lactobacillus helveticus R0052, Bifidobacterium longum ssp. infantis R0033, Bifidobacterium bifidum R0071, or placebo. Participants self-reported 2 outcomes for a 6-week period, which included final academic exams: daily level of stress (0=no stress to 10=extremely stressed) and weekly three diarrhoea-related symptoms (DS, 1=no discomfort to 7=severe discomfort) using the GI Symptom Rating Scale. Self-reported stress was positively related to DS (P=0.0068). Mean DS scores were lower with B. bifidum versus placebo at week 2 at the average level of stress and the average body mass index (BMI). DS scores were lower with B. bifidum at week 5 versus week 0 and 1 and with B. infantis R0033 at week 6 versus week 0. DS scores were higher when antibiotics were used in the prior week with placebo (P=0.0092). DS were not different with or without antibiotic use with the probiotics. Only B. bifidum had an effect on self-reported stress scores (P=0.0086). The self-reported stress score was also dependent on hours of sleep per day where it decreased by 0.13 for each additional hour of sleep. During a stressful period, B. bifidum R0071 decreases DS and self-reported stress scores. This trial was registered at clinicaltrials.gov as NCT01709825.

Diet quality improves for parents and children when almonds are incorporated into their daily diet: a randomized, crossover study

The health benefits of nuts may, in part, be due to the fiber that provides substrate for the maintenance of a healthy and diverse microbiota. We hypothesized that consuming almonds would benefit immune status through improving diet quality and modulation of microbiota composition in parents and their children, while improving gastrointestinal function. In a crossover trial, 29 parents (35 ± 0.6 years) and their children (n = 29; 4 ± 0.2 years; pairs) consumed 1.5 and 0.5 oz, respectively, of almonds and/or almond butter or control (no almonds) for 3 weeks followed by 4-week washouts. Parents completed daily questionnaires of stool frequency and compliance with nut intake. The Gastrointestinal Symptom Response Scale was administered weekly. Participants provided stools for microbiota analysis and saliva for secretory immunoglobulin A. Serum antioxidant/proinflammatory balance was determined in parents. From weekly dietary recalls (Automated Self-Administered 24-Hour Dietary Recall), nutrient and energy intake were assessed and Healthy Eating Index-2010 scores were calculated. Consuming almonds increased total Healthy Eating Index score from 53.7 ± 1.8 to 61.4 ± 1.4 (parents) and 53.7 ± 2.6 to 61.4 ± 2.2 (children; P < .001). Minimal changes in gastrointestinal symptoms and no change in stool frequency were noted with the almond intervention. Microbiota was stable at the phylum and family level, but genus-level changes occurred with nut intake, especially in children. No differences were observed for immune markers. Although higher intakes of almonds or longer interventions may be needed to demonstrate effects on immune status, a moderate intake of almonds improves diet quality in adults and their young children and modulates microbiota composition.

Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2 Ingestion Induces a Less Inflammatory Cytokine Profile and a Potentially Beneficial Shift in Gut Microbiota in Older Adults: A Randomized, Double-Blind, Placebo-Controlled, Crossover Study

OBJECTIVE

This study determined whether older adults who consumed a probiotic mixture would have a greater proportion of circulating CD4+ lymphocytes, altered cytokine production, and a shift in intestinal microbiota toward a healthier microbial community.

METHODS

Participants (70 ± 1 years [mean ± SEM]; n = 32) consumed a probiotic (Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM2) or a placebo twice daily for 3 weeks with a 5-week washout period between intervention periods. Blood and stools were collected before and after each intervention. The percentage of circulating CD4+ lymphocytes and ex vivo mitogen-stimulated cell cytokine production were measured. In stools, specific bacterial targets were quantified via quantitative polymerase chain reaction (qPCR) and community composition was determined via pyrosequencing.

RESULTS

During the first period of the crossover the percentage of CD4+ cells decreased with the placebo (48% ± 3% to 31% ± 3%, p < 0.01) but did not change with the probiotic (44% ± 3% to 42% ± 3%) and log-transformed concentrations of interleukin-10 increased with the probiotic (1.7 ± 0.2 to 3.4 ± 0.2, p < 0.0001) but not the placebo (1.7 ± 0.2 to 2.1 ± 0.2). With the probiotic versus the placebo a higher percentage of participants had an increase in fecal bifidobacteria (48% versus 30%, p < 0.05) and lactic acid bacteria (55% versus 43%, p < 0.05) and a decrease in Escherichia coli (52% versus 27%, p < 0.05). Several bacterial groups matching Faeacalibactierium prausnitzii were more prevalent in stool samples with the probiotic versus placebo.

CONCLUSIONS

The probiotic maintained CD4+ lymphocytes and produced a less inflammatory cytokine profile possibly due to the changes in the microbial communities, which more closely resembled those reported in healthy younger populations.

Consuming Lentinula edodes (Shiitake) Mushrooms Daily Improves Human Immunity: A Randomized Dietary Intervention in Healthy Young Adults

BACKGROUND

Mushrooms are widely cited for their medicinal qualities, yet very few human intervention studies have been done using contemporary guidelines.

OBJECTIVE

The aim of this study was to determine whether consumption of whole, dried Lentinula edodes (shiitake) mushrooms could improve human immune function. Primary objectives were to ascertain whether L. edodes consumption would improve γδ-T cell proliferation and activation responses, quantify a dose response, and elicit cytokine secretion patterns. Secondary objectives included determining changes in natural killer T (NK-T) cell proliferation and activation, secretory immunoglobulin A (sIgA) in saliva, and C-reactive protein (CRP) in serum.

DESIGN

Fifty-two healthy males and females, aged 21-41 years, participated in a 4-week parallel group study, consuming either 5 or 10 g of mushrooms daily. Each subject had blood drawn before and after 4 weeks of daily L. edodes consumption. Saliva and serum were also collected. Peripheral blood mononuclear cells were cultured in autologous serum for 24 hours or 6 days, stained, and examined by flow cytometry.

RESULTS

Eating L. edodes for 4 weeks resulted in increased ex vivo proliferation of γδ-T (60% more, p < 0.0001) and NK-T (2-fold more, p < 0.0001) cells. Both cell types also demonstrated a greater ability to express activation receptors, suggesting that consuming mushrooms improved cell effector function. The increase in sIgA implied improved gut immunity. The reduction in CRP suggested lower inflammation. The pattern of cytokines secreted before and after mushroom consumption was significantly different; consumption resulted in increased interleukin (IL)-4, IL-10, tumor necrosis factor (TNF)-α, and IL-1α levels, a decreased macrophage inflammatory protein-1α/chemokine C-C ligand 3 (MIP-1α/CCL3) level, and no change to IL-6, IL-1β, MIP-1β, IL-17 and interferon (IFN)-γ levels.

CONCLUSIONS

Regular L. edodes consumption resulted in improved immunity, as seen by improved cell proliferation and activation and increased sIgA production. The changes observed in cytokine and serum CRP levels suggest that these improvements occurred under conditions that were less inflammatory than those that existed before consumption.

The influence of study species selection on estimates of pesticide exposure in free-ranging birds

Field studies of pesticide effects on birds often utilize indicator species with the purpose of extrapolating to other avian taxa. Little guidance exists for choosing indicator species to monitor the presence and/or effects of contaminants that are labile in the environment or body, but are acutely toxic, such as anticholinesterase (anti-ChE) insecticides. Use of an indicator species that does not represent maximum exposure and/or effects could lead to inaccurate risk estimates. Our objective was to test the relevance of a priori selection of indicator species for a study on pesticide exposure to birds inhabiting fruit orchards. We used total plasma ChE activity and ChE reactivation to describe the variability in anti-ChE pesticide exposure among avian species in two conventionally managed fruit orchards. Of seven species included in statistical analyses, the less common species, chipping sparrow (Spizella passerina), showed the greatest percentage of exposed individuals and the greatest ChE depression, whereas the two most common species, American robins (Turdus migratorius) and gray catbirds (Dumatella carolinensis), did not show significant exposure. Due to their lower abundance, chipping sparrows would have been an unlikely choice for study. Our results show that selection of indicator species using traditionally accepted criteria such as abundance and ease of collection may not identify species that are at greatest risk. Our efforts also demonstrate the usefulness of conducting multiple-species pilot studies prior to initiating detailed studies on pesticide effects. A study such as ours can help focus research and resources on study species that are most appropriate.

Fecal lactic acid bacteria increased in adolescents randomized to whole-grain but not refined-grain foods, whereas inflammatory cytokine production decreased equally with both interventions

The intake of whole-grain (WG) foods by adolescents is reported to be approximately one-third the recommended intake of 48 g/d. This 6-wk randomized interventional study determined the effect of replacing grains within the diet with refined-grain (RG; n = 42) or WG (n = 41) foods/d on gastrointestinal and immune health in adolescents (aged 12.7 ± 0.1 y). A variety of grain-based foods were delivered weekly to participants and their families. Participants were encouraged to eat 3 different kinds of study foods (e.g., bread, cereals, snacks)/d with goals of 0 g/d (RG) and 80 g/d (WG). Stool samples were obtained during the prebaseline and final weeks to measure bifidobacteria and lactic acid bacteria (LAB) using qPCR. Stool frequency was recorded daily. Blood was drawn at baseline and at final visits for immune markers. Across groups, total-grain intake increased by one serving. The intake of WG was similar at baseline (18 ± 3 g) between groups but increased to 60 ± 5 g in the WG group and decreased to 4 ± 1 g in the RG group. Fecal bifidobacteria increased from baseline with both interventions, but LAB increased (P < 0.05) from baseline [2.4 ± 0.2 log(10) genome equivalents (eq)] to wk 6 (3.0 ± 0.2 log(10) genome eq) in the WG group but not in the RG group (baseline: 2.9 ± 0.2 log(10) genome eq; wk 6: 3.0 ± 0.1 log(10) genome eq). There was no difference in stool frequency, serum antioxidant potential, or in vitro LPS-stimulated mononuclear cell production of inflammatory cytokines between groups. However, across both groups the number of daily stools tended to increase (P = 0.08) by 0.0034 stools/g WG or by 0.2 stools with 60 g WG, mean antioxidant potential increased by 58%, and mean production of TNF-α, IL-1β, and IL-6 decreased by 24, 22, and 42%, respectively, between baseline and wk 6. Overall, incorporating either WG or RG foods increased serum antioxidant concentrations and decreased inflammatory cytokine production; however, WG study foods had more of an effect on aspects of gastrointestinal health.

PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker /.

Evolutionary history and phylodynamics of influenza A and B neuraminidase (NA) genes inferred from large-scale sequence analyses

Background

Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking.

Methodology/Principal findings

Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The d_N/d_S ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding.

Conclusions/Significance

The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance.

Pandemic (H1N1) 2009 virus revisited: an evolutionary retrospective

The pandemic (H1N1) 2009 virus is unique in many aspects, especially in its genetics and evolution. In this paper, we examine the molecular mechanisms underlying the evolution of this novel virus through a comprehensive bioinformatics analysis, and present results in the context of a review of the literature. The pandemic virus was found to arise from a reassortment of two swine viruses, each of which ultimately arose from interspecies transmission. It experienced fast evolutionary rates and strong selection pressures, diverging into two different clusters at the early pandemic stage. Cluster I became extinct at the end of 2009 whereas Cluster II continued to circulate at much lower rates in 2010. Therefore, on August 10 of 2010 the WHO declared the end of the pandemic. Important mutations associated with host specificity, virulence, and drug resistance were detected in the pandemic virus, indicating effective transmission and increased severity in humans. Much has been learned about the evolutionary dynamics of this pandemic virus; however, it is still impossible to predict when the next pandemic will occur and which virus will be responsible. Improved surveillance at different levels (both national and international) and in different hosts (especially in swine) appears to be crucial for early detection and prevention of future influenza pandemics.

Galactooligosaccharide supplementation reduces stress-induced gastrointestinal dysfunction and days of cold or flu: a randomized, double-blind, controlled trial in healthy university students

BACKGROUND

Acute psychological stress induced by academic exams is associated with dysregulated gastrointestinal and immune function.

OBJECTIVE

We examined whether supplementation with galactooligosaccharides reduced gastrointestinal dysfunction and the percentage of days with cold or flu in academically stressed undergraduate students.

DESIGN

In a randomized, double-blind study, subjects (n = 427) received 0, 2.5, or 5.0 g galactooligosaccharides for 8 wk around the time of fall final exams. Levels of stress and cold or flu symptom intensity (SI; 0 = not experiencing to 3 = severe) were recorded daily. The SI from 9 cold or flu symptoms was summed with 1 d of cold or flu defined as a sum >6. The Gastrointestinal Symptom Response Scale was completed weekly.

RESULTS

Stress was positively related to diarrhea, indigestion, and reflux syndromes and with abdominal pain, average daily cold or flu SI score, and the percentage of days with cold or flu. Gastrointestinal symptom scores for diarrhea (P = 0.0298), constipation (P = 0.0342), abdominal pain (P = 0.0058), and indigestion (P = 0.0003) syndromes were lower after galactooligosaccharide supplementation. The cold or flu SI score was affected by galactooligosaccharides and stress (P < 0.0001); 2.5 g was associated with a lower SI score across all levels of stress, but 5.0 g was protective only at lower levels of stress. The percentage of days with cold or flu was associated with galactooligosaccharides within different body mass index categories (P = 0.0002), wherein a 40% reduction in the percentage of days with cold or flu was observed in normal-weight individuals with 5.0 g galactooligosaccharides. This effect was not observed in overweight or obese individuals.

CONCLUSIONS

Acute psychological stress was directly related to symptoms of gastrointestinal dysfunction and cold or flu. Galactooligosaccharide supplementation reduced these symptoms and the number of days with cold or flu. This trial was registered at clinicaltrials.gov as NCT01137760.

SeqMaT: A sequence manipulation tool for phylogenetic analysis

Most bioinformatics tools require specialized input formats for sequence comparison and analysis. This is particularly true for molecular phylogeny programs, which accept only certain formats. In addition, it is often necessary to eliminate highly similar sequences among the input, especially when the dataset is large. Moreover, most programs have restrictions upon the sequence name. Here we introduce SeqMaT, a Sequence Manipulation Tool. It has the following functions: data format conversion,sequence name coding and decoding,redundant and highly similar sequence removal, anddata mining utilities. SeqMaT was developed using Java with two versions, web-based and standalone. A standalone program is convenient to manipulate a large number of sequences, while the web version will guarantee wide availability of the tool for researchers and practitioners throughout the Internet.

AVAILABILITY

The database is available for free at http://glee.ist.unomaha.edu/seqmat.

Social behavior drives the dynamics of respiratory disease in threatened tortoises

Since the early 1990s, morbidity and mortality in tortoise populations have been associated with a transmissible, mycoplasmal upper respiratory tract disease (URTD). Although the etiology, transmission, and diagnosis of URTD have been extensively studied, little is known about the dynamics of disease transmission in free-ranging tortoise populations. To understand the transmission dynamics of Mycoplasma agassizii, the primary etiological agent of URTD in wild tortoise populations, we studied 11 populations of free-ranging gopher tortoises (Gopherus polyphemus; n = 1667 individuals) over five years and determined their exposure to the pathogen by serology, by clinical signs, and by detection of the pathogen in nasal lavages. Adults tortoises (n = 759) were 11 times more likely to be seropositive than immature animals (n = 242) (odds ratio = 10.6, 95% CI = 5.7-20, P < 0.0001). Nasal discharge was observed in only 1.4% (4/296) of immature tortoises as compared with 8.6% (120/1399) of adult tortoises. Nasal lavages from all juvenile tortoises (n = 283) were negative by PCR for mycoplasmal pathogens associated with URTD. We tested for spatial segregation among tortoise burrows by size class and found no consistent evidence of clustering of either juveniles or adults. We suggest that the social behavior of tortoises plays a critical role in the spread of URTD in wild populations, with immature tortoises having minimal interactions with adult tortoises, thereby limiting their exposure to the pathogen. These findings may have broader implications for modeling horizontally transmitted diseases in other species with limited parental care and emphasize the importance of incorporating animal behavior parameters into disease transmission studies to better characterize the host-pathogen dynamics.

Short- and long-term movement patterns in complex confined environments in broiler chickens: the effects of distribution of cover panels and food resources

In captivity, the positioning of structural enrichment and food resources influences behavior and space use. The aim of this experiment was to examine the influence of cover panels and the positioning of food resources on the movement and space use of domestic fowl (Gallus gallus domesticus). Eight groups of 45 male chickens were used for this study. Each group was temporarily divided into 2 groups of 20 birds; each group was used to investigate the influence of cover panels and the effects of food resources. In the cover panel treatments, 20 birds were placed in the 10-m(2) testing enclosures that contained one 2-m cover panel in the center, four 0.5-m panels in a zigzag fashion, or had no panels (controls). In the food resource treatments, the position of the feed trays varied, with 1 feed tray in the center; 2 feed trays, one at each edge; or 4 feed trays, one at each corner of the enclosure. Locations of focal birds were collected through instantaneous scan sampling that was recorded as X,Y coordinates. From these X,Y coordinates, we calculated net and total distance moved, mean and maximum step lengths, and angular dispersion of the path of movement. To calculate long-term space use, 3 replications for each of 3 cover panel and food resource treatments were placed in nine 10-m(2) enclosures for 1 wk. Locations of focal birds in each group were collected by ad libitum scan sampling and data were used to calculate core areas by kernel estimates. Mixed model ANOVA was used to determine the effects of the distribution of cover panels and positioning of food resources on movement parameters during the study period, whereas 1-way ANOVA was used for core areas. Surprisingly, our analyses showed that long-term and short-term movement was not affected by changing the location of cover panels or food resources. Only net distance seemed to be affected to a certain degree by the presence of the cover and the distinctive availability of food resources.

Effects of contaminant exposure on reproductive success of ospreys (Pandion haliaetus) nesting in Delaware River and Bay, USA

Despite serious water-quality problems and pollutant loading and retention, Delaware River and Bay (USA) provide important wildlife habitat. In 2002, we conducted a comprehensive evaluation of contaminant exposure and reproduction of ospreys (Pandion haliaetus) breeding in Delaware River and Bay. Sample eggs were collected from 39 nests and analyzed for organochlorine pesticides, polychlorinated biphenyls (PCBs), and mercury; a subset of 15 eggs was analyzed for perfluorinated compounds and polybrominated diphenyl ethers (PBDEs). The fate of each nest was monitored weekly. Concentrations of 10 organochlorine pesticides or metabolites, total PCBs, and several toxic PCB congeners were greater (p < 0.05) in eggs collected between the Chesapeake and Delaware Canal (C and D Canal) and Trenton (Delaware River and northern Bay) compared to other sites. Concentrations of p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE; 0.785-3.84 microg/g wet wt) and total PCBs (5.50-14.5 microg/g wet wt) in eggs collected between the C and D Canal and Trenton were similar to levels recently found in the Chesapeake Bay. In all study segments, at least one young fledged from 66 to 75% of nests. Productivity for Delaware Inland Bays (reference area) and southern Delaware Bay was 1.17 and 1.42 fledglings/active nest, respectively; north of the C and D Canal, productivity was 1.00 fledgling/active nest, which is marginally adequate to maintain the population. Using these data, a logistic regression model found that contaminant concentrations (p,p'-DDE, heptachlor epoxide, chlordane and metabolites, and total PCBs) were predictive of hatching success. Several perfluorinated compounds and PBDEs were detected in eggs at concentrations approaching 1 microg/g wet weight. These findings provide evidence that contaminants continue to be a significant stressor on osprey productivity in the northern Delaware River and Bay.

Influence of phytase on water-soluble phosphorus in poultry and swine manure

The effect of dietary non-phytin phosphorus (NPP) and phytase (PHY) concentration on total phosphorus (TP) and water-soluble phosphorus (WSP) excretion was determined. Diets tested in broiler experiments were: National Research Council nutrient requirements for non-phytin phosphorus (NRC), NRC + PHY, reduced non-phytin phosphorus (RED), and RED + PHY. Turkey and swine experiment diets included NRC, RED, and RED + PHY. For all experiments, except broiler Experiment 1, excreta were: (i) boiled, antibiotic added, then frozen; (ii) boiled, antibiotic added, incubated (37 degrees C for 72 h), then frozen; and (iii) incubated, boiled, antibiotic added, then frozen. In Experiment 1, excreta were collected and frozen or incubated for 24 or 48 h. In broiler Experiment 1, WSP was not affected by phytase but increased with post-excretion incubation. In a broiler Experiment 2, reducing NPP resulted in reduced excreta TP and WSP (11.3 to 8.3 and 5.3 to 2.7 g kg(-1)). Feeding RED + PHY diets resulted in less TP and WSP (7.6 and 0.6 g kg(-1)) as compared with NRC + PHY (11.2 and 3.9 g kg(-1), Experiment 3). Incubation resulted in increased WSP, irrespective of phytase addition such that WSP as a percent of TP was similar among treatments. Addition of antibiotics before incubation prevented the increase in WSP. Similar results were observed with turkey and swine. Therefore, when phytase is used properly (i.e., with a simultaneous reduction of NPP), WSP or WSP as a percent of TP are not affected. The increase in WSP as a percent of TP post-excretion is a function of excreta microbial activity and not dietary phytase addition.

Inverse adaptive cluster sampling

Consider a population in which the variable of interest tends to be at or near zero for many of the population units but a subgroup exhibits values distinctly different from zero. Such a population can be described as rare in the sense that the proportion of elements having nonzero values is very small. Obtaining an estimate of a population parameter such as the mean or total that is nonzero is difficult under classical fixed sample-size designs since there is a reasonable probability that a fixed sample size will yield all zeroes. We consider inverse sampling designs that use stopping rules based on the number of rare units observed in the sample. We look at two stopping rules in detail and derive unbiased estimators of the population total. The estimators do not rely on knowing what proportion of the population exhibit the rare trait but instead use an estimated value. Hence, the estimators are similar to those developed for poststratification sampling designs. We also incorporate adaptive cluster sampling into the sampling design to allow for the case where the rare elements tend to cluster within the population in some manner. The formulas for the variances of the estimators do not allow direct analytic comparison of the efficiency of the various designs and stopping rules, so we provide the results of a small simulation study to obtain some insight into the differences among the stopping rules and sampling approaches. The results indicate that a modified stopping rule that incorporates an adaptive sampling component and utilizes an initial random sample of fixed size is the best in the sense of having the smallest variance.

Bootstrap confidence intervals for adaptive cluster sampling

Consider a collection of spatially clustered objects where the clusters are geographically rare. Of interest is estimation of the total number of objects on the site from a sample of plots of equal size. Under these spatial conditions, adaptive cluster sampling of plots is generally useful in improving efficiency in estimation over simple random sampling without replacement (SRSWOR). In adaptive cluster sampling, when a sampled plot meets some predefined condition, neighboring plots are added to the sample. When populations are rare and clustered, the usual unbiased estimators based on small samples are often highly skewed and discrete in distribution. Thus, confidence intervals based on asymptotic normal theory may not be appropriate. We investigated several nonparametric bootstrap methods for constructing confidence intervals under adaptive cluster sampling. To perform bootstrapping, we transformed the initial sample in order to include the information from the adaptive portion of the sample yet maintain a fixed sample size. In general, coverages of bootstrap percentile methods were closer to nominal coverage than the normal approximation.