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.

Three probiotic strains exert different effects on plasma bile acid profiles in healthy obese adults: randomised, double-blind placebo-controlled crossover study.

Microbial metabolism in the gut may alter human bile acid metabolism in a way that beneficially affects lipid homeostasis and therefore cardiovascular disease risk. Deconjugation of bile acids by microbes is thought to be key to this mechanism but has yet to be characterised in blood and stool while observing lipid markers. The aim of this study was to determine the effect of 3 different probiotic strains on plasma and stool bile acids in the context of lipid and glucose metabolism. In this 18-week, randomised, double-blind crossover study, healthy adults (53±8 years) with a high waist circumference underwent a 1-week pre-baseline period and were then randomised to receive 1 capsule/day of Bacillus subtilis R0179 (2.5×109 cfu/capsule; n=39), Lactobacillus plantarum HA-119 (5×109 cfu/capsule; n=38), Bifidobacterium animalis subsp. lactis B94 (5×109 cfu/capsule; n=37) or placebo for 6 weeks. Following a 3-week washout and second pre-baseline week, participants were crossed to the other intervention for 6 weeks followed by a 1-week post-intervention period. Blood and stool samples were collected at the beginning and end of each intervention to measure bile acids, serum lipid profiles, and glucose and insulin levels. Data from the placebo intervention were combined for all participants for analyses. In obese participants, the difference (final-baseline) in the sum of deconjugated plasma bile acids was greater with consumption of B. subtilis (691±378 nmol/l, P=0.01) and B. lactis (380±165 nmol/l, P=0.04) than with placebo (98±176 nmol/l, n=57). No significant differences were observed for any probiotics for stool bile acids, serum lipids, blood glucose or insulin. These data suggest that B. subtilis and B. lactis had no effect on glucose metabolism or serum cholesterol but increased deconjugated plasma bile acids in obese individuals. Additional studies should be conducted to confirm these findings and explore potential mechanisms. This trial was registered at clinicaltrials.gov as NCT01879098.

EMR documentation of physician-patient communication following genomic counseling for actionable complex disease and pharmacogenomic results.

Genomic risk information for potentially actionable complex diseases and pharmacogenomics communicated through genomic counseling (GC) may motivate physicians and patients to take preventive actions. The Ohio State University-Coriell Personalized Medicine Collaborative is a randomized trial to measure the effects of in-person GC on chronic disease patients provided with multiplex results. Nine personalized genomic risk reports were provided to patients through a web portal, and to physicians via electronic medical record (EMR). Active arm participants (98, 39% female) received GC within 1 month of report viewing; control arm subjects (101, 54% female) could access counseling 3-months post-report viewing. We examined whether GC affected documentation of physician-patient communication by reviewing the first clinical note following the patient's GC visit or report upload to the EMR. Multivariable logistic regression modeling estimated the independent effect of GC on physician-patient communication, as intention to treat (ITT) and per protocol (PP), adjusted for physician educational intervention. Counselees in the active arm had more physician-patient communications than control subjects [ITT, odds ratio (OR): 3.76 (95% confidence interval (CI): 1.38-10.22, p < 0.0094); PP, OR: 5.53 (95% CI: 2.20-13.90, p = 0.0017). In conclusion, GC appreciably affected physician-patient communication following receipt of potentially actionable genomic risk information.

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.

Direct-to-consumer genetic testing: Perspectives on its value in healthcare.

The direct-to-consumer genetic testing debate reached a fever pitch in November 2013 when the US Food and Drug Administration (FDA) instructed 23andMe to discontinue marketing and sale of their Personal Genome Service. In 2015, 23andMe emerged with FDA approval to market a carrier test for Bloom syndrome only, and plans to release additional reports. The dust has settled and it is time to ask: What have we learned, and where do we go from here?

Calcium phosphate supplementation increases faecal Lactobacillus spp. in a randomised trial of young adults.

The aim of the studies was to determine the effects of calcium carbonate and calcium phosphate supplementation on faecal Lactobacillus spp., with and without a probiotic supplement, in healthy adults. Study 1 comprised of a randomised, double-blind, crossover design; participants (n=15) received 2 capsules/d of 250 mg elemental calcium as calcium carbonate (Ca1) and calcium phosphate (Ca2) each for 2-week periods, with 2-week baseline and washout periods. Study 2 was a randomised, double-blind, crossover design; participants (n=17) received 2 capsules/d of Lactobacillus helveticus R0052 and Lactobacillus rhamnosus R0011 (probiotic) alone, the probiotic with 2 capsules/d of Ca1, and probiotic with 2 capsules/d of Ca2 each for 2-week periods with 2-week baseline and washout periods. In both studies, stools were collected during the baseline, intervention and washout periods for Lactobacillus spp. quantification and qPCR analyses. Participants completed daily questionnaires of stool frequency and compliance. In Study 1, neither calcium supplement influenced viable counts of resident Lactobacillus spp., genome equivalents of lactic acid bacteria or stool frequency. In Study 2, faecal Lactobacillus spp. counts were significantly enhanced from baseline when the probiotic was administered with Ca2 (4.83±0.30, 5.79±0.31) (P=0.02), but not with Ca1 (4.98±0.31) or with the probiotic alone (5.36±0.31, 5.55±0.29) (not significant). Detection of L. helveticus R0052 and L. rhamnosus R0011 was significantly increased with all treatments, but did not differ among treatments. There were no changes in weekly stool frequency. Calcium phosphate co-administration may increase gastrointestinal survival of orally-administered Lactobacillus spp.

Evaluation of Bacillus subtilis R0179 on gastrointestinal viability and general wellness: a randomised, double-blind, placebo-controlled trial in healthy adults.

A probiotic formulation of Enterococcus faecium R0026 and Bacillus subtilis R0179 has been evaluated in previous clinical trials. However, B. subtilis R0179 has not been evaluated as a single probiotic strain or in combination with other strains at doses higher than 0.1×109 cfu. To establish oral dose-response tolerance and gastrointestinal (GI) viability of B. subtilis R0179, a randomised, double-blind, placebo-controlled trial in healthy adults (n=81; 18-50 years old) was conducted. Participants received B. subtilis R0179 at 0.1, 1.0 or 10×109 cfu/capsule/day or placebo for four weeks. General wellness was assessed using a daily questionnaire evaluating GI, cephalic, ear-nose-throat, behavioural, emetic, and epidermal symptoms. GI symptoms were further evaluated using a weekly gastrointestinal symptom rating scale (GSRS). GI transit viability of B. subtilis R0179 was assessed by plating and microbiota analysis by 16S rRNA at baseline, week 4 of the intervention and washout. General wellness and GI function were not affected by oral consumption of B. subtilis R0179 at any dose. Daily questionnaire syndrome scores were not different from baseline and did not exceed a clinically significant score of 1. GSRS syndrome scores were not different from baseline and ranged from 1.1±0.1 to 1.9±0.2. Faecal viable counts of B. subtilis R0179 demonstrated a dose response: the placebo group (1.1±0.1 log10 cfu/g) differed from 0.1×109 (4.6±0.1 log10 cfu/g), 1×109 (5.6±0.1 log10 cfu/g) and 10×109 (6.4±0.1 log10 cfu/g) (P<0.0001). No significant changes in phyla were observed, but sequence reads binned to multiple operational taxonomic units matching closest to Ruminococci increased during probiotic supplementation. B. subtilis R0179 survives passage through the human GI tract and is well tolerated by healthy adults at intakes from 0.1 to 10×109 cfu/day. The trial has been registered at www.clinicaltrials.gov under NCT01802151.

Motivations and perceptions of early adopters of personalized genomics: perspectives from research participants.

BACKGROUND/AIMS: To predict the potential public health impact of personal genomics, empirical research on public perceptions of these services is needed. In this study, 'early adopters' of personal genomics were surveyed to assess their motivations, perceptions and intentions. METHODS: Participants were recruited from everyone who registered to attend an enrollment event for the Coriell Personalized Medicine Collaborative, a United States-based (Camden, N.J.) research study of the utility of personalized medicine, between March 31, 2009 and April 1, 2010 (n = 369). Participants completed an Internet-based survey about their motivations, awareness of personalized medicine, perceptions of study risks and benefits, and intentions to share results with health care providers. RESULTS: Respondents were motivated to participate for their own curiosity and to find out their disease risk to improve their health. Fewer than 10% expressed deterministic perspectives about genetic risk, but 32% had misperceptions about the research study or personal genomic testing. Most respondents perceived the study to have health-related benefits. Nearly all (92%) intended to share their results with physicians, primarily to request specific medical recommendations. CONCLUSION: Early adopters of personal genomics are prospectively enthusiastic about using genomic profiling information to improve their health, in close consultation with their physicians. This suggests that early users (i.e. through direct-to-consumer companies or research) may follow up with the health care system. Further research should address whether intentions to seek care match actual behaviors.

Replication of genome-wide association studies (GWAS) loci for fasting plasma glucose in African-Americans.

AIMS/HYPOTHESIS: Chronically elevated blood glucose (hyperglycaemia) is the primary indicator of type 2 diabetes, which has a prevalence that varies considerably by ethnicity in the USA, with African-Americans disproportionately affected. Genome-wide association studies (GWASs) have significantly enhanced our understanding of the genetic basis of diabetes and related traits, including fasting plasma glucose (FPG). However, the majority of GWASs have been conducted in populations of European ancestry. Thus, it is important to conduct replication analyses in populations with non-European ancestry to identify shared loci associated with FPG across populations. METHODS: We used data collected from non-diabetic unrelated African-American individuals (n = 927) who participated in the Howard University Family Study to attempt to replicate previously published GWASs of FPG. Of the 29 single nucleotide polymorphisms (SNPs) previously reported, we directly tested 20 in this study. In addition to the direct test, we queried a 500 kb window centred on all 29 reported SNPs for local replication of additional markers in linkage disequilibrium (LD). RESULTS: Using direct SNP and LD-based comparisons, we replicated multiple SNPs previously associated with FPG and strongly associated with type 2 diabetes in populations with European ancestry. The replicated SNPs included those in or near TCF7L2, SLC30A8, G6PC2, MTNR1B, DGKB-TMEM195 and GCKR. We also replicated additional variants in LD with the reported SNPs in ZMAT4 and adjacent to IRS1. CONCLUSIONS/INTERPRETATION: We identified multiple GWAS variants for FPG in our cohort of African-Americans. Using an LD-based strategy we also identified SNPs not previously reported, demonstrating the utility of using diverse populations for replication analysis.

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.

Evaluation of the broiler's ability to adapt to an early moderate deficiency of phosphorus and calcium.

We studied the ability of broiler chickens to adapt to early moderate P and Ca deficiencies by evaluating the impact of feeding different concentrations of P and Ca, from 1 to 18 d, on performance, bone characteristics, and nutrient absorption in the grower (Gr) period (18 to 32 d). Two starter (St) diets were fed from 1 to 18 d: a control (C) diet [0.45% nonphytate P (nPP) and 0.9% Ca] and a low (L) diet (0.30% nPP and 0.6% Ca). On d 19, half of the birds fed the St C diet were switched to a Gr C diet (0.40% nPP and 0.8% Ca), and the other half were switched to a Gr L diet (0.30% nPP and 0.6% Ca), whereas those fed the L diet in the St phase were fed the L diet in the Gr phase, resulting in a total of 3 treatments. Broiler chickens fed the St L diet weighed less (P < 0.05) than those fed the St C diet at 18 d; however, by 23 d they had they caught up to the C-C birds, and no BW differences (P > 0.05) were observed at 28 and 32 d. Feeding the St L diet resulted in decreased (P < 0.05) tibia ash at 18 d, but by 32 d their tibia ash was not different from that of birds fed the St C and Gr L diets. Broilers subjected to P and Ca restriction from hatch to 18 d absorbed more P and Ca during all times sampled than birds fed the St C and Gr C diets or those fed the St C and the Gr L diet. These results demonstrated that modern broilers exhibited a high adaptive capacity when they were exposed to early dietary P or Ca restrictions.

Influence of dietary calcium and phytase on phytate phosphorus hydrolysis in broiler chickens.

The effect of Ca and phytase on phytate phosphorus (PP) hydrolysis was studied in vitro and in vivo. In vitro, PP hydrolysis by a 3-phytase and a 6-phytase was studied at pH 2.5 and 6.5 with Ca added at levels equivalent to 0, 0.1, 0.2, 0.4, 0.7, or 0.9% of the diet. Irrespective of enzyme, Ca at a level as low as 0.1% reduced (P < 0.05) PP hydrolysis at pH 6.5. To test these effects in vivo, 22-d-old male broilers were fed 1 of 6 diets (10 replicate pens of 4 birds per diet) for 30 h. The experimental design was a 3 x 2 factorial arrangement of 3 phytase treatments (0, 500 U of phytase A/kg of diet, and 500 U of phytase B/kg of diet) and 2 added Ca levels (0 and 0.5% from CaCO3) to a corn-soy basal diet. Adding Ca to the diet resulted in a reduction (P < 0.05) in ileal PP disappearance from 69.2 to 25.4% when the 0 and 0.5% added Ca diets were fed, respectively, and in apparent ileal Ca and P absorption (46.3 to 33.6% and 67.9 to 29.4% when 0 and 0.5% Ca were added, respectively). Inclusion of a 3-phytase improved (P < 0.05) ileal PP disappearance from 25.4 to 58.9% in diets containing 0 and 0.5% added Ca, but the improvement was less pronounced with a 6-phytase. Apparent ileal Ca absorption was improved (P < 0.05) when Ca, phytase, or both were added to the diet.

Separase anxiety: dissolving the sister bond and more.

Separase is a protease that cleaves the bonds between sister chromatids during cell division. Until now, separase was thought to be a somewhat repressed protease, cleaving only a few substrates in a very controlled fashion. New findings in this issue raise the possibility that separase has some of the atavistic impulses that characterize caspases, its more destructive relatives.

Evidence that replication fork components catalyze establishment of cohesion between sister chromatids.

Accurate chromosome segregation requires that replicated sister chromatids are held together until anaphase, when their "cohesion" is dissolved, and they are pulled to opposite spindle poles by microtubules. Establishment of new cohesion between sister chromatids in the next cell cycle is coincident with replication fork passage. Emerging evidence suggests that this temporal coupling is not just a coincident timing of independent events, but rather that the establishment of cohesion is likely to involve the active participation of replication-related activities. These include PCNA, a processivity clamp for some DNA polymerases, Trf4/Pol final sigma (formerly Trf4/Pol kappa), a novel and essential DNA polymerase, and a modified Replication Factor C clamp--loader complex. Here we describe recent advances in how cohesion establishment is linked to replication, highlight important unanswered questions in this new field, and describe a "polymerase switch" model for how cohesion establishment is coupled to replication fork progression. Building the bridges between newly synthesized sister chromatids appears to be a fundamental but previously unrecognized function of the eukaryotic replication machinery.

Replication-related activities establish cohesion between sister chromatids.

Replicated sister chromatids are held together from their synthesis in S phase to their separation in anaphase. The process of sister chromatid cohesion is essential for the proper segregation of chromosomes in eukaryotic cells. Recent studies in Saccharomyces cerevisiae have advanced our understanding of how sister chromatid cohesion is established, maintained, and dissolved during the cell cycle. Historical observations have suggested that establishment of cohesion is roughly coincident with replication fork passage. Emerging evidence now indicates that replication fork components, such as PCNA, a novel DNA polymerase, Trf4p/Pol sigma (formerly Trf4p/Pol kappa), and a modified clamp-loader complex, actively participate in the process of the cohesion establishment. Here, we review the molecular events in the chromosome cycle with respect to cohesion. Failure of sister chromatid cohesion results in the aneuploidy characteristic of many birth defects and tumors in humans.

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.

Pol kappa: A DNA polymerase required for sister chromatid cohesion.

Establishment of cohesion between sister chromatids is coupled to replication fork passage through an unknown mechanism. Here we report that TRF4, an evolutionarily conserved gene necessary for chromosome segregation, encodes a DNA polymerase with beta-polymerase-like properties. A double mutant in the redundant homologs, TRF4 and TRF5, is unable to complete S phase, whereas a trf4 single mutant completes a presumably defective S phase that results in a failure of cohesion between the replicated sister chromatids. This suggests that TRFs are a key link in the coordination between DNA replication and sister chromatid cohesion. Trf4 and Trf5 represent the fourth class of essential nuclear DNA polymerases (designated DNA polymerase kappa) in Saccharomyces cerevisiae and probably in all eukaryotes.

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.