Rain, recreation and risk: Human activity and ecological disturbance create seasonal risk landscapes for the prey of an ambush predator.

Predation risk and prey responses exhibit fluctuations in space and time. Seasonal ecological disturbances can alter landscape structure and permeability to influence predator activity and efficacy, creating predictable patterns of risk for prey (seasonal risk landscapes). This may create corresponding seasonal shifts in antipredator behaviour, mediated by species ecology and trade-offs between risk and resources. Yet, how human recreation interacts with seasonal risk landscapes and antipredator behaviour remains understudied. In South Florida, we investigated the impact of a seasonal ecological disturbance, specifically flooding, which is inversely related to human activity, on interactions between Florida panthers (Puma concolor coryi) and white-tailed deer (Odocoileus virginianus). We hypothesized that human activity and ecological disturbances would interact with panther-deer ecology, resulting in the emergence of two distinct seasonal landscapes of predation risk and the corresponding antipredator responses. We conducted camera trap surveys across southwestern Florida to collect detection data on humans, panthers and deer. We analysed the influence of human site use and flooding on deer and panther detection probability, co-occurrence and diel activity during the flooded and dry seasons. Flooding led to decreased panther detections and increased deer detections, resulting in reduced deer-panther co-occurrence during the flooded season. Panthers exhibited increased nocturnality and reduced diel activity overlap with deer in areas with higher human activity. Supporting our hypothesis, panthers' avoidance of human recreation and flooding created distinct risk schedules for deer, driving their antipredator behaviour. Deer utilized flooded areas to spatially offset predation risk during the flooded season while increasing diurnal activity in response to human recreation during the dry season. We highlight the importance of understanding how competing risks and ecological disturbances influence predator and prey behaviour, leading to the generation of seasonal risk landscapes and antipredator responses. We emphasize the role of cyclical ecological disturbances in shaping dynamic predator-prey interactions. Furthermore, we highlight how human recreation may function as a 'temporal human shield,' altering seasonal risk landscapes and antipredator responses to reduce encounter rates between predators and prey.

Deer movement and resource selection during Hurricane Irma: implications for extreme climatic events and wildlife.

Extreme climatic events (ECEs) are increasing in frequency and intensity and this necessitates understanding their influence on organisms. Animal behaviour may mitigate the effects of ECEs, but field studies are rare because ECEs are infrequent and unpredictable. Hurricane Irma made landfall in southwestern Florida where we were monitoring white-tailed deer (Odocoileus virginianus seminolus) with GPS collars. We report on an opportunistic case study of behavioural responses exhibited by a large mammal during an ECE, mitigation strategies for reducing the severity of the ECE effects, and the demographic effect of the ECE based on known-fate of individual animals. Deer altered resource selection by selecting higher elevation pine and hardwood forests and avoiding marshes. Most deer left their home ranges during Hurricane Irma, and the probability of leaving was inversely related to home range area. Movement rates increased the day of the storm, and no mortality was attributed to Hurricane Irma. We suggest deer mobility and refuge habitat allowed deer to behaviourally mitigate the negative effects of the storm, and ultimately, aid in survival. Our work contributes to the small but growing body of literature linking behavioural responses exhibited during ECEs to survival, which cumulatively will provide insight for predictions of a species resilience to ECEs and improve our understanding of how behavioural traits offset the negative impacts of global climate change.

Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms.

Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish's long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (FST p-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.

Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI.

OBJECTIVE: Body mass index (BMI) is commonly used to assess obesity, which is associated with numerous diseases and negative health outcomes. BMI has been shown to be a heritable, polygenic trait, with close to 100 loci previously identified and replicated in multiple populations. We aim to replicate known BMI loci and identify novel associations in a trans-ethnic study population. SUBJECTS: Using eligible participants from the Population Architecture using Genomics and Epidemiology consortium, we conducted a trans-ethnic meta-analysis of 102 514 African Americans, Hispanics, Asian/Native Hawaiian, Native Americans and European Americans. Participants were genotyped on over 200 000 SNPs on the Illumina Metabochip custom array, or imputed into the 1000 Genomes Project (Phase I). Linear regression of the natural log of BMI, adjusting for age, sex, study site (if applicable), and ancestry principal components, was conducted for each race/ethnicity within each study cohort. Race/ethnicity-specific, and combined meta-analyses used fixed-effects models. RESULTS: We replicated 15 of 21 BMI loci included on the Metabochip, and identified two novel BMI loci at 1q41 (rs2820436) and 2q31.1 (rs10930502) at the Metabochip-wide significance threshold (P<2.5 × 10-7). Bioinformatic functional investigation of SNPs at these loci suggests a possible impact on pathways that regulate metabolism and adipose tissue. CONCLUSION: Conducting studies in genetically diverse populations continues to be a valuable strategy for replicating known loci and uncovering novel BMI associations.

The role of macrophages in the development of biliary injury in a lipopolysaccharide-aggravated hepatic ischaemia-reperfusion model.

INTRODUCTION: Endotoxins, in the form of lipopolysaccharides (LPS), are potent inducers of biliary injury. However the mechanism by which injury develops remains unclear. We hypothesized that hepatic macrophages are pivotal in the development of endotoxin-induced biliary injury and that no injury would occur in their absence. MATERIAL AND METHODS: Clodronate liposomes were used to deplete macrophages from the liver. Forty-eight rats were equally divided across six study groups: sham operation (sham), liposome treatment and sham operation (liposomes+sham), 1mg/kg LPS i.p. (LPS), liposome treatment and LPS administration (liposomes+LPS), hepatic ischaemia-reperfusion injury with LPS administration (IRI+LPS) and liposome treatment followed by IRI+LPS (liposomes+IRI+LPS). Following 6h of reperfusion, blood, bile, and liver tissue was collected for further analysis. Small bile duct injury was assessed, serum liver tests were performed and bile composition was evaluated. The permeability of the blood-biliary barrier (BBB) was assessed using intravenously administered horseradish peroxidase (HRP). RESULTS: The presence of hepatic macrophages was reduced by 90% in LPS and IRI+LPS groups pre-treated with clodronate liposomes (P<0.001). Severe small bile duct injury was not affected by macrophage depletion, and persisted in the liposomes+IRI+LPS group (50% of animals) and liposomes+LPS group (75% of animals). Likewise, BBB impairment persisted following macrophage depletion. LPS-induced elevation of the chemokine Mcp-1 in bile was not affected by macrophage depletion. CONCLUSIONS: Depletion of hepatic macrophages did not prevent development of biliary injury following LPS or LPS-enhanced IRI. Cholangiocyte activation rather than macrophage activation may underlie this injury. This article is part of a Special Issue entitled: Cholangiocytes in Health and Diseaseedited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.

A pilot intervention to reduce postpartum weight retention and central adiposity in first-time mothers: results from the mums OnLiNE (Online, Lifestyle, Nutrition & Exercise) study.

BACKGROUND: Postpartum weight retention (PPWR) increases the risk for obesity and complications during subsequent pregnancies. Few interventions have been successful in limiting PPWR in mothers. The present study assessed the effectiveness of the mums OnLiNE (Online, Lifestyle, Nutrition & Exercise) intervention with respect to reducing PPWR and improving diet, physical activity and sedentary behaviour. METHODS: A subsample of first-time mothers enrolled in the Extended Melbourne Infant Feeding Activity and Nutrition Trial (InFANT Extend) completed the nonrandomised mums OnLiNE intervention. Women in the intervention (I) group (n = 28) received access to an online calorie tracking program, smartphone app, three telephone counselling calls with a dietitian and written material. Women in two comparison groups (CI and C2) (n = 48; n = 43) were from the control (C1) and intervention (C2) arms of InFANT Extend and received no additional support. Weight and waist circumference were measured objectively. Written surveys assessed diet and physical activity. Sedentary behaviour was self-reported. Linear and logistic regression assessed changes in outcomes between groups from 9 to 18 months postpartum. RESULTS: Mean PPWR decreased in the (I) group (-1.2 kg) and the C2 group (-1.2 kg), although the changes were not significant. Mean waist circumference for all groups exceeded recommendations at baseline but decreased to below recommendations for women in the (I) group (78.3 cm) and significantly for the (I) group (-6.4 cm) compared to C1 (-1.1 cm; P = 0.002) and C2 (-3.3 cm; P = 0.001). Changes in diet, physical activity or sedentary behaviour were not significant. CONCLUSIONS: The online intervention reported in the present study shows promise with respect to reducing waist circumference in postpartum women. Further evidence of strategies that may improve weight and related behaviours in this target group is needed.

Image-based closed-loop feedback for highly mono-dispersed microdroplet production.

Micron-scale droplets isolated by an immiscible liquid can provide miniaturised reaction vessels which can be manipulated in microfluidic networks, and has seen a rapid growth in development. In many experiments, the precise volume of these microdroplets is a critical parameter which can be influenced by many external factors. In this work, we demonstrate the combination of imaging-based feedback and pressure driven pumping to accurately control the size of microdroplets produced in a microfluidic device. The use of fast-response, pressure-driving pumps allows the microfluidic flow to be quickly and accurately changed, while directly measuring the droplet size allows the user to define the more meaningful parameters of droplet size and generation frequency rather than flow rates or pressures. The feedback loop enables the drift correction of pressure based pumps, and leads to a large increase in the mono-dispersity of the droplets produced over long periods. We also show how this can be extended to control multiple liquid flows, allowing the frequency of droplet formation or the average concentration of living cells per droplet to be controlled and kept constant.

Fine-scale genetic structure due to adaptive divergence among microhabitats.

It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic-does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3-2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate ⩽1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.

What predicts children's active transport and independent mobility in disadvantaged neighborhoods?

This study examined two year changes in children's active transport and independent mobility and prospective associations between individual, social and physical environmental predictors of interest and these behaviors two years later. Overall, 43.5% of children (12.0±2.1 years) used active transport on the school journey at T1 and at T2 (p=0.77), and 35.3% engaged in independent mobility on the school journey at T1 and 29.6% at T2 (p=0.07). Enjoyment, parental safety concerns, and proximity to walking tracks were associated with independent mobility on the school journey. Road safety and social norms were associated with active transport and independent mobility to local destinations. These factors provide potential targets for interventions.

A mobile health intervention promoting healthy gestational weight gain for women entering pregnancy at a high body mass index: the txt4two pilot randomised controlled trial.

OBJECTIVE: To determine the feasibility and effectiveness of an mHealth intervention promoting healthy diet, physical activity and gestational weight gain in pregnant women. DESIGN: Randomised controlled trial (RCT). SETTING: Australian tertiary obstetric hospital. POPULATION: One hundred pregnant women who were overweight or obese prior to pregnancy. METHODS: Women recruited at the first antenatal clinic visit were randomised to either an intervention or a control group. The intervention consisted of a tailored suite of strategies delivered (from first antenatal visit until 36 weeks' gestation) via multiple modalities available on mobile devices. MAIN OUTCOME MEASURES: The primary outcome was intervention feasibility and secondary outcomes were objectively measured changes in gestational weight gain (GWG) and self-reported dietary intake and physical activity. RESULTS: Ninety-one women completed the study. Delivery to protocol provides evidence of program feasibility. Most women engaged regularly with the program, with the majority (97.6%) reporting that the intervention was helpful. Secondary outcomes demonstrated a significantly lower GWG in the intervention group (7.8 kg ± 4.7 versus 9.7 kg ± 3.9; P =0.041) compared with the control group at intervention completion. Intervention group women reported significantly smaller reductions in total, light- and moderate-intensity physical activity from baseline to completion of the intervention (P = 0.001) compared with the control group, but no differences in consumption frequencies of key food groups. CONCLUSION: An intervention that aimed to deliver healthy diet, physical activity and GWG guidance utilising innovative technology can be feasibly implemented and produce positive physical activity and GWG outcomes. TWEETABLE ABSTRACT: txt4two mHealth study improved gestational weight gain and physical activity in pregnant women with high BMIs.

Time to viral suppression is not related to achievement of SVR12 in HCV GT1-infected patients treated with ombitasvir/paritaprevir/ritonavir and dasabuvir with or without ribavirin.

High rates of sustained virologic response at post-treatment week 12 (SVR12) were achieved in six phase 3 trials of ombitasvir (OBV, an NS5A inhibitor), paritaprevir (an NS3/4A protease inhibitor) co-dosed with ritonavir (PTV/r) + dasabuvir (DSV, an NS5B RNA polymerase inhibitor) (ie, 3D regimen) with or without ribavirin (RBV) in adults with chronic genotype (GT) 1 hepatitis C virus (HCV) infection. We assessed whether time to first HCV RNA value below the lower limit of quantification in patients with and without cirrhosis was associated with achievement of SVR12. Data were analysed from GT1-infected patients enrolled in six phase 3 studies of 3D ± RBV. Patients who experienced non-virologic failure were excluded from analysis. HCV RNA was determined using the Roche COBAS TaqMan RT-PCR assay (lower limit of quantification, LLOQ =25 IU/mL). SVR12 was analysed by week of first HCV RNA suppression, defined as HCV RNA

Genomic variation among populations of threatened coral: Acropora cervicornis.

BACKGROUND: Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species' ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic. RESULTS: Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county. CONCLUSIONS: Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network.

Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE-PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of "precision medicine." The February 2015 eMERGE-PGx data release includes sequence-derived data from ∼5,000 clinical subjects. We present the variant frequency spectrum categorized by variant type, ancestry, and predicted function. We found 95.12% of genes have variants with a scaled Combined Annotation-Dependent Depletion score above 20, and 96.19% of all samples had one or more Clinical Pharmacogenetics Implementation Consortium Level A actionable variants. These data highlight the distribution and scope of genetic variation in relevant pharmacogenes, identifying challenges associated with implementing clinical sequencing for drug treatment at a broader level, underscoring the importance for multifaceted research in the execution of precision medicine.

Efficient continuous synthesis of high purity deep eutectic solvents by twin screw extrusion.

Mechanochemical synthesis has been applied to the rapid synthesis of Deep Eutectic Solvents (DESs), including Reline 200 (choline chloride : urea, 1 : 2), in a continuous flow methodology by Twin Screw Extrusion (TSE). This gave products in higher purity and with Space Time Yields (STYs), four orders of magnitude greater than for batch methods.

A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough.

The most common side effect of angiotensin-converting enzyme inhibitor (ACEi) drugs is cough. We conducted a genome-wide association study (GWAS) of ACEi-induced cough among 7080 subjects of diverse ancestries in the Electronic Medical Records and Genomics (eMERGE) network. Cases were subjects diagnosed with ACEi-induced cough. Controls were subjects with at least 6 months of ACEi use and no cough. A GWAS (1595 cases and 5485 controls) identified associations on chromosome 4 in an intron of KCNIP4. The strongest association was at rs145489027 (minor allele frequency=0.33, odds ratio (OR)=1.3 (95% confidence interval (CI): 1.2-1.4), P=1.0 × 10(-8)). Replication for six single-nucleotide polymorphisms (SNPs) in KCNIP4 was tested in a second eMERGE population (n=926) and in the Genetics of Diabetes Audit and Research in Tayside, Scotland (GoDARTS) cohort (n=4309). Replication was observed at rs7675300 (OR=1.32 (1.01-1.70), P=0.04) in eMERGE and at rs16870989 and rs1495509 (OR=1.15 (1.01-1.30), P=0.03 for both) in GoDARTS. The combined association at rs1495509 was significant (OR=1.23 (1.15-1.32), P=1.9 × 10(-9)). These results indicate that SNPs in KCNIP4 may modulate ACEi-induced cough risk.

Population Genomics of the Euryhaline Teleost Poecilia latipinna.

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.

Does food store access modify associations between intrapersonal factors and fruit and vegetable consumption?

BACKGROUND/OBJECTIVES: Existing theoretical frameworks suggest that healthy eating is facilitated by an individual's ability, motivation and environmental opportunities. It is plausible, although largely untested, that the importance of factors related to ability and motivation differ under varied environmental conditions. This study aimed to determine whether the magnitude of associations between fruit and vegetable consumption and intrapersonal factors (ability and motivation) were modified by differences in access to stores selling these items (environmental opportunities). SUBJECTS/METHODS: Cross-sectional analysis of 4335 women from socioeconomically disadvantaged neighbourhoods in the state of Victoria, Australia. Self-reported fruit and vegetable consumption was assessed against a number of ability- and motivation-related factors. To examine whether associations were modified by store access, interactions with access to supermarkets and greengrocers within 2 km of participants' households were tested. RESULTS: Of the two factors related to ability and seven factors related to motivation, almost all were associated with fruit and vegetable consumption. In general, associations were not modified by store access suggesting that these factors were not tempered by environmental opportunities. CONCLUSIONS: This study provides little support for the hypothesis that the importance of intra-personal factors to fruit and vegetable consumption is modified by food store access. Further research on this topic is required to inform behaviour change interventions.

Evaluation of phylogenetic relationships in Lemnaceae using nuclear ribosomal data.

Nuclear DNA sequence data are essential for obtaining a complete understanding of plant species relationships, yet these data have been conspicuously absent from phylogenetic analyses of Lemnaceae (duckweeds). Using a modified Sanger sequencing protocol, we obtained DNA sequences of duckweed nuclear ribosomal regions, including 18S and 26S rDNA genes, the external transcribed spacer (ETS) and the frequently used internal transcribed spacer (ITS). After obtaining sequence data for all Lemnaceae species, we ascertained that prior difficulty in sequencing the ITS regions likely resulted from extremely rigid secondary structures, precipitated by a high proportion of G/C nucleotides. In phylogenetic analyses, nuclear ribosomal data largely supported relationships that had been inferred using chloroplast DNA sequence data.

Genetic variation in the HLA region is associated with susceptibility to herpes zoster.

Herpes zoster, commonly referred to as shingles, is caused by the varicella zoster virus (VZV). VZV initially manifests as chicken pox, most commonly in childhood, can remain asymptomatically latent in nerve tissues for many years and often re-emerges as shingles. Although reactivation may be related to immune suppression, aging and female sex, most inter-individual variability in re-emergence risk has not been explained to date. We performed a genome-wide association analyses in 22,981 participants (2280 shingles cases) from the electronic Medical Records and Genomics Network. Using Cox survival and logistic regression, we identified a genomic region in the combined and European ancestry groups that has an age of onset effect reaching genome-wide significance (P>1.0 × 10(-8)). This region tags the non-coding gene HCP5 (HLA Complex P5) in the major histocompatibility complex. This gene is an endogenous retrovirus and likely influences viral activity through regulatory functions. Variants in this genetic region are known to be associated with delay in development of AIDS in people infected by HIV. Our study provides further suggestion that this region may have a critical role in viral suppression and could potentially harbor a clinically actionable variant for the shingles vaccine.