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Abstract Identifying transitional states is crucial for understanding protein conformational changes that underlie numerous biological processes. Markov state models (MSMs), built from Molecular Dynamics (MD) simulations, capture these dynamics through transitions among metastable conformational states, and have demonstrated success in studying protein conformational changes. However, MSMs face challenges in identifying transition states, as they partition MD conformations into discrete metastable states (or free energy minima), lacking description of transition states located at the free energy barriers. Here, we introduce Transition State identification via Dispersion and vAriational principle Regularized neural networks (TS-DAR), a deep learning framework inspired by out-of-distribution (OOD) detection in trustworthy artificial intelligence (AI). TS-DAR offers an end-to-end pipeline that can simultaneously detect all transition states between multiple free minima from MD simulations using the regularized hyperspherical embeddings in latent space. The key insight of TS-DAR lies in treating transition state structures as OOD data, recognizing that they are sparsely populated and exhibit a distributional shift from metastable states. We demonstrate the power of TS-DAR by applying it to a 2D potential, alanine dipeptide, and the translocation of a DNA motor protein on DNA, where it outperforms previous methods in identifying transition states.

Abstract Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to the proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance. Utilizing a benchmark dataset, MedReview, consisting of 8161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the performance of open-source models was all improved after fine-tuning. The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were manifested in both a human evaluation and a larger-scale GPT4-simulated evaluation.

Summary: Memory has been identified as the least heritable cognitive trait in canines, suggesting a significant influence of non-genetic factors. We observed a trend that overall memory scores (OMS) improve with age in a cohort of 27 young dogs, but considerable plasticity exists. Employing linear discriminant analysis of gut microbiome data from dogs exhibiting low and high OMS, a single bacterial species, Bifidobacterium pseudolongum, was identified and confirmed to be correlated with elevated OMS. Subsequent analysis using a random forest regression model revealed that sex, litter, and breed identity had minimal predictive importance. Age had some predictive value but failed to achieve statistical significance in this dataset. In sharp contrast, the abundance of 17 bacterial taxa in the microbiome showed a stronger predictive capacity for memory performance. Our findings provide insights into microbiome underpinnings of mammalian cognitive functions and suggest avenues for developing psychobiotics to enhance canine memory and learning.

Abstract Chronic kidney disease (CKD) is determined by an interplay of monogenic, polygenic, and environmental risks. Autosomal dominant polycystic kidney disease (ADPKD) and COL4A-associated nephropathy (COL4A-AN) represent the most common forms of monogenic kidney diseases. These disorders have incomplete penetrance and variable expressivity, and we hypothesize that polygenic factors explain some of this variability. By combining SNP array, exome/genome sequence, and electronic health record data from the UK Biobank and All-of-Us cohorts, we demonstrate that the genome-wide polygenic score (GPS) significantly predicts CKD among ADPKD monogenic variant carriers. Compared to the middle tertile of the GPS for noncarriers, ADPKD variant carriers in the top tertile have a 54-fold increased risk of CKD, while ADPKD variant carriers in the bottom tertile have only a 3-fold increased risk of CKD. Similarly, the GPS significantly predicts CKD in COL4A-AN carriers. The carriers in the top tertile of the GPS have a 2.5-fold higher risk of CKD, while the risk for carriers in the bottom tertile is not different from the average population risk. These results suggest that accounting for polygenic risk improves risk stratification in monogenic kidney disease.

Abstract Recent advances in large language models (LLMs) have demonstrated remarkable successes in zero- and few-shot performance on various downstream tasks, paving the way for applications in high-stakes domains. In this study, we systematically examine the capabilities and limitations of LLMs, specifically GPT-3.5 and ChatGPT, in performing zero-shot medical evidence summarization across six clinical domains. We conduct both automatic and human evaluations, covering several dimensions of summary quality. Our study demonstrates that automatic metrics often do not strongly correlate with the quality of summaries. Furthermore, informed by our human evaluations, we define a terminology of error types for medical evidence summarization. Our findings reveal that LLMs could be susceptible to generating factually inconsistent summaries and making overly convincing or uncertain statements, leading to potential harm due to misinformation. Moreover, we find that models struggle to identify the salient information and are more error-prone when summarizing over longer textual contexts.

Abstract Background Individuals that band together create new ecological opportunities for microorganisms. In vertical transmission, theory predicts a conserved microbiota within lineages, especially social bees. Bees exhibit solitary to social behavior among and/or within species, while life cycles can be annual or perennial. Bee nests may be used over generations or only once, and foraging ecology varies widely. To assess which traits are associated with bee microbiomes, we analyzed microbial diversity within solitary and social bees of Apidae, Colletidae, and Halictidae, three bee families in Panama’s tropical forests. Our analysis considered the microbiome of adult gut contents replicated through time, localities, and seasons (wet and dry) and included bee morphology and comparison to abdominal (dissected) microbiota. Diversity and distribution of tropical bee microbes (TBM) within the corbiculate bee clade were emphasized. Results We found the eusocial corbiculate bees tended to possess a more conserved gut microbiome, attributable to vertical transmission, but microbial composition varied among closely related species. Euglossine bees (or orchid bees), corbiculates with mainly solitary behavior, had more variable gut microbiomes. Their shorter-tongued and highly seasonal species displayed greater diversity, attributable to flower-visiting habits. Surprisingly, many stingless bees, the oldest corbiculate clade, lacked bacterial genera thought to predate eusociality, while several facultatively social, and solitary bee species possessed those bacterial taxa. Indeed, nearly all bee species displayed a range of affinities for single or multiple variants of the “socially associated” bacterial taxa, which unexpectedly demonstrated high sequence variation. Conclusions Taken together, these results call into question whether specific bacterial associates facilitate eusocial behavior, or are subsequently adopted, or indicate frequent horizontal transmission between perennial eusocial colonies and other social, facultatively social, and solitary bees. Video Abstract

While molecular testing is recommended for symptomatic patients suspected of having coronavirus disease 2019 (COVID-19), limited data are available examining real-world use of tests for severe acute respiratory syndrome coronavirus (SARS-CoV-2) and the impact of SARS-CoV-2 testing on patient outcomes. In this retrospective cohort study using de-identified administrative claims data in the Optum Labs Data Warehouse, we identified 2 groups of patients with ≥1 outpatient claims with a procedure code for SARS-CoV-2 testing between January 2021 and September 2022. Group 1 had ≥1 claims with CPT code 0240U or 0241U ("Xpert Xpress") (N = 51,602); Group 2 had ≥1 claims for laboratory-based molecular testing (N = 317,192). Outcomes assessed on the identification date and through the 90-day follow-up included claims evidence of use of SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) tests, diagnosis of active COVID-19, influenza, or RSV, and use of treatments (antivirals for COVID-19, influenza, and RSV and other treatments for COVID-19 and RSV). Patients in Group 1 had fewer tests for SARS-CoV-2, influenza, or RSV (mean ± standard deviation 1.6±1.4 versus 2.6±2.6, standardized difference -0.45), faster time to diagnosis of COVID-19 (median 0 versus 4 days, standardized difference -0.27) or influenza (median 0 versus 5 days, standardized difference -0.74), and faster time to treatment of COVID-19, influenza, or RSV (median 1 versus 5 days, standardized difference 0.16) than patients in Group 2. In this nationwide real-world study of outpatient testing, use of point-of-care molecular multiplex SARS-CoV-2 testing resulted in fewer claims for SARS-CoV-2, influenza, and RSV tests, faster time to diagnosis, and faster time to treatment than laboratory-based molecular testing.

Protecting diverse solitary ground-nesting bees remains a pivotal conservation concern. Ground-nesting bees are negatively impacted by anthropogenic land use change that often removes suitable nesting habitat from the landscape. Despite their enormous ecological and agricultural contributions to pollination, solitary, ground-nesting bees are often neglected, partly due to the significant obstacle of discovering exactly where these bees establish their nests. To address this limitation, we have developed a ‘community science’ project to map aggregations of ground-nesting bees globally. In certain locations, their abundances reach astounding levels, sometimes in the millions, but are scarcely known. Utilizing the iNaturalist platform, which permits geo-referencing of site observations and bee identification, we are providing public education and seeking public engagement to document bee aggregations in order to understand the nesting requirements of diverse species and open new opportunities for their conservation. Conservation priorities may then unequivocally be directed to areas of high species richness, nest densities, and nesting sites of rare bees. Such community-led efforts are vital for successful long-term management of native bees and the biotic and abiotic landscape data from nest-site localities can allow modeling to predict nest-site suitability and to readily test such predictions on the ground. Here, we summarize the progress, current limitations, and opportunities of using a global mapping project (GNBee) to direct conservation efforts and research toward solitary ground-nesting bees.

Abstract Introduction: Clinical research is critical for healthcare advancement, but participant recruitment remains challenging. Clinical research professionals (CRPs; e.g., clinical research coordinator, research assistant) perform eligibility prescreening, ensuring adherence to study criteria while upholding scientific and ethical standards. This study investigates the key information CRP prioritizes during eligibility prescreening, providing insights to optimize data standardization, and recruitment approaches. Methods: We conducted a freelisting survey targeting 150 CRPs from diverse domains (i.e., neurological disorders, rare diseases, and other diseases) where they listed essential information they look for from medical records, participant/caregiver inquiries, and discussions with principal investigators to determine a potential participant’s research eligibility. We calculated the salience scores of listed items using Anthropac, followed by a two-level analytic procedure to classify and thematically categorize the data. Results: The majority of participants were female (81%), identified as White (44%) and as non-Hispanic (64.5%). The first-level analysis universally emphasized age, medication list, and medical history across all domains. The second-level analysis illuminated domain-specific approaches in information retrieval: for instance, history of present illness was notably significant in neurological disorders during participant and principal investigator inquiries, while research participation was distinctly salient in potential participant inquiries within the rare disease domain. Conclusion: This study unveils the intricacies of eligibility prescreening, with both universal and domain-specific methods observed. Variations in data use across domains suggest the need for tailored prescreening in clinical research. Incorporating these insights into CRP training and refining prescreening tools, combined with an ethical, participant-focused approach, can advance eligibility prescreening practices.

Background:. Up to 25% of people with diabetes develop a diabetic foot ulcer (DFU) during their lifetime, which precedes approximately 85% of nontraumatic lower limb amputations. Diabetic limb salvage has been at the forefront of recent research, as major amputation is associated with 5-year mortality rates of 52%–80%. We sought to determine if ambulatory status before DFU diagnosis is predictive of amputations and outcomes within 1 year, as no studies have directly examined this relationship. Methods:. A retrospective review of patients diagnosed with DFUs from January 2011 to December 2021 was performed. Patients aged 18 years or more with type II diabetes were included. Ambulatory status was defined as the primary form of mobility reported by the patient before development of DFU, and was categorized as independent ambulation, ambulatory with assisting device (AWAD), or nonambulatory (NA). Statistical analyses included χ2, multinomial, and multivariable logistic regressions. Results:. After review, 506 patients were included. NA (OR = 5.10; P = 0.002) and AWAD status (OR = 2.77; P = 0.01) before DFU development were predictive of major (below or above-knee) amputation during hospitalization, emergency department visits within 30-days (NA: OR = 4.19; P = 0.01, AWAD: OR = 3.09; P = 0.02), and mortality within one-year (NA: OR = 4.19; P = 0.01, AWAD: OR = 3.09; P = 0.02). AWAD status was also associated with increased risk of hospital readmission (OR = 2.89; P < 0.001) within 30-days and any amputation (OR = 1.73; P = 0.01) within 1 year. Conclusions:. In patients with DFUs, NA and AWAD status were predictive of major amputation during hospitalization and are associated with poorer 1-year outcomes, including mortality. Ambulatory status assessment may be used to inform DFU treatment approaches.

Microbes, including diverse bacteria and fungi, play an important role in the health of both solitary and social bees. Among solitary bee species, in which larvae remain in a closed brood cell throughout development, experiments that modified or eliminated the brood cell microbiome through sterilization indicated that microbes contribute substantially to larval nutrition and are in some cases essential for larval development. To better understand how feeding larvae impact the microbial community of their pollen/nectar provisions, we examine the temporal shift in the bacterial community in the presence and absence of actively feeding larvae of the solitary, stem-nesting bee, Osmia cornifrons (Megachilidae). Our results indicate that the O. cornifrons brood cell bacterial community is initially diverse. However, larval solitary bees modify the microbial community of their pollen/nectar provisions over time by suppressing or eliminating rare taxa while favoring bacterial endosymbionts of insects and diverse plant pathogens, perhaps through improved conditions or competitive release. We suspect that the proliferation of opportunistic plant pathogens may improve nutrient availability of developing larvae through degradation of pollen. Thus, the health and development of solitary bees may be interconnected with pollen bacterial diversity and perhaps with the propagation of plant pathogens.

Understanding scaling relations of social and environmental attributes of urban systems is necessary for effectively managing cities. Urban scaling theory (UST) has assumed that population density scales positively with city size. We present a new global analysis using a publicly available database of 933 cities from 38 countries. Our results showed that (18/38) 47% of countries analyzed supported increasing density scaling (pop ~ area) with exponents ~⅚ as UST predicts. In contrast, 17 of 38 countries (~45%) exhibited density scalings statistically indistinguishable from constant population densities across cities of varying sizes. These results were generally consistent in years spanning four decades from 1975 to 2015. Importantly, density varies by an order of magnitude between regions and countries and decreases in more developed economies. Our results (i) point to how economic and regional differences may affect the scaling of density with city size and (ii) show how understanding country- and region-specific strategies could inform effective management of urban systems for biodiversity, public health, conservation and resiliency from local to global scales.200 word statement of contribution: Urban Scaling Theory (UST) is a general scaling framework that makes quantitative predictions for how many urban attributes spanning physical, biological and social dimensions scale with city size; thus, UST has great implications in guiding future city developments. A major assumption of UST is that larger cities become denser. We evaluated this assumption using a publicly available global dataset of 933 cities in 38 countries. Our scaling analysis of population size and area of cities revealed that while many countries analyzed showed increasing densities with city size, about 45% of countries showed constant densities across cities. These results question a key assumption of UST. Our results suggest policies and management strategies for biodiversity conservation, public health and sustainability of urban systems may need to be tailored to national and regional scaling relations to be effective.

The bacterium Bordetella bronchiseptica is responsible for serious respiratory disease in dogs, most often associated with ‘kennel cough’ (canine infectious tracheobronchitis). It is recommended that dogs are vaccinated against the bacterium every 6–12 months, either by oral or intranasal administration. Any impairment of dogs' olfactory capabilities due to medical treatments may impact their efficiency and accuracy in their jobs. This study examined (1) the effect of intranasal and oral vaccines on the olfactory capabilities of detection dogs; as well as (1) effects of the vaccines on canine behavior. Dogs that were vaccinated initially with the oral and 28 days later with intranasal B. bronchiseptica were generally slower to find the target odor than the dogs that were assigned intranasal then oral vaccine. This result prompted a second between-subjects study to further investigate any impact of intranasal administration of the B. bronchiseptica vaccine on the olfactory capabilities of dogs. The intranasal vaccine was of particular interest due to its prevalent use and potential for nasal inflammation leading to decreased olfactory capabilities. Neither odor threshold nor time spent searching for odor were affected by the intranasal vaccine. Behavioral analyses showed that behaviors associated with the dogs' positive and negative motivation affected their time spent finding the target odor; this suggests that behavior should be considered in future studies of olfactory performance.

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host's physiological capacities; however, the identity and functional role(s) of key members of the microbiome ("core microbiome") in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems' capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts' plastic and adaptive responses to environmental change requires (i) recognizing that individual host-microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

Plant diversity varies immensely over large-scale gradients in temperature, precipitation, and seasonality at global and regional scales. This relationship may be driven in part by climatic variation in the relative importance of abiotic and biotic interactions to the diversity and composition of plant communities. In particular, biotic interactions may become stronger and more host specific with increasing precipitation and temperature, resulting in greater plant species richness in wetter and warmer environments. This hypothesis predicts that the many defensive compounds found in plants’ metabolomes should increase in richness and decrease in interspecific similarity with precipitation, temperature, and plant diversity. To test this prediction, we compared patterns of chemical and morphological trait diversity of 140 woody plant species among seven temperate forests in North America representing 16.2°C variation in mean annual temperature (MAT), 2,115 mm variation in mean annual precipitation (MAP), and from 10 to 68 co-occurring species. We used untargeted metabolomics methods based on data generated with liquid chromatography-tandem mass spectrometry to identify, classify, and compare 13,480 unique foliar metabolites and to quantify the metabolomic similarity of species in each community with respect to the whole metabolome and each of five broad classes of metabolites. In addition, we compiled morphological trait data from existing databases and field surveys for three commonly measured traits (specific leaf area [SLA], wood density, and seed mass) for comparison with foliar metabolomes. We found that chemical defense strategies and growth and allocation strategies reflected by these traits largely represented orthogonal axes of variation. In addition, functional dispersion of SLA increased with MAP, whereas functional richness of wood density and seed mass increased with MAT. In contrast, chemical similarity of co-occurring species decreased with both MAT and MAP, and metabolite richness increased with MAT. Variation in metabolite richness among communities was positively correlated with species richness, but variation in mean chemical similarity was not. Our results are consistent with the hypothesis that plant metabolomes play a more important role in community assembly in wetter and warmer climates, even at temperate latitudes, and suggest that metabolomic traits can provide unique insight to studies of trait-based community assembly.

Feeding is critical for survival, and disruption in the mechanisms that govern food intake underlies disorders such as obesity and anorexia nervosa. It is important to understand both food intake and food motivation to reveal mechanisms underlying feeding disorders. Operant behavioral testing can be used to measure the motivational component to feeding, but most food intake monitoring systems do not measure operant behavior. Here, we present a new solution for monitoring both food intake and motivation in rodent home-cages: the Feeding Experimentation Device version 3 (FED3). FED3 measures food intake and operant behavior in rodent home-cages, enabling longitudinal studies of feeding behavior with minimal experimenter intervention. It has a programmable output for synchronizing behavior with optogenetic stimulation or neural recordings. Finally, FED3 design files are open-source and freely available, allowing researchers to modify FED3 to suit their needs.

CD4+ T cells are crucial for effective repression and elimination of cancer cells. Despite a paucity of CD4+ T cell receptor (TCR) clinical studies, CD4+ T cells are primed to become important therapeutics as they help circumvent tumor antigen escape and guide multifactorial immune responses. However, because CD8+ T cells directly kill tumor cells, most research has focused on the attributes of CD8+ TCRs. Less is known about how TCR affinity and CD4 expression affect CD4+ T cell activation in full length TCR (flTCR) and TCR single chain signaling (TCR-SCS) formats. Here, we generated an affinity panel of TCRs from CD4+ T cells and expressed them in flTCR and three TCR-SCS formats modeled after chimeric antigen receptors (CARs) to understand the contributions of TCR-pMHCII affinity, TCR format, and coreceptor CD4 interactions on CD4+ T cell activation. Strikingly, the coreceptor CD4 inhibited intermediate and high affinity TCR-construct activation by Lck-dependent and -independent mechanisms. These inhibition mechanisms had unique affinity thresholds dependent on the TCR format. Intracellular construct formats affected the tetramer staining for each TCR as well as IL-2 production. IL-2 production was promoted by increased TCR-pMHCII affinity and the flTCR format. Thus, CD4+ T cell therapy development should consider TCR affinity, CD4 expression, and construct format.

Integrated analyses of multiple large-scale screenings can be complicated by batch effects and technical artefacts. McFarland et al. introduce DEMETER2, a hierarchical model coupled with model-based normalization, which allows the assessment of differential dependencies across genes and cell lines.

Despite its known effects in brain reward centers, nicotine can be aversive in high doses. Here, the authors show that nicotine aversion depends on low-affinity nicotinic acetylcholine receptors expressed on projections from the interpeduncular nucleus to the laterodorsal tegmentum.

Abstract Adsorption and precipitation reactions often dictate the availability of phosphorus in soil environments. Tripolyphosphate (TPP) is considered a form of slow release P fertilizer in P limited soils, however, investigations of the chemical fate of TPP in soils are limited. It has been proposed that TPP rapidly hydrolyzes in the soil solution before adsorbing or precipitating with soil surfaces, but in model systems, TPP also adsorbs rapidly onto mineral surfaces. To study the adsorption behavior of TPP in calcareous soils, a short-term (48 h) TPP spike was performed under laboratory conditions. To determine the fate of TPP under field conditions, two different liquid TPP amendments were applied to a P limited subsurface field site via an in-ground injection system. Phosphorus speciation was assessed using X-ray absorption spectroscopy, total and labile extractable P, and X-ray diffraction. Adsorption of TPP to soil mineral surfaces was rapid (

Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve replicated metagenomic assessment. Mean bacterial genome size, GC content, total number of tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were all higher in the fertilized treatment, as predicted on the basis of the assumption that oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates. Contrasting changes in trait variances also suggested differences between traits in mediating assembly under copiotrophic versus oligotrophic conditions. Trade-offs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly because the major components of metabolism—information, energy, and nutrient requirements—are fine-tuned to an organism’s growth and trophic strategy.

Behavioral characteristics are the most influential factor in the success of a working dog. The need for highly capable detection dogs continues to rise; but reliable methods for early selection are lacking. The current study aimed to assess the reliability and validity of a behavioral test for assessing detection dog suitability. A cohort of candidate detection dog puppies (n = 60) were tested at 3; 5; and 11 months of age; as well as at the completion of training at approximately one year. Tests were designed to assess important detection dog behavioral characteristics such as search ability and fearfulness. Inter-rater reliability was high between independent observers. Convergent validity was demonstrated by comparing Principal Component Analysis (PCA) scores from the behavior test to trainer ratings using the Canine Behavioral Assessment and Research Questionnaire (C-BARQ) and a survey of detection dog traits. Performance on the behavior test predicted adult selection as a detection dog as early as 3 months. The methods reported will be valuable for improving selection measures and enhancing collaborations across breeding programs in order to increase the availability of highly capable detection dogs.

Kappa opioid receptors (KORs) are involved in a variety of aversive behavioral states, including anxiety. To date, a circuit-based mechanism for KOR-driven anxiety has not been described. Here, we show that activation of KORs inhibits glutamate release from basolateral amygdala (BLA) inputs to the bed nucleus of the stria terminalis (BNST) and occludes the anxiolytic phenotype seen with optogenetic activation of BLA-BNST projections. In addition, deletion of KORs from amygdala neurons results in an anxiolytic phenotype. Furthermore, we identify a frequency-dependent, optically evoked local dynorphin-induced heterosynaptic plasticity of glutamate inputs in the BNST. We also find that there is cell type specificity to the KOR modulation of the BLA-BNST input with greater KOR-mediated inhibition of BLA dynorphin-expressing neurons. Collectively, these results provide support for a model in which local dynorphin release can inhibit an anxiolytic pathway, providing a discrete therapeutic target for the treatment of anxiety disorders.

Though the last decade has seen accelerated advances in techniques and technologies to perturb neuronal circuitry in the brain, we are still poorly equipped to adequately dissect endogenous peptide release in vivo. To this end we developed a system that combines in vivo optogenetics with microdialysis and a highly sensitive mass spectrometry-based assay to measure opioid peptide release in freely moving rodents.

The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal–Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus–Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.

Global amphibian decline linked to fungal pathogens has galvanized research on applied amphibian conservation. Skin-associated bacterial communities of amphibians have been shown to mediate fungal skin infections and the development of probiotic treatments with antifungal bacteria has become an emergent area of research. While exploring the role of protective bacteria has been a primary focus for amphibian conservation, we aim to expand and study the other microbes present in amphibian skin communities including fungi and other micro-eukaryotes. Here, we characterize skin-associated bacteria and micro-eukaryotic diversity found across life stages of Cascades frog (Rana cascadae) and their associated aquatic environments using culture independent 16S and 18S rRNA marker-gene sequencing. Individuals of various life stages of Cascades frogs were sampled from a population located in the Trinity Alps in Northern California during an epidemic of the chytrid fungus, Batrachochytrium dendrobatidis. We filtered the bacterial sequences against a published database of bacteria known to inhibit B. dendrobatidis in co-culture to estimate the proportion of the skin bacterial community that is likely to provide defense against B. dendrobatidis. Tadpoles had a significantly higher proportion of B. dendrobatidis-inhibitory bacterial sequence matches relative to subadult and adult Cascades frogs. We applied a network analysis to examine patterns of correlation between bacterial taxa and B. dendrobatidis, as well as micro-eukaryotic taxa and B. dendrobatidis. Combined with the published database of bacteria known to inhibit B. dendrobatidis, we used the network analysis to identify bacteria that negatively correlated with B. dendrobatidis and thus could be good probiotic candidates in the Cascades frog system.

ABSTRACT Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology to enable stress survival remain unclear. Here we investigate the functions of transcription factors (TFs) within the global GRN of the stress-tolerant archaeal microorganism Halobacterium salinarum. We measured growth phenotypes of a panel of TF deletion mutants in high temporal resolution under heat shock, oxidative stress, and low-salinity conditions. To quantitate the noncanonical functional forms of the growth trajectories observed for these mutants, we developed a novel modeling framework based on Gaussian process regression and functional analysis of variance (FANOVA). We employ unique statistical tests to determine the significance of differential growth relative to the growth of the control strain. This analysis recapitulated known TF functions, revealed novel functions, and identified surprising secondary functions for characterized TFs. Strikingly, we observed that the majority of the TFs studied were required for growth under multiple stress conditions, pinpointing regulatory connections between the conditions tested. Correlations between quantitative phenotype trajectories of mutants are predictive of TF-TF connections within the GRN. These phenotypes are strongly concordant with predictions from statistical GRN models inferred from gene expression data alone. With genome-wide and targeted data sets, we provide detailed functional validation of novel TFs required for extreme oxidative stress and heat shock survival. Together, results presented in this study suggest that many TFs function under multiple conditions, thereby revealing high interconnectivity within the GRN and identifying the specific TFs required for communication between networks responding to disparate stressors. IMPORTANCE To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, salinity, and pH and under other conditions. In order to understand the cause-effect relationships between the dynamic function of the stress network and ultimate physiological consequences, this study characterized the physiological role of nearly one-third of all regulatory proteins known as transcription factors (TFs) in an archaeal organism. Using a unique quantitative phenotyping approach, we discovered functions for many novel TFs and revealed important secondary functions for known TFs. Surprisingly, many TFs are required for resisting multiple stressors, suggesting cross-regulation of stress responses. Through extensive validation experiments, we map the physiological roles of these novel TFs in stress response back to their position in the regulatory network wiring. This study advances understanding of the mechanisms underlying how microorganisms resist extreme stress. Given the generality of the methods employed, we expect that this study will enable future studies on how regulatory networks adjust cellular physiology in a diversity of organisms.

Increased tonic activity of locus coeruleus noradrenergic (LC-NE) neurons induces anxiety-like and aversive behavior. While some information is known about the afferent circuitry that endogenously drives this neural activity and behavior, the downstream receptors and anatomical projections that mediate these acute risk aversive behavioral states via the LC-NE system remain unresolved. Here we use a combination of retrograde tracing, fast-scan cyclic voltammetry, electrophysiology, and in vivo optogenetics with localized pharmacology to identify neural substrates downstream of increased tonic LC-NE activity in mice. We demonstrate that photostimulation of LC-NE fibers in the BLA evokes norepinephrine release in the basolateral amygdala (BLA), alters BLA neuronal activity, conditions aversion, and increases anxiety-like behavior. Additionally, we report that β-adrenergic receptors mediate the anxiety-like phenotype of increased NE release in the BLA. These studies begin to illustrate how the complex efferent system of the LC-NE system selectively mediates behavior through distinct receptor and projection-selective mechanisms.

Calcium phosphate minerals are typically the solubility-limiting phase for phosphate in calcareous soils. Magnesium (Mg), despite being present in high concentrations in calcareous soils, has been largely neglected in the study of formation and stabilization of soil phosphate minerals due to the high solubility of pure Mg phosphate phases. In this study, a series of four common calcium and magnesium phosphate minerals, hydroxyapatite/bobierrite and brushite/newberyite were synthesized in the presence of widely varying Mg concentrations to examine the effects of Mg substitution upon the local bonding environment and overall structure of the precipitates. Phosphorus K-edge X-Ray absorption near edge structure (XANES) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) provide insight into the local coordination environment, whereas synchrotron powder X-Ray diffraction (SP-XRD) and transmission electron microscopy (TEM) were used for structural analysis. In acidic to neutral pH, Mg-bearing brushite phases formed over a wide range of Ca:Mg ratios. In neutral to high pH systems, a short-range order amorphous calcium phosphate (ACP) with a local structure analogous with hydroxyapatite precipitated for a wide range of Ca to Mg ratios. It can be inferred that the presence of Mg in soils leads to stabilization of metastable phases: via cation substitution in brushite and via poisoning of crystal growth propagation for hydroxyapatite.

ABSTRACT Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals’ environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called omics, are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the K-S Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.

BackgroundFecal incontinence affects 7% to 12% of the US adult population, causing social, financial, and quality of life burdens.ObjectiveThe primary aim of this study was to evaluate the efficacy and safety of nonanimal stabilized hyaluronic acid/dextranomer through 36 months as a condition of postmarket approval application.DesignThis was a prospective, single-arm, multicenter, observational Food and Drug Administration-mandated postapproval clinical study.SettingsThis study was designed and executed by participating centers in 18 hospitals and colorectal health clinics in coordination with the Food and Drug Administration and the study sponsor.PatientsA total of 283 subjects who previously failed conservative therapy were enrolled across 18 US sites.InterventionsParticipants received 1 to 2 nonanimal stabilized hyaluronic acid/dextranomer treatments. The first treatment occurred within 30 days of baseline, and a second treatment was administered 1 to 3 months after initial treatment if determined necessary by the physician. Subjects were followed through 7 visits over 36 months after last treatment.Main outcome measuresEfficacy (as specified by the Food and Drug Administration) was measured as a fecal incontinence reintervention rate of

Networks of interacting transcription factors are central to the regulation of cellular responses to abiotic stress. Although the architecture of many such networks has been mapped, their dynamic function remains unclear. Here we address this challenge in archaea, microorganisms possessing transcription factors that resemble those of both eukaryotes and bacteria. Using genome-wide DNA binding location analysis integrated with gene expression and cell physiological data, we demonstrate that a bacterial-type transcription factor (TF), called RosR, and five TFIIB proteins, homologs of eukaryotic TFs, combinatorially regulate over 100 target genes important for the response to extremely high levels of peroxide. These genes include 20 other transcription factors and oxidative damage repair genes. RosR promoter occupancy is surprisingly dynamic, with the pattern of target gene expression during the transition from rapid growth to stress correlating strongly with the pattern of dynamic binding. We conclude that a hierarchical regulatory network orchestrated by TFs of hybrid lineage enables dynamic response and survival under extreme stress in archaea. This raises questions regarding the evolutionary trajectory of gene networks in response to stress.

Stress increases the risk of drug abuse, causes relapse to drug seeking, and potentiates the rewarding properties of both nicotine and cocaine. Understanding the mechanisms by which stress regulates the rewarding properties of drugs of abuse provides valuable insight into potential treatments for drug abuse. Prior reports have demonstrated that stress causes dynorphin release, activating kappa-opioid receptors (KOR) in monoamine circuits resulting in both potentiation and reinstatement of cocaine and nicotine conditioned place preference. Here we report that kappa-opioid dependent reinstatement of cocaine and nicotine place preference is reduced when the mice are exposed to a randomized chronic mild stress regime prior to training in a conditioned place preference-reinstatement paradigm. The chronic mild stress schedule involves seven different stressors (removal of nesting for 24hr, 5min forced swim stress at 15°C, 8hr food and water deprivation, damp bedding overnight, white noise, cage tilt and disrupted home cage lighting) rotated over a three-week period. This response is KOR-selective, because chronic mild stress does not protect against cocaine or nicotine drug-primed reinstatement. This protection from reinstatement is also observed following sub-chronic social defeat stress, where each mouse is placed in an aggressor mouse home cage for a period of 20 min over five days. In contrast, a single acute stressor resulted in a potentiation of KOR-induced reinstatement, similarly to previously reported. Prior studies have shown that stress alters sensitivity to opioids and prior stress can influence the pharmacodynamics of the opioid receptor system. Together, these findings suggest that exposure to different forms of stress may cause a dysregulation of kappa opioid circuitry and that changes resulting from mild stress can have protective and adaptive effects against drug relapse.

The discipline of sustainability science has emerged in response to concerns of natural and social scientists, policymakers, and lay people about whether the Earth can continue to support human population growth and economic prosperity. Yet, sustainability science has developed largely independently from and with little reference to key ecological principles that govern life on Earth. A macroecological perspective highlights three principles that should be integral to sustainability science: 1) physical conservation laws govern the flows of energy and materials between human systems and the environment, 2) smaller systems are connected by these flows to larger systems in which they are embedded, and 3) global constraints ultimately limit flows at smaller scales. Over the past few decades, decreasing per capita rates of consumption of petroleum, phosphate, agricultural land, fresh water, fish, and wood indicate that the growing human population has surpassed the capacity of the Earth to supply enough of these essential resources to sustain even the current population and level of socioeconomic development.