CeO2 nanoparticle dose and exposure modulate soybean development and plant-mediated responses in root-associated bacterial communities

Agricultural soils are increasingly undergoing inadvertent and purposeful exposures to engineered CeO2 nanoparticles (NPs), which can impact crops and root-associated microbial communities. However, interactions between NP concentration and exposure duration on plant-mediated responses of root-associated bacterial communities are not well understood. Soybeans seedlings were grown in soil with uncoated NPs added at concentrations of 0, 1 or 100 mg kg-1. Total soil exposure durations were either 190 days, starting 106 days before planting or 84 days with NP amendments coinciding with planting. We assessed plant development, bacterial diversity, differential abundance and inferred functional changes across rhizosphere, rhizoplane, and root tissue compartments. Plant non-monotonic dose responses were mirrored in bacterial communities. Most notably, effects were magnified in the rhizoplane under low-dose, short-exposures. Enriched metabolic pathways were primarily related to biosynthesis and degradation/utilization/assimilation, rather than responses to metals or oxidative stress. Our results indicate that plant-mediated bacterial responses were greater than direct NP impacts. Also, we identify needs for modeling non-monotonic legume stress responses that account for coinfection with mutualistic and parasitic bacteroids. Our findings provide new insights regarding effects of applications of soil amendments such as biosolids containing NPs or nano-enabled formulations used in cultivation of legumes and other crops.

Multigenerational, Indirect Exposure to Pyrethroids Demonstrates Potential Compensatory Response and Reduced Toxicity at Higher Salinity in Estuarine Fish

Estuarine environments are critical to fish species and serve as nurseries for developing embryos and larvae. They also undergo daily fluctuations in salinity and act as filters for pollutants. Additionally, global climate change (GCC) is altering salinity regimes within estuarine systems through changes in precipitation and sea level rise. GCC is also likely to lead to an increased use of insecticides to prevent pests from damaging agricultural crops as their habitats and mating seasons change from increased temperatures. This underscores the importance of understanding how insecticide toxicity to fish changes under different salinity conditions. In this study, larval Inland Silversides (Menidia beryllina) were exposed to bifenthrin (1.1 ng/L), cyfluthrin (0.9 ng/L), or cyhalothrin (0.7 ng/L) at either 6 or 10 practical salinity units (PSU) for 96 h during hatching, with a subset assessed for end points relevant to neurotoxicity and endocrine disruption by testing behavior, gene expression of a select suite of genes, reproduction, and growth. At both salinities, directly exposed F0 larvae were hypoactive relative to the F0 controls; however, the indirectly exposed F1 larvae were hyperactive relative to the F1 control. This could be evidence of a compensatory response to environmentally relevant concentrations of pyrethroids in fish. Effects on development, gene expression, and growth were also observed. Overall, exposure to pyrethroids at 10 PSU resulted in fewer behavioral and endocrine disruptive effects relative to those observed in organisms at 6 PSU.

LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules

Many RNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful, however, existing tools are either too simplistic or too slow. To address this issue, we present LinearCoFold, which approximates the complete minimum free energy structure of two strands in linear time, and LinearCoPartition, which approximates the cofolding partition function and base pairing probabilities in linear time. LinearCoFold and LinearCoPartition are orders of magnitude faster than RNAcofold. For example, on a sequence pair with combined length of 26,190 nt, LinearCoFold is 86.8× faster than RNAcofold MFE mode, and LinearCoPartition is 642.3× faster than RNAcofold partition function mode. Surprisingly, LinearCoFold and LinearCoPartition's predictions have higher PPV and sensitivity of intermolecular base pairs. Furthermore, we apply LinearCoFold to predict the RNA-RNA interaction between SARS-CoV-2 genomic RNA (gRNA) and human U4 small nuclear RNA (snRNA), which has been experimentally studied, and observe that LinearCoFold's prediction correlates better with the wet lab results than RNAcofold's.

Estimating fat content in barred owls (Strix varia) with predictive models developed from direct measures of proximate body composition

Body condition indices and related metrics can help assess habitat quality and other ecological processes, and ideally, these metrics are based on measures of lipids directly extracted from the species of interest. In recent decades, barred owls (Strix varia) have become a species of conservation concern as they invaded older forests of the US Pacific Northwest, and caused population declines of the closely related and federally threatened northern spotted owl (Strix occidentalis caurina). A simple and effective measure of barred owl body condition could help to understand how habitat quality varies within their new range, which in turn can inform their management and other aspects of their ecology. Using 77 barred owl carcasses collected during experimental removals in Washington and Oregon, USA, we measured the amount of lipid in each specimen with proximate body composition analysis. We then fit and compared (with adjusted R2 values) alternative linear regression models to estimate the percent lipids in dry mass of the owls based on morphometric body condition indices, a qualitative fat score of subcutaneous breast fat, sex and the time of year females were collected (relative to egg production). Adjusted R2 values for all models ranged from 0.49 to 0.87, with the best model including mass divided by foot-pad length, fat score, sex and the time of year a female was collected. Most models generated comparable estimates of percent lipids at a population level and we provided correction factors to apply these models when used with live barred owls, allowing for site-specific comparisons of body condition among individuals inhabiting a diversity of environmental conditions.

Induction of Aryl Hydrocarbon Receptor-Mediated Cancer Cell-Selective Apoptosis in Triple-Negative Breast Cancer Cells by a High-Affinity Benzimidazoisoquinoline

Triple-negative breast cancer (TNBC) remains a disease with a paucity of targeted treatment opportunities. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is involved in a wide range of physiological processes, including the sensing of xenobiotics, immune function, development, and differentiation. Different small-molecule AhR ligands drive strikingly varied cellular and organismal responses. In certain cancers, AhR activation by select small molecules induces cell cycle arrest or apoptosis via activation of tumor-suppressive transcriptional programs. AhR is expressed in triple-negative breast cancers, presenting a tractable therapeutic opportunity. Here, we identify a novel ligand of the aryl hydrocarbon receptor that potently and selectively induces cell death in triple-negative breast cancer cells and TNBC stem cells via the AhR. Importantly, we found that this compound, Analog 523, exhibits minimal cytotoxicity against multiple normal human primary cells. Analog 523 represents a high-affinity AhR ligand with potential for future clinical translation as an anticancer agent.

Assessment of a non-invasive approach to pregnancy diagnosis in gray whales through drone-based photogrammetry and faecal hormone analysis

Knowledge of baleen whales' reproductive physiology is limited and requires long-term individual-based studies and innovative tools. We used 6 years of individual-level data on the Pacific Coast Feeding Group gray whales to evaluate the utility of faecal progesterone immunoassays and drone-based photogrammetry for pregnancy diagnosis. We explored the variability in faecal progesterone metabolites and body morphology relative to observed reproductive status and estimated the pregnancy probability for mature females of unknown reproductive status using normal mixture models. Individual females had higher faecal progesterone concentrations when pregnant than when presumed non-pregnant. Yet, at the population level, high overlap and variability in progesterone metabolite concentrations occurred between pregnant and non-pregnant groups, limiting this metric for accurate pregnancy diagnosis in gray whales. Alternatively, body width at 50% of the total body length (W50) correctly discriminated pregnant from non-pregnant females at individual and population levels, with high accuracy. Application of the model using W50 metric to mature females of unknown pregnancy status identified eight additional pregnancies with high confidence. Our findings highlight the utility of drone-based photogrammetry to non-invasively diagnose pregnancy in this group of gray whales, and the potential for improved data on reproductive rates for population management of baleen whales generally.

Realigning theory with evidence to understand the role of care coordination in mental health services research

Current theoretical models intended to guide health services research and evaluation lack care coordination-its features and impacts. These aspects are critical for understanding the role of care coordination in healthcare use, quality, and outcomes. In this Focus article, we briefly review the well-known Andersen individual behavioral model (IBM) of healthcare use and the Donabedian health system and quality model (HSQM) together with recent practice-based evidence. We propose a new integrated theoretical model of healthcare and care coordination. The model can serve as a guide for future research to better understand the variation in care coordination services and delivery and its added value to improving mental health in different real-world settings.

Something to eat: experiences of food insecurity on the farm

The health of farm owners and farmworkers has significant impacts on farm businesses, farming families, and local rural communities where agriculture is an important driver of social and economic activity. Rural residents and farmworkers have higher rates of food insecurity, but little is known about food insecurity among farm owners and the collective experiences of farm owners and farmworkers. Researchers and public health practitioners have stressed the need for policies that target the health and well-being of farm owners and farmworkers while remaining sensitive to the nature of life on the farm, yet farm owner and farmworker lived experiences have been understudied, especially in relation to one another. In-depth qualitative interviews were conducted with 13 farm owners and 18 farmworkers in Oregon. Modified grounded theory was used to analyze interview data. Data were coded using a three-stage process to identify salient core characteristics of food insecurity. Farm owner and farmworker meanings and interpretations of their food insecurity were often contradicted by evaluated food security scores using validated quantitative measures. According to such measures, 17 experienced high food security, 3 had marginal food security, and 11 had low food security, but narrative experiences suggested higher rates. Narrative experiences were categorized by core characteristics of food insecurity, including seasonal food shortages, resource stretching, working extended hours most days of the week, limited use of food assistance, and the tendency to downplay hardship. These unique factors have important implications for developing responsive policies and programs to support the health and well-being of farm livelihoods whose work enables health and well-being among consumers. Future studies to test the relationships between the core characteristics of food insecurity identified in this study and farm owner and farmworker meanings and interpretations of food insecurity, hunger, and nourishment are warranted.

mtDNA heteroplasmy gives rise to a new maternal lineage in North Pacific humpback whales (Megaptera novaeangliae)

Heteroplasmy in the mitochondrial genome offers a rare opportunity to track the evolution of a newly arising maternal lineage in populations of non-model species. Here, we identified a previously unreported mitochondrial DNA haplotype while assembling an integrated database of DNA profiles and photo-identification records from humpback whales in southeastern Alaska (SEAK). The haplotype, referred to as A8, was shared by only 2 individuals, a mature female with her female calf, and differed by only a single base pair from a common haplotype in the North Pacific, referred to as A-. To investigate the origins of the A8 haplotype, we reviewed n = 1,089 electropherograms (including replicate samples) of n = 710 individuals with A- haplotypes from an existing collection. From this review, we found 20 individuals with clear evidence of heteroplasmy for A-/A8 (parental/derived) haplotypes. Of these, 15 were encountered in SEAK, 4 were encountered on the Hawaiian breeding ground (the primary migratory destination for whales in SEAK), and 1 was encountered in the northern Gulf of Alaska. We used genotype exclusion and likelihood to identify one of the heteroplasmic females as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. The mutation leading to this heteroplasmy and the fixation of the A8 haplotype provide an opportunity to document the population dynamics and regional fidelity of a newly arising maternal lineage in a population recovering from exploitation.

Ammonia Capture in Rhodium(II)-Based Metal-Organic Polyhedra via Synergistic Coordinative and H-Bonding Interactions

Ammonia (NH₃) is among the world's most widely produced bulk chemicals, given its extensive use in diverse sectors such as agriculture; however, it poses environmental and health risks at low concentrations. Therefore, there is a need for developing new technologies and materials to capture and store ammonia safely. Herein, we report for the first time the use of metal-organic polyhedra (MOPs) as ammonia adsorbents. We evaluated three different rhodium-based MOPs: [Rh₂(bdc)₂]₁₂ (where bdc is 1,3-benzene dicarboxylate); one functionalized with hydroxyl groups at its outer surface [Rh₂(OH-bdc)₂]₁₂ (where OH-bdc is 5-hydroxy-1,3-benzene dicarboxylate); and one decorated with aliphatic alkoxide chains at its outer surface [Rh₂(C₁₂O-bdc)₂]₁₂ (where C₁₂O-bdc is 5-dodecoxybenzene-1,3-benzene dicarboxylate). Ammonia-adsorption experiments revealed that all three Rh-MOPs strongly interact with ammonia, with uptake capacities exceeding 10 mmol/g_MOP. Furthermore, computational and experimental data showed that the mechanism of the interaction between Rh-MOPs and ammonia proceeds through a first step of coordination of NH₃ to the axial site of the Rh(II) paddlewheel cluster, which triggers the adsorption of additional NH₃ molecules through H-bonding interaction. This unique mechanism creates H-bonded clusters of NH₃ on each Rh(II) axial site, which accounts for the high NH₃ uptake capacity of Rh-MOPs. Rh-MOPs can be regenerated through their immersion in acidic water, and upon activation, their ammonia uptake can be recovered for at least three cycles. Our findings demonstrate that MOPs can be used as porous hosts to capture corrosive molecules like ammonia, and that their surface functionalization can enhance the ammonia uptake performance.

Design and fabrication of a stereo-video camera equipped unoccupied aerial vehicle for measuring sea turtles, sharks, and other marine fauna

The recent commercialization of unoccupied aerial vehicles (UAVs) has facilitated their incorporation into a variety of ecological studies. While UAVs are able to provide accurate visual data of marine species from an aerial perspective, these devices have some limitations that make measuring marine animals below the surface challenging. Many marine organisms are often visible from the air, but are deeper in the water column, and current methods cannot measure animals below the surface. Here, we developed and tested a stereo-video camera (SVC) system that was mounted onto a commercially-available UAV. We used the SVC-UAV to conduct remote body-size measurements for two marine species: the green sea turtle (Chelonia mydas) and the nurse shark (Ginglymostoma cirratum). When comparing SVC measurements to those taken by hand, the SVC-UAV had a mean absolute error (MAE) of 4.44 cm (n = 6; mean percent error (MPE) = 10.6%) for green sea turtles and 7.16 cm absolute error (n = 1; PE = 3.6%) for the nurse shark. Using a linear model, we estimated the slope of the SVC versus hand measurements for green sea turtles to be 1.085 (±0.099 SE), and accounting for the standard error, a measurement bias was not apparent. Using model selection, based on a global model predicting MAE from animal distance to the SVC and body size, the top ranked model was the intercept-only model. This indicates that neither animal distance nor body size strongly influenced measurement error. Incorporating SVC systems into UAVs can allow for relatively accurate measurements of near surface-dwelling marine species. To our knowledge, there is no other stand-alone SVC for UAVs available that offers similar accuracy and utility.

Impact of acute temperature and air pollution exposures on adult lung function: A panel study of asthmatics

Background

Individuals with respiratory conditions, such as asthma, are particularly susceptible to adverse health effects associated with higher levels of ambient air pollution and temperature. This study evaluates whether hourly levels of fine particulate matter (PM_2.5) and dry bulb globe temperature (DBGT) are associated with the lung function of adult participants with asthma.

Methods and findings

Global positioning system (GPS) location, respiratory function (measured as forced expiratory volume at 1 second (FEV₁)), and self-reports of asthma medication usage and symptoms were collected as part of the Exposure, Location, and Lung Function (ELF) study. Hourly ambient PM_2.5 and DBGT exposures were estimated by integrating air quality and temperature public records with time-activity patterns using GPS coordinates for each participant (n = 35). The relationships between acute PM_2.5, DBGT, rescue bronchodilator use, and lung function collected in one week periods and over two seasons (summer/winter) were analyzed by multivariate regression, using different exposure time frames.

In separate models, increasing levels in PM_2.5, but not DBGT, were associated with rescue bronchodilator use. Conversely DBGT, but not PM_2.5, had a significant association with FEV₁. When DBGT and PM_2.5 exposures were placed in the same model, the strongest association between cumulative PM_2.5 exposures and the use of rescue bronchodilator was identified at the 0–24 hours (OR = 1.030; 95% CI = 1.012–1.049; p-value = 0.001) and 0–48 hours (OR = 1.030; 95% CI = 1.013–1.057; p-value = 0.001) prior to lung function measure. Conversely, DBGT exposure at 0 hours (β = 3.257; SE = 0.879; p-value>0.001) and 0–6 hours (β = 2.885; SE = 0.903; p-value = 0.001) hours before a reading were associated with FEV₁. No significant interactions between DBGT and PM_2.5 were observed for rescue bronchodilator use or FEV₁.

Conclusions

Short-term increases in PM_2.5 were associated with increased rescue bronchodilator use, while DBGT was associated with higher lung function (i.e. FEV₁). Further studies are needed to continue to elucidate the mechanisms of acute exposure to PM_2.5 and DBGT on lung function in asthmatics.

Canine osteosarcoma cells exhibit basal accumulation of multiple chaperone proteins and are sensitive to small molecule inhibitors of GRP78 and heat shock protein function

Osteosarcoma is the most common type of bone cancer in dogs and humans, with significant numbers of patients experiencing treatment failure and disease progression. In our search for new approaches to treat osteosarcoma, we previously detected multiple chaperone proteins in the surface-exposed proteome of canine osteosarcoma cells. In the present study, we characterized expression of representative chaperones and find evidence for stress adaptation in canine osteosarcoma cells relative to osteogenic progenitors from normal bone. We compared the cytotoxic potential of direct (HA15) and putative (OSU-03012) inhibitors of Grp78 function and found canine POS and HMPOS osteosarcoma cells to be more sensitive to both compounds than normal cells. HA15 and OSU-03012 increased the thermal stability of Grp78 in intact POS cells at low micromolar concentrations, but each induced distinct patterns in Grp78 expression without significant change in Grp94. Both inhibitors were as effective alone as carboplatin and showed little evidence of synergy in combination treatment. However, HMPOS cells with acquired resistance to carboplatin were sensitive to inhibition of Grp78 (by HA15; OSU-03012), Hsp70 (by VER-155008), and Hsp90 (by 17-AAG) function. These results suggest that multiple nodes within the osteosarcoma chaperome may be relevant chemotherapeutic targets against platinum resistance.

Biogenesis and Biological Functions of Extracellular Vesicles in Cellular and Organismal Communication With Microbes

Extracellular vesicles (EVs) represent a prominent mechanism of transport and interaction between cells, especially microbes. Increasing evidence indicates that EVs play a key role in the physiological and pathological processes of pathogens and other symbionts. Recent research has focused on the specific functions of these vesicles during pathogen-host interactions, including trans-kingdom delivery of small RNAs, proteins and metabolites. Much current research on the function of EVs is focused on immunity and the interactions of microbes with human cells, while the roles of EVs during plant-microbe interactions have recently emerged in importance. In this review, we summarize recent research on the biogenesis of these vesicles and their functions in biology and pathology. Many key questions remain unclear, including the full structural and functional diversity of EVs, the roles of EVs in communication among microbes within microbiomes, how specific cargoes are targeted to EVs, whether EVs are targeted to specific destinations, and the full scope of EVs’ transport of virulence effectors and of RNA and DNA molecules.

Trends in Cardiovascular Disease by Asian American, Native Hawaiian, and Pacific Islander Ethnicity, Medicare Health Outcomes Survey 2011-2015

BACKGROUND

The burden of cardiovascular disease (CVD) is increasing in the aging population. However, little is known about CVD risk factors and outcomes for Asian American, Native Hawaiian, and Other Pacific Islander (NH/PI) older adults by disaggregated subgroups.

METHODS

Data were from the Centers for Medicare and Medicaid Services 2011-2015 Health Outcomes Survey, which started collecting expanded racial/ethnic data in 2011. Guided by Andersen and Newman's theoretical framework, multivariable logistic regression analyses were conducted to examine the prevalence and determinants of CVD risk factors (obesity, diabetes, smoking status, hypertension) and CVD conditions (coronary artery disease [CAD], congestive heart failure [CHF], myocardial infarction [MI], other heart conditions, stroke) for 10 Asian American and NH/PI subgroups and White adults.

RESULTS

Among the 639 862 respondents, including 26 853 Asian American and 4 926 NH/PI adults, 13% reported CAD, 7% reported CHF, 10% reported MI, 22% reported other heart conditions, and 7% reported stroke. CVD risk factors varied by Asian American and NH/PI subgroup. The prevalence of overweight, obesity, diabetes, and hypertension was higher among most Asian American and NH/PI subgroups than White adults. After adjustment, Native Hawaiians had significantly greater odds of reporting stroke than White adults.

CONCLUSIONS

More attention should focus on NH/PIs as a priority population based on the disproportionate burden of CVD risk factors compared with their White and Asian American counterparts. Future research should disaggregate racial/ethnic data to provide accurate depictions of CVD and investigate the development of CVD risk factors in Asian Americans and NH/PIs over the life course.

Is there no "I" in team? Potential bias in key informant interviews when asking individuals to represent a collective perspective

This paper sought to understand the extent to which, and how individuals use personal or collective language when asked to articulate sense of place from a collective perspective. Understanding a collective sense of place could illuminate place-based connections in natural resource industries, where it is as groups or as institutions that organizations interact with the environment rather than as individuals. While there are well known methods for collecting information about sense of place at the individual level, there is a gap in understanding the best method to collect information at a collective level. We examined the use of key-informant interviews as a method to understand collective sense of place. In Bocas del Toro, Panama, ecotourism and environmentally based organizations are becoming more prolific due to abundant natural resources, making it an interesting case study for understanding sense of place from an organizational perspective. The use of personal and collective language is examined though in-depth semi-structured interviews from 15 environmentally-oriented organizations with a total of 17 interviews. This study specifically examined whether and how key informants, when prompted to speak for their organization, spoke collectively, reflecting a collective perspective versus their own. Methods included both quantitative analysis of personal versus collective language use frequency, and qualitative examinations of how individuals used personal versus collective language. Our results indicated no difference in the frequency with which individuals use personal versus collective language. We found that how individuals situated their perspectives into an organization reflects a complex personal and collective point of view reflecting five themes of personal versus collective language use: 1) sole personal perspective, 2) sole collective perspective, 3) distinction between collective and personal perspective; 4) organization perspective with insertion of "I think"; and 5) personal and collective perspective about organization and greater community. Our research identifies a previously undiscussed potential bias of key informant interviews. These findings have implications for how researchers approach collecting information beyond the individual level.

The Restructuring-Induced CoO x Catalyst for Electrochemical Water Splitting

Restructuring is an important yet less understood phenomenon in the catalysis community. Recent studies have shown that a group of transition metal sulfide catalysts can completely or partially restructure during electrochemical reactions which then exhibit high activity even better than the best commercial standards. However, such restructuring processes and the final structures of the new catalysts are elusive, mainly due to the difficulty from the reaction-induced changes that cannot be captured by ex situ characterizations. To establish the true structure-property relationship in these in situ generated catalysts, we use multimodel operando characterizations including Raman spectroscopy, X-ray absorption spectroscopy, and X-ray reflectivity to investigate the restructuring of a representative catalyst, Co₉S₈, that shows better activity compared to the commercial standard RuO₂ during the oxygen evolution reaction (OER), a key half reaction in water-splitting for hydrogen generation. We find that Co₉S₈ ultimately converts to oxide cluster (CoO _x ) containing six oxygen coordinated Co octahedra as the basic unit which is the true catalytic center to promote high OER activity. The density functional theory calculations verify the in situ generated CoO _x consisting of edge-sharing CoO₆ octahedral clusters as the actual active sites. Our results also provide insights to design other transition-metal-based materials as efficient electrocatalysts that experience a similar restructuring in OER.

Influence of environmental change, harvest exposure, and human disturbance on population trends of greater sage-grouse

Hunter harvest of greater sage-grouse (Centrocercus urophasianus; hereafter “sage-grouse”) has been regulated by wildlife agencies during most of the past century. Hunting season regulations were maintained with the intention of providing sustainable hunting opportunities. Sage-grouse populations oscillate over time, and population growth can be influenced by seasonal weather and habitat disturbance. From 1995–2013, we compared sage-grouse lek trends from 22 relatively distinct sage-grouse population segments in 9 western U.S. states and 2 Canadian provinces. We stratified these populations into 3 broad categories (non-hunted [n = 8], continuously hunted [n = 10], and hunting season discontinued between 1996–2003 [n = 4]) with 8 different regulation histories to evaluate the potential impact of harvest on sage-grouse populations. Concomitantly, we assessed the effects of proportion burned, forested and cropland habitat; winter, spring, and summer precipitation; and human population, road, and oil and gas well densities on initial and time-varying lek counts. Density-dependent models fit lek trend data best for all regulation histories. In general, higher proportions of burnt, forested, and cropland habitat; and greater human population and oil and gas well densities were associated with lower equilibrium abundance (K). We found mixed results regarding the effect of hunting regulations on instantaneous growth rate (r). The cessation of harvest from 1996–2001 in approximately half of the largest sage-grouse population in our analysis was associated with higher r. Continuously harvested sage-grouse populations with permit hunting seasons had higher r during years with higher proportion of area exposed to permitted hunting rather than general upland game seasons. However, more liberal hunting regulations were positively associated with higher r in populations continuously harvested under general upland game hunts. Our results suggest that discontinuing harvest in the largest population resulted in greater population growth rates; however, this was not consistently the case for smaller populations. To no surprise, not all sage-grouse populations were influenced by the same environmental change or human disturbance factors. Our results will assist managers to understand factors associated with K, which provides the best targets for conservation efforts.

Sablefish (Anoplopoma fimbra Pallas, 1814) plasma biochemistry and hematology reference intervals including blood cell morphology

Plasma biochemistry and hematology reference intervals are integral health assessment tools in all medical fields, including aquatic animal health. As sablefish (Anoplopoma fimbria) are becoming aquaculturally and economically more important, this manuscript provides essential reference intervals (RI) for their plasma biochemistry and hematology along with reference photomicrographs of blood cells in healthy, fasted sablefish. Blood cell morphology can differ between fish species. In addition, blood cell counts and blood chemistry can vary between fish species, demographics, water conditions, seasons, diets, and culture systems, which precludes the use of RI's from other fish species. For this study, blood was collected for plasma biochemistry and hematology analysis between June 20 and July 18, 2019, from healthy, yearling sablefish, hatched and reared in captivity on a commercial diet. Overnight fast of 16-18 hours did not sufficiently reduce lipids in the blood, which led to visible lipemia and frequent rupture of blood cells during analysis. Therefore, sablefish should be fasted for 24 to 36 hours before blood is collected to reduce hematology artifacts or possible reagent interference in plasma biochemistry analysis. Lymphocytes were the most dominant leukocytes (98%), while eosinophils were rare, and basophils were not detected in sablefish. Neutrophils were very large cells with Döhle bodies. In mammals and avian species, Döhle bodies are usually signs of toxic change from inflammation, but no such association was found in these fish. In conclusion, lipemia can interfere with sablefish blood analysis, and available removal methods should be evaluated as fasting for up to 36 h might not always be feasible. Also, more studies are required to establish RI for different developmental stages and rearing conditions.

Rapid postglacial rebound amplifies global sea level rise following West Antarctic Ice Sheet collapse

Geodetic, seismic, and geological evidence indicates that West Antarctica is underlain by low-viscosity shallow mantle. Thus, as marine-based sectors of the West Antarctic Ice Sheet (WAIS) retreated during past interglacials, or will retreat in the future, exposed bedrock will rebound rapidly and flux meltwater out into the open ocean. Previous studies have suggested that this contribution to global mean sea level (GMSL) rise is small and occurs slowly. We challenge this notion using sea level predictions that incorporate both the outflux mechanism and complex three-dimensional viscoelastic mantle structure. In the case of the last interglacial, where the GMSL contribution from WAIS collapse is often cited as ~3 to 4 meters, the outflux mechanism contributes ~1 meter of additional GMSL change within ~1 thousand years of the collapse. Using a projection of future WAIS collapse, we also demonstrate that the outflux can substantially amplify GMSL rise estimates over the next century.

Shade, light, and stream temperature responses to riparian thinning in second-growth redwood forests of northern California

Resource managers in the Pacific Northwest (USA) actively thin second-growth forests to accelerate the development of late-successional conditions and seek to expand these restoration thinning treatments into riparian zones. Riparian forest thinning, however, may impact stream temperatures–a key water quality parameter often regulated to protect stream habitat and aquatic organisms. To better understand the effects of riparian thinning on shade, light, and stream temperature, we employed a manipulative field experiment following a replicated Before-After-Control-Impact (BACI) design in three watersheds in the redwood forests of northern California, USA. Thinning treatments were intended to reduce canopy closure or basal area within the riparian zone by up to 50% on both sides of the stream channel along a 100–200 m stream reach. We found that responses to thinning ranged widely depending on the intensity of thinning treatments. In the watersheds with more intensive treatments, thinning reduced shade, increased light, and altered stream thermal regimes in thinned and downstream reaches. Thinning shifted thermal regimes by increasing maximum temperatures, thermal variability, and the frequency and duration of elevated temperatures. These thermal responses occurred primarily during summer but also extended into spring and fall. Longitudinal profiles indicated that increases in temperature associated with thinning frequently persisted downstream, but downstream effects depended on the magnitude of upstream temperature increases. Model selection analyses indicated that local changes in shade as well as upstream thermal conditions and proximity to upstream treatments explained variation in stream temperature responses to thinning. In contrast, in the study watershed with less intensive thinning, smaller changes in shade and light resulted in minimal stream temperature responses. Collectively, our data shed new light on the stream thermal responses to riparian thinning. These results provide relevant information for managers considering thinning as a viable restoration strategy for second-growth riparian forests.

Measuring the additive effects of predation on prey survival across spatial scales

The degree to which predation is an additive vs. compensatory source of mortality is fundamental to understanding the effects of predation on prey populations and evaluating the efficacy of predator management actions. In the Columbia River basin, USA, predation by Caspian Terns (Hydroprogne caspia) on U.S. Endangered Species Act (ESA)-listed juvenile salmonids (smolts; Oncorhynchus spp.) has led to predator management actions to reduce predation; however, the assumption that reduced predation translates into greater salmonid survival, either within the life stage where predation occurs or across their lifetime, has remained untested. To address this critical uncertainty, we analyzed a long-term (2008-2018) mark-recapture-recovery data set of ESA-listed steelhead trout (O. mykiss) that were tagged (n = 78,409) and subsequently exposed to predation during smolt out-migration through multiple river reaches (spatial scales), jointly estimating weekly probabilities of steelhead survival, mortality due to bird predation, and mortality due to other causes. This concurrent estimation across time-stratified cohorts allowed for the direct measurement of the strength, magnitude, and direction of relationships between survival and Caspian Tern predation. Estimates of Tern predation on steelhead were substantial in most years, with cumulative annual estimates ranging from 0.075 (95% creditable interval = 0.058-0.099) to 0.375 (0.290-0.461). Increases in Tern predation probabilities were associated with statistically significant decreases in steelhead survival probabilities in all evaluated years and salmonid life stages (smolt out-migration and smolt-to-adult returns). Results provide novel evidence that predation by Caspian Terns may have been a super-additive source of mortality during the smolt life stage and a partially additive source of mortality to the adult life stage. Annual estimates of the difference between observed survival and baseline survival (i.e., in the absence of Tern predation) ranged from 0.052 (0.017-0.103) to 0.314 (0.172-0.459) during the steelhead smolt life stage and from 0.011 (0.001-0.029) to 0.049 (0.025-0.078) to the adult life stage. The estimated levels of compensation have important implications for predator management actions aimed at increasing the survival of endangered salmonids, and the modeling approach developed herein provides a framework to directly quantify the impacts of source-specific mortality factors on prey populations.

A Review of the Functional Roles of the Zebrafish Aryl Hydrocarbon Receptors

Over the last 2 decades, the zebrafish (Danio rerio) has emerged as a stellar model for unraveling molecular signaling events mediated by the aryl hydrocarbon receptor (AHR), an important ligand-activated receptor found in all eumetazoan animals. Zebrafish have 3 AHRs-AHR1a, AHR1b, and AHR2, and studies have demonstrated the diversity of both the endogenous and toxicological functions of the zebrafish AHRs. In this contemporary review, we first highlight the evolution of the zebrafish ahr genes, and the characteristics of the receptors including developmental and adult expression, their endogenous and inducible roles, and the predicted ligands from homology modeling studies. We then review the toxicity of a broad spectrum of AHR ligands across multiple life stages (early stage, and adult), discuss their transcriptomic and epigenetic mechanisms of action, and report on any known interactions between the AHRs and other signaling pathways. Through this article, we summarize the promising research that furthers our understanding of the complex AHR pathway through the extensive use of zebrafish as a model, coupled with a large array of molecular techniques. As much of the research has focused on the functions of AHR2 during development and the mechanism of TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) toxicity, we illustrate the need to address the considerable knowledge gap in our understanding of both the mechanistic roles of AHR1a and AHR1b, and the diverse modes of toxicity of the various AHR ligands.

Remote sensing: generation of long-term kelp bed data sets for evaluation of impacts of climatic variation

A critical tool in assessing ecosystem change is the analysis of long-term data sets, yet such information is generally sparse and often unavailable for many habitats. Kelp forests are an example of rapidly changing ecosystems that are in most cases data poor. Because kelp forests are highly dynamic and have high intrinsic interannual variability, understanding how regional-scale drivers are driving kelp populations-and particularly how kelp populations are responding to climate change-requires long-term data sets. However, much of the work on kelp responses to climate change has focused on just a few, relatively long-lived, perennial, canopy-forming species. To understand how kelp populations with different life history traits are responding to climate-related variability, we leverage 35 yr of Landsat satellite imagery to track the population size of an annual, ruderal kelp, Nereocystis luetkeana, across Oregon. We found high levels of interannual variability in Nereocystis canopy area and varying population trajectories over the last 35 yr. Surprisingly, Oregon Nereocystis population sizes were unresponsive to a 2014 marine heat wave accompanied by increases in urchin densities that decimated northern California Nereocystis populations. Some Oregon Nereocystis populations have even increased in area relative to pre-2014 levels. Analysis of environmental drivers found that Nereocystis population size was negatively correlated with estimated nitrate levels and positively correlated with winter wave height. This pattern is the inverse of the predicted relationship based on extensive prior work on the perennial kelp Macrocystis pyrifera and may be related to the annual life cycle of Nereocystis. This article demonstrates (1) the value of novel remote sensing tools to create long-term data sets that may challenge our understanding of nearshore marine species and (2) the need to incorporate life history traits into our theory of how climate change will shape the ocean of the future.

Space use of Pacific harbor seals (Phoca vitulina richardii) from two haulout locations along the Oregon coast

BACKGROUND

There are approximately 10,000-12,000 Pacific harbor seals (Phoca vitulina richardii) inhabiting the Oregon coast, and unlike other species of pinnipeds in this region, are reliably present year-round. Despite this, and drastic rebounds in population since the enactment of the Marine Mammal Protection Act, limited data is available for the present period regarding their space use at sea, and within estuarine, riverine, or bay areas within the state.

OBJECTIVE

To examine site-based differences in space use for 24 adult Pacific harbor seals captured and outfitted with satellite transmitters at two predominant haulout sites on the Oregon Coast, USA.

DESIGN

We captured 24 adult harbor seals from two haulout sites on the Central Oregon coast between September 2014-16 and fitted them with external Wildlife Computers SPOT5 satellite transmitters to track movement. Using state-space modeled locations derived from satellite telemetry data, we evaluated spatial behavior of these animals using a correlated random walk model via R package crawl. Kernel density estimation was subsequently used to calculate home range and core area for each animal. Percent use of open ocean habitat versus use of estuaries, rivers and bays was quantified, as was an initial examination of presence within five newly-established marine reserves in Oregon. Examination of haulout site-related differences in spatial behavior were examined for seals captured in Netarts and Alsea Bays, Oregon and haul out behavior related to time of day, season, and tidal level was also investigated.

RESULTS

The average individual home range for seals was 364.47 ± 382.87 km2 with seals captured in Alsea bay demonstrating a significantly higher home range area than those captured in Netarts Bay. Alsea bay seals also tended to range farther from shore than Netarts Bay animals. The average calculated core area for seals encompassed on average 29.41 ± 29.23 km2 per animal, however the home range of one animal was so small, core area could not be calculated. Use of marine reserves was limited for animals in this study, representing less than 2% of locations with a majority occurring in Cape Perpetua Marine Reserve and North Marine Protected Area. Seals were more likely to haul out during low tides and periods of low light (dusk, night and dawn), and hauling out behavior increased in winter months.

SIGNIFICANCE

These findings demonstrate the first major documentation of space use of harbor seals in the state for nearly three decades, and lends itself to future comparison and formation of mechanistically-based hypotheses for behavior of a common marine mammal in the highly productive northern California Current System.

Evidence for lasting alterations to aquatic food webs with short-duration reservoir draining

Large dams and their respective reservoirs provide renewable energy and water security, but also can profoundly alter riverine ecosystems. Here, we present evidence of changing aquatic food web structure in the seasons following short-duration, extreme manipulation of water levels in a reservoir (i.e., draining of the reservoir to the original riverbed during fall to assist outmigration of juvenile Chinook Salmon). We find unintended and lagged consequences of transitioning from a lake to a river, even temporarily, that resulted in trophic shifts away from piscivory and towards feeding at lower trophic levels for two common piscivorous fishes in reservoirs. Using natural abundances of nitrogen stable isotopes, we observed lower trophic level of feeding for invasive Largemouth Bass (Micropterus salmoides) and native Rainbow Trout (Oncorhynchus mykiss) during the summers following reservoir refilling than in nearby reference reservoirs that were not temporarily drained during fall. Declines in trophic levels of aquatic top predators have been rarely documented outside of controlled laboratory conditions. While useful for assisting outmigration of juvenile salmonids, the temporary draining of a reservoir to riverbed can also result in novel shifts in foodweb dynamics including reduced piscivory. As large dams continue to be operated and constructed worldwide, increased understanding of the community and ecosystem-level effects of reservoir management will be critical to evaluating trade-offs between human water needs, conservation of high value species, and ecosystem services impacted by river fragmentation.

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features

BACKGROUND

We previously reported on CERENKOV, an approach for identifying regulatory single nucleotide polymorphisms (rSNPs) that is based on 246 annotation features. CERENKOV uses the xgboost classifier and is designed to be used to find causal noncoding SNPs in loci identified by genome-wide association studies (GWAS). We reported that CERENKOV has state-of-the-art performance (by two traditional measures and a novel GWAS-oriented measure, AVGRANK) in a comparison to nine other tools for identifying functional noncoding SNPs, using a comprehensive reference SNP set (OSU17, 15,331 SNPs). Given that SNPs are grouped within loci in the reference SNP set and given the importance of the data-space manifold geometry for machine-learning model selection, we hypothesized that within-locus inter-SNP distances would have class-based distributional biases that could be exploited to improve rSNP recognition accuracy. We thus defined an intralocus SNP "radius" as the average data-space distance from a SNP to the other intralocus neighbors, and explored radius likelihoods for five distance measures.

RESULTS

We expanded the set of reference SNPs to 39,083 (the OSU18 set) and extracted CERENKOV SNP feature data. We computed radius empirical likelihoods and likelihood densities for rSNPs and control SNPs, and found significant likelihood differences between rSNPs and control SNPs. We fit parametric models of likelihood distributions for five different distance measures to obtain ten log-likelihood features that we combined with the 248-dimensional CERENKOV feature matrix. On the OSU18 SNP set, we measured the classification accuracy of CERENKOV with and without the new distance-based features, and found that the addition of distance-based features significantly improves rSNP recognition performance as measured by AUPVR, AUROC, and AVGRANK. Along with feature data for the OSU18 set, the software code for extracting the base feature matrix, estimating ten distance-based likelihood ratio features, and scoring candidate causal SNPs, are released as open-source software CERENKOV2.

CONCLUSIONS

Accounting for the locus-specific geometry of SNPs in data-space significantly improved the accuracy with which noncoding rSNPs can be computationally identified.

Nanoalginates via Inverse-Micelle Synthesis: Doxorubicin-Encapsulation and Breast Cancer Cytotoxicity

Crosslinked-biopolymer nanoparticles provide a convenient platform for therapeutic encapsulation and delivery. Here, we present a robust inverse-micelle process to load water-soluble drugs into a calcium-crosslinked alginate matrix. The utility of the resulting nanoalginate (NALG) carriers was assessed by a doxorubicin (DOX) formulation (NALG-DOX) and evaluating its potency on breast cancer cells (4T1). This facile synthesis process produced doxorubicin-containing particles of ~ 83 nm by hydrodynamic size and zeta potential ~ 7.2 mV. The cyclohexane/dodecylamine microemulsion yielded uniform and spherical nanoparticles as observed by electron microscopy. The uptake of the drug from the NALG-DOX formulation in 4T1 cells was observed by fluorescence microscopy employing doxorubicin's inherent fluorescence. Therapeutic efficacy of the NALG-DOX against 4T1 cells was demonstrated qualitatively through a LIVE/DEAD fluorescence assay and quantitatively via cell viability assay (Alamar Blue). In addition, IC50 values were determined, with encapsulated doxorubicin having a slightly higher value. No toxicity of the empty NALG carrier was observed. Overall, these results demonstrate the utility of this synthesis process for encapsulation of hydrophilic therapeutics and NALG to function as a drug carrier.

A Computational Systems Biology Approach for Identifying Candidate Drugs for Repositioning for Cardiovascular Disease

We report an in silico method to screen for receptors or pathways that could be targeted to elicit beneficial transcriptional changes in a cellular model of a disease of interest. In our method, we integrate: (1) a dataset of transcriptome responses of a cell line to a panel of drugs; (2) two sets of genes for the disease; and (3) mappings between drugs and the receptors or pathways that they target. We carried out a gene set enrichment analysis (GSEA) test for each of the two gene sets against a list of genes ordered by fold-change in response to a drug in a relevant cell line (HL60), with the overall score for a drug being the difference of the two enrichment scores. Next, we applied GSEA for drug targets based on drugs that have been ranked by their differential enrichment scores. The method ranks drugs by the degree of anti-correlation of their gene-level transcriptional effects on the cell line with the genes in the disease gene sets. We applied the method to data from (1) CMap 2.0; (2) gene sets from two transcriptome profiling studies of atherosclerosis; and (3) a combined dataset of drug/target information. Our analysis recapitulated known targets related to CVD (e.g., PPARγ; HMG-CoA reductase, HDACs) and novel targets (e.g., amine oxidase A, δ-opioid receptor). We conclude that combining disease-associated gene sets, drug-transcriptome-responses datasets and drug-target annotations can potentially be useful as a screening tool for diseases that lack an accepted cellular model for in vitro screening.

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish

Growing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genus Pseudomonas appeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome's interaction with environmental chemicals.