The interplay between hydrogen and halogen bonding: substituent effects and their role in the hydrogen bond enhanced halogen bond

The hydrogen bond enhanced halogen bond (HBeXB) has recently been used to effectively improve anion binding, organocatalysis, and protein structure/function. In this study, we present the first systematic investigation of substituent effects in the HBeXB. NMR analysis confirmed intramolecular HBing between the amine and the electron-rich belt of the XB donor (N-H⋯I). Gas-phase density functional theory studies showed that the influence of HBing on the halogen atom is more sensitive to substitution on the HB donor ring (R1). The NMR studies revealed that the intramolecular HBing had a significant impact on receptor performance, resulting in a 50-fold improvement. Additionally, linear free energy relationship (LFER) analysis was employed for the first time to study the substituent effect in the HBeXB. The results showed that substituents on the XB donor ring (R2) had a competing effect where electron donating groups strengthened the HB and weakened the XB. Therefore, selecting an appropriate substituent on the adjacent HB donor ring (R1) could be an alternative and effective way to enhance an electron-rich XB donor. X-ray crystallographic analysis demonstrated that intramolecular HBing plays an important role in the receptor adopting the bidentate conformation. Taken together, the findings imply that modifying distal substituents that affect neighboring noncovalent interactions can have a similar impact to conventional para substitution substituent effects.

SODA: a TypeScript/JavaScript library for visualizing biological sequence annotation

We present SODA, a lightweight and open-source visualization library for biological sequence annotations that enables straightforward development of flexible, dynamic and interactive web graphics. SODA is implemented in TypeScript and can be used as a library within TypeScript and JavaScript.

Towns and trails drive carnivore movement behaviour, resource selection, and connectivity

BACKGROUND

Global increases in human activity threaten connectivity of animal habitat and populations. Protection and restoration of wildlife habitat and movement corridors require robust models to forecast the effects of human activity on movement behaviour, resource selection, and connectivity. Recent research suggests that animal resource selection and responses to human activity depend on their behavioural movement state, with increased tolerance for human activity in fast states of movement. Yet, few studies have incorporated state-dependent movement behaviour into analyses of Merriam connectivity, that is individual-based metrics of connectivity that incorporate landscape structure and movement behaviour.

METHODS

We assessed the cumulative effects of anthropogenic development on multiple movement processes including movement behaviour, resource selection, and Merriam connectivity. We simulated movement paths using hidden Markov movement models and step selection functions to estimate habitat use and connectivity for three landscape scenarios: reference conditions with no anthropogenic development, current conditions, and future conditions with a simulated expansion of towns and recreational trails. Our analysis used 20 years of grizzly bear (Ursus arctos) and gray wolf (Canis lupus) movement data collected in and around Banff National Park, Canada.

RESULTS

Carnivores increased their speed of travel near towns and areas of high trail and road density, presumably to avoid encounters with people. They exhibited stronger avoidance of anthropogenic development when foraging and resting compared to travelling and during the day compared to night. Wolves exhibited stronger avoidance of anthropogenic development than grizzly bears. Current development reduced the amount of high-quality habitat between two mountain towns by more than 35%. Habitat degradation constrained movement routes around towns and was most pronounced for foraging and resting behaviour. Current anthropogenic development reduced connectivity from reference conditions an average of 85%. Habitat quality and connectivity further declined under a future development scenario.

CONCLUSIONS

Our results highlight the cumulative effects of anthropogenic development on carnivore movement behaviour, habitat use, and connectivity. Our strong behaviour-specific responses to human activity suggest that conservation initiatives should consider how proposed developments and restoration actions would affect where animals travel and how they use the landscape.

Physiological acclimation of elk during population restoration in the Missouri Ozarks, USA

Conservation translocations-the intentional movement of animals to restore populations-have increased over the past 30 years to halt and reverse species declines and losses. However, there are many challenges translocated animals face that should be considered for restoration programs to be successful. Understanding how long it takes for translocated animals to acclimate to these challenges and their new landscape is a critical component of post-release population management. Physiological measures such as hormone responses are increasingly used to assess animal responses and acclimation to disturbances including translocation. We determined the physiological acclimation period of elk (Cervus canadensis) translocated to the Missouri Ozarks, USA, as part of a restoration effort. From 2011 to 2013, we translocated 108 GPS-radio-collared elk from Kentucky, USA, to Missouri, USA, and collected faecal samples for glucocorticoid metabolite extraction to use as an indicator of physiological acclimation. We modelled the response of population-wide faecal glucocorticoid metabolites (fGCMs) across the initial 9 years of the restoration in response to days following release and additional site-specific covariates. Presence of white-tailed deer (Odocoileus virginianus) hunts and monthly precipitation levels were positively and negatively associated with fGCM levels, respectively. Concurrent with influences from site-specific conditions on the release landscape, fGCM levels declined following release. We identified a breakpoint in fGCM decline at ~42 days following translocation releases suggesting elk acclimated physiologically relatively quickly compared to other species. The fast physiological acclimation by Missouri elk suggests effective use of temporary post-release management efforts. Determining how quickly animals acclimate following translocations allows researchers to tailor post-release management plans to each species' needs, thus maximizing the success of future translocation efforts while minimizing costs.

Pushing the Limits of the Hydrogen Bond Enhanced Halogen Bond —The Case of the C–H Hydrogen Bond

C–H hydrogen bonds have remarkable impacts on various chemical systems. Here we consider the influence of C–H hydrogen bonds to iodine atoms. Positioning a methyl group between two iodine halogen bond donors of the receptor engendered intramolecular C–H hydrogen bonding (HBing) to the electron-rich belt of both halogen bond donors. When coupled with control molecules, the role of the C–H hydrogen bond was evaluated. Gas-phase density functional theory studies indicated that methyl C–H hydrogen bonds help bias a bidentate binding conformation. Interaction energy analysis suggested that the charged C–H donors augment the halogen bond interaction—producing a >10 kcal mol⁻¹ enhancement over a control lacking the C–H⋯I–C interaction. X-ray crystallographic analysis demonstrated C–H hydrogen bonds and bidentate conformations with triflate and iodide anions, yet the steric bulk of the central functional group seems to impact the expected trends in halogen bond distance. In solution, anion titration data indicated elevated performance from the receptors that utilize C–H Hydrogen Bond enhanced Halogen Bonds (HBeXBs). Collectively, the results suggest that even modest hydrogen bonds between C–H donors and iodine acceptors can influence molecular structure and improve receptor performance.

C–H hydrogen bonds to iodine halogen bond donors are shown to improve halogen bonding and molecular preorganization.

Habitat selection by wolves and mountain lions during summer in western Montana

In the Northern Rockies of the United States, predators like wolves (Canis lupus) and mountain lions (Puma concolor) have been implicated in fluctuations or declines in populations of game species like elk (Cervus canadensis) and mule deer (Odocoileus hemionus). In particular, local distributions of these predators may affect ungulate behavior, use of space, and dynamics. Our goal was to develop generalizable predictions of habitat selection by wolves and mountain lions across western Montana. We hypothesized both predator species would select habitat that maximized their chances of encountering and killing ungulates and that minimized their chances of encountering humans. We assessed habitat selection by these predators during summer using within-home range (3^rd order) resource selection functions (RSFs) in multiple study areas throughout western Montana, and tested how generalizable RSF predictions were by applying them to out-of-sample telemetry data from separate study areas. Selection for vegetation cover-types varied substantially among wolves in different study areas. Nonetheless, our predictions of 3^rd order selection by wolves were highly generalizable across different study areas. Wolves consistently selected simple topography where ungulate prey may be more susceptible to their cursorial hunting mode. Topographic features may serve as better proxies of predation risk by wolves than vegetation cover-types. Predictions of mountain lion distribution were less generalizable. Use of rugged terrain by mountain lions varied across ecosystem-types, likely because mountain lions targeted the habitats of different prey species in each study area. Our findings suggest that features that facilitate the hunting mode of a predator (i.e. simple topography for cursorial predators and hiding cover for stalking predators) may be more generalizable predictors of their habitat selection than features associated with local prey densities.

Evaluating corticosterone as a biomarker for amphibians exposed to increased salinity and ambient corticosterone

Physiological biomarkers are commonly used to assess the health of taxa exposed to natural and anthropogenic stressors. Glucocorticoid (GC) hormones are often used as indicators of physiological stress in wildlife because they affect growth, reproduction and survival. Increased salinity from human activities negatively influences amphibians and their corticosterone (CORT; the main amphibian GC) physiology; therefore, CORT could be a useful biomarker. We evaluated whether waterborne CORT could serve as a biomarker of salt stress for three free-living amphibian species that vary in their sensitivity to salinity: boreal chorus frogs (Pseudacris maculata), northern leopard frogs (Rana pipiens) and barred tiger salamanders (Ambystoma mavortium). Across a gradient of contamination from energy-related saline wastewaters, we tested the effects of salinity on baseline and stress-induced waterborne CORT of larvae. Stress-induced, but not baseline, CORT of leopard frogs increased with increasing salinity. Salinity was not associated with baseline or stress-induced CORT of chorus frogs or tiger salamanders. Associations between CORT and salinity were also not related to species-specific sensitivities to salinity. However, we detected background environmental CORT (ambient CORT) in all wetlands and spatial variation was high within and among wetlands. Higher ambient CORT was associated with lower waterborne CORT of larvae in wetlands. Therefore, ambient CORT likely confounded associations between waterborne CORT and salinity in our analysis and possibly influenced physiology of larvae. We hypothesize that larvae may passively take up CORT from their environment and downregulate endogenous CORT. Although effects of some hormones (e.g. oestrogen) and endocrine disruptors on aquatic organisms are well described, studies investigating the occurrence and effects of ambient CORT are limited. We provide suggestions to improve collection methods, reduce variability and avoid confounding effects of ambient CORT. By making changes to methodology, waterborne CORT could still be a promising, non-invasive conservation tool to evaluate effects of salinity on amphibians.

Migration ecology of western gray catbirds

BACKGROUND

For many songbirds in North America, we lack movement details about the full annual cycle, notably outside the breeding season. Understanding how populations are linked spatially between breeding and overwintering periods (migratory connectivity) is crucial to songbird conservation and management. We assessed migratory connectivity for 2 breeding populations of Gray Catbirds (Dumetella carolinensis) west of and within the Rocky Mountains by determining migration routes, stopover sites, and overwintering locations. Additionally, we compared apparent annual survivorship for both populations.

METHODS

We deployed 39 archival light-level geolocators and 21 Global Positioning System (GPS) tags on catbirds in the South Okanagan Valley, British Columbia, Canada, and 32 geolocators and 52 GPS tags in the Bitterroot River Valley, Montana, USA. These devices allowed us to determine migration routes, stopover sites, overwintering locations, and migratory connectivity. Migratory connectivity was quantified using Mantel's correlation. We used mark-recapture of colour banded catbirds in both sites to estimate apparent annual survivorship.

RESULTS

We retrieved 6 geolocators and 19 GPS tags with usable data. Gray Catbirds from both populations passed through the Rocky Mountains eastward before heading south towards their overwintering locations in northeastern Mexico and Texas. Stopover sites during fall migration occurred primarily in Montana, Kansas, Oklahoma, and Arkansas. Overwintering locations spanned Texas and 5 states in northeastern Mexico. Individual catbirds used up to 4 distinct sites during the overwintering period. Catbirds separated by almost 500 km during the breeding season overlapped during the non-breeding season, suggesting weak migratory connectivity among western populations (Mantel's correlation = 0.013, P-value = 0.41). Catbird apparent annual survivorship estimates were higher in British Columbia (0.61 ± 0.06 females; 0.64 ± 0.05 males) than in Montana (0.34 ± 0.05 females; 0.43 ± 0.04 males), though the main driver of these differences remain unclear.

CONCLUSIONS

Our results provide high precision geographic details during the breeding, migration, and overwintering phases of the annual cycle for western Gray Catbirds. Notably, we found that western catbirds followed the Central Flyway as opposed to the Pacific Flyway. We document that catbirds used multiple sites over winter, contrary to the popular belief that this phase of the annual cycle is stationary for most songbirds.

Lack of phenological shift leads to increased camouflage mismatch in mountain hares

Understanding whether organisms will be able to adapt to human-induced stressors currently endangering their existence is an urgent priority. Globally, multiple species moult from a dark summer to white winter coat to maintain camouflage against snowy landscapes. Decreasing snow cover duration owing to climate change is increasing mismatch in seasonal camouflage. To directly test for adaptive responses to recent changes in snow cover, we repeated historical (1950s) field studies of moult phenology in mountain hares (Lepus timidus) in Scotland. We found little evidence that population moult phenology has shifted to align seasonal coat colour with shorter snow seasons, or that phenotypic plasticity prevented increases in camouflage mismatch. The lack of responses resulted in 35 additional days of mismatch between 1950 and 2016. We emphasize the potential role of weak directional selection pressure and low genetic variability in shaping the scope for adaptive responses to anthropogenic stressors.

Is there a role for sarcolipin in avian facultative thermogenesis in extreme cold?

Endotherms defend their body temperature in the cold by employing shivering (ST) and/or non-shivering thermogenesis (NST). Although NST is well documented in mammals, its importance to avian heat generation is unclear. Recent work points to a prominent role for the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) in muscular NST. SERCA's involvement in both ST and NST, however, posits a tradeoff between these two heat-generating mechanisms. To explore this tradeoff, we assayed pectoralis gene expression of adult songbirds exposed to chronic temperature acclimations. Counter to mammal models, we found that cold-acclimated birds downregulated the expression of sarcolipin (SLN), a gene coding for a peptide that promotes heat generation by uncoupling SERCA Ca2+ transport from ATP hydrolysis, indicating a reduced potential for muscular NST. We also found differential expression of many genes involved in Ca2+ cycling and muscle contraction and propose that decreased SLN could promote increased pectoralis contractility for ST. Moreover, SLN transcript abundance negatively correlated with peak oxygen consumption under cold exposure (a proxy for ST) across individuals, and higher SLN transcript abundance escalated an individual's risk of hypothermia in acute cold. Our results therefore suggest that SLN-mediated NST may not be an important mechanism of-and could be a hindrance to-avian thermoregulation in extreme cold.

Importance of considering soils in seed transfer zone development: evidence from a study of the native Bromus marginatus

Seed transfer zones, which define the geographical relationship between adaptive traits and environmental factors, are increasingly used to determine the source populations that can be combined in restoration and revegetation. Climatic variables have been the most commonly used environmental data in transfer zone development, even though soils are also a primary selective force on plants. We assessed the importance of including soils in seed transfer zones using Bromus marginatus, a native grass used for restoration and revegetation in the western United States, as an example. Seeds were collected from 64 populations across Montana and Idaho and grown in a common garden for two years. We assessed among-population variation based on 11 traits related to germination rate, plant size, vigor, inflorescence number, survival, and carbon isotope discrimination (∆¹³ ), and used this variation to develop seed transfer zone maps using two approaches: (1) a conventional approach, using only climatic variables (climate only) and (2) an expanded approach that included soils and climatic variables (soils + climate). The most influential drivers of trait variation were factors related to soil water availability: soil order, available water content (AWC), and organic carbon levels. Populations from areas with andic soils, which have high soil AWC and soil organic carbon, had low germination, limited first-year survival, low ∆¹³ , and small seeds. Growing season length and winter temperatures were also predictive of trait variation. In comparison to climate-only models, soils + climate models explained 11% more variance (120% relative increase) for ∆¹³ and an average of 4.5% more (27% relative increase) for growth traits and survival. The transfer zone map developed using soils + climate differed from the climate-only map in both spatial pattern of ecotypic variation and number of transfer zones; the soils + climate map had more zones and a higher proportion of small (<4 km² ) transfer zone patches, while the climate-only map had more large patches >37 km² . Including soils in transfer zone development may identify adaptive trait variation that is obscured by large-scale differences in climate and could improve plant materials used for ecosystem management.

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets

Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.

Ecological momentary assessment of daily discrimination experiences and nicotine, alcohol, and drug use among sexual and gender minority individuals

OBJECTIVE

Sexual and gender minority (SGM) individuals experience elevated rates of minority stress, which has been linked to higher rates of nicotine and substance use. Research on this disparity to date is largely predicated on methodology that is insensitive to within day SGM-based discrimination experiences, or their relation to momentary nicotine and substance use risk. We address this knowledge gap in the current study using ecological momentary assessment (EMA).

METHOD

Fifty SGM individuals, between 18 and 45 years of age, were recruited from an inland northwestern university, regardless of their nicotine or substance use history, and invited to participate in an EMA study. Each were prompted to provide data, six times daily (between 10:00 a.m. and 10:00 p.m.) for 14 days, regarding SGM-based discrimination, other forms of mistreatment, and nicotine, drug, and alcohol use since their last prompt.

RESULTS

Discrimination experiences that occurred since individuals' last measurement prompt were associated with greater odds of nicotine and substance use during the same measurement window. Substance use was also more likely to occur in relation to discrimination reported two measurements prior in lagged models. Relative to other forms of mistreatment, discrimination effects were consistently larger in magnitude and became stronger throughout the day/evening.

CONCLUSION

This study adds to existing minority stress research by highlighting the both immediate and delayed correlates of daily SGM-based discrimination experiences. These results also contribute to our understanding of daily stress processes and provide insight into ways we might mitigate these effects using real-time monitoring and intervention technology. (PsycINFO Database Record