modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.

Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides and aptamers can incorporate various modified nucleic acids to target specific biomolecules for various therapeutic activities. Molecular dynamics simulations can accelerate the design and development of these systems with noncanonical nucleic acids by observing intricate dynamic properties and relative stability on the all-atom level.

Influence of sea ice concentration, sex and chick age on foraging flexibility and success in an Arctic seabird.

Declining sea ice and increased variability in sea ice dynamics are altering Arctic marine food webs. Changes in sea ice dynamics and prey availability are likely to impact pagophilic (ice-dependent and ice-associated) species, such as thick-billed murres (), through changes in foraging behaviour and foraging success. At the same time, extrinsic factors, such as chick demand, and intrinsic factors, such as sex, are also likely to influence foraging behaviour and foraging success of adult murres.

An arctic breeding songbird overheats during intense activity even at low air temperatures.

Birds maintain some of the highest body temperatures among endothermic animals. Often deemed a selective advantage for heat tolerance, high body temperatures also limits birds' thermal safety margin before reaching lethal levels. Recent modelling suggests that sustained effort in Arctic birds might be restricted at mild air temperatures, which may require reductions in activity to avoid overheating, with expected negative impacts on reproductive performance.

An interspecific foraging association with polar bears increases foraging opportunities for avian predators in a declining Arctic seabird colony.

Interspecific foraging associations (IFAs) are biological interactions where two or more species forage in association with each other. Climate-induced reductions in Arctic sea ice have increased polar bear () foraging in seabird colonies, which creates foraging opportunities for avian predators. We used drone video of bears foraging within a common eider () colony on East Bay Island (Nunavut, Canada) in 2017 to investigate herring gull () foraging in association with bears.

van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.

Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald's methods became routine.

A colonial-nesting seabird shows limited heart rate responses to natural variation in threats of polar bears.

Several predator-prey systems are in flux as an indirect result of climate change. In the Arctic, earlier sea-ice loss is driving polar bears () onto land when many colonial nesting seabirds are breeding. The result is a higher threat of nest predation for birds with potential limited ability to respond.

Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.

Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields.

Do foraging ecology and contaminants interactively predict parenting hormone levels in common eider?

Global climate change is causing abiotic shifts such as higher air and ocean temperatures, and disappearing sea ice in Arctic ecosystems. These changes influence Arctic-breeding seabird foraging ecology by altering prey availability and selection, affecting individual body condition, reproductive success, and exposure to contaminants such as mercury (Hg). The cumulative effects of alterations to foraging ecology and Hg exposure may interactively alter the secretion of key reproductive hormones such as prolactin (PRL), important for parental attachment to eggs and offspring and overall reproductive success.

A colonial-nesting seabird shows no heart-rate response to drone-based population surveys.

Aerial drones are increasingly being used as tools for ecological research and wildlife monitoring in hard-to-access study systems, such as in studies of colonial-nesting birds. Despite their many advantages over traditional survey methods, there remains concerns about possible disturbance effects that standard drone survey protocols may have on bird colonies. There is a particular gap in the study of their influence on physiological measures of stress.

Breeding stage and tissue isotopic consistency suggests colony-level flexibility in niche breadth of an Arctic marine bird.

Organisms must overcome environmental limitations to optimize their investment in life history stages to maximize fitness. Human-induced climate change is generating increasingly variable environmental conditions, impacting the demography of prey items and, therefore, the ability of consumers to successfully access resources to fuel reproduction. While climate change effects are especially pronounced in the Arctic, it is unknown whether organisms can adjust foraging decisions to match such changes.

Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains.

Protein flexible loop regions were once thought to be simple linkers between other more functional secondary structural elements. However, as it becomes clearer that these loop domains are critical players in a plethora of biological processes, accurate conformational sampling of 3D loop structures is vital to the advancement of drug design techniques and the overall growth of knowledge surrounding molecular systems. While experimental techniques provide a wealth of structural information, the resolution of flexible loop domains is sometimes low or entirely absent due to their complex and dynamic nature.

Systematic review: Perceptions of type 2 diabetes of people of African descent living in high-income countries.

Aims: To describe how people of African descent perceive and understand type 2 diabetes, and to examine the impact of their perceptions and beliefs on the uptake of diet, exercise, weight control and adherence to medication recommendations.

Design: Systematic literature review of quantitative and qualitative studies.

Data Sources: We searched MEDLINE, CINAHL Complete, Psych INFO, Academic Search Premier, Education Research Complete, Web of Science and Scopus, World Health Organization (WHO), Diabetes UK and American Diabetes Association for articles published from January 1999 to December 2019.

Favorable spring conditions can buffer the impact of winter carryover effects on a key breeding decision in an Arctic-breeding seabird.

The availability and investment of energy among successive life-history stages is a key feature of carryover effects. In migratory organisms, examining how both winter and spring experiences carryover to affect breeding activity is difficult due to the challenges in tracking individuals through these periods without impacting their behavior, thereby biasing results.Using common eiders , we examined whether spring conditions at an Arctic breeding colony (East Bay Island, Nunavut, Canada) can buffer the impacts of winter temperatures on body mass and breeding decisions in birds that winter at different locations (Nuuk and Disko Bay, Greenland, and Newfoundland, Canada; assessed by analyzing stable isotopes of 13-carbon in winter-grown claw samples).

Drought at a coastal wetland affects refuelling and migration strategies of shorebirds.

Droughts can affect invertebrate communities in wetlands, which can have bottom-up effects on the condition and survival of top predators. Shorebirds, key predators at coastal wetlands, have experienced widespread population declines and could be negatively affected by droughts. We explored, in detail, the effects of drought on multiple aspects of shorebird stopover and migration ecology by contrasting a year with average wet/dry conditions (2016) with a year with moderate drought (2017) at a major subarctic stopover site on southbound migration.

Exposure to cumulative stressors affects the laying phenology and incubation behaviour of an Arctic-breeding marine bird.

Wildlife are exposed to multiple stressors across life-history stages, the effects of which can be amplified as human activity surges globally. In Arctic regions, increasing air and ocean temperatures, more severe weather systems, and exposure to environmental contaminants all represent stressors occurring simultaneously. While Arctic vertebrates, including marine birds, are expected to be at risk of adverse effects from these individual stressors, few studies have researched their combined impacts on breeding behaviour and reproductive success.

The Circadian Clock Gene, Bmal1, Regulates Intestinal Stem Cell Signaling and Represses Tumor Initiation.

Background & Aims: Circadian rhythms are daily physiological oscillations driven by the circadian clock: a 24-hour transcriptional timekeeper that regulates hormones, inflammation, and metabolism. Circadian rhythms are known to be important for health, but whether their loss contributes to colorectal cancer is not known. We tested the nonredundant clock gene Bmal1 in intestinal homeostasis and tumorigenesis, using the Apc model of colorectal cancer.

Limited heat tolerance in a cold-adapted seabird: implications of a warming Arctic.

The Arctic is warming at approximately twice the global rate, with well-documented indirect effects on wildlife. However, few studies have examined the direct effects of warming temperatures on Arctic wildlife, leaving the importance of heat stress unclear. Here, we assessed the direct effects of increasing air temperatures on the physiology of thick-billed murres (Uria lomvia), an Arctic seabird with reported mortalities due to heat stress while nesting on sun-exposed cliffs.

Researcher perspectives on challenges and opportunities in conservation physiology revealed from an online survey.

Conservation physiology represents a recently emerging arm of conservation science that applies physiological tools and techniques to understand and solve conservation issues. While a multi-disciplinary toolbox can only help to address the global biodiversity crisis, any field can face challenges while becoming established, particularly highly applied disciplines that require multi-stakeholder involvement. Gaining first-hand knowledge of the challenges that conservation physiologists are facing can help characterize the current state of the field and build a better foundation for determining how it can grow.

Habitat loss on the breeding grounds is a major contributor to population declines in a long-distance migratory songbird.

Many migratory species are declining and for most, the proximate causes of their declines remain unknown. For many long-distance Neotropical migratory songbirds, it is assumed that habitat loss on breeding or non-breeding grounds is a primary driver of population declines. We integrated data collected from tracking technology, community science and remote sensing data to quantify migratory connectivity (MC), population trends and habitat loss.