A Translational Model for Venous Thromboembolism: MicroRNA Expression in Hibernating Black Bears.

BACKGROUND: Hibernating American black bears have significantly different clotting parameters than their summer active counterparts, affording them protection against venous thromboembolism during prolonged periods of immobility. We sought to evaluate if significant differences exist between the expression of microRNAs in the plasma of hibernating black bears compared with their summer active counterparts, potentially contributing to differences in hemostasis during hibernation. MATERIALS AND METHODS: MicroRNA sequencing was assessed in plasma from 21 American black bears in summer active (n = 11) and hibernating states (n = 10), and microRNA signatures during hibernating and active state were established using both bear and human genome. MicroRNA targets were predicted using messenger RNA (mRNA) transcripts from black bear kidney cells. In vitro studies were performed to confirm the relationship between identified microRNAs and mRNA expression, using artificial microRNA and human liver cells. RESULTS: Using the bear genome, we identified 15 microRNAs differentially expressed in the plasma of hibernating black bears. Of these microRNAs, three were significantly downregulated (miR-141-3p, miR-200a-3p, and miR-200c-3p), were predicted to target SERPINC1, the gene for antithrombin, and demonstrated regulatory control of the gene mRNA expression in cell studies. CONCLUSIONS: Our findings suggest that the hibernating black bears' ability to maintain hemostasis and achieve protection from venous thromboembolism during prolonged periods of immobility may be due to changes in microRNA signatures and possible upregulation of antithrombin expression.

The Hunt for the Closed Conformation of the Fruit-Ripening Enzyme 1-Aminocyclopropane-1-carboxylic Oxidase: A Combined Electron Paramagnetic Resonance and Molecular Dynamics Study.

1-Aminocyclopropane-1-carboxylic oxidase (ACCO) is a non-heme iron(II)-containing enzyme involved in the biosynthesis of the phytohormone ethylene, which regulates fruit ripening and flowering in plants. The active conformation of ACCO, and in particular that of the C-terminal part, remains unclear and open and closed conformations have been proposed. In this work, a combined experimental and computational study to understand the conformation and dynamics of the C-terminal part is reported. Site-directed spin-labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy was used. Mutagenesis experiments were performed to generate active enzymes bearing two paramagnetic labels (nitroxide radicals) anchored on cysteine residues, one in the main core and one in the C-terminal part. Inter-spin distance distributions were measured by pulsed EPR spectroscopy and compared with the results of molecular dynamics simulations. The results reveal the existence of a flexibility of the C-terminal part. This flexibility generates several conformations of the C-terminal part of ACCO that correspond neither to the existing crystal structures nor to the modelled structures. This highly dynamic region of ACCO raises questions on its exact function during enzymatic activity.

Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory.

Blue copper proteins, such as azurin, show dramatic changes in Cu2+ /Cu+ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high-level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Šfrom the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long-range electrostatic changes and hence can be modeled accurately with continuum electrostatics.

Kibble-Zurek Scaling during Defect Formation in a Nematic Liquid Crystal.

Symmetry-breaking phase transitions are often accompanied by the formation of topological defects, as in cosmological theories of the early universe, superfluids, liquid crystals or solid-state systems. This scenario is described by the Kibble-Zurek mechanism, which predicts corresponding scaling laws for the defect density ρ. One such scaling law suggests a relation ρ≈τQ-1/2 with τQ the change of rate of a control parameter. In contrast to the scaling of the defect density during annihilation with ρ≈t-1 , which is governed by the attraction of defects of the same strength but opposite sign, the defect formation process, which depends on the rate of change of a physical quantity initiating the transition, has only rarely been investigated. Herein, we use nematic liquid crystals as a different system to demonstrate the validity of the predicted scaling relation for defect formation. It is found that the scaling exponent is independent of temperature and material employed, thus universal, as predicted.

Pyrethroid Pesticides as Endocrine Disruptors: Molecular Mechanisms in Vertebrates with a Focus on Fishes.

Pyrethroids are now the fourth most used group of insecticides worldwide. Employed in agriculture and in urban areas, they are detected in waterways at concentrations that are lethally and sublethally toxic to aquatic organisms. Highly lipophilic, pyrethroids accumulate in sediments and bioaccumulate in fishes. Additionally, these compounds are demonstrated to act as endocrine disrupting compounds (or EDCs) in mammals and fishes, and therefore interfere with endocrine signaling by blocking, mimicking, or synergizing endogenous hormones through direct receptor interactions, and indirectly via upstream signaling pathways. Pyrethroid metabolites have greater endocrine activity than their parent structures, and this activity is dependent on the enantiomer present, as some pyrethroids are chiral. Many EDCs studied thus far in fish have known estrogenic or antiestrogenic effects, and as such cause the inappropriate or altered expression of genes or proteins (i.e., Vtg-vitellogenin, Chg-choriogenin), often leading to physiological or reproductive effects. Additionally, these compounds can also interfere with other endocrine pathways and immune response. This review highlights studies that focus on the mechanisms of pyrethroid biotransformation and endocrine toxicity to fishes across a broad range of different pyrethroid types, and integrates literature on the in vitro and mammalian responses that inform these mechanisms.

Mental fatigue negatively influences manual dexterity and anticipation timing but not repeated high-intensity exercise performance in trained adults.

This study examined the impact of a period of mental fatigue on manual dexterity, anticipation timing and repeated high intensity exercise performance. Using a randomised, repeated measures experimental design, eight physically trained adults (mean age = 24.8 ± 4.1 years) undertook a 40 minute vigilance task to elicit mental fatigue or a control condition followed by four repeated Wingate anaerobic performance tests. Pre, post fatigue/control and post each Wingate test, manual dexterity (Seconds), coincidence anticipation (absolute error) were assessed. A series of two (condition) by six (time) ways repeated measures ANOVAs indicated a significant condition by time interactions for manual dexterity time (p = 0.021) and absolute error (p = 0.028). Manual dexterity and coincidence anticipation were significantly poorer post mental fatigue compared with control. There were no significant differences in mean power between conditions or across trials (all p > 0.05).

Using holography to measure extinction.

This work presents a new concept to measure the extinction cross section for a single particle in situ. The concept involves recording the hologram produced by the interference of a particle's forward-scattered light with the incident light. This interference pattern is fundamentally connected to the energy flow that gives rise to extinction, and, by integrating this measured pattern, one obtains an approximation for the cross section. Mie theory is used to show that this approximation can be as little as 1% in error of the true value for many cases of practical interest. Moreover, since an image of the particle can be computationally reconstructed from a measured hologram using the Fresnel-Kirchhoff diffraction theory, one can obtain the cross section simultaneously with the particle shape and size.

Interactions between the protein barnase and co-solutes studied by NMR.

Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.

Backscatter digital holography of microparticles.

This work investigates a method for digital holographic imaging of microparticles. Traditional digital holographic techniques use a particle's forward scattered light to form the hologram, whereas here we use the backscattered light. Images of a particle are then computationally reconstructed from the backscatter hologram, and several examples of such reconstructions are presented. A potential advantage of this technique is that the backscatter holograms may be more sensitive to particle-surface details.

Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1.

Protein structures calculated using NMR data are less accurate and less well-defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.

Genetic architecture and evolution of color variation in American black bears.

Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.

Behavioral responses of terrestrial mammals to COVID-19 lockdowns.

COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.

The accuracy of protein structures in solution determined by AlphaFold and NMR.

In the recent Critical Assessment of Structure Prediction (CASP) competition, AlphaFold2 performed outstandingly. Its worst predictions were for nuclear magnetic resonance (NMR) structures, which has two alternative explanations: either the NMR structures were poor, implying that Alpha-Fold may be more accurate than NMR, or there is a genuine difference between crystal and solution structures. Here, we use the program Accuracy of NMR Structures Using RCI and Rigidity (ANSURR), which measures the accuracy of solution structures, and show that one of the NMR structures was indeed poor. We then compare Alpha-Fold predictions to NMR structures and show that Alpha-Fold tends to be more accurate than NMR ensembles. There are, however, some cases where the NMR ensembles are more accurate. These tend to be dynamic structures, where Alpha-Fold had low confidence. We suggest that Alpha-Fold could be used as the model for NMR-structure refinements and that Alpha-Fold structures validated by ANSURR may require no further refinement.

Novel missense WFS1 variant causing autosomal dominant atypical Wolfram syndrome.

BACKGROUND: In contrast to the classic autosomal recessive Wolfram syndrome, Wolfram-like syndrome (WLS) is an autosomal dominant disease caused by heterozygous variants in the WFS1 gene. Here, we present deep phenotyping of a mother and son with a WFS1 variant NM_006005.3:c.2508 G > T, p. (Lys836Asn) detected with next-generation sequencing, which is novel at the nucleotide level. In this Greek family, the proband and mother had sensorineural hearing loss and mild non-progressive vision loss with optic nerve atrophy. An initial optic atrophy panel that did not test for WFS1 was unremarkable, but a broader inherited retinal dystrophy panel found the WFS1 variant. CONCLUSION: This study highlights the importance of including WFS1 sequencing in the evaluation of optic nerve atrophy to discover syndromic conditions.

Anatomical and functional outcomes of bevacizumab treatment in pediatric autosomal recessive bestrophinopathy.

PURPOSE: To report functional and anatomical outcomes of anti-VEGF treatment in eyes with autosomal recessive Bestrophinopathy (ARB) presenting in the first decade of life. METHODS: Case series of four eyes from two siblings with compound heterozygous mutations in the BEST1 gene who were treated with eight monthly intravitreal bevacizumab (IVB) injections. Response to treatment was analyzed using fundus photography (CFP), fundus autofluorescence (FAF), optical coherence tomography (OCT), OCT angiography (OCTA), and Microperimetry (MP). RESULTS: Patient-1 (male, age 9 yrs.) with visual acuity of 20/20 OD and 20/50 OS. Patient-2 (female, age 10 yrs.), with visual acuity of 20/25 OD, 20/20 OS. All eyes had multifocal subretinal deposition of lipofuscin, subretinal fluid and three had choroidal neovascularization (CNV). Lipofuscin material reabsorbed in 2/4 eyes, the CNV regressed in 3/3, a bacillary detachment resolved (1/1) but the subretinal fluid did not change. Functional improvement in visual acuity was noted but MP showed scattered areas of reduced retinal sensitivity. No ocular or systemic side effects were detected. CONCLUSION: Anti-VEGF treatment of choroidal neovascularization in eyes with ARB resulted in anatomical changes that were only clinically significant in the eye with decreased visual acuity. The hyporeflective subretinal material remained unchanged suggesting a non-exudative cause. These findings provide new insights into the management of ARB, especially in pediatric subjects with CNV.

White-tailed deer exploit temporal refuge from multi-predator and human risks on roads.

Although most prey have multiple predator species, few studies have quantified how prey respond to the temporal niches of multiple predators which pose different levels of danger. For example, intraspecific variation in diel activity allows white-tailed deer (Odocoileus virginianus) to reduce fawn activity overlap with coyotes (Canis latrans) but finding safe times of day may be more difficult for fawns in a multi-predator context. We hypothesized that within a multi-predator system, deer would allocate antipredation behavior optimally based on combined mortality risk from multiple sources, which would vary depending on fawn presence. We measured cause-specific mortality of 777 adult (>1-year-old) and juvenile (1-4-month-old) deer and used 300 remote cameras to estimate the activity of deer, humans, and predators including American black bears (Ursus americanus), bobcats (Lynx rufus), coyotes, and wolves (Canis lupus). Predation and vehicle collisions accounted for 5.3 times greater mortality in juveniles (16% mortality from bears, coyotes, bobcats, wolves, and vehicles) compared with adults (3% mortality from coyotes, wolves, and vehicles). Deer nursery groups (i.e., ≥1 fawn present) were more diurnal than adult deer without fawns, causing fawns to have 24-38% less overlap with carnivores and 39% greater overlap with humans. Supporting our hypothesis, deer nursery groups appeared to optimize diel activity to minimize combined mortality risk. Temporal refuge for fawns was likely the result of carnivores avoiding humans, simplifying diel risk of five species into a trade-off between diurnal humans and nocturnal carnivores. Functional redundancy among multiple predators with shared behaviors may partially explain why white-tailed deer fawn predation rates are often similar among single- and multi-predator systems.

Variable effects of wolves on niche breadth and density of intraguild competitors.

The parallel niche release hypothesis (PNR) indicates that reduced competition with dominant competitors results in greater density and niche breadth of subordinate competitors and which may support an adaptive advantage.We assessed support for the PNR by evaluating relationships between variation in niche breadth and intra- and interspecific density (an index of competition) of wolves (Canis lupus) coyotes (C. latrans), and bobcats (Lynx rufus).We estimated population density (wolf track surveys, coyote howl surveys, and bobcat hair snare surveys) and variability in space use (50% core autocorrelated kernel density home range estimators), temporal activity (hourly and overnight speed), and dietary (isotopic δ13C and δ15N) niche breadth of each species across three areas of varying wolf density in the Upper Peninsula of Michigan, USA, 2010-2019.Densities of wolves and coyotes were inversely related, and increased variability in space use, temporal activity, and dietary niche breadth of coyotes was associated with increased coyote density and decreased wolf density supporting the PNR. Variability in space use and temporal activity of wolves and dietary niche breadth of bobcats also increased with increased intraspecific density supporting the PNR.Through demonstrating decreased competition between wolves and coyotes and increased coyote niche breadth and density, our study provides multidimensional support for the PNR. Knowledge of the relationship between niche breadth and population density can inform our understanding of the role of competition in shaping the realized niche of species.

Short-term outcomes in patients with center-involving diabetic macular edema after a single dose of intravitreal bevacizumab.

BACKGROUND: A significant portion of diabetic macular edema (DME) is refractory to anti-vascular endothelial growth factor (anti-VEGF) agents. This study investigates morphological and functional outcomes to a single intravitreal bevacizumab (IVB) injection in patients with center-involving DME (ciDME) at 4-6 weeks and compares treatment responders and non-responders based on spectral domain optical coherence tomography (SD-OCT) features. METHODS: IRB approved observational, retrospective chart review of patients with ciDME, identified by ICD-10 code, who received IVB and underwent baseline and 4-6 weeks follow-up SD-OCT imaging between January 1, 2016 and January 19, 2021. Patients who had received previous treatment with anti-VEGF or intraocular steroids within 1 year were excluded. Variables included best-corrected visual acuity (BCVA), central subfield thickness (CST) and total macular volume (TMV). Eyes were classified as responders if CST reduction was greater than 10%. OCT scans were graded qualitatively by two masked graders using Imagivault software. Paired Student's t-tests, Wilcoxon signed rank tests and Chi-Square tests were used for analysis. RESULTS: A total of 334 prospective subjects were identified, and after applying exclusion criteria 52 eyes from 46 patients (mean age 64.22 ± 8.12 years, 58.7% male) were included. Mean BCVA did not significantly change with treatment, 63.9 ETDRS letters (~ 20/50) at baseline and 65.9 ETDRS letters (~ 20/50) post-treatment (p = 0.07). Mean CST decreased from 466 ± 123 µm at baseline to 402 ± 86 µm post-treatment (p < 0.001). 22 (42.3%) of eyes were categorized as responders and 30 (57.7%) as non-responders. Average change in CST from baseline in responders was -164 µm (p < 0.001) and + 9 µm in non-responders (p = 0.47). Vitreomacular adhesion (VMA) was more prevalent in non-responders (28.7% vs. 4.8%, p = 0.03). In addition, cyst location in the inner nuclear layer (INL) was present more frequently in responders (95.5% vs. 73.3%, p = 0.037) as was subretinal fluid (45.5% vs. 13.3%, p = 0.01). CONCLUSION: The short-term response to a single IVB was sub-optimal with structural but no functional improvements. Greater baseline CST, presence of INL cysts and subretinal fluid may represent factors indicative of a better treatment response.

Quantifying anthropogenic wolf mortality in relation to hunting regulations and landscape attributes across North America.

Understanding the types and magnitude of human-caused mortality is essential for maintaining viable large carnivore populations. We used a database of cause-specific mortality to examine how hunting regulations and landscape configurations influenced human-caused mortality of North American gray wolves (Canis lupus). Our dataset included 21 studies that monitored the fates of 3564 wolves and reported 1442 mortalities. Human-caused mortality accounted for 61% of mortality overall, with 23% due to illegal harvest, 16% due to legal harvest, and 12% the result of management removal. The overall proportion of anthropogenic wolf mortality was lowest in areas with an open hunting season compared to areas with a closed hunting season or mixed hunting regulations, suggesting that harvest mortality was neither fully additive nor compensatory. Proportion of mortality from management removal was reduced in areas with an open hunting season, suggesting that legal harvest may reduce human-wolf conflicts or alternatively that areas with legal harvest have less potential for management removals (e.g., less livestock depredation). Proportion of natural habitat was negatively correlated with the proportion of anthropogenic and illegal harvest mortality. Additionally, the proportion of mortality due to illegal harvest increased with greater natural habitat fragmentation. The observed association between large patches of natural habitat and reductions in several sources of anthropogenic wolf mortality reiterate the importance of habitat preservation to maintain wolf populations. Furthermore, effective management of wolf populations via implementation of harvest may reduce conflict with humans. Effective wolf conservation will depend on holistic strategies that integrate ecological and socioeconomic factors to facilitate their long-term coexistence with humans.

Factors influencing lion movements and habitat use in the western Serengeti ecosystem, Tanzania.

Protected areas that restrict human activities can enhance wildlife habitat quality. Efficacy of protected areas can be improved with increased protection from illegal activities and presence of buffer protected areas that surround a core protected area. Habitat value of protected areas also can be affected by seasonal variation in anthropogenic pressures. We examined seasonal space use by African lions (Panthera leo) within a core protected area, Serengeti National Park, Tanzania, and surrounding buffer protected areas with varying protection strengths. We used lion locations in logistic regression models during wet and dry seasons to estimate probability of use in relation to protection strength, distance to protected area edge, human and livestock density, distance to roads and rivers, and land cover. Lions used strongly protected buffer areas over the core protected area and unprotected areas, and moved away from protected area boundaries toward the core protected area when buffer protected areas had less protection. Lions avoided high livestock density in the wet season and high human density in the dry season. Increased strength of protection can decrease edge effects on buffer areas and help maintain habitat quality of core protected areas for lions and other wildlife species.