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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Marginal support for a trophic cascade among sympatric canids in peripheral wolf range.

Trophic cascades reportedly structure ecological communities through indirect species interactions. Though the predator-herbivore-autotroph relationship has received much attention, mechanistic evidence supporting intraguild trophic cascades is rare. We established 348 remote camera sites (1 August-5 September 2019) across seven study areas of varying wolf (Canis lupus) density including one study area where wolves were absent in northern Michigan, USA. Using multi-species occupancy modeling at species-relevant spatial scales, we evaluated the hypothesis that increased wolf occurrence suppresses coyote (C. latrans) occurrence with corresponding increased red fox (Vulpes vulpes) occurrence mediated by land cover edge density, human presence, and temporal partitioning. Remote cameras recorded >600,000 images and included 6,370, 10,137, and 4,876 detections of wolves, coyotes, and foxes, respectively. Fox occupancy probability was more than three times as high (0.29) at camera sites where wolves were present, relative to sites wolves were absent (0.09). Pairwise species interactions supported expected size-based dominance patterns among canids and insignificant effects were directionally consistent with reported reduced strength of top-down effects in peripheral wolf range. Increased edge density also increased co-occurrence of coyote and wolves, likely a function of increased prey availability and refugia for coyotes. Though foxes occurred in spatial proximity to wolves, competition was limited by greater temporal partitioning than observed between coyotes and foxes that were spatially segregated. Collectively, our results provide marginal support for the reported trophic cascade among wolves, coyotes, and foxes wherein top-down effects may be reduced near the edge of current wolf distributions. As predators continue to recolonize portions of their historic range, knowledge of the effects on intraguild predators has implications for species management and predicting prey population responses.

The accuracy of NMR protein structures in the Protein Data Bank.

The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a need for more experimental restraints in loops. Currently, the best predictors of accuracy are Ramachandran distribution and the number of NOE restraints per residue. The precision of structures within the ensemble correlates well with accuracy, as does the number of hydrogen bond restraints per residue. Structure accuracy is improved when other components (such as additional polypeptide chains or ligands) are included.

Acute-onset central serous retinopathy after immunization with COVID-19 mRNA vaccine.

PURPOSE: We report the case of a 33-year-old male who presented with unilateral central serous retinopathy three days after the injection of a COVID-19 vaccine. OBSERVATIONS: A 33-year-old healthy Hispanic male referred to the ophthalmology service due to blurry vision and metamorphopsia in the right eye without any flashes, floaters, eye redness or pain. The patient reported that 69 hours prior to presentation he received the first dose of the Pfizer-BioNTech BNT162b2 mRNA COVID-19 vaccine. He denied any past ocular history or pertinent medical history. He does not take any medicines and denies stressful factors in his life. The clinical examination and imaging tests were consistent with central serous retinopathy that resolved in three months. CONCLUSIONS AND IMPORTANCE: This is the first report of an ocular complication potentially associated with a COVID-19 vaccination. Our case contributes information of a side effect potentially related to this new vaccine.

American martens use vigilance and short-term avoidance to navigate a landscape of fear from fishers at artificial scavenging sites.

Where two sympatric species compete for the same resource and one species is dominant, there is potential for the subordinate species to be affected through interference competition or energetic costs of avoiding predation. Fishers (Pekania pennanti) and American martens (Martes americana) often have high niche overlap, but fishers are considered dominant and potentially limiting to martens. We observed presence and vigilance of fishers and martens at winter carcass sites using remote cameras in Michigan, USA, to test the hypothesis that interference competition from fishers creates a landscape of fear for martens. Within winters, fishers co-occupied 78-88% of sites occupied by martens, and martens co-occupied 79-88% of sites occupied by fishers. Fishers displaced martens from carcasses during 21 of 6117 marten visits, while martens displaced fishers during 0 of 1359 fisher visits. Martens did not alter diel activity in response to fisher use of sites. Martens allocated 37% of time to vigilance compared to 23% for fishers, and martens increased vigilance up to 8% at sites previously visited by fishers. Fishers increased vigilance by up to 8% at sites previously visited by martens. Our results indicate that fishers were dominant over martens, and martens had greater baseline perception of risk than fishers. However, fishers appeared to be also affected as the dominant competitor by putting effort into scanning for martens. Both species appeared widespread and common in our study area, but there was no evidence that fishers spatially or temporally excluded martens from scavenging at carcasses other than occasional short-term displacement when a fisher was present. Instead, martens appeared to mitigate risk from fishers by using vigilance and short-term avoidance. Multiple short-term anti-predator behaviors within a landscape of fear may facilitate coexistence among carnivore species.

Multimodal imaging and genetic findings in a case of ARSG-related atypical Usher syndrome.

Background: Atypical Usher syndrome has recently been associated with arylsulfatase G (ARSG) variants. In these cases, characteristic findings include progressive sensorineural hearing loss (SNHL) without vestibular involvement and ring-shaped late-onset retinitis pigmentosa (RP).Materials and Methods: One patient with atypical Usher syndrome and a novel homozygous ARSG variant was included in this study. The patient underwent a comprehensive ophthalmic examination, including multimodal imaging and genetic testing.Results: A 60-year-old male of Persian decent presented to our clinic with a history of 20 years of progressive SNHL, and 10 years of progressive peripheral vision loss and pigmentary retinopathy. Consistent with previous reports of ARSG-related atypical Usher syndrome, fundus examination revealed ring-shaped retinal hyperpigmentation and fundus autofluorescence (FAF) demonstrated a six-zone pattern of autofluorescence. Optical coherence tomography (OCT) showed extensive cystoid spaces concentrated in the ganglion cell layer. Widefield OCT angiography at the level of the choriocapillaris showed signs of atrophy that corresponded to the FAF hypofluorescent zone. The patient was homozygous for a novel ARSG variant c. 1270 C > T, p. Arg424Cys.Conclusion: We report a novel ARSG variant in a case of atypical Usher syndrome and describe multimodal imaging findings that further characterize the effect of ARSG in the pathogenesis of atypical Usher syndrome.

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.

A method for validating the accuracy of NMR protein structures.

We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.

Conformational exchange in the potassium channel blocker ShK.

ShK is a 35-residue disulfide-linked polypeptide produced by the sea anemone Stichodactyla helianthus, which blocks the potassium channels Kv1.1 and Kv1.3 with pM affinity. An analogue of ShK has been developed that blocks Kv1.3 > 100 times more potently than Kv1.1, and has completed Phase 1b clinical trials for the treatment of autoimmune diseases such as psoriasis and rheumatoid arthritis. Previous studies have indicated that ShK undergoes a conformational exchange that is critical to its function, but this has proved difficult to characterise. Here, we have used high hydrostatic pressure as a tool to increase the population of the alternative state, which is likely to resemble the active form that binds to the Kv1.3 channel. By following changes in chemical shift with pressure, we have derived the chemical shift values of the low- and high-pressure states, and thus characterised the locations of structural changes. The main difference is in the conformation of the Cys17-Cys32 disulfide, which is likely to affect the positions of the critical Lys22-Tyr23 pair by twisting the 21-24 helix and increasing the solvent exposure of the Lys22 sidechain, as indicated by molecular dynamics simulations.