Measurement of microclimates in a warming world: problems and solutions.

As the world warms, it will be tempting to relate the biological responses of terrestrial animals to air temperature. But air temperature typically plays a lesser role in the heat exchange of those animals than does radiant heat. Under radiant load, animals can gain heat even when body surface temperature exceeds air temperature. However, animals can buffer the impacts of radiant heat exposure: burrows and other refuges may block solar radiant heat fully, but trees and agricultural shelters provide only partial relief. For animals that can do so effectively, evaporative cooling will be used to dissipate body heat. Evaporative cooling is dependent directly on the water vapour pressure difference between the body surface and immediate surroundings, but only indirectly on relative humidity. High relative humidity at high air temperature implies a high water vapour pressure, but evaporation into air with 100% relative humidity is not impossible. Evaporation is enhanced by wind, but the wind speed reported by meteorological services is not that experienced by animals; instead, the wind, air temperature, humidity and radiation experienced is that of the animal's microclimate. In this Commentary, we discuss how microclimate should be quantified to ensure accurate assessment of an animal's thermal environment. We propose that the microclimate metric of dry heat load to which the biological responses of animals should be related is black-globe temperature measured on or near the animal, and not air temperature. Finally, when analysing those responses, the metric of humidity should be water vapour pressure, not relative humidity.

Living in Western Australia induces some physiological adaptations of seasonal acclimatisation in the surgical burns team.

Seasonal acclimatization is known to result in adaptations that can improve heat tolerance. Staff who operate on burn injuries are exposed to thermally stressful conditions and seasonal acclimatization may improve their thermoeffector responses during surgery. Therefore, the aim of this study was to assess the physiological and perceptual responses of staff who operate on burn injuries during summer and winter, to determine whether they become acclimatized to the heated operating theater. Eight staff members had physiological and perceptual responses compared during burn surgeries conducted in thermoneutral (CON: 24.1 ± 1.2°C, 45 ± 7% relative humidity [RH]) and heated (HOT: 31.3 ± 1.6°C, 44 ± 7% RH) operating theaters, in summer and winter. Physiological parameters that were assessed included core temperature, heart rate, total sweat loss, sweat rate, and urinary specific gravity. Perceptual responses included ratings of thermal sensation and comfort. In summer, CON compared to winter CON, baseline (85 ± 15 bpm VS 94 ± 18 bpm), mean (84 ± 16 bpm VS 93 ± 18 bpm), and peak HR (94 ± 17 bpm VS 105 ± 19 bpm) were lower (p < 0.05), whereas core temperature was not different between seasons in either condition (p > 0.05). In HOT, ratings of discomfort were higher in summer (15 ± 3) than winter (13 ± 3; p > 0.05), but ratings of thermal sensation and sweat rate were similar between seasons (p > 0.05). The surgical team in burns in Western Australia can obtain some of the physiological adaptations that result from seasonal acclimatization, but not all. That is most likely due to a lower than required amount of outdoor heat exposure in summer, to induce all physiological and perceptual adaptations.

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore.

Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The high-quality filtered RNA-seq raw reads were deposited in a public database which provides approximately 54 billion high-quality paired-end sequencing reads in total, with an average mapping rate of ~93.92%. Transcriptome databases represent valuable resources that can be used to study patterns of gene expression, and pathways that are related to key biological processes, including important economic traits in herbivores.

Behavioural and physiological responses to stressors in sheep with temperament classified by genotype or phenotype.

The single nucleotide polymorphism (SNP) rs107856856, located in the tryptophan hydroxylase-2 gene, is associated with the behavioural phenotype for sheep temperament measured at weaning. Here, we tested the association between that SNP and physiological and behavioural responses to stressors in adult sheep. Two groups of adult sheep, one with genotype A/A (calm genotype) and the other with G/G (nervous genotype) in rs107856856, were selected from 160 sheep and were exposed, twice, to an open-field arena and an isolation box test (IBT). During each repeat, the behaviour and physiological responses (cortisol, prolactin, dehydroepiandrosterone [DHEA], brain derived neurotrophic factor [BDNF], characteristics of the response of body temperature, and oxidative stress) were measured. The behavioural and physiological responses of the sheep were compared between genotypes and also between groups classified on their phenotype as assessed by their initial isolation box score ("low responders" and "high responders"). The SNP rs107856856 had some effects on the behavioural phenotype (IBT score) but no effects on the physiological response to stress (cortisol, prolactin, DHEA, BDNF, oxidative stress or changes in body temperature) in the adult sheep, probably because the sheep were exposed, and therefore had adapted, to human contact during their life.

Optimal sampling interval for characterisation of the circadian rhythm of body temperature in homeothermic animals using periodogram and cosinor analysis.

Core body temperature (T c) is a critical aspect of homeostasis in birds and mammals and is increasingly used as a biomarker of the fitness of an animal to its environment. Periodogram and cosinor analysis can be used to estimate the characteristics of the circadian rhythm of T c from data obtained on loggers that have limited memory capacity and battery life. The sampling interval can be manipulated to maximise the recording period, but the impact of sampling interval on the output of periodogram or cosinor analysis is unknown. Some basic guidelines are available from signal analysis theory, but those guidelines have never been tested on T c data. We obtained data at 1-, 5- or 10-min intervals from nine avian or mammalian species, and re-sampled those data to simulate logging at up to 240-min intervals. The period of the rhythm was first analysed using the Lomb-Scargle periodogram, and the mesor, amplitude, acrophase and adjusted coefficient of determination (R 2) from the original and the re-sampled data were obtained using cosinor analysis. Sampling intervals longer than 60 min did not affect the average mesor, amplitude, acrophase or adjusted R 2, but did impact the estimation of the period of the rhythm. In most species, the period was not detectable when intervals longer than 120 min were used. In all individual profiles, a 30-min sampling interval modified the values of the mesor and amplitude by less than 0.1°C, and the adjusted R 2 by less than 0.1. At a 30-min interval, the acrophase was accurate to within 15 min for all species except mice. The adjusted R 2 increased as sampling frequency decreased. In most cases, a 30-min sampling interval provides a reliable estimate of the circadian T c rhythm using periodogram and cosinor analysis. Our findings will help biologists to select sampling intervals to fit their research goals.

Social media as a tool to understand the distribution and ecology of elusive mammals.

Comparatively little is known about the distribution and ecology of Aardvark (Orycteropus afer) and Temminck's Ground Pangolin (Smutsia temminckii). Both are elusive species that are normally nocturnal, solitary, and fossorial. Formally collected records have been used to map the distribution of these species, and social media records provide a tool to gather information on their distribution and ecology. We obtained 680 photographs and videos of aardvarks and 790 of ground pangolins in southern Africa from publicly available posts on Facebook and Instagram (2010-2019). The images provide new insights into the distribution, activity, drinking, and predation-and confirm that aardvarks are more diurnally active when they are in poor body condition. Social media can provide useful supplementary information for understanding of elusive mammals. These "soft" data can be applied to other species.

Finding biomarkers of experience in animals.

At a time when there is a growing public interest in animal welfare, it is critical to have objective means to assess the way that an animal experiences a situation. Objectivity is critical to ensure appropriate animal welfare outcomes. Existing behavioural, physiological, and neurobiological indicators that are used to assess animal welfare can verify the absence of extremely negative outcomes. But welfare is more than an absence of negative outcomes and an appropriate indicator should reflect the full spectrum of experience of an animal, from negative to positive. In this review, we draw from the knowledge of human biomedical science to propose a list of candidate biological markers (biomarkers) that should reflect the experiential state of non-human animals. The proposed biomarkers can be classified on their main function as endocrine, oxidative stress, non-coding molecular, and thermobiological markers. We also discuss practical challenges that must be addressed before any of these biomarkers can become useful to assess the experience of an animal in real-life.

Functional interactions between coat structure and colour in the determination of solar heat load on arid living kangaroos in summer: balancing crypsis and thermoregulation.

Interactions of solar radiation with mammal fur are complex. Reflection of radiation in the visible spectrum provides colour that has various roles, including sexual display and crypsis, i.e., camouflage. Radiation that is absorbed by a fur coat is converted to heat, a proportion of which impacts on the skin. Not all absorption occurs at the coat surface, and some radiation penetrates the coat before being absorbed, particularly in lighter coats. In studies on this phenomenon in kangaroos, we found that two arid zone species with the thinnest coats had similar effective heat load, despite markedly different solar reflectances. These kangaroos were Red Kangaroos (Osphranter rufus) and Western Grey Kangaroos (Macropus fuliginosus).Here we examine the connections between heat flow patterns associated with solar radiation, and the physical structure of these coats. Also noted are the impacts of changing wind speed. The modulation of solar radiation and resultant heat flows in these coats were measured at wind speeds from 1 to 10 m s-1 by mounting them on a heat flux transducer/temperature-controlled plate apparatus in a wind tunnel. A lamp with a spectrum like solar radiation was used as a proxy for the sun. The integrated reflectance across the solar spectrum was higher in the red kangaroos (40 ± 2%) than in the grey kangaroos (28 ± 1%). Fur depth and insulation were not different between the two species, but differences occurred in fibre structure, notably in fibre length, fibre density and fibre shape. Patterns of heat flux within the species' coats occurred despite no overall difference in effective solar heat load. We consider that an overarching need for crypsis, particularly for the more open desert-adapted red kangaroo, has led to the complex adaptations that retard the penetrance of solar radiation into its more reflective fur.

Neurotrophic factor MANF regulates autophagy and lysosome function to promote proteostasis in C. elegans.

The conserved mesencephalic astrocyte-derived neurotrophic factor (MANF) protects dopaminergic neurons but also functions in several other tissues. Previously, we showed that Caenorhabditis elegans manf-1 null mutants have increased ER stress, dopaminergic neurodegeneration, protein aggregation, slower growth, and a reduced lifespan. The multiple requirements of MANF in different systems suggest its essential role in regulating cellular processes. However, how intracellular and extracellular MANF regulates broader cellular function remains unknown. Here, we report a novel mechanism of action for manf-1 that involves the autophagy transcription factor HLH-30/TFEB-mediated signaling to regulate lysosomal function and aging. We generated multiple transgenic strains overexpressing MANF-1 and found that animals had extended lifespan, reduced protein aggregation, and improved neuronal health. Using a fluorescently tagged MANF-1, we observed different tissue localization of MANF-1 depending on the ER retention signal. Further subcellular analysis showed that MANF-1 localizes within cells to the lysosomes. These findings were consistent with our transcriptomic studies and, together with analysis of autophagy regulators, demonstrate that MANF-1 regulates protein homeostasis through increased autophagy and lysosomal activity. Collectively, our findings establish MANF as a critical regulator of the stress response, proteostasis, and aging.

Effect of Neck-Deep Immersion in Cool or Thermoneutral Water on Blood Glucose Levels in Individuals With Type 1 Diabetes.

Context: It is unclear whether immersion in cool water, typical of many beaches, increases the concentration of blood glucose in individuals with type 1 diabetes mellitus (T1DM). Objective: To test the hypothesis in individuals with T1DM that immersion neck-deep in cool water (COOL) causes an increase in blood glucose concentration, but not exposure to thermoneutral water (THERMO) or thermoneutral air. Methods: Eight overnight-fasted participants with T1DM were exposed for 60 minutes on separate days to 3 experimental conditions: cool water (COOL, 23 °C); thermoneutral water (THERMO, 33.5 °C); or thermoneutral air (24 °C). They then recovered for 60 minutes on land at 24 °C. At time intervals, we measured: blood glucose and plasma insulin concentration, rate of carbohydrate and fat oxidation, skin and core temperature, subcutaneous blood flow, and shivering via electromyography. Results: There was no change in blood glucose concentration during the 3 experimental conditions (P > .05). During recovery after COOL, blood glucose increased (P < .05) but did not change in the other 2 conditions. The rate of carbohydrate oxidation during and early after COOL was higher than in the other 2 conditions (P < .05), and COOL led to a decrease in subcutaneous blood flow and the concentration of plasma insulin (P < .05). Conclusion: Cool or thermoneutral neck-deep immersion in water does not cause a change in the concentration of blood glucose in people with T1DM, but on-land recovery from COOL causes an increase in blood glucose that may be due, at least in part, to the accompanying decrease in plasma insulin.

Correction: Could the ketogenic diet induce a shift in thyroid function and support a metabolic advantage in healthy participants? A pilot randomized-controlled-crossover trial.

[This corrects the article DOI: 10.1371/journal.pone.0269440.].

Effect of starvation on electrotaxis response.

Caenorhabditis elegans is an ideal model for investigating the effects of extrinsic and intrinsic conditions on the behavioral changes of animals. Our group previously showed how different conditions influence the behavior of worms following an electric stimulus in a microfluidic channel, known as electrotaxis. In this study we describe the effect of starvation on the electrotaxis movement of animals. We show that acute starvation did not affect the electrotaxis response or dopaminergic neurons but extended the lifespan of animals.

Cold and Hungry: Heterothermy Is Associated with Low Leptin Levels in a Bulk Grazer during a Drought.

AbstractReduced energy intake can compromise the ability of a mammal to maintain body temperature within a narrow 24-h range, leading to heterothermy. To investigate the main drivers of heterothermy in a bulk grazer, we compared abdominal temperature, body mass, body condition index, and serum leptin levels in 11 subadult Cape buffalo (Syncerus caffer caffer) during a drought year and a nondrought year. Low food availability during the drought year (as indexed by grass biomass, satellite imagery of vegetation greenness, and fecal chlorophyll) resulted in lower body condition index, lower body mass relative to that expected for an equivalent-aged buffalo, and lower leptin levels. The range of 24-h body temperature rhythm was 2°C during the nondrought year and more than double that during the drought year, and this was caused primarily by a lower minimum 24-h body temperature rhythm during the cool dry winter months. After rain fell and vegetation greenness increased, the minimum 24-h body temperature rhythm increased, and the range of 24-h body temperature rhythm was smaller than 2°C. In order of importance, poor body condition, low minimum 24-h air temperature, and low serum leptin levels were the best predictors of the increase in the range of 24-h body temperature rhythm. While the thermoregulatory role of leptin is not fully understood, the association between range of 24-h body temperature rhythm and serum leptin levels provides clues about the underlying mechanism behind the increased heterothermy in large mammals facing food restriction.

Finding motifs using DNA images derived from sparse representations.

MOTIVATION: Motifs play a crucial role in computational biology, as they provide valuable information about the binding specificity of proteins. However, conventional motif discovery methods typically rely on simple combinatoric or probabilistic approaches, which can be biased by heuristics such as substring-masking for multiple motif discovery. In recent years, deep neural networks have become increasingly popular for motif discovery, as they are capable of capturing complex patterns in data. Nonetheless, inferring motifs from neural networks remains a challenging problem, both from a modeling and computational standpoint, despite the success of these networks in supervised learning tasks. RESULTS: We present a principled representation learning approach based on a hierarchical sparse representation for motif discovery. Our method effectively discovers gapped, long, or overlapping motifs that we show to commonly exist in next-generation sequencing datasets, in addition to the short and enriched primary binding sites. Our model is fully interpretable, fast, and capable of capturing motifs in a large number of DNA strings. A key concept emerged from our approach-enumerating at the image level-effectively overcomes the k-mers paradigm, enabling modest computational resources for capturing the long and varied but conserved patterns, in addition to capturing the primary binding sites. AVAILABILITY AND IMPLEMENTATION: Our method is available as a Julia package under the MIT license at https://github.com/kchu25/MOTIFs.jl, and the results on experimental data can be found at https://zenodo.org/record/7783033.

Seasonal activities of the phyllosphere microbiome of perennial crops.

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

Tourniquet use during primary total knee arthroplasty-a survey of Irish orthopaedic surgeons in 2022.

BACKGROUND: Tourniquet use during primary total knee arthroplasty is a debated topic in the literature with no consensus on its optimal use. AIM: To analyse current tourniquet practice amongst Irish orthopaedic surgeons performing primary total knee arthroplasty surgery. To evaluate if there has been a shift in practice in recent years and to explore potential reasons behind this. METHODS: An eleven-question online survey was developed using the online platform SurveyMonkey. This was distributed by email to Irish orthopaedic surgeons via the Irish Institute of Trauma and Orthopaedic Surgery. RESULTS: Fifty responses were included in the final analysis of this study. Eighteen (36%) respondents reported changing their tourniquet use in the past 5 years. Thirty-one (62%) respondents reported inflating the tourniquet for the entire case, with the remaining never applying a tourniquet (n = 6, 12%), applying a tourniquet but not routinely inflating it (n = 3, 6%), or inflating the tourniquet only during cementation (n = 5, 10%). The number of years of experience as a consultant appeared to impact tourniquet use in a bimodal pattern. CONCLUSION: While the majority of Irish orthopaedic surgeons in this survey inflate a tourniquet for the entire surgical procedure, there is a definite shift towards reduced tourniquet use compared to previous Irish, UK, and American surveys.

Point-of-Care Tenofovir Urine Testing for the Prediction of Treatment Failure and Drug Resistance During Initial Treatment for Human Immunodeficiency Virus Type 1 (HIV-1) Infection.

BACKGROUND: Viral rebound during antiretroviral treatment (ART) is most often driven by suboptimal adherence in the absence of drug resistance. We assessed the diagnostic performance of point-of-care (POC) tenofovir (TFV) detection in urine for the prediction of viral rebound and drug resistance during ART. METHODS: We performed a nested case-control study within the ADVANCE randomized clinical trial (NCT03122262) in Johannesburg, South Africa. Adults with human immunodeficiency virus (HIV) and newly initiating ART were randomized to receive either dolutegravir or efavirenz, tenofovir disoproxil fumarate or alafenamide, and emtricitabine. All participants with rebound ≥200 copies/mL between 24 and 96 weeks of follow-up were selected as cases and matched to controls with virological suppression <50 copies/mL. Rapid POC urine-TFV detection was performed retrospectively. RESULTS: We included 281 samples from 198 participants. Urine-TFV was detectable in 30.7% (70/228) of cases and in 100% (53/53) of controls. Undetectable urine-TFV predicted rebound with a sensitivity of 69% [95% confidence interval {CI}: 63-75] and specificity of 100% [93-100]. In cases with virological failure and sequencing data (n = 42), NRTI drug resistance was detected in 50% (10/20) of cases with detectable urine-TFV versus in 8.3% (2/24) of cases with undetectable urine-TFV. Detectable urine-TFV predicted NRTI resistance (odds ratio [OR] 10.4 [1.8-114.4] P = .005) with a sensitivity of 83% [52-98] and specificity of 69% [50-84]. CONCLUSIONS: POC objective adherence testing using a urine-TFV test predicted viral rebound with high specificity. In participants with rebound, urine-TFV testing predicted the selection of drug resistance. Objective adherence testing may be used to rapidly provide insight into adherence, suppression, and drug resistance during ART.

Pekin ducks are motivated to lay in their preferred nest substrate.

Nest design is one factor contributing to floor-laying in farmed poultry. We investigated: (i) if ducks (Anas platyrhynchos) prefer a particular nest substrate; and (ii) how important that preference is to them, indicated by stress-induced hyperthermia, egg albumen corticosterone, and behaviour. Twelve female ducks that were trained in a push-door task had temperature data loggers implanted. Preference testing identified the most and least preferred nest substrates between sawdust, astroturf, and hemp fibres. A behavioural demand test then required the ducks to use push-doors to access nests containing either the most or least preferred substrate. The preferred substrate door was loaded with increasing weight (0-120% of bodyweight, four nights per workload) and eventually blocked to prevent nest access. The least preferred substrate door remained unweighted. The overall rank order of substrate preferences was sawdust > hemp > astroturf. Six of the 12 birds pushed all workloads and attempted to push the blocked door. The area under the curve (AUC) of hyperthermia was larger when the preferred substrate door was blocked compared with 0%. The AUC did not differ between nights 2-4 of the blocked door compared with night 1. Egg albumen corticosterone was unaffected. We conclude that laying Pekin ducks prefer manipulatable nest substrates and accessing one is important enough to pay a cost. The results indicate that a manipulatable substrate should be provided to commercially farmed nesting ducks.