Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy.

Neurotransmitter:sodium symporters (NSSs) play critical roles in neural signaling by regulating neurotransmitter uptake into cells powered by sodium electrochemical gradients. Bacterial NSSs orthologs, including MhsT from Bacillus halodurans, have emerged as model systems to understand the structural motifs of alternating access in NSSs and the extent of conservation of these motifs across the family. Here, we apply a computational/experimental methodology to illuminate the conformational landscape of MhsT alternating access. Capitalizing on our recently developed method, Sampling Protein Ensembles and Conformational Heterogeneity with AlphaFold2 (SPEACH_AF), we derived clusters of MhsT models spanning the transition from inward-facing to outward-facing conformations. Systematic application of double electron-electron resonance (DEER) spectroscopy revealed ligand-dependent movements of multiple structural motifs that underpin MhsT's conformational cycle. Remarkably, comparative DEER analysis in detergent micelles and lipid nanodiscs highlights the profound effect of the environment on the energetics of conformational changes. Through experimentally derived selection of collective variables, we present a model of ion and substrate-powered transport by MhsT consistent with the conformational cycle derived from DEER. Our findings not only advance the understanding of MhsT's function but also uncover motifs of conformational dynamics conserved within the broader context of the NSS family and within the LeuT-fold class of transporters. Importantly, our methodological blueprint introduces an approach that can be applied across a diverse spectrum of transporters to describe their conformational landscapes.

Haemolysis overestimates plasma oxidative stress biomarkers in a free-ranging mammal: The case of roe deer.

Quantifying oxidative stress has garnered extensive interest in evolutionary ecology and physiology since proposed as a mediator of life histories. However, while the theoretical framework of oxidative stress ecology is well-supported by laboratory-based studies, results obtained in wild populations on oxidative damage and antioxidant biomarkers have shown inconsistent trends. We propose that red blood cell lysis could be a source of bias affecting measurements of oxidative stress biomarkers, distorting the conclusions drawn from them. Using an experimental approach consisting of enriching plasma from roe deer with lysed red blood cells, we show that the values of commonly used oxidative stress biomarkers linearly increase with the degree of haemolysis - assayed by haemoglobin concentration. This result concerns oxidized proteins (carbonyls) and lipids (TBARS), as well as enzymatic (superoxide dismutase) and non-enzymatic (trolox assay, OXY assay) antioxidant markers. Based on 707 roe deer blood samples collected in the field, we next show that the occurrence of haemolysis in plasma samples is negatively related to age. Finally, we illustrate that considering the variance explained by age-related haemolysis improves explanatory models for inter-individual variability in plasma oxidative stress biomarkers, without substantially altering the estimates of the parameters studied here. Our results raise the question of the veracity of the conclusions if the degree of haemolysis in plasma is not considered in animal models such as roe deer, for which the occurrence and severity of haemolysis vary according to individual characteristics. We recommend measuring and controlling for the degree of haemolysis be considered in future studies that investigate the causes and consequences of oxidative stress in ecophysiological studies.

Relationship between Plasma and Saliva Urea Nitrogen Concentrations in New Zealand Red Deer Calves (Cervus elaphus).

Red deer (Cervus elaphus), like other ruminants, excrete approximately 70% of the nitrogen they ingest. Developing ways in which to reduce the rate of loss, such as manipulating the diet or selecting for efficiency of growth, requires close monitoring of the plasma urea N (PUN) concentration which, in turn, requires a simple, safe, and reliable method for collecting samples. Saliva is easier to collect than blood, but the relationship between the salivary urea N (SUN) and the PUN is not known for red deer. This was therefore evaluated in two strains of mixed-sex red deer calves (Cervus elaphus): a phenotype with a high seasonality of growth (H, n = 10) and a phenotype with a low seasonality of growth (L, n = 13). Both phenotypes were divided into two groups, which were each offered one of two forage-based diets ad libitum: a medium-quality diverse treatment and a low-quality perennial ryegrass-white clover treatment. Blood and saliva samples for the determination of the PUN and SUN were collected at dawn every four weeks for five months (April to September 2022). There was a strong linear relationship between the PUN and SUN in the pooled sample (R2 = 0.65, p < 0.001). The estimations of the PUN were significantly improved by adding diet and the date of sampling into the model (p < 0.001), but not phenotype (p > 0.75). SUN represents a reliable index of the PUN, and collecting saliva therefore represents a simple and inexpensive alternative to collecting blood samples in studies of nitrogen metabolism in red deer.

Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling methods.

Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure-function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.

Expression of the cellular prion protein by mast cells in white-tailed deer carotid body, cervical lymph nodes and ganglia.

Chronic wasting disease (CWD) is a transmissible and fatal prion disease that affects cervids. While both oral and nasal routes of exposure to prions cause disease, the spatial and temporal details of how prions enter the central nervous system (CNS) are unknown. Carotid bodies (CBs) are structures that are exposed to blood-borne prions and are densely innervated by nerves that are directly connected to brainstem nuclei, known to be early sites of prion neuroinvasion. All CBs examined contained mast cells expressing the prion protein which is consistent with these cells playing a role in neuroinvasion following prionemia.

Report of Giardia duodenalis in a non-captive chital Axis axis (Erxleben 1777) in Santa Catarina, South of Brazil.

Giardiasis is an infection of the small intestine by protozoa of the genus Giardia, which has a wide range of susceptible hosts, including domestic and wild animals and humans. Giardia is a zoonotic agent and represents one of the main human parasites, with high prevalence and great importance in public health. This report aims to describe the parasitism of a non-captive Chital deer (Axis axis) by Giardia duodenalis. The animal, after being rescued by soldiers from the 2nd Platoon of the 2nd Company of the 2nd Battalion of the Environmental Military Police of the State of Santa Catarina, was sent to the Wildlife Studies Center (NEVS) of the University of Western Santa Catarina (UNOESC). During clinical care, an exposed fracture in the left pelvic limb and signs of acute respiratory failure were found. Fecal samples were collected for later parasitological diagnosis. Two techniques were applied: centrifugal flotation with zinc sulfate, to diagnose parasites of the gastrointestinal system, and Baermann, to search for parasitism in the respiratory tract. The investigation revealed the presence of Giardia duodenalis. The animal died on the same day of its arrival due to a cardiorespiratory arrest. The presence of this parasite in an invasive exotic deer species highlights its epidemiological importance, as it can act as a source of infection and spread the disease to humans and other animals.

Giardíase é uma infecção do intestino delgado por protozoários do gênero Giardia, o qual apresenta uma ampla variedade de hospedeiros suscetíveis, incluindo animais domésticos, selvagens e também humanos. Giardia é um agente zoonótico, e representa um dos principais parasitas de humanos, com alta prevalência e grande importância em saúde pública. Este relato tem como objetivo descrever o parasitismo de um indivíduo de cervo Chital (Axis axis) de vida livre por Giardia duodenalis. O animal, após ser resgatado por soldados do 2º Pelotão da 2ª Companhia do 2º Batalhão da Polícia Militar Ambiental do Estado de Santa Catarina, foi encaminhado ao Núcleo de Estudos em Vida Selvagem (NEVS) da Universidade do Oeste de Santa Catarina (UNOESC). Durante o atendimento clínico foi constatada fratura exposta no membro pélvico esquerdo e sinais de insuficiência respiratória aguda. Amostras de fezes foram coletadas para posterior diagnóstico parasitológico. Para isso, foram usadas duas técnicas: centrífugo-flutuação em sulfato de zinco, com o objetivo de diagnosticar parasitas do sistema gastrointestinal, e Baermann, com o objetivo de pesquisar parasitas do trato respiratório. Os achados revelaram presença de cistos de Giardia duodenalis. O animal morreu no mesmo dia de sua chegada, devido a uma parada cardiorrespiratória. A presença desse parasito em uma espécie de cervídeo exótico invasor destaca sua importância epidemiológica, pois o mesmo pode atuar como fonte de infecção e de disseminação da doença para o ser humano e/ou outros animais.

The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) from Jartai Pass Site in Xinjiang, China, and its phylogenetic relationships.

The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as NJ26S from Jartai Pass Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition of the mitochondrial genome is 28.17% A, 25.01% T, 11.89% G, 19.72% C, and 15.21% missing data with an AT composition of 53.18%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2 + I + G4 model. This study presents molecular evidence indicating the presence of Capreolus pygargus in the Xinjiang Uygur Autonomous Region in China more than 3,000 years ago.

Temporal Characterization of Prion Shedding in Secreta of White-Tailed Deer in Longitudinal Study of Chronic Wasting Disease, United States.

Chronic wasting disease (CWD) affects cervids in North America, Asia, and Scandinavia. CWD is unique in its efficient spread, partially because of contact with infectious prions shed in secreta. To assess temporal profiles of CWD prion shedding, we collected saliva, urine, and feces from white-tailed deer for 66 months after exposure to low oral doses of CWD-positive brain tissue or saliva. We analyzed prion seeding activity by using modified amyloid amplification assays incorporating iron oxide bead extraction, which improved CWD detection and reduced false positives. CWD prions were detected in feces, urine, and saliva as early as 6 months postinfection. More frequent and consistent shedding was observed in deer homozygous for glycine at prion protein gene codon 96 than in deer expressing alternate genotypes. Our findings demonstrate that improved amplification methods can be used to identify early antemortem CWD prion shedding, which might aid in disease surveillance of cervids.

The role of wild red deer on soil physical properties in a Mediterranean ecosystem: insights from a Portuguese mountain.

In this study we aimed to assess the role of wild red deer, along with other ungulates such as roe deer and wild boar, in the soil's physical properties, namely soil penetration resistance and depth (used as a proxy for soil compaction), hydraulic conductivity (a proxy for water infiltration), and the proportion of soil stable aggregates. Results showed that, at the density level found in our study area, red deer have a neutral effect at the soil level, not causing significant soil compaction or significantly influencing measured soil functions.

Theileria orientalis Ikeda infection detected in red deer but not dogs or horses in New Zealand.

AIMS: To determine whether evidence for infection with Theileria orientalis (Ikeda) could be identified in samples of commercial red deer (Cervus elaphus), horses, and working farm dogs in New Zealand. METHODS: Blood samples were collected during October and November 2019 from a convenience sample of red deer (n = 57) at slaughter. Equine blood samples (n = 50) were convenience-sampled from those submitted to a veterinary pathology laboratory for routine testing in January 2020. Blood samples, collected for a previous study from a convenience sample of Huntaway dogs (n = 115) from rural regions throughout the North and South Islands of New Zealand between August 2018 and December 2020, were also tested. DNA was extracted and quantitative PCR was used to detect the T. orientalis Ikeda major piroplasm surface protein (MPSP) gene. A standard curve of five serial 10-fold dilutions of a plasmid carrying a fragment of the T. orientalis MPSP gene was used to quantify the number of T. orientalis organisms in the samples. MPSP amplicons obtained by end-point PCR on positive samples were isolated and subjected to DNA sequencing. The resulting sequences were compared to previously published T. orientalis sequences. RESULTS: There were 6/57 (10%) samples positive for T. orientalis Ikeda from the deer and no samples positive for T. orientalis Ikeda from the working dogs or horses. The mean infection intensity for the six PCR-positive deer was 5.1 (min 2.2, max 12.4) T. orientalis Ikeda organisms/µL. CONCLUSIONS AND CLINICAL RELEVANCE: Red deer can potentially sustain low infection intensities of T. orientalis Ikeda and could act as reservoirs of infected ticks. Further studies are needed to determine whether naïve ticks feeding on infected red deer can themselves become infected. ABBREVIATIONS: Cq: Quantification cycle; LOQ: Limits of quantification; MPSP: Major piroplasm surface protein; qPCR: Quantitative polymerase chain reaction.

Pulse EPR Methods in the Angstrom to Nanometre Scale Shed Light on the Conformational Flexibility of a Fluoride Riboswitch.

Riboswitches control gene regulation upon external stimuli such as environmental factors or ligand binding. The fluoride sensing riboswitch from Thermotoga petrophila is a complex regulatory RNA proposed to be involved in resistance to F- cytotoxicity. The details of structure and dynamics underpinning the regulatory mechanism are currently debated. Here we demonstrate that a combination of pulsed electron paramagnetic resonance (ESR/EPR) spectroscopies, detecting distances in the angstrom to nanometre range, can probe distinct regions of conformational flexibility in this riboswitch. PELDOR (pulsed electron-electron double resonance) revealed a similar preorganisation of the sensing domain in three forms, i.e. the free aptamer, the Mg2+-bound apo, and the F--bound holo form. 19F ENDOR (electron-nuclear double resonance) was used to investigate the active site structure of the F--bound holo form. Distance distributions without a priori structural information were compared with in silico modelling of spin label conformations based on the crystal structure. While PELDOR, probing the periphery of the RNA fold, revealed conformational flexibility of the RNA backbone, ENDOR indicated low structural heterogeneity at the ligand binding site. Overall, the combination of PELDOR and ENDOR with sub-angstrom precision gave insight into structural organisation and flexibility of a riboswitch, not easily attainable by other biophysical techniques.

Variation in the prion protein gene (PRNP) open reading frame sequence in French cervids.

The recent emergence of chronic wasting disease (CWD) in Europe has become a new public health risk for monitoring of wild and farmed cervids. This disease, due to prions, has proliferated in North America in a contagious manner. In several mammalian species, polymorphisms in the prion protein gene (PRNP) play a crucial role in the susceptibility to prions and their spread. To obtain a reliable picture of the distribution of PRNP polymorphisms in the two most common cervid species in France, we sequenced the open reading frame (ORF) of this gene in 2114 animals, 1116 roe deer (Capreolus capreolus) and 998 red deer (Cervus elaphus). Selection criteria such as historical origin, spatial distribution and sex ratio have been integrated to establish this sample collection. Except for one heterozygous animal with a non-synonymous mutation at codon 37 (G37A), all the 1116 French roe deer were monomorphic. Red deer showed greater variation with two non-synonymous substitutions (T98A; Q226E), three synonymous substitutions (codons 21, 78 and 136) and a new 24pb deletion (Δ69-77). We found significant regional variations between French regions in the frequency of the identified substitutions. After cloning of the PRNP ORF from animals presenting multiple non-synonymous polymorphisms, we identified six haplotypes and obtained a total of twelve genotypes. As in other European countries, we highlighted the apparent homogeneity of PRNP in the French roe deer and the existence of a greater diversity in the red deer. These results were in line with European phylogeographic studies on these two species.

Host-pathogen associations inferred from bloodmeal analyses of Ixodes scapularis ticks in a low biodiversity setting.

Tick-borne pathogen emergence is dependent on the abundance and distribution of competent hosts in the environment. Ixodes scapularis ticks are generalist feeders, and their pathogen infection prevalence depends on their relative feeding on local competent and non-competent hosts. The ability to determine what host a larval life stage tick fed on can help predict infection prevalence, emergence, and spread of certain tick-borne pathogens and the risks posed to public health. Here, we use a newly developed genomic target-based technique to detect the source of larval bloodmeals by sampling questing nymphs from Block Island, RI, a small island with a depauperate mammalian community. We used previously designed specific assays to target all known hosts on this island and analyzed ticks for four human pathogenic tick-borne pathogens. We determined the highest proportion of larvae fed on avian species (42.34%), white-footed mice (36.94%), and white-tailed deer (20.72%) and occasionally fed on feral cats, rats, and voles, which are in low abundance on Block Island. Additionally, larvae that had fed on white-footed mice were significantly more likely to be infected with Borrelia burgdorferi and Babesia microti, while larvae that had fed on white-footed mice or white-tailed deer were significantly more likely to be infected with, respectively, mouse- and deer-associated genotypes of Anaplasma phagocytophilum. The ability to detect a nymph's larval host allows for a better understanding of tick feeding behavior, host distribution, pathogen prevalence, and zoonotic risks to humans, which can contribute to better tick management strategies. IMPORTANCE: Tick-borne diseases, such as Lyme disease, babesiosis, and anaplasmosis, pose significant public health burdens. Tick bloodmeal analysis provides a noninvasive sampling method to evaluate tick-host associations and combined with a zoonotic pathogen assay, can generate crucial insights into the epidemiology and transmission of tick-borne diseases by identifying potential key maintenance hosts. We investigated the bloodmeals of questing Ixodes scapularis nymphs. We found that avian hosts, white-footed mice, and white-tailed deer fed the majority of larval ticks and differentially contributed to the prevalence of multiple tick-borne pathogens and pathogen genotypes in a low biodiversity island setting. Unraveling the intricate network of host-vector-pathogen interactions will contribute to improving wildlife management and conservation efforts, to developing targeted surveillance, and vector and host control efforts, ultimately reducing the incidence of tick-borne diseases and improving public health.

Agouti-Signaling Protein and Melanocortin-1-Receptor Mutations Associated with Coat Color Phenotypes in Fallow Deer (Dama dama).

Four dominant coat color phenotypes are found in fallow deer (Dama dama). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals (772 brown, 62 black, 126 menil, and 38 white) were examined for mutations in the ASIP, MC1R, TYR, and SLC45A2 genes. In ASIP, two mutations (ASIP-M-E2, located at the boundary from exon 2 to intron 2; and ASIP-M-E3, an InDel of five nucleotides) were found, leading to black fallow deer being either homozygous or heterozygous in combination. There were also two mutations found in MC1R. Whereby the mutation MC1R-M1 (leucine to proline, L48P) homozygous leads to a white coat, while the mutation MC1R-M2 (glycine to aspartic acid, G236D) homozygous is associated with the menil phenotype. When both mutations occur together in a heterozygous character state, it results in a menil coat. Since the mutations in the two genes are only present alternatively, 36 genotypes can be identified that form color clusters to which all animals can be assigned. No mutations were found in the TYR and SLC45A2 genes. Our investigations demonstrate that the four dominant coat colors in fallow deer can be explained by ASIP and MC1R mutations only.

Adult Offspring of Deer Mouse Breeding Pairs Selected for Normal and Compulsive-Like Large Nesting Expression Invariably Show the Same Behavior Without Prior In-Breeding.

Obsessive-compulsive disorder is a neuropsychiatric condition with notable genetic involvement. Against this background, laboratory-housed deer mice of both sexes varyingly present with excessive and persistent large nesting behavior (LNB), which has been validated for its resemblance of clinical compulsivity. Although LNB differs from normal nesting behavior (NNB) on both a biological and cognitive level, it is unknown to what extent the expression of LNB and NNB is related to familial background. Here, we randomly selected 14 NNB- and 14 LNB-expressing mice (equally distributed between sexes) to constitute 7 breeding pairs of each phenotype. Pairs were allowed to breed two successive generations of offspring, which were raised until adulthood (12 weeks) and assessed for nesting expression. Remarkably, our findings show that offspring from LNB-expressing pairs build significantly larger nests compared to offspring from NNB-expressing pairs and the nesting expression of the offspring of each breeding pair, irrespective of parental phenotype or litter, is family specific. Collectively, the results of this investigation indicate that LNB can be explored for its potential to shed light on heritable neurocognitive mechanisms that may underlie the expression of specific persistent behavioral phenotypes.

Machine Learning Meets Meta-Heuristics: Bald Eagle Search Optimization and Red Deer Optimization for Feature Selection in Type II Diabetes Diagnosis.

This article investigates the effectiveness of feature extraction and selection techniques in enhancing the performance of classifier accuracy in Type II Diabetes Mellitus (DM) detection using microarray gene data. To address the inherent high dimensionality of the data, three feature extraction (FE) methods are used, namely Short-Time Fourier Transform (STFT), Ridge Regression (RR), and Pearson's Correlation Coefficient (PCC). To further refine the data, meta-heuristic algorithms like Bald Eagle Search Optimization (BESO) and Red Deer Optimization (RDO) are utilized for feature selection. The performance of seven classification techniques, Non-Linear Regression-NLR, Linear Regression-LR, Gaussian Mixture Models-GMMs, Expectation Maximization-EM, Logistic Regression-LoR, Softmax Discriminant Classifier-SDC, and Support Vector Machine with Radial Basis Function kernel-SVM-RBF, are evaluated with and without feature selection. The analysis reveals that the combination of PCC with SVM-RBF achieved a promising accuracy of 92.85% even without feature selection. Notably, employing BESO with PCC and SVM-RBF maintained this high accuracy. However, the highest overall accuracy of 97.14% was achieved when RDO was used for feature selection alongside PCC and SVM-RBF. These findings highlight the potential of feature extraction and selection techniques, particularly RDO with PCC, in improving the accuracy of DM detection using microarray gene data.

Ticks and Tick-Borne Pathogens: Occurrence and Host Associations over Four Years of Wildlife Surveillance in the Liguria Region (Northwest Italy).

Tick-borne diseases (TBDs) are a considerable public health problem worldwide. The occurrence of Anaplasma spp., Borrelia burgdorferi s.l., Coxiella burnetii, Rickettsia spp., and tick-borne encephalitis virus (TBEv) was investigated via PCR and sequencing in 683 ticks collected from 105 roe deer, 61 wild boars, 49 fallow deer, and 2 chamois, in the Liguria region, northwest Italy, between 2019 and 2022. The ticks were morphologically identified. Four different tick species were found: Ixodes ricinus (66.8% of the collected ticks), Dermacentor marginatus (15.8%), Rhipicephalus sanguineus s.s. (15.7%), and Haemaphysalis punctata (0.9%). Six ticks (0.9%) were only identified as Rhipicephalus spp. Of the 222 pools analyzed, 27.9% were positive. Most pools (n = 58, 26.1% of pools analyzed) were positive for Rickettsia spp., and several species were found: Rickettsia slovaca was the dominant species (15.3%), followed by R. monacensis (8.1%), while R. helvetica (1.8%), R. massiliae (0.5%), and R. raoultii (0.5%) were found only sporadically. Anaplasma phagocytophilum was identified in three pools and B. burgdorferi s.l. in one pool. All samples were negative for C. burnetii and TBEv. Significant associations were found between I. ricinus and roe deer, D. marginatus and wild boar, and between R. monacensis and I. ricinus. The prevalence of Rickettsia spp. differed significantly between tick and host species. This updated picture of tick species and TBPs in wild ungulates in Liguria, where the population of these animals is increasing, shows a widespread presence of potentially zoonotic Rickettsia spp. Continuous monitoring and public information on preventive measures are needed.

Effects of Probiotic Supplementation on Body Weight, Growth Performance, Immune Function, Intestinal Microbiota and Metabolites in Fallow Deer.

Intestinal diseases are one of the diseases that affect the growth and immunity of deer. Currently, more lactic acid bacteria (LAB) are available as feed additives to improve the intestinal ecological balance of ruminants in production practices. In this study, Enterococcus faecalis was supplemented in the feed of fallow deer for 170 d, and body weights, blood indices and immune levels of fallow deer were counted at 35, 65 and 170 d. The effects of Enterococcus faecalis on the intestinal microbiota and the metabolism of fallow deer were analysed using 16S rDNA and UPLC-MS/MS methods. The results showed that the addition of Enterococcus faecalis to the diet improved body weight and immune function and increased the aggregation of gut microbiota in fallow deer. The addition of Enterococcus faecalis altered the community structure of intestinal microorganisms in fallow deer and increased the number of beneficial bacteria. In addition, combined with metabolomics analysis, it was found that supplementation with Enterococcus faecalis significantly altered the metabolites of fallow deer, mainly regulating lipid metabolism, carbohydrate metabolism and phospholipid metabolism. In conclusion, this study presents, for the first time, evidence that the LAB strain Enterococcus faecalis can be used as a potential probiotic for deer and points to a new direction for the treatment of intestinal disorders in the deer family.

Causes of mortality in farmed white-tailed deer in the midwestern United States, 2004-2023.

Farmed cervids are of growing economic importance in the midwestern United States. Although diseases of wild and captive cervids have been examined in more northerly climates, little information exists on the health challenges of deer in the Midwest. We characterized and summarized the causes of mortality in farmed white-tailed deer (Odocoileus virginianus) submitted to the University of Missouri Veterinary Medical Diagnostic Laboratory (Columbia, MO, USA) over a 19-y period (2004-2023). Of 388 cases examined, 253 (65%) were carcasses submitted for autopsy, and 135 (35%) cases were tissue samples harvested by field veterinarians. Infectious disease was the most common cause of mortality (n = 335; 86.3%). Of infectious causes, primary pneumonia was most common (n = 140; 41.7%), followed by septicemia (n = 68; 20.1%), and primary enteritis (n = 64; 19.1%). Viruses were detected in 18% of pneumonia cases. The most common non-infectious diagnoses were emaciation and trauma (both 4 each; 1%). Thirteen animals (3.4%) died of unknown causes. Forty-nine percent of cases were juvenile deer <1-y-old. Most cases were received in the summer (212; 54.6%). Infectious diseases, particularly bacteria and viruses, pose a significant health challenge to farmed deer in the midwestern United States.

Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness.

This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patterns of autozygosity across individuals especially in 2 out of the 8 farms, exhibiting elevated ROH levels and mean genome coverage under ROH segments. The prevalence of shorter ROH segments (0.5-4 Mb) suggests historical relatedness and potential selective pressures within these populations. Intriguingly, despite observed variations in ROH profiles, the overall genomic inbreeding coefficient (FROH) remained relatively low across all farms, indicating a discernible degree of genetic exchange and effective mitigation of inbreeding within the studied Sika deer populations. Consensus ROH (cROH) were found to harbor genes for important functions viz., EGFLAM gene which is involved in the vision function of the eye, SKP2 gene which regulates cell cycle, CAPSL involved in adipogenesis, SPEF2 which is essential for sperm flagellar assembly, DCLK3 involved in the heat stress. This first ever study on ROH in Sika deer, to shed light on the adaptive role of genes in these homozygous regions. The insights garnered from this study have broader implications in the management of genetic diversity in this vulnerable species.