A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus.

Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recreational, commercial, and food source value for many households. We present a genome generated using DNA from a single Illinois white-tailed sequenced on the PacBio Sequel II platform and assembled using Wtdbg2. Omni-C chromatin conformation capture sequencing was used to scaffold the genome contigs. The final assembly was 2.42 Gb, consisting of 508 scaffolds with a contig N50 of 21.7 Mb, a scaffold N50 of 52.4 Mb, and a BUSCO complete score of 93.1%. Thirty-six chromosome pseudomolecules comprised 93% of the entire sequenced genome length. A total of 20 651 predicted genes using the BRAKER pipeline were validated using InterProScan. Chromosome length assembly sequences were aligned to the genomes of related species to reveal corresponding chromosomes.

River otters as biomonitors for organochlorine pesticides, PCBs, and PBDEs in Illinois.

The North American river otter (Lontra canadensis) is a biomonitor for organohalogenated compounds (OHCs) associated with a wide range of deleterious health effects in wildlife and humans. We determined concentrations of twenty OHCs in livers of 23 river otters salvaged by the Illinois Department of Natural Resources from 2009 to 2011, determined sex-dependent distribution of OHCs, and compared our results to the reported concentrations of four OHCs in Illinois river otters from 1984 to 1989. Since these contaminants have been banned for over 30 years, we predicted smaller mean concentrations than those previously reported in Illinois otters. We detected eleven of twenty OHCs; PCBs (polychlorinated biphenyls), dieldrin, and 4,4'-DDE (dichlorodiphenyldichloroethylene) were present in the greatest mean concentrations. We report the largest mean concentration of dieldrin to date in the liver of North American river otters (mean: 174, range: 14.4-534 parts per billion wet wt [ppb]). Mean PCB concentrations were significantly higher in males (mean: 851; range: 30-3450 ppb) than females (mean: 282; range: 40-850 ppb; p=0.04). Mean concentrations of dieldrin were greater than those detected in otters from 1984 to 1989 (mean: 90; range: 30-130 ppb; p<0.05). Our results suggest OHC exposure remains a concern. Future research in Illinois should focus on evaluating OHCs exposures, particularly dieldrin, at the watershed level.

The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus).

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks.

Impact of landcover composition and density of localized deer culling sites on chronic wasting disease prevalence.

Chronic Wasting Disease (CWD), the prion disease of the Cervidae family, has been managed in Illinois deer since it was first detected in the Fall of 2002. Management uses a state-sponsored localized focus culling (LFC) program, implemented as close as possible to previously identified CWD-infected locations (TRSs (township/range/section)). We used hunter-harvest and LFC deer from 4621 and 435 unique TRSs, respectively, over 16 years of surveillance and management (2003-2017). We divided the study area into groups of TRSs with similar landcover types (SPLT) to assess CWD hunter-harvest prevalence at LFC and non-LFC sites by landcover composition. We also evaluate the importance of the month when LFC was implemented and determine whether the density of LFC sites or the total number of deer removed by LFC predicts hunter-harvest CWD prevalence. The percentage of CWD positive samples from hunters was lower than for LFC samples (for the study area and SPLTs). The probability of CWD increased by 5.24% for all the SPLT groups combined in the study area, by 4.6% from areas without an LFC nearby, and by 1.21% for areas with a prior LFC nearby. For all the TRS in the study area, low CWD odds (<1) in hunter-harvest deer were found in three SPLTs, in two SPLTs within TRSs with non-LFC, and five in five SPLTs within TRSs with LFC. The results suggest the importance of accounting for landcover composition to implement and sustain management in habitats with a higher risk of CWD. Our findings support that hunter-harvest alone cannot control CWD and the critical need for continued LFC intervention. For the whole study area-regardless of landcover composition-LFC in January was more important in decreasing hunter-harvest CWD prevalence than when LFC was conducted in March. However, the LFC conducted in January, February, and March were equally important when evaluating the month per habitat. Furthermore, the density of LFC sites in proximity to known infected areas is a better predictor of CWD than the number of deer removed by LFC, suggesting that increasing the density of LFC sites has a greater impact on CWD. The proximity of LFC to infected areas helps control CWD. Ultimately, landowners' and hunters' collaborations with the CWD surveillance and management programs are critical to protecting the Illinois wild deer herd; this study demonstrates their ongoing and valuable contributions to protecting this natural and public resource.

Evaluating the ability of a locally focused culling program in removing chronic wasting disease infected free-ranging white-tailed deer in Illinois, USA, 2003-2020.

In northern Illinois, chronic wasting disease (CWD) was first identified in free-ranging white-tailed deer (Odocoileus virginianus; hereafter referred to as "deer") in 2002. To reduce CWD transmission rates in Illinois, wildlife biologists have conducted locally focussed culling of deer since 2003 in areas where CWD has been detected. We used retrospective spatial, temporal and space-time scan statistical models to identify areas and periods where culling removed higher than expected numbers of CWD-positive deer. We included 490 Public Land Survey "sections" (∼2.59 km2 ) from 15 northern Illinois counties in which at least one deer tested positive for CWD between 2003 and 2020. A negative binomial regression model compared the proportion of CWD positive cases removed from sections with at least one CWD case detected in the previous years, "local area 1 (L1)," to the proportion of CWD cases in adjacent sections-L2, L3, and L4-designated by their increasing distance from L1. Of the 14,661 deer removed and tested via culling, 325 (2.22 %) were CWD-positive. A single temporal CWD cluster occurred in 2020. Three spatial clusters were identified, with a primary cluster located at the border of Boone and Winnebago counties. Four space-time clusters were identified with a primary cluster in the northern portion of the study area from 2003 to 2005 that overlapped with the spatial cluster. The proportion of CWD cases removed from L1 (3.92, 95% CI, 2.56-6.01) and L2 (2.32, 95% CI, 1.50-3.59) were significantly higher compared to L3. Focussing culling efforts on accessible properties closest to L1 areas results in more CWD-infected deer being removed, which highlights the value of collaborations among landowners, hunters, and wildlife management agencies to control CWD. Continuous evaluation and updating of the culling and surveillance programs are essential to mitigate the health burden of CWD on deer populations in Illinois.

Bluetongue and Epizootic Hemorrhagic Disease in the United States of America at the Wildlife-Livestock Interface.

Bluetongue (BT) and epizootic hemorrhagic disease (EHD) cases have increased worldwide, causing significant economic loss to ruminant livestock production and detrimental effects to susceptible wildlife populations. In recent decades, hemorrhagic disease cases have been reported over expanding geographic areas in the United States. Effective BT and EHD prevention and control strategies for livestock and monitoring of these diseases in wildlife populations depend on an accurate understanding of the distribution of BT and EHD viruses in domestic and wild ruminants and their vectors, the Culicoides biting midges that transmit them. However, national maps showing the distribution of BT and EHD viruses and the presence of Culicoides vectors are incomplete or not available at all. Thus, efforts to accurately describe the potential risk of these viruses on ruminant populations are obstructed by the lack of systematic and routine surveillance of their hosts and vectors. In this review, we: (1) outline animal health impacts of BT and EHD in the USA; (2) describe current knowledge of the distribution and abundance of BT and EHD and their vectors in the USA; and (3) highlight the importance of disease (BT and EHD) and vector surveillance for ruminant populations.

Spatial analysis of chronic wasting disease in free-ranging white-tailed deer (Odocoileus virginianus) in Illinois, 2008-2019.

Understanding the geographic distribution and clustering of chronic wasting disease (CWD) among free-ranging white-tailed deer (Odocoileus virginianus) populations can inform disease management practices. We used a retrospective analysis of surveillance data to evaluate CWD's spatial and temporal dynamics within 16 CWD-infected northern Illinois counties. Of 42,541 deer samples collected and tested for CWD from recreational hunter harvest between 2008 and 2019, we recorded 359 (0.84%) CWD-positive samples. We observed variability in CWD cases over time and space. By county, the median CWD-positive proportion was 0.84%, varying from a minimum of 0.14% in McHenry County to a maximum of 6.28% in Boone County. Across years, there were differences among CWD-positive proportions with a median of 0.90%, ranging from a minimum of 0.27% in 2012 to a maximum of 1.60% in 2019. We used a retrospective discrete Poisson scan statistic model to evaluate the space-time clustering of CWD-positive deer. We identified a statistically significant (p < .001) primary cluster C1 (area = 23.59 km2 ; RR = 10.48), occurring from 2010 to 2015 in the north-central part of the study area, and a secondary cluster C2, occurring from 2014 to 2019 (area = 9.27 km2 ; RR = 3.88) in the north-west of the study area. Detected CWD-positive space-time clusters suggest that the risk of CWD is not random. Space-time clusters of CWD can be used to evaluate the effectiveness of the Illinois CWD management programme. The area surrounding the older C1 cluster has undergone longer and more intense CWD management compared with C2. Currently, the older C1 cluster is no longer as high risk compared with the newer cluster C2, suggesting that management efforts in C2 should be increased. However, all CWD clusters should be targeted with surveillance, prevention and management programmes, including reducing deer densities to limit further spread of CWD.

Chronic Wasting Disease In Cervids: Prevalence, Impact And Management Strategies.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) that affects members of the cervidae family. The infectious agent is a misfolded isoform (PrPSC) of the host prion protein (PrPC). The replication of PrPSC initiates a cascade of developmental changes that spread from cell to cell, individual to individual, and that for some TSEs, has crossed the species barrier. CWD can be transmitted horizontally and vertically, and it is the only TSE that affects free-ranging wildlife. While other TSEs are under control and even declining, infection rates of CWD continue to grow and the disease distribution continues to expand in North America and around the world. Since the first reported case in 1967, CWD has spread infecting captive and free-ranging cervids in 26 states in the US, 3 Canadian provinces, 3 European countries and has been found in captive cervids in South Korea. CWD causes considerable ecologic, economic and sociologic impact, as this is a 100% fatal highly contagious infectious disease, with no treatment or cure available. Because some TSEs have crossed the species barrier, the zoonotic potential of CWD is a concern for human health and continues to be investigated. Here we review the characteristics of the CWD prion protein, mechanisms of transmission and the role of genetics. We discuss the characteristics that contribute to prevalence and distribution. We also discuss the impact of CWD and review the management strategies that have been used to prevent and control the spread of CWD.

Clay content and pH: soil characteristic associations with the persistent presence of chronic wasting disease in northern Illinois.

Environmental reservoirs are important to infectious disease transmission and persistence, but empirical analyses are relatively few. The natural environment is a reservoir for prions that cause chronic wasting disease (CWD) and influences the risk of transmission to susceptible cervids. Soil is one environmental component demonstrated to affect prion infectivity and persistence. Here we provide the first landscape predictive model for CWD based solely on soil characteristics. We built a boosted regression tree model to predict the probability of the persistent presence of CWD in a region of northern Illinois using CWD surveillance in deer and soils data. We evaluated the outcome for possible pathways by which soil characteristics may increase the probability of CWD transmission via environmental contamination. Soil clay content and pH were the most important predictive soil characteristics of the persistent presence of CWD. The results suggest that exposure to prions in the environment is greater where percent clay is less than 18% and soil pH is greater than 6.6. These characteristics could alter availability of prions immobilized in soil and contribute to the environmental risk factors involved in the epidemiological complexity of CWD infection in natural populations of white-tailed deer.

Cytokine-hormone interactions: tumor necrosis factor alpha impairs biologic activity and downstream activation signals of the insulin-like growth factor I receptor in myoblasts.

TNFalpha is elevated following damage to skeletal muscle. Here we provide evidence that TNFalpha acts on muscle cells to induce a state of IGF-I receptor resistance. We establish that TNFalpha inhibits IGF-I-stimulated protein synthesis in primary porcine myoblasts. Similar results were observed in C(2)C(12) murine myoblasts, where as little as 0.01 ng/ml TNFalpha significantly inhibits protein synthesis induced by IGF-I. TNFalpha also impairs the ability of IGF-I to induce expression of a key myogenic transcription factor, myogenin. The inhibition by TNFalpha of IGF-I-induced protein synthesis and expression of myogenin is not due to direct killing of myoblasts by TNFalpha. Although IGF-I induces an approximately 19-fold induction in tyrosine phosphorylation of the beta-chains of its receptor, TNFalpha does not inhibit this autophosphorylation. Instead, TNFalpha significantly reduces by approximately 50% IGF-I-stimulated tyrosine phosphorylation of two of the major downstream receptor docking molecules, insulin receptor substrate (IRS)-1 and IRS-2. These results establish that low picogram concentrations of TNFalpha acts on both porcine and murine myoblasts to impair tyrosine phosphorylation of both IRS-1 and IRS-2, but not the receptor itself. These data are consistent with the notion that very low physiological concentrations of TNFalpha interfere with both protein synthesis and muscle cell development by inducing a state of IGF-I receptor resistance.

Influence of landscape factors and management decisions on spatial and temporal patterns of the transmission of chronic wasting disease transmission in white-tailed deer.

Chronic wasting disease (CWD) has been reported in white-tailed deer at the border of the US states of Illinois and Wisconsin since 2002. Transmission of infectious prions between animals and from the environment has resulted in spatial and temporal structure observable in the spatio-temporal patterns of reported cases. Case locations of 382 positive cases from 28,954 deer tested between 2002 and 2009 provided insight into the potential risk factors and landscape features associated with transmission using a combination of clustering, generalised linear modelling and descriptive evaluations of a risk map of predicted cases of CWD. A species distribution map of white-tailed deer developed using MaxEnt provided an estimate of deer locations. We found that deer probability increased in areas with larger forests and less urban and agricultural lands. Spatial clustering analysis revealed a core area of persistent CWD transmission in the northern part of the region. The regression model indicated that larger and more compact forests were associated with higher risk for CWD. High risk areas also had soils with less clay and more sand than other parts of the region. The transmission potential was higher where landscape features indicated the potential for higher deer concentrations. The inclusion of spatial lag variables improved the model. Of the 102 cases reported in the study area in the two years following the study period, 89 (87%) of those were in the 32% of the study area with the highest 50% of predicted risk of cases.

Properties of Frankfurters Processed with Different Levels of Sodium Bicarbonate 1.

The effect of substituting sodium bicarbonate for sodium chloride in frankfurters was evaluated using chemical and sensory criteria. Frankfurters were formulated and prepared using one of three treatments: (a) 2% sodium chloride control, (b) 1% sodium bicarbonate and 1% sodium chloride or (c) 2% sodium bicarbonate. Substitution of sodium bicarbonate raised the pH from 6.0 to 7.5 and 8.2 (treatments a, b and c, respectively). Percent free water decreased with sodium bicarbonate substitution from 41.3 to 31.7 and 21.6. Sodium bicarbonate substitution did not significantly affect Warner-Bratzler shear force values or sensory determination of moistness or tenderness. However, sensory evaluations of texture and mouthfeel and off-flavor intensity were less desirable with increased sodium bicarbonate content. Visual evaluations indicated that substitution of sodium bicarbonate for sodium chloride resulted in frankfurters having a darker brown color. Scanning electron microscopic evaluation of frankfurters did not show evidence of major structural differences. Frankfurters in vacuum-packaged bags were stored for up to 30 d in a 4°C lighted retail case. Total plate counts were not significantly different between treatments on days 0, 15 or 30 of storage. These results indicate a potential use of sodium bicarbonate to alter pH and percent free water of emulsified meat products; however, some sensory properties are diminished when sodium chloride is replaced with sodium bicarbonate.

IL-1beta impairs insulin-like growth factor i-induced differentiation and downstream activation signals of the insulin-like growth factor i receptor in myoblasts.

Proinflammatory cytokines are elevated in disorders characterized by muscle wasting and weakness, such as inflammatory myopathies and AIDS wasting. We recently demonstrated that TNF-alpha impairs the ability of insulin-like growth factor (IGF)-I to promote protein synthesis in muscle precursor cells. In this study we extend these findings by showing that low concentrations of IL-1beta impair IGF-I-dependent differentiation of myoblasts, as assessed by expression of the muscle specific protein, myosin heavy chain. In the absence of exogenous IGF-I, IL-1beta (1 ng/ml) did not impair muscle cell development. However, in the presence of IGF-I, 100-fold lower concentrations of IL-1beta (0.01 ng/ml) significantly suppressed myoblast differentiation, protein synthesis, and myogenin expression. Increasing IL-1beta to 1 ng/ml completely blocked the anabolic actions of IGF-I in murine C(2)C(12) myoblasts. Similarly, IL-1beta inhibited IGF-I-stimulated protein synthesis in primary porcine myoblasts. IL-1beta impaired the actions of IGF-I at a point distal to the IGF receptor, and this was not due to IL-1beta-induced cell death. Instead, IL-1beta inhibited the ability of IGF-I to phosphorylate tyrosine residues on both of its downstream docking proteins, insulin receptor substrate 1 and insulin receptor substrate 2. These data establish that physiological concentrations of IL-1beta block the ability of IGF-I to promote protein synthesis, leading to reduced expression of the myogenic transcription factor, myogenin, and the subsequent development of more mature differentiated cells that express myosin heavy chain. Collectively, the results are consistent with the notion that very low concentrations of IL-1beta significantly impair myogenesis, but they are unable to do so in the absence of the growth factor IGF-I.