POPULATION ECOLOGY OF THE NORTHERN SLIMY SALAMANDER (PLETHODON GLUTINOSUS) IN EAST-CENTRAL ILLINOIS

The importance of plethodontid salamanders in forested habitats has been recognized for decades and more recently plethodontids have been touted as a model taxon for monitoring ecosystem integrity and recovery. However, basic demographic data that are crucial to conservation and management plans are currently lacking for many species and regions. The objectives of our study were to characterize the population density, biomass, and capture success of a peripheral population of Plethodon glutinosus to provide a comparison for eastern populations and set a baseline for future monitoring of Midwestern populations. We estimated the population density of P. glutinosus at our site to be 0.41 salamanders/m2, with an estimated biomass of 0.70 g/m2. We did not find any evidence for temperature or precipitation affecting capture success. Our results showed that our density estimate falls within the range of other population ecology studies of Plethodon and sets a baseline for other peripheral Midwestern populations

A simple technique for eliminating tracheal buckling on lateral neck roentgenograms

Brief, gentle extrinsic pressure on the trachea at the level of the cricothyroid membrane during lateral roentgenography of the neck is suggested as a safe, simple, and reliable means of evaluating the retrotracheal pre-cervical soft tissues in infants and children.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46690/1/247_2004_Article_BF00972851.pd

Quality Assurance Project Plan (QAPP) for Wetland Program Development Grant No. CD-00E00963-0

In order to evaluate overall ecological health and function of seasonal and semi-permanent wetlands in Illinois, we will sample 240 wetlands distributed across 60 state managed lands over three field seasons (2012-2014; see attached map for preliminary site locations). During each field season, we will conduct sampling on 20 state managed properties and 4 wetlands will be sampled at each site (n = 80 wetlands per season). At each wetland surveys will be conducted during four time periods over a five month span (February-June) to increase the probability of species detection. Additionally, due to fluctuations in population sizes, variability in breeding phenologies, and suspected detection rates between taxonomic groups (i.e. rare species have lower detection rates than common species), wetlands will be sampled for three nights per period (n =12 total samples in a season). By repeatedly sampling wetlands during the field season, we can estimate occupancy and detection rates using program PRESENCE 3.1. Each state managed property (and associated wetlands) will be sampled during only one field season to increase the number of overall sites sampled during the study and all wetlands will be located on Illinois Department of Natural Resources (IDNR) managed properties to ensure accessibility. Wetland health and function will be assessed by examining three critical components of wetlands ecosystems: 1) Amphibian diversity and abundance; 2) Reptile diversity and abundance; and 3) Macroinvertebrate diversity and abundance. Each of these primary components will Date: 04 January 2012 Revision 0 9 be incorporated into an index of biological integrity (IBI) to determine how well the wetland is functioning within the ecosystem.U.S. Environmental Protection Agency Wetland Program Development Grant No. CD-00E00963-0unpublishednot peer reviewedOpe

Knee maturation as a differentiating sign between congenital rubella and cytomegalovirus infections

Knee epiphyseal maturation is retarded in most neonates with congenital rubella infection, whereas neonates with congenital cytomegalovirus infection have relatively normal maturation. Assessment of knee maturation is useful in differentiating rubella from cytomegalovirus infection in the neonate.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46720/1/247_2004_Article_BF00973813.pd

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Elevated serum urate levels cause gout and correlate with cardiometabolic diseases via poorly understood mechanisms. We performed a trans-ancestry genome-wide association study of serum urate in 457,690 individuals, identifying 183 loci (147 previously unknown) that improve the prediction of gout in an independent cohort of 334,880 individuals. Serum urate showed significant genetic correlations with many cardiometabolic traits, with genetic causality analyses supporting a substantial role for pleiotropy. Enrichment analysis, fine-mapping of urate-associated loci and colocalization with gene expression in 47 tissues implicated the kidney and liver as the main target organs and prioritized potentially causal genes and variants, including the transcriptional master regulators in the liver and kidney, HNF1A and HNF4A. Experimental validation showed that HNF4A transactivated the promoter of ABCG2, encoding a major urate transporter, in kidney cells, and that HNF4A p.Thr139Ile is a functional variant. Transcriptional coregulation within and across organs may be a general mechanism underlying the observed pleiotropy between urate and cardiometabolic traits.The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Variant annotation was supported by software resources provided via the Caché Campus program of the InterSystems GmbH to Alexander Teumer

Human Dectin-1 Deficiency Impairs Macrophage-Mediated Defense Against Phaeohyphomycosis

Subcutaneous phaeohyphomycosis typically affects immunocompetent individuals following traumatic inoculation. Severe or disseminated infection can occur in CARD9 deficiency or after transplantation, but the mechanisms protecting against phaeohyphomycosis remain unclear. We evaluated a patient with progressive, refractory Corynespora cassiicola phaeohyphomycosis and found that he carried biallelic deleterious mutations in CLEC7A encoding the CARD9-coupled, β-glucan-binding receptor, Dectin-1. The patient\u27s PBMCs failed to produce TNF-α and IL-1β in response to β-glucan and/or C. cassiicola. To confirm the cellular and molecular requirements for immunity against C. cassiicola, we developed a mouse model of this infection. Mouse macrophages required Dectin-1 and CARD9 for IL-1β and TNF-α production, which enhanced fungal killing in an interdependent manner. Deficiency of either Dectin-1 or CARD9 was associated with more severe fungal disease, recapitulating the human observation. Because these data implicated impaired Dectin-1 responses in susceptibility to phaeohyphomycosis, we evaluated 17 additional unrelated patients with severe forms of the infection. We found that 12 out of 17 carried deleterious CLEC7A mutations associated with an altered Dectin-1 extracellular C-terminal domain and impaired Dectin-1-dependent cytokine production. Thus, we show that Dectin-1 and CARD9 promote protective TNF-α- and IL-1β-mediated macrophage defense against C. cassiicola. More broadly, we demonstrate that human Dectin-1 deficiency may contribute to susceptibility to severe phaeohyphomycosis by certain dematiaceous fungi

Kankakee Sands Ornate Box Turtle (Terrapene ornata) Population and Ecosystem Assessment

ID: 8982; Wildlife Preservation Fund Grant IDNR RC03L21W and Nature Conservancy Grant: Nature Conserv 1131626100 Final Report issued December 4, 2003INHS Technical Report prepared for Illinois Department of Natural Resources and Nature Conservanc

Survey and assessment of threatened and endangered freshwater mussels, fishes, amphibians, and reptiles of the I-90 tollway improvement corridor from IL Rte 47 to I-39

INHS Technical Report Prepared for Illinois Toll Highway Authorit

Assessment of Wetland Quality in Illinois Conservation Areas

Seasonal and semi-permanent wetlands are shallow, depressional wetlands that occur throughout the Midwestern and Eastern United States. Distribution and abundance of seasonal wetlands are regarded as an indicator of overall ecosystem health and are especially important to numerous species of plants and wildlife. In addition to their biological importance, these wetlands play critical roles in hydrology (surface water storage and groundwater exchange), biogeochemical cycling, and energy exchange (via amphibian production and dispersal) to adjacent terrestrial habitat. Despite their ecological significance within the landscape, seasonal and semi-permanent wetlands typically receive minimal regulatory protection at both the federal and state levels because they are often small and hydrologically isolated. Animals such as amphibians, semi-aquatic reptiles, and macroinvertebrates depend on wetlands for all or part of their life cycle, which means that their survival is directly linked to the presence and ecological health of wetlands. In Illinois, 32 of the 41 amphibians and 47 of the 61 reptiles are wetland dependent species, in addition to the numerous macroinvertebrate taxa found across the state. While the US loses approximately 60,000 acres of wetlands each year, wetland conversion and drainage in Illinois has been especially extensive where an estimated 90% of original wetland area has been lost; therefore assessment and protection of wetlands is a high priority within the state. Further, Action Item 3 of the Wetlands Campaign in the Illinois Wildlife Action Plan is to fill information gaps and develop conservation actions to address remaining wetlands in Illinois. Specifically, the action item calls for: 1) updated inventory of wetland habitat in Illinois; 2) research on the ecological aspects of high-quality wetland sites; and 3) assessment of the status and distribution of wetland-dependent amphibians and reptiles. The primary objectives of this project were to provide the following: 1) development of an integrated index of biological integrity (IBI) to assess wetland condition; 2) evaluation of sampling schemes; 3) establishment of reference (baseline) wetland conditions for each part of the state of Illinois; 4) identification of high quality wetland sites in Illinois; 5) identification of deficient wetland sites in Illinois; 6) identify important habitat features of high quality wetlands in Illinois; 7) report on the overall xiii health of wetlands on public lands in Illinois and provide recommendations to IDNR for areas in need of protection and restoration; and 8) contribution of information to the management plans of imperiled wetland-dependent species. In order to evaluate overall ecological health and function of seasonal and semipermanent wetlands in Illinois, we sampled 242 wetlands distributed across 45 managed lands (hereafter conservation areas) over three years (2012-2014). At each wetland, surveys were conducted during four time periods over a five month span (February-June) to increase the probability of species detection. Additionally, due to fluctuations in population sizes, variability in breeding phenologies, and suspected variability in detection rates between taxonomic groups (i.e. rare species have lower detection rates than common species), wetlands were sampled for three days per period (n =12 total samples per wetland). Each conservation area (and associated wetlands) was sampled during only one year to increase the number of overall sites sampled during the study. Wetland health and function were assessed by examining three critical components of wetlands ecosystems: 1) amphibian diversity and abundance; 2) reptile diversity and abundance; and 3) macroinvertebrate diversity and abundance. Each of these primary components was incorporated into an index of biological integrity (IBI) to determine how well the wetland was functioning within the ecosystem. As a result of this study, we have generated the following major conclusions: 1) reptiles are not good biological indicators for assessment of seasonal and semi-permanent wetland health due to low capture numbers; 2) wetland macroinvertebrate life history and distribution information is inadequate in Illinois for using macroinvertebrates as a biological indicator group; however this study is a crucial first step in providing some of that needed information; 3) amphibians are good biological indicators for assessment of seasonal and semi-permanent wetlands; however a proper sampling protocol (appropriate sample times and numbers) is critical for successful wetland evaluations; 4) high quality seasonal and semi-permanent wetlands are concentrated along the eastern side of the state (Wabash Border division) and into southern Illinois (Southern Till Plain and Coastal Plain divisions); and 5) a diversity of wetland types (physical parameters and proximity to forest) are needed for increased wildlife persistence. Lastly, we have identified 3 major areas of need for future research: 1) additional macroinvertebrate sampling in seasonal xiv and semi-permanent wetlands to fill the previously identified information gaps for this taxon; 2) assessment of anthropogenic effects on wetlands in highly urbanized environments (e.g., the Chicago region); and 3) establishment of a bank of long-term wetland monitoring sites throughout the state of Illinois to assess the impacts of climate change on wetland ecological health and function. While our distribution of sampling sites covered a large part of the state, we did not sample many properties in the northeastern part of the state. We focused on IDNR state properties for this study and the majority of public lands in the Chicago region are held by county forest preserve districts. With the dramatic effects that urbanization can have on wetlands, we believe it is imperative that wetlands in this region be sampled to set a baseline for ecological function and identify areas in need of wetland restoration and creation. Further, to fully understand the effects that climate change has had or may have on the ecological function of seasonal and semi-permanent wetlands in Illinois, a network of wetland monitoring sites is needed to collect the longitudinal datasets for climate change analyses. Ultimately, to continue to further the goals of the EPA and IDNR wetlands programs in Illinois, each of these three research items must be addressed.U.S. Environmental Protection Agency, Region 5, CD00E00963unpublishednot peer reviewedOpe

Using species distribution and occupancy modeling to guide survey efforts and assess species status

Habitat loss and fragmentation continue to be major issues affecting the persistence and conservation of species, but identification of critical habitat remains a challenge. Species distribution modeling and occupancy modeling are both approaches that have been used to predict species distributions and can identify critical habitat characteristics associated with species occurrence. Additionally, occupancy sampling can provide measures of detectability, increasing the confidence that a species is truly absent when not detected. While increasingly popular, these methods are infrequently used in synergy, and rarely at fine spatial scales. We provide a case study of using distribution and occupancy modeling in unison to direct survey efforts, provide estimates of species presence/absence, and to identify local and landscape features important for species occurrence. The focal species for our study was Ambystoma jeffersonianum, a threatened salamander in the state of Illinois, U.S.A. We found that fine-scale distribution models accurately discriminated occupied from unoccupied breeding ponds (78–91% accuracy), and surveys could be effectively guided using a well-fit model. We achieved a high detection rate (0.774) through occupancy sampling, and determined that A. jeffersonianum never used ponds inhabited by fish, and the probability of a pond being used for breeding increased as canopy cover increased. When faced with limited resources, combining fine-scale distribution modeling with a robust occupancy sampling design can expedite survey efforts, confidently designate species occupancy status, prioritise habitat for future surveys and/or restoration, and identify critical habitat features. This approach is broadly applicable to other taxa that have specific habitat requirements