In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements.

Purpose: DNA methylation is a well-characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of transcription is controlled by proteins that regulate recruitment and activity of RNA polymerase by binding to specific cis-regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell-specific gene expression. Although much is known about the functions and DNA binding specificity of CRX, little is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements. Methods: We used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO, PDE6B, PAX6, and LINE1 retrotransposon repeats. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences. Results: In this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to the DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate changes in the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX-dependent transcription. Conclusions: Collectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.

Dnmt1, Dnmt3a and Dnmt3b cooperate in photoreceptor and outer plexiform layer development in the mammalian retina.

Characterizing the role of epigenetic regulation in the mammalian retina is critical for understanding fundamental mechanisms of retinal development and disease. DNA methylation, an epigenetic modifier of genomic DNA, plays an important role in modulating networks of tissue and cell-specific gene expression. However, the impact of DNA methylation on retinal development and homeostasis of retinal neurons remains unclear. Here, we have created a tissue-specific DNA methyltransferase (Dnmt) triple mutant mouse in an effort to characterize the impact of DNA methylation on retinal development and homeostasis. An Rx-Cre transgene was used to drive targeted mutation of all three murine Dnmt genes in the mouse retina encoding major DNA methylation enzymes DNMT1, DNMT3A and DNMT3B. The triple mutant mice represent a hypomorph model since Dnmt1 catalytic activity was still present and excision of Dnmt3a and Dnmt3b had only about 90% efficiency. Mutation of all three Dnmts resulted in global genomic hypomethylation and dramatic reorganization of the photoreceptor and synaptic layers within retina. Transcriptome and proteomic analyses demonstrated enrichment of dysregulated phototransduction and synaptic genes. The 5 mC signal in triple mutant retina was confined to the central heterochromatin but reduced in the peripheral heterochromatin region of photoreceptor nuclei. In addition, we found a reduction of the 5 mC signal in ganglion cell nuclei. Collectively, this data suggests cooperation of all three Dnmts in the formation and homeostasis of photoreceptors and other retinal neurons within the mammalian retina, and highlight the relevance of epigenetic regulation to sensory retinal disorders and vision loss.

Aflatoxin contamination in corn sold for wildlife feed in texas.

Supplemental feeding with corn to attract and manage deer is a common practice throughout Texas. Other species, including northern bobwhites (Colinus virginianus), are commonly seen feeding around supplemental deer feeders. In many cases, supplemental feeding continues year-round so feed supply stores always have supplemental corn in stock. Fluctuating weather and improper storage of corn can lead to and/or amplify aflatoxin contamination. Due to the recent decline of bobwhites throughout the Rolling Plains ecoregion of Texas, there has been interest in finding factors such as toxins that could be linked to their decline. In this study, we purchased and sampled supplemental corn from 19 locations throughout this ecoregion to determine if aflatoxin contamination was present in individual bags prior to being dispersed to wildlife. Of the 57 bags sampled, 33 bags (approximately 58%) contained aflatoxin with a bag range between 0.0-19.91 parts per billion (ppb). Additionally, three metal and three polypropylene supplemental feeders were each filled with 45.4 kg of triple cleaned corn and placed in an open field to study long-term aflatoxin buildup. Feeders were sampled every 3 months from November 2013-November 2014. Average concentration of aflatoxin over the year was 4.08 ± 2.53 ppb (±SE) in metal feeders, and 1.43 ± 0.89 ppb (±SE) in polypropylene feeders. The concentration of aflatoxins is not affected by the type of feeder (metal vs polypropylene), the season corn was sampled, and the location in the feeder (top, middle, bottom) where corn is sampled. It is unlikely that corn used in supplemental feeders is contributing to the bobwhite decline due to the low levels of aflatoxin found in purchased corn and long-term storage of corn used in supplemental feeders.

Caecal worm, Aulonocephalus pennula, infection in the northern bobwhite quail, Colinus virginianus.

Parasitic nematodes that infect quail have been understudied and long been dismissed as a problem in quail management. Within the Rolling Plains ecoregion of Texas, an area that has experienced quail population "boom and bust" cycles and ultimately a general decline, the need to determine why Northern bobwhite (Colinus virginianus) populations are diminishing has increased in priority. Previously, caecal parasites have been documented to cause inactivity, weight loss, reduced growth, inflammation to the caecal mucosa, and even death. The caecal worm Aulonocephalus pennula is an intestinal nematode parasite that is commonly found within the caecum of quail, as well as many other avian species. In the Rolling Plains ecoregion, A. pennula has been documented to have as high as a 98% prevalence in bobwhite quail samples; however, the effect it has on its host is not well understood. The present study documents A. pennula causes no pathological changes within the caeca of the Northern bobwhite. However, there is concern for disruption of digestion and the possible implications of infection for wild bobwhite quail survival are discussed.

Oxyspirura petrowi infection leads to pathological consequences in Northern bobwhite (Colinus virginianus).

Debilitating ocular diseases are often reported in avian species. By and large, helminth parasites have been overlooked in avian diseases and regarded as inconsequential. The decline of Northern bobwhite quail (Colinus virginianus) in the Rolling Plains ecoregion of Texas has prompted an investigation of the factors influencing their disappearance. Infection by the eyeworm (Oxyspirura petrowi) has been documented in many avian species; however, the effect it has on its host is not well understood. Heavy eyeworm infection has been documented in Northern bobwhites throughout this ecoregion, leading to eye pathology in this host species. The present study further documents and supports the pathological changes associated with O. petrowi in bobwhites.

A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus).

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53-0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population.

A survey of neonicotinoid use and potential exposure to northern bobwhite (Colinus virginianus) and scaled quail (Callipepla squamata) in the Rolling Plains of Texas and Oklahoma.

Northern bobwhite (quail) (Colinus virginianus) and scaled quail (Callipepla squamata) populations have declined dramatically in the Rolling Plains ecoregion of Texas and Oklahoma (USA). There is rising concern about potential toxicity of neonicotinoids to birds. To investigate this concern, the authors examined crops of 81 northern bobwhite and 17 scaled quail to determine the presence or absence of seeds treated with 3 neonicotinoids (clothianidin, imidacloprid, and thiamethoxam). No treated seeds were found in the 98 crops examined. Liver samples from all 98 quail were collected and analyzed for neonicotinoid residues. Analysis revealed very low concentrations of neonicotinoids within the quail liver samples. The results suggest there is little to no risk of direct toxicity to quail from neonicotinoids. Environ Toxicol Chem 2016;35:1511-1515. © 2015 SETAC.

EYEWORMS (OXYSPIRURA PETROWI) IN NORTHERN BOBWHITES (COLINUS VIRGINIANUS) FROM THE ROLLING PLAINS ECOREGION OF TEXAS AND OKLAHOMA, 2011-13.

The Northern Bobwhite ( Colinus virginianus ) has been steadily declining throughout much of its historic range for decades. The Rolling Plains ecoregion of Texas and western Oklahoma, historically rich with wild Northern Bobwhites and one of the last remaining quail strongholds, also has a declining population. During August and October in 2011-13, 348 Northern Bobwhites from the Rolling Plains were examined for eyeworms (Oxyspirura petrowi). Of these 348 Northern Bobwhites, 144 (41.4%) were infected with 1,018 total eyeworms. Eyeworm abundance (mean±SE) was 2.9±0.4 (range 0-64), with an intensity (mean±SE) of 7.1±0.6. Eyeworm prevalence was significantly higher in adult Northern Bobwhites (58.7%) than in juveniles (35.4%). Recent research suggests that eyeworms have the potential to cause cellular tissue damage to the eye, but it is unknown how these worms affect host survivability. This study further expands the regional distribution of O. petrowi in Northern Bobwhites in the Rolling Plains ecoregion and assesses the prevalence and abundance of infection across host age, host sex, and year. Further research is warranted on the life history of O. petrowi and assessing the impacts of eyeworms on their definitive host at individual and population levels.

Evidence of Oxyspirura petrowi in migratory songbirds found in the rolling plains of West Texas, USA.

Three Northern Mockingbirds (Mimus polyglottos) and one Curve-billed Thrasher (Toxostoma curvirostre) from the Rolling Plains of Texas, USA were sampled for eyeworms in September 2013. All four birds were infected with the eyeworm Oxyspirura petrowi.

The parasitic eyeworm Oxyspirura petrowi as a possible cause of decline in the threatened lesser prairie-chicken (Tympanuchus pallidicinctus).

Lesser prairie-chickens (Tympanuchus pallidicinctus) have been declining range wide since the early 1900's despite efforts to establish conservation and improve their habitat. In early 2014, the lesser prairie-chicken was listed as a threatened species under the U.S Endangered Species Act and the need to find out why they are declining is more important than ever. Nine hunter shot lesser prairie-chickens were donated and sampled for the presence or absence of the eyeworm Oxyspirura petrowi, a known parasite that can cause damage to the eye of its host, and common environmental contaminants. Eyeworm infection was found in 7 of 9 birds (78% infection rate) with an infection range between 0-16 O. petrowi per bird. Breast, liver, and fat tissue samples from the lesser prairie-chickens were analyzed for the frequency of 20 organochlorine pesticides. Femurs and livers were also tested on these birds for metal contaminants. Pesticides were found in several samples above the detection limits but were still in the low ng/g range. Notable was the ubiquitous presence of endrin aldehyde across all tissues. One femur showed 5.66 µg/g of lead (Pb) but this is still relatively low. No liver samples had elevated mercury (Hg) above detection limits. The presence of these organochlorines is consistent with the historic use of pesticides in this region. With pesticide and metals found in such low levels and parasitic nematode infections at rather high levels, it is recommended that these parasites be further evaluated as a contributing factor to the decline of the lesser prairie-chicken.

Evidence of an Oxyspirura petrowi epizootic in northern bobwhites (Colinus virginianus), Texas, USA.

We captured 36 Northern Bobwhites (Colinus virginianus) in Mitchell County, Texas in June-September 2013, and examined them for the eyeworm Oxyspirura petrowi. We recovered 334 eyeworms from 28 of 29 adult bobwhites (97%); infections ranged from 1-40 worms and mean (± SD) abundance of 11.9 ± 13.0. Three of seven juveniles were infected, and those infected had one eyeworm each. Prevalence of eyeworms was similar among months. However, mean abundance of eyeworms peaked in July and August (3.3 ± 2.1, 13.5 ± 15.0, and 16.9 ± 15.5), and decreased in September (6.3 ± 3.0). We suggest that several previous studies may underreport prevalence and abundance because in those studies only the eye surface and nictitating membrane were examined, and not eye-associated tissue, ducts, glands, or sinuses.