Aqueous Humor TGF-ß2 and Its Association With Intraocular Pressure in a Naturally Occurring Large Animal Model of Glaucoma.

Purpose: Transforming growth factor (TGF)-ß2 has been widely implicated in human glaucoma pathology. The purpose of this study was to determine the source of TGF-ß2 in aqueous humor (AH) and its relationship with intraocular pressure (IOP) in an inherited large animal model of glaucoma. Methods: Sixty-six glaucomatous cats homozygous for LTBP2 mutation, and 42 normal cats were studied. IOP was measured weekly by rebound tonometry. AH was collected by anterior chamber paracentesis from each eye under general anesthesia, and serum samples collected from venous blood concurrently. Concentrations of total, active and latent TGF-ß2 in AH and serum samples were measured by quantitative sandwich immunoassay. For comparisons between groups, unpaired t-test or Mann Whitney test were used, with P < 0.05 considered significant. The relationships between TGF-ß2 concentrations and IOP values were examined by Pearson's correlation coefficient and generalized estimating equation. Results: IOP and AH TGF-ß2 concentrations were significantly higher in glaucomatous than in normal cats. AH TGF-ß2 showed a significant, robust positive correlation with IOP in glaucomatous cats (r = 0.83, R2 = 0.70, P < 0.0001). Serum TGF-ß2 did not correlate with AH TGF-ß2 and was not significantly different between groups. TGF-ß2 mRNA and protein expression were significantly increased in local ocular tissues in glaucomatous cats. Conclusions: Enhanced, local ocular production of TGF-ß2 with a robust positive association with IOP was identified in this spontaneous feline glaucoma model, providing a foundation for preclinical testing of novel therapeutics to limit disease-associated AH TGF-ß2 elevation and signaling in glaucoma.

Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome.

Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration's GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.

Analysis of Plant Root Gravitropism.

Gravity is a powerful element in shaping plant development, with gravitropism, the oriented growth response of plant organs to the direction of gravity, leading to each plant's characteristic form both above and below ground. Despite being conceptually simple to follow, monitoring a plant's directional growth responses can become complex as variation arises from both internal developmental cues as well as effects of the environment. In this protocol, we discuss approaches to gravitropism assays, focusing on automated analyses of root responses. For Arabidopsis, we recommend a simple 90° rotation using seedlings that are 5-8 days old. If images are taken at regular intervals and the environmental metadata is recorded during both seedling development and gravitropic assay, these data can be used to reveal quantitative kinetic patterns at distinct stages of the assay. The use of software that analyzes root system parameters and stores this data in the RSML format opens up the possibility for a host of root parameters to be extracted to characterize growth of the primary root and a range of lateral root phenotypes.

Nonparametric bounds in two-sample summary-data Mendelian randomization: Some cautionary tales for practice.

Recently, in genetic epidemiology, Mendelian randomization (MR) has become a popular approach to estimate causal exposure effects by using single nucleotide polymorphisms from genome-wide association studies (GWAS) as instruments. The most popular type of MR study, a two-sample summary-data MR study, relies on having summary statistics from two independent GWAS and using parametric methods for estimation. However, little is understood about using a nonparametric bound-based analysis, a popular approach in traditional instrumental variables frameworks, to study causal effects in two-sample MR. In this article, we explore using a nonparametric, bound-based analysis in two-sample MR studies, focusing primarily on implications for practice. We also propose a framework to assess how likely one can obtain more informative bounds if we used a different MR design, notably a one-sample MR design. We conclude by demonstrating our findings through two real data analyses concerning the causal effect of smoking on lung cancer and the causal effect of high cholesterol on heart attacks. Overall, our results suggest that while a bound-based analysis may be appealing due to its nonparametric nature, it is far more conservative in two-sample settings than in one-sample settings to get informative bounds on the causal exposure effect.

Mapping retinal ganglion cell somas in a large-eyed glaucoma model.

Purpose: The purpose of this study was to identify a robust, representative region of interest (ROI) for studies of retinal ganglion cell (RGC) soma loss in feline congenital glaucoma (FCG), a spontaneous, large-eyed glaucoma model. Methods: Seven FCG and three wild-type (wt) eyes were collected from 10 adult cats of both sexes. Eyes enucleated postmortem were immediately fixed overnight in 4% paraformaldehyde and then stored in 0.1 M PBS at 4 °C. The retinas were wholemounted, Nissl stained with cresyl violet, and imaged using light microscopy. Somas of RGCs were manually identified according to long-established morphological criteria and quantified using a semiautomated method; their coordinates were used to create density maps and plots of the retinal topography. The RGC axon counts for the corresponding eyes were obtained from glutaraldehyde-fixed, resin-embedded optic nerve cross-sections stained with 0.1% p-phenylenediamine (PPD) using a semiautomated counting method. Correlations between total optic nerve axons and RGC soma counts were assessed by linear regression. A k-means cluster algorithm was used to identify a retinal ROI, with further definition using a probability density algorithm. Results: Interindividual variability in RGC total soma counts was more pronounced in FCG cats (mean = 83,244, range: 0-155,074) than in wt cats (mean = 117,045, range: 97,373-132,972). In general, RGC soma counts were lower in FCG cats than they were in wt cats. RGC axon counts in the optic nerve cross-sections were lower than, but strongly correlated to, the total RGC soma count across all cats (in wt and FCG retinas; R2 = 0.88) and solely FCG eyes (R2 = 0.92). The k-means cluster algorithm indicated a region of the greatest mean difference between the normal wt retinas and FCG-affected retinas within the temporal retina, incorporating the region of the area centralis. Conclusions: As in other species, RGC soma count and topography are heterogeneous between individual cats, but we identified an ROI in the temporal retina for future studies of RGC soma loss or preservation in a large-eyed model of congenital glaucoma. Many of the methods refined and established to facilitate studies in this FCG model will be broadly applicable to studies in other large-eyed models.

Precursors and Development of Geographic Atrophy with Autofluorescence Imaging: Age-Related Eye Disease Study 2 Report Number 18.

PURPOSE: To describe the sequence of events leading to development of geographic atrophy (GA) in age-related macular degeneration with fundus autofluorescence (FAF) imaging. DESIGN: Post hoc analysis of FAF images from the Age-Related Eye Disease Study 2. PARTICIPANTS: Fundus autofluorescence images of 120 eyes (109 patients) with incident GA and at least 2 years of preceding FAF images. METHODS: Images of incident GA were stacked and aligned over FAF images of preceding annual visits. The regions of retina where incident GA developed were assessed on prior years' FAF images. These regions, defined as precursor lesions, were classified into minimal change autofluorescence, predominant hypoautofluorescence (decreased autofluorescence), predominant hyperautofluorescence (increased autofluorescence), and mixed autofluorescence. The natural progression in precursor lesions leading to GA formation and their associations with incident GA size and GA enlargement rate were evaluated. MAIN OUTCOME MEASURES: Incident GA area and enlargement rate and precursor pattern frequency. RESULTS: Incident GA had a mean area of 1.00 mm2 (range, 0.15-8.22 mm2) and an enlargement rate of 0.97 mm2/year (standard deviation, 1.66 mm2/year). Predominant hypoautofluorescence was the most common precursor lesion, increasing from 42% to 81% over 3 years before onset of GA. Almost 30% of eyes showed minimal change autofluorescence 3 years before GA. Among the other precursors, 70% progressed to predominant hypoautofluorescence before GA developed. The type of precursor lesions was not associated with incident GA area. Geographic atrophy evolving from minimal change autofluorescence precursor lesions was associated with faster GA enlargement rates compared with other precursor lesion classes. CONCLUSIONS: Using image registration, we identified changes in autofluorescence images before the onset of GA. Decreased autofluorescence was the most common change, although minimal changes also were seen in one third of the images. Incident GA that arises from predominantly normal autofluorescence is associated with faster enlargement rates compared with GA arising from abnormal autofluorescence. Faster GA enlargement rates also were associated with incident GA size, area of surround abnormal autofluorescence, and presence of reticular pseudodrusen.

Relationship between corneal sensitivity, corneal thickness, corneal diameter, and intraocular pressure in normal cats and cats with congenital glaucoma.

OBJECTIVE: To determine the effect of feline congenital glaucoma (FCG) on corneal sensitivity, and relationships between corneal sensitivity, central corneal thickness (CT), and corneal diameter (CD). ANIMALS AND PROCEDURES: Corneal sensitivity (estimated by corneal touch threshold [CTT] using Cochet-Bonnet esthesiometry); CT using ultrasonic pachymetry; intraocular pressure (IOP) using rebound tonometry; and maximal horizontal CD were measured in 16 normal and 14 FCG cats, both males and females, aged 7 months-3.5 years. All procedures complied with an Institutional Animal Care and Use Committee-approved protocol. Data were analyzed by linear regression: paired Student's t tests for between-eye comparisons, and unpaired Student's t tests for comparisons between groups. Relationships between parameters were evaluated by Pearson correlation coefficients and linear mixed effects modeling. For statistical tests, with the exception of values that were Benjamini-Hochberg adjusted for multiple comparisons, P-values < 0.05 were considered significant. RESULTS: Mean CTT and CT values were lower in FCG eyes relative to normal eyes, but differences were not statistically significant. Mean CD was significantly larger in FCG eyes relative to normal eyes, and there was a significant negative correlation between CD and CTT in FCG (r = -0.8564, corrected P = 0.005). These associations were confirmed in linear mixed effects models. CONCLUSIONS: Eyes with FCG have significantly larger CDs when compared with normal eyes, and larger CDs correlated with decreased corneal sensitivity in this group. Further studies are warranted to explore the effect of buphthalmos and corneal enlargement on corneal sensitivity and innervation in feline subjects with chronic glaucoma.

Validation of Peek Acuity application in pediatric screening programs in Paraguay.

AIM: To validate the Peek Acuity mobile phone application in pediatric populations and compare its utility, both economic and diagnostic, against conventional screening methods using a pediatric ophthalmologist examination as the gold standard. METHODS: A cohort of 393 subjects from Fernando de la Mora, Paraguay (ages 6-16y) were enrolled in the study. Subjects were randomly assigned a starting screening modality among: Peek Acuity, a single line of tumbling E optotypes set at 20/40, and Spot Vision Screener. Once completing the first screening modality, the subjects completed the two remaining techniques. Referral criteria were established based on the most current American Association of Pediatric Ophthalmology and Strabismus (AAPOS) recommendations: 20/40 for Peek Acuity and the tumbling E, and refractive error detection for the Spot Vision Screener. Subjects that failed to achieve the cut-off for any of the three screening techniques or subjects that passed the screening but were randomly selected to perform a comprehensive eye exam to determine the false negative rate, were evaluated by a pediatric ophthalmologist. This evaluation was considered the gold standard, and included vision assessment by a Snellen chart, strabismus evaluation, and cycloplegic refraction with dilated fundoscopy. RESULTS: We obtained 48% sensitivity, 83% specificity, 43% positive predictive value, and 86% negative predictive value for Peek Acuity's ability to refer compared to evaluation by a pediatric ophthalmologist, failing to achieve a desired sensitivity for implementation. Peek Acuity trended to overestimate the subject's visual acuity, providing a higher visual acuity that would not indicate referral for a comprehensive eye examination. However, its high specificity accurately predicted a significant number of children who did not need further evaluation. When comparing the three screening methods, no single screening modality outperformed the others. Peek Acuity represented a technology that was economically feasible compared to other screening modalities in low income settings, due to the prevalence of cell phone use. CONCLUSION: Peek Acuity represents an efficient tool that has potential for implementation in school screenings with different strategies aimed at pediatric populations due to its low cost and high specificity. An increase in sensitivity would improve detection of children with refractive errors.

Absence of a secondary glucocorticoid response in C57BL/6J mice treated with topical dexamethasone.

Glucocorticoids such as dexamethasone can cause an increase in intraocular pressure (IOP) in some of the population, but not all. In this paper we used a mouse model of glucocorticoid induced ocular hypertension to examine the changes in the anterior segment of the eye in mice that failed to respond to glucocorticoid treatment with a sustained increase in IOP. C57BL/6J mice were treated with either 0.1% dexamethasone sodium phosphate ophthalmic solution or sterile PBS 3 times daily for up to 5 weeks. IOP was measured weekly at approximately the same time of the day. After 3-5 weeks of treatment, eyes were enucleated and evaluated for changes associated with steroid induced glaucoma. These studies showed that IOP was significantly elevated in dexamethasone (DEX) treated mice compared to PBS treated mice after 3 weeks of treatment, but IOP in DEX treated mice returned to baseline levels after 5 weeks of treatment. All the mice demonstrated a response to the glucocorticoid treatments and showed an elevation in FKBP5 expression after both 3 and 5 weeks of DEX treatment (primary glucocorticoid response protein) and a weight loss. Western blot analysis of anterior segments from treated mice, however, did not show an increase in secondary glucocorticoid response proteins such as ß3 integrin or myocilin. Fibronectin levels were also not statistically different. The data suggest that in mice, which do not exhibit a prolonged increase in IOP in response to the DEX treatment, there is a compensatory mechanism that can prevent or turn off the secondary glucocorticoid response.

Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus.

BACKGROUND: The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. RESULTS: A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus. CONCLUSION: Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances.

Meta-analysis of transcriptomic changes in optic nerve injury and neurodegenerative models reveals a fundamental response to injury throughout the central nervous system.

Purpose: Injury to the central nervous system (CNS) leads to transcriptional changes that effect tissue function and govern the process of neurodegeneration. Numerous microarray and RNA-Seq studies have been performed to identify these transcriptional changes in the retina following optic nerve injury and elsewhere in the CNS following a variety of insults. We reasoned that conserved transcriptional changes between injury paradigms would be important contributors to the neurodegenerative process. Therefore, we compared the expression results from heterogeneous studies of optic nerve injury and neurodegenerative models. Methods: Expression data was collected from the Gene Expression Omnibus. A uniform method for normalizing expression data and detecting differentially expressed (DE) genes was used to compare the transcriptomes from models of acute optic nerve injury (AONI), chronic optic nerve injury (CONI) and brain neurodegeneration. DE genes were split into genes that were more or less prevalent in the injured condition than the control condition (enriched and depleted, respectively) and transformed into their human orthologs so that transcriptomes from different species could be compared. Biologic significance of shared genes was assessed by analyzing lists of shared genes for gene ontology (GO) term over-representation and for representation in KEGG pathways. Results: There was significant overlap of enriched DE genes between transcriptomes of AONI, CONI and neurodegeneration studies even though the overall concordance between datasets was low. The depleted DE genes identified between AONI and CONI models were significantly overlapping, but this significance did not extend to comparisons between optic nerve injury models and neurodegeneration studies. The GO terms overrepresented among the enriched genes shared between AONI, CONI and neurodegeneration studies were related to innate immune processes like the complement system and interferon signaling. KEGG pathway analysis revealed that transcriptional alteration between JAK-STAT, PI3K-AKT and TNF signaling, among others, were conserved between all models that were analyzed. Conclusions: There is a conserved transcriptional response to injury in the CNS. This transcriptional response is driven by the activation of the innate immune system and several regulatory pathways. Understanding the cellular origin of these pathways and the pathological consequences of their activation is essential for understanding and treating neurodegenerative disease.

Combinations of Osmolytes, Including Monosaccharides, Disaccharides, and Sugar Alcohols Act in Concert During Cryopreservation to Improve Mesenchymal Stromal Cell Survival.

There is demand for non-dimethyl sulfoxide (DMSO) cryoprotective agents that maintain cell viability without causing poor postthaw function or systemic toxicity. The focus of this investigation involves expanding our understanding of multicomponent osmolyte solutions and their ability to preserve cell viability during freezing. Controlled cooling rate freezing, Raman microscopy, and differential scanning calorimetry (DSC) were utilized to evaluate the differences in recovery and ice crystal formation behavior for solutions containing multiple cryoprotectants, including sugars, sugar alcohols, and small molecule additives. Postthaw recovery of mesenchymal stem cells (MSCs) in solutions containing multiple osmolytes have been shown to be comparable or better than that of MSCs frozen in 10% DMSO at 1°C/min when the solution composition is optimized. Maximum postthaw recovery was observed in these multiple osmolyte solutions with incubation times of up to 2 h before freezing. Raman images demonstrate large ice crystal formation in cryopreserved cells incubated for shorter periods of time (∼30 min), suggesting that longer permeation times are needed for these solutions. Recovery was dependent upon the concentration of each component in solution, and was not strongly correlated with osmolarity. It is noteworthy that the postthaw recovery varied significantly with the composition of solutions containing the same three components and this variation exhibited an inverted U-shape behavior, indicating that there may be a "sweet spot" for different combinations of osmolytes. Raman images of freezing behavior in different solution compositions were consistent with the observed postthaw recovery. Phase change behavior (solidification patterns and glass-forming tendency) did not differ for solutions with similar osmolarity, but differences in postthaw recovery suggest that biological, not physical, methods of protection are at play. Lastly, molecular substitution of glucose (a monosaccharide) for sucrose (a disaccharide) resulted in a significant drop in recovery. Taken together, the information from these studies increases our understanding of non-DMSO multicomponent cryoprotective solutions and the manner by which they enhance postthaw recovery.