Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium

Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects of variants across the genome, it is believed that gene-gene interactions can help elucidate part of the missing heritability by allowing for the test of interactions between genetic variants to mimic the complex nature of biology. To explain the etiology of glaucoma, we first performed a genome-wide association study (GWAS) on glaucoma case-control samples obtained from electronic medical records (EMR) to establish the utility of EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype. Our findings from GWAS suggest consistent evidence of several known associations in POAG. We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value <0.01) and observed interesting findings in the electronic MEdical Records and GEnomics Network (eMERGE) network dataset. Genes from the top epistatic interactions from eMERGE data (Likelihood Ratio Test i.e. LRT p-value <1e-05) were then tested for replication in the NEIGHBOR consortium dataset. To replicate our findings, we performed a gene-based SNP-SNP interaction analysis in NEIGHBOR and observed significant gene-gene interactions (p-value <0.001) among the top 17 gene-gene models identified in the discovery phase. Variants from gene-gene interaction analysis that we found to be associated with POAG explain 3.5% of additional genetic variance in eMERGE dataset above what is explained by the SNPs in genes that are replicated from previous GWAS studies (which was only 2.1% variance explained in eMERGE dataset); in the NEIGHBOR dataset, adding replicated SNPs from gene-gene interaction analysis explain 3.4% of total variance whereas GWAS SNPs alone explain only 2.8% of variance. Exploring gene-gene interactions may provide additional insights into many complex traits when explored in properly designed and powered association studies.     

Meeting Report on the Conference on Fathers’ Role in Children’s Weight‐Related Behaviors and Outcomes

On September 22, 2017, “Engaging the Forgotten Parent: Conference of Experts on Fathers’ Role in Children’s Weight‐Related Behaviours and Outcomes” brought researchers, students, health professionals, community stakeholders, and knowledge users from Canada, Australia, and the United States together to Toronto, Ontario, for a 1‐day gathering focused on furthering scientific understanding of effective strategies to recruit, engage, and retain fathers in family‐based obesity research. Furthermore this conference focused on identifying key knowledge gaps and opportunities for collaborative research to further our understanding of fathers’ roles in the development of their children’s behaviors and weight outcomes. The following four themes emerged from the conference: (1) underrepresentation of fathers in family‐based obesity research, (2) fathers’ engagement in children’s weight‐related behaviors and desire to participate in research, (3) best practices in recruiting, engaging, and retaining fathers in research, and (4) key lessons learned from fatherhood research in developmental science.     

Functional roles for beta1,4-N-acetlygalactosaminyltransferase-A in Drosophila larval neurons and muscles

Adult Drosophila mutant for the glycosyltransferase beta1,4-N-acetlygalactosaminyltransferase-A (beta4GalNAcTA) display an abnormal locomotion phenotype, indicating a role for this enzyme, and the glycan structures that it generates, in the neuromuscular system. To investigate the functional role of this enzyme in more detail, we turned to the accessible larval neuromuscular system and report here that larvae mutant for beta4GalNAcTA display distinct nerve and muscle phenotypes. Mutant larvae exhibit abnormal backward crawling, reductions in nerve terminal bouton number, decreased spontaneous transmitter-release frequency, and short, wide muscles. This muscle shape change appears to result from hypercontraction since the individual sarcomeres are shorter in mutant muscles. Analysis of muscle calcium signals showed altered calcium handling in the mutant, suggesting a mechanism by which hypercontraction could occur. All of these phenotypes can be rescued by a transgene carrying the beta4GalNAcTA genomic region. Tissue-specific expression, using the Gal4-UAS system, reveals that neural expression rescues the mutant crawling phenotype, while muscle expression rescues the muscle defect. Tissue-specific expression did not appear to rescue the decrease in neuromuscular junction bouton number, suggesting that this defect arises from cooperation between nerve and muscle. Altogether, these results suggest that beta4GalNAcTA has at least three distinct functional roles.     

Ecology of Listeria monocytogenes and Listeria species in India: the occurrence,resistance to biocides,genomic landscape and biocontrol

Listeria monocytogenes, the causative agent of listeriosis, has been implicated in increasing foodborne outbreaks worldwide. The disease is manifested in various forms ranging from severe sepsis in immune-compromised individuals, febrile gastroenteritis, still birth, abortions and meningoencephalitis. In India, data from studies on the detection and molecular epidemiological analysis of L. monocytogenes are only recently emerging. The presence of Listeria in different ecological niches has been recorded from India, including foods, soil, vegetables, mangrove swamps, seafood, freshwater fishes, clinical cases, and also insects. The organism has also been isolated from women with spontaneous abortions, miscarriage or recurrent obstetric history, aborted foetuses, animal clinical cases and wildlife samples. A novel species of Listeria has also been characterized. Listeria monocytogenes strains isolated from clinical, environmental, and foods showed biofilm-forming abilities. Listeria monocytogenes serotype 4b isolates of ST328, a predominant and unique ST observed in India, was repeatedly isolated from different sources, times, and geographical locations. Here, we reviewed the occurrence of Listeria in different sources in India, its resistance to biocides, and provide epidemiological analysis on its genomic landscape.     

Status and distribution of jaguarundi in Texas and Northeastern México: Making the case for extirpation and initiation of recovery in the United States

The jaguarundi (Puma yagouaroundi) is a small felid with a historical range from central Argentina through southern Texas. Information on the current distribution of this reclusive species is needed to inform recovery strategies in the United States where its last record was in 1986 in Texas. From 2003 to 2021, we conducted camera‐trap surveys across southern Texas and northern Tamaulipas, México to survey for medium‐sized wild cats (i.e., ocelots [Leopardus pardalis], bobcats [Lynx rufus], and jaguarundi). After 350,366 trap nights at 685 camera sites, we did not detect jaguarundis at 16 properties or along 2 highways (1050 km²) in Texas. However, we recorded 126 jaguarundi photographic detections in 15,784 trap nights on 2 properties (125.3 km²) in the northern Sierra of Tamaulipas, Tamaulipas, México. On these properties, latency to detection was 72 trap nights, with a 0.05 probability of detection per day and 0.73 photographic event rate every 100 trap nights. Due to a lack of confirmed class I sightings (e.g., specimen, photograph) in the 18 years of this study, and no other class I observations since 1986 in the United States, we conclude that the jaguarundi is likely extirpated from the United States. Based on survey effort and results from México, we would have expected to detect jaguarundis over the course of the study if still extant in Texas. We recommend that state and federal agencies consider jaguarundis as extirpated from the United States and initiate recovery actions as mandated in the federal jaguarundi recovery plan. These recovery actions include identification of suitable habitat in Texas, identification of robust populations in México, and re‐introduction of the jaguarundi to Texas.     

MnSOD antisense treatment and exercise-induced protection against arrhythmias

Exercise provides protection against ischemia-reperfusion (I-R)-induced arrhythmias, myocardial stunning, and infarction. An exercise-induced increase in myocardial manganese superoxide dismutase (MnSOD) activity has been reported to be vital for protection against infarction. However, whether MnSOD is essential for exercise-induced protection against ventricular arrhythmias is unknown. We determined the effects of preventing the exercise-induced increase in MnSOD activity on arrhythmias during I-R resulting in myocardial stunning. Male rats remained sedentary or were subjected to successive bouts of endurance exercise. During in vivo myocardial I-R, the incidence of arrhythmias was significantly lower in the exercise-trained rats than in the sedentary rats as evidenced by the arrhythmia. When exercised rats were pretreated with antisense oligonucleotides directed against MnSOD, protection from arrhythmias was attenuated. Moreover, I-R resulted in significant increases in nitro-tyrosine (NT) in the sedentary group. Exercise abolished this I-R-induced NT formation but this protection was unchanged by antisense treatment. Protein carbonyls were increased by I-R, but neither exercise nor antisense treatment impacted carbonyl formation. These data demonstrate that an exercise-induced increase in MnSOD activity is important for protection against arrhythmias. The mechanism by which MnSOD provides protection does not appear to be linked to protein nitrosylation or oxidation.     

A meta-analysis of randomized controlled trials comparing endoscopic and open carpal tunnel decompression

Controversy exists regarding the benefit of endoscopic carpal tunnel release versus open carpal tunnel release in terms of grip/pinch strength, scar tenderness, pain, return to work, reversible/irreversible nerve damage, and adverse effects. Although a number of randomized controlled trials and systematic reviews have been published on the subject, to date, no large definitive randomized controlled trial or meta-analysis has been performed comparing endoscopic to open carpal tunnel release. This meta-analysis was undertaken to address the effectiveness of endoscopic carpal tunnel release relative to open carpal tunnel release. Key outcome measures from 13 randomized controlled trials were extracted and statistically combined. Heterogeneity was observed in three of the outcomes (i.e., grip strength, pain, and return to work), but the causes of heterogeneity could not be explained because of insufficient detail in the reported studies. Using the Jadad et al. scale, nine of 13 studies were of low methodologic quality. The effect sizes were compared between the studies that were rated as high quality and the studies that were rated as low quality on the Jadad et al. scale. Similarly, the studies that were rated as high quality on the Gerritsen et al. scale were compared with those that were rated as low quality. No clinically significant difference in effect sizes was apparent between studies of high and low methodologic quality. This meta-analysis supports the conclusion that endoscopic carpal tunnel release is favored over the open carpal tunnel release in terms of a reduction in scar tenderness and increase in grip and pinch strength at a 12-week follow-up. With regard to symptom relief and return to work, the data are inconclusive. Irreversible nerve damage is uncommon in either technique; however, there is an increased susceptibility to reversible nerve injury that is three times as likely to occur with endoscopic carpal tunnel release than with open carpal tunnel release.