Investigating the Pathogenecity of CHL1 Leu17Phe Polymorphism in Schizophrenia

Schizophrenia is a devastating brain disorder that affects a surprising 1% of the world\u27s population. Despite this prevalence, little is known about the molecular aspects of this disorder making it both difficult to diagnose and treat. Several studies have identified the CHL1 gene (Close Homolog of L1), sometimes referred to as CALL, as a risk gene for schizophrenia. CHL1, a neural cell adhesion molecule, has major roles in cell migration, and the development of dendritic and axonal projections. Therefore any deficiency in CHL1 may result in brain defects similar to those identified in schizophrenic populations. Moreover, in genetically engineered mice, studies have shown that deficiency of the CHL1 gene results in altered emotional reactivity (such as altered fear responses) and motor coordination, reduced sensorimotor gating and impaired working memory and spatial-temporal integration, similar characteristics to those seen in patients with schizophrenia. The focus of this study is to assess the research literature available for CHL1 as well as investigate a single point mutation in the CHL1 sequence altering a leucine residue to a phenylalanine in the signal peptide of the protein (Leu17Phe) in order to produce a functional deficit of the CHL1 gene. This missense polymorphism has been identified as a risk factor for schizophrenia in Asian populations. Through this mutagenesis, we are able to study CHL1 protein recruitment to the cell membrane in order to understand CHL1\u27s role in schizophrenia at a molecular level

Genetic Variation in DNA Repair Pathways and Risk of Non-Hodgkin's Lymphoma

Molecular and genetic evidence suggests that DNA repair pathways may contribute to lymphoma susceptibility. Several studies have examined the association of DNA repair genes with lymphoma risk, but the findings from these reports have been inconsistent. Here we provide the results of a focused analysis of genetic variation in DNA repair genes and their association with the risk of non-Hodgkin's lymphoma (NHL). With a population of 1,297 NHL cases and 1,946 controls, we have performed a two-stage case/control association analysis of 446 single nucleotide polymorphisms (SNPs) tagging the genetic variation in 81 DNA repair genes. We found the most significant association with NHL risk in the ATM locus for rs227060 (OR = 1.27, 95% CI: 1.13–1.43, p = 6.77×10−5), which remained significant after adjustment for multiple testing. In a subtype-specific analysis, associations were also observed for the ATM locus among both diffuse large B-cell lymphomas (DLBCL) and small lymphocytic lymphomas (SLL), however there was no association observed among follicular lymphomas (FL). In addition, our study provides suggestive evidence of an interaction between SNPs in MRE11A and NBS1 associated with NHL risk (OR = 0.51, 95% CI: 0.34–0.77, p = 0.0002). Finally, an imputation analysis using the 1,000 Genomes Project data combined with a functional prediction analysis revealed the presence of biologically relevant variants that correlate with the observed association signals. While the findings generated here warrant independent validation, the results of our large study suggest that ATM may be a novel locus associated with the risk of multiple subtypes of NHL

Naturally acquired antibodies to gametocyte antigens are associated with reduced transmission of Plasmodium vivax gametocytes to Anopheles arabiensis mosquitoes

Naturally acquired antibodies may reduce the transmission of Plasmodium gametocytes to mosquitoes. Here, we investigated associations between antibody prevalence and P. vivax infectivity to mosquitoes. A total of 368 microscopy confirmed P. vivax symptomatic patients were passively recruited from health centers in Ethiopia and supplemented with 56 observations from asymptomatic P. vivax parasite carriers. Direct membrane feeding assays (DMFA) were performed to assess mosquito infectivity; for selected feeds these experiments were also performed after replacing autologous plasma with malaria naïve control serum (n=61). The prevalence of antibodies against 6 sexual stage antigens (Pvs47, Pvs48/45, Pvs230, PvsHAP2, Pvs25 and PvCelTOS) and an array of asexual antigens was determined by ELISA and multiplexed bead-based assays. Gametocyte (ρ< 0.42; p = 0.0001) and parasite (ρ = 0.21; p = 0.0001) densities were positively associated with mosquito infection rates. Antibodies against Pvs47, Pvs230 and Pvs25 were associated with 23 and 34% reductions in mosquito infection rates (p<0.0001), respectively. Individuals who showed evidence of transmission blockade in serum-replacement DMFAs (n=8) were significantly more likely to have PvsHAP2 or Pvs47 antibodies. Further studies may demonstrate causality for the observed associations, improve our understanding of the natural transmission of P. vivax and support vaccine development

ICU-free days as a more sensitive primary outcome for clinical trials in critically ill pediatric patients.

BACKGROUND: Our objective was to assess the association between intensive care unit (ICU)-free days and patient outcomes in pediatric prehospital care and to evaluate whether ICU-free days is a more sensitive outcome measure for emergency medical services research in this population. METHODS: This study used data from a previous pediatric prehospital trial. The original study enrolled patients ≤12 years of age and compared bag-valve-mask-ventilation (BVM) versus endotracheal intubation (ETI) during prehospital resuscitation. For the current study, we defined ICU-free days as 30 minus the number of days in the ICU (range, 0-30 days) and assigned 0 ICU-free days for death within 30 days. We compared ICU-free days between the original study treatment groups (BVM vs ETI) and with the original trial outcomes of survival to hospital discharge and Pediatric Cerebral Performance Category (PCPC). RESULTS: Median ICU-free days for the BVM group (n = 404) versus ETI group (n = 416) was not statistically different: 0 ICU-free days (interquartile range, 0-10) versus 0 (0-0), P = 0.219. Median ICU-free days were greater for BVM group in 3 subgroups: foreign body aspiration 30 (0-30) versus 0 (0-21), P = 0.028; child maltreatment 0 (0-14.2) versus 0 (0-0), P = 0.004; and respiratory arrest 25 (1-29) versus 7.5 (0-27.7), P = 0.015. In the original trial, neither survival nor PCPC demonstrated differences in all 3 subgroups-survival was greater with BVM for child maltreatment and respiratory arrest and favorable PCPC was greater with BVM for foreign body aspiration. Overall, in the current study, patients with more ICU-free days also had greater survival to hospital discharge and more favorable PCPC scores. CONCLUSIONS: This initial study of the association between ICU-free days and patient outcomes during prehospital pediatric resuscitation appears to support the use of ICU-free days as a clinical endpoint in this population. ICU-free days may be more sensitive than either mortality or PCPC alone while capturing aspects of both measures

The source of elevated free carbon dioxide at the state fish hatchery, Springville, Utah

The Utah Division of Wildlife Resources operates the Springville State Fish Hatchery for raising rainbow trout for stocking lakes and ponds throughout Utah. Since February 2011 the hatchery has observed excessive physical activity among the trout, including jumping out of the hatchery raceways onto the concrete walkways, which can result from free CO2 levels above 15 ppm. Free CO2 levels in the hatchery water have been measured as high as 40 ppm, although the temporal variation has not been well-documented. Thus far, the problem has been addressed by passing the water through aerators before it enters the hatchery and by greatly reducing the food intake of the trout, which both increase costs and reduce production. Current mitigation measures have reduced free CO2 levels at the hatchery entrance by only 5 ppm, which is roughly equal to the increase in CO2 due to fish respiration from the hatchery entrance to exit. The objective of this study has been to determine the source of elevated free CO2 and provide the hatchery with recommendations for mitigation of the problem. The water source for the hatchery is a shallow pond, which is fed by 10 springs, both warm and cold. The pond was formerly used as a receptor for municipal stormwater and the bottom of the pond includes several feet of organic-rich mud, which may be a product of stormwater input. The objective was first addressed by collecting unfiltered water samples from each spring, the pond outlet, the hatchery entrance (outlet of aerator) and exit, and measuring temperature, pH, electrical conductivity, dissolved O2, and free CO2 on-site. The Hach DR-2700 Spectrophotometer was used to measure Cu, Fe, Zn, ammonia, nitrite and hardness, which are the most common stressors of rainbow trout. The discharge of each spring was estimated based upon flow over sharp-crested weirs. Mixing calculations showed that the chemistry and discharge of the springs predicted the chemistry of the pond outlet within (2-9) % for all parameters except Cu, Fe and Zn. The free CO2 at the pond outlet was over-predicted by 9%, indicating that the organic mud in the pond is not a significant contributor of free CO2. The heavy metals Fe, Cu and Zn were under-predicted by (22-27) %, suggesting that the organic mud is a sink for heavy metals. Mixing calculations showed further that the free CO2 level at the hatchery entrance could be reduced as low as 12 ppm with acceptable discharge and other chemical parameters by diverting the four springs with the highest CO2 levels. Current research involves improved documentation of the daily variation in free CO2 levels at the pond outlet and hatchery entrance and exit along with monthly collection of both filtered and unfiltered samples and on-site measurements at all of the above-mentioned sites. In addition to measuring nitrite, ammonia and hardness with the spectrophotometer, Ag, As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Ti are being measured using the PerkinElmer Optima-8000 ICP-OES. Further results will be reported at the meeting

Orthogonal NGS for High Throughput Clinical Diagnostics

Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly

Assessment of <i>SLX4</i> Mutations in Hereditary Breast Cancers

<div><p>Background</p><p><i>SLX4</i> encodes a DNA repair protein that regulates three structure-specific endonucleases and is necessary for resistance to DNA crosslinking agents, topoisomerase I and poly (ADP-ribose) polymerase (PARP) inhibitors. Recent studies have reported mutations in <i>SLX4</i> in a new subtype of Fanconi anemia (FA), FA-P. Monoallelic defects in several FA genes are known to confer susceptibility to breast and ovarian cancers.</p><p>Methods and Results</p><p>To determine if <i>SLX4</i> is involved in breast cancer susceptibility, we sequenced the entire <i>SLX4</i> coding region in 738 (270 Jewish and 468 non-Jewish) breast cancer patients with 2 or more family members affected by breast cancer and no known <i>BRCA1</i> or <i>BRCA2</i> mutations. We found a novel nonsense (c.2469G>A, p.W823*) mutation in one patient. In addition, we also found 51 missense variants [13 novel, 23 rare (MAF<0.1%), and 15 common (MAF>1%)], of which 22 (5 novel and 17 rare) were predicted to be damaging by Polyphen2 (score = 0.65–1). We performed functional complementation studies using p.W823* and 5 <i>SLX4</i> variants (4 novel and 1 rare) cDNAs in a human <i>SLX4</i>-null fibroblast cell line, RA3331. While wild type <i>SLX4</i> and all the other variants fully rescued the sensitivity to mitomycin C (MMC), campthothecin (CPT), and PARP inhibitor (Olaparib) the p.W823* <i>SLX4</i> mutant failed to do so.</p><p>Conclusion</p><p>Loss-of-function mutations in <i>SLX4</i> may contribute to the development of breast cancer in very rare cases.</p></div