A Quantitative Method to Measure the Kinetics of Elemental Mercury Emissions From Black Shale (Nova Scotia, Canada)

A controlled chamber method using continuous gold trap atomic fluorescence spectroscopy (AFS) (Tekran 2537X) for the analysis of Hg(0) emissions from moderate mass rock samples was developed and tested. A series of black shale and other bedrock samples from Nova Scotia, Canada, were used to test the method and its reproducibility. Hg(0) emissions at 170°C were measured to quantify both free surficial Hg(0) and Hg(0) that had penetrated the rock structure. High volumes of chamber air (45 L) were sampled using 30 min collection times to achieve detectable elemental mercury (Hg(0)) emissions. We found higher percentage masses of Hg(0) were released (1.1%-4.1% of total Hg mass present) in black shale samples as compared to granite and basalt samples from the same region (0.0%-0.3% released) over 350 h of continuous analysis time. The pseudo first order emission rate constants ranged from 0.015-0.245 h-1 (mean 0.063 h-1, standard deviation (SD) 0.102) for the black shale samples analyzed and was 0.004 h-1 for the granite sample. The 24-h zero-order emission rate constants ranged between 0.41 and 3.54 ng h-1 (mean 1.4 ng h-1, SD 1.3) for the black shale samples analyzed and were ~ 0.01 ng h-1 for the granite and basalt samples. This technique has useful implications for examining rock properties and Hg(0) emission rates.

Tumor Voxel Dose-Response Matrix Prediction Using Deep Learning

PURPOSE/OBJECTIVE(S)

Tumor voxel dose-response matrix (DRM) can be assessed using a series of FDG-PET/CT feedback images acquired during radiotherapy. Predicting the tumor voxel DRM earlier is crucial for effectively implementing adaptive treatment management. However, it is also challenging due to FDG uptake dynamic fluctuation in tumor cells. This study investigated the feasibility of predicting tumor voxel DRM during the early treatment weeks using the advanced deep learning (DL) technique.

MATERIALS/METHODS

Serial FDG-PET/CT images were acquired at the pretreatment (pre-Tx), the 2nd and 4th treatment weeks during standard chemo-radiotherapy (35 × 2 Gy) from each of the 50 patients with head and neck squamous cell carcinomas (HNSCC). The reference value of tumor voxel DRM (DRMref), representing the average metabolic change ratio during the treatment, was determined using a linear regression performed on the standard uptake values (SUV)s obtained at the pre-Tx (SUV0), the 2nd (SUV2) and the 4th (SUV4) treatment weeks following deformable PET/CT image registration. A DL model, 3D residual-Unet with a total of 3.4 million parameters, was trained to predict the tumor voxel DRMref with using the SUV0 and SUV2 matrices as inputs. The performance of the DL model was evaluated using 10-fold cross-validation and was compared to that of a linear regression (LR) model determined on the SUV0 and SUV2 matrices.

RESULTS

The mean (SD) of the tumor voxel DRMref was 0.46 (0.2) over all 34612 tumor voxels. The predicted tumor voxel DRM was 0.5 (0.38) and 0.46 (0.15) for the LR model and the DL model, respectively. For those resistant voxels (23.7% of all tumor voxels) with a DRMref > 0.6, the DRM deviation was 0.13 (0.4) and -0.11 (0.13) for the LR model and the DL model, respectively. For those sensitive voxels (76.3%) with a DRMref ≤ 0.6, the DRM deviation was 0.01 (0.23) and 0.03 (0.08) for the LR model and the DL model, respectively.

CONCLUSION

The proposed DL model can predict the tumor voxel DRM with a single FDG-PET feedback image acquired during the 2nd treatment week of radiotherapy for HNSCC patients. The prediction accuracy was improved compared to that of the LR model with a substantial reduction in the variances of the prediction errors. This work demonstrates the great potential of utilizing DL techniques to improve the efficiency of tumor response assessment and adaptive treatment management.

Characterizing Determinants of Near-Road Ambient Air Quality for an Urban Intersection and a Freeway Site

INTRODUCTION

Near-road ambient air pollution concentrations that are affected by vehicle emissions are typically characterized by substantial spatial variability with respect to distance from the roadway and temporal variability based on the time of day, day of week, and season. The goal of this work is to identify variables that explain either temporal or spatial variability based on case studies for a freeway site and an urban intersection site. The key hypothesis is that dispersion modeling of near-road pollutant concentrations could be improved by adding estimates or indices for site-specific explanatory variables, particularly related to traffic. Based on case studies for a freeway site and an urban intersection site, the specific aims of this project are to (1) develop and test regression models that explain variability in traffic-related air pollutant (TRAP) ambient concentration at two near-roadway locations; (2) develop and test refined proxies for land use, traffic, emissions and dispersion; and (3) prioritize inputs according to their ability to explain variability in ambient concentrations to help focus efforts for future data collection and model development.

The key pollutants that are the key focus of this work include nitrogen oxides (NOx), carbon monoxide (CO), black carbon (BC), fine particulate matter (PM2.5; PM ≤ 2.5 μm in aerodynamic diameter), ultrafine particles (UFPs; PM ≤ 0.1 μm in aerodynamic diameter), and ozone (O3). NOx, CO, and BC are tracers of vehicle emissions and dispersion. PM2.5 is influenced by vehicle table emissions and regional sources. UFPs are sensitive to primary vehicle emissions. Secondary particles can form near roadways and on regional scales, influencing both PM2.5 and UFP concentrations. O3 concentrations are influenced by interaction with NOx near the roadway. Nitrogen dioxide (NO2), CO, PM2.5, and O3 are regulated under the National Ambient Air Quality Standards (NAAQS) because of demonstrated health effects. BC and UFPs are of concern for their potential health effects. Therefore, these pollutants are the focus of this work.

METHODS

The methodological approach includes case studies for which variables are identified and assesses their ability to explain either temporal or spatial variability in pollutant ambient concentrations. The case studies include one freeway location and one urban intersection. The case studies address (1) temporal variability at a fixed monitor 10 meters from a freeway; (2) downwind concentrations perpendicular to the same location; (3) variability in 24-hour average pollutant concentrations at five sites near an urban intersection; and (4) spatiotemporal variability along a walking path near that same intersection.

The study boundary encompasses key factors in the continuum from vehicle emissions to near-road exposure concentrations. These factors include land use, transportation infrastructure and traffic control, vehicle mix, vehicle (traffic) flow, on-road emissions, meteorology, transport and evolution (transformation) of primary emissions, and production of secondary pollutants, and their resulting impact on measured concentrations in the near-road environment. We conducted field measurements of land use, traffic, vehicle emissions, and near-road ambient concentrations in the vicinity of two newly installed fixed-site monitors. One is a monitoring station jointly operated by the U.S. Environmental Protection Agency (U.S. EPA) and the North Carolina Department of Environmental Quality (NC DEQ) on I-40 between Airport Boulevard and I-540 in Wake County, North Carolina. The other is a fixed-site monitor for measuring PM2.5 at the North Carolina Central University (NCCU) campus on E. Lawson Street in Durham, North Carolina. We refer to these two locations as the freeway site and the urban site, respectively. We developed statistical models for the freeway and urban sites.

RESULTS

We quantified land use metrics at each site, such as distances to the nearest bus stop. For the freeway site, we quantified lane-by-lane total vehicle count, heavy vehicle (HV) count, and several vehicle-activity indices that account for distance from each lane to the roadside monitor. For the urban site, we quantified vehicle counts for all 12 turning movements through the intersection. At each site, we measured microscale vehicle tailpipe emissions using a portable emission measurement system.

At the freeway site, we measured the spatial gradient of NOx, BC, UFPs, and PM, quantified particle size distributions at selected distances from the roadway and assessed partitioning of particles as a function of evolving volatility. We also quantified fleet-average emission factors for several pollutants.

At the urban site, we measured daily average concentrations of nitric oxide (NO), NOx, O3, and PM2.5 at five sites surrounding the intersection of interest; we also measured high resolution (1-second to 10-second averages) concentrations of O3, PM2.5, and UFPs along a pedestrian transect. At both sites, the Research LINE-source (R-LINE) dispersion model was applied to predict concentration gradients based on the physical dispersion of pollution.

Statistical models were developed for each site for selected pollutants. With variables for local wind direction, heavy-vehicle index, temperature, and day type, the multiple coefficient of determination (R2) was 0.61 for hourly NOx concentrations at the freeway site. An interaction effect of the dispersion model and a real-time traffic index contributed only 24% of the response variance for NOx at the freeway site. Local wind direction, measured near the road, was typically more important than wind direction measured some distance away, and vehicle-activity metrics directly related to actual real-time traffic were important. At the urban site, variability in pollutant concentrations measured for a pedestrian walk-along route was explained primarily by real-time traffic metrics, meteorology, time of day, season, and real-world vehicle tailpipe emissions, depending on the pollutant. The regression models explained most of the variance in measured concentrations for BC, PM, UFPs, NO, and NOx at the freeway site and for UFPs and O3 at the urban site pedestrian transect.

CONCLUSIONS

Among the set of candidate explanatory variables, typically only a few were needed to explain most of the variability in observed ambient concentrations. At the freeway site, the concentration gradients perpendicular to the road were influenced by dilution, season, time of day, and whether the pollutant underwent chemical or physical transformations. The explanatory variables that were useful in explaining temporal variability in measured ambient concentrations, as well as spatial variability at the urban site, were typically localized real-time traffic-volume indices and local wind direction. However, the specific set of useful explanatory variables was site, context (e.g., next to road, quadrants around an intersection, pedestrian transects), and pollutant specific. Among the most novel of the indicators, variability in real-time measured tailpipe exhaust emissions was found to help explain variability in pedestrian transect UFP concentrations. UFP particle counts were very sensitive to real-time traffic indicators at both the freeway and urban sites. Localized site-specific data on traffic and meteorology contributed to explaining variability in ambient concentrations. HV traffic influenced near-road air quality at the freeway site more so than at the urban site. The statistical models typically explained most of the observed variability but were relatively simple. The results here are site-specific and not generalizable, but they are illustrative that near-road air quality can be highly sensitive to localized real-time indicators of traffic and meteorology.

Improved Food Access for Vulnerable Older Adults During COVID19 Pandemic: Findings From a Hospital-Farm Distribution Program

Objectives

In response to the COVID19 pandemic, a Hospital-Farm partnership adapted their Farmers’ Market Program (FMP) to meet the needs of older adults in three Boston-area communities. Adaptations included pre-bagging produce, an option for home-delivery, and informational zoom sessions, instead of pre-pandemic Farmers’ Market-style operations. The objective of this study is to assess the revised (FMP) on food access among participants in the midst of a public health crisis.

Methods

Trained interviewers conducted surveys including demographics, Fruit/Vegetable (F/V) access, intake, quality, and variety, and food-related behaviors, via phone.

Results

Respondents (n = 116 of 176 participants) were more likely to be female (82%), White (90%), aged 70 to 79 years (41.8%), age range 50 to 99 years, had at least one chronic disease (83%), and as likely to live alone or with others (50%). Respondents reported increased F/V access (78.1%), intake (68.6%), quality (76.2%), and variety (80.9%) after participation compared to before the program. The most vulnerable (older, living alone, annual incomes below $30,000) participants had the greatest benefit. Specifically, greater improved F/V access (37% vs 16%), intake (27% vs 17%), quality (35% vs 13%) and variety (36% vs 16%), aged 70 years and older compared to below 70 years, respectively. Living alone had greater improved access (41% vs 37%), intake (39% vs 29%), quality (42% vs 35%) and variety (44% vs 38%) compared to those living with others. Incomes below $30,000 reported greater improved access (44% vs 25%), intake (37% vs 22%), quality (40% vs 26%) and variety (43% vs 30%) compared to those with higher incomes. One or more chronic disease reported greater improved access (35% vs 14%), intake (24% vs 11%), quality (36% vs 15%) and variety (35% vs 14%) compared to respondents with no reported chronic disease.

Conclusions

FMP improved F/V access, intake, quality and variety among older adults and COVID19-related program revisions may have had greater impacts on F/V outcomes among vulnerable populations.

Funding Sources

NIFA, USDA, CAFÉ UMass Amherst.

Using Dictyostelium discoideum as a model for phagocytosis resistance in Escherichia coli

Escherichia coli related illnesses continue to be a problem around the world, especially in developing countries that lack clean water and proper sanitation. Dictyostelium discoideum is a soil dwelling amoeba that phagocytizes bacteria for nutrients. D. discoideum is a great model to study host pathogen interactions, and it has been used to identify virulence factors in bacteria. Our objective is to use Dictyostelium discoideum as a model to identify bacterial genes involved in resistance to phagocytosis. We hypothesize that D. discoideum can be used as a model organism to identify virulence genes associated with E. coli. The aims of this study are to identify E. coli genes predicted to grant resistance to D. discoideum grazing and phagocytosis and further characterize genes identified as potential virulence factors and observe the genes’ effects on D. discoideum grazing and phagocytic killing. Intestinal pathogenic, extraintestinal pathogenic, and laboratory E. coli strains were classified according to grazing phenotype. Previous comparative genomic analysis by large-scale BLAST score ratio (LS-BSR) identified genes prevalent amongst strains resistant to D. discoideum grazing. The gene gipA (growth in Peyer’s patches) was one gene found in various E. coli strains resistant to D. discoideum grazing. We are currently working to characterize the role of E. coli genes associated with resistance to D. discoideum grazing by manipulating E. coli strains for expression of these genes. We will observe the interactions between these strains and D. discoideum grazing and phagocytosis. This experiment will give insight into bacterial genes and virulence factors responsible for evading phagocytosis and the immune system.

This project was funded in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institute of Health, and Department of Health and Human Services under grant number U19 AI110820. Dr. M. Snyder was funded by an NIH NIGMS grant F33 GM116618, a Franklin Research Grant from the American Philosophical Society and a grant from the TU FDRC committee. This research was also supported by an NIH NIGMS R25 GM19970. 

NADase activity found in bacterial TIR proteins may aid in innate immune evasion

Pathogenic microbes have evolved various mechanisms to evade recognition by host immune responses, which can lead to the prevalence of disease and infection. Many strains of pathogenic bacteria contain genes encoding Toll/Interleukin-1 receptor (TIR) domain-containing proteins that function through the inhibition of TLR and myeloid differentiation factor 88 (MyD88) signaling. Previous research has also revealed that prokaryotic TIR domains may regulate bacterial and host metabolic pathways by acting as NAD+ glycohydrolases (NADases). We hypothesize that this NADase activity may contribute to the role of bacterial TIRs as virulence factors. In order to test this hypothesis, we observed the effects of TIR NADase activity on the binding interactions between bacterial TIRs and host MyD88, and on the ability of bacterial TIRs to block NF-kB signaling. For this, we have identified amino acids predicted to play a role in TIR NADase activity and have expressed and purified recombinant bacterial TIR proteins that have incorporated these mutations. We then tested the NADase activity of these mutants in comparison with that of wild-type TIR proteins and TIRs with a mutation known to inhibit NADase activity. We are now using TIRs with deficiencies in NADase activity in pull-down assays to test their binding to MyD88 and utilizing RT-PCR to analyze the effects of these mutant TIRs on innate cell activation. This information will allow us to gain a deeper understanding into the relationship between NADase activity in bacterial TIRs and their virulence activity and can potentially uncover new mechanisms for pathogenic evasion of host immune defenses.

Supported by grant from NIH (R25 GM119970 04)

Structure of NAD+ consuming Acinetobacter baumannii TIR domain

Toll-like and Interleukin-1/18 receptor (TIR) resistance proteins have been identified across biology to function as important multimodal signal transduction and immune regulatory molecules. Select TIR domain containing proteins identified in both eukaryotic and prokaryotic species have also been found to have NAD+ hydrolase activity in bacteria, plants and in mammalian cells. We report the crystal structure of the Acinetobacter baumannii Toll-Interleukin-1 receptor resistance domain protein (AbTIR) determined to a resolution of 2.8 Å, confirm its enzymatic function in NAD+ hydrolysis and map its interaction with NAD+ using HDX-MS. Additionally, we have developed a novel assay for measuring AbTIR’s enzymatic activity in live bacteria using label-free quantitative two-photon fluorescence lifetime (FLT) imaging microscopy (2p-FLIM). These studies provide new insight into TIR protein mechanisms and their varying roles across biology.

Supported by R01 AI-082299, R21 CA191726-01 

POS0443 EXPLORING NOVEL TENOSYNOVITIS AND COMBINED INFLAMMATION IMAGING OUTCOMES: RESULTS FROM A RANDOMISED CONTROLLED TRIAL IN EARLY RHEUMATOID ARTHRITIS

Background:

Magnetic resonance imaging (MRI) trial outcomes have largely focused on synovitis, bone marrow oedema (BME) and erosions. Tenosynovitis is a common manifestation of rheumatoid arthritis (RA), but is relatively understudied; a combined inflammation score (CIS) summing synovitis, BME and tenosynovitis may be a highly responsive measure. We previously showed the responsiveness of the Outcome Measures in Rheumatology (OMERACT) RA MRI scoring system (RAMRIS) and a machine-learning derived automated tool (RAMRIQ) in a randomised controlled trial (RCT) of tofacitinib and methotrexate (MTX) in MTX-naïve patients (pts) with early RA.1

Objectives:

This post hoc analysis assessed the impact of tofacitinib ± MTX on MRI tenosynovitis and CIS in pts with early RA using semiquantitative and quantitative MRI outcomes.

Methods:

Study A3921068 (NCT01164579), a 1-year, exploratory, Phase 2, RCT, compared tofacitinib 10 mg twice daily (BID) ± MTX, and MTX monotherapy, in MTX-naïve pts with early RA.1 MRI of unilateral wrist and metacarpophalangeal joints was performed at screening/baseline (BL) and Months (M)1/3/6/12. MRI tenosynovitis and CIS were assessed using RAMRIS and RAMRIQ. Changes from BL (Δ) in RAMRIS and RAMRIQ tenosynovitis and CIS were evaluated at M1/3/6/12. Data were assessed using a mixed-effect model for repeated measures, with treatment arms as factors and BL values as covariates. Using data pooled across treatment arms, Spearman’s rank correlation coefficients were calculated for associations between BL RAMRIS and BL RAMRIQ tenosynovitis and CIS vs BL Disease Activity Score in 28 joints, C-reactive protein (DAS28-4[CRP]), and ΔRAMRIS and ΔRAMRIQ tenosynovitis and CIS at M12 vs ΔDAS28-4(CRP) at M12.

Results:

In total, 109 pts were randomised and treated. ΔRAMRIS and ΔRAMRIQ tenosynovitis and CIS were generally significantly greater at M3/6/12 in pts receiving tofacitinib ± MTX vs MTX, while ΔRAMRIQ CIS was also significantly greater at M1 (Figure 1). Compared with RAMRIS, RAMRIQ outcomes were generally more responsive to treatment with tofacitinib ± MTX. Significant correlations were seen between BL RAMRIS and BL RAMRIQ tenosynovitis and BL RAMRIS CIS vs BL DAS28-4(CRP), and between ΔRAMRIS and ΔRAMRIQ tenosynovitis and CIS at M12 vs ΔDAS28-4(CRP) at M12 (Table 1). In general, stronger correlations were seen between BL DAS28-4(CRP) and BL RAMRIS vs BL RAMRIQ parameters, while correlations were similar between ΔDAS28-4(CRP) at M12 and ΔRAMRIS and ΔRAMRIQ parameters at M12.

Table 1.

Correlations between a) BL RAMRIS and BL RAMRIQ tenosynovitis and CIS vs BL DAS28-4(CRP) (N=109) and b) ΔRAMRIS and ΔRAMRIQ tenosynovitis and CIS at M12 vs ΔDAS28-4(CRP) at M12 (N=73) across treatment armsa

a)BL DAS28-4(CRP)b)ΔDAS28-4(CRP)BL imaging featureCorrelationp valueΔImaging featureCorrelationp valueRAMRIStenosynovitis0.3660.0001RAMRIStenosynovitis0.531<0.0001RAMRIS CIS0.399<0.0001RAMRIS CIS0.554<0.0001RAMRIQtenosynovitis0.2050.037RAMRIQtenosynovitis0.543<0.0001RAMRIQ CIS0.1800.062RAMRIQ CIS0.564<0.0001

aData were pooled across the tofacitinib 10 mg BID ± MTX and MTX monotherapy arms

Spearman’s rank correlation coefficients and p values were calculated for associations between RAMRIS and RAMRIQ parameters and DAS28-4(CRP); tenosynovitis and CIS were assessed using combined data from metacarpophalangeal and wrist joints; CIS is the sum of synovitis, BME and tenosynovitis values

Δ, change from BL; N, number of pts with values at BL/timepoint of interest

Conclusion:

Responsiveness of RAMRIS and RAMRIQ tenosynovitis and CIS was demonstrated with significant improvements through M12 in pts receiving tofacitinib 10 mg BID ± MTX vs MTX. Construct validity for RAMRIS and RAMRIQ tenosynovitis and CIS was evident from correlations with DAS28-4(CRP). Further work is needed to validate these novel imaging biomarkers in terms of relative responsiveness and prediction of later structural progression.

References:

[1]Conaghan et al. Ann Rheum Dis 2016; 75: 1024-1033.

Acknowledgements:

Study sponsored by Pfizer Inc. Medical writing support was provided by Jennifer Arnold, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests:

Philip G Conaghan Speakers bureau: AbbVie, Novartis, Consultant of: AbbVie, Bristol-Myers Squibb, Eli Lilly, Flexion, Galapagos, Gilead Sciences, GlaxoSmithKline, Janssen, Novartis, Pfizer Inc, Regeneron, Mikkel Østergaard Speakers bureau: AbbVie, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Eli Lilly, GlaxoSmithKline, Hospira, Janssen, Merck, Mundipharma, Novartis, Novo, Orion, Pfizer Inc, Regeneron, Roche, Schering-Plough, Takeda, UCB, Wyeth, Consultant of: AbbVie, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Eli Lilly, GlaxoSmithKline, Hospira, Janssen, Merck, Mundipharma, Novartis, Novo, Orion, Pfizer Inc, Regeneron, Roche, Schering-Plough, Takeda, UCB, Wyeth, Grant/research support from: AbbVie, Centocor, Merck, Orrin Troum Speakers bureau: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Horizon, Novartis, Pfizer Inc, Sanofi-Genzyme, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Eli Lilly, Horizon, Pfizer Inc, Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Centocor, Corrona, Novartis, Pfizer Inc, Zhiyong Xie Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Alan Brett Shareholder of: Stryker Corp, Employee of: Stryker Corp, Mark Snyder Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Abbas Ebrahim Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Douglass Chapman Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Gosford Sawyerr Consultant of: Pfizer Inc, Employee of: Syneos Health, John Andrews Shareholder of: Pfizer Inc, Employee of: Pfizer Inc

Adaptation of a CURE course aimed at characterization of host-pathogen interactions for on-line learning

Course-based undergraduate research experiences (CUREs) aim to engage a large, diverse group of students in authentic research, promote student research skills, content knowledge, scientific literacy, critical thinking and analysis skills, support student self-efficacy, and at the same time provide a means to advance faculty research productivity. Addressing each of these varied goals of a CURE course is a challenge, and became even more challenging when classes were forced on-line for the COVID-19 pandemic. In Fall of 2020, we adapted our CURE course, which seeks to engage students at Towson University with research ongoing at the University of Maryland, School of Medicine, for virtual learning. To move the course on-line, we focused on activities that could easily be adapted to a virtual environment, such as those focusing on bioinformatics analysis, research design, data analysis, scientific writing and on-line lab simulations. Students were tasked with becoming ‘project managers’—designing hypotheses and protocols and choosing experimental variables and controls, while instructors and an undergraduate learning assistant carried out the experiments, videotaping so students could become familiar with the techniques. While the drawbacks of the virtual CURE course were many, including the lack of student involvement in hands-on bench work, benefits of the virtual CURE included more time and attention devoted to critical skills such as research design, data analysis and scientific writing. Future designs of CURE courses may benefit from increased attention to these skills, even upon return to in-person learning.

Contribution of the NADase function of bacterial TIR domain proteins to the inhibition of innate immune responses

Pathogenic microbes have evolved various mechanisms to evade recognition by host immune responses, which can lead to the prevalence of disease and infection. Many strains of pathogenic bacteria contain genes encoding Toll/Interleukin-1 receptor (TIR) domain-containing proteins that function through the inhibition of TLR and myeloid differentiation factor 88 (MyD88) signaling. Previous research has also revealed that prokaryotic TIR domains may regulate bacterial and host metabolic pathways by acting as NAD+ glycohydrolases (NADases). We hypothesize that this NADase activity may contribute to the role of bacterial TIRs as virulence factors. In order to test this hypothesis, we observed the effects of TIR NADase activity on the binding interactions between bacterial TIRs and host MyD88, and on the ability of bacterial TIRs to block NF-kB signaling. For this, we have identified amino acids predicted to play a role in TIR NADase activity and have expressed and purified recombinant bacterial TIR proteins that have incorporated these mutations. We then tested the NADase activity of these mutants in comparison with that of wild-type TIR proteins and TIRs with mutations already known to inhibit NADase activity. We are now using mutant TIRs with deficiencies in NADase activity in pull-down assays to test their binding to MyD88 and utilizing reporter assays to analyze the effects of these mutant TIRs on NF-kB signaling. This information will allow us to gain a deeper understanding into the relationship between NADase activity in bacterial TIRs and their virulence activity, and can potentially uncover new mechanisms for pathogenic evasion of host immune defenses.

Hydroxide promotes ion pairing in the NaNO2-NaOH-H2O system

Nitrite (NO2-) is a prevalent nitrogen oxyanion in environmental and industrial processes, but its behavior in solution, including ion pair formation, is complex. This solution phase complexity impacts industries such as nuclear waste treatment, where NO2- significantly affects the solubility of other constituents present in sodium hydroxide (NaOH)-rich nuclear waste. This work provides molecular scale information into sodium nitrite (NaNO2) and NaOH ion-pairing processes to provide a physical basis for later development of thermodynamic models. Solubility isotherms of NaNO2 in aqueous mixtures with NaOH and total alkalinity were also measured. Spectroscopic characterization of these solutions utilized high-field nuclear magnetic resonance spectroscopy (NMR) and Raman spectroscopy, with additional solution structure detailed by X-ray total scattering pairwise distribution function analysis (X-ray PDF). Despite the NO2- deformation Raman band's insensitivity to added NaOH in saturated NaNO2 solutions, 23Na and 15N NMR studies indicated the Na+ and NO2- chemical environments change likely due to ion pairing. The ion pairing correlates with a decrease in diffusion coefficient of solution species as measured by pulsed field gradient 23Na and 1H NMR. Two-dimensional correlation analyses of the 2800-4000 cm-1 Raman region and X-ray PDF indicated that saturated NaNO2 and NaOH mixtures disrupt the hydrogen network of water into a new structure where the length of the OO correlations is contracted relative to the typical H2O structure. Beyond describing the solubility of NaNO2 in a multicomponent electrolyte mixture, these results also indicate that nitrite exhibits greater ion pairing in mixtures of concentrated NaNO2 and NaOH than in comparable solutions with only NaNO2.

Identification and characterization of Escherichia coli genes associated with grazing resistance to the social amoeba Dictyostelium discoideum

Pathogenic Escherichia coli strains remain a significant health challenge, particularly in developing countries. The social amoeba, Dictyostelium discoideum, which phagocytizes bacteria for nutritional purposes, serves as a host model for several pathogenic bacteria, including E. coli. Here we have characterized the interactions of D. discoideum with 35 representative E. coli strains and identified strains sensitive and resistant to D. discoideum grazing in each E. coli pathotype. Whole genome phylogenomic analysis revealed that grazing resistance is distributed among the phylotypes, although resistant strains are enriched in the B2 phylogenomic group. Comparative genomic analysis identified genes more prevalent among strains resistant to D. discoideum grazing, including genes associated with adhesion, carbohydrate modification, iron transport, signaling and metabolism. Interestingly, the gipA (growth in Peyer’s Patches) gene, which has been found associated with microbiota in patients with Crohn’s disease, was widely present in E. coli strains resistant for D. discoideum grazing. We are currently working to characterize the role of E. coli genes associated with resistance to phagocytosis and killing by D. discoideum, through creation and analysis of E. coli strains manipulated for expression of the identified genes. Such characterization is aimed at providing insight into potentially novel E. coli virulence factors.

Development of a CURE course aimed at characterization of bacterial Toll/interleukin 1 receptor (TIR) domain-containing proteins

Course-based undergraduate research experiences (CUREs) can engage a large, diverse group of students in authentic research, promote student research skills, student content knowledge, scientific literacy, critical thinking and analysis skills, support student self-efficacy, and at the same time provide a means to advance faculty research productivity. These varied goals of a CURE course, at times, can prove to be competing. For example, courses aimed at providing advanced levels of student input in design of research questions, hypotheses and protocols can veer from faculty research goals. In an effort to balance these competing objectives, we designed a CURE course engaging students at Towson University with research ongoing at the University of Maryland, School of Medicine aimed at characterizing the function of bacterial Toll/interleukin 1 receptor (TIR) domain containing proteins. Bacterial TIR proteins were originally characterized as virulence factors that impede mammalian innate immune signaling, but recently also have been shown to exhibit enzymatic NADase activity. Students in the CURE course used bioinformatics analysis of modeled structures of bacterial TIRs to predict sites for NADase function and hypothesized the effects of mutations of these sites on TIR functions. Students then designed and created recombinantly-expressed proteins mutated at their predicted sites and tested their mutant proteins for both NADase function and potential inhibition of mammalian innate immune signaling. This course outline thus allowed student engagement in project design and hypothesis formation, while also maintaining projects aimed at advancing a specific faculty research program.

Characterization of a potential Escherichia coli virulence factor identified in a screen using the social amoeba phagocyte, Dictyostelium discoideum

Escherichia coli are a typical component of mammalian gut microbiota; however, a number of pathogenic strains remain a health challenge for developing countries. To identify novel bacterial virulence factors, we used the social amoeba, Dictyostelium discoideum, which preys upon soil bacteria, including E. coli, as a model for mammalian phagocytic cells. Using random mutagenesis, screening for mutant E. coli strains resistant to killing upon phagocytosis, and genomic sequencing of these resistant strains, we identified mutations in several potential genes of interest, including an E. coli gene of unknown function, yfaT. Preliminary results suggest that D. discoideum Erk signaling is reduced in response to yfaT-deficient E. coli. Furthermore, mammalian TLR4 signaling in response to yfaT-deficient E. coli also appears attenuated. Our current studies focus on characterizing differences in growth patterns for wild-type and yfaT-deficient E. coli using Biolog screenings, as well as analyzing potential differences in LPS structure in these strains. These studies are aimed at identification and characterization of novel mechanisms that may be involved in bacterial virulence. In addition, given that the development of mechanisms to resist D. discoideum predation may have contributed to the selection and maintenance of bacterial virulence factors, such as yfaT, against mammalian hosts, these studies may provide insight on the evolution of host-pathogen interactions.

Identification and characterization of Escherichia coli genes associated with grazing resistance to the social amoeba Dictyostelium discoideum

Pathogenic Escherichia coli strains remain a significant health challenge, particularly in developing countries. The social amoeba, Dictyostelium discoideum, which phagocytizes bacteria for nutritional purposes, serves as a host model for several pathogenic bacteria, including E. coli. Here we have characterized the interactions of D. discoideum with 35 representative E. coli strains, and found that strains sensitive and resistant to D. discoideum grazing were found in each E. coli pathotype. Whole genome phylogenomic analysis revealed that grazing resistance is distributed among the phylotypes, although resistant strains are enriched in the B2 phylogenomic group. Comparative genomic analysis identified genes more prevalent among strains resistant to D. discoideum grazing, including genes associated with adhesion, carbohydrate modification, iron transport, signaling and metabolism. Interestingly, the gipA (growth in Peyer’s Patches) gene, which has been found associated with microbiota in patients with Crohn’s disease, was widely present in E. coli strains resistant for D. discoideum grazing. We are currently working to characterize the role that E. coli genes that have been found associated with grazing-resistance might play in resistance to phagocytosis by D. discoideum, through creation and analysis of E. coli strains manipulated for expression of the identified genes. Such characterization is aimed at providing insight into potentially novel E. coli virulence factors.

Student Outcomes in a CURE Course Using Simple Model Organisms to Characterize Host-Pathogen Interactions

Course-based undergraduate research experiences (CUREs) can increase the inclusivity of scientific research by breaking down both barriers associated with student awareness and confidence in seeking research experiences, as well as faculty biases in selection of student researchers. We developed a CURE using the social amoeba Dictyostelium discoideum and its bacterial prey Escherichia coli as a model for host-pathogen interactions. D. discoideum phagocytize bacteria and can be used as a simple model to characterize innate immune processes. Our CURE course focuses on characterization of genes potentially associated with resistance to phagocytic killing, which were identified in a screen for mutant E. coli strains with enhanced survival upon D. discoideum phagocytosis. These mutant E. coli strains were sequenced, and students in the course use bioinformatics tools to identify mutated genes. From there, students work with E. coli strains deficient for the mutated genes, performing assays to characterize both bacterial phenotypes as well as D. discoideum phagocytic and signaling responses to these mutant strains. Using various tools, including pre- and post-tests, interviews and the SURE survey to assess student outcomes, we found significant gains in student knowledge and skills, as well as student-reported gains in knowledge of the research process, confidence in working in a research team, and ability to interpret results. Our CURE course was used as a model for implementation of the TU-Research Enhancement Program (TU-REP), which is funded by the HHMI Inclusive Excellence initiative, and seeks to transform the scientific curriculum at TU by offering opportunities for students to engage early and often in authentic research.

Comparative genomic analysis of Escherichia coli strains resistant to grazing by the social amoeba Dictyostelium discoideum

Diarrheagenic Escherichia coli remain a significant health challenge, particularly in developing countries. Challenges in the use of small animal models for enteric infections highlight the need for development of alternative model systems. The social amoeba, Dictyostelium discoideum, which phagocytizes bacteria for nutritional purposes, serves as a host model for several pathogenic bacteria, including E. coli. Previous studies characterized interactions of D. discoideum with commensal and extraintestinal E. coli. In the current study, we extend this characterization to analyze the grazing interactions of D. discoideum with 35 representative diarrheagenic, extraintestinal and commensal E. coli strains. We found that E. coli strains sensitive and resistant to D. discoideum grazing are present in each pathotype. Whole genome phylogenomic analysis revealed that grazing resistance to D. discoideum is distributed among the phylotypes, although resistant strains are enriched in the B2 phylogenomic group. Comparative genomic analysis identified genes that were more prevalent among strains resistant to D. discoideum grazing. While not providing direct insight into conserved mechanisms of resistance, these identified genes do provide avenues for further investigation. Phenotypic analysis revealed that E. coli strains resistant to D. discoideum grazing also exhibited increased resistance to the reducing agent, β-ME. These data extend the characterization of interactions between D. discoideum and E. coli, and through comparative genomics identify candidate E. coli genes that may be associated with resistance to grazing by the model phagocyte D. discoideum, and by extension with resistance to phagocytic immune cells.

Influential factors affecting black carbon trends at four sites of differing distance from a major highway in Las Vegas

Elevated air pollution levels adjacent to major highways are an ongoing topic of public health concern worldwide. Black carbon (BC), a component of particulate matter (PM) emitted by diesel and gasoline vehicles, was measured continuously via a filter-based light absorption technique over ~ 16 months at four different stations positioned on a perpendicular trajectory to a major highway in Las Vegas, NV. During downwind conditions (winds from the west), BC at 20 m from the highway was 32 and 60% higher than concentrations at 100 and 300 m from the roadway, respectively. Overall highest roadside (20-m site) BC concentrations were observed during the time period of 4 a.m.-8 a.m. under low-speed variable winds (3.02 μg/m³) or downwind conditions (2.84 μg/m³). The 20-m site BC concentrations under downwind conditions are 85% higher on weekday periods compared to weekends during the time period of 4 a.m.-8 a.m. Whereas total traffic volume was higher on weekdays versus weekends and differed by approximately 3% on weekdays versus weekends, similarly, the detected heavy-duty fraction was higher on weekdays versus weekends and differed by approximately 21% on weekdays versus weekend. Low wind speeds predominated during early morning hours, leading to higher BC concentrations during early morning hours despite the maximum traffic volume occurring later in the day. No noticeable impact from the airport or nearby arterial roadways was observed, with the 300-m site remaining the lowest of the four-site network when winds were from the east. Multivariate linear regression analysis revealed that heavy-duty traffic volume, light-duty traffic volume, wind speed, weekday versus weekend, surface friction velocity, ambient temperature, and the background BC concentration were significant predictors of roadside BC concentrations. Comparison of BC and PM_2.5 downwind concentration gradients indicates that the BC component contributes substantially to the PM_2.5 increase in roadside environments. These results suggest that BC is an important indicator to assess the contribution of primary traffic emissions to near-road PM_2.5 concentrations, providing opportunities to evaluate the feasibility and effectiveness of mitigation strategies.

NO to NO2 Conversion Rate Analysis and Implications for Dispersion Model Chemistry Methods using Las Vegas, Nevada Near-Road Field Measurements

The nitrogen dioxide/oxides of nitrogen (NO₂/NO_X) ratio is an important surrogate for NO to NO₂ chemistry in dispersion models when estimating NO_X impacts in a near-road environment. Existing dispersion models use different techniques and assumptions to represent NO to NO₂ conversion and do not fully characterize all of the important atmospheric chemical and mechanical processes. Thus, "real-world" ambient measurements must be analyzed to assess the behavior of NO₂/NO_X ratios near roadways. An examination of NO₂/NO_X ratio data from a field study conducted in Las Vegas, Nevada (NV), from mid-December, 2008 through mid-December, 2009 provides insights into the appropriateness of assumptions about the NO₂/NO_X ratio included in dispersion models. Data analysis indicates multiple factors affect the downwind NO₂/NO_X ratio. These include spatial gradient, background ozone (O₃), source emissions of NO and NO₂, and background NO₂/NO_X ratio. Analysis of the NO₂/NO_X ratio spatial gradient indicates that under high O₃ conditions, the change in the ratio is fairly constant once a certain O₃ threshold (≥ 30 ppb) is reached. However, under low O₃ conditions (< 30 ppb), there are differences between weekdays and weekends, most likely due to a decline in O₃ concentrations during the weekday morning hours, reducing the O₃ available to titrate the emitted NO, allowing lower NO₂/NO_X ratios. These results suggest that under high O₃ conditions, NO_X chemistry is driving the NO₂/NO_X ratios whereas under low O₃ conditions, atmospheric mixing is the driving factor.

Estimation of on-road NO2 concentrations, NO2/NOX ratios, and related roadway gradients from near-road monitoring data

This paper describes a new regression modeling approach to estimate on-road nitrogen dioxide (NO2) and oxides of nitrogen (NOX) concentrations and near-road spatial gradients using data from a near-road monitoring network. Field data were collected in Las Vegas, NV at three monitors sited 20, 100, and 300 m from Interstate-15 between December, 2008 and January, 2010. Measurements of NO2 and NOX were integrated over 1-hour intervals and matched with meteorological data. Several mathematical transformations were tested for regressing pollutant concentrations against distance from the roadway. A logit-ln model was found to have the best fit (R2 = 94.7%) and also provided a physically realistic profile. The mathematical model used data from the near-road monitors to estimate on-road concentrations and the near-road gradient over which mobile source pollutants have concentrations elevated above background levels. Average and maximum on-road NO2 concentration estimates were 33 ppb and 105 ppb, respectively. Concentration gradients were steeper in the morning and late afternoon compared with overnight when stable conditions preclude mixing. Estimated on-road concentrations were also highest in the late afternoon. Median estimated on-road and gradient NO2 concentrations were lower during summer compared with winter, with a steeper gradient during the summer, when convective mixing occurs during a longer portion of the day On-road concentration estimates were higher for winds perpendicular to the road compared with parallel winds and for atmospheric stability with neutral-to-unstable atmospheric conditions. The concentration gradient with increasing distance from the road was estimated to be sharper for neutral-to-unstable conditions when compared with stable conditions and for parallel wind conditions compared with perpendicular winds. A regression of the NO2/NOX ratios yielded on-road ratios ranging from 0.25 to 0.35, substantially higher than the anticipated tail-pipe emissions ratios. The results from the ratios also showed that the diurnal cycle of the background NO2/NOX ratios were a driving factor in the on-road and downwind NO2/NOX ratios.

Marking 15 years of the Genetic and Rare Diseases Information Center

BACKGROUND:

The Genetic and Rare Diseases Information Center (GARD), a program of the National Center for Advancing Translational Sciences, was established in 2002 to assist the public in finding reliable, timely, and easy-to-understand information about genetic and/or rare diseases in English or Spanish.

OBJECTIVE:

A review of longitudinal data on GARD inquiries from 2002 to 2016 and assessment of the results of two user satisfaction surveys were conducted to understand the demographics and needs of GARD customers over time.

METHODS:

Since 2002, GARD has collected anonymized data while responding to questions received via e-mail, website, telephone, fax, letter, or TTY. Between 2002 and 2016 GARD received a total of 60,106 inquiries. User satisfaction surveys were conducted in 2006 and 2014, in which users self-selected to participate.

RESULTS:

The annual number of inquiries has risen steadily since 2002. Inquiries are overwhelmingly from educated female patients, family, and friends seeking disease-specific information, treatment options, referrals, and research studies. Most users report satisfaction with the experience.

CONCLUSIONS:

Rare disease patients and their families face challenges in finding information about their symptoms or diagnosis, prognosis, treatment options, significance for family members, and research opportunities. Lack of available clinical expertise can leave patients, their family, and friends with little choice but to become knowledgeable on their own. GARD fills a critical need by providing the public with vetted, evidence-based information that empowers people to engage in their own health care and seek research studies of relevance.

Identification of Virulence and Virulence Regulatory Factors in Escherichia coli using Dictyostelium discoideum as a Model Phagocyte

Escherichia coli is normally found as part of the human gut microbiota, however there exist a number of diarrheagenic strains. Identification and disruption of the virulence factors that promote infection could lead to a reduction in infection period of these E. coli strains and potentially of other species with similar means of virulence. To identify E. coli strains with altered virulence, we used Dictyostelium discoideum, a social amoeba that phagocytizes bacteria for nutritional purposes. Using random mutagenesis, we created mutant stocks of E. coli, each. These stocks were subjected to several rounds of phagocytosis by D. discoideum, enriching the culture and selecting for mutants resistant to intracellular killing. Resistant mutants were isolated and we found that some of the resistant strains showed increased survival when compared to the wild-type strain. Once isolated, the full genomes of our resistant mutant strains were sequenced using Illumina’s next generation MiSeq technology. While analyzing the sequencing data from these mutant strains, we found several potential genes of interest, including genes related to flagella, oxidoreductases, and acid resistance. We have begun to characterize genes of interest through various qualitative and quantitative assays using individual gene knockout strains. These studies should allow for identification of novel factors associated with regulation of virulence in E. coli. In addition, given that the development of mechanisms to resist D. discoideum predation may have contributed to the selection and maintenance of bacterial virulence factors against mammalian hosts, these studies may provide insight on the evolution of host-pathogen interactions.

Abstract P6-05-01: Low BRCA2 levels cause epigenetic activation of growth adaptive pathways without inducing recurrent genomic mutations

The development of therapeutics to prevent cancer onset is hindered by a lack of robust cell systems to study the earliest steps of malignant transformation. Significant barriers to studying cancer-initiating events include intrinsic cellular pathways to prevent cell proliferation in the setting of activating oncogenes or genomic instability. To circumvent this limitation, we studied in vitro transient depletion of breast cancer tumor suppressor genes followed by selective growth conditions to enrich for de novo mutations or stable epigenetic alterations that can confer a growth advantage to non-transformed breast epithelial cells. We report that transient BRCA2 depletion, but not depletion of other breast cancer genes, leads to a selective growth advantage in EGF-free media. This is due to a failure of BRCA2 inactivated cells to enact a mesenchymal-to-epithelial transition upon withdrawal of EGF. Genomic profiling and biochemical approaches indicate that transient loss of BRCA2 induces chromatin remodeling in concert with NF-κB signaling and histone H2B deacetylation to repress genes associated with the epithelial state. Notably, this process did not appear to require recurrent driver mutations, nor DNA methylation changes, but was dependent on ATR signaling. Overall, our work suggests that transiently low BRCA2 levels are sufficient to induce aberrant cell proliferation under certain conditions and that targeting epigenetic modifiers may be an approach to prevent BRCA2-induced malignancy.

Citation Format: Gruber JJ, Snyder M. Low BRCA2 levels cause epigenetic activation of growth adaptive pathways without inducing recurrent genomic mutations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-05-01.

207 EFFICIENT GENERATION OF MYOSTATIN PROMOTER MUTATIONS IN BOVINE EMBRYOS USING THE CRISPR/Cas9 SYSTEM

The myostatin gene or growth differentiation factor 8 is a member of the transforming growth factor-β superfamily that acts as a negative regulator of muscle growth. Mutations inactivating this gene occur naturally in Piedmontese and Belgian Blue cattle breeds, resulting in a dramatic increase in muscle mass, albeit with unwanted consequences of increased dystocia and decreased fertility. Modulation of muscle mass increase without the unwanted effects would be of great value for improving livestock growth and economic value of livestock. The objective of our work was to use the CRISPR-Cas9 genetic engineering tool to generate deletions of different elements in the myostatin promoter in order to decrease the level of expression and obtain an attenuated phenotype without the detrimental consequences of an inactivating mutation. To achieve this objective 4 different small guide RNA (sgRNA) targeting the promoter near the mutation were designed with PAM positions from transcription starting site of −1577, −689, −555, and −116. These sgRNA were cloned individually into the Cas9 plasmids (px461, and px462; Addgene®). These plasmids allow for a dual puromycin resistance (px462) and green fluorescent protein (px461) selection. We first tested the functionality of these sgRNA in vitro by co-transfecting bovine fetal fibroblasts with a combination of both plasmids (Set 1 = sgRNA 1–4; Set 2 = sgRNA 2–3). Cells were exposed to puromycin (0.2 µg mL−1) for 72 h, then single and mixed colonies positive for green fluorescent protein expression were separated for propagation. The DNA was extracted for PCR amplification of the targeted region. Multiple deletions and a few insertion events were observed after PCR, bands were cloned into TOPO® vector (Thermo Fisher Scientific, Waltham, MA, USA) and sequenced. Sequencing results confirmed the PCR products as insertions or deletions in the myostatin promoter region. We proceeded to modify the myostatin promoter directly in bovine zygotes. For this, IVF-derived zygotes were randomly assigned to 3 different treatment groups Set 1, Set 2, or Null (no sgRNA) for microinjections. Each zygote was injected with ~100 pL of trophectoderm buffer containing 50 ng µL−1 of total sgRNA, 10 ng µL−1 of Cas9 mRNA, and 30 ng µL−1 of Cas9 protein with 1 mg mL−1 of fluorescent dextran. Day 7 post-IVF blastocysts were lysed and DNA was extracted for PCR amplification of the target region. In Set 1, 16 of 19 embryos (94.12%) were successfully edited, whereas in Set 2 there were 11 of 17 embryos (64.7%) edited. In both sets of sgRNA there was a high degree of mosaicism, with only 1 embryo demonstrating a homozygous deletion. In conclusion, CRISPR/Cas9 acts over the course of the first few cleavage divisions Further research is necessary to refine the CRISPR/Cas9 system for inducing genetic mutations in bovine embryos.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. 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Development of Dictyostelium discoideum as a model to identify evolutionarily-conserved virulence factors in Escherichia coli

Escherichia coli are a typical component of mammalian gut microbiota; however, a number of pathogenic strains remain a health concern for developing countries. Identification and disruption of virulence factors that promote infection could lead to reduction in infection. To identify novel bacterial virulence factors, we are using the soil amoeba, Dictyostelium discoideum, which preys upon bacteria, including E. coli, in the soil, as a model for mammalian phagocytic cells. Using random mutagenesis, we have created mutant stocks of MG1655 E. coli. These stocks were fed to D. discoideum, enriching the culture and selecting for mutants that were resistant to killing upon phagocytosis. After several rounds of selection, resistant mutant strains were isolated, and we found that some strains showed up to 100-fold increase in survival over a 2 h period. Once isolated, the genomes of the resistant mutant strains were sequenced and the sequences compared to that of the initial WT strain using Illumina’s MiSeq technology. While analyzing the sequences from these mutant strains, we found mutations in several potential genes of interest and are working to characterize their roles in the cell. We are testing E. coli strains reconstituted with specific mutations to identify particular mutations that are associated with phagocytosis-resistant phenotypes. These studies are aimed at identifying particular bacterial genes that may be involved in regulation of virulence. In addition, given that the development of mechanisms to resist D. discoideum predation may have contributed to the selection and maintenance of bacterial virulence factors against mammalian hosts, these studies may provide insight on the evolution of host-pathogen interactions.

94 EFFECTS OF 6- OR 12-HOUR CULTURE IN A Micro Q STRAW INCUBATOR ON DEVELOPMENT OF IN VITRO-PRODUCED BOVINE EMBRYOS

Transporting in vitro-produced (IVP) embryos can be challenging when an embryo transfer destination is more than 6 h away or electricity is not available on site to unload embryos for transfer. The objective of this study was to determine if development rates would be compromised for Day 6.5 IVP embryos when placed in warmed Vigro holding medium (Vetoquinol, Pullman, WA, USA) loaded and plugged into 1/4 cc straws (Professional Embryo Transfer Services, Canton, TX, USA) for a period of either 6 or 12 h in a 38.5°C Micro Q straw block incubator (Micro Q iQ1T 64). Bovine oocytes were shipped and matured in transit from a commercial abattoir (DeSoto Biosciences, Seymour, TN, USA), fertilized (IVF = Day 0) with frozen-thawed semen, and cultured in Bovine Evolve (Zenith Biotech, Guilford, CT, USA) supplemented with 4 mg mL–1 BSA (Probumin, EMD Millipore, Norcross, GA, USA) under oil in a 5% CO2, 5%O2, 90% N2 humidified incubator (Pryor et al. 2011 Theriogenology 75, 24–33). Cleavage rates of 87.7% (664/757) from three replicates produced 273 (36.0%) viable embryos on Day 6.5 post-IVF, which were evenly distributed by IETS stage (4–7) and grade (1 and 2) into three treatment groups (0 = control, 6 or 12 h straw incubation) before in vitro culture for an additional 24 h. For each replicate, the average embryo stage was calculated by multiplying the number of embryos in each treatment by their IETS stage and dividing by total embryos per group. The change in stage for each treatment was calculated by subtracting the initial average stage from the final average stage on Day 8. Grade 1 and 2 embryos at stage 6–8 were counted and used to calculate total viable rates. Day 8 (post-IVF) embryos were fixed in cold methanol, washed in PBS/0.1%Tween 20, mounted in 10 μg mL–1 Hoechst 33342/glycerol and viewed under UV light to count nuclei. Percentage data were transformed using arcsine square root function before analysis, and means were compared using a one-way ANOVA and Tukey’s HSD. Although viability decreased with increasing time in straw incubation, there were no statistical differences between control, 6 and 12 h treatments for total viable rates (90.8, 80.3, and 70.8%, respectively). Average embryo stage on Day 8 for control, 6 and 12 h (7.0 ± 0.66, 6.6 ± 0.24, and 6.2 ± 0.30 s.e.m., respectively) was not different, but tended to be higher in control (P = 0.08). The change in stage, however, was different between control and 12 h (1.46 ± 0.33 and 0.66 ± 0.24, respectively; P < 0.05). Likewise, cell numbers were greater in control and 6 h embryos compared with 12 h straw incubation (149.8 ± 9.14, 138.7 ± 7.94, and 101.8 ± 5.29; n = 47, 50, and 46, respectively P < 0.01). In conclusion, 6.5 day IVP embryos held in warm Vigro holding medium for 12 h in 1/4 cc straws fail to develop at the same rate and incurred lower cell counts than either control or 6 h treatments. Further research to evaluate pregnancy rates following transfer and utilising different incubation or media and/or temperature is warranted to further evaluate the utility of in straw incubation for extended periods of time.