Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance.

Generally repressed by epigenetic mechanisms, retrotransposons represent around 40% of the murine genome. At the Agouti viable yellow (Avy) locus, an endogenous retrovirus (ERV) of the intracisternal A particle (IAP) class retrotransposed upstream of the agouti coat-color locus, providing an alternative promoter that is variably DNA methylated in genetically identical individuals. This results in variable expressivity of coat color that is inherited transgenerationally. Here, a systematic genome-wide screen identifies multiple C57BL/6J murine IAPs with Avy epigenetic properties. Each exhibits a stable methylation state within an individual but varies between individuals. Only in rare instances do they act as promoters controlling adjacent gene expression. Their methylation state is locus-specific within an individual, and their flanking regions are enriched for CTCF. Variably methylated IAPs are reprogrammed after fertilization and re-established as variable loci in the next generation, indicating reconstruction of metastable epigenetic states and challenging the generalizability of non-genetic inheritance at these regions.

Omics in Chlamydomonas for Biofuel Production.

In response to demands for sustainable domestic fuel sources, research into biofuels has become increasingly important. Many challenges face biofuels in their effort to replace petroleum fuels, but rational strain engineering of algae and photosynthetic organisms offers a great deal of promise. For decades, mutations and stress responses in photosynthetic microbiota were seen to result in production of exciting high-energy fuel molecules, giving hope but minor capability for design. However, '-omics' techniques for visualizing entire cell processing has clarified biosynthesis and regulatory networks. Investigation into the promising production behaviors of the model organism C. reinhardtii and its mutants with these powerful techniques has improved predictability and understanding of the diverse, complex interactions within photosynthetic organisms. This new equipment has created an exciting new frontier for high-throughput, predictable engineering of photosynthetically produced carbon-neutral biofuels.

Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic.

The expression of endogenous retrotransposable elements, including long interspersed nuclear element 1 (LINE-1 or L1) and human endogenous retrovirus, accompanies neoplastic transformation and infection with viruses such as HIV. The ability to engender immunity safely against such self-antigens would facilitate the development of novel vaccines and immunotherapies. In this article, we address the safety and immunogenicity of vaccination with these elements. We used immunohistochemical analysis and literature precedent to identify potential off-target tissues in humans and establish their translatability in preclinical species to guide safety assessments. Immunization of mice with murine L1 open reading frame 2 induced strong CD8 T cell responses without detectable tissue damage. Similarly, immunization of rhesus macaques with human LINE-1 open reading frame 2 (96% identity with macaque), as well as simian endogenous retrovirus-K Gag and Env, induced polyfunctional T cell responses to all Ags, and Ab responses to simian endogenous retrovirus-K Env. There were no adverse safety or pathological findings related to vaccination. These studies provide the first evidence, to our knowledge, that immune responses can be induced safely against this class of self-antigens and pave the way for investigation of them as HIV- or tumor-associated targets.

Investigating the Unique Ability of Trichodesmium To Fix Carbon and Nitrogen Simultaneously Using MiMoSA.

The open ocean is an extremely competitive environment, partially due to the dearth of nutrients. Trichodesmium erythraeum, a marine diazotrophic cyanobacterium, is a keystone species in the ocean due to its ability to fix nitrogen and leak 30 to 50% into the surrounding environment, providing a valuable source of a necessary macronutrient to other species. While there are other diazotrophic cyanobacteria that play an important role in the marine nitrogen cycle, Trichodesmium is unique in its ability to fix both carbon and nitrogen simultaneously during the day without the use of specialized cells called heterocysts to protect nitrogenase from oxygen. Here, we use the advanced modeling framework called multiscale multiobjective systems analysis (MiMoSA) to investigate how Trichodesmium erythraeum can reduce dimolecular nitrogen to ammonium in the presence of oxygen. Our simulations indicate that nitrogenase inhibition is best modeled as Michealis-Menten competitive inhibition and that cells along the filament maintain microaerobia using high flux through Mehler reactions in order to protect nitrogenase from oxygen. We also examined the effect of location on metabolic flux and found that cells at the end of filaments operate in distinctly different metabolic modes than internal cells despite both operating in a photoautotrophic mode. These results give us important insight into how this species is able to operate photosynthesis and nitrogen fixation simultaneously, giving it a distinct advantage over other diazotrophic cyanobacteria because they can harvest light directly to fuel the energy demand of nitrogen fixation. IMPORTANCE Trichodesmium erythraeum is a marine cyanobacterium responsible for approximately half of all biologically fixed nitrogen, making it an integral part of the global nitrogen cycle. Interestingly, unlike other nitrogen-fixing cyanobacteria, Trichodesmium does not use temporal or spatial separation to protect nitrogenase from oxygen poisoning; instead, it operates photosynthesis and nitrogen fixation reactions simultaneously during the day. Unfortunately, the exact mechanism the cells utilize to operate carbon and nitrogen fixation simultaneously is unknown. Here, we use an advanced metabolic modeling framework to investigate and identify the most likely mechanisms Trichodesmium uses to protect nitrogenase from oxygen. The model predicts that cells operate in a microaerobic mode, using both respiratory and Mehler reactions to dramatically reduce intracellular oxygen concentrations.

Voltammetric determination of inorganic arsenic in mildly acidified (pH 4.7) groundwaters from Mexico and India.

Routine monitoring of inorganic arsenic in groundwater using sensitive, reliable, easy-to-use and affordable analytical methods is integral to identifying sources, and delivering appropriate remediation solutions, to the widespread global issue of arsenic pollution. Voltammetry has many advantages over other analytical techniques, but the low electroactivity of arsenic(V) requires the use of either reducing agents or relatively strong acidic conditions, which both complicate the analytical procedures, and require more complex material handling by skilled operators. Here, we present the voltammetric determination of total inorganic arsenic in conditions of near-neutral pH using a new commercially available 25 µm diameter gold microwire (called the Gold Wirebond), which is described here for the first time. The method is based on the addition of low concentrations of permanganate (10 µM MnO4-) which fulfils two roles: (1) to ensure that all inorganic arsenic is present as arsenate by chemically oxidising arsenite to arsenate and, (2) to provide a source of manganese allowing the sensitive detection of arsenate by anodic stripping voltammetry at a gold electrode. Tests were carried out in synthetic solutions of various pH (ranging from 4.7 to 9) in presence/absence of chloride. The best response was obtained in 0.25 M chloride-containing acetate buffer resulting in analytical parameters (limit of detection of 0.28 µg L-1 for 10 s deposition time, linear range up to 20 µg L-1 and a sensitivity of 63.5 nA ppb-1. s-1) better than those obtained in acidic conditions. We used this new method to measure arsenic concentrations in contrasting groundwaters: the reducing, arsenite-rich groundwaters of India (West Bengal and Bihar regions) and the oxidising, arsenate-rich groundwaters of Mexico (Guanajuato region). Very good agreement was obtained in all groundwaters with arsenic concentrations measured by inductively coupled plasma-mass spectrometry (slope = +1.029, R2 = 0.99). The voltammetric method is sensitive, faster than other voltammetric techniques for detection of arsenic (typically 10 min per sample including triplicate measurements and 2 standard additions), easier to implement than previous methods (no acidic conditions, no chemical reduction required, reproducible sensor, can be used by non-voltammetric experts) and could enable cheaper groundwater surveying campaigns with in-the-field analysis for quick data reporting, even in remote communities.

Regulation of apoAI processing by procollagen C-proteinase enhancer-2 and bone morphogenetic protein-1.

Given the increased prevalence of cardiovascular disease in the world, the search for genetic variations controlling the levels of risk factors associated with the development of the disease continues. Multiple genetic association studies suggest the involvement of procollagen C-proteinase enhancer-2 (PCPE2) in modulating HDL-C levels. Therefore biochemical and mechanistic studies were undertaken to determine whether there might be a basis for a role of PCPE2 in HDL biogenesis. Our studies indicate that PCPE2 accelerates the proteolytic processing of pro-apolipoprotein (apo) AI by enhancing the cleavage of the hexapeptide extension present at the N terminus of apoAI. Surface Plasmon Resonance and immunoprecipitation studies indicate that PCPE2 interacts with BMP-1 and pro-apoAI to form a ternary pro-apoAI/BMP-1/PCPE2 complex. The most favorable interaction among these proteins begins with the association of BMP-1 to pro-apoAI followed by the binding of PCPE2 which further stabilizes the complex. PCPE2 resides, along with apoAI, on the HDL fraction of lipoproteins in human plasma supporting a relationship between HDL and PCPE2. Taken together, the findings from our studies identify a new player in the regulation of apoAI post-translational processing and open a new avenue to the study of mechanisms involved in the regulation of apoAI synthesis, HDL levels, and potentially, cardiovascular disease.

Monte Carlo-based adaptive EPID dose kernel accounting for different field size responses of imagers.

The aim of this study is to present an efficient method to generate imager-specific Monte Carlo (MC)-based dose kernels for amorphous silicon-based electronic portal image device dose prediction and determine the effective backscattering thicknesses for such imagers. EPID field size-dependent responses were measured for five matched Varian accelerators from three institutions with 6 MV beams at the source to detector distance (SDD) of 105 cm. For two imagers, measurements were made with and without the imager mounted on the robotic supporting arm. Monoenergetic energy deposition kernels with 0-2.5 cm of water backscattering thicknesses were simultaneously computed by MC to a high precision. For each imager, the backscattering thickness required to match measured field size responses was determined. The monoenergetic kernel method was validated by comparing measured and predicted field size responses at 150 cm SDD, 10 x 10 cm2 multileaf collimator (MLC) sliding window fields created with 5, 10, 20, and 50 mm gaps, and a head-and-neck (H&N) intensity modulated radiation therapy (IMRT) patient field. Field size responses for the five different imagers deviated by up to 1.3%. When imagers were removed from the robotic arms, response deviations were reduced to 0.2%. All imager field size responses were captured by using between 1.0 and 1.6 cm backscatter. The predicted field size responses by the imager-specific kernels matched measurements for all involved imagers with the maximal deviation of 0.34%. The maximal deviation between the predicted and measured field size responses at 150 cm SDD is 0.39%. The maximal deviation between the predicted and measured MLC sliding window fields is 0.39%. For the patient field, gamma analysis yielded that 99.0% of the pixels have gamma < 1 by the 2%, 2 mm criteria with a 3% dose threshold. Tunable imager-specific kernels can be generated rapidly and accurately in a single MC simulation. The resultant kernels are imager position independent and are able to predict fields with varied incident energy spectra and a H&N IMRT patient field. The proposed adaptive EPID dose kernel method provides the necessary infrastructure to build reliable and accurate portal dosimetry systems.

Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems.

In natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in 'ideal' laboratory environments, cells can experience a high degree of heterogeneity in their environments. Unfortunately, most of the metabolic modeling approaches that are currently used assume ideal conditions and that each cell is identical, limiting their application to pure cultures in well-mixed vessels. Here we describe our development of Multiscale Multiobjective Systems Analysis (MiMoSA), a metabolic modeling approach that can track individual cells in both space and time, track the diffusion of nutrients and light and the interaction of cells with each other and the environment. As a proof-of concept study, we used MiMoSA to model the growth of Trichodesmium erythraeum, a filamentous diazotrophic cyanobacterium which has cells with two distinct metabolic modes. The use of MiMoSA significantly improves our ability to predictively model metabolic changes and phenotype in more complex cell cultures.

Comparison of two methods to compute the absorbed dose to water for photon beams.

Cross-validation was performed between an in-house dose-to-water (D(water)) calculation method used at Virginia Commonwealth University and the VMC++ D(water) calculation during particle transport. The effect of Monte Carlo statistical precision was observed. The results of the two calculations on homogeneous phantoms with densities varying from 0.3 g cm(-3) to 2.95 g cm(-3) were compared. Depth and field size dependence were tested. D(water) calculations were compared in a bone-lung-bone phantom to observe how the calculations differed in steep density gradients. The methods were compared for five prostate and five head-and-neck (H/N) patient cases as well. In all phantom tests, the differences between the two D(water) calculations were less than 1%. The largest differences in patient cases was a prostate case in which 1% of the voxels with doses greater than 50% of the maximum dose had a systematic difference corresponding to 1.16% of the maximum dose. All differences were clinically insignificant.

The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum.

BACKGROUND: Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we have created the first genome-scale metabolic network reconstruction of the nitrogen fixing cyanobacterium T. erythraeum and used genome-scale modeling approaches to investigate carbon and nitrogen fluxes as well as growth and equilibrium population composition. RESULTS: We created a genome-scale reconstruction of T. erythraeum with 971 reactions, 986 metabolites, and 647 unique genes. We then used data from previous studies as well as our own laboratory data to establish a biomass equation and two distinct submodels that correspond to the two cell types formed by T. erythraeum. We then use flux balance analysis and flux variability analysis to generate predictions for how metabolism is distributed to account for the unique productivity of T. erythraeum. Finally, we used in situ data to constrain the model, infer time dependent population compositions and metabolite production using dynamic Flux Balance Analysis. We find that our model predicts equilibrium compositions similar to laboratory measurements, approximately 15.5% diazotrophs for our model versus 10-20% diazotrophs reported in literature. We also found that equilibrium was the most efficient mode of growth and that equilibrium was stoichiometrically mediated. Moreover, the model predicts that nitrogen leakage is an essential condition of optimality for T. erythraeum; cells leak approximately 29.4% total fixed nitrogen when growing at the optimal growth rate, which agrees with values observed in situ. CONCLUSION: The genome-metabolic network reconstruction allows us to use constraints based modeling approaches to predict growth and optimal cellular composition in T. erythraeum colonies. Our predictions match both in situ and laboratory data, indicating that stoichiometry of metabolic reactions plays a large role in the differentiation and composition of different cell types. In order to realize the full potential of the model, advance modeling techniques which account for interactions between colonies, the environment and surrounding species need to be developed.

Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay.

Cyclic GMP-AMP synthase (cGAS) initiates the innate immune system in response to cytosolic dsDNA. After binding and activation from dsDNA, cGAS uses ATP and GTP to synthesize 2', 3' -cGAMP (cGAMP), a cyclic dinucleotide second messenger with mixed 2'-5' and 3'-5' phosphodiester bonds. Inappropriate stimulation of cGAS has been implicated in autoimmune disease such as systemic lupus erythematosus, thus inhibition of cGAS may be of therapeutic benefit in some diseases; however, the size and polarity of the cGAS active site makes it a challenging target for the development of conventional substrate-competitive inhibitors. We report here the development of a high affinity (KD = 200 nM) inhibitor from a low affinity fragment hit with supporting biochemical and structural data showing these molecules bind to the cGAS active site. We also report a new high throughput cGAS fluorescence polarization (FP)-based assay to enable the rapid identification and optimization of cGAS inhibitors. This FP assay uses Cy5-labelled cGAMP in combination with a novel high affinity monoclonal antibody that specifically recognizes cGAMP with no cross reactivity to cAMP, cGMP, ATP, or GTP. Given its role in the innate immune response, cGAS is a promising therapeutic target for autoinflammatory disease. Our results demonstrate its druggability, provide a high affinity tool compound, and establish a high throughput assay for the identification of next generation cGAS inhibitors.

Determination of perchlorate in drinking water by ion chromatography using macrocycle-based concentration and separation methods.

Macrocycle-based ion chromatography provides a convenient, reliable method for the determination of perchlorate ion, which is currently of great interest to the environmental community. This study shows that effective perchlorate determinations can be made using standard conductimetric detection by combining an 18-crown-6-based mobile phase with an underivatized reversed-phase mobile phase ion chromatography (MPIC) column. One unique feature of this method is the flexibility in column capacity that is achieved through simple variations in eluent concentrations of 18-crown-6 and KOH, facilitating the separation of target analyte anions such as perchlorate. Using a standard anion exchange column as concentrator makes possible the determination of perchlorate as low as 0.2 ug/L in low ionic strength matrices. Determination of perchlorate at the sub-ug/L level in pure water and in spiked local city hard water samples with high background ion concentrations can be achieved this way. However, like other IC techniques, this method is challenged to achieve analyses at the ug/L level in the demanding high ionic strength matrix described by the United States Environmental Protection Agency (EPA) (1,000 mg/L chloride, sulfate and carbonate). We approached this challenge by use of the Cryptand C1 concentrator column, provided by Dionex Corporation, to effectively preconcentrate perchlorate while reducing background ion concentrations in the high ionic strength matrix. The retention characteristics of the concentrator column were studied in order to maximize its effectiveness for perchlorate determinations. The method makes possible the determination of perchlorate at the 5 ug/L level in the highest ionic strength matrix described by the EPA.

Sensory characteristics of chronic non-specific low back pain: a subgroup investigation.

It has been proposed that patients with chronic non-specific low back pain (CNSLBP) can be broadly classified based on clinical features that represent either predominantly a mechanical pain (MP) or non-mechanical pain (NMP) profile. The aim of this study was to establish if patients with CNSLBP who report features of NMP demonstrate differences in pain thresholds compared to those who report MP characteristics and pain-free controls. This study was a cross-sectional design investigating whether pressure pain threshold (PPT) and/or cold pain threshold (CPT) at three anatomical locations differed between patients with mechanical CNSLBP (n = 17) versus non-mechanical CNSLBP (n = 19 and healthy controls (n = 19) whilst controlling for confounders. The results of this study provide evidence of increased CPT at the wrist in the NMP profile group compared to both the MP profile and control subjects, when controlling for gender, sleep and depression (NMP versus MP group Odds Ratio (OR): 18.4, 95% confidence interval (CI): 2.5-133.1, p = 0.004). There was no evidence of lowered PPT at any site after adjustment for confounding factors. Those with an MP profile had similar pain thresholds to pain-free controls, whereas the NMP profile group demonstrated elevated CPT's consistent with central amplification of pain. These findings may represent different pain mechanisms associated with these patient profiles and may have implications for targeted management.

Development and characterization of a JAK-2-specific antibody suitable for immunohistochemical investigative studies.

Janus kinases (JAKs) are tyrosine kinases called JAK-1, JAK-2, JAK-3, and Tyk-2, which have been shown to participate in the signaling pathways of several cytokines that are believed to play a key role in several autoimmune-mediated disorders including rheumatoid arthritis (RA). However, the availability of JAK-specific antibodies to be used in investigative efficacy studies in RA models is very limited. Therefore, in this study we developed and characterized a JAK-2-specific antibody that was used to evaluate its immunohistochemical expression in the joints of a rat adjuvant-induced arthritis (rAIA) RA preclinical model. An immunogen peptide sequence design was used to generate JAK-2-specific mouse, rat, and human polyclonal antibodies. JAK-2 plasmid cDNA was then generated and HEK293 transfected cell lines, gel electrophoresis, immunoblotting, and immunohistochemistry were used to further characterize the generated JAK-2 antibodies. We show that the generated JAK-2 antibody exhibits specificity and lacks cross-reactivity to JAK-1 and JAK-3. In addition, marked JAK-2 expression is shown in the rAIA in mixed inflammatory cells (macrophages and neutrophils), mast cells, and bone marrow elements. In conclusion, we show the development and characterization of a JAK-2-specific antibody that can be used in investigative and mechanistic studies such as preclinical efficacy models.

Comparison of sources of exit fluence variation for IMRT.

The fluence exiting a patient during beam delivery can be used as treatment delivery quality assurance, either by direct comparison with expected exit fluences or by backprojection to reconstruct the patient dose. Multiple possible sources of measured exit fluence deviations exist, including changes in the beam delivery and changes in the patient anatomy. The purpose of this work is to compare the deviations caused by these sources. Machine delivery-related variability is measured by acquiring multiple dosimetric portal images (DPIs) of several test fields without a patient/phantom in the field over a time period of 2 months. Patient anatomy-related sources of fluence variability are simulated by computing transmission DPIs for a prostate patient using the same incident fluence for 11 different computed tomography (CT) images of the patient anatomy. The standard deviation (SD) and maximum deviation of the exit fluence, averaged over 5 mm x 5 mm square areas, is calculated for each test set. Machine delivery fluence SDs as large as 1% are observed for a sample patient field and as large as 2.5% for a picket-fence dMLC test field. Simulations indicate that day-to-day patient anatomy variations induce exit fluence SDs as large as 3.5%. The largest observed machine delivery deviations are 4% for the sample patient field and 7% for the picket-fence field, while the largest difference for the patient anatomy-related source is 8.5%. Since daily changes in patient anatomy can result in substantial exit fluence deviations, care should be taken when applying fluence back-projection to ensure that such deviations are properly attributed to their source.

Anion binding by a tetradipicolylamine-substituted resorcinarene cavitand.

Anion binding has been achieved with a resorcinarene substituted with four 2,2'-dipicolylamine moieties on the upper rim. The four dipicolylamine groups reside in proximity on one rim of the cavitand. The dipicolylamine groups were protonated with triflic acid to provide the cationic ammonium sites for anion binding. This anion receptor binds strongly to anions of different geometries, such as H(2)PO(4)(-), Cl(-), F(-), CH(3)CO(2)(-), HSO(4)(-), and NO(3)(-). The association constants for binding these anions are large, on the order of log K = 5 in CD(3)CN, a solvent of intermediate dielectric constant. These values represent significant binding compared to other cavitands with nitrogen pendant groups. Evidence suggests that the cavitand provides two identical receptor sites formed by two dipicolylamine groups, facilitating the simultaneous binding of two anions. Intramolecular binding of anions between two protonated dipicolylamine groups is indicated on the basis of the comparison to a structurally similar monomeric analogue and by semiempirical PM3 molecular modeling. Titrations with the analogue result in much weaker anion association, even at high concentrations, indicating the importance of proximity and preorganization of sites on the cavitand upper rim.