Histone H2AX Is Phosphorylated at Sites of Retroviral DNA Integration but Is Dispensable for Postintegration Repair

The histone variant H2AX is rapidly phosphorylated (denoted {gamma}H2AX) in large chromatin domains (foci) flanking double strand DNA (dsDNA) breaks that are produced by ionizing radiation or genotoxic agents and during V(D)J recombination. H2AX-deficient cells and mice demonstrate increased sensitivity to dsDNA break damage, indicating an active role for {gamma}H2AX in DNA repair; however, {gamma}H2AX formation is not required for V(D)J recombination. The latter finding has suggested a greater dependence on {gamma}H2AX for anchoring free broken ends versus ends that are held together during programmed breakage-joining reactions. Retroviral DNA integration produces a unique intermediate in which a dsDNA break in host DNA is held together by the intervening viral DNA, and such a reaction provides a useful model to distinguish {gamma}H2AX functions. We found that integration promotes transient formation of {gamma}H2AX at retroviral integration sites as detected by both immunocytological and chromatin immunoprecipitation methods. These results provide the first direct evidence for the association of newly integrated viral DNA with a protein species that is an established marker for the onset of a DNA damage response. We also show that H2AX is not required for repair of the retroviral integration intermediate as determined by stable transduction. These observations provide independent support for an anchoring model for the function of {gamma}H2AX in chromatin repair

Mapping pneumonia research: a systematic analysis of UK investments and published outputs 1997–2013

BackgroundThe burden of pneumonia continues to be substantial, particularly among the poorest in global society. We describe here the trends for UK pneumonia R&D investment and published outputs, and correlate with 2013 global mortality.MethodsData related to awards to UK institutions for pneumonia research from 1997 to 2013 were systematically sourced and categorised by disease area and type of science. Investment was compared to mortality figures in 2010 and 2013 for pneumonia, tuberculosis and influenza. Investment was also compared to publication data.ResultsOf all infectious disease research between 2011 and 2013 (£917.0 million), £28.8 million (3.1%) was for pneumonia. This was an absolute and proportionate increase from previous time periods. Translational pneumonia research (33.3%) received increased funding compared with 1997–2010 where funding was almost entirely preclinical (87.5%, here 30.9%), but high-burden areas such as paediatrics, elderly care and antimicrobial resistance received little investment. Annual investment remains volatile; publication temporal trends show a consistent increase. When comparing investment to global burden with a novel ‘investment by mortality observed’ metric, tuberculosis (£48.36) and influenza (£484.21) receive relatively more funding than pneumonia (£43.08), despite investment for pneumonia greatly increasing in 2013 compared to 2010 (£7.39). Limitations include a lack of private sector data and the need for careful interpretation of the comparisons with burden, plus categorisation is subjective.ConclusionsThere has been a welcome increase for pneumonia funding awarded to UK institutions in 2011–2013 compared with 1997–2010, along with increases for more translational research. Published outputs relating to pneumonia rose steadily from 1997 to 2013. Investment relative to mortality for pneumonia has increased, but it remains low compared to other respiratory infections and clear inequities remain. Analyses that measure investments in pneumonia can provide an insight into funding trends and research gaps.Research in contextPneumonia continues to be a high-burden illness around the globe. This paper shows that although research funding is increasing in the UK (between 1997 and 2013), it remains poorly funded compared to other important respiratory infectious diseases such as tuberculosis and influenza. Publications about pneumonia have been steadily increasing over time, indicating continuing academic and clinical interest in the topic. Though global mortality of pneumonia is declining, it should still be an area of high priority for funders, policymakers and researchers

Environmental Tobacco Smoke Avoidance Among Pregnant African-American Nonsmokers

Background—Environmental tobacco smoke (ETS) exposure during pregnancy contributes to adverse infant health outcomes. Limited previous research has focused on identifying correlates of ETS avoidance. This study sought to identify proximal and more distal correlates of ETS avoidance early in pregnancy among African-American women. Methods—From a sample of low-income, black women (n=1044) recruited in six urban, prenatal care clinics (July 2001–October 2003), cotinine-confirmed nonsmokers with partners, household/ family members, or friends who smoked (n=450) were identified and divided into two groups: any past-7-day ETS exposure and cotinine-confirmed ETS avoidance. Bivariate and multivariate logistic regression analyses identified factors associated with ETS avoidance. Data were initially analyzed in 2004. Final models were reviewed and revised in 2007 and 2008. Results—Twenty-seven percent of pregnant nonsmokers were confirmed as ETS avoiders. In multivariate logistic regression analysis, the odds of ETS avoidance were increased among women who reported household smoking bans (OR=2.96; 95% CI=1.83, 4.77; p Conclusions—Social contextual factors were the strongest determinants of ETS avoidance during pregnancy. Results highlight the importance of prenatal screening to identify pregnant nonsmokers at risk, encouraging household smoking bans, gaining support from significant others, and fully understanding the interpersonal context of a woman’s pregnancy before providing behavioral counseling and advice to prevent ETS exposure

Wall-Modeled Lattice Boltzmann and Navier-Stokes Approaches for Separated Flows

Lattice Boltzmann (LB) and hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) methods within the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are applied to NASA's Revolutionary Computational Aerosciences (RCA) standard test cases for separated flows. A detailed comparison between the performance and accuracy of the two emerging numerical methodologies for turbulence resolving simulations, i.e. the LB and hybrid RANS/LES methods will be presented. This contribution addresses the RCA technical challenge to identify and down-select critical turbulence, transition, and numerical method technologies for 40% reduction in predictive error for standard turbulence separated flow test cases. Results for the 2D NASA wall-mounted hump and the axisymmetric transonic bump including time-averaged pressure coefficient, skin friction, and velocity pro les, as well as resolved and modeled Reynolds stresses for both numerical approaches will be presented and differences between LB and hybrid RANS/LES will be discussed

Genomic Counter-Stress Changes Induced by the Relaxation Response

Background: Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. It is believed to be the counterpart of the stress response that exhibits a distinct pattern of physiology and transcriptional profile. We hypothesized that RR elicitation results in characteristic gene expression changes that can be used to measure physiological responses elicited by the RR in an unbiased fashion. Methods/Principal Findings: We assessed whole blood transcriptional profiles in 19 healthy, long-term practitioners of daily RR practice (group M), 19 healthy controls (group $N_1$), and 20 $N_1$ individuals who completed 8 weeks of RR training (group $N_2$). 2209 genes were differentially expressed in group M relative to group $N_1$ (p<0.05) and 1561 genes in group $N_2$ compared to group $N_1$ (p<0.05). Importantly, 433 (p<$10_{−10}$) of 2209 and 1561 differentially expressed genes were shared among long-term (M) and short-term practitioners ($N_2$). Gene ontology and gene set enrichment analyses revealed significant alterations in cellular metabolism, oxidative phosphorylation, generation of reactive oxygen species and response to oxidative stress in long-term and short-term practitioners of daily RR practice that may counteract cellular damage related to chronic psychological stress. A significant number of genes and pathways were confirmed in an independent validation set containing 5 $N_1$ controls, 5 $N_2$ short-term and 6 M long-term practitioners. Conclusions/Significance: This study provides the first compelling evidence that the RR elicits specific gene expression changes in short-term and long-term practitioners. Our results suggest consistent and constitutive changes in gene expression resulting from RR may relate to long term physiological effects. Our study may stimulate new investigations into applying transcriptional profiling for accurately measuring RR and stress related responses in multiple disease settings

Relaxation Response Induces Temporal Transcriptome Changes in Energy Metabolism, Insulin Secretion and Inflammatory Pathways

The relaxation response (RR) is the counterpart of the stress response. Millennia-old practices evoking the RR include meditation, yoga and repetitive prayer. Although RR elicitation is an effective therapeutic intervention that counteracts the adverse clinical effects of stress in disorders including hypertension, anxiety, insomnia and aging, the underlying molecular mechanisms that explain these clinical benefits remain undetermined. To assess rapid time-dependent (temporal) genomic changes during one session of RR practice among healthy practitioners with years of RR practice and also in novices before and after 8 weeks of RR training, we measured the transcriptome in peripheral blood prior to, immediately after, and 15 minutes after listening to an RR-eliciting or a health education CD. Both short-term and long-term practitioners evoked significant temporal gene expression changes with greater significance in the latter as compared to novices. RR practice enhanced expression of genes associated with energy metabolism, mitochondrial function, insulin secretion and telomere maintenance, and reduced expression of genes linked to inflammatory response and stress-related pathways. Interactive network analyses of RR-affected pathways identified mitochondrial ATP synthase and insulin (INS) as top upregulated critical molecules (focus hubs) and NF-κB pathway genes as top downregulated focus hubs. Our results for the first time indicate that RR elicitation, particularly after long-term practice, may evoke its downstream health benefits by improving mitochondrial energy production and utilization and thus promoting mitochondrial resiliency through upregulation of ATPase and insulin function. Mitochondrial resiliency might also be promoted by RR-induced downregulation of NF-κB-associated upstream and downstream targets that mitigates stress

Correction: Genomic Counter-Stress Changes Induced by the Relaxation Response

The Competing Interests statement is incorrect. The correct Competing Interests statement is: The following authors hold or have held positions at the Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, which is paid by patients and their insurers for running the SMART-3RP and related relaxation/mindfulness clinical programs, markets related products such as books, DVDs, CDs and the like, and holds a patent pending (PCT/ US2012/049539 filed August 3, 2012) entitled Quantitative Genomics of the Relaxation Response : JAD, ALW, HB

Correction: Genomic Counter-Stress Changes Induced by the Relaxation Response

The Competing Interests statement is incorrect. The correct Competing Interests statement is: The following authors hold or have held positions at the Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, which is paid by patients and their insurers for running the SMART-3RP and related relaxation/mindfulness clinical programs, markets related products such as books, DVDs, CDs and the like, and holds a patent pending (PCT/ US2012/049539 filed August 3, 2012) entitled Quantitative Genomics of the Relaxation Response : JAD, ALW, HB