Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects.

BACKGROUND: Smoking remains one of the leading preventable causes of death. Smoking leaves a strong signature on the blood methylome as shown in multiple studies using the Infinium HumanMethylation450 BeadChip. Here, we explore novel blood methylation smoking signals on the Illumina MethylationEPIC BeadChip (EPIC) array, which also targets novel CpG-sites in enhancers. METHOD: A smoking-methylation meta-analysis was carried out using EPIC DNA methylation profiles in 1407 blood samples from four UK population-based cohorts, including the MRC National Survey for Health and Development (NSHD) or 1946 British birth cohort, the National Child Development Study (NCDS) or 1958 birth cohort, the 1970 British Cohort Study (BCS70), and the TwinsUK cohort (TwinsUK). The overall discovery sample included 269 current, 497 former, and 643 never smokers. Replication was pursued in 3425 trans-ethnic samples, including 2325 American Indian individuals participating in the Strong Heart Study (SHS) in 1989-1991 and 1100 African-American participants in the Genetic Epidemiology Network of Arteriopathy Study (GENOA). RESULTS: Altogether 952 CpG-sites in 500 genes were differentially methylated between smokers and never smokers after Bonferroni correction. There were 526 novel smoking-associated CpG-sites only profiled by the EPIC array, of which 486 (92%) replicated in a meta-analysis of the American Indian and African-American samples. Novel CpG sites mapped both to genes containing previously identified smoking-methylation signals and to 80 novel genes not previously linked to smoking, with the strongest novel signal in SLAMF7. Comparison of former versus never smokers identified that 37 of these sites were persistently differentially methylated after cessation, where 16 represented novel signals only profiled by the EPIC array. We observed a depletion of smoking-associated signals in CpG islands and an enrichment in enhancer regions, consistent with previous results. CONCLUSION: This study identified novel smoking-associated signals as possible biomarkers of exposure to smoking and may help improve our understanding of smoking-related disease risk.

Increasing Access to Physical Activity Within Low Income and Diverse Communities: A Systematic Review.

OBJECTIVE: The purpose of this review is to uncover some best practices for increasing access to physical activity opportunities by examining efforts used within low income and diverse communities. The theoretical lens used is from the Active Living by Design (ALbD) Community Action Model, with a focus on the 6 essential practices (health equity focus, community engagement, facilitative leadership, sustainable thinking, culture of learning, and strategic communication) describing how partnerships can guide and sustain meaningful change in a community. METHODS: A 2-step process guided the literature search. In step 1, 4 databases (PubMed, Psych INFO, Social Science Citation Index, and Cochrane Library) were searched using Boolean connections and variations in the key terms. Step 2 assessed articles by title, abstract, and full text to determine whether the studies met the inclusion and exclusion criteria guided by Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Additionally, included articles were compared against the 6 essential practices outlined by the ecological framework, ALbD. RESULTS: Of 1775 total articles, 14 studies met inclusion criteria. Most of the studies were case studies located in the United States using several different approaches including, changes in the built environment, implementation of a community-based physical activity program, creating partnerships to leverage resources, and policy change. This review compared the 14 studies against the 6 essential practices of the ALbD model and found 2 studies that met all 6 criteria, and only a few studies meeting more than 2 criteria. CONCLUSIONS: Overall, the conclusions are 2-fold, (1) only 14 cases demonstrate success in increasing access to physical activity opportunities, suggesting that more can be done to address inequalities. (2) Of the existing efforts, few utilize crucial components to create a sustainable change in the community. Future research should take into consideration the ALbD ecological framework, the best existing theory for this type of work, to guide the creation and implementation of a sustainable community access effort.

Childhood adversity and DNA methylation in two population-based cohorts.

Childhood adversity affects later health, but the underlying molecular mechanisms are unclear. Although there is some evidence from animal models and case-control studies of a role for DNA methylation, evidence from human population-based studies is limited. In two cohorts (mothers from the Avon Longitudinal Study of Parents and Children, ALSPAC, n = 780 and women from the MRC National Survey of Health and Development, NSHD, n = 552), we assessed the association of seven adverse childhood experiences (ACEs: parental physical illness, parental mental illness, parental death, parental separation, suboptimal maternal bonding, childhood illness and child maltreatment) as well as their combination (ACE score) with genome-wide DNA methylation levels measured using the Illumina Infinium HumanMethylation450 BeadChip in peripheral blood at mean age 47 years (ALSPAC) and in buccal cells at age 53 years (NSHD). CpG sites with a genome-wide false discovery rate (FDR) below 0.05 and differentially methylated regions (DMRs) with one-step Sidák correction p-values below 0.05 in each cohort were examined in the other cohort. No individual CpG sites replicated across cohorts. However, nine DMRs replicated across cohorts respectively associated with the ACE score (one region), parental mental illness (two regions), parental physical illness (three regions) and parental death (three regions). These observations indicate that some adverse childhood experiences, notably those related to parental health, may leave imprints on peripheral DNA methylation that persist to mid-life.

25-hydroxyvitamin D, APOE ɛ4 genotype and cognitive function: findings from the 1958 British birth cohort.

Both high and low vitamin D statuses have been associated with lower memory function. Apolipoprotein E (APOE) ɛ4 alleles have been associated with reduced memory function, and separately with higher vitamin D concentrations. This report aims to examine if the presence of APOE ɛ4 alleles contributes to the relationship between vitamin D and memory function. A total of 4848 (46% female) participants from the 1958 British birth cohort had information on APOE genotypes and completed memory tests at 50 years, where 4644 also had 25-hydroxyvitamin D (25(OH)D) concentrations measured at 45 years. Both low and high 25(OH)D concentrations were associated with lower memory function after adjustment for number of APOE ɛ4 alleles (P curvature=0.02). There was evidence of interaction between APOE ɛ4 and 25(OH)D, suggesting the association between 25(OH)D concentrations and memory function is different for those with two APOE ɛ4 alleles compared with those with zero or one APOE ɛ4 alleles (recessive model P interaction=0.01). Among participants with two APOE ɛ4 alleles, higher 25(OH)D concentrations were associated with higher memory function, whereas in others, memory scores were slightly lower for individuals with higher versus lower concentrations. Further studies are required to replicate these findings.

Saccharomyces cerevisiae Rbg1 protein and its binding partner Gir2 interact on Polyribosomes with Gcn1.

Rbg1 is a previously uncharacterized protein of Saccharomyces cerevisiae belonging to the Obg/CgtA subfamily of GTP-binding proteins whose members are involved in ribosome function in both prokaryotes and eukaryotes. We show here that Rbg1 specifically associates with translating ribosomes. In addition, in this study proteins were identified that interact with Rbg1 by yeast two-hybrid screening and include Tma46, Ygr250c, Yap1, and Gir2. Gir2 contains a GI (Gcn2 and Impact) domain similar to that of Gcn2, an essential factor of the general amino acid control pathway required for overcoming amino acid shortage. Interestingly, we found that Gir2, like Gcn2, interacts with Gcn1 through its GI domain, and overexpression of Gir2, under conditions mimicking amino acid starvation, resulted in inhibition of growth that could be reversed by Gcn2 co-overexpression. Moreover, we found that Gir2 also cofractionated with polyribosomes, and this fractionation pattern was partially dependent on the presence of Gcn1. Based on these findings, we conclude that Rbg1 and its interacting partner Gir2 associate with ribosomes, and their possible biological roles are discussed.

Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques.

Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16 degrees C and 37 degrees C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.

The Vibrio harveyi GTPase CgtAV is essential and is associated with the 50S ribosomal subunit.

It was previously reported that unlike the other obg/cgtA GTPases, the Vibrio harveyi cgtAV is not essential. Here we show that cgtAV was not disrupted in these studies and is, in fact, essential for viability. Depletion of CgtAV did not result in cell elongation. CgtAV is associated with the large ribosomal particle. In light of our results, we predict that the V. harveyi CgtAV protein plays a similar essential role to that seen for Obg/CgtA proteins in other bacteria.

Biochemical properties of the Vibrio harveyi CgtAV GTPase.

Bacteria encode a number of relatively poorly characterized GTPases, including the essential, ribosome-associated Obg/CgtA proteins. In contrast to Ras-like proteins, it appears that the Obg/CgtA proteins bind guanine nucleotides with modest affinity and hydrolyze GTP relatively slowly. We show here that the Vibrio harveyi CgtA(V) exchanges guanine nucleotides rapidly and has a modest affinity for nucleotides, suggesting that these features are a universal property of the Obg/CgtA family. Interestingly, CgtA(V) possesses a significantly more rapid GTP hydrolysis rate than is typical of other family members, perhaps reflecting the diversity and specificity of bacterial ecological niches.

The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase.

CgtA(E)/Obg(E)/YhbZ is an Escherichia coli guanine nucleotide binding protein of the Obg/GTP1 subfamily whose members have been implicated in a number of cellular functions including GTP-GDP sensing, sporulation initiation, and translation. Here we describe a kinetic analysis of CgtA(E) with guanine nucleotides and show that its properties are similar to those of the Caulobacter crescentus homolog CgtA(C). CgtA(E) binds both GTP and GDP with moderate affinity, shows high guanine nucleotide exchange rate constants for both nucleotides, and has a relatively low GTP hydrolysis rate. We show that CgtA(E) is associated predominantly with the 50S ribosomal subunit. Interestingly, CgtA(E) copurifies with SpoT, a ribosome-associated ppGpp hydrolase/synthetase involved in the stress response. The interaction between CgtA(E) and SpoT was confirmed by reciprocal coprecipitation experiments and by two-hybrid assays. These studies raise the possibility that the ribosome-associated CgtA(E) is involved in the SpoT-mediated stress response.

Reactive sulfides relationship with metals in sediments from an eutrophicated estuary in Southeast Brazil.

The potential association of acid-volatile sulfides (AVS) and reactive (HCl soluble) Fe with the distribution of reactive trace metals (Cu, Cd, Ni, Pb and Zn) was investigated in sediment cores collected in the Iguaçu river estuarine system (Guanabara bay, Brazil), within the river (core R) and the bay (core B) areas. Moderate to extremely high AVS concentrations (33-314 micromol g(-1)) were found in the rapidly-accumulated sediments of this eutrophicated estuary. AVS showed significant correlations with Fe, Ni and Pb in core B, whereas no correlation between AVS and metals was observed in core R. Results suggest that the AVS:Fe molar ratio may often reflect the diagenetic conditions controlling the distribution of Cd and Cu in core B better than AVS and Fe levels themselves. A shift in the biogeochemical controls of metal distribution from the river to the open bay sediments is suggested, with a greater association of most metals with AVS and Fe in bay sediments.

TlpC, a novel chemotaxis protein in Rhodobacter sphaeroides, localizes to a discrete region in the cytoplasm.

TlpC is encoded in the second chemotaxis operon of Rhodobacter sphaeroides. This protein shows some homology to membrane-spanning chemoreceptors of many bacterial species but, unlike these, is essential for R. sphaeroides chemotaxis to all compounds tested. Genomic replacement of tlpC with a C-terminal gfp fusion demonstrated that TlpC localized to a discrete cluster within the cytoplasm. Immunogold electron microscopy also showed that TlpC localized to a cytoplasmic electron-dense region. Correct TlpC-GFP localization depended on the downstream signalling proteins, CheW3, CheW4 and CheA2, and was tightly linked to cell division. Newly divided cells contained a single cluster but, as the cell cycle progressed, a second cluster appeared close to the initial cluster. As elongation continued, these clusters moved apart so that, on septation, each daughter cell contained a single TlpC cluster. The data presented suggest that TlpC is either a cytoplasmic chemoreceptor responding to or integrating global signals of metabolic state or a novel and essential component of the chemotaxis signalling pathway. These data also suggest that clustering is essential for signalling and that a mechanism may exist for targeting and localizing proteins within the bacterial cytoplasm.

Analysis of the outer membrane proteome of Caulobacter crescentus by two-dimensional electrophoresis and mass spectrometry.

Caulobacter crescentus, a Gram negative alpha-purple bacterium that displays an invariant asymmetric cell division pattern, has become a key model system for the study of bacterial development. Membrane proteins play key roles in cell cycle events, both as components of landmark morphological structures and as critical elements in regulation of the cell cycle. Recent advances for the isolation and solubilization of bacterial membrane proteins prior to isoelectric focusing have significantly improved the separation of outer membrane proteins by two-dimensional (2-D) electrophoresis. In this work we describe the analysis of the outer membrane proteome of Caulobacter crescentus. Proteins were identified using 2-D gel electrophoresis and peptide mass fingerprinting by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. We identified 54 unique proteins out of which 41 were outer membrane proteins. Of the outer membrane proteins, 16 were identified as TonB-dependent receptor proteins. These studies were executed simultaneously with the Caulobacter genome sequencing project and advantages and limitations of proteomic analysis of a nonannotated genome are discussed. Finally, protein levels between cells grown in rich and minimal media are compared which demonstrates that many of the TonB-dependent receptor proteins are found at higher levels in minimal medium.

Impact of skin cancer prevention on outdoor aquatics staff: the Pool Cool program in Hawaii and Massachusetts.

BACKGROUND: Aquatic staff, including lifeguards, are exposed to intense sunlight for many hours each day and are likely to be at a relatively high risk for developing skin cancer. However, no interventions have been specifically directed to staff at outdoor swimming pool sites. METHODS: We conducted a randomized controlled trial among aquatic staff at 28 outdoor pool sites in Hawaii and Massachusetts. Intervention pools received sun protection education and control pools received education on child injury prevention. Staff in both arms received orientation sessions and led instruction during swim lessons. Analysis of covariance was used to compare and test for changes in outcome variables (sun protection habits and sunburning rates of aquatic staff) and pool protection policies. Surveys were completed at the beginning and end of the summer. RESULTS: Surveys were completed by 220 aquatics staff at baseline; 194 surveys were completed at posttest. Compared with staff at control pools, sun protection policies (P < 0.04) and sunburning rates (P < 0.05) improved at sun protection pools from baseline to posttest. However, the difference in the mean score of all sun protection habits between the two study groups was nonsignificant. CONCLUSION: The Pool Cool sun protection intervention had significant effects on lifeguards' sunburn rates and pool sun safety policies but did not improve reported sun protection behaviors. More intensive strategies may be needed to influence aquatics workers who have already begun to adopt skin cancer prevention practices.

The College Alcohol Problems Scale.

A short, reliable two-factor instrument measuring drinking-related negative consequences was developed from a previous measure using two samples of college students. In Study I, data on alcohol use and problems associated with alcohol use were collected on 382 introductory psychology students. The original College Alcohol Problems Scale (CAPS) was tested and found to fit the data poorly. Sequential methods were used to develop a revised instrument. Principal components analyses (PCA) on half of the sample were conducted on 20 items written to measure negative consequences related to college student drinking. Results indicated a two-factor solution measuring social and emotional problems. Confirmatory factor analyses (CFA) on the other half of the sample confirmed the two-factor structure. Further refinement of the instrument resulted in the revised CAPS (CAPS-r), an eight-item two-factor scale. In Study II, the response format was altered to coincide with the Young Adult Problem Screening Test. A total of 726 students completed the instrument as part of a university-wide random sample. CFA showed that the hypothesized model fit well across all measures of model fit and the factor structure was invariant across gender. Additional analyses revealed that the scale was internally consistent and externally valid. A short reliable and valid measure of alcohol-related problems is needed to enable low-cost data collection on college campuses across the nation, as well as to facilitate program evaluation and routine epidemiological surveillance and monitoring.

Environmental risk increase due to heavy metal contamination caused by a copper mining activity in Southern Brazil.

The Camaquã Copper Mines (CCM) were the main sulphide deposit in Southern Brazil and have been in operation from last century to 1996. To evaluate water contamination and environmental risk increase by heavy metals from mining operations, two points on the João Dias Creek were sampled (Station 1, background area and Station 2, contaminated area). Mining activity increased the natural weakly heavy metal fluxes by approximately 5424 kg. (approximately 60%) of the total metal flux, 1542 kg. (approximately 49%) of dissolved and 3881 kg (approximately 66%) of particulate metal flux. Total metal flux of anthropic origin was mostly due to Fe followed by Cu > Zn > Mn whereas Cd, As and Pb fluxes were negligible. The potential human health hazards and risk assessment related to daily intake of water from João Dias Creek are mostly due to Mn and should be of concern for the contaminated area. The ingestion of water from station 2 represents incremental risks of 130% and 59% respectively, considering the non-carcinogenic and the carcinogenic effects. The real increase of human health hazards may be greater than those related to the total concentrations since Mn and As dissolved concentrations were 5.5 and 2.0 higher than acceptable, respectively.

Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins.

Many bacterial outer membrane proteins (OMPs) are missing from two-dimensional (2-D) gel proteome maps. Recently, we developed a technique for 2-D electrophoresis (2-DE) of Escherichia coli OMPs using alkaline pH incubation for isolation of OMPs, followed by improved solubilization conditions for array by 2-DE using immobilized pH gradients. In this report, we expanded our study, examining protein components from the outer membranes of two enteric bacteria, Salmonella typhimurium and Klebsiella pneumoniae (also known as Klebsiella aerogenes), as well as the unrelated, free-living alpha-proteobacteria Caulobacter crescentus. Patterns of OMPs expression appeared remarkably conserved between members of the Enterobacteriaceae, while C. crescentus was unique, displaying a greater number of clusters of higher-molecular-weight proteins (>80 kDa). Peptide mass fingerprinting (PMF) was used for protein identification, and despite matching across-species boundaries, proved useful for first-pass protein assignment of enteric OMPs. In contrast, identification of C. crescentus OMPs was successful only when searching against its recently completed genome. For all three microorganisms examined, the majority of proteins identified on the 2-D gel appear localized to the outer membrane, a result consistent with our previous finding in Escherichia coli. In addition, we discuss some of the benefits and limitations of PMF in cross-species searching.

A randomized trial of the Hawaii SunSmart program's impact on outdoor recreation staff.

BACKGROUND: Skin cancer is the most common form of cancer in the United States and one of the most preventable. Prevention programs for children at outdoor recreation sites may influence not only the youth, but the staff, or caregivers, as well. By teaching children about sun protection, staff may also change their sun protection behaviors. OBJECTIVE: We report on the impact of a childhood skin cancer prevention program (SunSmart) on staff at outdoor recreation sites where a child-focused intervention was conducted. METHODS: The intervention included staff training, on-site activities delivered by staff, distribution of sunscreen, and the promotion of sun-safe environments. It was hypothesized that by teaching children about sun protection, staff would change their sun protection behaviors. A randomized trial at 14 recreation sites (n = 176 staff) in Hawaii tested the efficacy of education only, and education plus environmental changes, compared with a control condition. RESULTS: Results showed significant positive changes in knowledge, sun protection habits, norms, and sun protection policies. The education plus environment group was not superior to education alone. CONCLUSION: Changes in staff behavior and attitudes are important for their own health, as positive role models, and for the dissemination of skin cancer control programs.