Radon Potential, Geologic Formations, and Lung Cancer Risk

OBJECTIVE: Exposure to radon is associated with approximately 10% of U.S. lung cancer cases. Geologic rock units have varying concentrations of uranium, producing fluctuating amounts of radon. This exploratory study examined the spatial and statistical associations between radon values and geological formations to illustrate potential population-level lung cancer risk from radon exposure. METHOD: This was a secondary data analysis of observed radon values collected in 1987 from homes (N = 309) in Kentucky and geologic rock formation data from the Kentucky Geological Survey. Radon value locations were plotted on digital geologic maps using ArcGIS and linked to specific geologic map units. Each map unit represented a package of different types of rock (e.g., limestone and/or shale). Log-transformed radon values and geologic formation categories were compared using one-way analysis of variance. RESULTS: Observed radon levels varied significantly by geologic formation category. Of the 14 geologic formation categories in north central Kentucky, four were associated with median radon levels, ranging from 8.10 to 2.75 pCi/L. CONCLUSION: Radon potential maps that account for geologic factors and observed radon values may be superior to using observed radon values only. Knowing radon-prone areas could help target population-based lung cancer prevention interventions given the inequities that exist related to radon

The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy

BACKGROUND: DNA microarrays are a powerful tool with important applications such as global gene expression profiling. Construction of bacterial DNA microarrays from genomic sequence data using a two-stage PCR amplification approach for the production of arrayed DNA is attractive because it allows, in principal, the continued re-amplification of DNA fragments and facilitates further utilization of the DNA fragments for additional uses (e.g. over-expression of protein). We describe the successful construction and use of DNA microarrays by the two-stage amplification approach and discuss the technical challenges that were met and resolved during the project. RESULTS: Chimeric primers that contained both gene-specific and shared, universal sequence allowed the two-stage amplification of the 3,168 genes identified on the genome of Synechocystis sp. PCC6803, an important prokaryotic model organism for the study of oxygenic photosynthesis. The gene-specific component of the primer was of variable length to maintain uniform annealing temperatures during the 1(st ) round of PCR synthesis, and situated to preserve full-length ORFs. Genes were truncated at 2 kb for efficient amplification, so that about 92% of the PCR fragments were full-length genes. The two-stage amplification had the additional advantage of normalizing the yield of PCR products and this improved the uniformity of DNA features robotically deposited onto the microarray surface. We also describe the techniques utilized to optimize hybridization conditions and signal-to-noise ratio of the transcription profile. The inter-lab transportability was demonstrated by the virtual error-free amplification of the entire genome complement of 3,168 genes using the universal primers in partner labs. The printed slides have been successfully used to identify differentially expressed genes in response to a number of environmental conditions, including salt stress. CONCLUSIONS: The technique detailed here minimizes the cost and effort to replicate a PCR-generated DNA gene fragment library and facilitates several downstream processes (e.g. directional cloning of fragments and gene expression as affinity-tagged fusion proteins) beyond the primary objective of producing DNA microarrays for global gene expression profiling

Atmospheric observation-based estimation of fossil fuel CO_2 emissions from regions of central and southern California

Combustion of fossil fuel is the dominant source of greenhouse gas emissions to the atmosphere in California. Here, we describe radiocarbon (^(14)CO_2) measurements and atmospheric inverse modeling to estimate fossil fuel CO_2 (ffCO_2) emissions for 2009–2012 from a site in central California, and for June 2013–May 2014 from two sites in southern California. A priori predicted ffCO_2 mixing ratios are computed based on regional atmospheric transport model (WRF-STILT) footprints and an hourly ffCO_2 prior emission map (Vulcan 2.2). Regional inversions using observations from the central California site suggest that emissions from the San Francisco Bay Area (SFBA) are higher in winter and lower in summer. Taking all years together, the average of a total of fifteen 3-month inversions from 2009 to 2012 suggests ffCO_2 emissions from SFBA were within 6 ± 35% of the a priori estimate for that region, where posterior emission uncertainties are reported as 95% confidence intervals. Results for four 3-month inversions using measurements in Los Angeles South Coast Air Basin (SoCAB) during June 2013–May 2014 suggest that emissions in SoCAB are within 13 ± 28% of the a priori estimate for that region, with marginal detection of any seasonality. While emissions from the SFBA and SoCAB urban regions (containing ~50% of prior emissions from California) are constrained by the observations, emissions from the remaining regions are less constrained, suggesting that additional observations will be valuable to more accurately estimate total ffCO_2 emissions from California as a whole

Short Sleep Is Associated With Low Bone Mineral Density and Osteoporosis in the Women’s Health Initiative

Short sleep duration, recognized as a public health epidemic, is associated with adverse health conditions, yet little is known about the association between sleep and bone health. We tested the associations of usual sleep behavior and bone mineral density (BMD) and osteoporosis. In a sample of 11,084 postmenopausal women from the Women’s Health Initiative (WHI; mean age 63.3â years, SD = 7.4), we performed a crossâ sectional study of the association of selfâ reported usual hours of sleep and sleep quality (WHI Insomnia Rating Score) with whole body, total hip, femoral neck, and spine BMD using linear regression models. We also studied the association of sleep duration and quality with dualâ energy Xâ ray absorptiometry (DXA)â defined low bone mass (Tâ scoreâ <â â 2.5 to <â 1) and osteoporosis (Tâ scoreâ â ¤â â 2.5) using multinomial regression models. We adjusted for age, DXA machine, race, menopausal symptoms, education, smoking, physical activity, body mass index, alcohol use, physical function, and sleep medication use. In adjusted linear regression models, women who reported sleeping 5â hours or less per night had on average 0.012 to 0.018â g/cm2 significantly lower BMD at all four sites compared with women who reported sleeping 7â hours per night (reference). In adjusted multinomial models, women reporting 5â hours or less per night had higher odds of low bone mass and osteoporosis of the hip (odds ratio [OR] =â 1.22; 95% confidence interval [CI] 1.03â 1.45, and 1.63; 1.15â 2.31, respectively). We observed a similar pattern for spine BMD, where women with 5â hours or less per night had higher odds of osteoporosis (adjusted OR = 1.28; 95% CI 1.02â 1.60). Associations of sleep quality and DXA BMD failed to reach statistical significance. Short sleep duration was associated with lower BMD and higher risk of osteoporosis. Longitudinal studies are needed to confirm the crossâ sectional effects of sleep duration on bone health and explore associated mechanisms. © 2019 American Society for Bone and Mineral Research.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154418/1/jbmr3879_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154418/2/jbmr3879.pd

Galaxy Clusters in the Line of Sight to Background Quasars: II. Environmental effects on the sizes of baryonic halo sizes

Based on recent results on the frequency of MgII absorption line systems in the "QSO behind RCS clusters" survey (QbC), we analyse the effects of the cluster environment on the sizes of baryonic haloes around galaxies. We use two independent models, i) an empirical halo occupation model which fits current measurements of the clustering and luminosity function of galaxies at low and high redshifts, and ii) the GALFORM semi-analytic model of galaxy formation, which follows the evolution of the galaxy population from first principles, adjusted to match the statistics of low and high redshift galaxies. In both models we constrain the MgII halo sizes of field and cluster galaxies using observational results on the observed MgII statistics. Our results for the field are in good agreement with previous works, indicating a typical \mgii\ halo size of $r_MgII ~ 50h_71^-1kpc in the semi-analytic model, and slightly lower in the halo occupation number approach. For the cluster environment, we find that both models require a median MgII halo size of r_MgII< 10h_71^-1kpc in order to reproduce the observed statistics on absorption line systems in clusters of galaxies. Based on the Chen & Tinker (2008) result that stronger systems occur closer to the MgII halo centre, we find that strong absorption systems in clusters of galaxies occur at roughly a fixed fraction of the cold-warm halo size out to 1h_71^-1Mpc from the cluster centres. In contrast, weaker absorption systems appear to occur at progressively shorter relative fractions of this halo as the distance to the cluster centre decreases.Comment: 12 pages, 8 figures, accepted for publication in MNRA

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules

Quantification of CO2 removal in a large-scale enhanced weathering field trial on an oil palm plantation in Sabah, Malaysia

Modeling studies show that large-scale deployment of enhanced rock weathering on croplands has the potential to reduce levels of atmospheric carbon dioxide by the end of the century. There is, however, a pressing need to verify model predictions through long-term field trials. Here we report results from the first 3 years of an ongoing enhanced weathering field trial, carried out on an oil palm plantation in Sabah, Malaysia. Crushed silicate rock was applied to three hydrologically isolated catchments, and three adjacent (paired) reference catchments were left untreated. The drawdown of atmospheric CO2 was quantified via the export of alkalinity in stream waters and changes in soil carbonate content. The amended and reference catchments were found to have a similar extent of CO2 drawdown via alkalinity export [respectively, 3.8 ± 0.8 (1 SD) and 3.7 ± 0.6 (1 SD) tCO2 ha−1] when all catchments were averaged over the study period (October 2018 to July 2021). However, differences were observed between the different catchment pairs (plots): two of the plots displayed a similar extent of CO2 removal for both the amended and reference catchments, but the third amended catchment had a higher extent of CO2 removal of ~1 tCO2 ha−1 relative to its adjacent reference catchment. The difference in CO2 removal rates determined for this plot can likely be attributed to increased weathering of silicate minerals in the amended catchment. Soil carbonate concentrations were on average < 0.2 wt% CaCO3, but we report a small increase of ~0.03 wt% CaCO3 in the top 30 cm of soil in the amended soils relative to the reference catchments. The magnitude of CO2 drawdown via alkalinity export determined for these agricultural catchments is around an order of magnitude higher than in natural forested catchments in Sabah and similar to that of basaltic catchments. We show that these high weathering rates are primarily driven by weathering of carbonate fertilizers. The data presented from this field trial provide vital contextual information on the real-world efficacy and practicalities associated with the implementation of enhanced weathering for atmospheric CO2 removal that will help to inform further trials as well as wider-scale deployment

Atmospheric observation-based estimation of fossil fuel CO_2 emissions from regions of central and southern California

Combustion of fossil fuel is the dominant source of greenhouse gas emissions to the atmosphere in California. Here, we describe radiocarbon (^(14)CO_2) measurements and atmospheric inverse modeling to estimate fossil fuel CO_2 (ffCO_2) emissions for 2009–2012 from a site in central California, and for June 2013–May 2014 from two sites in southern California. A priori predicted ffCO_2 mixing ratios are computed based on regional atmospheric transport model (WRF-STILT) footprints and an hourly ffCO_2 prior emission map (Vulcan 2.2). Regional inversions using observations from the central California site suggest that emissions from the San Francisco Bay Area (SFBA) are higher in winter and lower in summer. Taking all years together, the average of a total of fifteen 3-month inversions from 2009 to 2012 suggests ffCO_2 emissions from SFBA were within 6 ± 35% of the a priori estimate for that region, where posterior emission uncertainties are reported as 95% confidence intervals. Results for four 3-month inversions using measurements in Los Angeles South Coast Air Basin (SoCAB) during June 2013–May 2014 suggest that emissions in SoCAB are within 13 ± 28% of the a priori estimate for that region, with marginal detection of any seasonality. While emissions from the SFBA and SoCAB urban regions (containing ~50% of prior emissions from California) are constrained by the observations, emissions from the remaining regions are less constrained, suggesting that additional observations will be valuable to more accurately estimate total ffCO_2 emissions from California as a whole