An Environmental and Energy Information System

The Environmental Information System Office (EISO) at Oak Ridge National Laboratory (ORNL) provides information support for researchers and administrators involved with energy and environmental policy and progress. Multiple EISO activities for various governmental agencies have resulted in establishment of compatible data bases concerned with energy and environmental information, methods for effectively developing these, development and computer display of numerical data summaries, and reports evaluating published information. Direction is provided by continuing dialogue between users and information system staff

Exploring the Pathogenic and Drug Resistance Mechanisms of Staphylococcus aureus

We have previously identified σS, an ECF sigma factor that is important in the virulence and stress response of S. aureus. Transcriptional profiling of sigS revealed that it is differentially regulated in a variety of laboratory and clinical strains of S. aureus, suggesting that there exists a regulatory network that modulates its expression. In order to identify direct regulators of sigS expression, we performed a biotin pull down assay in tandem with mass spectrometry. We identified CymR as a direct regulator and observed that sigS expression is increased in cells lacking cymR. In addition, transposon mutagenesis was performed to identify regulators of sigS expression. We identified insertions in genes that are transcriptional regulators, and elements involved in amino acid biosynthesis and DNA replication, recombination and repair as influencing sigS expression. Finally, methyl nitro-nitrosoguanidine mutagenesis in conjunction with whole genome sequencing was employed and revealed mutations in the lactose repressor, lacR, and the membrane sensor histidine kinase, kdpD, as negatively effecting sigS expression. EMSAs revealed that LacR is an indirect regulator of sigS expression, while the response regulator KdpE is a direct repressor. These results indicate that a complex regulatory network is in place for sigS that modulates its expression. In a continuation of studies on σS regulation, we next explored interplay with the products of genes conserved within the sigS locus. We determined that this region is conserved amongst all the sequenced staphylococci, and includes four genes: SAUSA300_1721 (a conserved hypothetical protein), as well as sigS, ecfX, and ecfY. In order to investigate the relationship between EcfX and σS we performed protein pull down assays and observed that these two protein interact. Further to this, transcriptional analysis of sigS in an ecfX mutant reveal that expression of sigS is decreased, indicating that it is an activator. Architectural analysis of the sigS locus via RNAseq revealed that the majority of transcription in this region comes from ecfY, a gene that is downstream and divergent to sigS. We demonstrate that inactivation of ecfY leads to a significant increase in sigS expression, and that ecfY null strains are more resistant to DNA damaging agents such as UV, H2O2, MMS, and ethidium bromide, which we have previously demonstrated that a sigS mutant is highly sensitive to. Our studies also revealed that an ecfY null strain is better able to survive intracellularly following phagocytosis by RAW 264.7 cell and demonstrates increased survival in whole-human blood, which is again opposed to that previously observed for sigS deficient strains. Because the ecfY null strain overexpresses sigS, we investigated the regulon of this sigma factor using this mutant in conjunction with RNAseq analysis. We identified that genes putatively under the control of σS are involved in DNA damage and repair, virulence, amino acid starvation and nucleic acid biosynthesis. Collectively, our results indicate that σS is regulated via a unique mechanism: positively through an apparent need for an activator protein (EcfX) and negatively via RNA-RNA interaction (the 3’ UTR of ecfY). We suggest that the evidence presented here greatly adds not only to our understanding of the regulatory circuits extant within S. aureus, but also to alternative sigma factor biology in general. Finally, we evaluated the efficacy of a novel library of quinazoline-based compounds against a highly drug resistant strain of S. aureus. We performed structure activity and structure property relationship assays in order to identify lead compounds. These methods lead to the identification of N2,N4-disubstituted quinazoline-2,4-diamines that had low minimum inhibitory concentrations, along with favorable physiochemical properties. Evaluation of their biological activity demonstrated limited potential for resistance of to our quinazoline based compounds, low toxicity to human epithelial cells, and strong efficacy in vivo. Taken together, our findings support the use of quinazoline derivatives as potential new antimicrobials against multidrug resistant S. aureus

Examination of dietary intake of UK preschool children by varying carers : evidence from the 2008-2016 UK National Diet and Nutrition Survey

Early years caregivers can play a key role in young children’s eating and the prevention of childhood obesity. The UK National Diet and Nutrition Survey (NDNS) is a large representative survey collecting detailed food and nutrition consumption data. Using these data, the aim of this study was to investigate the relationship between dietary intake of preschool children in the UK aged two to four years old and accompanying adult/s. Nutrition consumption data from 1,218 preschool children from years one to eight of the NDNS (2008 to 2016) were accessed. Dietary data was captured using three or four day estimated food diaries. Regression analyses were performed to explore the association between dietary intake and accompanying adult. There were significant differences in consumption when children were not accompanied by their parents. Compared to when children were with parents, children consumed significantly more energy (15kcal, 95% CI 7-23kcal) sodium (−19mg, 95% CI 6-32mg), added sugars (0.6g, 95% CI 0.1-1.1g), vegetables (3g, 95% CI 1-4g), total grams (12g, 95% CI 3-21g) and saturated fat (0.2g, 95% CI 0.1-0.4g) per eating occasion when accompanied by wider family. When children were accompanied by a formal carer they consumed significantly less added sugars (−1.6g, 95% CI −2.4-0.8g) and more fruit (12g, 95% CI 3-21g) per eating occasion than when they were with their parents. The results demonstrate that non-parental caregivers might be an important target to promote healthy eating in young children. Further research is needed to establish which caregivers would benefit most

Programming of embryonic development

Assisted reproductive techniques (ART) and parental nutritional status have profound effects on embryonic/fetal and placental development, which are probably mediated via “programming” of gene expression, as reflected by changes in their epigenetic landscape. Such epigenetic changes may underlie programming of growth, development, and function of fetal organs later in pregnancy and the offspring postnatally, and potentially lead to long-term changes in organ structure and function in the offspring as adults. This latter concept has been termed developmental origins of health and disease (DOHaD), or simply developmental programming, which has emerged as a major health issue in animals and humans because it is associated with an increased risk of non-communicable diseases in the offspring, including metabolic, behavioral, and reproductive dysfunction. In this review, we will briefly introduce the concept of developmental programming and its relationship to epigenetics. We will then discuss evidence that ART and periconceptual maternal and paternal nutrition may lead to epigenetic alterations very early in pregnancy, and how each pregnancy experiences developmental programming based on signals received by and from the dam. Lastly, we will discuss current research on strategies designed to overcome or minimize the negative consequences or, conversely, to maximize the positive aspects of developmental programming

Development of All-Solid-State Sensors for Measurement of Nitric Oxide and Ammonia Concentrations by Optical Absorption in Particle-Laden Combustion Exhaust Streams

An all-solid-state continuous-wave (cw) laser system for ultraviolet absorption measurements of the nitric oxide (NO) molecule has been developed and demonstrated. For the NO sensor, 250 nW of tunable cw ultraviolet radiation is produced by sum-frequency-mixing of 532-nm radiation from a diode-pumped Nd:YAG laser and tunable 395-nm radiation from an external cavity diode laser (ECDL). The sum-frequency-mixing process occurs in a beta-barium borate crystal. The nitric oxide absorption measurements are performed by tuning the ECDL and scanning the sum-frequency-mixed radiation over strong nitric oxide absorption lines near 226 nm. In Year 1 of the research, the nitric oxide sensor was used for measurements in the exhaust of a coal-fired laboratory combustion facility. The Texas A&M University boiler burner facility is a 30 kW (100,000 Btu/hr) downward-fired furnace with a steel shell encasing ceramic insulation. Measurements of nitric oxide concentration in the exhaust stream were performed after modification of the facility for laser based NOx diagnostics. The diode-laser-based ultraviolet absorption measurements were successful even when the beam was severely attenuated by particulate in the exhaust stream and window fouling. Single-laser-sweep measurements were demonstrated with an effective time resolution of 100 msec, limited at this time by the scan rate of our mechanically tuned ECDL system. In Year 2, the Toptica ECDL in the original system was replaced with a Sacher Lasers ECDL. The mode-hop-free tuning range and tuning rate of the Toptica ECDL were 25 GHz and a few Hz, respectively. The mode-hop-free tuning range and tuning rate of the Sacher Lasers ECDL were 90 GHz and a few hundred Hz, respectively. The Sacher Lasers ECDL thus allows us to scan over the entire NO absorption line and to determine the absorption baseline with increased accuracy and precision. The increased tuning rate is an advantage in that data can be acquired much more rapidly and the absorption measurements are less susceptible to the effects of transient fluctuations in the properties of the coal combustor exhaust stream. Gas cell measurements were performed using the NO sensor with the new ECDL, and a few spectra were acquired from the coal exhaust stream. However, the laser diode in the new ECDL failed during the coal combustor tests. In Year 3, however, we obtained a new GaN laser diode for our ECDL system, installed it, and completed an extensive series of measurements in the Texas A&M coal-fired laboratory combustion facility. The combustor was operated with coal and coal/biomass as fuels, with and without reburn, and with and without ammonia injection. Several different fuel equivalence ratios were investigated for each operating condition. A series of spectral simulations was performed using the HITRAN code to investigate the potential sensitivity of absorption measurements of ammonia in different spectral regions. It was concluded that ammonia absorption features in the 3000-nm spectral region would be hard to measure due to water vapor interferences. We will concentrate on the spectral region near 1530 nm, where other researchers have had some success in measuring ammonia

Improving temperature‐based predictions of the timing of flowering in cotton

Key management recommendations for cotton (Gossypium hirsutum L.) management require estimates of the timing of crop phenology. Most commonly growing day degree (DD) (thermal time) approaches are used. Currently, across many cotton production regions, there is no consistent approach to predicting first square and flower timing. Day degree approaches vary considerably, with base thresholds different (12.0–15.6 °C) with no consistency using an optimum temperature threshold (i.e., temperature where development ceases to increase). As cotton is grown in variable and changing climates, and cultivars change, there is a need to ensure the accuracy of this approach for predicting timing of flowering for assisting cotton management. In this study new functions to predict first square and first flower were developed and validated using data collected in multiple seasons and regions (Australia and the United States). Earlier controlled environment studies that monitored crop development were used to assess in more detail how temperatures were affecting early cotton development. New DD functions developed predicted first square and first flower better than the existing Australian and U.S. approaches. The best performing functions had base temperatures like those of existing U.S. functions (15.6 °C) and an optimum threshold temperature of 32.0 °C. New universal DD targets for first square (343 DD [°C]) and first flower (584 DD) were developed. Controlled environment studies supported this base temperature outcome; however, it was less clear that 32.0 °C was the optimum threshold temperature from these data. Precise predictions of cotton development will facilitate accurate growth stage assessments and hence better cotton management decisions

Scaling and root planing with and without periodontal flap surgery

. Complete removal of calculus is a primary part of achieving a “biologically acceptable” tooth surface in the treatment of periodontitis. Rabbani et al. reported that a single episode of scaling did not completely remove subgingival calculus and that the deeper the periodontal pocket, the less complete the calculus removal. The purpose of the present study was to evaluate the effectiveness of scaling relative to calculus removal following reflection of a periodontal flap. Each of 21 patients who required multiple extractions had 2 teeth scaled, 2 teeth scaled following the reflection of a periodontal flap, and 2 teeth serve as controls. Local anesthesia was used. Following extraction, the % of subgingival tooth surfaces free of calculus was determined using the method described by Rabbani with a stereomicroscope. Results showed that while scaling only (SO) and scaling with a flap (SF) increased the % of root surface without calculus, scaling following the reflection of a flap aided calculus removal in pockets 4 mm and deeper. Comparison of SO versus SF at various pocket depths for % of tooth surfaces completely free of calculus showed 1 to 3 mm pockets to be 86% versus 86%, 4 to 6 mm pockets to be 43% versus 76% and >6 mm pockets to be 32% versus 50%. The extent of residual calculus was directly related to pocket depth, was greater following scaling only, and was greatest at the CEJ or in association with grooves, fossae or furcations. No differences were noted between anterior and posterior teeth or between different tooth surfaces.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73823/1/j.1600-051X.1986.tb01461.x.pd