Measurement of oxidatively induced DNA damage and its repair,by mass spectrometric techniques

Abstract

Oxidatively induced damage caused by free radicals and other DNA-damaging agents generate a plethora of products in the DNA of living organisms. There is mounting evidence for the involvement of this type of damage in the etiology of numerous diseases including carcinogenesis. For a thorough understanding of the mechanisms, cellular repair, and biological consequences of DNA damage, accurate measurement of resulting products must be achieved. There are various analytical techniques, with their own advantages and drawbacks, which can be used for this purpose. Mass spectrometric techniques with isotope dilution, which include gas chromatography (GC) and liquid chromatography (LC), provide structural elucidation of products and ascertain accurate quantification, which are absolutely necessary for reliable measurement. Both gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS), in single or tandem versions, have been used for the measurement of numerous DNA products such as sugar and base lesions, 8,5’-cyclopurine-2’-deoxynucleosides, base-base tandem lesions, and DNA-protein crosslinks, in vitro and in vivo. This article reviews these techniques and their applications in the measurement of oxidatively induced DNA damage and its repair.     

Energy and Carbon Management Systems

This article examines an important class of information system that serves as the foundation for corporate energy and greenhouse gas (GHG) accounting: energy and carbon management systems (ECMS). Investors, regulators, customers, and employees increasingly demand that organizations provide information about their organizational energy use and GHG emissions. However, there is little transparency about how organizations use ECMS to meet such demands. To shed light on ECMS implementation and application, we collected extensive qualitative interview data from two service‐sector organizations: one that uses a spreadsheet‐based ECMS and another that implemented an ECMS provided by a third‐party vendor. Our analysis of collected data revealed numerous challenges in the areas of business processes, managerial capabilities, data capture and integration, and data quality. Though our study is built on only two organizations and requires confirmation in large‐sample surveys, we provide several recommendations for organizations regarding ECMS. We also provide suggestions for future studies to build on our tentative results.     

CYANOBACTERIAL BUOYANCY REGULATION: THE PARADOXICAL ROLES OF CARBON1

In stratified lakes, dominance of the phytoplankton by cyanobacteria is largely the result of their buoyancy and depth regulation. Bloom-forming cyanobacteria regulate the gas vesicle and storage polymer contents of their cells in response to interactive environmental factors, especially light and nutrients. While research on the roles of nitrogen and phosphorus in cyanobacterial buoyancy regulation has reached a consensus, evaluations of the roles of carbon have remained open to dispute. We investigated the various effects of changes in carbon availability on cyanobacterial buoyancy with continuous cultures of Microcystis aeruginosa Kuetz. emend. Elenkin (1924), a notorious bloom-former. Although CO₂ limitation of photosynthesis can promote buoyancy in the short term by preventing the collapse of turgor-sensitive gas vesicles and/or by limiting polysaccharide accumulation, we found that sustained carbon limitation restricts buoyancy regulation by limiting gas vesicle as well as polysaccharide synthesis. These results provide an explanation for the positive effects of bicarbonate enrichment on cyanobacterial nitrogen uptake and bloom formation in lake experiments and may help to explain the pattern of cyanobacterial dominance in phosphorus-enriched, low-carbon lakes.     

三株亚肉座菌乙酸乙酯提取物生物活性及GC-MS分析

采用乙酸乙酯提取3株亚肉座菌菌丝体,测试虫生真菌乙酸乙酯提取物（EAE）的抗肿瘤、抗菌和抗氧化活性,并借助GC-MS方法分析各提取物中的化学成分。结果发现2株亚肉座菌的菌丝体EAE对HepG2细胞的抑制活性较强,IC₅₀均小于9μmol/L;抗菌结果表明2株真菌的提取物具有抑制细菌生长的作用;1株供试菌的EAE表现出较强的DPPH自由基清除活性（清除率可达85%）。GC-MS分析表明从亚肉座菌JXJG201717、JXJG201720和ARSEF7697的EAE中分别鉴定出21、35和39种成分,主要成分为酯类、醇类和酸类;盘状亚肉座菌JXJG201720与ARSEF7697有相同化合物13个,与暹罗亚肉座菌JXJG201717存在7个相同化合物。本研究表明虫生亚肉座菌具有产生丰富活性成分的能力,彰显出多种利用价值。     

Carbohydrate-rich supplements can improve nitrogen use efficiency and mitigate nitrogenous gas emissions from the excreta of dairy cows grazing temperate grass

Temperate pasture species constitute a source of protein for dairy cattle. On the other hand, from an environmental perspective, their high N content can increase N excretion and nitrogenous gas emissions by livestock. This work explores the effect of energy supplementation on N use efficiency (NUE) and nitrogenous gas emissions from the excreta of dairy cows grazing a pasture of oat and ryegrass. The study was divided into two experiments: an evaluation of NUE in grazing dairy cows, and an evaluation of N-NH₃ and N-N₂O volatilizations from dairy cow excreta. In the first experiment, 12 lactating Holstein × Jersey F1 cows were allocated to a double 3 × 3 Latin square (three experimental periods of 17 days each) and subjected to three treatments: cows without supplementation (WS), cows supplemented at 4.2 kg DM of corn silage (CS) per day, and cows supplemented at 3.6 kg DM of ground corn (GC) per day. In the second experiment, samples of excreta were collected from the cows distributed among the treatments. Aliquots of dung and urine of each treatment plus one blank (control – no excreta) were allotted to a randomized block design to evaluate N-NH₃ and N-N₂O volatilization. Measurements were performed until day 25 for N-NH₃ and until day 94 for N-N₂O. Dietary N content in the supplemented cows was reduced by 20% (P < 0.001) compared with WS cows, regardless of the supplement. Corn silage cows had lower N intake (P < 0.001) than WS and GC cows (366 v. 426 g/day, respectively). Ground corn supplementation allowed cows to partition more N towards milk protein compared with the average milk protein of WS cows or those supplemented with corn silage (117 v. 108 g/day, respectively; P < 0.01). Thus, even though they were in different forms, both supplements were able to increase (P < 0.01) NUE from 27% in WS cows to 32% in supplemented cows. Supplementation was also effective in reducing N excretion (761 v. 694 g/kg of N_intake; P < 0.001), N-NH₃ emission (478 v. 374 g/kg of N_milk; P < 0.01) and N-N₂O emission (11 v. 8 g/kg of N_milk; P < 0.001). Corn silage and ground corn can be strategically used as feed supplements to improve NUE, and they have the potential to mitigate N-NH₃ and N-N₂O emissions from the excreta of dairy cows grazing high-protein pastures.     

Variation in the phenology of photosynthesis among eastern white pine provenances in response to warming

In higher‐latitude trees, temperature and photoperiod control the beginning and end of the photosynthetically active season. Elevated temperature (ET) has advanced spring warming and delayed autumn cooling while photoperiod remains unchanged. We assessed the effects of warming on the length of the photosynthetically active season of three provenances of Pinus strobus L. seedlings from different latitudes, and evaluated the accuracy of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI) for tracking the predicted variation in spring and autumn phenology of photosynthesis among provenances. Seedlings from northern, local and southern P. strobus provenances were planted in a temperature‐free‐air‐controlled enhancement (T‐FACE) experiment and exposed to ET (+1.5/3°C; day/night). Over 18 months, we assessed photosynthetic phenology by measuring chlorophyll fluorescence, gas exchange, leaf spectral reflectance and pigment content. During autumn, all seedlings regardless of provenance followed the same sequence of phenological events with the initial downregulation of photosynthesis, followed by the modulation of non‐photochemical quenching and associated adjustments of zeaxanthin pool sizes. However, the timing of autumn downregulation differed between provenances, with delayed onset in the southern provenance (SP) and earlier onset in the northern relative to the local provenance, indicating that photoperiod at the provenance origin is a dominant factor controlling autumn phenology. Experimental warming further delayed the downregulation of photosynthesis during autumn in the SP. A provenance effect during spring was also observed but was generally not significant. The vegetation indices PRI and CCI were both effective at tracking the seasonal variations of energy partitioning in needles and the differences of carotenoid pigments indicative of the stress status of needles. These results demonstrate that PRI and CCI can be useful tools for monitoring conifer phenology and for the remote monitoring of the length of the photosynthetically active season of conifers in a changing climate.     

Changes in Nkx2.1, Sox2, Bmp4, and Bmp16 expression underlying the lung‐to‐gas bladder evolutionary transition in ray‐finned fishes

The key to understanding the evolutionary origin and modification of phenotypic traits is revealing the responsible underlying developmental genetic mechanisms. An important organismal trait of ray‐finned fishes is the gas bladder, an air‐filled organ that, in most fishes, functions for buoyancy control, and is homologous to the lungs of lobe‐finned fishes. The critical morphological difference between lungs and gas bladders, which otherwise share many characteristics, is the general direction of budding during development. Lungs bud ventrally and the gas bladder buds dorsally from the anterior foregut. We investigated the genetic underpinnings of this ventral‐to‐dorsal shift in budding direction by studying the expression patterns of known lung genes (Nkx2.1, Sox2, and Bmp4) during the development of lungs or gas bladder in three fishes: bichir, bowfin, and zebrafish. Nkx2.1 and Sox2 show reciprocal dorsoventral expression patterns during tetrapod lung development and are important regulators of lung budding; their expression during bichir lung development is conserved. Surprisingly, we find during gas bladder development, Nkx2.1 and Sox2 expression are inconsistent with the hypothesis that they regulate the direction of gas bladder budding. Bmp4 is expressed ventrally during lung development in bichir, akin to the pattern during mouse lung development. During gas bladder development, Bmp4 is not expressed. However, Bmp16, a paralogue of Bmp4, is expressed dorsally in the developing gas bladder of bowfin. Bmp16 is present in the known genomes of Actinopteri (ray‐finned fishes excluding bichir) but absent from mammalian genomes. We hypothesize that Bmp16 was recruited to regulate gas bladder development in the Actinopteri in place of Bmp4.     

Methane emissions reduce the radiative cooling effect of a subtropical estuarine mangrove wetland by half

The role of coastal mangrove wetlands in sequestering atmospheric carbon dioxide (CO₂) and mitigating climate change has received increasing attention in recent years. While recent studies have shown that methane (CH₄) emissions can potentially offset the carbon burial rates in low‐salinity coastal wetlands, there is hitherto a paucity of direct and year‐round measurements of ecosystem‐scale CH₄ flux (F_CH4) from mangrove ecosystems. In this study, we examined the temporal variations and biophysical drivers of ecosystem‐scale F_CH4 in a subtropical estuarine mangrove wetland based on 3 years of eddy covariance measurements. Our results showed that daily mangrove F_CH4 reached a peak of over 0.1 g CH₄‐C m^?2 day^?1 during the summertime owing to a combination of high temperature and low salinity, while the wintertime F_CH4 was negligible. In this mangrove, the mean annual CH₄ emission was 11.7 ± 0.4 g CH₄‐C m^–2 year^?1 while the annual net ecosystem CO₂ exchange ranged between ?891 and ?690 g CO₂‐C m^?2 year^?1, indicating a net cooling effect on climate over decadal to centurial timescales. Meanwhile, we showed that mangrove F_CH4 could offset the negative radiative forcing caused by CO₂ uptake by 52% and 24% over a time horizon of 20 and 100 years, respectively, based on the corresponding sustained‐flux global warming potentials. Moreover, we found that 87% and 69% of the total variance of daily F_CH4 could be explained by the random forest machine learning algorithm and traditional linear regression model, respectively, with soil temperature and salinity being the most dominant controls. This study was the first of its kind to characterize ecosystem‐scale F_CH4 in a mangrove wetland with long‐term eddy covariance measurements. Our findings implied that future environmental changes such as climate warming and increasing river discharge might increase CH₄ emissions and hence reduce the net radiative cooling effect of estuarine mangrove forests.