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.     

Discovery of the oldest known Pterygota in the Lower Carboniferous of the Upper Silesian Basin in the Czech Republic (Insecta: Archaeorthoptera)

The earliest pterygote (winged insect), dated from the Lower Carboniferous (Namurian A/E1, circa 324 millions years ago) is described from the Upper Silesian Basin in the Czech Republic. On the basis of its wing venation, it is attributed to the Archaeorthoptera Béthoux and Nel, 2002, crown group of the “Orthoptera”. Besides Apterygota (Collembola and Archaeognatha) known from the Lower Devonian, extremely rare pterygote insects are known from Lower Carboniferous deposits when they first appeared. The present discovery supports the hypothesis of the presence of the ancestor lineage of the orthopteroid in the Lower Carboniferous ecosystems.     

Detection and identification of phytoplasma associated with witches’ broom and little leaf disease in Arundo donax: first report from India

During the survey of two successive years 2012–2013, in nearby places of Gorakhpur districts, Uttar Pradesh, India, Arundo donax plants were found to be exhibiting witches’ broom, excessive branching accompanied with little leaf symptoms with considerable disease incidence. Nested PCR carried out with universal primers pair R16F2n/R16R2 employing the PCR (P1/P7) product as a template DNA (1:20) resulted in expected size positive amplification ~1.2 kb in all symptom-bearing plants suggested the association of phytoplasma with witches’ broom disease of Narkat plants. BLASTn analysis of the 16S rRNA gene sequence showed the highest (99%) sequence identity with Candidatus phytoplasma asteris (16SrI group). In phylogenetic analysis, the sequence data showed close relationships with the members of 16SrI phytoplasma and clustered within a single clade of 16SrI group and closed to B subgroup representatives. This is a first report of 16Sr I-B group phytoplasma associated with witches’ broom accompanied with little leaf disease of Narkat in India.     

Stream hierarchy defines riverscape genetics of a North American desert fish

Global climate change is apparent within the Arctic and the south‐western deserts of North America, with record drought in the latter reflected within 640 000 km² of the Colorado River Basin. To discern the manner by which natural and anthropogenic drivers have compressed Basin‐wide fish biodiversity, and to establish a baseline for future climate effects, the Stream Hierarchy Model (SHM) was employed to juxtapose fluvial topography against molecular diversities of 1092 Bluehead Sucker (Catostomus discobolus). MtDNA revealed three geomorphically defined evolutionarily significant units (ESUs): Bonneville Basin, upper Little Colorado River and the remaining Colorado River Basin. Microsatellite analyses (16 loci) reinforced distinctiveness of the Bonneville Basin and upper Little Colorado River, but subdivided the Colorado River Basin into seven management units (MUs). One represents a cline of three admixed gene pools comprising the mainstem and its lower‐gradient tributaries. Six others are not only distinct genetically but also demographically (i.e. migrants/generation <9.7%). Two of these (i.e. Grand Canyon and Canyon de Chelly) are defined by geomorphology, two others (i.e. Fremont‐Muddy and San Raphael rivers) are isolated by sharp declivities as they drop precipitously from the west slope into the mainstem Colorado/Green rivers, another represents an isolated impoundment (i.e. Ringdahl Reservoir), while the last corresponds to a recognized subspecies (i.e. Zuni River, NM). Historical legacies of endemic fishes (ESUs) and their evolutionary potential (MUs) are clearly represented in our data, yet their arbiter will be the unrelenting natural and anthropogenic water depletions that will precipitate yet another conservation conflict within this unique but arid region.     

Century‐long apparent decrease in intrinsic water‐use efficiency with no evidence of progressive nutrient limitation in African tropical forests

Forests exhibit leaf‐ and ecosystem‐level responses to environmental changes. Specifically, rising carbon dioxide (CO₂) levels over the past century are expected to have increased the intrinsic water‐use efficiency (iWUE) of tropical trees while the ecosystem is gradually pushed into progressive nutrient limitation. Due to the long‐term character of these changes, however, observational datasets to validate both paradigms are limited in space and time. In this study, we used a unique herbarium record to go back nearly a century and show that despite the rise in CO₂ concentrations, iWUE has decreased in central African tropical trees in the Congo Basin. Although we find evidence that points to leaf‐level adaptation to increasing CO₂—that is, increasing photosynthesis‐related nutrients and decreasing maximum stomatal conductance, a decrease in leaf δ¹³C clearly indicates a decreasing iWUE over time. Additionally, the stoichiometric carbon to nitrogen and nitrogen to phosphorus ratios in the leaves show no sign of progressive nutrient limitation as they have remained constant since 1938, which suggests that nutrients have not increasingly limited productivity in this biome. Altogether, the data suggest that other environmental factors, such as increasing temperature, might have negatively affected net photosynthesis and consequently downregulated the iWUE. Results from this study reveal that the second largest tropical forest on Earth has responded differently to recent environmental changes than expected, highlighting the need for further on‐ground monitoring in the Congo Basin.     

Comparison of methods for the demarcation between earlywood and latewood in tree rings of Norway spruce

The precise demarcation between earlywood and latewood is important for the detailed analysis of intra-annual tree ring features. Different techniques based on visual assessment, wood anatomy analysis and X-ray densitometry have been developed and are currently used for this purpose. Depending on the chosen method, tree species and environmental conditions, the results can significantly vary. Thus, it is important to determine the technique optimal for a particular research. Here, we investigated Norway spruce (Picea abies) tree rings to examine the agreement among the following demarcation methods: (1) direct visual assessment, (2) Mork’s index (anatomical definition of the transition from earlywood to latewood based on cell wall-lumen ratio) and (3) fixed and floating density thresholds applied to intra-ring density profiles. The aim was to modify both the Mork’s criterion and density thresholds on the basis of reference values given by visual identification of earlywood/latewood transition. A total of 231 tree rings were analysed by all methods. Our results showed that the usage of floating threshold (defined for each ring separately based on density profiles) is more reliable in comparison with fixed threshold (the same threshold value used for all tree rings and samples). Statistical analysis revealed the best correspondence between visual identification of earlywood/latewood transition and demarcation based on the standard Mork’s index and the floating density threshold derived as 80 % of maximum latewood density. In terms of Mork’s index calibration, the results showed that to determine latewood cells in Norway spruce trees growing in temperate conditions, it is sufficient to use an index value equal to 0.83. The results are applicable for the studied spruce population growing in a temperate climate. The methodology itself, however, is universal and can help to calibrate criteria for earlywood-latewood demarcation under specific conditions.