The PARP inhibitor Olaparib disrupts base excision repair of 5-aza-2′-deoxycytidine lesions

Decitabine (5-aza-2′-deoxycytidine, 5-azadC) is used in the treatment of Myelodysplatic syndrome (MDS) and Acute Myeloid Leukemia (AML). Its mechanism of action is thought to involve reactivation of genes implicated in differentiation and transformation, as well as induction of DNA damage by trapping DNA methyltranferases (DNMT) to DNA. We demonstrate for the first time that base excision repair (BER) recognizes 5-azadC-induced lesions in DNA and mediates repair. We find that BER (XRCC1) deficient cells are sensitive to 5-azadC and display an increased amount of DNA single- and double-strand breaks. The XRCC1 protein co-localizes with DNMT1 foci after 5-azadC treatment, suggesting a novel and specific role of XRCC1 in the repair of trapped DNMT1. 5-azadC-induced DNMT foci persist in XRCC1 defective cells, demonstrating a role for XRCC1 in repair of 5-azadC-induced DNA lesions. Poly (ADP-ribose) polymerase (PARP) inhibition prevents XRCC1 relocation to DNA damage sites, disrupts XRCC1–DNMT1 co-localization and thereby efficient BER. In a panel of AML cell lines, combining 5-azadC and Olaparib cause synthetic lethality. These data suggest that PARP inhibitors can be used in combination with 5-azadC to improve treatment of MDS and AML.     

Second Generation Inactivated Eastern Equine Encephalitis Virus Vaccine Candidates Protect Mice against a Lethal Aerosol Challenge

Currently, there are no FDA-licensed vaccines or therapeutics for eastern equine encephalitis virus (EEEV) for human use. We recently developed several methods to inactivate CVEV1219, a chimeric live-attenuated eastern equine encephalitis virus (EEEV). Dosage and schedule studies were conducted to evaluate the immunogenicity and protective efficacy of three potential second-generation inactivated EEEV (iEEEV) vaccine candidates in mice: formalin-inactivated CVEV1219 (fCVEV1219), INA-inactivated CVEV1219 (iCVEV1219) and gamma-irradiated CVEV1219 (gCVEV1219). Both fCVEV1219 and gCVEV1219 provided partial to complete protection against an aerosol challenge when administered by different routes and schedules at various doses, while iCVEV1219 was unable to provide substantial protection against an aerosol challenge by any route, dose, or schedule tested. When evaluating antibody responses, neutralizing antibody, not virus specific IgG or IgA, was the best correlate of protection. The results of these studies suggest that both fCVEV1219 and gCVEV1219 should be evaluated further and considered for advancement as potential second-generation inactivated vaccine candidates for EEEV.     

Excessive use of nitrogen in Chinese agriculture results in high N2O/(N2O+N2) product ratio of denitrification,primarily due to acidification of the soils

China is the world's largest producer and consumer of fertilizer N, and decades of overuse has caused nitrate leaching and possibly soil acidification. We hypothesized that this would enhance the soils' propensity to emit N₂O from denitrification by reducing the expression of the enzyme N₂O reductase. We investigated this by standardized oxic/anoxic incubations of soils from five long‐term fertilization experiments in different regions of China. After adjusting the nitrate concentration to 2 mM, we measured oxic respiration (R), potential denitrification (D), substrate‐induced denitrification, and the denitrification product stoichiometry (NO, N₂O, N₂). Soils with a history of high fertilizer N levels had high N₂O/(N₂O+N₂) ratios, but only in those field experiments where soil pH had been lowered by N fertilization. By comparing all soils, we found a strong negative correlation between pH and the N₂O/(N₂O+N₂) product ratio (r² = 0.759, P < 0.001). In contrast, the potential denitrification (D) was found to be a linear function of oxic respiration (R), and the ratio D/R was largely unaffected by soil pH. The immediate effect of liming acidified soils was lowered N₂O/(N₂O+N₂) ratios. The results provide evidence that soil pH has a marginal direct effect on potential denitrification, but that it is the master variable controlling the percentage of denitrified N emitted as N₂O. It has been known for long that low pH may result in high N₂O/(N₂O+N₂) product ratios of denitrification, but our documentation of a pervasive pH‐control of this ratio across soil types and management practices is new. The results are in good agreement with new understanding of how pH may interfere with the expression of N₂O reductase. We argue that the management of soil pH should be high on the agenda for mitigating N₂O emissions in the future, particularly for countries where ongoing intensification of plant production is likely to acidify the soils.     

Oxidation of atmospheric methane in Northern European soils, comparison with other ecosystems, and uncertainties in the global terrestrial sink

This paper reports the range and statistical distribution of oxidation rates of atmospheric CH₄ in soils found in Northern Europe in an international study, and compares them with published data for various other ecosystems. It reassesses the size, and the uncertainty in, the global terrestrial CH₄ sink, and examines the effect of land‐use change and other factors on the oxidation rate. Only soils with a very high water table were sources of CH₄; all others were sinks. Oxidation rates varied from 1 to nearly 200 μg CH₄ m^?2 h^?1; annual rates for sites measured for ≥1 y were 0.1–9.1 kg CH₄ ha^?1 y^?1, with a log‐normal distribution (log‐mean ≈ 1.6 kg CH₄ ha^?1 y^?1). Conversion of natural soils to agriculture reduced oxidation rates by two‐thirds –‐ closely similar to results reported for other regions. N inputs also decreased oxidation rates. Full recovery of rates after these disturbances takes > 100 y. Soil bulk density, water content and gas diffusivity had major impacts on oxidation rates. Trends were similar to those derived from other published work. Increasing acidity reduced oxidation, partially but not wholly explained by poor diffusion through litter layers which did not themselves contribute to the oxidation. The effect of temperature was small, attributed to substrate limitation and low atmospheric concentration. Analysis of all available data for CH₄ oxidation rates in situ showed similar log‐normal distributions to those obtained for our results, with generally little difference between different natural ecosystems, or between short‐and longer‐term studies. The overall global terrestrial sink was estimated at 29 Tg CH₄ y^?1, close to the current IPCC assessment, but with a much wider uncertainty range (7 to > 100 Tg CH₄ y^?1). Little or no information is available for many major ecosystems; these should receive high priority in future research.     

Identification of Renibacterium salmoninarum surface proteins by radioiodination

Abstract Treatment of Clostridium perfringens alpha toxin with aminopeptidase resulted in no effect on various activities of the toxin. Aminopeptidase did not hydrolyze the native toxin or the toxin treated with urea in the presence of EDTA. Treatment with carboxypeptidase for 30 min resulted in a 75% decrease in these activities. Incubation of the native toxin with carboxypeptidase for 30 min released approximately 15 amino acids from the C-terminus of the toxin. The biological activities of a mutant toxin lacking 20 C-terminal residues of the toxin (AT_1–350) showed about 59–87% of the activity of native toxin. The mutant toxin showed partial antigenic identity with the native toxin. These data suggest that the C-terminal domain contributes to maintaining the active form of the toxin.     

Separation and Purification of Bacteria from Soil

Bacteria were released and separated from soil by a simple blending-centrifugation procedure. The percent yield of bacterial cells (microscopic counts) in the supernatants varied over a wide range depending on the soil type. The superantants contained large amounts of noncellular organic material and clay particles. Further purification of the bacterial cells was obtained by centrifugation in density gradients, whereby the clay particles and part of the organic materials sedimented. A large proportion of the bacteria also sedimented through the density gradient, showing that they had a buoyant density above 1.2 g/ml. Attachment to clay minerals and humic material may account for this apparently high buoyant density. The percent yield of cells was negatively correlated with the clay content of the soils, whereas the purity was positively correlated with it. The cell size distribution and the relative frequency of colony-forming cells were similar in the soil homogenate, the supernatants after blending-centrifugation, and the purified bacterial fraction. In purified bacterial fraction from a clay loam, the microscopically measured biomass could account for 20 to 25% of the total C and 30 to 40% of the total N as cellular C and N. The amount of cellular C and N may be higher, however, owing to an underestimation of the cell diameter during fluorescence. A part of the contamination could be ascribed to extracellular structures as well as partly decayed cells, which were not revealed by fluorescence microscopy.     

Regulation of foraging trips and costs of incubation shifts in the Antarctic petrel (Thalassoica antarctica)

In species where incubation is shared by both parents, the mate'sability to fast on the nest may constrain the time availablefor foraging. The decision to return to the nest should thereforebe a compromise between an animal's own foraging success andits mate's ability to fast on the nest. To examine how the bodyconditions of incubating Antarctic petrels, Thalassoica antarctica,influence both the length of foraging trips and incubation shifts,we experimentally handicapped females by increasing their flightcosts during a foraging trip by adding lead weights to theirlegs. Handicapped females spent more time at sea and had lowerbody conditions at arrival to the colony than controls, and,moreover, females in poor body condition at arrival to the colonyspent generally more time at sea than those with higher bodycondition. The prolonged time period spent at sea by handicappedfemales was associated with higher desertion rates than amongcontrols. The time the incubating mates fasted increased withtheir body condition at arrival to the colony, suggesting thata high body condition of the incubating bird may reduce theprobability of nest desertion. Accordingly, our results suggestthat the time spent foraging is adjusted to the body conditionsof both the foraging and incubating mate.     

MRS study of glutamate metabolism in cultured neurons/glia

[U-¹³C]Glutamate metabolism was studied in primary brain cell cultures. Cell extracts as well as redissolved lyophilized media were subjected to nuclear magnetic resonance spectroscopy in order to identify¹³C labeled metabolites. Both neurons and astrocytes metabolized glutamate extensively with¹³C label appearing in aspartate in all cultures. Additionally, GABA is synthesized in the GABAergic cortical neurons. Labeling of lactate and glutamine was prominent in medium from astrocytes, but not detectable in cerebral cortical neurons. Cerebellar granule neurons showed some labeling of lactate. Glutamate derived from the first turn of the tricarboxylic acid cycle (1,2,3-¹³C₃-isotopomer) is present in all cell types analyzed. However, glutamate derived from the second turn of the cycle was only detected in granule neurons. In astrocytes, the transaminase inhibitor aminooxyacetic acid not only abolished the appearance of aspartate, but also of the 1,2,3-¹³C₃-isotopomer of glutamate, thus showing that transmination is necessary for the conversion of 2-oxoglutarate to glutamate. The entry of glutamate into the tricarboxylic acid cycle was, however, not seriously impaired. 3-nitropropionic acid abolished the appearance of aspartate, the 1,2,3-¹³C₃-isotopomer of glutamate and lactate in cerebellar granule neurons. Special issue dedicated to Dr. Herman Bachelard.     

Mortality and lamb body mass growth in free‐ranging domestic sheep – environmental impacts including lethal and non‐lethal impacts of predators

The management and recovery of large predator populations in areas where human persecution has driven them to ecological extinction requires a solid understanding of the effects of both predation and food limitation on prey populations. We used 11 yr of data on reported losses among 17.3 million free‐ranging sheep Ovis aries in the Norwegian farming industry to elucidate the relative roles of climate, vegetation characteristics, sheep densities, lamb body mass and densities of predators and alternative prey on the number of lambs and ewes lost on summer pastures. We first examined whether predator densities predicted autumn lamb body mass through possible impacts of predators on body growth (non‐lethal effects) but found no evidence for such effects in our study system. This might be due to weak anti‐predator behavioral responses in domesticated sheep. However, autumn lamb body mass was predicted by both sheep density and winter and spring weather conditions, probably through food availability. Losses of both lambs and ewes were positively and strongly related to the density of Eurasian lynx Lynx lynx, wolverine Gulo gulo and brown bear Ursus arctos. In addition, food availability and spring weather conditions were associated to losses of lambs, while precipitation in May predicted losses of ewes. There was little evidence for interaction effects of predator species on losses, suggesting that most of the effects of the predators were additive to each other. Given the strong effect of predator densities on sheep losses, we conclude that changing livestock husbandry practices towards a system that actively protects sheep and/or active management of predator densities may be necessary to reduce sheep losses where predators are recolonizing.