Preservation of ancient DNA in thermally damaged archaeological bone

Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.     

Applicability of the Arrhenius model for ammonia oxidizing bacteria subjected to temperature time gradients

The aim of this work is to identify the range of applicability of Arrhenius type temperature dependence for Ammonia Oxidizing Bacteria (AOB) subjected to temperature time gradients through continuous titrimetric tests. An innovative online differential titrimetric technique was used to continuously monitor the maximum biologic ammonia oxidation rate of the biomass selected in a pilot scale membrane bioreactor, as a function of temperature time gradients. The monitoring technique is based on the measurement of alkalinity and hydrogen peroxide consumption rates in two parallel reactors operated in non-limiting substrate conditions for AOB; both reactors were continuously fed with mixed liquor and in one of them AOB were inhibited with allylthiourea. The effects of temperature decrease rates in the range 1 to 4°C·h⁻¹ were evaluated by controlling the titrimetric reactor in the temperature range 10°C–20°C. The dependence of growth kinetics on temperature time gradients and the range of applicability of Arrhenius model for temperature dependency of AOB growth kinetics were assessed. The Arrhenius model was found to be accurate only with temperature gradients lower than 2°C·h⁻¹. The estimated Arrhenius coefficients (θ) were shown to increase from 1.07 to 1.6 when the temperature decrease rate reached 4°C·h⁻¹.     

Alpha-male paternity in elephant seals

The aim of this study was to assess paternity of males that dominated mating in harems at northern (Mirounga angustirostris) and southern (M. leonina) elephant seal rookeries using DNA fingerprinting and microsatellite DNA analysis. Southern alpha males had greater reproductive success than most northern alphas at similar-sized harems. Comparison of the relatedness between pups within harems also suggested that fewer males achieved matings in the southern elephant seal population. This was consistent with behavioral observations that suggest greater competition for mates in northern elephant seal harems. Reproductive success was consistent with estimates of mating success in some cases, but lower than expected for some northern elephant seal alpha males. A lower reproductive success than predicted from mating behavior may arise from a variety of factors including sperm competition, male sperm depletion from frequent mating, or reduced fertility. The alternatives are discussed in the context of environmental and historical factors. Received: 17 August 1998 / Received in revised form: 28 March 1999 / Accepted: 30 May 1999     

Effects of climate change on surface-water photochemistry: a review

Information concerning the link between surface-water photochemistry and climate is presently very scarce as only a few studies have been dedicated to the subject. On the basis of the limited knowledge that is currently available, the present inferences can be made as follows: (1) Warming can cause enhanced leaching of ionic solutes from the catchments to surface waters, including cations and more biologically labile anions such as sulphate. Preferential sulphate biodegradation followed by removal as organic sulphides in sediment could increase alkalinity, favouring the generation of the carbonate radical, CO₃ ^·?. However, this phenomenon would be easily offset by fluctuations of the dissolved organic carbon (DOC), which is strongly anticorrelated with CO₃ ^·?. Therefore, obtaining insight into DOC evolution is a key issue in understanding the link between photochemistry and climate. (2) Climate change could exacerbate water scarcity in the dry season in some regions. Fluctuations in the water column could deeply alter photochemistry that is usually favoured in shallower waters. However, the way water is lost would strongly affect the prevailing photoinduced processes. Water outflow without important changes in solute concentration would mostly favour reactions induced by the hydroxyl and carbonate radicals (·OH and CO₃ ^·?). In contrast, evaporative concentration would enhance reactions mediated by singlet oxygen (¹O₂) and by the triplet states of chromophoric dissolved organic matter (³CDOM*). (3) In a warmer climate, the summer stratification period of lakes would last longer, thereby enhancing photochemical reactions in the epilimnion but at the same time keeping the hypolimnion water in the dark for longer periods.     

Effects of repeated-low level sodium chlorate administration on ruminal and fecal coliforms in sheep

Abstract

The objective of this study was to evaluate the efficacy of oral sodium chlorate administration on reducing total coliform populations in ewes. A 30% sodium chlorate product or a sodium chloride placebo was administered to twelve lactating Dorper X Blackbelly or Pelibuey crossbred ewes averaging 65 kg body weight. The ewes were adapted to diet and management. Ewes were randomly assigned (4/treatment) to one of three treatments which were administered twice daily by oral gavage for five consecutive days: a control (TC) consisting of 3 g sodium chloride/animal/d, a T3 treatment consisting of 1.8 g of sodium chlorate/animal/d, and a T9 treatment consisting of 5.4 g sodium chlorate/animal/d; the latter was intended to approximate a lowest known effective dose. Ruminal samples collected by stomach tube and freshly voided fecal samples were collected daily beginning 3 days before treatment initiation and for 6 days thereafter. Contents were cultured quantitatively to enumerate total coliforms. There were no significant differences in total coliform numbers (log₁₀ cfu/g) in the feces between treatments (P = 0.832). There were differences (P < 0.02) in ruminal coliform counts (log₁₀ cfu/mL) between treatments (4.1, 4.3 and 5.0 log₁₀/mL contents in TC, T3 and T9 Treatments, respectively) which tended to increase from the beginning of treatment until the 5th day of treatment (P < 0.05). Overall, we did not obtain the expected results with oral administration of sodium chloride at the applied doses. By comparing the trends in coliform populations in the rumen contents in all treatments, there was an increase over the days. The opposite trend occurred in the feces, due mainly to differences among rumen contents and feces in ewes administered the T9 treatment (P = 0.06). These results suggest that the low chlorate doses used here were suboptimal for the control of coliforms in the gastrointestinal tract of ewes.     

On-Road Vehicle Particulate Matter and Gaseous Emission Distributions in Las Vegas,Nevada, Compared with Other Areas

Abstract

During the spring and summer of 2000, 2001, and 2002, gaseous and particulate matter (PM) fuel-based emission factors for ～150,000 low-tailpipe, individual vehicles in the Las Vegas, NV, area were measured via on-road remote sensing. For the gaseous pollutants (carbon monoxide, hydrocarbons, and nitrogen oxide), a commercial vehicle emissions remote sensing system (VERSS) was used. The PM emissions were determined using a Lidar-based VERSS. Emission distributions and their shapes were analyzed and compared with previous studies. The large skewness of the distributions is evident for both gaseous pollutants and PM and has important implications for emission reduction policies, because the majority of emissions are attributed to a small fraction of vehicles. Results of this Las Vegas study and studies at other geographical locations were compared. The gaseous pollutants were found to be close to those measured by VERSS in other U.S. cities. The PM emission factors for spark ignition and diesel vehicles are in the range of previous tunnel and dynamometer studies.     

Quantifying food losses and the potential for reduction in Switzerland

A key element in making our food systems more efficient is the reduction of food losses across the entire food value chain. Nevertheless, food losses are often neglected. This paper quantifies food losses in Switzerland at the various stages of the food value chain (agricultural production, postharvest handling and trade, processing, food service industry, retail, and households), identifies hotspots and analyses the reasons for losses. Twenty-two food categories are modelled separately in a mass and energy flow analysis, based on data from 31 companies within the food value chain, and from public institutions, associations, and from the literature. The energy balance shows that 48% of the total calories produced (edible crop yields at harvest time and animal products, including slaughter waste) is lost across the whole food value chain. Half of these losses would be avoidable given appropriate mitigation measures. Most avoidable food losses occur at the household, processing, and agricultural production stage of the food value chain. Households are responsible for almost half of the total avoidable losses (in terms of calorific content).     

Life Cycle Assessment and Carbon Footprint in the Wine Supply-Chain

Global warming represents one of the most critical internationally perceived environmental issues. The growing, and increasingly global, wine sector is one of the industries which is under increasing pressure to adopt approaches for environmental assessment and reporting of product-related greenhouse gas emissions. The International Organization for Vine and Wine has recently recognized the need to develop a standard and objective methodology and a related tool for calculating carbon footprint (CF). This study applied this tool to a wine previously analyzed using the life cycle assessment (LCA) methodology. The objective was to test the tool as regards both its potential and possible limitations, and thus to assess its suitability as a standard tool. Despite the tool's user-friendliness, a number of limitations were noted including the lack of accurate baseline data, a partial system boundary and the impossibility of dealing with the multi-functionality issue. When the CF and LCA results are compared in absolute terms, large discrepancies become obvious due to a number of different assumptions, as well as the modeling framework adopted. Nonetheless, in relative terms the results seem to be quite consistent. However, a critical limitation of the CF methodology was its focus on a single issue, which can lead to burden shifting. In conclusion, the study confirmed the need for both further improvement and adaptation to additional contexts and further studies to validate the use of this tool in different companies.     

Performance of some biotic indices in the real variable world: A case study at different spatial scales in North-Western Mediterranean Sea

The aim of this study was to analyse the variability of four different benthic biotic indices (AMBI, BENTIX, H′, M-AMBI) in two marine coastal areas of the North-Western Mediterranean Sea. In each coastal area, 36 replicates were randomly selected according to a hierarchical sampling design, which allowed estimating the variance components of the indices associated with four different spatial scales (ranging from metres to kilometres). All the analyses were performed at two different sampling periods in order to evaluate if the observed trends were consistent over the time. The variance components of the four indices revealed complex trends and different patterns in the two sampling periods. These results highlighted that independently from the employed index, a rigorous and appropriate sampling design taking into account different scales should always be used in order to avoid erroneous classifications and to develop effective monitoring programs.