Identification of a novel type of spacer element required for imprinting in fission yeast

Asymmetrical segregation of differentiated sister chromatids is thought to be important for cellular differentiation in higher eukaryotes. Similarly, in fission yeast, cellular differentiation involves the asymmetrical segregation of a chromosomal imprint. This imprint has been shown to consist of two ribonucleotides that are incorporated into the DNA during laggingstrand synthesis in response to a replication pause, but the underlying mechanism remains unknown. Here we present key novel discoveries important for unravelling this process. Our data show that cis-acting sequences within the mat1 cassette mediate pausing of replication forks at the proximity of the imprinting site, and the results suggest that this pause dictates specific priming at the position of imprinting in a sequence-independent manner. Also, we identify a novel type of cis-acting spacer region important for the imprinting process that affects where subsequent primers are put down after the replication fork is released from the pause. Thus, our data suggest that the imprint is formed by ligation of a not-fullyprocessed Okazaki fragment to the subsequent fragment. The presented work addresses how differentiated sister chromatids are established during DNA replication through the involvement of replication barriers

Spatial distribution of soils determines export of nitrogen and dissolved organic carbon from an intensively managed agricultural landscape

The surrounding landscape of a stream has crucial impacts on the aquatic environment. This study pictures the hydro-biogeochemical situation of the Tyrebækken creek catchment in central Jutland, Denmark. The intensively managed agricultural landscape is dominated by rotational croplands. The small catchment mainly consist of sandy soil types besides organic soils along the streams. The aim of the study was to characterise the relative influence of soil type and land use on stream water quality. Nine snapshot sampling campaigns were undertaken during the growing season of 2009. Total dissolved nitrogen (TDN), nitrate (NO3-), ammonium nitrogen and dissolved organic carbon (DOC) concentrations were measured, and dissolved organic nitrogen (DON) was calculated for each grabbed sample. Electrical conductivity, pH and flow velocity were measured during sampling. Statistical analyses showed significant differences between the northern, southern and converged stream parts, especially for NO3- concentrations with average values between 1.4 mg N l-1 and 9.6 mg N l-1. Furthermore, throughout the sampling period DON concentrations increased to 2.8 mg N l-1 in the northern stream contributing up to 81% to TDN. Multiple-linear regression analyses performed between chemical data and landscape characteristics showed a significant negative influence of organic soils on instream N concentrations and corresponding losses in spite of their overall minor share of the agricultural land (12.9%). On the other hand, organic soil frequency was positively correlated to the corresponding DOC concentrations. Croplands also had a significant influence but with weaker correlations. For our case study we conclude that the fractions of coarse textured and organic soils have a major influence on N and DOC export in this intensively used landscape. Meanwhile, the contribution of DON to the total N losses was substantial

Food safety and environmental risks based on meat and dairy consumption surveys

This paper gives an overview of the possibilities of using meat and dairy consumption studies in food safety and environmental risk scenarios. For both types of risk-based scenarios, common denominators are consumption patterns such as frequency and quantity of consumed food, demographic profile of consumers and food safety hazard or environmental impact of a specific type of food. This type of data enables development of simulation models where the Monte Carlo method is considered as a useful mathematical tool. Synergy of three dimensions - field research used in consumption studies, advanced chemometric tools necessary for quantifying chemical food safety hazards or environmental impacts and simulation models - has the potential to adapt datasets from various sources into useful food safety and/or environmental information

Gradient microfluidics enables rapid bacterial growth inhibition testing

Bacterial growth inhibition tests have become a standard measure of the adverse effects of inhibitors for a wide range of applications, such as toxicity testing in the medical and environmental sciences. However, conventional well-plate formats for these tests are laborious and provide limited information (often being restricted to an end-point assay). In this study, we have developed a microfluidic system that enables fast quantification of the effect of an inhibitor on bacteria growth and survival, within a single experiment. This format offers a unique combination of advantages, including long-term continuous flow culture, generation of concentration gradients, and single cell morphology tracking. Using Escherichia coli and the inhibitor amoxicillin as one model system, we show excellent agreement between an on-chip single cell-based assay and conventional methods to obtain quantitative measures of antibiotic inhibition (for example, minimum inhibition concentration). Furthermore, we show that our methods can provide additional information, over and above that of the standard well-plate assay, including kinetic information on growth inhibition and measurements of bacterial morphological dynamics over a wide range of inhibitor concentrations. Finally, using a second model system, we show that this chip-based systems does not require the bacteria to be labeled and is well suited for the study of naturally occurring species. We illustrate this using Nitrosomonas europaea, an environmentally important bacteria, and show that the chip system can lead to a significant reduction in the period required for growth and inhibition measurements (<4 days, compared to weeks in a culture flask)

Using fuzzy PROMETHEE to select countries for developmental Aid

Wealthy nations continue to demonstrate their unwavering support to improving conditions and the general well-being of poor countries in spite of the recent economic crises. However, as developmental aid relatively shrinks, both Aid donors and recipient countries have shown keen interest in methodologies used in evaluating developmental assistance programs. Evaluation of aid programs is seen as a complex task mainly because of the several non-aid factors that tend to affect overall outcomes. Adding to the complexity are the subjective sets of criteria used in Aid evaluations programs. This paper proposes a two stage framework of fuzzy TOPSIS and sensitivity analysis to demonstrate how aid-recipient countries can be evaluated to deepen transparency, fairness, value for money and sustainability of such aid programs. Using the Organisation for Economic Co-operation and Development (OECD) set of subjective criteria for evaluating aid programs; a numerical examplepre-defined by linguistic terms parameterized by triangular fuzzy numbers is provided to evaluate aid programs. Fuzzy PROMETHEE is used in the first stage to evaluate and rank aid-recipients followed by a comparative analysis with Fuzzy VIKOR and Fuzzy TOPSIS to ascertain an accurateness of the method used. A sensitivity analysis is further added that anticipates possible influences from lobbyists and examines the effect of that bias in expert ratings on the evaluation process. The result shows a framework that can be employed in evaluating aid effectiveness of recipient-countries

Sensory, microbiological and chemical changes in vacuum-packaged Blue Spotted Emperor (Lethrinus sp), Saddletail Snapper (Lutjanus malabaricus), Crimson Snapper (Lutjanus erythropterus), Barramundi (Lates calcarifer) and Atlantic Salmon (Salmo salar) fillets stored at 4°C

Quality assessment of finfish fillets during storage is important to be able to predict the shelf life of the fresh product during distribution. Microbial, chemical (pH, TMA, and TVB‐N), and sensory (Quality index assessment QIA, Torry scheme) changes in vacuum‐packaged blue‐spotted emperor (Lethrinus sp), saddletail (Lutjanus malabaricus), crimson snapper (Lutjanus erythropterus), barramundi (Lates calcarifer), and Atlantic salmon (Salmo salar) fillets stored at 4°C were evaluated for 5 days. Microbiological study included evaluation of TVC (total viable counts), total psychrotrophic organisms, and H2S‐producing bacteria. Numbers increased during storage time and reached an average of 8.5, 8.5, and 9.2 log10 cfu/g, respectively, for the five different fish species. These levels were above accepted microbiological limits for fish fillets. Although the sensory analyses showed a decrease in quality, none of the finfish fillets were considered unacceptable at the end of the storage trial. Chemically, there was a slight pH increase, but trimethylamine (TMA) levels remained low. However, total volatile basic nitrogen (TVB‐N) levels increased over time, reaching levels above 35 mg/100 g for blue spotted emperor, saddletail snapper, and crimson snapper by the end of the storage period. Results show that the deterioration of finfish fillet quality is a complex event of biochemical, sensory, and microbial factors, and multiple analyses may be required to define acceptability

Repeated evolution of self-compatibility for reproductive assurance

Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes evolutionary mechanisms such as hermaphroditism and self-fertilisation have repeatedly evolved. Combining insight from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes were readily evolving under selection in experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions governing the evolution of self-compatibility