Parallel post-source decay for increasing protein identification confidence levels from 2-D gels

Peptide mass fingerprinting (PMF) has over the years become one of the most commonly used tools for high-throughput analysis and identification of proteins. This method is applicable when relatively simple samples have to be analysed and it is commonly used for analysing proteins previously separated by 2-DE. The most common type of instrument used for this approach is the MALDI-TOF that has proved to be particularly suitable for the PMF analysis because of its characteristics of speed, robustness, sensitivity and automation. We have used a MALDI-TOF equipped with a novel parallel PSD capability (MALDI micro MX), to perform the analysis of two sets of different biological samples isolated by 2-DE. By using a method that integrates the data obtained by PMF analysis with the PSD data obtained in the same experiment, we show that the new multiplexed PSD solution increases the protein identification rate compared to the normal PMF approach. We also investigated the use of a charge-directed fragmentation modification reagent to improve the identification rate and confidence levels.     

Molecular regulation of sink–source transition in rice leaf sheaths during the heading period

The upper leaf sheath of rice (Oryza sativa L.) serves as a temporary starch sink before heading, subsequently becoming a carbon source tissue to the growing panicle at the post-heading stage. The time of sink–source transition in upper leaf sheaths is highly correlated to the panicle exsertion. Here, we found that the expression profiles of starch synthesis genes such as ADP-glucose pyrophosphorylase large subunit 2, granule-bound starch synthase II, soluble starch synthase I, starch branching enzyme (SBE) I, SBEIII, and SBEIV were highly correlated with starch content changes during the heading period in the second leaf sheath below the flag leaf. In addition, the α-amylase2A and β-amylase were considered as major genes that were in charge of starch degradation at the post-heading period. Of the five sucrose transporter (OsSUT) genes, OsSUT1 and OsSUT4 appeared to play an important role in sucrose loading into the phloem of source leaf sheaths. Moreover, the microarray-based data implied that the dominant processes associated with functional leaf sheath transition from sink to source were carbohydrate metabolism and the translocation of the carbon and nitrogen sources and inorganic phosphate.     

Pollen productivity estimates and relevant source area of pollen for selected plant taxa in a pasture woodland landscape of the Jura Mountains (Switzerland)

Relevant source area of pollen (RSAP) and pollen productivity for 11 key taxa characteristic of the pasture woodland landscape of the Jura Mountains, Switzerland, were estimated using pollen assemblages from moss polsters at 20 sites. To obtain robust pollen productivity estimates (PPEs), we used vegetation survey data at a fine spatial-resolution (1 × 1 m²) and randomized locations for sampling sites, techniques rarely used in palynology. Three Extended R value (ERV) submodels and three distance-weighting methods for plant abundance calculation were applied. Different combinations of the submodels and distance-weighting methods provide slightly different estimates of RSAP and PPEs. Although ERV submodel 1 using 1/d (d = distance in meters) best fits the dataset, PPE values for heavy pollen types (e.g. Abies) were sensitive to the method used for distance-weighting. Taxon-specific distance-weighting methods, such as Prentice’s model, emphasize the intertaxonomic differences in pollen dispersal and deposition, and are thus theoretically sound. For the dataset obtained in this project, Prentice’s model was more appropriate than other distance-weighting methods to estimate PPEs. Most of the taxa have PPEs equal to (Fagus, Plantago media and Potentilla-type), or higher (Abies, Picea, Rubiaceae and Trollius europaeus) than Poaceae (PPE = 1). Acer, Cyperaceae, and Plantago montana-type are low pollen producers. This set of PPEs will be useful for reconstructing heterogeneous, mountainous pasture woodland landscapes from fossil pollen records. The RSAP for moss polsters in this semi-open landscape region is ca. 300 m.     

The use of modelling and simulation approach in reconstructing past landscapes from fossil pollen data: a review and results from the POLLANDCAL network

Information on past land cover in terms of absolute areas of different landscape units (forest, open land, pasture land, cultivated land, etc.) at local to regional scales is needed to test hypotheses and answer questions related to climate change (e.g. feedbacks effects of land-cover change), archaeological research, and nature conservancy (e.g. management strategy). The palaeoecological technique best suited to achieve quantitative reconstruction of past vegetation is pollen analysis. A simulation approach developed by Sugita (the computer model POLLSCAPE) which uses models based on the theory of pollen analysis is presented together with examples of application. POLLSCAPE has been adopted as the central tool for POLLANDCAL (POLlen/LANdscape CALibration), an international research network focusing on this topic. The theory behind models of the pollen–vegetation relationship and POLLSCAPE is reviewed. The two model outputs which receive greatest attention in this paper are the relevant source area of pollen (RSAP) and pollen loading in mires and lakes. Six examples of application of POLLSCAPE are presented, each of which explores a possible use of the POLLANDCAL tools and a means of validating or evaluating the models with empirical data. The landscape and vegetation factors influencing the size of the RSAP, the importance of pollen productivity estimates (PPEs) for the model outputs, the detection of small and rare patches of plant taxa in pollen records, and quantitative reconstructions of past vegetation and landscapes are discussed on the basis of these examples. The simulation approach is seen to be useful both for exploring different vegetation/landscape scenarios and for refuting hypotheses.     

A survey of unresolved problems in life cycle assessment

Background, aims, and scope  Life cycle assessment (LCA) stands as the pre-eminent tool for estimating environmental effects caused by products and processes from ‘cradle to grave’ or ‘cradle to cradle.’ It exists in multiple forms, claims a growing list of practitioners, and remains a focus of continuing research. Despite its popularity and codification by organizations such as the International Organization for Standards and the Society of Environmental Toxicology and Chemistry, life cycle assessment is a tool in need of improvement. Multiple authors have written about its individual problems, but a unified treatment of the subject is lacking. The following literature survey gathers and explains issues, problems and problematic decisions currently limiting LCA’s goal and scope definition and life cycle inventory phases. Main features  The review identifies 15 major problem areas and organizes them by the LCA phases in which each appears. This part of the review focuses on the first 7 of these problems occurring during the goal and scope definition and life cycle inventory phases. It is meant as a concise summary for practitioners interested in methodological limitations which might degrade the accuracy of their assessments. For new researchers, it provides an overview of pertinent problem areas toward which they might wish to direct their research efforts. Results and discussion  Multiple problems occur in each of LCA’s four phases and reduce the accuracy of this tool. Considering problem severity and the adequacy of current solutions, six of the 15 discussed problems are of paramount importance. In LCA’s first two phases, functional unit definition, boundary selection, and allocation are critical problems requiring particular attention. Conclusions and recommendations  Problems encountered during goal and scope definition arise from decisions about inclusion and exclusion while those in inventory analysis involve flows and transformations. Foundational decisions about the basis of comparison (functional unit), bounds of the study, and physical relationships between included processes largely dictate the representativeness and, therefore, the value of an LCA. It is for this reason that problems in functional unit definition, boundary selection, and allocation are the most critical examined in the first part of this review.

Biodegradation of 2,4-dichlorophenol by a <Emphasis Type="Italic">Bacillus</Emphasis> consortium

As part of our effort at establishing microbial consortia of relevance for the bioremediation of xenobiotics polluted environments in Mexico, we assessed the aerobic biodegradation of 2,4-dichlorophenol (2,4-DCP) by a consortium of four Bacillus species that were isolated from a polluted soil by enrichment using a mixture of chlorophenols. The bacterial consortium effectively biodegraded 2-chlorophenol, 3-chlorophenol and 2,4-dichlorophenol at degradation rates of between 1.7 and 6.7 μmoles l⁻¹ h⁻¹. In the presence of NH₄Cl or KNO₂ as nitrogen sources_, 2,4-DCP was variously degraded. Under both conditions, cell biomass attained highest values of 350 and 450 mg l⁻¹ respectively, while the amounts of 2,4-DCP metabolized in 21 days reached peak values of 2.1 and 2.5 mM representing between 70 and 85% degradation respectively. Chloride releases during the same period were highest at 4.7 mM and 5.3 mM in the presence of the two nitrogen sources. The presence of free-chloride in the culture medium had a significant impact on the catabolism of 2,4-dichlorophenol.     

Partitioning direct and indirect human-induced effects on carbon sequestration of managed coniferous forests using model simulations and forest inventories

Temperate forest ecosystems have recently been identified as an important net sink in the global carbon budget. The factors responsible for the strength of the sinks and their permanence, however, are less evident. In this paper, we quantify the present carbon sequestration in Thuringian managed coniferous forests. We quantify the effects of indirect human‐induced environmental changes (increasing temperature, increasing atmospheric CO₂ concentration and nitrogen fertilization), during the last century using BIOME‐BGC, as well as the legacy effect of the current age‐class distribution (forest inventories and BIOME‐BGC). We focused on coniferous forests because these forests represent a large area of central European forests and detailed forest inventories were available. The model indicates that environmental changes induced an increase in biomass C accumulation for all age classes during the last 20 years (1982–2001). Young and old stands had the highest changes in the biomass C accumulation during this period. During the last century mature stands (older than 80 years) turned from being almost carbon neutral to carbon sinks. In high elevations nitrogen deposition explained most of the increase of net ecosystem production (NEP) of forests. CO₂ fertilization was the main factor increasing NEP of forests in the middle and low elevations. According to the model, at present, total biomass C accumulation in coniferous forests of Thuringia was estimated at 1.51 t C ha^?1 yr^?1 with an averaged annual NEP of 1.42 t C ha^?1 yr^?1 and total net biome production of 1.03 t C ha^?1 yr^?1 (accounting for harvest). The annual averaged biomass carbon balance (BCB: biomass accumulation rate‐harvest) was 1.12 t C ha^?1 yr^?1 (not including soil respiration), and was close to BCB from forest inventories (1.15 t C ha^?1 yr^?1). Indirect human impact resulted in 33% increase in modeled biomass carbon accumulation in coniferous forests in Thuringia during the last century. From the forest inventory data we estimated the legacy effect of the age‐class distribution to account for 17% of the inventory‐based sink. Isolating the environmental change effects showed that these effects can be large in a long‐term, managed conifer forest.     

不同地区根霉分离株的RAPD多样性分析

为了研究微生物的分子多样性,在获得系列米根霉分离物的基础上,应用经筛选的13条随机引物,对来自不同地区的18株米根霉分离物进行了RAPD分析,聚类结果表明,18株分离物在0.75的相异水平上可以聚为6个群体,其分子多样性同地理来源之间具有一定的相关性。