Making marine life count: a new baseline for policy

The Census of Marine Life aids practical work of the Convention on Biological Diversity, discovers and tracks ocean biodiversity, and supports marine environmental planning.     

Thioredoxin affinity chromatography: a useful method for further understanding the thioredoxin network

Thioredoxin affinity chromatography can be used to recognize the target proteins of thioredoxin or thioredoxin-related proteins in whole cells or certain cellular compartments. In the last couple of years, many potential target proteins have been identified from various organelles and organisms by this method. Based on the information on the target proteins provided by these studies, the complete thioredoxin-related redox networks can now be efficiently described.     

Rapid synthesis of oligodeoxyribonucleotides: a new solid-phase method.

A method is described that makes use of a new polyamide resin for the rapid synthesis of short oligodeoxyribonucleotides. The method is illustrated by the preparation of two heptadeoxyribonucleotides, d(pT6-C) and d(pC-A-G-T-G-A-T) using a phosphodiester approach. A further development involved use of phenyl isocyanate as an in situ drying agent, which obviated the need for solvent co-evaporation prior tothe internucleotidic coupling steps. Improved fractionation of thymidyl oligonucleotides was obtained by use of a new microparticulate, silica-based anion-exchanger.     

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

Background  

Constraint-based flux analysis of metabolic network model quantifies the reaction flux distribution to characterize the state of cellular metabolism. However, metabolites are key players in the metabolic network and the current reaction-centric approach may not account for the effect of metabolite perturbation on the cellular physiology due to the inherent limitation in model formulation. Thus, it would be practical to incorporate the metabolite states into the model for the analysis of the network.     

Applications of biotope mapping for spatial environmental planning and policy: case studies in urban ecosystems in Korea

The purpose of this paper is to investigate the current status and method of biotope mapping for practical use for landscape planning and environmental policy in urban ecosystem in Korea. We examine current ecological mapping of Seoul, Seongnam, Daegu, and Yongin. Ecological mapping is examined closely in terms of investigation methodology, investigation subject, classification of urban landscape, and the present condition of application. Biotope mapping in Seoul and Seongnam were carried out by the city governments concerned with the pre-set budgets earmarked for mapping. In order to promote the utilization of biotope maps for city planning in Korea, the following actions should be considered. First, the survey method should be standardized by introducing a uniform standard with respect to the scope of survey, the quality of primary data used, the survey method, and the level of the survey. Second, it is necessary to identify a basic category of biotope for each area by consolidating the outcome of the previous surveys. Third, it is highly desirable to minimize the differences between the evaluation criteria and the assessment factors. Fourth, it is ideal to apply the results of the biotope evaluation to city planning in an indirect manner through reflecting the results first in the landscape plans. In order to facilitate this alternative utilization, it is necessary to strengthen the control provisions contained in the ordinances of the city concerned or to enact a set of new provisions in the ordinances so that biotope mapping could be used more widely as a criterion for the spatial environmental impact assessment.     

Impact of environmental inputs on reverse-engineering approach to network structures

Background  

Uncovering complex network structures from a biological system is one of the main topic in system biology. The network structures can be inferred by the dynamical Bayesian network or Granger causality, but neither techniques have seriously taken into account the impact of environmental inputs.     

A new model and method for understanding Wolbachia-induced cytoplasmic incompatibility

Wolbachia are intracellular bacteria transmitted almost exclusively vertically through eggs. In response to this mode of transmission, Wolbachia strategically manipulate their insect hosts' reproduction. In the most common manipulation type, cytoplasmic incompatibility, infected males can only mate with infected females, but infected females can mate with all males. The mechanism of cytoplasmic incompatibility is unknown; theoretical and empirical findings need to converge to broaden our understanding of this phenomenon. For this purpose, two prominent models have been proposed: the mistiming-model and the lock-key-model. The former states that Wolbachia manipulate sperm of infected males to induce a fatal delay of the male pronucleus during the first embryonic division, but that the bacteria can compensate the delay by slowing down mitosis in fertilized eggs. The latter states that Wolbachia deposit damaging "locks" on sperm DNA of infected males, but can also provide matching "keys" in infected eggs to undo the damage. The lock-key-model, however, needs to assume a large number of locks and keys to explain all existing incompatibility patterns. The mistiming-model requires fewer assumptions but has been contradicted by empirical results. We therefore expand the mistiming-model by one quantitative dimension to create the new, so-called goalkeeper-model. Using a method based on formal logic, we show that both lock-key- and goalkeeper-model are consistent with existing data. Compared to the lock-key-model, however, the goalkeeper-model assumes only two factors and provides an idea of the evolutionary emergence of cytoplasmic incompatibility. Available cytological evidence suggests that the hypothesized second factor of the goalkeeper-model may indeed exist. Finally, we suggest empirical tests that would allow to distinguish between the models. Generalizing our results might prove interesting for the study of the mechanism and evolution of other host-parasite interactions.     

Clinical governance implementation in a selected teaching emergency department: a systems approach

ABSTRACT: BACKGROUND: Clinical governance (CG) is among the different frameworks proposed to improve the quality of healthcare. Iran, like many other countries, has put healthcare quality improvement in its top health policy priorities. In November 2009, implementation of CG became a task for all hospitals across the country. However, it has been a challenge to clarify the notion of CG and the way to implement it in Iran. The purpose of this action research study is to understand how CG can be defined and implemented in a selected teaching emergency department (ED).Methods/designWe will use Soft Systems Methodology for both designing the study and inquiring into its content. As we considered a complex problem situation regarding the quality of care in the selected ED, we initially conceptualized CG as a cyclic set of purposeful activities designed to explore the situation and find relevant changes to improve the quality of care. Then, implementation of CG will conceptually be to carry out that set of purposeful activities. The activities will be about: understanding the situation and finding out relevant issues concerning the quality of care; exploring different stakeholders' views and ideas about the situation and how it can be improved; and defining actions to improve the quality of care through structured debates and development of accommodations among stakeholders. We will flexibly use qualitative methods of data collection and analysis in the course of the study. To ensure the study rigor, we will use different strategies. DISCUSSION: Successful implementation of CG, like other quality improvement frameworks, requires special consideration of underlying complexities. We believe that addressing the complex situation and reflections on involvement in this action research will make it possible to understand the concept of CG and its implementation in the selected setting. By describing the context and executed flexible methods of implementation, the results of this study would contribute to the development of implementation science and be employed by boards and executives governing other clinical settings to facilitate CG implementation.     

RNAi assay in primary cells: a new method for gene function analysis in marine bivalve

RNA interference (RNAi) is an effective approach for gene function analysis, which is well developed in mammal cell lines. However, RNAi has rarely been reported in marine bivalve species. To provide support on functional analysis of bivalve genes, for the first time to our knowledge, we conducted RNAi assay on primary cell of clam Meretrix meretrix in this study. Firstly we explored the method of culturing primary cells of M. meretrix to ensure the cells to live at high activity for at least 2 weeks. Ferritin gene was chosen as the target gene and RNAi assay was conducted through soaking the primary cells of M. meretrix digestive gland in medium containing dsRNA of ferritin gene. Realtime PCR, western blot and immunocytochemistry analysis were used to analyze the inhibition of gene expression after RNAi. Results showed the ferritin mRNA was significantly down-regulated by 66.11% after RNAi. Western blot result showed that the expression level of ferritin protein was also depressed post RNAi. The method developed in this study proved to be reliable and effective for RNAi assay on marine bivalve cells. It would be an efficient tool for gene function analysis in marine bivalves and more studies based on primary cells of marine bivalves can be expected.     

Genomic fluidity of Bordetella pertussis assessed by a new method for chromosomal mapping.

The genomic organization of Bordetella pertussis strains has been examined by using a new method. This method does not depend on the prior determination of a restriction map of the bacterial chromosome but is based on the ability to measure directly the distance between two genes. This is accomplished through the integration at each gene of a suicide vector containing a cleavage site for the intron-encoded endonuclease I-SceI, which is not otherwise found in the chromosome. Integration is mediated by homologous recombination between the chromosomal and cloned plasmid copies of a gene of interest. Digestion with I-SceI gives rise to a fragment the size of which represents the distance between the two genes. Multiple pairwise determinations within a set of genes provide sufficient information to derive a map of the relative gene positions. Mapping a set of 11 to 13 genes for five strains of B. pertussis and one strain of B. parapertussis revealed extensive divergence of gene order between B. pertussis Tohama I, B. pertussis 18-323, and B. parapertussis ATCC 15311. Less extensive divergence of gene order was observed between B. pertussis Tohama I and B. pertussis Tohama III, BP165, and Wellcome 28, with most of the observed differences explainable by large inversions.     

A new method of DNA denaturation mapping.

Described is a new method for DNA denaturation mapping utilizing glyoxal (ethanedial) to stabilize the denatured regions. The extent of glyoxal reaction can be easily and sensitively measured using an assay based on the intercalation of ethidium into duplex DNA. Thus denturation maps can be produced in a controlled way under a wide variety of conditions.     

Metastable secondary structures in ribosomal RNA: a new method for analyzing the titration behavior of rRNA

The pH titration behavior of E. coli rRNA in the acid range has been analyzed by combining spectrophotometric and potentiometric titration data. The “simplest” model for the system, which considers as possible reactions the protonation of adenine (A), cytosine (C), and guanine (G) residues along with the opening of A·U and G·C base pairs, does not adequately account for the titration properties. It is postulated that extra reactions may occur in addition to those in the “simplest” model, and a new analytical method was developed to deal with this situation. Our approach yields the ultraviolet spectral changes which accompany the extra reactions, from which the nature of these reactions can in principle be deduced. The calculations also give, at each pH, the extents of the extra reactions as well as the extents of those reactions which comprise the “simplest” model. We infer that in acidic RNA solutions of 0.1M ionic strength there occur at least two extra reactions, each of which involves G residues. We propose that in the pH range 6.0 ≥ pH ≥ 3.8 triple-stranded helical sequences, presumably protonated G·C·G, are formed. These regions are replaced at lower pH by acid-stable structures involving G·G and A·A base pairs. In solutions of lower ionic strength (I = 0.01M) no triple strands are formed, but G·G and A·A regions seem to develop even at pH values as high as 6.0. At I = 0.1M, an acid–base titration cycle between pH 7 and 2.8 is not reversible; rRNA shows true hysteresis behavior. We conclude that in ribosomal RNA's, which are generally G-rich, guanine residues may participate in hitherto unpredicted conformations, some of which may be metastable while others are equilibrium structures.     

Haligena salina: a new marine pyrenomycete

EARRANT, C. A. & JONES, E. B. G., 1986. Haligena salina: a new marine pyrenomycete. Haligena salina sp. Nova (Ascomycotina, Sphaeriales, Halosphaeriaceae) collected on wood from San Juan Island, Washington State, U.S.A., and on reeds from Pisa, Italy is described. The species is compared with Haligena elaterophoraj. Kohlmeyer and species in the genus Remispora Linder.     

Rapid increase in fish numbers follows creation of world's largest marine reserve network

No-take marine reserves (NTMRs) are much advocated as a solution to managing marine ecosystems, protecting exploited species and restoring natural states of biodiversity [1,2]. Increasingly, it is becoming clear that effective marine conservation and management at ecosystem and regional scales requires extensive networks of NTMRs [1,2]. The world's largest network of such reserves was established on Australia's Great Barrier Reef (GBR) in 2004. Closing such a large area to all fishing has been socially and politically controversial, making it imperative that the effectiveness of this new reserve network be assessed. Here we report evidence, first, that the densities of the major target species of the GBR reef line fisheries were significantly higher in the new NTMRs, compared with fished sites, in just two years; and second, that the positive differences were consistent for multiple marine reserves over an unprecedented spatial scale (>1,000 km).