Foot differentiation and genomic plasticity in Hydra: lessons from the PPOD gene family

In Hydra, developmental processes are permanently active to maintain a simple body plan consisting of a two-layered, radially symmetrical tube with two differentiated structures, head and foot. Foot formation is a dynamic process and includes terminal differentiation of gastric epithelial cells into mucous secreting basal disc cells. A well-established marker for this highly specialized cell type is a locally expressed peroxidase (Hoffmeister et al. 1985). Based on the foot-specific peroxidase activity, the gene PPOD1 has been identified (Hoffmeister-Ullerich et al. 2002). Unexpectedly, this approach led to the identification of a second gene, PPOD2, with high sequence similarity to PPOD1 but a strikingly different expression pattern. Here, we characterize PPOD2 in more detail and show that both genes, PPOD1 and PPOD2, are members of a gene family with differential complexity and expression patterns in different Hydra species. At the genomic level, differences in gene number and structure within the PPOD gene family, even among closely related species, support a recently proposed phylogeny of the genus Hydra and point to unexpected genomic plasticity within closely related species of this ancient metazoan taxon. Electronic supplementary material Supplementary material is available in the online version of this article at     

Factors that influence decisions by families to donate brain tissue for medical research

Whilst mainstream transplant literature provides valuable insights into the influences on families to donate organs and tissues for transplant, the relevance of these findings in relation to organ donation for research remain speculative. The present study aims to expand the research donation literature, by exploring factors that influence a family’s decision to donate brain tissue to neuroscience research. The verbal responses of the senior available next-of-kin (NOK), to the question of brain donation for research, are analysed. The donation rate was high (54%) over the 5-year-period. NOK relationship to the deceased, and post mortem interval were the main factors associated with a positive donation. Parents were most likely to donate and this may result from a lifetime of decision-making on behalf of the deceased. Also, the longer the interval between death of the potential donor and the question being asked, the greater the likelihood of donation.     

Rethinking of risk communication: lessons from the decision sciences

Risk communication involves three primary elements: process, content and intent. Much has been written about the first two. Much is known, for example, about the guiding principles that should be considered during the design of a risk communication. Likewise, many studies have been conducted about how best to establish the technical and informational content of a risk communication. Very little attention, by contrast, has been devoted to the intent of risk communication, which is to inform decision making for risk management. While appropriate information upon which to base risk management decisions is important, so to is an understanding of how people instinctively approach decision making under conditions of risk. Work in the decision sciences provides this often-missing perspective for many risk communication efforts and is, therefore, the focus of this paper.

Cultivating participatory policy processes for genetic resources policy: lessons from the Genetic Resources Policy Initiative (GRPI) project

The purpose of the paper is to draw lessons and document experiences from the Genetic Resources Policy Initiative (GRPI) project, a project which has been underway in six countries and two sub-regions during the last 5 years. Its focus has been to experiment an approach to participatory policy processes, coined by the project, called the multi-stakeholder, multi-disciplinary and multi-sector or in short the 3M. This approach, which was demand-driven due to the nature of the policy problems being examined, aims to create a platform to address competing interests inherent in genetic resources issues from multiple perspectives. It is meant to enable different stakeholders to balance issues they diverge and/or converge upon in genetic resources management, thereby harmonizing trade-offs, objectives and strategies. Experiences from the project in applying the 3M in Egypt, Nepal, Vietnam Peru and Zambia highlight several lessons in participatory policy processes. The experiences show that the success or otherwise of participatory policy making processes is dependent on various factors that have to do with stakeholder capacities, process orientation, shared understanding versus vested interests and institutional functions. They highlight that the most effective approach to stakeholder engagement in policy processes is to construct them around an actively engaged ‘process leader’ that possesses, or has the potential to champion the process by mobilising the required cognitive knowledge and institutional engagement. They further suggest that since genetic resources policy issues are cross-cutting, they will demand a more holistic approach with a clear identification of impact pathways through which policy changes can be expected to influence the outcome variables. Since policy making processes are perpetual, the question of sustaining project ideas and recommendations beyond the life of a project has to be part of the planning exercise in any participatory genetic resources policy research and formulation.

Microarray data quality analysis: lessons from the AFGC project

Genome-wide expression profiling with DNA microarrays has and will provide a great deal of data to the plant scientific community. However, reliability concerns have required the development data quality tests for common systematic biases. Fortunately, most large-scale systematic biases are detectable and some are correctable by normalization. Technical replication experiments and statistical surveys indicate that these biases vary widely in severity and appearance. As a result, no single normalization or correction method currently available is able to address all the issues. However, careful sequence selection, array design, experimental design and experimental annotation can substantially improve the quality and biological of microarray data. In this review, we discuss these issues with reference to examples from the Arabidopsis Functional Genomics Consortium (AFGC) microarray project.     

Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family

Background  

Chitinases (EC.3.2.1.14) hydrolyze the β-1,4-linkages in chitin, an abundant N-acetyl-β-D-glucosamine polysaccharide that is a structural component of protective biological matrices such as insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 (GH18) family of chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Mammals are not known to synthesize chitin or metabolize it as a nutrient, yet the human genome encodes eight GH18 family members. Some GH18 proteins lack an essential catalytic glutamic acid and are likely to act as lectins rather than as enzymes. This study used comparative genomic analysis to address the evolutionary history of the GH18 multiprotein family, from early eukaryotes to mammals, in an effort to understand the forces that shaped the human genome content of chitinase related proteins.     

Making a better case for biodiversity conservation: the BESAFE project

This Editorial to the BESAFE special issue introduces the project and its approach and case studies. The BESAFE (EC 7th Framework programme) project investigated how the effectiveness of different types of arguments for biodiversity conservation depends on the context in which they are used. Our results show that tailoring of argumentation to audience within the course of decision processes is the main factor determining effectiveness. We consistently found arguments linked to intrinsic value (e.g. moral or ethical obligation arguments) as shared and supported widely, and thus offering common ground between parties. Economic arguments are effective as additional ones, but not as replacements. Next generation biodiversity conservation strategies can probably improve their effectiveness by emphasizing and better explaining the synergies between traditional conservation and especially regulating and cultural services.     

S28 peptidases: lessons from a seemingly 'dysfunctional' family of two

A recent paper in BMC Structural Biology reports the crystal structure of human prolylcarboxypeptidase (PRCP), one of the two members of the S28 peptidase family. Comparison of the substrate-binding site of PRCP with that of its family partner, dipeptidyl dipeptidase 7 (DPP7), helps to explain the different enzymatic activities of these structurally similar proteins, and also reveals a novel apparent charge-relay system in PRCP involving the active-site catalytic histidine.     

Human brain reflexes: from stimulus to recognition and from decision to action

The paper presents a survey of the data, obtained in laboratories, directed by the author, on the problem of the brain bases of psychics. Phenomena of perception, thinking and taking decision about behavioural response correspond to the afferent, central and efferent parts of the reflex arch. Psychic function arises on the basis of complex organization and integration of the processes in the brain. It is shown that sensation is based on the synthesis in the cortical projection area of the information on physical and signal properties of the stimulus. By means of the method developed in the laboratory, of mapping of intracortical interaction the participation is studied of different cortical zones in the process of mental creation of visual image. The process of taking decision is studied by a new method: "reaction choice potential" recorded in the case of decision, about the character of reaction to signal controlled by consciousness.     

Towards new enzymes for biofuels: lessons from chitinase research

Enzymatic conversion of structural polysaccharides in plant biomass is a key issue in the development of second generation ('lignocellulosic') bioethanol. The efficiency of this process depends in part on the ability of enzymes to disrupt crystalline polysaccharides, thus gaining access to single polymer chains. Recently, new insights into how enzymes accomplish this have been obtained from studies on enzymatic conversion of chitin. First, chitinolytic microorganisms were shown to produce non-hydrolytic accessory proteins that increase enzyme efficiency. Second, it was shown that a processive mechanism, which is generally considered favorable because it improves substrate accessibility, might in fact slow down enzymes. These findings suggest new focal points for the development of enzyme technology for depolymerizing recalcitrant polysaccharide biomass. Improving substrate accessibility should be a key issue because this might reduce the need for using processive enzymes, which are intrinsically slow and abundantly present in current commercial enzyme preparations for biomass conversion. Furthermore, carefully selected substrate-disrupting accessory proteins or domains might provide novel tools to improve substrate accessibility and thus contribute to more efficient enzymatic processes.     

Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project

Structural studies of multi-protein complexes, whether by X-ray diffraction, scattering, NMR spectroscopy or electron microscopy, require stringent quality control of the component samples. The inability to produce 'keystone' subunits in a soluble and correctly folded form is a serious impediment to the reconstitution of the complexes. Co-expression of the components offers a valuable alternative to the expression of single proteins as a route to obtain sufficient amounts of the sample of interest. Even in cases where milligram-scale quantities of purified complex of interest become available, there is still no guarantee that good quality crystals can be obtained. At this step, protein engineering of one or more components of the complex is frequently required to improve solubility, yield or the ability to crystallize the sample. Subsequent characterization of these constructs may be performed by solution techniques such as Small Angle X-ray Scattering and Nuclear Magnetic Resonance to identify 'well behaved' complexes. Herein, we recount our experiences gained at protein production and complex assembly during the European 3D Repertoire project (3DR). The goal of this consortium was to obtain structural information on multi-protein complexes from yeast by combining crystallography, electron microscopy, NMR and in silico modeling methods. We present here representative set case studies of complexes that were produced and analyzed within the 3DR project. Our experience provides useful insight into strategies that are more generally applicable for structural analysis of protein complexes.     

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research

The Zebrafish Information Network, ZFIN, is a WWW community resource of zebrafish genetic, genomic and developmental research information (http://zfin.org). ZFIN provides an anatomical atlas and dictionary, developmental staging criteria, research methods, pathology information and a link to the ZFIN relational database (http://zfin. org/ZFIN/). The database, built on a relational, object-oriented model, provides integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish research community. The database is populated with curated published data, user submitted data and large dataset uploads. A broad range of data types including text, images, graphical representations and genetic maps supports the data. ZFIN incorporates links to other genomic resources that provide sequence and ortholog data. Zebrafish nomenclature guidelines and an automated registration mechanism for new names are provided. Extensive usability testing has resulted in an easy to learn and use forms interface with complex searching capabilities.     

Molecular cloning, genomic organization and expression analysis of the gene encoding bovine (Bos taurus) B-cell activating factor belonging to the TNF family (BAFF)

A novel bovine cDNA has been isolated by EST assembly and subsequently confirmed by using RT-PCR and designated bovine B-cell activating factor belonging to TNF family (bBAFF). The open reading frame (ORF) of this cDNA covers 843 bp, encoding 280 amino acids. The functional soluble part of bBAFF (bsBAFF) shows 96% and 91% identity with its pig and human counterparts, respectively, at the level of the primary protein structure. The bBAFF genomic sequence consists of six exons and five introns, is approximately 30 kb in size, and maps to bovine chromosome 12q. Southern blotting analysis indicated that the bBAFF gene is a single copy gene. Real-time quantitative PCR (qPCR) analysis revealed that bBAFF is predominantly expressed in bovine lymphoid tissues PBLs and spleen. The predicted three dimensional (3D) structure of the bsBAFF monomer analyzed by "comparative protein modeling" revealed that it is very similar to its human counterpart. In western blotting analysis, His6-tagged bsBAFF protein expressed in E. coli could be recognized not only by an anti-His6.tag mAb but also by an anti-human sBAFF mAb, indicating immunological cross-reactivity occurs between bovine and human sBAFF protein.