Analyzing the function of a hox gene: an evolutionary approach

We present an evolutionary approach to dissecting conserved developmental mechanisms. We reason that important mechanisms for making the bodyplan will act early, to generate the major features of the body and that they will be conserved in evolution across many metazoa, and thus, that they will be available in very different animals. This led to our specific approach of microarrays to screen for very early conserved developmental regulators in parallel in an insect, Drosophila and a vertebrate, Xenopus. We screened for the earliest conserved targets of the ectopically expressed hox gene Hoxc6/Antennapedia in both species and followed these targets up, using in situ hybridization, in the Xenopus system. The results indicate that relatively few of the early Hox target genes are conserved: these are mainly involved in the specification of the antero-posterior body axis and in gastrulation.     

Towards building the silicon cell: a modular approach

Systems Biology aims to understand quantitatively how properties of biological systems can be understood as functions of the characteristics of, and interactions between their macromolecular components. Whereas, traditional biochemistry focused on isolation and characterization of cellular components, the challenge for Systems Biology lies in integration of this knowledge and the knowledge about molecular interactions. Computer models play an important role in this integration. We here discuss an approach with which we aim to link kinetic models on small parts of metabolism together, so as to form detailed kinetic models of larger chunks of metabolism, and ultimately of the entire living cell. Specifically, we will discuss techniques that can be used to model a sub-network in isolation of a larger network of which it is a part, while still maintaining the dynamics of the larger complete network. We will start by outlining the JWS online system, the silicon cell project, and the type of models we propose. JWS online is a model repository, which can be used for the storage, simulation and analysis of kinetic models. We advocate to integrate a top-down approach, where measurements on the complete system are used to derive fluxes in a detailed structural model, with a bottom-up approach, consisting of the integration of molecular mechanism-based detailed kinetic models into the structural model.     

Improving protein solubility: the use of the Escherichia coli dihydrofolate reductase gene as a fusion reporter

We have devised a strategy for screening mutant libraries for enzyme variants with enhanced solubility. The method is based on the observation that Escherichia coli can become insensitive to the antibiotic trimethoprim (TMP) if dihydrofolate reductase (DHFR) is expressed at an appropriate level. DHFR is a very soluble protein and can be expressed at levels that exceed normally lethal concentrations of TMP. In our approach, the gene encoding an insoluble target protein is placed in a vector so that the translated protein will be fused to DHFR. The resulting fusion protein will form inclusion bodies and inactivate DHFR-the cells will be susceptible to TMP. Mutations to the target protein that make it more soluble will also make the fusion protein more soluble so that DHFR will be at least partially active-the cells will be resistant to TMP. As the solubility of the target protein increases, the cells will become more resistant to TMP. The system was tested with a putative acetyltransferase (ACE) from a strain of the marine bacterium Vibrio fischerii. The gene encoding this protein was of interest since it is part of a mobile gene cassette within an integron array of the strain in question. After multiple rounds of shuffling and selection, ACE mutants were produced that had significantly improved solubility.     

Functional activation studies of word processing in the recovery from aphasia

Some reviews on theories of recovery in aphasia put an emphasis on neural network models based on empirical data from evoked-potentials in aphasia as an approach to mapping recovery of cognitive function to neural structure. We will focus here on what we call an "anatomical" approach to look at recovery in aphasia. "Anatomical" theories of recovery stated by classical aphasiologists have contributed to the understanding of language representations in the human brain. But many aspects of these theories can only be investigated by using modern techniques of lesion analysis, psychometric assessment and functional imaging. Whereas structure-function relations have been primarily established by looking for the association of deficit symptoms with certain lesions, functional activation methods offer a means to study more directly the functional anatomy of recovered or retained functions in neuropsychological patients. To falsify or build up anatomical theories of recovery we will propose a stepwise approach of inference. The methodological pitfalls of this approach will be discussed by focussing on anatomical hypotheses of semantic word comprehension and its impairment and recovery in aphasia.     

The cell cycle hypothesis of Alzheimer's disease: suggestions for drug development

The cell cycle of hypothesis of neural dysfunction in chronic neurodegenerative conditions such as Alzheimer's disease (AD) offers a unified approach to understanding both existing and novel strategies for drug development. At the present time, a ligand based approach is a pragmatic solution for identifying new chemical leads on which to base future discovery and optimisation. We have pursued a ligand based approach on the basis of public domain data to identify existing compounds capable of abrogating the cell cycle at the G0-G1 interface. Selected on this basis, irrespective of the tissue under study, we identified several classes of compounds as potential chemical leads. Of these compounds, at least ten have already been shown to be neuroprotective in animal models of acute neurodegeneration. Such compounds could form the basis of a screening exercise after development of suitable screening tools. Progressing of chemical leads through such an approach will be more efficient if future leads display relevant "drug-like" properties. Further, drug development in this arena should take account of the special concerns raised by targeting an elderly population. This will involve accounting for frequent polypharmacy in the aging population, and age-related alterations in physiology.     

The conserved genome organisation of non-falciparum malaria species: the need to know more

The current knowledge on genomes of non-falciparum malaria species and the potential of model malaria parasites for functional analyses are reviewed and compared with those of the most pathogenic human parasite, Plasmodium falciparum. There are remarkable similarities in overall genome composition among the different species at the level of chromosome organisation and chromosome number, conserved order of individual genes, and even conserved functions of specific gene domains and regulatory control elements. With the initiative taken to sequence the genome of P. falciparum, a wealth of information is already becoming available to the scientific community. In order to exploit the biological information content of a complete genome sequence, simple storage of the bulk of sequence data will be inadequate. The requirement for functional analyses to determine the biological role of the open reading frames is commonly accepted and knowledge of the genomes of the animal model malaria species will facilitate these analyses. Detailed comparative genome information and sequencing of additional Plasmodium genomes will provide a deeper insight into the evolutionary history of the species, the biology of the parasite, and its interactions with the mammalian host and mosquito vector. Therefore, an extended and integrated approach will enhance our knowledge of malaria and will ultimately lead to a more rational approach that identifies and evaluates new targets for anti-malarial drug and vaccine development.     

The European Union and Ocean Use Management: The Marine Strategy and the Maritime Policy

Problems resulting from contemporary patterns of ocean use and threats to the viability of the marine environment have led to reconsideration of ocean use governance in a number of states, including the United States, Australia, and Canada. For its part, the European Union has been working on the development of a Marine Strategy to safeguard the environment and a more encompassing Maritime Policy into which the Marine Strategy would be folded. The desired Maritime Policy would reflect a holistic perspective of ocean space, embody an ecosystem-based approach to ocean use management, and provide a broad framework for ocean/coastal management. As has been seen elsewhere, developing such a governance system is difficult both in terms of conceptualization and, subsequently, in operationalization. The June 2006 European Commission Green Paper on Maritime Policy sets the stage for a year of consultations designed to develop an effective governance system for ocean management. Institutional and policy changes will be needed and it will be necessary to balance the objectives of economic growth and protection of environmental sustainability. This article examines current developments in efforts to devise a coherent and integrated European Union approach to ocean management.     

Personalized medicine: revolutionizing drug discovery and patient care.

Advances in human genome research are opening the door to a new paradigm for practising medicine that promises to transform healthcare. Personalized medicine, the use of marker-assisted diagnosis and targeted therapies derived from an individual's molecular profile, will impact the way drugs are developed and medicine is practiced. Knowledge of the molecular basis of disease will lead to novel target identification, toxicogenomic markers to screen compounds and improved selection of clinical trial patients, which will fundamentally change the pharmaceutical industry. The traditional linear process of drug discovery and development will be replaced by an integrated and heuristic approach. In addition, patient care will be revolutionized through the use of novel molecular predisposition, screening, diagnostic, prognostic, pharmacogenomic and monitoring markers. Although numerous challenges will need to be met to make personalized medicine a reality, with time, this approach will replace the traditional trial-and-error practice of medicine.     

On the possibilities to apply the result from an LCA disclosed to public

Aim, Scope and background  Given the communication limitation of a damage-oriented approach, the question addressed in this paper is how normalisation can be developed instead. Normalisation of product service systems without value choices is, in accordance to ISO 14042, suitable for external communication. Reason normalisation approaches use a geographically-defined baseline year of emissions, optionally combined with politically established target emissions (Guinée 2002, Stranddorf et al. 2001). In contradiction to these approaches, this paper aims to draw up the general structure of an alternative normalisation procedure. The normalisation procedure suggested here is based on environmental quality objectives (EQO), in order to streamline the result to include as few output parameters as possible, without compromising the scientific robustness of the method. Main Features  This article describes a normalisation procedure based on environmental quality objectives. Comparison between this approach and a damage-oriented approach is conducted. The relevant working area concerning dose and effect is evaluated. Then a discussion is conducted focusing on the trade-off necessary to achieve an integrated category indicator, covering the following issues; model reliability, user applicability and the unambiguously of the result. Result  A damage-oriented approach will have to take into account all the defined consequences from all impact categories that affect the safeguards in parallel. In other words, each impact category indicator and its potential effects on all safeguards must be evaluated and accounted for. In the case where a single category indicator cannot be found without utilising value choices, a number of category indicators will then have to constitute an intermediate category indicator result, where weighting must be applied in order to streamline the result. In contrast to the above approach, the suggested normalisation procedure utilises the precautionary principle with respect to the essential EQO in order to achieve a category indicator result, called a critical load category indicator result. In practice, this means that the number of figures in an LCIA-profile based on critical load will always be the same as the number of impact categories. Conclusions  The suggested EQO normalisation procedure forms a set of critical loads per impact category, where each is defined by a critical load function where linearity is defined between a zero load and the critical load. This procedure will affect the temporal resolution and the field of application of the LCIA method. The positive aspect is that the suggested normalisation procedure renders the method applicable for long-lived products like, for example, buildings or other infrastructures. This aspect is gained by reducing the damage-oriented resolution. Consequently, for long-lived products where the main environmental loads will appear in the future, it is hard to assess by a damage-oriented LCIA method (if all boundary conditions are not assumed to be fixed). The EQO normalisation method will, in this respect, improve the overall reliability of the outcome of an LCA when long-lived products are assessed. For short-lived products, adequate boundary conditions can be achieved, and for this reason a damage-oriented approach will have the possibility to address current consequences. Nevertheless, a damage-oriented approach working area is not applicable beneath thresholds unlike the EQO normalisation procedure. The most effective decision support of short-lived products is therefore achieved when both approaches are applied. Outlook  A complementary paper will be produced where the described normalisation procedure is exemplified in a case study, with special interest on assessment of chemical substances.     

Integrated Human and Ecological Risk Assessment: A Case Study of Organophosphorous Pesticides in the Environment

This study was chosen as an example of integrated risk assessment because organophosphorous esters (OPs) share exposure characteristics for different species, including human beings and because a common mechanism of action can be identified. The “Framework for the integration of health and ecological risk assessment” is being tested against a deterministic integrated environmental health risk assessment for OPs used in a typical farming community. It is argued that the integrated approach helps both the risk manager and the risk assessor in formulating a more holistic approach toward the risk of the use of OP-esters. It avoids conclusions based on incomplete assessments or on separate assessments. The database available can be expanded and results can be expressed in a more coherent manner. In the integrated exposure assessment of OPs, the risk assessments for human beings and the environment share many communalities with regards to sources and emissions, distribution routes and exposure scenarios. The site of action of OPs, acetylcholinesterase, has been established in a vast array of species, including humans. It follows that in the integrated approach the effects assessment for various species will show communalities in reported effects and standard setting approaches. In the risk characterization, a common set of evidence, common criteria, and common interpretations of those criteria are used to determine the cause of human and ecological effects that co-occur or are apparently associated with exposure to OPs. Results of health and ecological risk assessments are presented in a common format that facilitates comparison of results. It avoids acceptable risk conclusions with regard to the environment, which are unacceptable with regard to human risk and vice versa. Risk managers will be prompted to a more balanced judgement and understanding and acceptance of risk reduction measures will be facilitated.     

The duration of residence approach to a dynamic stochastic model of internal migration: A test of the axiom of cumulative inertia

Abstract

The data presented indicate a definite trend that tends to support the axiom of cumulative inertia. The probabilities of movement decline by increasing duration of residence for each year. Not only is information on duration of residence an important element in any study of migration, but it also provides a necessary modification for the Markov chain approach to migration probabilities. Future studies of the mathematical model will require data that will satisfy the criteria stipulated in this paper and will be of sufficient quantity to assure reliable within‐cell probabilities of movement.     

DNA Taxonomy and the identification of immature insect stages: the true larva of Tauriphila argo (Hagen 1869) (Odonata: Anisoptera: Libellulidae)

For many insect taxa, larval morphology plays a decisive role in various fields like taxonomy, phylogeny or ecology. However, species identification is usually based on imaginal characters and the identification of larvae depends upon an established link to unequivocally identified imagines. This taxonomic correspondence of larvae and imagines is far from being established in many odonate species. We have employed a molecular approach to link larval and adult specimens in Tauriphila argo (Hagen, 1869). The sequenced mt SSU gene fragments of the reared female, supposedly a T. argo female, and a clearly identified male specimen of the species were identical. However, the larva of the reared female clearly differed from the described T. argo larva, previously matched to the species. From this observation, we conclude that the previously described larva of T. argo does not belong to this species because of too many phenotypic differences that far exceed the generally observed intraspecific variation.

It can be foreseen that the molecular approach will prove to be effective in identifying unknown larvae in many insect species. Additionally, the discrimination of sibling species or the linkage of allotypes and holotypes will become feasible with this approach.     

Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates

Measurements provide the basis for process monitoring and control as well as for model development and validation. Systematic approaches to increase the accuracy and credibility of the empirical data set are therefore of great value. In (bio)chemical conversions, linear conservation relations such as the balance equations for charge, enthalpy, and/or chemical elements, can be employed to relate conversion rates. In a pactical situation, some of these rates will be measured (in effect, be calculated directly from primary measurements of, e.g., concentrations and flow rates), as others can or cannot be calculated from the measured ones. When certain measured rates can also be calculated from other measured rates, the set of equations, the accuracy and credibility of the measured rates can indeed be improved by, respectively, balancing and gross error diagnosis. The balanced conversion rates are more accurate, and form a consistent set of data, which is more suitable for further application (e.g., to calculate nonmeasured rates) than the raw measurements. Such an approach has drawn attention in previous studies. The current study deals mainly with the problem of mathematically classifying the conversion rates into balanceable and calculable rates, given the subset of measured rates. The significance of this problem is illustrated with some examples. It is shown that a simple matrix equation can be derived that contains the vector of measured conversion rates and the redundancy matrix R. Matrix R plays a predominant role in the classification problem. In supplementary articles, significance of the redundancy matrix R for an improved gross error diagnosis approach will be shown. In addition, efficient equations have been derived to calculate the balanceable and/or calculable rates. The method is completely based on matrix algebra (principally different from the graph-theoretical approach), and it is easily implemented into a computer program. (c) 1994 John Wiley & Sons, Inc.     

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation

We have developed a formalism and a computational method for analyzing the potential functional consequences of non-synonymous single nucleotide polymorphisms. Our approach uses a structural model and phylogenetic information to derive a selection of structure and sequence-based features serving as indicators of an amino acid polymorphim's effect on function. The feature values can be integrated into a probabilistic assessment of whether an amino acid polymorphism will affect the function or stability of a target protein. The method has been validated with data sets of unbiased mutations in the lac repressor and lysoyzyme. Applying our methodology to recent surveys of genetic variation in the coding regions of clinically important genes, we estimate that approximately 26-32 % of the natural non-synonymous single nucleotide polymorphisms have effects on function. This estimate suggests that a typical person will have about 6240-12,800 heterozygous loci that encode proteins with functional variation due to natural amino acid polymorphism.     

Gene mapping of the mammalian genome: The CEPH and genethon initiative

Over the past four years, the CEPH (Jean Dausset Foundation) has expanded its linkage mapping effort to include physical mapping and, in 1990, co-founded the Genethon to ensure that a combined physical and genetic map of the entire human genome would be achieved. The Genethon has applied methods developed at CEPH on an industrial scale to accomplish the colossal task of constructing an integrated map. It is the role of such an integrated map to accelerate the search for the genes responsible for inherited diseases, and the results of the past 12 months encourage our optimism that this goal will be realized rapidly. These discoveries are providing not only an approach to the diagnosis of genetically based disease but also some of the first breakthroughs in the area of gene therapy.     

Finite Element Method (FEM) Modeling of Freeze-drying: Monitoring Pharmaceutical Product Robustness During Lyophilization

Lyophilization is an approach commonly undertaken to formulate drugs that are unstable to be commercialized as ready to use (RTU) solutions. One of the important aspects of commercializing a lyophilized product is to transfer the process parameters that are developed in lab scale lyophilizer to commercial scale without a loss in product quality. This process is often accomplished by costly engineering runs or through an iterative process at the commercial scale. Here, we are highlighting a combination of computational and experimental approach to predict commercial process parameters for the primary drying phase of lyophilization. Heat and mass transfer coefficients are determined experimentally either by manometric temperature measurement (MTM) or sublimation tests and used as inputs for the finite element model (FEM)-based software called PASSAGE, which computes various primary drying parameters such as primary drying time and product temperature. The heat and mass transfer coefficients will vary at different lyophilization scales; hence, we present an approach to use appropriate factors while scaling-up from lab scale to commercial scale. As a result, one can predict commercial scale primary drying time based on these parameters. Additionally, the model-based approach presented in this study provides a process to monitor pharmaceutical product robustness and accidental process deviations during Lyophilization to support commercial supply chain continuity. The approach presented here provides a robust lyophilization scale-up strategy; and because of the simple and minimalistic approach, it will also be less capital intensive path with minimal use of expensive drug substance/active material.     

Solvated docking: introducing water into the modelling of biomolecular complexes

MOTIVATION: Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes. METHODS: We present a solvated docking approach that explicitly accounts for the presence of water in protein-protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water layer is present in-between the molecules. It mimics the pathway from this initial complex towards the final assembly in which most waters have been expelled from the interface. Docking is performed from solvated biomolecules and waters are removed in a biased Monte Carlo procedure based on water-mediated contact propensities obtained from an analysis of high-resolution crystal structures. RESULTS: We demonstrate the feasibility of this approach for protein-protein complexes representing both 'wet' and 'dry' interfaces. Solvated docking leads to improvements both in quality and scoring. Water molecules are recovered that closely match the ones in the crystal structures. AVAILABILTY: Solvated docking will be made available in the future release of HADDOCK version 2.0 (http://www.nmr.chem.uu.nl/haddock).