Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the x-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the x-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA- M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.

Header design for flow equalization in microstructured reactors

To enhance the uniformity of fluid flow distribution in microreactors, a header configuration consisting of a cone diffuser connected to a thick-walled screen has been proposed. The thick-walled screen consists of two sections: the upstream section constitutes a set of elongated parallel upstream channels and the downstream section constitutes a set of elongated parallel downstream channels positioned at an angle of 90 with respect to the upstream channels. In this approach the problem of flow, equalization reduces to that of flow equalization in the first and second downstream channels of the thick-walled screen. In turn, this requires flow equalization in the corresponding cross sections of the upstream channels. The computational fluid dynamics analysis of the fluid flow maldistribution shows that eight parallel upstream channels with a width of 300-600 pm are required per 1 cm of length for flow equalization. The length to width ratio of these channels has to be > 15. The numerical results suggest that the proposed header-configuration can effectively improve the performance of the downstream microstructured devices, decreasing the ratio of the maximum flow velocity to the mean flow velocity from 2 to 1.005 for a wide range of Reynolds numbers (0.5-10). 2006 American Institute of Chemical Engineers AlChE J, 53: 28-38, 2007.

Pilgrimstad revisited - a multi-proxy reconstruction of Early/Middle Weichselian climate and environment at a key site in central Sweden

The site Pilgrimstad in central Sweden has often been cited as a key locality for discussions of ice-free/ice-covered intervals during the Early and Middle Weichselian. Multi-proxy investigations of a recently excavated section at Pilgrimstad now provide a revised picture of the climatic and environmental development between similar to 80 and 36 ka ago. The combination of sedimentology, geochemistry, OSL and 14C dating, and macrofossil, siliceous microfossil and chironomid analyses shows: (i) a lower succession of glaciofluvial/fluvial, lacustrine and glaciolacustrine sediments; (ii) an upper lacustrine sediment sequence; and (iii) Last Glacial Maximum till cover. Microfossils in the upper lacustrine sediments are initially characteristic for oligo- to mesotrophic lakes, and macrofossils indicate arctic/sub-arctic environments and mean July temperatures > 8 degrees C. These conditions were, however, followed by a return to a low-nutrient lake and a cold and dry climate. The sequence contains several hiatuses, as shown by the often sharp contacts between individual units, which suggests that ice-free intervals alternated with possible ice advances during certain parts of the Early and Middle Weichselian.

Site choices in recreational demand: a matter of utility maximization or regret minimization?

This paper compares the Random Regret Minimization and the Random Utility Maximization models for determining recreational choice. The Random Regret approach is based on the idea that, when choosing, individuals aim to minimize their regret – regret being defined as what one experiences when a non-chosen alternative in a choice set performs better than a chosen one in relation to one or more attributes. The Random Regret paradigm, recently developed in transport economics, presents a tractable, regret-based alternative to the dominant choice paradigm based on Random Utility. Using data from a travel cost study exploring factors that influence kayakers’ site-choice decisions in the Republic of Ireland, we estimate both the traditional Random Utility multinomial logit model (RU-MNL) and the Random Regret multinomial logit model (RR-MNL) to gain more insights into site choice decisions. We further explore whether choices are driven by a utility maximization or a regret minimization paradigm by running a binary logit model to examine the likelihood of the two decision choice paradigms using site visits and respondents characteristics as explanatory variables. In addition to being one of the first studies to apply the RR-MNL to an environmental good, this paper also represents the first application of the RR-MNL to compute the Logsum to test and strengthen conclusions on welfare impacts of potential alternative policy scenarios.

Environmental, lifestyle, and familial/ethnic factors associated with myeloproliferative neoplasms

Myeloproliferative neoplasms (MPNs) are characterized by overproduction of mature functional blood cells and are often associated with an acquired genetic mutation of Janus Kinase 2V617F. The etiology of MPNs remains unknown. The aim of this article was to review and collate all known published data investigating environmental and lifestyle factors associated with MPNs. Medline, Embase, PubMed, Cochrane, and Web of Science were systematically searched using terms for MPNs and observational study designs to identify studies investigating the risk factors for MPNs published before March 2010. Of 9,156 articles identified, 19 met the selection criteria. Although the studies exhibited heterogeneity, in case definitions, study design, and risk factors investigated, several themes emerged. A strong association was found with Jewish descent, and with a family history of MPNs. Autoimmune conditions, specifically Crohn's disease, were more common in patients with MPNs. Certain occupational groups were significantly associated with MPNs including occupations with potential exposure to benzene and/or petroleum. Blood donation was associated with an increased risk of polycythemia vera specifically. The vast heterogeneity in studies identified as part of this review suggests that large scale systematic assessment of etiological factors associated with MPNs is warranted. (C) 2011 Wiley-Liss, Inc.

FACTORIAL EXPERIMENTAL-DESIGN FOR CONCRETE DURABILITY RESEARCH

It is widely accepted that concrete designed to perform satisfactorily in adverse environmental conditions must have a high cement content and a low water-cement ratio. In addition, in order to enhance its durability, many types of additive and admixture such as super-plasticizers, fly ash, silica fume, ggbfs, etc., have been used in the past. However, a close study of the published literature indicates that the effect of mix variables on the durability and the interaction between the various ingredients are not fully understood. Some of these apparent contradictions are due to the limitations in the design of the experimental programme. For instance, it is evident that relatively higher concentrations of aggregates increase the tortuosity of the flow path and hence reduce the permeability, which results in an improvement in the durability. Therefore, an increase in cement content without a proportional decrease in water-cement ratio may reduce the durability. In such cases, the interactive effects of factors can be established by resorting to a properly designed experimental programme, such as the factorial experimental design.

Confined site construction: An empirical analysis of factors impacting health and safety management

Purpose – The purpose of this paper is to identify, clarify and tabulate the various managerial issues encountered, to aid in the management of the complex health and safety concerns which occur within a confined construction site environment.

Design/methodology/approach – This is achieved through conducting extensive qualitative and qualitative research in the form of case studies, interviews and questionnaire survey.

Findings – The leading managerial issues in the management of health and safety on a confined construction site are found to be: “Difficulty to move materials around site safely”; “Lack of adequate room for the effective handling of materials”; “Difficulty in ensuring site is tidy and all plant and materials are stored safely”; “Close proximity of individuals to operation of large plant and machinery”; and joint fifth “Difficulty in ensuring proper arrangement and collection of waste materials on-site” along with “Difficulty in controlling hazardous materials and equipment on site”.

Practical implications – The resulting implication for practice of these results can be summarised by identifying that with sustained development of urban centres on a global scale, coupled with the increasing complexity of architectural designs, the majority of on-site project management professionals are faced with the onerous task of completing often intricate designs within a limited spatial environment, under strict health and safety parameters.

Originality/value – The subsequent value of the findings are such that just as on-site management professionals successfully identify the various managerial issues highlighted, the successful management of health and safety on a confined construction site is attainable.

Degradation of carbon disulphide (CS2) in soils and groundwater from a CS2 -contaminated site

This study is the first investigation of biodegradation of carbon disulphide (CS₂) in soil that provides estimates of degradation rates and identifies intermediate degradation products and carbon isotope signatures of degradation. Microcosm studies were undertaken under anaerobic conditions using soil and groundwater recovered from CS₂-contaminated sites. Proposed degradation mechanisms were validated using equilibrium speciation modelling of concentrations and carbon isotope ratios. A first-order degradation rate constant of 1.25 × 10-2 h-1 was obtained for biological degradation with soil. Carbonyl sulphide (COS) and hydrogen sulphide (H₂S) were found to be intermediates of degradation, but did not accumulate in vials. A 13C/12C enrichment factor of -7.5 ± 0.8 ‰ was obtained for degradation within microcosms with both soil and groundwater whereas a 13C/12C enrichment factor of -23.0 ± 2.1 ‰ was obtained for degradation with site groundwater alone. It can be concluded that biological degradation of both CS2-contaminated soil and groundwater is likely to occur in the field suggesting that natural attenuation may be an appropriate remedial tool at some sites. The presence of biodegradation by-products including COS and H₂S indicates that biodegradation of CS₂ is occurring and stable carbon isotopes are a promising tool to quantify CS₂ degradation.

An Analytical Study of Surplus Value using a Value Driven Design Methodology

People are now becoming more environmentally aware and as a consequence of this, industries such as the aviation industry are striving to design more environmentally friendly products. To achieve this, the current design methodologies must be modified to ensure these issues are considered from product conception through to disposal. This paper discusses the environmental problems in relation to the aviation industry and highlights some logic for making the change from the traditional Systems Engineering approach to the recent design paradigm known as Value Driven Design. Preliminary studies have been undertaken to aid in the understanding of this methodology and the existing surplus value objective function. The main results from the work demonstrate that surplus value works well bringing disparate issues such as manufacture and green taxes together to aid decision making. Further, to date studies on surplus value have used simple sensitivity analysis, but deeper consideration shows non-linear interactions between some of the variables and further work will be needed to fully account for complex issues such as environmental impact and taxes.

Validated ligand binding sites in CCK receptors. Next step: Computer aided design of novel CCK ligands

Computer-aided drug design becomes an important part of G-protein coupled receptors (GPCR) drug discovery process that is applied for improving the efficiency of derivation and optimization of novel ligands. It represents the combination of methods that-use-structural information of a receptor binding site of known ligands to design new ligands. In this report, we give a brief description of ligand binding sites in cholecystokinin and gastrin receptors (CK1R and CCK2R) which were delineated using experimental and computational methods, and then, we show how the validated ligand binding sites can be used to design and improve novel ligands. The translation of the knowledge of ligand-binding sites of different GPCRs to computer-aided design of novel ligands is summarized.

Binding site of AMPA-receptor allosteric modulator

The computer molecular docking of piperonyl acid piperidide (BDP) and some its analogs already known as ampakins was conducted for estimating their possible binding with AMPA-receptor glutamate domains in cyclothiazide binding area and for further design of new structures maximally complimentary to the receptor. On the base of the conducted docking it can be suggested that the binding site of BDP (amides of benzodioxane-6-carboxylic and piperonyl acids) analogs is located in AMPA-receptor cyclothiazide binding pocket. It is shown that formation of protein-ligand complexes of AMPA-receptor with benzodioxane-6-carboxylic and piperonyl acid derivatives, similarly to cyclothiazide, proceeds with interaction with Ser497, Leu751, which significance is confirmed by site-specific mutagenesis.

CoMFA and homology-based models of the glycine binding site of N-methyl-D-aspartate receptor

Homology modeling was used to build 3D models of the N-methyl-D-aspartate (NMDA) receptor glycine binding site on the basis of an X-ray structure of the water-soluble AMPA-sensitive receptor. The docking of agonists and antagonists to these models was used to reveal binding modes of ligands and to explain known structure-activity relationships. Two types of quantitative models, 3D-QSAR/CoMFA and a regression model based on docking energies, were built for antagonists (derivatives of 4-hydroxy-2-quinolone, quinoxaline-2,3-dione, and related compounds). The CoMFA steric and electrostatic maps were superimposed on the homology-based model, and a close correspondence was marked. The derived computational models have permitted the evaluation of the structural features crucial for high glycine binding site affinity and are important for the design of new ligands.

Improving multi-site benefit functions via Bayesian model averaging: A new approach to benefit transfer

A benefit function transfer obtains estimates of willingness-to-pay (WTP) for the evaluation of a given policy at a site by combining existing information from different study sites. This has the advantage that more efficient estimates are obtained, but it relies on the assumption that the heterogeneity between sites is appropriately captured in the benefit transfer model. A more expensive alternative to estimate WTP is to analyze only data from the policy site in question while ignoring information from other sites. We make use of the fact that these two choices can be viewed as a model selection problem and extend the set of models to allow for the hypothesis that the benefit function is only applicable to a subset of sites. We show how Bayesian model averaging (BMA) techniques can be used to optimally combine information from all models. The Bayesian algorithm searches for the set of sites that can form the basis for estimating a benefit function and reveals whether such information can be transferred to new sites for which only a small data set is available. We illustrate the method with a sample of 42 forests from U.K. and Ireland. We find that BMA benefit function transfer produces reliable estimates and can increase about 8 times the information content of a small sample when the forest is 'poolable'. © 2008 Elsevier Inc. All rights reserved.