Characterizing groundwater flow at Fort Leonard Wood using universal cokriging with trend removal

Groundwater elevation interpolation is necessary for the prediction of groundwater flow direction and contaminant transport. Kriging is a geostatistical tool commonly used to interpolate groundwater elevation. Kriging requires a relatively large number of monitoring wells at the site of interest. The variogram model is a crucial element to the kriging equations. The variogram modelling process is an iterative procedure that is often very time consuming. This study presents a literature based approach that provides a point of departure for the variogram modelling process as well as other kriging parameters. A literature database is developed in order to provide insight and a measure of reasonableness to the variogram parameters developed at a groundwater interpolation site. A case study was performed on the Fort Leonard Wood Military Reservation located in Missouri. A data quality analysis was performed on the dataset and spatial outliers were removed. The results from before and after spatial outlier removal are shown. Compliance points were developed using data gaps observed from the standard error maps produced during kriging. The number of wells for the Fort Leonard Wood site were reduced from 61 wells to 45, 30, and 15 wells. Three realizations were performed for each well reduction and results were averaged. Results indicate that when the number of wells are reduced to 15 wells the contour maps are inconsistent with the baseline contour map, each other, as well as the conceptual model. The literature based approach can be easily applied as a point of departure for kriging groundwater elevations --Abstract, page iv

Public Support of the Processing and Marketing of Agricultural Products: A Driver of Innovation in the Food Industry?

At issue in this paper is the role of innovation within the public support of food-industries under EU rural development policy. It is focused on the questions: Are there fundamental economic characteristics of highly innovative in comparison to less innovative enterprises? And, what are successful strategies to promote innovations by intervention of the state. Baseline information is given through the data ascertainment of investment grant applications and collaboration with local state departments.Innovation, industrial policy, investment assistance, food-industry, state-intervention, Agribusiness, Agricultural and Food Policy, Marketing,

Proceedings of the European Workshop on the Evaluation of Farm Investment Support, Investment Support for Improvement of Processing and Marketing of Agricultural Products

Contents: i - Angela Bergschmidt, Walter Dirksmeyer and Bernhard Forstner - Proceedings of the European Evaluation Workshop – Foreword -- PAPERS PRESENTED IN THE PLENARY SESSIONS -- 3 - Stefan Meyer - Methods for the Evaluation of Investment Support -- 15 - Andrea Pufahl - Programme Evaluation of Rural Development Plans – Purpose, Approaches and Exemplary Results -- 27 - Carel Gosselink - Agri Finance: Lost without Support? -- 33 - Anne Margarian - How to Evaluate a Measure without Goals – Considerations on the Basis of the Paradigmatic Example of Farm Investment Support in Germany -- 45 - Rudy Ooijen - Ex Ante Evaluations of Rural Development Programmes – Not just an Appraisal -- PAPERS PRESENTED IN THE SESSION ON FARM INVESTMENT SUPPORT -- 61 - Angela Bergschmidt and Walter Dirksmeyer - A Comparison of Farm Investment Support in Selected EU Member States -- 69 - Monika Beck and Thomas Dogot - The Use of Impact Indicators for the Evaluation of Farm Investment Support – A Case Study Based on the Rural Development Programme for Wallonia (2000 – 2006) -- 79 - Barbara Costantini and Maria Cristina Sibilla - Implementation of Farm Investment Support in Italy – Mid-Term Analysis -- 93 - Pawel Chmielinski - Regional Absorption Capacity of Farm Investment Support in Poland -- 105 - Luis A. Collado Cueto - Effectiveness and Impacts of Farm Investment Support in Spain – The Experience of the Updated Mid-Term Evaluation (2000 – 2006) -- 121 - Dimitros Lianos and Triantafyllia Giotopoulou - The Experience of the Evaluation of Farm Investment Support in Greece -- 133 - Bernhard Forstner - Evaluation of Farm Investment Support in Germany – Lessons Learned from the Application of Different Approaches -- 147 - Stephan Pfefferli - Impact Analysis of Investment Support for Agricultural Buildings in Switzerland -- 159 - Justyna Ziólkowska, Joanna Nargiello and Cezary Klimkowski - The Analysis of Changes in Farm Investment Support Policy in Poland after Joining the European Union -- PAPERS PRESENTED IN THE SESSION ON INVESTMENT SUPPORT FOR IMPROVEMENT OF PROCESSING AND MARKETING OF AGRICULTURAL PRODUCTS -- 177 - Inge Uetrecht, Heinz Wendt, Volker Krah and Annette Trefflich - The Implementation of Investment Support for Improving Processing and Marketing of Agricultural Products in the EU Member States – An Overview -- 187 -Andreas Pölking - Synthesis of the RDP Mid-Term Evaluation in Germany (16 Länder) and EC 15 in 2005 – Methodologies, Possibilities, Pitfalls and some Selected Results -- 195 - Julia Neuwirth and Karlheinz Pistrich - Improving Processing and Marketing of Agricultural Products – Organisation, Problems and Results of Evaluation in Austria -- 201 - Alois Grabner - Improving of Processing and Marketing of Agricultural Products – Assessment of Projects -- 205 - Pedro Serrano - Support to Processing and Marketing of Agricultural Products in Portugal -- 215 - Mark Temple - Two Approaches to Evaluation – The Case of the Processing and Marketing Grant in England -- 227 - Jochen Nölle and Josef Efken - Does Complete Field Research Build a Good Basis to Evaluating the Measure? -- CLOSURE OF THE EUROPEAN EVALUATION WORKSHOP -- 241 - Bernhard Forstner and Heinz Wendt - Summary and Final Discussion --

Golgi positioning during cell migration

Investigation of crucial aspects of cellular function in live cells frequently requires the loss of expression of a specific protein to gain insight into its function. It is also beneficial to combine this with either the enforced re-expression of a tagged version of the protein of interest to validate the phenotype, or the expression of fluorescently tagged marker proteins to investigate a particular phenomenon. Modifications to a short hairpin RNA-mediated knock-down lenti-viral delivery system described here enable the simultaneous expression of short hairpin RNA and a fluorescently-tagged rescue or marker protein to investigate specific cellular processes. The knock-down phenotype of capping protein [beta] was rescued by the simultaneous expression of a fluorescently tagged knock-down resistant version. Chromophore-assisted laser inactivation of capping protein [beta] demonstrated the acute loss of function phenotype and highlighted the necessity of loss of endogenous protein expression for the effects to be observed. Another modification in the lenti-viral vector system was used to demonstrate a role for coronin 1B in modulating the rate of actin retrograde flow. A final modification to the lenti-viral system enabled the simultaneous expression of two different fluorescent markers. This was used to investigate Golgi and nucleus positioning during migration. In Rat2 cells at the edge of an artificial wound, the Golgi and centrosome were positioned coincident to one another and were polarized to the front of the nucleus relative to the wound edge. Freely migrating cells expressing fluorescent markers of the Golgi and nucleus did not exhibit such polarity. Instead, Golgi positioning remained fairly constant relative to the nucleus independent of the direction of migration. Nucleus and Golgi positioning relative to the direction of migration was also independent of the speed or directional persistence. Lamellipodial dynamics such as the distance, duration or rate of protrusion were not substantially different along the nuclear-Golgi axis relative to other areas of the cell periphery. Together these data suggest that Golgi positioning in freely migrating cells is independent of the events at the periphery of the cell that are involved in migration

Assembly pathway of hepatitis B core virus-like particles from genetically fused dimers

Macromolecular complexes are responsible for many key biological processes. However, in most cases details of the assembly/disassembly of such complexes are unknown at the molecular level, as the low abundance and transient nature of assembly intermediates make analysis challenging. The assembly of virus capsids is an example of such a process. The hepatitis B virus capsid (core) can be composed of either 90 or 120 dimers of coat protein. Previous studies have proposed a trimer of dimers as an important intermediate species in assembly, acting to nucleate further assembly by dimer addition. Using novel genetically-fused coat protein dimers, we have been able to trap higher-order assembly intermediates and to demonstrate for the first time that both dimeric and trimeric complexes are on pathway to virus-like particle (capsid) formation

Fucose Binding Cancels out Mechanical Differences between Distinct Human Noroviruses

The majority of nonbacterial gastroenteritis in humans and livestock is caused by noroviruses.Like most RNA viruses, frequent mutations result in various norovirus variants. The strain-dependentbinding profiles of noroviruses to fucose are supposed to facilitate norovirus infection. It remains unclear, however, what the molecular mechanism behind strain-dependent functioning is. In this study,by applying atomic force microscopy (AFM) nanoindentation technology, we studied norovirus-likeparticles (noroVLPs) of three distinct human norovirus variants. We found differences in viral mechanical properties even between the norovirus variants from the same genogroup. The noroVLPswere then subjected to fucose treatment. Surprisingly, after fucose treatment, the previously foundconsiderable differences in viral mechanical properties among these variants were diminished. Weattribute a dynamic switch of the norovirus P domain upon fucose binding to the reduced differencesin viral mechanical properties across the tested norovirus variants. These findings shed light on themechanisms used by norovirus capsids to adapt to environmental changes and, possibly, increasecell infection. Hereby, a new step towards connecting viral mechanical properties to viral prevalenceis taken.<br/

Golgi polarity does not correlate with speed or persistence of freely migrating fibroblasts

The polarization of the Golgi has long been thought to be important for cell migration. Here we show that Rat2 cells at the edge of an artificial wound repolarize the Golgi relative to the nucleus to face the direction of migration into the wound. However, in the absence of cues from neighboring cells, individual cells do not display Golgi polarity relative to the direction in which they are moving. Instead, the positioning of the Golgi relative to the nucleus remains relatively constant over time and does not reflect changes in the direction of migration. Consistent with this observation, we observe only a slight bias in Golgi positioning to the front of the nucleus and this bias is not higher during periods of time when the cell is moving in a persistent manner. Taken together, these data suggest that Golgi polarity is not a requirement for cell migration

Using ion mobility spectrometry-mass spectrometry to decipher the conformational and assembly characteristics of the hepatitis B capsid protein.

The structural and functional analysis of the core protein of hepatitis B virus is important for a full understanding of the viral life cycle and the development of novel therapeutic agents. The majority of the core protein (CP149) comprises the capsid assembly domain, and the C-terminal region (residues 150-183) is responsible for nucleic acid binding. Protein monomers associate to form dimeric structural subunits, and helices 3 and 4 (residues 50-111 of the assembly domain) have been shown to be important for this as they constitute the interdimer interface. Here, using mass spectrometry coupled with ion mobility spectrometry, we demonstrate the conformational flexibility of the CP149 dimer. Limited proteolysis was used to locate involvement in this feature to the C-terminal region. A genetically fused CP dimer was found to show decreased disorder, consistent with a more restricted C-terminus at the fusion junction. Incubation of CP149 dimer with heteroaryldihydropyrimidine-1, a small molecule known to interfere with the assembly process, was shown to result in oligomers different in shape to the capsid assembly-competent oligomers of the fused CP dimer. We suggest that heteroaryldihydropyrimidine-1 affects the dynamics of CP149 dimer in solution, likely affecting the ratio between assembly active and inactive states. Therefore, assembly of the less dynamic fused dimer is less readily misdirected by heteroaryldihydropyrimidine-1. These studies of the flexibility and oligomerization properties of hepatitis B virus core protein illustrate both the importance of C-terminal dynamics in function and the utility of gas-phase techniques for structural and dynamical biomolecular analysis

The crystal structure of mycobacterial epoxide hydrolase A

The human pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis resulting in over 1 million fatalities every year, despite decades of research into the development of new anti-TB compounds. Unlike most other organisms M. tuberculosis has six putative genes for epoxide hydrolases (EH) of the α/β-hydrolase family with little known about their individual substrates, suggesting functional significance for these genes to the organism. Due to their role in detoxification, M. tuberculosis EH’s have been identified as potential drug targets. Here, we demonstrate epoxide hydrolase activity of M. thermoresistibile epoxide hydrolase A (Mth-EphA) and report its crystal structure in complex with the inhibitor 1,3-diphenylurea at 2.0 Å resolution. Mth-EphA displays high sequence similarity to its orthologue from M. tuberculosis and generally high structural similarity to α/β-hydrolase EHs. The structure of the inhibitor bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor. Comparison to other EHs from mycobacteria allows insight into the active site plasticity with respect to substrate specificity. We speculate that mycobacterial EHs may have a narrow substrate specificity providing a potential explanation for the genetic repertoire of epoxide hydrolase genes in M. tuberculosis

Ion mobility-mass spectrometry reveals conformational flexibility in the deubiquitinating enzyme USP5

Many proteins exhibit conformation flexibility as part of their biological function, whether through the presence of a series of well-defined states or by the existence of intrinsic disorder. Ion mobility spectrometry, in combination with MS (IM–MS), offers a rapid and sensitive means of probing ensembles of protein structures through measurement of gas-phase collisional cross sections. We have applied IM–MS analysis to the multidomain deubiquitinating enzyme ubiquitin specific protease 5 (USP5), which is believed to exhibit significant conformational flexibility. Native ESI–MS measurement of the 94-kDa USP5 revealed two distinct charge-state distributions: [M + 17H]+ to [M + 21H]+ and [M + 24H]+ to [M + 29H]+. The collisional cross sections of these ions revealed clear groupings of 52 ± 4 nm2 for the lower charges and 66 ± 6 nm2 for the higher charges. Molecular dynamics simulation of a compact form of USP5, based on a crystal structure, produced structures of 53–54 nm2 following 2 ns in the gas phase, while simulation of an extended form (based on small-angle X-ray scattering data) led to structures of 64 nm2. These data demonstrate that IM–MS is a valuable tool in studying proteins with different discrete conformational states