bluuebunny/crossref_metadata_2025 huggingface dataset:
Stochastic Simulations of Spatial Variability Based on Multifractal Characteristics
Authors: Kravchenko A. N.
Published: May 2008

Using multifractal characteristics in the stochastic simulation of environmental and agronomic variables has the potential for producing simulations that better represent features of interest, including distribution properties of the high and low values, than simulations based on geostatistical characteristics. The objective of this study was to compare the performance of stochastic simulations that reproduce certain multifractal characteristics with simulations that reproduce variogram model parameters. Data on corn (Zea mays L.) and wheat (Triticum aestivum L.) yields collected at 1100 and 880 sampling locations, respectively, were used in the simulations. Wheat data represented an example of a variable exhibiting a multifractal scaling and corn an example of a variable exhibiting a monofractal scaling. The conditional simulations were conducted using a simulated annealing procedure. Two simulation scenarios were compared. The first scenario consisted of using the order of the structure function q = 2, which is equivalent to simulating a data set with a certain variogram, that is, a monofractal simulation. The second scenario used the histogram and the structure function with exponent values for q ranging from 1 to 5, a multifractal simulation. Based on 50 simulations, the performances of the two scenarios in representing the highest and lowest values were compared. There was no significant difference in performance of monofractal and multifractal simulations for the variable exhibiting monofractal scaling (corn). For the variable with multifractal scaling (wheat), however, multifractal simulations performed better in predicting low values. For soil or agronomic variables exhibiting multifractal scaling, stochastic simulations based on multifractal characteristics could be preferable to those based on variogram parameters.
Multifractal Analysis of Pore Size Distributions as Affected by Simulated Rainfall
Authors: Vázquez E. Vidal , Ferreiro J. Paz , Miranda J. G. V. , González A. Paz
Published: May 2008

Rainfall changes the physical state, pore system geometry, and structure of soils. Characterization of the soil pore system provides a realistic base to understand the retention and movement of water in soil. The objective of this work was to estimate multifractal parameters from Hg injection porosimetry data on the uppermost soil surface layer as affected by simulated rainfall. Soil aggregates were sampled at the 0‐ to 2‐cm depth in a loamy soil, both on a recently tilled soil surface and on its disturbed counterpart after 260‐mm cumulative rainfall. Pore size distributions (PSDs) were determined by Hg intrusion porosimetry from 0.005‐ to about 100‐μm pore diameters on 10 samples per surface stage. The rainfall reduced aggregate pore volume, showing significant differences between the pore space of the reference and the disturbed soil surfaces. A multifractal analysis was performed by means of scaling of the moments ranging from −10 < q < 10 for all PSDs. Mean values of the entropy dimension, D1, and correlation dimension, D2, in the aggregate set sampled after rain disturbance were lower than those of the reference stage; however, mean values of the difference Δ(D1 − D2), the Hölder exponent of order zero, α0, and widths of the left (α0 − αq+) and right (αq− − α0) hand sides of the singularity spectra f(α) after rainfall action were higher than those of the initial soil surface. Entropy dimension, D1, and the width of the left (α0 − αq+) hand side of the f(α) spectra best discriminated between PSDs of the reference initial soil surface vs. soil surface disturbed by rain.
A Comparison of SWAT Model‐Predicted Potential Evapotranspiration Using Real and Modeled Meteorological Data
Authors: Earls Julie , Dixon Barnali
Published: May 2008

Adequate characterization of potential evapotranspiration (PET) plays a critical role in hydrologic budgets, rainfall–runoff models, infiltration calculations, and drought prediction models (to name a few applications). The availability of reliable and continuous meteorological data remains a challenge; therefore, it is common to use modeled (simulated) meteorological data. This research used the Soil and Water Assessment Tool (SWAT) to estimate PET using different meteorological input data (simulated vs. real data) and the three commonly used PET calculation methods (viz. Penman–Monteith, Hargreaves, and Priestley‐Taylor). The overall goal of this research was to determine the accuracy of prediction using simulated and real meteorological data when used with three PET calculation methods. Initial input layers to SWAT were: digital elevation models, soils, and land use. Real meteorological data were obtained from three local meteorological stations, whereas simulated meteorological data were generated by SWAT using one nearby national meteorological site. The model‐predicted PET results were validated using independent PET measurements from Florida Automated Weather Network sites. The results of the study indicate that the difference in predicted PET between simulated (modeled) and real meteorology for a given PET calculation method is not significant; however, it is significant across the methods of PET calculation.
Multifractal Analysis of Soil Surface Roughness
Authors: Moreno R. García , Álvarez M. C. Díaz , Requejo A. Saa , Tarquis A. M.
Published: May 2008

Soil surface roughness (SSR) is a parameter highly suited to the study of soil susceptibility to wind and water erosion. The development of a methodology for quantifying SSR is therefore instrumental to soil evaluation. We developed such a method, based on the multifractal analysis (MFA) of soil elevation measurements collected at the intersections on a 2‐ by 2‐cm2 grid in a 200‐ by 200‐cm2 plot. Samples were defined using the gliding box algorithm (GB), in which a box of a given size “glides” across the grid map in all possible directions. The advantage of the GB over the box counting algorithm is that it yields a greater number of large sample sizes, which usually leads to better statistical results. Standard deviation, semivariogram fractal dimension, and semivariogram crossover length were estimated for all scenarios to compare the results of SSR multifractal analysis to indices found with traditional techniques. For its high sensitivity to the spatial arrangement implicit in a data set, MFA appears to be better suited than classical indices to compare plots tilled under different management criteria. The results showed that MFA is able to effectively reflect the heterogeneity and complexity of agricultural SSR. Based on this type of analysis, two new indices have been defined to compare the multifractal spectrum characteristics of the raw data to the characteristics of a random field with the same average and SD.
Multiscale Entropy‐based Analysis of Soil Transect Data
Authors: Tarquis A. M. , Bird N. R. A. , Whitmore A. P. , Cartagena M. C. , Pachepsky Yakov
Published: May 2008

A deeper understanding of the spatial variability of soil properties and the relationships between them is needed to scale up measured soil properties and to model soil processes. The object of this study was to describe the spatial scaling properties of a set of soil physical properties measured on a common 1024‐m transect across arable fields at Silsoe in Bedfordshire, east‐central England. Properties studied were volumetric water content (θ), total porosity (π), pH, and N2O flux. We applied entropy as a means of quantifying the scaling behavior of each transect. Finally, we examined the spatial intrascaling behavior of the correlations between θ and the other soil variables. Relative entropies and increments in relative entropy calculated for θ, π, and pH showed maximum structure at the 128‐m scale, while N2O flux presented a more complex scale dependency at large and small scales. The intrascale‐dependent correlation between θ and π was negative at small scales up to 8 m. The rest of the intrascale‐dependent correlation functions between θ with N2O fluxes and pH were in agreement with previous studies. These techniques allow research on scale effects localized in scale and provide the information that is complementary to the information about scale dependencies found across a range of scales.
MODFLOW SURFACT: A State‐of‐the‐Art Use of Vadose Zone Flow and Transport Equations and Numerical Techniques for Environmental Evaluations
Authors: Panday Sorab , Huyakorn Peter S.
Published: May 2008

MODFLOW SURFACT is a state‐of‐the‐art simulator that utilizes vadose zone flow and transport equations to provide practical solutions to the analysis of flow and contaminant transport at various levels of complexity and sophistication as needed for site evaluation and closure. The variably saturated flow equation can be solved with standard retention functions or with bimodal or multimodal relative permeability curves for unsaturated flow in porous and fractured systems. The equation can further be solved with pseudo‐soil retention functions for confined–unconfined simulations and for use in wellbore hydraulics. Finally, the equation can be cast in terms of air phase flow to analyze subsurface air flow behavior. The variably saturated transport equation can be solved for an unsaturated medium or can be used for confined–unconfined situations. The passive phase of flow can be included in the equation to include both air and water phases in the transport situation. An immobile multicomponent nonaqueous phase liquid (NAPL) phase can further be included in the transport simulation with equilibrium partitioning providing mass transfer between phases, which adjusts NAPL saturations. Dual domain equations can be condensed into the transport equation to provide capabilities for analyzing transport in fractured media. General reaction capabilities provide analyses of complex environmental and geochemical interactions. Two examples are provided to demonstrate the value of a comprehensive simulation capability for site investigations.
Modeling of Processes in Subsurface Flow Constructed Wetlands: A Review
Authors: Langergraber Günter
Published: May 2008

Constructed wetlands (CWs) provide a natural way for simple, inexpensive, and robust wastewater treatment. Detailed understanding of CW functioning is difficult, because a large number of physical, chemical, and biological processes occur in parallel and influence each other. For this reason, CWs have long been seen as “black boxes” where wastewater enters and treated water leaves the system. Numerical models describing the biochemical transformation and degradation processes in CWs are promising tools to better understand CW functioning. The first part of this paper reviews published mechanistic models for CWs. Horizontal flow systems can be simulated when only water flow saturated conditions are considered; six models have been reviewed whereby a series or network of completely stirred tank reactors is most frequently used to describe the hydraulics. For modeling vertical flow CWs with intermittent loading, transient variably saturated flow models are required. Due to the intermittent loading, these systems are highly dynamic, adding to the complexity of the overall system. Five models of different complexity have been reviewed; three use the Richards equation to describe variably saturated flow, whereas the two others use simplified approaches. In the second part of the paper, the multicomponent reactive transport module CW2D is demonstrated. Simulation results for CWs treating domestic wastewater, combined sewer overflow, and surface water are presented. In general, a good match between simulation results and measured data could be achieved if the hydraulic behavior of the system could be described well. Based on the experience from these examples, the need for further model development is determined.
Advanced Vadose Zone Simulations Using TOUGH
Authors: Finsterle S. , Doughty C. , Kowalsky M.B. , Moridis G. J. , Pan L. , Xu T. , Zhang Y. , Pruess K.
Published: May 2008

The vadose zone can be characterized as a complex subsurface system in which intricate physical and biogeochemical processes occur in response to a variety of natural forces and human activities. This makes it difficult to describe, understand, and predict the behavior of this specific subsurface system. The TOUGH nonisothermal multiphase flow simulators are well suited to perform advanced vadose zone studies. The conceptual models underlying the TOUGH simulators are capable of representing features specific to the vadose zone, and of addressing a variety of coupled phenomena. Moreover, the simulators are integrated into software tools that enable advanced data analysis, optimization, and system‐level modeling. We discuss fundamental and computational challenges in simulating vadose zone processes, review recent advances in modeling such systems, and demonstrate some capabilities of the TOUGH suite of codes using illustrative examples.
Advances of Modeling Water Flow in Variably Saturated Soils with SWAP
Authors: van Dam Jos C. , Groenendijk Piet , Hendriks Rob F.A. , Kroes Joop G.
Published: May 2008

The Soil Water Atmosphere Plant (SWAP) model simulates transport of water, solutes, and heat in the vadose zone in interaction with vegetation development. Special features of the model are generic crop growth, versatile top boundary conditions, macroporous flow, and interaction of soil water with groundwater and surface water. We discuss typical model applications that have appeared in recent scientific literature. New model developments are explained with respect to the numerical solution of Richards' equation, macroporous flow, evapotranspiration, and interactions with groundwater and surface water. We describe case studies on agricultural water productivity, regional nutrient management, and groundwater conservation by surface water management. Finally we envision model developments with respect to SWAP for the coming 5 to 10 yr.
New Tool RhizoMath for Modeling Coupled Transport and Speciation in the Rhizosphere
Authors: Szegedi Krisztian , Vetterlein Doris , Nietfeld Heino , Jahn Reinhold , Neue Heinz‐Ulrich
Published: May 2008

The transfer of nutrients and contaminants from bulk soil to roots and into plants depends on many plant and soil processes. The RhizoMath approach for modeling co‐occurring processes in the rhizosphere, including speciation in the soil solution, is based on coupling the mathematical package MATLAB with the geochemical code PHREEQC. In addition to the built‐in initialization module that performs calibration against experimental data, RhizoMath's greatest advantage is that different geochemical models (with and without charge balance) and geometries (planar and radial) are already included. Moreover, due to its graphical user interface, the tool can be applied without changing the source code or a complex input file. The model was verified using a benchmark and experimental data: (i) the initialization module was successfully applied to describe concentrations measured in soil solution samples; (ii) the theoretical problem “diffusion of K toward a single root” was used to demonstrate that the performance of applied numerical methods is comparable to other approaches; and (iii) for compartment system experiments involving more complex speciation, RhizoMath was able to describe the observed effects of citrate exudates on the simultaneous transport of arsenate and phosphate that compete for surface binding sites with each other and with other oxyanions such as citrate.
Modeling Nonequilibrium Flow and Transport Processes Using HYDRUS
Authors: Šimůnek Jirka , van Genuchten Martinus Th.
Published: May 2008

Accurate process‐based modeling of nonequilibrium water flow and solute transport remains a major challenge in vadose zone hydrology. Our objective here was to describe a wide range of nonequilibrium flow and transport modeling approaches available within the latest version of the HYDRUS‐1D software package. The formulations range from classical models simulating uniform flow and transport, to relatively traditional mobile‐immobile water physical and two‐site chemical nonequilibrium models, to more complex dual‐permeability models that consider both physical and chemical nonequilibrium. The models are divided into three groups: (i) physical nonequilibrium transport models, (ii) chemical nonequilibrium transport models, and (iii) physical and chemical nonequilibrium transport models. Physical nonequilibrium models include the Mobile‐Immobile Water Model, Dual‐Porosity Model, Dual‐Permeability Model, and Dual‐Permeability Model with Immobile Water. Chemical nonequilibrium models include the One Kinetic Site Model, the Two‐Site Model, and the Two Kinetic Sites Model. Finally, physical and chemical nonequilibrium transport models include the Dual‐Porosity Model with One Kinetic Site and the Dual‐Permeability Model with Two‐Site Sorption. Example calculations using the different types of nonequilibrium models are presented. Implications for the formulation of the inverse problem are also discussed. The many different models that have been developed over the years for nonequilibrium flow and transport reflect the multitude of often simultaneous processes that can govern nonequilibrium and preferential flow at the field scale.
Inverse Modeling of Subsurface Flow and Transport Properties: A Review with New Developments
Authors: Vrugt Jasper A. , Stauffer Philip H. , Wöhling Th. , Robinson Bruce A. , Vesselinov Velimir V.
Published: May 2008

Many of the parameters in subsurface flow and transport models cannot be estimated directly at the scale of interest, but can only be derived through inverse modeling. During this process, the parameters are adjusted in such a way that the behavior of the model approximates, as closely and consistently as possible, the observed response of the system under study for some historical period of time. We briefly review the current state of the art of inverse modeling for estimating unsaturated flow and transport processes. We summariz how the inverse method works, discuss the historical background that led to the current perspectives on inverse modeling, and review the solution algorithms used to solve the parameter estimation problem. We then highlight our recent work at Los Alamos related to the development and implementation of improved optimization and data assimilation methods for computationally efficient calibration and uncertainty estimation in complex, distributed flow and transport models using parallel computing capabilities. Finally, we illustrate these developments with three different case studies, including (i) the calibration of a fully coupled three‐dimensional vapor extraction model using measured concentrations of volatile organic compounds in the subsurface near the Los Alamos National Laboratory, (ii) the multiobjective inverse estimation of soil hydraulic properties in the HYDRUS‐1D model using observed tensiometric data from an experimental field plot in New Zealand, and (iii) the simultaneous estimation of parameter and states in a groundwater solute mixture model using data from a multitracer experiment at Yucca Mountain, Nevada.
Modeling the Spatial Distribution of Nitrogen Leaching from Dairy Farmland
Authors: Wang Fuli
Published: May 2008

Urine patches on dairy farmland may cause extra loss of nitrogen through leaching and thus lead to potential contamination of groundwater in underlying aquifers. In this study, mathematical models and numerical simulations were used to quantitatively investigate the most important factors affecting the total quantity and spatial distribution of N‐leaching from dairy farmland soils. A comprehensive two‐dimensional model was derived by integrating models on pasture growth, heat transport, water flow and solute transport, and various N transformation processes. Through numerical simulations, the influence of soil texture (hydraulic conductivity, dispersivity, immobile water content, and “diffusion” path length and conductivity of macropores), urine patch density, quantity of irrigation and N fertilizer application on total N‐leaching, and spatial variations in N‐leaching were analyzed. Results showed that for all cases investigated, spatial variations in N‐leaching at the bottom of root zone were very large, which is the major reason urine patches would introduce extra N‐leaching losses. Spatial variations in N‐leaching were strongly affected by the density of urine patch coverage, soil hydraulic conductivity, dispersivity, preferential flow in macropores, and irrigation, but little by N fertilizer application and the presence of soil immobile water. Total N‐leaching was strongly affected by density of urine patch coverage, soil hydraulic conductivity, irrigation, N fertilizer application, and preferential flow, but only slightly by the dispersivity and immobile water.
Quasi Steady‐State Simulation of the Unsaturated Zone in Groundwater Modeling of Lowland Regions
Authors: van Walsum Paul E. V. , Groenendijk Piet
Published: May 2008

Well‐conceived and detailed simulation of soil‐moisture processes is a prerequisite for accurate watershed‐scale modeling of water quantity and quality processes. For this purpose, Richards' equation (and its extensions) is the conceptually preferable option. Applying the equation on the watershed scale, however, may overstretch available computer resources. At the other extreme, methods based on lumping are oversimplified. Approaches are therefore needed that are efficient and just accurate enough, and that provide the required detail in the vertical column. We have developed a quasi‐steady‐state model that uses a sequence of steady‐state water content profiles for performing dynamic simulations. The appropriate profiles are—for each time level—selected on the basis of water balances at the aggregate scale of control volumes. The groundwater coupling scheme involves an iteration cycle for the phreatic storage coefficient. In the postprocessing stage, the values of state variables obtained using the coupled model are disaggregated, thus delivering pressure heads, moisture contents, and fluxes at the detailed scale of compartments of a Richards‐type model. The plausibility of the simplified approach was tested by comparing its results to those of a Richards‐type model. The results appear promising for at least three‐quarters of the area of the Netherlands with a shallow groundwater elevation (within 2 m of the soil surface) and a thin root zone (<0.5 m thick). Customizing the modeling method used to the situation conserves computational resources, allowing more room for doing sensitivity analyses. This could be instrumental for quantification of model reliability.
Oxidative Stress as a Major Culprit in Kidney Disease in Diabetes
Authors: Forbes Josephine M. , Coughlan Melinda T. , Cooper Mark E.
Published: May 2008

It is postulated that localized tissue oxidative stress is a key component in the development of diabetic nephropathy. There remains controversy, however, as to whether this is an early link between hyperglycemia and renal disease or develops as a consequence of other primary pathogenic mechanisms. In the kidney, a number of pathways that generate reactive oxygen species (ROS) such as glycolysis, specific defects in the polyol pathway, uncoupling of nitric oxide synthase, xanthine oxidase, NAD(P)H oxidase, and advanced glycation have been identified as potentially major contributors to the pathogenesis of diabetic kidney disease. In addition, a unifying hypothesis has been proposed whereby mitochondrial production of ROS in response to chronic hyperglycemia may be the key initiator for each of these pathogenic pathways. This postulate emphasizes the importance of mitochondrial dysfunction in the progression and development of diabetes complications including nephropathy. A mystery remains, however, as to why antioxidants per se have demonstrated minimal renoprotection in humans despite positive preclinical research findings. It is likely that the utility of current study approaches, such as vitamin use, may not be the ideal antioxidant strategy in human diabetic nephropathy. There is now an increasing body of data to suggest that strategies involving a more targeted antioxidant approach, using agents that penetrate specific cellular compartments, may be the elusive additive therapy required to further optimize renoprotection in diabetes.
Electric conductance method to study the contact of injected liquid with fluidized particles
Authors: Portoghese Federica , House Peter , Berruti Franco , Briens Cedric , Adamiak Kazimierz , Chan Edward
Published: May 2008

A sensitive and reliable experimental technique was developed to assess the performance of gas‐atomization nozzles injecting liquid into a gas‐solid fluidized bed. Gas atomizers are used to inject liquid feeds into industrial fluid cokers, fluid catalytic crackers, and gas‐phase polymerization reactors. In the fluid coking process, for example, both liquid yields and reactor operability are affected by how well the injected liquid contacts the fluidized particles. The new experimental method assesses the quality of the liquid‐solid contact from the electric conductance of the bed solids wetted with the injected liquid. The validity of the method was corroborated by direct comparison with the results provided by alternative experimental techniques, as well as by numerical modeling of the evolution of the bed conductance for various types of liquid distribution within the bed solids. The electric conductance technique can help optimize liquid injection into fluidized beds. © 2008 American Institute of Chemical Engineers AIChE J, 2008
Individual strategy preferences and decisional fit
Authors: Betsch Cornelia , Kunz Justus J.
Published: May 2008

The present research introduces the concept of decisional fit. A decision maker experiences decisional fit when the individually preferred decision strategy fits the actually applied strategy. In accordance to other fit‐concepts in psychology (e.g., person–environment fit), we expected positive effects of decisional fit. Five studies examine the effects of a fit between the individual preference for intuition and deliberation (PID) and the actually used decision strategy (intuition or deliberation). A comparison of extreme types (according to participants' values on the PID scale) revealed that decisional fit enhances the perceived value of the chosen or evaluated object (Studies 1–3). In Studies 4 and 5, participants experienced less regret after decisional fit. The findings highlight the importance of considering individual differences when comparing intuitive and deliberate decision making, because strategy preferences interact with applied strategies. Copyright © 2008 John Wiley & Sons, Ltd.
Calcium phosphate transfection generates mammalian recombinant cell lines with higher specific productivity than polyfection
Authors: Chenuet Sebastien , Martinet Danielle , Besuchet‐Schmutz Nathalie , Wicht Marianne , Jaccard Nicolas , Bon Anne‐Charlotte , Derouazi Madiha , Hacker David L. , Beckmann Jacques S. , Wurm Florian M.
Published: May 2008

Transfection with polyethylenimine (PEI) was evaluated as a method for the generation of recombinant Chinese hamster ovary (CHO DG44) cell lines by direct comparison with calcium phosphate‐DNA coprecipitation (CaPO4) using both green fluorescent protein (GFP) and a monoclonal antibody as reporter proteins. Following transfection with a GFP expression vector, the proportion of GFP‐positive cells as determined by flow cytometry was fourfold higher for the PEI transfection as compared to the CaPO4 transfection. However, the mean level of transient GFP expression for the cells with the highest level of fluorescence was twofold greater for the CaPO4 transfection. Fluorescence in situ hybridization on metaphase chromosomes from pools of cells grown under selective pressure demonstrated that plasmid integration always occurred at a single site regardless of the transfection method. Importantly, the copy number of integrated plasmids was measurably higher in cells transfected with CaPO4. The efficiency of recombinant cell line recovery under selective pressure was fivefold higher following PEI transfection, but the average specific productivity of a recombinant antibody was about twofold higher for the CaPO4‐derived cell lines. Nevertheless, no difference between the two transfection methods was observed in terms of the stability of protein production. These results demonstrated the feasibility of generating recombinant CHO‐derived cell lines by PEI transfection. However, this method appeared inferior to CaPO4 transfection with regard to the specific productivity of the recovered cell lines. Biotechnol. Bioeng. © 2008 Wiley Periodicals, Inc.
Ribosome display selection of a metal‐binding motif from an artificial peptide library
Authors: Wada Akira , Sawata Shinya Y. , Ito Yoshihiro
Published: May 2008

A new ribosome display system was applied for the in vitro selection of a metal‐binding motif from an artificial peptide library. The display system consisted of an mRNA‐associating protein, a ribosome, and mRNA. The protein part of this display system was designed to provide a random peptide library and to stabilize the ribosome display. The random peptide library was newly designed to isolate stable metal‐binding motifs. We employed the system for in vitro selection and found several new proteins and peptides that bind Co(II)‐immobilized resin and Co(II)‐complex, respectively. This newly developed system can be conveniently applied to the in vitro selection of peptide aptamers. Biotechnol. Bioeng. © 2008 Wiley Periodicals, Inc.
Single‐cell analysis demonstrates how nutrient deprivation creates apoptotic and quiescent cell populations in tumor cylindroids
Authors: Kim Byoung‐jin , Forbes Neil S.
Published: May 2008

Understanding how quiescent and apoptotic populations form in tumors is necessary because these cell types can considerably diminish therapeutic efficacy. Most cancer therapeutics are ineffective against quiescent cells because they target rapidly proliferating cells. Distinguishing apoptosis is important because apoptotic cells are committed to death and do not require treatment. Regrowth of quiescent cell can lead to tumor reoccurrence and metastasis, which are the leading causes of cancer mortality. We hypothesized that cylindroid cultures and acridine orange staining could be used to determine how nutrient diffusion creates apoptotic and quiescent regions in tumors. To test this hypothesis we developed a microscopy technique to measure cellular DNA and RNA content in single cells using thin cylindroids and acridine orange staining. Cell classification was compared to flow cytometry of cells grown in defined monolayer cultures. The presence of apoptosis was confirmed by morphological nuclear analysis. The effect of diffusion was determined by varying incubation time, cylindroid size, and exposing cylindroids to nutrient‐deficient media. Four overlapping regions were identified as a function of cylindroid radius: an outer viable/quiescent region; a second quiescent/apoptotic region; a third late‐stage apoptotic region; and an inner dead region. In monolayer cultures the absence of glutamine and growth factors induced apoptosis and hypoxia induced quiescence. Treating with nutrient‐deficient media suggested that cells became quiescent near the periphery because of glucose and oxygen limitations, and became apoptotic and died further from the edge because of glutamine and growth factor limitations. These results show that cellular microenvironments can be identified in cylindroids using simple acridine orange staining and that single cell florescence can be measured in three‐dimensional culture. The developed techniques will be useful for developing cancer therapies and determining how cell death and apoptosis are induced in three‐dimensional tumor tissue. Biotechnol. Bioeng. 2008;101: 797–810. © 2008 Wiley Periodicals, Inc.
Thermostability and molecular encapsulation within an engineered caged protein scaffold
Authors: Dalmau Mercè , Lim Sierin , Chen Helen C. , Ruiz Cesar , Wang Szu‐Wen
Published: May 2008

Self‐assembling biological complexes such as viral capsids have been manipulated to function in innovative nanotechnology applications. The E2 component of pyruvate dehydrogenase from Bacillus stearothermophilus forms a dodecahedral complex and potentially provides another platform for these purposes. In this investigation, we show that this protein assembly exhibits unusual stability and can be modified to encapsulate model drug molecules. To distill the E2 protein down to its structural scaffold core, we synthesized a truncated gene optimized for expression in Escherichia coli. The correct assembly and dodecahedral structure of the resulting scaffold was confirmed with dynamic light scattering and transmission electron microscopy. Using circular dichroism and differential scanning calorimetry, we found the thermostability of the complex to be unusually high, with an onset temperature of unfolding at 81.1 ± 0.9°C and an apparent midpoint unfolding temperature of 91.4 ± 1.4°C. To evaluate the potential of this scaffold for encapsulation of guest molecules, we made variants at residues 381 and 239 which altered the physicochemical properties of the hollow internal cavity. These mutants, yielding 60 and 120 mutations within this cavity, assembled into the correct architecture and exhibited high thermostability that was comparable to the wild‐type scaffold. To show the applicability of this scaffold, two different fluorescent dye molecules were covalently coupled to the cysteine mutant at site 381. We demonstrate that these mutations can introduce non‐native functionality and enable molecular encapsulation within the cavity while still retaining the dodecahedral structure. The unusually robust nature of this scaffold and its amenability to internal changes reveal its potential for nanoscale applications. Biotechnol. Bioeng. 2008;101: 654–664. © 2008 Wiley Periodicals, Inc.
Retail brand extension—perceived fit, risks and trust
Authors: Laforet Sylvie
Published: May 2008

This study examines consumer fit perception, risks and trust in retail brand extension in financial services. Respondents (324) living in Sheffield were involved in the consumer survey, conducted on three major British supermarkets. Mean scores were compared between four groups of respondents. Discriminant analysis was used to determine the factor(s) distinguishing the retailers. Retailers A and B were perceived as trusted brands with respect to financial services. Retailer A was perceived as a trusted brand regardless of the product category. Retailer B was seen as a trusted brand when product performance and financial risks were low while Retailer C was perceived unfit and risky by non‐users and the non‐intend‐to‐buy groups. Age, gender and income influenced fit, risks and trust perception. When consumers knew the store or were store loyal, they tended to trust the store brand extension whereas when consumers did not know or were new to the store, fit and risks were perceived. Implications for corporate branding, brand extension decision‐making and implementations are sought.

Copyright © 2008 John Wiley & Sons, Ltd.
Mitochondrial AIF protein involved in skeletal muscle regeneration
Authors: Qiu Xiao‐zhong , Yu Lei , Lai Gui‐hua , Wang Le‐yu , Chen Bing , Ouyang Jun
Published: May 2008

The mitochondrial flavoprotein apoptosis‐inducing factor (AIF) has proved to be either the main mediator of apoptosis or an anti‐apoptotic factor via its putative oxidoreductase and peroxide scavenging activities. We report here that 100 µM hydrogen peroxide (H2O2) induced the proliferation of C2C12 myoblasts and over‐expression of AIF simultaneously in vitro. Immunofluorescence showed that the over‐expression of AIF was located in the cytoplasm. The immunopositive AIF was detected in nuclei 27 days after denervation of skeletal muscle, but in the cytoplasm it was detected 27 days after fiber‐damaged skeletal muscle. AIF may be a factor involved in skeletal muscle regeneration. Copyright © 2008 John Wiley & Sons, Ltd.
4‐Amino‐3‐acetylquinoline‐induced apoptosis of murine L1210 leukemia cells involves ROS‐mitochondrial‐mediated death signaling and activation of p38 MAPK
Authors: Jantová S. , Repický A. , Letašiová S. , Čipák L.
Published: May 2008

Quinolines are known to be multitarget agents with a broad spectrum of biological activity. In a previous study, we showed that newly prepared 4‐amino‐3‐acetylquinoline (AAQ) possesses strong anticancer activities. In this study, we investigated whether AAQ has cytotoxicity in murine L1210 leukemia cells. Results from cell proliferation assays showed that AAQ caused significant decrease in cell number in a dose‐dependent manner. The cell death induced by AAQ appeared to involve apoptosis, based on evidence from apoptotic DNA fragmentation, flow cytometry, fluorescence microscopy, and Western blot analyses. We found that AAQ‐treated cells had activated p38 MAPK and that apoptosis was processed through a reactive oxygen species (ROS)‐dependent mitochondrial pathway. In summary, our results suggest that AAQ can induce apoptosis, at least in part, through the activation of the p38 MAPK pathway in L1210 leukemia cells. Copyright © 2008 John Wiley & Sons, Ltd.
Reassembly of Anthramycin Biosynthetic Gene Cluster by Using Recombinogenic Cassettes
Authors: Hu Yunfeng , Phelan Vanessa V. , Farnet Chris M. , Zazopoulos Emmanuel , Bachmann Brian O.
Published: May 2008

The reassembly and heterologous expression of complete gene clusters in shuttle vectors has enabled investigations of several large biosynthetic pathways in recent years. With a gene cluster in a mobile construct, the interrogation of gene functions from both culturable and nonculturable organisms is greatly accelerated and large pathway engineering efforts can be executed to produce “new” natural products. However, the genetic manipulation of complete natural product biosynthetic gene clusters is often complicated by their sheer size (10–200 kbp), which makes standard restriction/ligation‐based methods impracticable. To circumvent these problems, alternative recombinogenic methods, which depend on engineered homology‐based recombination have recently arisen as a powerful alternative. Here, we describe a new general technique that can be used to reconstruct large biosynthetic pathways from overlapping cosmids by retrofitting each cosmid with a “recombinogenic cassette” that contains a shared homologous element and orthogonal antibiotic markers. We employed this technique to reconstruct the anthramycin biosynthetic gene cluster of the thermotolerant actinomycete Streptomyces refuineus, from two >30 kbp cosmids into a single cosmid and integrate it into the genome of Streptomyces lividans. Anthramycin production in the heterologous Streptomyces host confirmed the integrity of the reconstructed pathway and validated the proposed boundaries of the gene cluster. Notably, anthramycin production by recombinant S. lividans was seen only during growth at high temperature—a property also shown by the natural host. This work provides tools to engineer the anthramycin biosynthetic pathway and to explore the connection between anthramycin production and growth at elevated temperatures.
Enantioselective Epoxidation of Electrophilic Olefins by Using Glycosyl Hydroperoxides
Authors: Kośnik Wioletta , Bocian Wojciech , Kozerski Lech , Tvaroška Igor , Chmielewski Marek
Published: May 2008

Anomeric hydroperoxides derived from 3,4,6‐tri‐O‐benzyl‐galactose and glucose were used for enantioselective epoxidation of naphthoquinone (12), chalcone (13), (E)‐1,2‐dibenzoyl ethylene (14) and (E)‐iso‐butyryl‐phenyl ethylene (15). In the presence of sodium hydroxide, the epoxidations showed exceptional high asymmetric induction. The exchange of sodium by a potassium ion resulted in a low asymmetric induction. These results pointed to the crucial role of the counterion and strongly suggested that coordination of the alkaline ion occurs in the transition state of the epoxidation process by both reagents, hydroperoxide and the olefin. Theoretical studies of the reaction mechanism at the DFT B3LYP/6‐31G* level fitted very well with experimental results.
Untersuchungen zum Einfluss elektrokinetischer Wechselwirkungen auf die Adsorptionsmechanismen bei der Tiefenfiltration
Authors: Sartor M. , Kaschek M. , Mavrov V. , Chmiel H.
Published: May 2008

Die Filtration von Biosuspensionen wird häufig durch das Biofouling an der Oberfläche des Filtermaterials limitiert. Um einen zufriedenstellenden Fluss zu ermöglichen, werden hohe Druckdifferenzen benötigt. Das Ziel dieser Arbeit ist es, den Einfluss elektrokinetischer Wechselwirkungen auf die Adsorptionsmechanismen zu untersuchen, die das Biofouling in Filterbetten verursachen. Verschiedene Filtermittel werden eingesetzt, um den Einfluss der elektrokinetischen Kräfte zu ermitteln. Es kann gezeigt werden, dass bei Wahl des geeigneten Filtermittels die suspendierten Partikel selektiv entweder mittels elektrokinetischer Abstoßungskräfte im Schüttbett zurückgehalten werden können oder auf der Oberfläche des Schüttbetts am Filtermittel adsorbieren. Durch die Berücksichtigung der elektrokinetischen Wechselwirkungen bei der Auswahl des geeigneten Filtermittels lässt sich die Tiefenfiltration für die selektive Entfernung von suspendierten Partikeln wie z. B. Mikroorganismen aus Biosuspensionen optimieren.
Überblick zur Gewinnung von Phytoextrakten
Authors: Ondruschka B. , Klemm W.
Published: May 2008

Die Gewinnung von Naturstoffen als qualitätsgerechte Komponenten für Produkte der Lebensmittel‐ sowie pharmazeutischen und kosmetischen Industrie hat in den letzten Jahren stark zugenommen. Aus wirtschaftlichen Gründen kommt den Extraktionsprozessen, zusammengefasst unter dem Begriff der Phytoextraktion, eine besondere Bedeutung zu. Hier soll über den gegenwärtigen Stand der Technologien zur Gewinnung von Naturstoffen berichtet werden, insbesondere über die Anwendung in der Industrie. Ein wesentlicher Gesichtspunkt ist dabei die Anwendung Mikrowellen‐assistierter Trennverfahren. In einer Übersicht über den Markt und die derzeit bevorzugt verwendeten Herstellungsverfahren sowie Anlagen wird die Zukunftsaussicht ihrer technischen Realisierung an Hand von Literaturrecherchen und persönlichen Anfragen an Hersteller von Produkten und Anlagen untersucht. Das Ergebnis ist, dass die Mikrowellen‐assistierte Technologie zwar für die Qualitäts‐ und Inhaltsstoffanalytik eine große Bedeutung gewonnen, aber aus technischen und daraus resultierenden wirtschaftlichen Gründen derzeit keine Aussicht auf eine Produktionseinführung hat.
Isolierung von Plasmid‐DNA durch inversmizellare Zweiphasensysteme – Optimierung der Rückextraktion
Authors: Streitner N. , Voß C. , Flaschel E.
Published: May 2008

Die Verteilung von RNA und Plasmid‐DNA wurde in einem inversmizellaren Zweiphasensystem bestehend aus Trioctylmethylammoniumchlorid (TOMAC) und Isooctan untersucht. Die Auswirkung verschiedener Salze und Alkohole auf den Transfer der Nukleinsäuren wurde vor allem unter dem Gesichtspunkt einer hohen Wiederfindung der Plasmid‐DNA nach der Rückextraktion betrachtet. Systeme, die eine Trennung von Plasmid‐DNA und RNA ermöglichen, wurden eingesetzt, um RNA aus bakteriellem Klarlysat zu entfernen.
Gewinnung und Potenziale des Biopolymers Chitosan
Authors: Ondruschka J. , Trutnau M. , Bley T.
Published: May 2008

In der Natur konnte Chitosan bisher nur in den Zellwänden weniger Pilze (z. B. Mucorales) gefunden werden. Auf Grund struktureller Eigenschaften, der geringen Toxizität, Biokompatibilität und biologischen Abbaubarkeit besitzt Chitosan ein breites Anwendungspotenzial. Wegen entfallender Entsorgungs‐ und Umweltprobleme ist es zusätzlich als Rohstoff attraktiv. Chitosan wird bisher aus Chitin gewonnen, das überwiegend aus Schalenresten der Krabben‐ und Shrimpsherstellung stammt. Eigene Untersuchungen zeigen, dass sich Chitosan aus verschiedenen Pilzmycelien, die als Restprodukte bei biotechnologischen Prozessen (Enzymproduktion, Bierbrauerei) anfallen, besonders günstig gewinnen und aufarbeiten ließe. Unter Umständen ist sogar ein Fermentationsprozess mit Zygomycota rentabel, weil in der Zellwand dieser filamentösen Pilze bereits Chitosan in vivo enthalten ist und so auf den Aufarbeitungsschritt der Deacetylierung verzichtet werden kann. Analysen ergaben, dass Chitosan aus Pilzmycelien gleiche Eigenschaften wie Krabbenchitosan hinsichtlich des Deacetylierungsgrades und der Wasserlöslichkeit bei weniger Aufarbeitungsschritten zeigt. Außerdem lässt es sich protein‐ und schwermetallfrei herstellen, was für Anwendungen im medizinischen Bereich besonders wichtig ist.
Aptamere in der Biosensorik
Authors: Walter J.‐G. , Stahl F.
Published: May 2008

In der Biotechnologie und der Bioprozesstechnik wird es zukünftig verstärkt zum Vermessen von Zielsubstanzen des Proteoms kommen. Traditionell dienen dabei als Biorezeptoren in Biosensoren vor allem Antikörper. Die Empfindlichkeit von Antikörpern führt insbesondere bei der Vermessung komplexer Proben wie Fermentationsbrühen zu einer begrenzten Haltbarkeit der Sensoren. Durch den Einsatz von Aptameren als alternative Biorezeptoren lässt sich diese Limitierung umgehen. Im Vergleich zu Antikörpern sind diese funktionellen Nukleinsäuren wesentlich robuster und können zielgerichtet modifiziert werden, wodurch eine definierte Immobilisierung an festen Oberflächen möglich ist. Aufgrund dieser Vorteile eröffnen Aptamere in der Biosensorik neue Möglichkeiten. Dieser Übersichtsartikel beschreibt die Entwicklung von Aptameren und gibt einen Überblick über aptamerbasierte Biosensoren. Darüber hinaus wird der Einsatz von Aptameren in der Protein‐Microarray‐Technologie beschrieben.
Untersuchungen zur Proteinseparation mittels magnetischer Mikrosorbentien in Kombination mit wässrigen Zweiphasen‐Systemen
Authors: Becker J. , Raffelt S. , Franzreb M.
Published: May 2008

Sowohl wässrige Zweiphasen‐Systeme als auch magnetische Mikro‐ und Nanosorbentien werden seit einigen Jahren als potenzielle Kandidaten für neuartige Aufarbeitungsprozesse biotechnologischer Produkte wie z. B. therapeutischer Proteine gehandelt. Der kombinierte Einsatz von magnetischen Sorbentien und Extraktionsphasen kann die technologische Nutzung beider Komponenten vereinfachen und bietet zudem verfahrenstechnische Möglichkeiten zur Optimierung kritischer Prozessparameter wie Selektivität und Produktivität. Im Folgenden werden ein neuartiges, aus einer derartigen Kombination hervorgegangenes, Verfahrenskonzept zur Bioproduktisolierung sowie erste experimentelle Ergebnisse vorgestellt.
Perspektiven der Biothermodynamik – Teil II. Adsorption von Proteinen
Authors: Keller J. U.
Published: May 2008

Die Anwendung von Begriffen und Methoden der Thermodynamik der Gleichgewichte und der Vorgänge auf Systeme und Prozesse der Biotechnologie haben zur Bildung eines neuen Fachgebietes geführt, der Technischen Biothermodynamik. Der vorliegende Artikel ist der zweite einer Reihe, in der versucht wird, einen Überblick über die Grundlagen und Möglichkeiten, die dieses Gebiet dem Bioverfahrensingenieur eröffnen, zu geben und dies auch an einzelnen Beispielen zu demonstrieren. Im vorliegenden Artikel wird die Thermodynamik der Adsorption von Proteinen aus Lösungen an festen Oberflächen entwickelt. Dabei werden Gleichgewichte und Prozesse, Einkomponenten‐ und Vielkomponentensysteme von Proteinen in Lösungen betrachtet. Einige Bemerkungen zum Phänomen der Multikontakt‐Adsorption von Proteinen und der Denaturierung von Proteinen durch Adsorption beschließen den Artikel. Die Adsorption von Molekülen eines Lösungsmittels, insbesondere von Wasser auf und in Proteinen wird hier nicht besprochen sondern ist einem Folgeartikel vorbehalten.