bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fabrication and characterization of biomaterial film from gland silk of muga and eri silkworms
Authors: Dutta Saranga , Talukdar Bijit , Bharali Rupjyoti , Rajkhowa Rangam , Devi Dipali 
Published: October 2012

AbstractThis study discusses the possibilities of liquid silk (Silk gland silk) of Muga and Eri silk, the indigenous non mulberry silkworms of North Eastern region of India, as potential biomaterials. Silk protein fibroin of Bombyx mori, commonly known as mulberry silkworm, has been extensively studied as a versatile biomaterial. As properties of different silk‐based biomaterials vary significantly, it is important to characterize the non mulberry silkworms also in this aspect. Fibroin was extracted from the posterior silk gland of full grown fifth instars larvae, and 2D film was fabricated using standard methods. The films were characterized using SEM, Dynamic contact angle test, FTIR, XRD, DSC, and TGA and compared with respective silk fibers. SEM images of films reveal presence of some globules and filamentous structure. Films of both the silkworms were found to be amorphous with random coil conformation, hydrophobic in nature, and resistant to organic solvents. Non mulberry silk films had higher thermal resistance than mulberry silk. Fibers were thermally more stable than the films. This study provides insight into the new arena of research in application of liquid silk of non mulberry silkworms as biomaterials. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 292–333, 2013.
Reviewprobing protein electron transfer mechanisms from the molecular to the cellular length scales
Authors: Skourtis Spiros S. 
Published: October 2012

AbstractThe mechanisms of bridge‐mediated electron transfer (ET) reactions vary from coherent deep tunneling to thermally activated hopping. This short review focuses on some developments in the study of protein ET mechanisms at the molecular and at the cellular levels. It explains experimental and theoretical work on the influence of electronic‐energy and electronic‐coupling fluctuations on ET rates and on the switch from the tunneling to the hopping regimes. It also describes recent work on extracellular ET, in particular on bacterial nanowires which support ET over micron length scales. Future directions in these research areas are discussed. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 82–92, 2013.
Laminar shear stress elicit distinct endothelial cell e‐selectin expression pattern via TNFα and IL‐1β activation
Authors: Huang Ryan B. , Gonzalez Anjelica L. , Eniola‐Adefeso Omolola 
Published: October 2012

AbstractThe ability to discriminate cell adhesion molecule expression between healthy and inflamed endothelium is critical for therapeutic intervention in many diseases. This study explores the effect of laminar flow on TNFα‐induced E‐selectin surface expression levels in human umbilical vein endothelial cells (HUVECs) relative to IL‐1β‐induced expression via flow chamber assays. HUVECs grown in static culture were either directly (naïve) activated with cytokine in the presence of laminar shear or pre‐exposed to 12 h of laminar shear (shear‐conditioned) prior to simultaneous shear and cytokine activation. Naïve cells activated with cytokine in static served as control. Depending on the cell shear history, fluid shear is found to differently affect TNFα‐induced relative to IL‐1β‐induced HUVEC expression of E‐selectin. Specifically, E‐selectin surface expression by naïve HUVECs is enhanced in the 8–12 h activation time range with simultaneous exposure to shear and TNFα (shear‐TNFα) relative to TNFα static control whereas enhanced E‐selectin expression is observed in the 4–24 h range for shear‐IL‐1β treatment relative to IL‐1β static control. While exposure of HUVECs to shear preconditioning mutes shear‐TNFα‐induced E‐selectin expression, it enhances or down‐regulates shear‐IL‐1β‐induced expression dependent on the activation period. Under dual‐cytokine‐shear conditions, IL‐1β signaling dominates. Overall, a better understanding of E‐selectin expression pattern by human ECs relative to the combined interaction of cytokines, shear profile and history can help elucidate many disease pathologies. Biotechnol. Bioeng. 2013; 110: 999–1003. © 2012 Wiley Periodicals, Inc.
Analyzing the effect of decreasing cytosolic triosephosphate isomerase onSolanum tuberosumhairy root cells using a kinetic–metabolic model
Authors: Valancin Alexandre , Srinivasan Balasubrahmanyan , Rivoal Jean , Jolicoeur Mario 
Published: October 2012

AbstractA kinetic–metabolic model ofSolanum tuberosumhairy roots is presented in the interest of understanding the effect on the plant cell metabolism of a 90% decrease in cytosolic triosephosphate isomerase (cTPI, EC 5.3.1.1) expression by antisense RNA. The model considers major metabolic pathways including glycolysis, pentose phosphate pathway, and TCA cycle, as well as anabolic reactions leading to lipids, nucleic acids, amino acids, and structural hexoses synthesis. Measurements were taken from shake flask cultures for six extracellular nutrients (sucrose, fructose, glucose, ammonia, nitrate, and inorganic phosphate) and 15 intracellular compounds including sugar phosphates (G6P, F6P, R5P, E4P) and organic acids (PYR, aKG, SUCC, FUM, MAL) and the six nutrients. From model simulations and experimental data it can be noted that plant cell metabolism redistributes metabolic fluxes to compensate for the cTPI decrease, leading to modifications in metabolites levels. Antisense roots showed increased exchanges between the pentose phosphate pathway and the glycolysis, an increased oxygen uptake and growth rate. Biotechnol. Bioeng. 2013; 110: 924–935. © 2012 Wiley Periodicals, Inc.
A reliable simulator for dynamic flux balance analysis
Authors: Höffner K. , Harwood S. M. , Barton P. I. 
Published: October 2012

AbstractDynamic flux balance analysis (DFBA) provides a platform for detailed design, control and optimization of biochemical process technologies. It is a promising modeling framework that combines genome‐scale metabolic network analysis with dynamic simulation of the extracellular environment. Dynamic flux balance analysis assumes that the intracellular species concentrations are in equilibrium with the extracellular environment. The resulting underdetermined stoichiometric model is solved under the assumption of a biochemical objective such as growth rate maximization. The model of the metabolism is coupled with the dynamic mass balance equations of the extracellular environment via expressions for the rates of substrate uptake and product excretion, which imposes additional constraints on the linear program (LP) defined by growth rate maximization of the metabolism. The linear program is embedded into the dynamic model of the bioreactor, and together with the additional constraints this provides an accurate model of the substrate consumption, product secretion, and biomass production during operation. A DFBA model consists of a system of ordinary differential equations for which the evaluation of the right‐hand side requires not only function evaluations, but also the solution of one or more linear programs. The numerical tool presented here accurately and efficiently simulates large‐scale dynamic flux balance models. The main advantages that this approach has over existing implementation are that the integration scheme has a variable step size, that the linear program only has to be solved when qualitative changes in the optimal flux distribution of the metabolic network occur, and that it can reliably simulate behavior near the boundary of the domain where the model is defined. This is illustrated through large‐scale examples taken from the literature. Biotechnol. Bioeng. 2013; 110: 792–802. © 2012 Wiley Periodicals, Inc.
Cell mass and cell cycle dynamics of an asynchronous budding yeast population: Experimental observations, flow cytometry data analysis, and multi‐scale modeling
Authors: Fernandes Rita Lencastre , Carlquist Magnus , Lundin Luisa , Heins Anna‐Lena , Dutta Abhishek , Sørensen Søren J. , Jensen Anker D. , Nopens Ingmar , Lantz Anna Eliasson , Gernaey Krist V. 
Published: October 2012

AbstractDespite traditionally regarded as identical, cells in a microbial cultivation present a distribution of phenotypic traits, forming a heterogeneous cell population. Moreover, the degree of heterogeneity is notably enhanced by changes in micro‐environmental conditions. A major development in experimental single‐cell studies has taken place in the last decades. It has however not been fully accompanied by similar contributions within data analysis and mathematical modeling. Indeed, literature reporting, for example, quantitative analyses of experimental single‐cell observations and validation of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distributions, of a population of Saccharomyces cerevisiae, in response to the substrate consumption observed during batch cultivation. The good agreement between the proposed multi‐scale model (a population balance model [PBM] coupled to an unstructured model) and experimental data (both the overall physiology and cell size and cell cycle distributions) indicates that a mechanistic model is a suitable tool for describing the microbial population dynamics in a bioreactor. This study therefore contributes towards the understanding of the development of heterogeneous populations during microbial cultivations. More generally, it consists of a step towards a paradigm change in the study and description of cell cultivations, where average cell behaviors observed experimentally now are interpreted as a potential joint result of various co‐existing single‐cell behaviors, rather than a unique response common to all cells in the cultivation. Biotechnol. Bioeng. 2013; 110: 812–826. © 2012 Wiley Periodicals, Inc.
Gene delivery to overcome astrocyte inhibition of axonal growth: An in vitro Model of the glial scar
Authors: Tuinstra Hannah M. , Ducommun Melissa M. , Briley William E. , Shea Lonnie D. 
Published: October 2012

AbstractAfter injury to the central nervous system, a glial scar develops that physically and biochemically inhibits axon growth. In the scar, activated astrocytes secrete inhibitory extracellular matrix, of which chondroitin sulfate proteoglycans (CSPGs) are considered the major inhibitory component. An inhibitory interface of CSPGs forms around the lesion and prevents axons from traversing the injury, and decreasing CSPGs can enhance axon growth. In this report, we established an in vitro interface model of activated astrocytes and subsequently investigated gene delivery as a means to reduce CSPG levels and enhance axon growth. In the model, a continuous interface of CSPG producing astrocytes was created with neurons seeded opposite the astrocytes, and neurite crossing, stopping, and turning were evaluated as they approached the interface. We investigated the efficacy of lentiviral delivery to degrade or prevent the synthesis of CSPGs, thereby removing CSPG inhibition of neurite growth. Lentiviral delivery of RNAi targeting two key CSPG synthesis enzymes, chondroitin polymerizing factor and chondroitin synthase‐1, decreased CSPGs, and reduced inhibition by the interface. Degradation of CSPGs by lentiviral delivery of chondroitinase also resulted in less inhibition and more neurites crossing the interface. These results indicate that the interface model provides a tool to investigate interventions that reduce inhibition by CSPGs, and that gene delivery can be effective in promoting neurite growth across an interface of CSPG producing astrocytes. Biotechnol. Bioeng. 2013; 110: 947–957. © 2012 Wiley Periodicals, Inc.
Co‐culture with mesenchymal stem cells enhances metabolic functions of liver cells in bioartificial liver system
Authors: Yang Ying , Li Jianzhou , Pan Xiaoping , Zhou Pengcheng , Yu Xiaopeng , Cao Hongcui , Wang Yingjie , Li Lanjuan 
Published: October 2012

AbstractBioartificial liver provides a combination of three‐dimensional support, matrix interactions, and extracellular cues to create a bio‐mimic microenvironment for maintaining hepatic‐specific functions of liver cells in vitro. However, its transformal and metabolic functions are not yet satisfactory for clinic application. In this study, hepatoma‐derived C3A cells were co‐cultured with human placental mesenchymal stem cells (hPMSC) in microspheres placed in a fluidized bioreactor. The secretion of albumin and urea, the expression of metabolizing enzymes at both transcriptional and translational levels and the drug metabolism functions of co‐cultured C3A cells were determined. With the three‐dimensional culture system, when C3A cells were co‐cultured with hPMSCs in separate microspheres, the secretion of albumin and activity of CYP1A2 were significantly improved although the enhancement of urea synthesis and CYP3A4 activity was less prominent. Combining co‐culture system with fluidization significantly increased the secretion of urea and the activities of CYP1A2, CYP3A4 but not the albumin synthesis. Interestingly, the levels of phospho‐PKA (Thr 197), phospho‐PKC, phospho‐ERK1/2 (Thr 202/Tyr 204) and CaMKII were all found to decrease in co‐cultured C3A cells, implicating suppressed signaling pathways in those cells. Taken together, our results suggest that co‐culturing of liver cells with hPMSC cells in three‐dimensional fluidized bioreactor significantly improved the preservation of liver cells' metabolic functions which may greatly enhance the efficacy of bioartificial liver treatment. Biotechnol. Bioeng. 2013; 110: 958–968. © 2012 Wiley Periodicals, Inc.
A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors
Authors: Tang Youneng , Ontiveros‐Valencia Aura , Feng Liang , Zhou Chen , Krajmalnik‐Brown Rosa , Rittmann Bruce E. 
Published: October 2012

AbstractThis work presents a multispecies biofilm model that describes the co‐existence of nitrate‐ and sulfate‐reducing bacteria in the H2‐based membrane biofilm reactor (MBfR). The new model adapts the framework of a biofilm model for simultaneous nitrate and perchlorate removal by considering the unique metabolic and physiological characteristics of autotrophic sulfate‐reducing bacteria that use H2 as their electron donor. To evaluate the model, the simulated effluent H2, UAP (substrate‐utilization‐associated products), and BAP (biomass‐associated products) concentrations are compared to experimental results, and the simulated biomass distributions are compared to real‐time quantitative polymerase chain reaction (qPCR) data in the experiments for parameter optimization. Model outputs and experimental results match for all major trends and explain when sulfate reduction does or does not occur in parallel with denitrification. The onset of sulfate reduction occurs only when the nitrate concentration at the fiber's outer surface is low enough so that the growth rate of the denitrifying bacteria is equal to that of the sulfate‐reducing bacteria. An example shows how to use the model to design an MBfR that achieves satisfactory nitrate reduction, but suppresses sulfate reduction. Biotechnol. Bioeng. 2013; 110: 763–772. © 2012 Wiley Periodicals, Inc.
Dye free automated cell counting and analysis
Authors: Dehlinger Dietrich , Suer Lynn , Elsheikh Maher , Peña José , Naraghi‐Arani Pejman 
Published: October 2012

AbstractWe have developed an automated cell counting method that uses images obtained at multiple focal heights to enumerate cells in confluent culture. By taking the derivative of image intensity with respect to focal height using two complementary images, we are able to count high‐density monolayers of cells over a large image area. Our method resists errors arising from variability in the focal plane caused by flatness or tilt non‐uniformities with a minimal amount of focal plane alignment, allowing the automated collection of images across a large area. Biotechnol. Bioeng. © 2013 Wiley Periodicals, Inc.
Protein analysis by dynamic light scattering: Methods and techniques for students
Authors: Lorber Bernard , Fischer Frédéric , Bailly Marc , Roy Hervé , Kern Daniel 
Published: October 2012

AbstractDynamic light scattering (DLS) analyses are routinely used in biology laboratories to detect aggregates in macromolecular solutions, to determine the size of proteins, nucleic acids, and complexes or to monitor the binding of ligands. This article is written for graduate and undergraduate students with access to DLS and for faculty members who wish to incorporate DLS into a lab activity, a practical course or research. It reviews the basic concepts of light scattering measurements and addresses four critical aspects of the analysis and interpretation of DLS results. To ensure reproducible quantitative data, attention should be paid to controlling the preparation and handling of proteins or assemblies because variations in the state of aggregation, induced by minor changes in experimental condition or technique, might compromise DLS results and affect protein activity. Variables like temperature, solvent viscosity, and inter‐particle interactions may also influence particle size determination. Every point is illustrated by case studies, including a commercially available albumin, a small RNA virus isolated from plants, as well as four soluble proteins and a ribonucleoprotein assembly purified and characterized by students in the frame of their master degree. © 2012 by The International Union of Biochemistry and Molecular Biology
Alginate as Template in the Preparation of Active Titania Photocatalysts
Authors: Buaki‐Sogo Mireia , Serra Marco , Primo Ana , Alvaro Mercedes , Garcia Hermenegildo 
Published: October 2012

AbstractA simple and reliable procedure to prepare TiO2 and Au/TiO2 samples with high photocatalytic activity for hydrogen generation from water/methanol mixtures is reported, which uses natural alginate as the templating agent. Aqueous solutions of sodium alginate are flocculated as beads by TiO2+ ions in the presence or absence of AuCl4−. The resulting alginate beads containing approximately 25 wt % of Ti and various Au contents are dehydrated by ethanol washings before drying under supercritical CO2 conditions. The key step in the preparation method is to obtain Au/Ti‐containing alginate aerogels of approximately 700 m2 g−1 Brunauer–Emmett–Teller surface area. The surface area of the TiO2 and Au/TiO2 samples obtained after calcination of the organic biopolymer at 450 °C under air ranges from 187 to 136 m2 g−1, and the Au content has been varied from 1.3 to 0.05 wt % to optimize the photocatalytic activity of the samples. TiO2 forms in the anatase phase according to XRD and Raman spectroscopy. The highest activity Au/TiO2 sample (containing 0.556 wt % of Au) prepared by means of the biopolymer templating method was approximately eight times more active for hydrogen generation using a solar simulator than was an analogous Au‐containing TiO2 P25 sample prepared by means of the conventional deposition–precipitation method.
Efficient Photoinduced Energy Transfer in a Newly Developed Hybrid SBA‐15 Photonic Antenna
Authors: Cucinotta Fabio , Carniato Fabio , Devaux André , De Cola Luisa , Marchese Leonardo 
Published: October 2012

AbstractA new hybrid photostable donor–acceptor mesoporous SBA‐15 silica system was designed and prepared. It consists of an encapsulated donor, the Super Yellow (SY) polymer, which transfers the photoexcitation energy directly to an acceptor dye that is linked outside the framework. The obtained composite material was characterized by X‐ray diffraction, nitrogen‐physisorption porosimetry, diffuse‐reflectance (DR)‐UV/Vis spectroscopy and photoluminescence, space‐ and time‐resolved confocal microscopy. The physico‐chemical analyses showed that the system behaves as an efficient Förster resonance energy transfer (FRET) pair, and high photoluminescence was observed from the acceptor. The presented photonic antenna is the first example of dye sensitization by polymer‐loaded mesoporous silica and represents a step forward in the search for new efficient and stable materials with opto‐electronic applications.
Free‐Amine‐Directed Alkenylation of C(sp2)H and Cycloamination by Palladium Catalysis
Authors: Liang Zunjun , Ju Long , Xie Yongju , Huang Lehao , Zhang Yuhong 
Published: October 2012

AbstractA new protocol for the palladium‐catalyzed free‐amine‐directed alkenylation of C(sp2)H bonds and cycloamination is described. Substituted biaryl‐2‐amines react with various alkenes, including electron‐deficient alkenes, aryl alkenes and alkyl alkenes, to give the corresponding phenanthridines with exclusive regioselectivity. The use of α‐branched styrenes leads to the formation of tricyclic compounds with a seven‐membered amine ring. The method operates through a free‐amine‐directed alkenylation and a subsequent hydroamination cyclization reaction.
Design of Hybrid Distillation/Melt Crystallization Processes for Separation of Close‐Boiling Mixtures
Authors: Micovic Jovana , Beierling Thorsten , Lutze Philip , Sadowski Gabriele , Górak Andrzej 
Published: October 2012

AbstractDie Kombination aus Rektifikation und Schmelzekristallisation in einem hybriden Trennverfahren hat großes Potenzial für die Prozessintensivierung. Allerdings stellt die Auslegung solcher Verfahren aufgrund der Vielzahl struktureller und operativer Freiheitsgrade eine große Herausforderung dar. Für die Auslegung hybrider Trennverfahren hat sich eine dreistufige Auslegungsmethode durchgesetzt, die aber nur dann angewendet werden kann, wenn alle Modellparameter für die Kristallisation a priori bekannt sind. Da dies oft nicht der Fall ist, wird hier eine vierstufige Entwurfsmethode vorgeschlagen. Die Eignung der Methode sowie entwickelte Werkzeuge werden an einem Fallbeispiel der Trennung langkettiger isomerer Aldehyde vorgestellt.
Synthesis and Biological Evaluation of N‐Substituted Noscapine Analogues
Authors: DeBono Aaron J. , Xie Jin Han , Ventura Sabatino , Pouton Colin W. , Capuano Ben , Scammells Peter J. 
Published: October 2012

AbstractNoscapine is a phthalideisoquinoline alkaloid isolated from the opium poppy Papaver somniferum. It has long been used as an antitussive agent, but has more recently been found to possess microtubule‐modulating properties and anticancer activity. Herein we report the synthesis and pharmacological evaluation of a series of 6′‐substituted noscapine derivatives. To underpin this structure–activity study, an efficient synthesis of N‐nornoscapine and its subsequent reduction to the cyclic ether derivative of N‐nornoscapine was developed. Reaction of the latter with a range of alkyl halides, acid chlorides, isocyanates, thioisocyanates, and chloroformate reagents resulted in the formation of the corresponding N‐alkyl, N‐acyl, N‐carbamoyl, N‐thiocarbamoyl, and N‐carbamate derivatives, respectively. The ability of these compounds to inhibit cell proliferation was assessed in cell‐cycle cytotoxicity assays using prostate cancer (PC3), breast cancer (MCF‐7), and colon cancer (Caco‐2) cell lines. Compounds that showed activity in the cell‐cycle assay were further evaluated in cell viability assays using PC3 and MCF‐7 cells.