bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and Characterization of a Clinically Compliant Xeno-Free Culture Medium in Good Manufacturing Practice for Human Multipotent Mesenchymal Stem Cells
Authors: Chase Lucas G. , Yang Sufang , Zachar Vladimir , Yang Zheng , Lakshmipathy Uma , Bradford Jolene , Boucher Shayne E. , Vemuri Mohan C.
Published: October 2012

Human multipotent mesenchymal stem cell (MSC) therapies are currently being tested in clinical trials for Crohn's disease, multiple sclerosis, graft-versus-host disease, type 1 diabetes, bone fractures, cartilage damage, and cardiac diseases. Despite remarkable progress in clinical trials, most applications still use traditional culture media containing fetal bovine serum or serum-free media that contain serum albumin, insulin, and transferrin. The ill-defined and variable nature of traditional culture media remains a challenge and has created a need for better defined xeno-free culture media to meet the regulatory and long-term safety requirements for cell-based therapies. We developed and tested a serum-free and xeno-free culture medium (SFM-XF) using human bone marrow- and adipose-derived MSCs by investigating primary cell isolation, multiple passage expansion, mesoderm differentiation, cellular phenotype, and gene expression analysis, which are critical for complying with translation to cell therapy. Human MSCs expanded in SFM-XF showed continual propagation, with an expected phenotype and differentiation potential to adipogenic, chondrogenic, and osteogenic lineages similar to that of MSCs expanded in traditional serum-containing culture medium (SCM). To monitor global gene expression, the transcriptomes of bone marrow-derived MSCs expanded in SFM-XF and SCM were compared, revealing relatively similar expression profiles. In addition, the SFM-XF supported the isolation and propagation of human MSCs from primary human marrow aspirates, ensuring that these methods and reagents are compatible for translation to therapy. The SFM-XF culture system allows better expansion and multipotentiality of MSCs and serves as a preferred alternative to serum-containing media for the production of large scale, functionally competent MSCs for future clinical applications.
La relation musique-danse dans le genre du ballet au Mali : organisation, évolution et émancipation
Authors: Djebbari Elina
Published: October 2012

Pendant longtemps, la danse dite « africaine » a été considérée comme une expression corporelle que l’on ne pouvait distinguer du « tam-tam », censé l’accompagner à tout moment. Depuis sa création après l’indépendance en 1960, le Ballet national du Mali a contribué à donner du sens à ce stéréotype en faisant du tambour jembe l’instrument-roi de ce genre musico-chorégraphique. Cet article propose de nous interroger sur les techniques musicales et chorégraphiques qui permettent l’interaction musique-danse lors de la performance scénique, sur les rapports de hiérarchie qui s’en dégagent, la façon dont ces valeurs peuvent s’inverser ou se transformer selon les contextes et les pratiques et, enfin, d’appréhender comment la création artistique contemporaine de ce genre musico-chorégraphique semble pouvoir s’orienter vers une dissociation de ces deux éléments alors que leur complémentarité en déterminait justement la caractéristique principale.
Danse et musique, deux arts en dialogue chez Anne Teresa De Keersmaeker
Authors: Guisgand Philippe
Published: October 2012

À la suite de mon travail de thèse, j’ai noué avec le musicien Jean-Luc Plouvier un dialogue à propos de l’oeuvre d’Anne Teresa De Keersmaeker. Une des spécificités de cette chorégraphe est de travailler majoritairement sur la musique occidentale écrite. Cette collaboration entre un musicien et un danseur permet de questionner des termes tels que « dialoguer vraiment », « rapport entre musique et danse », « demande et adresse des arts entre eux » ou encore « faille entre écriture et réception ». Il s’agira dans cet article de dresser un état des lieux de cette collaboration et de montrer – du point de vue de la danse – ce que les démarches analytiques et esthétiques issues de la musique apportent au champ des études chorégraphiques.
Music and Movement in Dialogue: Exploring Gesture in Soundpainting
Authors: Minors Helen Julia
Published: October 2012

Using “Soundpainting” as a case study, this paper examines how musicians and dancers can create and contribute to a dialogue between, across and within the arts. Interviews with the “Soundpainter” Walter Thompson provide a practical and applied basis for analysis, and a major goal of the article is to illustrate how music-dance dialogues are formed in this creative sign language.
Time trends and correlates of late presentation for HIV care in Northern Greece during the decade 2000 to 2010
Authors: Metallidis Simeon , Pilalas Dimitrios , Skoura Lemonia , Haidich Anna‐Bettina , Tsachouridou Olga , Papaioannou Maria , Chrysanthidis Theofilos , Bakaimi Isidora , Antoniadou Zoe A , Margariti Apostolia , Malisiovas Nicolaos , Nikolaidis Pavlos
Published: October 2012

Background

The aim of our study was to assess the extent of late presentation for HIV care in Northern Greece during the period 2000 to 2010 and to explore correlations aiming to provide guidance for future interventions.

Methods

HIV‐positive patients with no prior history of HIV care at presentation and with a CD4 T cell count within three months from the first confirmatory Western blot result were eligible for this study. Late presentation and advanced HIV disease were defined in concordance with the recommendations of the European Late Presenter Consensus working group. Time trends in presentation status and risk factors linked to late presentation and advanced HIV disease were identified in multivariable logistic regression models. Additional analyses after multiple imputation of missing values were performed to assess the robustness of our findings.

Results

The status at presentation was evaluated for 631 eligible HIV‐positive individuals. Overall, 52.5% (95% CI: 48.6% to 56.4%) of patients presented late for HIV care and 31.2% (95% CI: 27.6% to 34.8%) presented with advanced HIV disease. Time trends were consistent with an improvement in the presentation status of our study population (p<0.001). Risk factors associated with late presentation in multivariable logistic regression were intravenous drug use, heterosexual HIV transmission, immigrant status and age at diagnosis.

Conclusions

Despite the trend for improvement, a significant proportion of newly diagnosed HIV‐positive patients present late for care. Targeted interventions with focus on social groups such as the elderly, persons who inject drugs, immigrants and individuals at risk for heterosexual HIV transmission are mandated.
Time Series Analysis of the Geospatial Distribution of Distance Education Learners: Implications for Student Support
Authors: Bagarinao Ricardo T.
Published: October 2012

Distance Education (DE) is a new field in education that is entirely separated from the standard, classroom-based, classical instructional model. It is believed to attract geographically diverse learners. A time series enrolment data (2005-2010) of UPOU was categorized by province, and fed into a GIS-data analysis environment Visual analysis was conducted to analyze the temporal and spatial behavior of the data; identify major spatial units of students ‘concentration; and extract the implications of this behavior on the development of student support system. Data were visualized as maps, tables, and graphs. Results indicate that enrolment in UPOU is increasing within the period of analysis, and enrolment data were widespread in 2005 but tend to aggregate in urban centers in the succeeding years. The increasing trend in enrolment data may be due to the convenience factor of online learning. On the other hand, the geospatial distribution patterns over time highlight the equity and accessibility issue, and the importance of mobile communication facilities as supplemental learning platforms. It is recommended that a mobile-learning environment that is equivalent to the online learning management system may be developed.   Keywords - distance education, student support, UP Open University, geospatial, GIS, student support, time series analysis
Dehydrogenative Silylation of Terminal Alkynes with Hydrosilanes under Zinc–Pyridine Catalysis
Authors: Tsuchimoto Teruhisa , Fujii Masakazu , Iketani Yoshihiko , Sekine Masaru
Published: October 2012

A combination of zinc triflate and pyridine in a nitrile medium was found to act as an effective catalytic system for dehydrogenative silylation with flexible pieces of terminal alkynes and hydrosilanes, thereby producing diverse alkynylsilanes in high to excellent yields.
Correlation of interferon‐inducible chemokine plasma levels with disease severity in systemic sclerosis
Authors: Liu Xiaochun , Mayes Maureen D. , Tan Filemon K. , Wu Minghua , Reveille John D. , Harper Brock E. , Draeger Hilda T. , Gonzalez Emilio B. , Assassi Shervin
Published: October 2012

Objective

To measure interferon (IFN)–inducible chemokines in the plasma of patients with systemic sclerosis (SSc) and investigate whether the chemokine levels are correlated with disease severity.

Methods

Plasma levels of the IFN‐inducible chemokines IFNγ‐inducible protein 10 (IP‐10/CXCL10), IFN‐inducible T cell α chemoattractant (I‐TAC/CXCL11), and monocyte chemoattractant protein 1 (CCL2) were measured in SSc patients and examined for correlation with the IFN gene expression signature. A composite IFN‐inducible chemokine score was generated for chemokines showing a correlation with the IFN gene signature (IP‐10 and I‐TAC), and this score was compared between 266 patients with SSc enrolled in the Genetics versus Environment in Scleroderma Outcome Study (GENISOS) cohort and 97 matched control subjects. Subsequently, the correlation between the IFN‐inducible chemokine score at baseline and markers of disease severity was assessed. In addition, the course of the IFN‐inducible chemokine score over time was examined.

Results

The plasma IFN‐inducible chemokine score correlated with the IFN gene expression signature, and this score was higher in SSc patients compared to controls. The IFN‐inducible chemokine score was also associated with the absence of anti–RNA polymerase III antibodies and presence of anti–U1 RNP antibodies, but not with disease duration, disease type, or other autoantibodies. The chemokine score correlated with concomitantly obtained scores on the Medsger Severity Index for muscle, skin, and lung involvement in SSc, as well as the forced vital capacity, diffusing capacity for carbon monoxide, and creatine kinase levels. The association of the chemokine score with disease severity was independent of the presence of anti–U1 RNP or other potential confounders (age, sex, ethnicity, disease duration, and treatment with immunosuppressive agents). Finally, there was not a significant change in the IFN‐inducible chemokine score over time.

Conclusion

The IFN‐inducible chemokine score is a stable serologic marker of a more severe form of SSc and may be useful for risk stratification of patients, regardless of disease type (limited or diffuse) or duration of disease.
IgG anti–NR2 glutamate receptor autoantibodies from patients with systemic lupus erythematosus activate endothelial cells
Authors: Yoshio Taku , Okamoto Hiroshi , Hirohata Shunsei , Minota Seiji
Published: October 2012

Objective

To investigate the possibility that IgG anti–NR2 glutamate receptor antibodies (anti‐NR2) derived from patients with systemic lupus erythematosus (SLE) cause an immunologic interaction with endothelial cells (ECs) in the blood–brain barrier, resulting in inflammation of the blood–brain barrier, allowing the entrance of these autoantibodies into the cerebrospinal fluid.

Methods

Purified IgG anti‐NR2 antibodies from 14 patients with SLE were tested for their ability to bind to double‐stranded DNA (dsDNA) and ECs, to modulate endothelial adhesion molecule expression and cytokine production by ECs, and to activate the NF‐κB pathways in the ECs. Purified IgG from 5 normal subjects was used as a negative control.

Results

Purified IgG anti‐NR2 antibodies bound to dsDNA in an IgG‐dose–dependent manner. This interaction up‐regulated the expression of endothelial leukocyte adhesion molecule 1, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 on the EC surface and increased the production of interleukin‐6 (IL‐6) and IL‐8, but not tumor necrosis factor α or IL‐1β, by ECs. Purified IgG anti‐NR2 also activated the degradation of cytoplasmic IκB, indicating the activation of NF‐κB in the ECs.

Conclusion

EC activation through the NF‐κB signaling pathway induced by IgG anti‐NR2 antibodies in the central nervous system of SLE patients may lead to inflammation of the blood–brain barrier, initiating the pathogenesis of neuropsychiatric SLE.
Alternative Copolymerization of a Conjugated Segment and a Flexible Segment and Fabrication of a Fluorescent Sensing Film for HCl in the Vapor Phase
Authors: Wang Hongyue , Cui Hong , Liu Xinglei , Li Lanlan , Cao Yuan , Liu Taihong , Fang Yu
Published: October 2012

A novel fluorescently active co‐oligomer (P1) was designed and prepared by alternative co‐polymerization of oligo(p‐phenyleneethynylene) (OPE), possessing two cholesterol‐containing side chains, and ethanediamine. A control co‐oligomer (P2) possessing similar structure to P1 was also prepared, but in this case the OPE bears no side chains. P1 and P2 have been used for the fabrication of two fluorescent films, film 1 and film 2, respectively. Fluorescence studies demonstrated that the emission of film 1 is sensitive and selective to the presence of trace amounts of HCl in air. In contrast, film 2 shows no such response. The quenching has been attributed to the protonation of the imino groups within the oligomer chains, and the difference in the sensing behaviors of the two films was rationalized by supposing the existence of molecular channels in film 1. The proposed mechanism is supported by the results from additional experiments and theoretical calculations. Furthermore, the film as fabricated is robust, and thereby it is believed that film 1 has the potential to be developed into a new generation of sensitive and selective HCl sensor.
Testing independence between two sequential gap times in the presence of covariates
Authors: Pénichoux Juliette , Moreau Thierry , Meyer Laurence , Boufassa Faroudy , Huber Catherine , Latouche Aurélien
Published: October 2012

In the risk analysis of sequential events, the successive gap times are often correlated, e.g. as a result of an individual heterogeneity. Correlation is usually accounted for by using a shared gamma‐frailty model, where the variance φ of the random individual effect quantifies the correlation between gap times. This method is known to yield satisfactory estimates of covariate effects, but underestimates φ, which could result in a lack of power of the test of independence. We propose a new test of independence between two sequential gap times where the first is the time elapsed from the origin. The test is based on an approximation of the hazard of the second event given the first gap time in a frailty model, with a frailty distribution belonging to the power variance function family. Simulation results show an increased power of the new test compared with the test derived from the gamma‐frailty model. In the realistic case where hazards are event specific, and using event‐specific approaches, the proposed estimation of the variance of the frailty is less biased than the gamma‐frailty based estimation for a wide range of values ( with the set of parameters considered), and similar for higher values. As an illustration, the methods are applied to a previously analysed asthma prevention trial with results showing a significant positive association between the successive times to asthmatic events. We also analyse data from a cohort of HIV‐seropositive patients in order to assess the effect of risk factors on the occurrence of two successive markers of progression of the HIV disease. The results demonstrate the ability of the proposed model to account for negative correlations between gap times.
Differential expression of centrosome‐associated proteins in human brain tumors: A possible role of hNinein isoform 6 in cell differentiation
Authors: Loh Joon‐Khim , Lieu Ann‐Shung , Chou Chia‐Hua , Lin Ching‐Chih , Yang Ming‐Chang , Lin Fang‐Yi , Hong Yi‐Ren , Howng Shen‐Long
Published: October 2012

Dysregulated centrosomal expression has been observed in high grade gliomas. Thus, this study aimed to examine the expression of Aurora family kinase and various centrosomal proteins, including centrin, γ‐tubulin, and hNinein isoforms, in human brain tumors, including 29 meningiomas, 34 astrocytomas, 6 pituitary adenomas, and 6 metastatic tumors. mRNA expression was evaluated using reverse transcription polymerase chain reaction. The role of hNinein isoform 6 expression in cell differentiation was assessed in BrdU‐treated IMR‐32 cells. Differential expression of centrosomal proteins of brain tumors and cell lines was observed. Specifically, centrin 2 and centrin 3 expression levels were classified as moderate or abundant in >97% of samples in the meningioma group, 63% of astrocytomas, >83% of metastatic and pituitary tumors. Alternatively, hNinein isoform 6 expression was only detected in normal brain and astrocytoma tumors (17/34); however, it was not expressed in meningioma (0/29), metastatic tumors (0/6) (P < 0.001). Of the six neuroblastoma cell lines analyzed only IMR‐32 cells expressed hNinein isoform 6. Furthermore, downregulated expression of hNinein isoform 6 and upregulation of γ‐tubulin was correlated to astrocytoma tumor grade (P < 0.001). Increased hNinein isoform 6 mRNA expression was observed in response to BrdU treatment, and its expression was greater in teratomas as compared to embryonic stem cells. Further studies are necessary to determine if hNinein isoform 6 functions as a tumor‐suppressor gene in brain tumors. Differential centrosomal protein expression may result in altered centrosome function that is observed the in progression of various brain tumors. © 2012 International Union of Biochemistry and Molecular Biology, Inc.
A bioreactor system for interfacial culture and physiological perfusion of vascularized tissue equivalents
Authors: Groeber Florian , Kahlig Alexander , Loff Steffan , Walles Heike , Hansmann Jan
Published: October 2012

A pivotal requirement for the generation of vascularized tissue equivalents is the development of culture systems that provide a physiological perfusion of the vasculature and tissue‐specific culture conditions. Here, we present a bioreactor system that is suitable to culture vascularized tissue equivalents covered with culture media and at the air–medium interface, which is a vital stimulus for skin tissue. For the perfusion of the vascular system a new method was integrated into the bioreactor system that creates a physiological pulsatile medium flow between 80 and 120 mmHg to the arterial inflow of the equivalent's vascular system. Human dermal microvascular endothelial cells (hDMECs) were injected into the vascular system of a biological vascularized scaffold based on a decellularized porcine jejunal segment and cultured in the bioreactor system for 14 days. Histological analysis and 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) staining revealed that the hDMECs were able to recolonize the perfused vascular structures and expressed endothelial cell specific markers such as platelet endothelial cell adhesion molecule and von Willebrand factor. These results indicate that our bioreactor system can serve as a platform technology to generate advanced bioartificial tissues with a functional vasculature for future clinical applications.
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

This 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

The 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

The 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

A 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

Dynamic 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

Despite 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

After 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

Bioartificial 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

This 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

We 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

Dynamic 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

A 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

A 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

A 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

Die 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

Noscapine 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.
Delayed and asynchronous ganglionic maturation during cephalopod neurogenesis as evidenced by Sof‐elav1 expression in embryos of Sepia officinalis (Mollusca, Cephalopoda)
Authors: Buresi Auxane , Canali Ester , Bonnaud Laure , Baratte Sébastien
Published: October 2012

Among the Lophotrochozoa, centralization of the nervous system reaches an exceptional level of complexity in cephalopods, where the typical molluscan ganglia become highly developed and fuse into hierarchized lobes. It is known that ganglionic primordia initially emerge early and simultaneously during cephalopod embryogenesis but no data exist on the process of neuron differentiation in this group. We searched for members of the elav/hu family in the cuttlefish Sepia officinalis, since they are one of the first genetic markers of postmitotic neural cells. Two paralogs were identified and the expression of the most neural‐specific gene, Sof‐elav1, was characterized during embryogenesis. Sof‐elav1 is expressed in all ganglia at one time of development, which provides the first genetic map of neurogenesis in a cephalopod. Our results unexpectedly revealed that Sof‐elav1 expression is not similar and not coordinated in all the prospective ganglia. Both palliovisceral ganglia show extensive Sof‐elav1 expression soon after emergence, showing that most of their cells differentiate into neurons at an early stage. On the contrary, other ganglia, and especially both cerebral ganglia that contribute to the main parts of the brain learning centers, show a late extensive Sof‐elav1 expression. These delayed expressions in ganglia suggest that most ganglionic cells retain their proliferative capacities and postpone differentiation. In other molluscs, where a larval nervous system predates the development of the definitive adult nervous system, cerebral ganglia are among the first to mature. Thus, such a difference may constitute a cue in understanding the peculiar brain evolution in cephalopods. J. Comp. Neurol. 521:1482–1496, 2013. © 2012 Wiley Periodicals, Inc.
Synaptic alterations in the rTg4510 mouse model of tauopathy
Authors: Kopeikina Katherine J. , Polydoro Manuela , Tai Hwan‐Ching , Yaeger Erich , Carlson George A. , Pitstick Rose , Hyman Bradley T. , Spires‐Jones Tara L.
Published: October 2012

Synapse loss, rather than the hallmark amyloid‐β (Aβ) plaques or tau‐filled neurofibrillary tangles (NFT), is considered the most predictive pathological feature associated with cognitive status in the Alzheimer's disease (AD) brain. The role of Aβ in synapse loss is well established, but despite data linking tau to synaptic function, the role of tau in synapse loss remains largely undetermined. Here we test the hypothesis that human mutant P301L tau overexpression in a mouse model (rTg4510) will lead to age‐dependent synaptic loss and dysfunction. Using array tomography and two methods of quantification (automated, threshold‐based counting and a manual stereology‐based technique) we demonstrate that overall synapse density is maintained in the neuropil, implicating synapse loss commensurate with the cortical atrophy known to occur in this model. Multiphoton in vivo imaging reveals close to 30% loss of apical dendritic spines of individual pyramidal neurons, suggesting these cells may be particularly vulnerable to tau‐induced degeneration. Postmortem, we confirm the presence of tau in dendritic spines of rTg4510‐YFP mouse brain by array tomography. These data implicate tau‐induced loss of a subset of synapses that may be accompanied by compensatory increases in other synaptic subtypes, thereby preserving overall synapse density. Biochemical fractionation of synaptosomes from rTg4510 brain demonstrates a significant decrease in expression of several synaptic proteins, suggesting a functional deficit of remaining synapses in the rTg4510 brain. Together, these data show morphological and biochemical synaptic consequences in response to tau overexpression in the rTg4510 mouse model. J. Comp. Neurol., 521:1334–1353, 2013. © 2012 Wiley Periodicals, Inc.