bluuebunny/crossref_metadata_2025 huggingface dataset:
Source attribution of the changes in atmospheric methane for 2006–2008
Authors: Bousquet P. , Ringeval B. , Pison I. , Dlugokencky E. J. , Brunke E.-G. , Carouge C. , Chevallier F. , Fortems-Cheiney A. , Frankenberg C. , Hauglustaine D. A. , Krummel P. B. , Langenfelds R. L. , Ramonet M. , Schmidt M. , Steele L. P. , Szopa S. , Yver C. , Ciais P.
Published: November 2010

Abstract. The recent increase of atmospheric methane is investigated by using two atmospheric inversions to quantify the global distribution of sources and sinks for the 2006–2008 period, and a process-based model of CH4 emissions by natural wetland ecosystems. Global emissions derived from inversions are found to have increased by 19 Tg on average in 2007 (16 to 21 Tg) and by 13 Tg in 2008 (6 to 20 Tg), as compared to the 1999–2006 period. A positive anomaly of tropical emissions is found to be the main contributor to the global emission anomaly of 2007 (~60–75%), with a dominant share attributed to natural wetlands (~66%). Abnormally high wetlands emissions from high latitudes are also detected by both inversions in 2007, contributing 15–30% of the global anomaly. Good agreement is found between the results of the wetland ecosystem model and the inversions for 2007. The inferred distribution of the source anomaly in 2007 is shown to be consistent with the observation of a more pronounced increase in near surface methane atmospheric growth rate at high latitudes, because the dilution of surface fluxes by convection is strong in the tropics and weak at high latitudes. The source anomaly in 2008 is found to be much larger in the wetland ecosystem model than in the inversions, suggesting a too strong sensitivity of bottom-up modeled emissions to precipitation. Changes in OH radicals during 2006–2008 are found to be less than 1% in inversions, with only a small impact on the inferred methane emissions.
Non-invasive monitoring of endocrine status in laboratory primates: methods, guidelines and applications
Authors: Heistermann M.
Published: November 2010

Abstract. During the past three decades, non-invasive methods for assessing physiological, in particular endocrine, status have revolutionized almost all areas of primatology, including behavioural ecology, reproductive biology, stress research, conservation and last but not least management of primates in captivity where the technology plays an integral role in assisting the husbandry, breeding and welfare of many species. Non-invasive endocrine methods make use of the fact that hormones circulating in blood are secreted into saliva or deposited in hair and are eliminated from the body via urinary and faecal excretion. The choice of which matrix to use for hormonal assessment depends on a range of factors, including the type of information required, the measurement techniques involved, species differences in hormone metabolism and route of excretion and the practicality of sample collection. However, although sample collection is usually relatively easy, analysing hormones from these non-invasively collected samples is not as easy as many people think, particularly not when dealing with a new species. In this respect, the importance of a careful validation of each technique is essential in order to generate meaningful and accurate results. This paper aims to provide an overview of the available non-invasive endocrine-based methodologies, their relative merits and their potential areas of application for assessing endocrine status in primates, with special reference to captive environments. In addition, general information is given about the most important aspects and caveats researchers have to be aware of when using these methodologies.
Direct contribution of nitrogen deposition to nitrous oxide emissions in a temperate beech and spruce forest – a 15N tracer study
Authors: Eickenscheidt N. , Brumme R. , Veldkamp E.
Published: November 2010

Abstract. The impact of atmospheric nitrogen (N) deposition on nitrous oxide (N2O) emissions in forest ecosystems is still unclear. The objective of our study was to investigate the direct contribution of N deposition to N2O emissions in temperate forests exposed to chronic high N deposition using a 15N labelling technique. In a Norway spruce stand (Picea abies) and in a beech stand (Fagus sylvatica) in the Solling, Germany, we added a low concentrated 15N-labelled ammoniumnitrate solution to simulate N deposition. Nitrous oxide fluxes and 15N isotope abundances in N2O were measured using the closed chamber method combined with 15N isotope analyses. Emissions of N2O were higher in the beech stand (2.6 ± 0.6 kg N ha−1 yr−1) than in the spruce stand (0.3 ± 0.1 kg N ha−1 yr−1). We observed a direct effect of N input on 15N2O emissions, which lasted less than three weeks and was mainly caused by denitrification. No progressive increase in 15N enrichment of N2O occurred over a one-year experiment, which we explained by immobilisation of deposited N. The annual emission factor for N2O from deposited N was 0.1% for the spruce stand and 0.6% for the beech stand. Standard methods used in the literature applied to the same stands grossly overestimated emission factors with values of up to 25%. Only 6–13% of the total N2O emissions were derived from direct N deposition. Whether the remaining emissions resulted from accumulated anthropogenic N deposition or native N, can not be distinguish with the applied methods. The 15N tracer technique represents a precise tool, which may improve estimates of the current contribution of N deposition on N2O emissions.
Structural and Electrical Characterization of ZnO Films Grown by Spray Pyrolysis and Their Application in Thin‐Film Transistors
Authors: Adamopoulos George , Bashir Aneeqa , Gillin William P. , Georgakopoulos Stamatis , Shkunov Maxim , Baklar Mohamed A. , Stingelin Natalie , Bradley Donal D. C. , Anthopoulos Thomas D.
Published: November 2010

The role of the substrate temperature on the structural, optical, and electronic properties of ZnO thin films deposited by spray pyrolysis using a zinc acetate precursor solution is reported. Analysis of the precursor compound using thermogravimentry and differential scanning calorimetry indicates complete decomposition of the precursor at around 350 °C. Film characterization using Fourier Transform Infrared Spectroscopy (FTIR), photoluminescence spectroscopy (PL), and ultraviolet–visible (UV–Vis) optical transmission spectroscopy suggests the onset of ZnO growth at temperatures as low as 100 °C as well as the transformation to a polycrystalline phase at deposition temperatures >200 °C. Atomic force microscopy (AFM) and X‐ray diffraction (XRD) reveal that as‐deposited films exhibit low surface roughness (rms ≈ 2.9 nm at 500 °C) and a crystal size that is monotonously increasing from 8 to 32 nm for deposition temperatures in the range of 200–500 °C. The latter appears to have a direct impact on the field‐effect electron mobility, which is found to increase with increasing ZnO crystal size. The maximum mobility and current on/off ratio is obtained from thin‐film transistors fabricated using ZnO films deposited at >400 °C yielding values on the order of 25 cm2 V−1s−1 and 106, respectively.
Enantioselective Cyclopropanation Reactions with Planar‐Chiral Pyridinium Ylides: A Substituent Effect and a Remote Steric Effect
Authors: Kanomata Nobuhiro , Sakaguchi Ryo , Sekine Kazuki , Yamashita Satomi , Tanaka Hiroko
Published: November 2010

Novel planar‐chiral pyridinium ylides were designed, and generated in situ from the corresponding pyridinium salts with triethylamine. Ylides with a common parapyridinophane skeleton reacted efficiently with electron‐deficient dicyanoalkenes, or malononitriles, to produce optically active cyclopropane derivatives with high enantioselectivity (up to 99% ee). Remote steric effects were observed on the enantioselectivities, where the R2 groups of the pyridinophane core resulted in higher ee values of the products. Density function theory (DFT) calculations are in good agreement with our experimental results: the energetically favored transition state leads to the major stereoisomer, namely the trans‐cyclopropane products.
Dibutyltin Dimethoxide‐Catalyzed Cyano Transfer to Aldehydes and Imines
Authors: Yanagisawa Akira , Matsumoto Takuya , Kushihara Naoyuki , Yoshida Kazuhiro
Published: November 2010

A novel reaction involving cyano transfer from benzophenone cyanohydrin to aldehydes and imines was realized by using dibutyltin dimethoxide as a catalyst. Various cyanohydrins and α‐amino nitriles were obtained in moderate to high yields by this reaction. Ketimines also showed remarkable reactivity as cyano acceptors under conventional reaction conditions. This catalytic reaction was further applied to a three‐component condensation reaction of aldehydes, aniline, and benzophenone cyanohydrin in the presence of Drierite®.
Superparamagnetic Nanoparticle‐Supported (S)‐Diphenyl‐ prolinol Trimethylsilyl Ether as a Recyclable Catalyst for Asymmetric Michael Addition in Water
Authors: Wang Bang Gen , Ma Bao Chun , Wang Qiong , Wang Wei
Published: November 2010

A new superparamagnetic nanoparticle‐supported (S)‐diphenylprolinol trimethylsilyl ether (Jørgensen–Hayashi catalyst) was synthesized and applied for the asymmetric Michael addition of aldehydes to nitroalkenes in water, which gives products in moderate to good yields (up to 96%), good enantioselectivity (up to 90% ee) and diastereoselectivities (up to 99:1). The immobilized catalyst could be easily separated from the reaction by an external magnet and recycled for four times without significant loss of catalytic efficiency.
The financing of clinical genetics research by disease advocacy organizations: A review of funding disclosures in biomedical journals
Authors: Sharp Richard R. , Landy David C.
Published: November 2010

Anecdotal reports suggest that disease‐advocacy groups (DAOs) participate in multiple aspects of clinical research. No systemic analysis of the extent of DAO involvement in clinical genetics research has been conducted to date. We conducted a systematic review of journal articles published in 2004 and 2005 reporting clinical research on 50 genetic diseases to assess the extent to which DAOs financed the studies reported, assisted in subject recruitment, or participated in other aspects of research. Of 513 articles, 350 (68%) included a statement regarding research support. Of these articles, 114 (33%) acknowledged DAO funding. The proportion of articles reporting financial support from a DAO varied greatly by disease. Articles reporting financial support from a DAO often identified at least one additional source of support (73%). Of the articles examined, 19 (4%) acknowledged DAO assistance with subject recruitment and 11 (2%) included an author affiliated with a DAO. DAOs provide financial support for numerous clinical research studies in genetics, often in partnership with government agencies and for‐profit corporations. DAOs also participate in other aspects of clinical research, including subject recruitment. Future studies should seek to characterize these research partnerships more fully. © 2010 Wiley‐Liss, Inc.
Fingolimod provides long‐term protection in rodent models of cerebral ischemia
Authors: Wei Ying , Yemisci Muge , Kim Hyung‐Hwan , Yung Lai Ming , Shin Hwa Kyoung , Hwang Seo‐Kyoung , Guo Shuzhen , Qin Tao , Alsharif Nafiseh , Brinkmann Volker , Liao James K , Lo Eng H , Waeber Christian
Published: November 2010

Objective:

The sphingosine‐1‐phosphate (S1P) receptor agonist fingolimod (FTY720), that has shown efficacy in advanced multiple sclerosis clinical trials, decreases reperfusion injury in heart, liver, and kidney. We therefore tested the therapeutic effects of fingolimod in several rodent models of focal cerebral ischemia. To assess the translational significance of these findings, we asked whether fingolimod improved long‐term behavioral outcomes, whether delayed treatment was still effective, and whether neuroprotection can be obtained in a second species.

Methods:

We used rodent models of middle cerebral artery occlusion and cell‐culture models of neurotoxicity and inflammation to examine the therapeutic potential and mechanisms of neuroprotection by fingolimod.

Results:

In a transient mouse model, fingolimod reduced infarct size, neurological deficit, edema, and the number of dying cells in the core and periinfarct area. Neuroprotection was accompanied by decreased inflammation, as fingolimod‐treated mice had fewer activated neutrophils, microglia/macrophages, and intercellular adhesion molecule‐1 (ICAM‐1)‐positive blood vessels. Fingolimod‐treated mice showed a smaller infarct and performed better in behavioral tests up to 15 days after ischemia. Reduced infarct was observed in a permanent model even when mice were treated 4 hours after ischemic onset. Fingolimod also decreased infarct size in a rat model of focal ischemia. Fingolimod did not protect primary neurons against glutamate excitotoxicity or hydrogen peroxide, but decreased ICAM‐1 expression in brain endothelial cells stimulated by tumor necrosis factor alpha.

Interpretation:

These findings suggest that anti‐inflammatory mechanisms, and possibly vasculoprotection, rather than direct effects on neurons, underlie the beneficial effects of fingolimod after stroke. S1P receptors are a highly promising target in stroke treatment. ANN NEUROL, 2010
Eating and hypothalamus changes in behavioral‐variant frontotemporal dementia
Authors: Piguet Olivier , Petersén Åsa , Yin Ka Lam Bonnie , Gabery Sanaz , Murphy Karen , Hodges John R. , Halliday Glenda M.
Published: November 2010

Objective

Behavioral‐variant frontotemporal dementia (bvFTD) is a progressive neurodegenerative brain disorder, clinically characterized by changes in cognition, personality, and behavior. Marked disturbances in eating behavior, such as overeating and preference for sweet foods, are also commonly reported. The hypothalamus plays a critical role in feeding regulation, yet the relation between pathology in this region and eating behavior in FTD is unknown. This study aimed to address this issue using 2 complementary approaches.

Methods

First, 18 early stage bvFTD patients and 16 healthy controls underwent high‐resolution structural magnetic resonance imaging and assessment of eating behavior. Hypothalamic volumes were traced manually on coronal images. Second, postmortem analyses of 12 bvFTD cases and 6 matched controls were performed. Fixed hypothalamic tissue sections were stained for a cell marker and for peptides regulating feeding behaviors using immunohistochemistry. Stereological estimates of the hypothalamic volume and the number of neurons and glia were performed.

Results

Significant atrophy of the hypothalamus in bvFTD was present in both analyses. Patients with high feeding disturbance exhibited significant atrophy of the posterior hypothalamus. Neuronal loss, which was observed only in bvFTD cases with Tar DNA protein‐43 deposition, was also predominant posteriorly. In contrast, orexin (hypocretin), neuropeptide Y, cocaine‐ and amphetamine‐regulating transcript, and vasopressin‐containing neurons that regulate appetite were spared in posterior nuclei known to participate in feeding regulation.

Interpretation

Degeneration and consequent dysregulation within the hypothalamus relates to significant feeding disturbance in bvFTD. These findings provide a basis for the development of therapeutic models. Ann Neurol 2011
Palladium(II) complexes of Y,C,Y‐chelated phosphines: synthesis, structure, and catalytic activity in Suzuki–Miyaura reaction
Authors: Řezníček Tomáš , Dostál Libor , Růžička Aleš , Kulhánek Jiří , Bureš Filip , Jambor Roman
Published: November 2010

The phosphines L1PPh2 (1) and L2PPh2 (2) containing different Y,C,Y‐chelating ligands, L1 = 2,6‐(tBuOCH2)2C6H3− and L2 = 2,6‐(Me2NCH2)2C6H3−, were treated with PdCl2 and di‐µ‐chloro‐bis[2‐[(N,N‐dimethylamino)methyl]phenyl‐C,N]‐dipalladium(II) and yielded complexes trans‐{[2,6‐(tBuOCH2)2C6H3]PPh2}2PdCl2 (3), {[2,6‐(Me2NCH2)2C6H3]PPh2} PdCl2 (4), {[2,6‐(tBuOCH2)2C6H3]PPh2}Pd(Cl)[2‐(Me2NCH2)C6H4] (5) and {[2,6‐(Me2NCH2)2C6H3]PPh2}Pd(Cl)[2‐(Me2NCH2)C6H4] (6) as the result of different ability of starting phosphines 1 and 2 to complex PdCl2. Compounds 3–6 were characterized by 1H, 13C, 31P NMR spectroscopy and ESI‐MS. The molecular structures of 3,4 and 6 were also determined by X‐ray diffraction analysis. The catalytic activity of complexes 3–6 was evaluated in the Suzuki‐Miyaura cross‐coupling reaction. Copyright © 2010 John Wiley & Sons, Ltd.
Catalytic dehydrogenative coupling of diorganotindihydrides by lanthanide diamide complexes
Authors: Schittelkopf Kathrin , Fischer Roland C. , Meyer Sarah , Wilfling Petra , Uhlig Frank
Published: November 2010

Despite the fact that sterically demanding 1,2‐dihydrodistannanes are versatile synthons, their synthesis is typically a tedious, low‐yield procedure, which limits synthetic applications. Looking for generally applicable and high‐yield routes, we examined the dehydrogenative coupling of sterically crowded diorganotindihydrides. Herein, we report the application of lanthanide diamide‐based catalysts (CH2)3‐1,3‐[N(Dipp)]2LnBr (Ln = La,Ce,Nd,Dy) to generate polystannanes and distannanes, depending on the size of the aromatic substituents. Reaction of tBu2SnH2 resulted in the quantitative formation of 1,1,2,2‐tetra‐tert‐butyldistannane while conversion of sterically encumbered Mes2SnH2 yielded 1,1,2,2‐tetramesityldistannane. Copyright © 2010 John Wiley & Sons, Ltd.
The Relationship Between Aquaporin‐4 Expression and Blood‐Brain and Spinal Cord Barrier Permeability Following Experimental Autoimmune Encephalomyelitis in the Rat
Authors: Huang Xiang‐Nan , Wang Wei‐Zhi , Fu Jin , Wang Hua‐Bing
Published: November 2010

Aquaporin 4(AQP4) is a water channel protein strongly expressed in the central nervous system in perimicrovessel astrocyte foot processes, the glia limitans, and ependyma. Expression of AQP4 is highest at the blood‐brain barrier and blood‐spinal cord barrier, supporting its critical function in material transport across these structures. Recently, presence of the anti‐aquaporin‐4 antibody in sera has been used as an important diagnostic tool for neuromyelitis optica, suggesting a potential role in central nervous system inflammation. The aim of the present study was to examine AQP4 protein expression in the cerebellum and spinal cord from rats with experimental autoimmune encephalomyelitis. By western blot analysis, AQP4 expression increased during experimental autoimmune encephalomyelitis development, and peaked at onset (lumbar enlargement) or climax (cerebellum) of neurological signs of experimental autoimmune encephalomyelitis. There was also a faster and more pronounced increase in permeability in the cerebellar blood‐brain barrier and the lumbar enlargement blood‐spinal cord barrier consistent with AQP4 expression, which was manifested by increased Evans Blue leakage and reduced tight junction protein expression. In conclusion, aquaporin upregulation may be involved in the development of inflammation in the acute phase of experimental autoimmune encephalomyelitis, and may correlate with damage to central nervous system barrier function. Anat Rec, 2010. © 2010 Wiley‐Liss, Inc.
Nasal Septal and Premaxillary Developmental Integration: Implications for Facial Reduction in Homo
Authors: Holton Nathan E. , Franciscus Robert G. , Marshall Steven D. , Southard Thomas E. , Nieves Mary Ann
Published: November 2010

The influence of the chondrocranium in craniofacial development and its role in the reduction of facial size and projection in the genus Homo is incompletely understood. As one component of the chondrocranium, the nasal septum has been argued to play a significant role in human midfacial growth, particularly with respect to its interaction with the premaxilla during prenatal and early postnatal development. Thus, understanding the precise role of nasal septal growth on the facial skeleton is potentially informative with respect to the evolutionary change in craniofacial form. In this study, we assessed the integrative effects of the nasal septum and premaxilla by experimentally reducing facial length in Sus scrofa via circummaxillary suture fixation. Following from the nasal septal‐traction model, we tested the following hypotheses: (1) facial growth restriction produces no change in nasal septum length; and (2) restriction of facial length produces compensatory premaxillary growth due to continued nasal septal growth. With respect to hypothesis 1, we found no significant differences in septum length (using the vomer as a proxy) in our experimental (n = 10), control (n = 9) and surgical sham (n = 9) trial groups. With respect to hypothesis 2, the experimental group exhibited a significant increase in premaxilla length. Our hypotheses were further supported by multivariate geometric morphometric analysis and support an integrative relationship between the nasal septum and premaxilla. Thus, continued assessment of the growth and integration of the nasal septum and premaxilla is potentially informative regarding the complex developmental mechanisms that underlie facial reduction in genus Homo evolution. Anat Rec, 2010. © 2010 Wiley‐Liss, Inc.
Regional and Zonal Histo‐Morphological Characteristics of the Lapine Menisci
Authors: Killian Megan L. , Lepinski Nicole M. , Haut Roger C. , Haut Donahue Tammy L.
Published: November 2010

The menisci have crucial weight‐bearing roles in the knee. Regional variations in structure and cellularity of the meniscus have only been minimally investigated. Therefore, the goal of this study was to illustrate the regional cell density, tissue area, and structure of healthy lapine menisci. Skeletally mature Flemish Giant rabbits were used for this study. Upon sacrifice, menisci were removed, fixed in formalin, and cryosectioned. Histological analysis was performed for the detection of sulfated glycosaminoglycans (GAG), collagen Types I and II, cellular density, and tissue area. ANOVA and paired t tests were used for testing of statistical significance. Glycosaminoglycan coverage of the medial meniscus significantly varied between regions, with the anterior region demonstrating significantly more GAG coverage than the posterior region. Inter‐ and intra‐meniscal comparisons revealed variations between zones, with trends that outer zones of the medial menisci had less GAG coverage. Collagen Types I and II had marked characteristics and varying degrees of coverage across regions. Tissue area varied between regions for both medial and lateral menisci. Cellular density was dependent on region in the lateral meniscus. This is the first study to illustrate regional and zonal variation in glycosaminoglycan coverage, size, and cellular density for healthy lapine meniscal tissue. This data provides baseline information for future investigations in meniscal injury models in rabbits. Anat Rec, 2010. © 2010 Wiley‐Liss, Inc.
AMMA information system: an efficient cross‐disciplinary tool and a legacy for forthcoming projects
Authors: Fleury Laurence , Boichard Jean‐Luc , Brissebrat Guillaume , Cloché Sophie , Eymard Laurence , Mastrorillo Laurence , Moulaye Oumarou , Ramage Karim , Asencio Nicole , Coppeaux Jean , Devic Marie‐Pierre , Favot Florence , Ginoux Karine , Lafore Jean‐Philippe , Polcher Jan , Redelsperger Jean‐Luc , Roussot Odile , Tytéca Michel
Published: November 2010

In the framework of the African Monsoon Multidisciplinary Analyses (AMMA) programme, several tools have been developed in order to facilitate and speed up data and information exchange between researchers from different disciplines. The AMMA information system includes a multidisciplinary user‐friendly distributed data management and distribution system, a reports and quick looks archive associated with a display website and scientific papers exchange systems. All the applications have been developed by several French institutions and fully duplicated in Niamey, Niger. Copyright © 2010 Royal Meteorological Society
Metabolic engineering of Escherichia coli for the production of 1,2‐propanediol from glycerol
Authors: Clomburg James M. , Gonzalez Ramon
Published: November 2010

Due to its availability, low‐price, and high degree of reduction, glycerol has become an attractive carbon source for the production of fuels and reduced chemicals. Using the platform we have established from the identification of key pathways mediating fermentative metabolism of glycerol, this work reports the engineering of Escherichia coli for the conversion of glycerol into 1,2‐propanediol (1,2‐PDO). A functional 1,2‐PDO pathway was engineered through a combination of overexpression of genes involved in its synthesis from the key intermediate dihydroxyacetone phosphate (DHAP) and the manipulation of the fermentative glycerol utilization pathway. The former included the overexpression of methylglyoxal synthase (mgsA), glycerol dehydrogenase (gldA), and aldehyde oxidoreductase (yqhD). Manipulation of the glycerol utilization pathway through the replacement of the native E. coli PEP‐dependent dihydroxyacetone kinase (DHAK) with an ATP‐dependent DHAK from C. freundii increased the availability of DHAP allowing for higher 1,2‐PDO production. Analysis of the major fermentative pathways indentified ethanol as a required co‐product while increases in 1,2‐PDO titer and yield were achieved through the disruption of the pathways for acetate and lactate production. Combination of these key metabolic manipulations resulted in an engineered E. coli strain capable of producing 5.6 g/L 1,2‐PDO, at a yield of 21.3% (w/w). This strain also performed well when crude glycerol, a by‐product of biodiesel production, was used as the substrate. The titer and yield achieved in this study were favorable to those obtained with the use of E. coli for the production of 1,2‐PDO from common sugars. Biotechnol. Bioeng. 2011; 108:867–879. © 2010 Wiley Periodicals, Inc.
Micropatterns of cell adhesive proteins with poly(ethylene oxide)‐block‐Poly(4‐vinylpyridine) diblock copolymer
Authors: Racine J. , Cheradame H. , Chu Y.S. , Thiery J.P. , Rodriguez I.
Published: November 2010

Control of cell shape and behavior through the micropattern technique by spatial immobilization of adhesive proteins on a surface has provided novel insights in several aspects of cell biology, such as tissue morphogenesis, cell growth and cell differentiation, and apoptosis. In this work, we present the use of poly(ethylene oxide‐block‐poly(4‐vinylpyridine) (PEO‐b‐P4VP) as a non‐adhesive background to construct micropatterns of cell adhesive proteins. In the method presented, PEO‐b‐P4VP is used for its antifouling properties and at the same time, as a photosensitive material to define the micropatterns. The irradiation of PEO‐b‐P4VP with a short wavelength UV light through photolithographic mask, causes the polymer to crosslink and immobilize in the areas exposed. In the areas non‐exposed the polymer can be removed. These areas can be subsequent back filled with the adhesive protein of interest to produce the final micropatterned cell chips. Biotechnol. Bioeng. 2011; 108:983–987. © 2010 Wiley Periodicals, Inc.
In situ metabolic flux analysis to quantify the liver metabolic response to experimental burn injury
Authors: Izamis Maria‐Louisa , Sharma Nripen S. , Uygun Basak , Bieganski Robert , Saeidi Nima , Nahmias Yaakov , Uygun Korkut , Yarmush Martin L. , Berthiaume Francois
Published: November 2010

Trauma such as burns induces a hypermetabolic response associated with altered central carbon and nitrogen metabolism. The liver plays a key role in these metabolic changes; however, studies to date have evaluated the metabolic state of liver using ex vivo perfusions or isotope labeling techniques targeted to specific pathways. Herein, we developed a unique mass balance approach to characterize the metabolic state of the liver in situ, and used it to quantify the metabolic changes to experimental burn injury in rats. Rats received a sham (control uninjured), 20% or 40% total body surface area (TBSA) scald burn, and were allowed to develop a hypermetabolic response. One day prior to evaluation, all animals were fasted to deplete glycogen stores. Four days post‐burn, blood flow rates in major vessels of the liver were measured, and blood samples harvested. We combined measurements of metabolite concentrations and flow rates in the major vessels entering and leaving the liver with a steady‐state mass balance model to generate a quantitative picture of the metabolic state of liver. The main findings were: (1) Sham‐burned animals exhibited a gluconeogenic pattern, consistent with the fasted state; (2) the 20% TBSA burn inhibited gluconeogenesis and exhibited glycolytic‐like features with very few other significant changes; (3) the 40% TBSA burn, by contrast, further enhanced gluconeogenesis and also increased amino acid extraction, urea cycle reactions, and several reactions involved in oxidative phosphorylation. These results suggest that increasing the severity of injury does not lead to a simple dose‐dependent metabolic response, but rather leads to qualitatively different responses. Biotechnol. Bioeng. 2011; 108:839–852. © 2010 Wiley Periodicals, Inc.
Topology optimized microbioreactors
Authors: Schäpper Daniel , Lencastre Fernandes Rita , Lantz Anna Eliasson , Okkels Fridolin , Bruus Henrik , Gernaey Krist V.
Published: November 2010

This article presents the fusion of two hitherto unrelated fields—microbioreactors and topology optimization. The basis for this study is a rectangular microbioreactor with homogeneously distributed immobilized brewers yeast cells (Saccharomyces cerevisiae) that produce a recombinant protein. Topology optimization is then used to change the spatial distribution of cells in the reactor in order to optimize for maximal product flow out of the reactor. This distribution accounts for potentially negative effects of, for example, by‐product inhibition. We show that the theoretical improvement in productivity is at least fivefold compared with the homogeneous reactor. The improvements obtained by applying topology optimization are largest where either nutrition is scarce or inhibition effects are pronounced. Biotechnol. Bioeng. 2011; 108:786–796. © 2010 Wiley Periodicals, Inc.
Production of new‐to‐nature sophorolipids by cultivating the yeast Candida bombicola on unconventional hydrophobic substrates
Authors: Van Bogaert Inge , Fleurackers Steve , Van Kerrebroeck Simon , Develter Dirk , Soetaert Wim
Published: November 2010

The naturally occurring sophorolipids synthesized by Candida bombicola possess—despite their overall heterogeneity—little variation in the length of the lipid tail. The range is limited to C16–C18 fatty acids and is governed by the specificity of a cytochrome P450 monooxygenase. However, incorporation of fatty acids differing from the conventional C16–C18 range could broaden up the application potential of sophorolipids. The incorporation of medium‐chain fatty acids should render the molecules more hydrophilic and consequently improve their water solubility. Two strategies to circumvent this C16–C18 preference are described in this paper. The first one skips the controlling action of the cytochrome P450 enzyme by supplying the yeast with already hydroxylated substrates, while the other method is based on the deception of the enzyme by presenting it substrates structurally resembling stearic acid. This later strategy can be applied to create very specific tailor‐made sophorolipids when combined with post‐fermentive modification. Biotechnol. Bioeng. 2011; 108:734–741. © 2010 Wiley Periodicals, Inc.
Construction of a novel glucose‐sensing molecule based on a substrate‐binding protein for intracellular sensing
Authors: Sakaguchi‐Mikami Akane , Taniguchi Akiyoshi , Sode Koji , Yamazaki Tomohiko
Published: November 2010

A novel transcriptional regulator responding to glucose was designed with a substrate‐binding protein (SBP) as a probe towards intracellular sensing system for glucose in mammalian cells. A chimeric protein of an SBP for glucose (GBP) and a LacI‐type regulator, LacI (SLCPGL), was designed, constructed and characterized using Escherichia coli recombinant protein. We report that SLCPGL has a glucose‐specific binding ability and an operator‐sequence specific DNA‐binding ability. The loss of its DNA‐binding ability in the presence of glucose suggests a role as a transcriptional regulator in vitro. The glucose‐dependent gene regulation function of SLCPGL in cells was investigated using mammalian cells co‐transfected with SLCPGL and Lac operator‐fused luciferase gene constructs. The luciferase activity of the transfected cells increased with the glucose concentration in the medium, showing that the expression of the luciferase gene is regulated by SLCPGL, which can dissociate from DNA in a glucose concentration‐dependent manner. Therefore, we demonstrated that SLCPGL functions as a glucose‐sensitive transcriptional regulator in mammalian cells. These results reveal the possibility of developing an SBP‐based regulator as a probe of intracellular sensing and gene regulation system for mammalian cells in response to a desired ligands depending on the SBP ligand specificity. Biotechnol. Bioeng. 2011; 108:725–733. © 2010 Wiley Periodicals, Inc.
Evaluation of oxygen transfer rates in stirred‐tank bioreactors for clinical manufacturing
Authors: Bellucci Joseph J. , Hamaker Kent H.
Published: November 2010

Several methods are available for determining the volumetric oxygen transfer coefficient in bioreactors, though their application in industrial bioprocess has been limited. To be practically useful, mass transfer measurements made in nonfermenting systems must be consistent with observed microbial respiration rates. This report details a procedure for quantifying the relationship between agitation frequency and oxygen transfer rate that was applied in stirred‐tank bioreactors used for clinical biologics manufacturing. The intrinsic delay in dissolved oxygen (DO) measurement was evaluated by shifting the bioreactor pressure and fitting a first‐order mathematical model to the DO response. The dynamic method was coupled with the DO lag results to determine the oxygen transfer rate in Water for Injection (WFI) and a complete culture medium. A range of agitation frequencies was investigated at a fixed air sparge flow rate, replicating operating conditions used in Pichia pastoris fermentation. Oxygen transfer rates determined by this method were in excellent agreement with off‐gas calculations from cultivation of the organism (P = 0.1). Fermentation of Escherichia coli at different operating parameters also produced respiration rates that agreed with the corresponding dynamic method results in WFI (P = 0.02). The consistency of the dynamic method results with the off‐gas data suggests that compensation for the delay in DO measurement can be combined with dynamic gassing to provide a practical, viable model of bioreactor oxygen transfer under conditions of microbial fermentation. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
Automated computational framework for the analysis of electrostatic similarities of proteins
Authors: Kieslich Chris A. , Morikis Dimitrios , Yang Jianfeng , Gunopulos Dimitrios
Published: November 2010

Charge plays an important role in protein–protein interactions. In the case of excessively charged proteins, their electrostatic potentials contribute to the processes of recognition and binding with other proteins or ligands. We present an automated computational framework for determining the contribution of each charged amino acid to the electrostatic properties of proteins, at atomic resolution level. This framework involves computational alanine scans, calculation of Poisson–Boltzmann electrostatic potentials, calculation of electrostatic similarity distances (ESDs), hierarchical clustering analysis of ESDs, calculation of solvation free energies of association, and visualization of the spatial distributions of electrostatic potentials. The framework is useful to classify families of mutants with similar electrostatic properties and to compare them with the parent proteins in the complex. The alanine scan mutants introduce perturbations in the local electrostatic properties of the proteins and aim in delineating the contribution of each mutated amino acid in the spatial distribution of electrostatic potential, and in biological function when electrostatics is a dominant contributing factor in protein–protein interactions. The framework can be used to design new proteins with tailored electrostatic properties, such as immune system regulators, inhibitors, and vaccines, and in guiding experimental studies. We present an example for the interaction of the immune system protein C3d (the d‐fragment of complement protein C3) with its receptor CR2, and we discuss our data in view of a binding site controversy. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
A comparative study of the regioselectivity of the β‐galactosidases from Kluyveromyces lactis and Bacillus circulans in the enzymatic synthesis of N‐Acetyl‐lactosamine in aqueous media
Authors: Bridiau Nicolas , Maugard Thierry
Published: November 2010

The enzymatic synthesis of N‐acetyl‐lactosamine (LacNAc) was studied in aqueous media with high substrate concentrations using the transgalactosylation of N‐acetyl‐D‐glucosamine (GlcNAc), starting from lactose as a galactosyl donor. The efficiency and regioselectivity of the β‐galactosidases from Kluyveromyces lactis (KlβGal) and Bacillus circulans (BcβGal) were compared. The reaction was optimized by varying the experimental conditions (pH, catalytic activity concentration, and mass concentration ratio of the substrates), which enhanced the synthesis yields with both enzymes and especially with BcβGal. BcβGal catalyzed the formation of the maximal LacNAc concentration obtained (101 mM or 39 g L−1, corresponding to a yield of 11% on the basis of GlcNAc conversion), after 5 h at pH 6.5 and for a substrate mass concentration ratio of 1. This enzyme also gave an optimal synthesis yield of about 17.5%. No change in regioselectivity was observed when using KlβGal, whereas the regioselectivity of BcβGal proved to be subject to variations, the 1–4 and 1–6 linkages being favored under kinetic and thermodynamic control conditions, respectively. Finally, it was demonstrated that the N‐acetyl‐allolactosamine synthesized during the GlcNAc transgalactosylation catalyzed by BcβGal was a thermodynamic product and did not result from a chemical and/or enzymatic isomerization of LacNAc. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
Phenolics removal from transgenic Lemna minor extracts expressing mAb and impact on mAb production cost
Authors: Barros Georgia O. F. , Woodard Susan L. , Nikolov Zivko L.
Published: November 2010

Transgenic Lemna minor has been used successfully to produce several biotherapeutic proteins. For plant‐produced mAbs specifically, the cost of protein A capture step is critical as the economic benefits of plant production systems could be erased if the downstream processing ends up being expensive. To avoid potential modification of mAb or fouling of expensive protein A resins, a rapid and efficient removal of phenolics from plant extracts is desirable. We identified major phenolics in Lemna extracts and evaluated their removal by adsorption to PVPP, XAD‐4, IRA‐402, and Q‐Sepharose. Forms of apigenin, ferulic acid, and vitexin comprised ∼75% of the total phenolics. Screening of the resins with pure ferulic acid and vitexin indicated that PVPP would not be efficient for phenolics removal. Analysis of the breakthrough fractions of phenolics adsorption to XAD‐4, IRA‐402, and Q‐Sepharose showed differences in adsorption with pH and in the type of phenolics adsorbed. Superior dynamic binding capacities (DBC) were observed at pH 4.5 than at 7.5. To evaluate the cost impact of a phenolics removal step before protein A chromatography, a mAb purification process was simulated using SuperPro Designer 7.0. The economic analysis indicated that addition of a phenolics adsorption step would increase mAb production cost only 20% by using IRA‐402 compared to 35% for XAD‐4 resin. The cost of the adsorption step is offset by increasing the lifespan of protein A resin and a reduction of overall mAb production cost could be achieved by using a phenolics removal step. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
Synthesis and Nootropic Activity of Some 2,3‐Dihydro‐1H‐isoindol‐1‐one Derivatives Structurally Related with Piracetam
Authors: Reyes Adelfo , Huerta Leticia , Alfaro Marisol , Navarrete Andrés
Published: November 2010

Three 2,3‐dihydro‐1H‐isoindol‐1‐ones structurally related with piracetam (=2‐oxopyrrolidine‐1‐acetamide) have been synthesized and tested for their nootropic effects in the passive avoidance test in mice. Compounds (RS)‐2, (R,R)‐3, and (R,S)‐3 were obtained in good yields in only two steps starting from methyl dl‐phthaloylalanine. Compound (RS)‐2 exhibited nootropic activity at lower doses than piracetam, used as reference drug, but it showed lower efficacy. Whereas diastereoisomers (R,R)‐3 and (R,S)‐3 were as potent as piracetam to revert amnesia induced by scopolamine, (R,S)‐3 showed lower efficacy than (R,R)‐3. Only (R,R)‐3 showed myorelaxant effect at doses of 10 and 30 mg/kg; other compounds did not exhibit any anticonvulsant, sedative, myorelaxant, or impaired motor‐coordination effect in mice. These synthesized 2,3‐dihydro‐1H‐isoindol‐1‐one derivatives constitute a new kind of nootropic compounds.
Secondary Metabolites of Plants from the Genus Saussurea: Chemistry and Biological Activity
Authors: Wang Yu‐Fang , Ni Zhi‐Yu , Dong Mei , Cong Bin , Shi Qing‐Wen , Gu Yu‐Cheng , Kiyota Hiromasa
Published: November 2010

The Asteraceae family comprises ca. 1000 genera, mainly distributed in Asia and Europe. Saussurea DC., as the largest subgenus of this family, comprises ca. 400 species worldwide, of which ca. 300 species occur in China. Most plants in China grow wild in the alpine zone of the Qingzang Plateau and adjacent regions at elevations of 4000 m. Plants of the genus Saussurea (Asteraceae) are used in both traditional Chinese folk medicine and Tibet folklore medicine, since they are efficacious in relieving internal heat or fever, harmonizing menstruation, invigorating blood circulation, stopping bleeding, alleviating pain, increasing energy, and curing rheumatic arthritis. A large number of biologically active compounds have been isolated from this genus. This review shows the chemotaxonomy of these compounds (215 compounds) such as sesquiterpenoids (101 compounds), flavonoids (19 compounds), phytosterols (15 compounds), triterpenoids (25 compounds), lignans (32 compounds), phenolics (23 compounds), and chlorophylls (11 compounds). Biological activities (anti‐inflammatory, anticancer, antitumor, hepatoprotective, anti‐ulcer, cholagogic, immunosuppressive, spasmolytic, antimicrobial, antiparasitic, antifeedant, CNS depressant, antioxidant, etc.) of these compounds, including structure–activity relationships, are also discussed.
Antimicrobial Activity of Fatty Acids from Fruits of Peucedanum cervaria and P. alsaticum
Authors: Skalicka‐Woźniak Krystyna , Los Renata , Głowniak Kazimierz , Malm Anna
Published: November 2010

Plants of the genus Peucedanum have been used in traditional medicine for a long time to treat different diseases including infectious diseases. The hexane fruits extracts of Peucedanum cervaria and P. alsaticum were examined for antimicrobial activity and analyzed for their fatty acid content. Fatty acid composition of oils were analyzed by GC/FID in methyl ester form. Minimal inhibitory concentrations (MICs) of fatty acid fractions against twelve reference bacterial and yeast strains were performed by the twofold serial microdilution broth method. Fourteen fatty acids were identified. Oleic and linoleic acids were found to be dominant. The extracts from both plants examined exhibited inhibitory effects against Gram‐positive strains tested with different MIC values (0.25–2 mg/ml); however, extract from P. alsaticum possessed stronger antibacterial properties and a broader spectrum. The growth of Gram‐negative bacteria and Candida spp. strains was not inhibited even at the highest extract concentration used (MIC>4 mg/ml). Standard fatty acids exhibited inhibitory effects towards all bacterial and yeast strains used in this study; however, the majority of bacteria were more sensitive to linoleic than to oleic acid. These results revealed, for the first time, that hexane extracts obtained from fruits of P. alsaticum and P. cervaria possess moderate in vitro antibacterial activity against Gram‐positive bacteria including staphylococci. Linoleic and oleic acids appear to be the compounds responsible for this effect, and a synergistic antimicrobial effect between these two fatty acids was indicated.
Chemical Composition and Antimicrobial Activity of Volatiles from Degenia velebitica, a European Stenoendemic Plant of the Brassicaceae Family
Authors: Mastelić Josip , Blažević Ivica , Kosalec Ivan
Published: November 2010

Free and glucosidic bound leaf volatiles of Degenia velebitica were isolated and fractionated simultaneously into H2O‐soluble, H2O‐insoluble, and highly volatile compounds by hydrodistillation–adsorption (HDA) and analyzed by GC/MS. Among the 24 constituents identified, the main compounds obtained by the HDA method were S‐ and/or N‐atom containing compounds, i.e., 6‐(methylsulfanyl)hexanenitrile (10; 26.78%), dimethyl trisulfide (6; 26.35%), 3,4,5‐trimethylpyrazole (17; 13.33%), hex‐5‐enenitrile (2; 10.11%), dimethyl tetrasulfide (8; 4.93%), and pent‐4‐enyl isothiocyanate (7; 4.45%). In addition, O‐glycosidically bound volatiles and free volatiles were isolated by solvent extraction. Sixteen volatile O‐aglycones and twelve free volatile components were identified. The main O‐aglycones were eugenol (19; 24.15%), 2‐methoxy‐4‐vinylphenol (11; 11.50%), and benzyl alcohol (20; 9.49%), and the main free volatiles were (9Z,12Z)‐octa‐9,12‐dienic acid (38.35%), hexadecanoic acid (22.64%), and phytol (5.80%). The H2O‐soluble volatile fraction obtained by HDA, containing mostly glucosinolate degradation products and 3,4,5‐trimethylpyrazole (17), was evaluated for antimicrobial activity by determining inhibition zones with the diffusion method as well as minimal inhibitory concentrations (MIC) and minimal microbicidal concentrations (MMC) with the micro‐dilution method. The fraction expressed activity against the tested Gram‐positive and Gram‐negative bacteria as well as against yeast, with MIC values equal to or lower than 16.7 μg/ml.
Induced Production of Halogenated Diphenyl Ethers from the Marine‐Derived Fungus Penicillium chrysogenum
Authors: Yang Guohua , Yun Keumja , Nenkep Viviane N. , Choi Hong Dae , Kang Jung Sook , Son Byeng Wha
Published: November 2010

Manipulation of the fermentation of the marine‐derived fungus Penicillium chrysogenum by addition of CaBr2 resulted in induced production of bromodiphenyl ether analogs. Two new free‐radical‐scavenging polybrominated diphenyl ethers, 1 and 2, and three known diphenyl ethers, 3,3′‐dihydroxy‐5,5′‐dimethyldiphenyl ether (3), and an inseparable mixture of violacerol‐I (4) and violacerol‐II (5) were isolated. The structures of the two new polybromodiphenyl ethers 1 and 2 were assigned by combined spectroscopic‐data analysis, including deuterium‐induced isotope effect. Compounds 1–3, and a mixture of 4 and 5 exhibited radical‐scavenging activities against 1,1‐diphenyl‐2‐picrylhydrazyl with IC50 values of 18, 15, 42, and 6 μM, respectively. With the exception of 3, the compounds were, therefore, more active than the positive control, ascorbic acid (IC50 20 μM).