bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature dependence of amino acid side chain IR absorptions in the amide I' region
Authors: Anderson Benjamin A. , Literati Alex , Ball Borden , Kubelka Jan 
Published: October 2013

ABSTRACTAmide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side‐chains that overlap the amide I' may significantly complicate the structural analyses. While the side‐chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side‐chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D2O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side‐chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side‐chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN3H5+ bending signal, although a linear fit can account for this change to within ~1/3 cm‐1. The applicability of the determined spectral parameters for estimations of temperature‐dependent side‐chain absorptions in peptides and proteins are discussed. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 536–548, 2014.
Isothermal amplification of DNA using quadruplex primers with fluorescent pteridine base analogue 3‐methyl isoxanthopterin
Authors: Gogichaishvili Shota , Johnson John , Gvarjaladze David , Lomidze Levan , Kankia Besik 
Published: October 2013

ABSTRACTWe previously developed a method, known as quadruplex priming amplification (QPA), which greatly simplifies DNA amplification and quantification assays. QPA employs specific primers based on GGGTGGGTGGGTGGG (G3T) sequence, which upon polymerase elongation spontaneously dissociates from the target and folds into a stable quadruplex. Fluorescent nucleotide analogs, when incorporated into these primers, emit light upon quadruplex formation and permit simple, specific, and sensitive quantification without the attachment of probe molecules. Here, we studied optical [fluorescence and circular dichroism (CD)] and thermodynamic properties of the G3T sequence and variants incorporating 3‐methylisoxanthopterin (3MI), a highly fluorescent nucleotide analog suitable for QPA. CD studies demonstrate that the incorporation of 3MI does not change the overall tertiary structure of G3T; however, thermal unfolding experiments revealed that it significantly destabilizes the quadruplex. Enzymatic studies revealed that Taq and Bst are practically unable to incorporate any nucleotides opposite to template 3MI. Based on this knowledge, we designed QPA assays with truncated targets that demonstrate efficient amplification around 55°C. Overall, these studies suggest that 3MI‐based QPA is a useful assay for DNA amplification and detection. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 583–590, 2014.
Cis‐suppression to arrest protein aggregation in mammalian cells
Authors: Gregoire Simpson , Zhang Shaojie , Costanzo Joseph , Wilson Kelly , Fernandez Erik J. , Kwon Inchan 
Published: October 2013

ABSTRACTProtein misfolding and aggregation are implicated in numerous human diseases and significantly lower production yield of proteins expressed in mammalian cells. Despite the importance of understanding and suppressing protein aggregation in mammalian cells, a protein design and selection strategy to modulate protein misfolding/aggregation in mammalian cells has not yet been reported. In this work, we address the particular challenge presented by mutation‐induced protein aggregation in mammalian cells. We hypothesize that an additional mutation(s) can be introduced in an aggregation‐prone protein variant, spatially near the original mutation, to suppress misfolding and aggregation (cis‐suppression). As a model protein, we chose human copper, zinc superoxide dismutase mutant (SOD1A4V) containing an alanine to valine mutation at residue 4, associated with the familial form of amyotrophic lateral sclerosis. We used the program RosettaDesign to identify Phe20 in SOD1A4V as a key residue responsible for SOD1A4V conformational destabilization. This information was used to rationally develop a pool of candidate mutations at the Phe20 site. After two rounds of mammalian‐cell based screening of the variants, three novel SOD1A4V variants with a significantly reduced aggregation propensity inside cells were selected. The enhanced stability and reduced aggregation propensity of the three novel SOD1A4V variants were verified using cell fractionation and in vitro stability assays. Biotechnol. Bioeng. 2014;111: 462–474. © 2013 Wiley Periodicals, Inc.
Drug susceptibility of matrix‐encapsulated Candida albicans nano‐biofilms
Authors: Srinivasan Anand , Gupta Celia Macias , Agrawal C. Mauli , Leung Kai P. , Lopez‐Ribot Jose L. , Ramasubramanian Anand K. 
Published: October 2013

ABSTRACTThe rise in the use of biomedical devices and implants has seen a concomitant surge in the advent of device‐related nosocomial (hospital‐acquired) infections of bacterial and fungal origins. The most common nosocomial fungal infection is candidiasis caused mainly by Candida albicans biofilms. Candidiasis is associated with an unacceptably high mortality rate, and there is an urgent need for the discovery of new antifungal drugs that prevent or control biofilm formation. To this end, we recently developed an ultra‐high‐throughput microarray platform consisting of nano‐scale biofilms of C. albicans encapsulated in collagen or alginate hydrogel matrices for antifungal drug screening. Here, we report that the choice of matrix influences the apparent susceptibility of C. albicans to the common antifungal drugs, amphotericin B, and caspofungin. While amphotericin B is equally effective against biofilms grown in collagen and alginate matrices, caspofungin is effective only against biofilms grown only in alginate, but not in collagen. We demonstrate differences in the distribution of the drugs in the two matrices may contribute to the susceptibility of C. albicans nano‐biofilms. In a larger context, our results highlight the importance of the choice of matrix as a parameter in 3D cell encapsulation, and suggest a screening strategy to predict drug performance in vivo. Biotechnol. Bioeng. 2014;111: 418–424. © 2013 Wiley Periodicals, Inc.
Combinatorial engineering of mevalonate pathway for improved amorpha‐4,11‐diene production in budding yeast
Authors: Yuan Jifeng , Ching Chi Bun 
Published: October 2013

ABSTRACTCombinatorial genome integration of mevalonate pathway genes was performed with the aim of optimizing the metabolic flux for improved production of terpenoids in budding yeast. In the present study, we developed a novel δ‐integration platform to achieve multiple genome integrations through modulating the concentration of antibiotics. By exploiting carotenoid biosynthesis as screening module, we successfully created a library of yeast colonies appeared with various intensities of orange color. As proof‐of‐concept that carotenoid overproducers could serve to boost the titer of other terpenoids, we further tested engineered strains for the production of amorpha‐4,11‐diene, an important precursor for antimalarial drug. However, we experienced some limitations of the carotenoid‐based screening approach as it was only effective in detecting a small range of pathway activity improvement and further increasing mevalonate pathway activity led to a decreased orange color. By far, we were only able to obtain one mutant strain yielded more than 13‐fold amorpha‐4,11‐diene over parental strains, which was approximately 64 mg/L of caryophyllene equivalents. Further qPCR studies confirmed that erg10, erg13, thmg1 and erg12 involved in mevalonate pathway were overexpressed in this mutant strain. We envision the current δ‐integration platform would form the basis of a generalized technique for multiple gene integrations in yeast—a method that would be of significant interest to the metabolic engineering community. Biotechnol. Bioeng. 2014;111: 608–617. © 2013 Wiley Periodicals, Inc.
Simultaneous method for analyzing dimerization and signaling of G‐protein‐coupled receptor in yeast by dual‐color reporter system
Authors: Nakamura Yasuyuki , Takemoto Norika , Ishii Jun , Kondo Akihiko 
Published: October 2013

ABSTRACTUnderstanding the role of G‐protein‐coupled receptor (GPCR) dimerization in cellular function has now become a major research focus. The potentially large functional and physiological diversity of dimerization among GPCRs is expected to provide opportunities for novel drug discovery. However, there is currently a lack of cell‐based assays capable of specific profiling for the functional consequences of dimerization linked to ligand‐mediated signaling. Here, we present an advanced method to simultaneously analyze the dimerization and ligand response of GPCRs using two yeast‐based systems for split‐ubiquitin two‐hybrid assay and G‐protein signaling assay. To permit simultaneous detection, we established a two‐color (dual‐color) fluorescence reporter gene assay using enhanced green fluorescent protein (EGFP) and a far‐red derivative of the tetrameric fluorescent protein DsRed‐Express2 (E2‐Crimson). In the present study, we tested our method first by analyzing dimerization and ligand‐mediated signaling by the yeast endogenous pheromone receptor (Ste2p). Second, we showed that the system facilitated mutational analysis of domains involved in dimerization and signaling by Ste2p. Third, we successfully demonstrated that the system could simultaneously monitor homo‐ and hetero‐dimerization and somatostatin‐induced signaling in the test case of the human SSTR5 somatostatin receptor. Our strategy is expected to provide a useful tool for the elucidation of molecular biological functions of GPCR dimers and for the screening of GPCR dimer‐specific agonistic ligands. Biotechnol. Bioeng. 2014;111: 586–596. © 2013 Wiley Periodicals, Inc.
Hydrocarbon production in high density Botryococcus braunii race B continuous culture
Authors: Khatri Waqas , Hendrix Robert , Niehaus Tom , Chappell Joe , Curtis Wayne R. 
Published: October 2013

ABSTRACTContinuous cultures of Botryococcus braunii race B were maintained at photosynthetic cell densities as high as 20 g dry weight per liter for up to 3 months. Growth associated triterpene hydrocarbon accumulation was nearly constant at 22.5% of dry weight for a range of growth rates maintained by daily replacement of 5–15% of the respective cultures. The ability to achieve high cell concentrations and oil levels of roughly 5 g triterpene oil/L resulted from a combination of high light (∼ 1/4 full sun for 15 h/day) and replenishing stoichiometrically balanced growth medium. Due to light‐limited growth conditions, cell concentration dropped nearly linearly with increased dilution rate. This reduction in cell number resulted in increased productivity per cell at higher dilution rates and was accompanied by a dramatic increase in algae colony size from 0.09 to 0.343 mm at high dilution rate. This change in colony size resulted in an equally dramatic change in optical density (OD) per gram dry weight, which precluded use of simple correlations of OD and cell concentration. A trickle‐film photobioreactor was also demonstrated as a scalable approach to achieving these ultra‐high cell concentrations. Additional media analysis revealed a steady increase in photobioreactor conductivity suggesting an accumulation of ions may be the reason for rapid culture crash and washout observed at all dilution rates after several months of continuous operation. The volumetric productivity of 22.5 mg oil/L/photo‐h reported here is more than an order of magnitude higher than previous reports for B. braunii race B, reflecting the high cell densities used in this work and substantiating a higher metabolic rate for B. braunii race B than previously surmised from its relatively long doubling times. Biotechnol. Bioeng. 2014;111: 493–503. © 2013 Wiley Periodicals, Inc.
Oxygen allows Shewanella oneidensis MR‐1 to overcome mediator washout in a continuously fed bioelectrochemical system
Authors: TerAvest Michaela A. , Rosenbaum Miriam A. , Kotloski Nicholas J. , Gralnick Jeffrey A. , Angenent Largus T. 
Published: October 2013

ABSTRACTMany bioelectrochemical systems (BESs) harness the ability of electrode‐active microbes to catalyze reactions between electrodes and chemicals, often to perform useful functions such as wastewater treatment, fuel production, and biosensing. A microbial fuel cell (MFC) is one type of BES, which generates electric power through microbial respiration with an anode as the electron acceptor, and typically with oxygen reduction at the cathode to provide the terminal electron acceptor. Oxygen intrusion into MFCs is typically viewed as detrimental because it competes with anodes for electrons and lowers the coulombic efficiency. However, recent evidence suggests that it does not necessarily lead to lower performances—particularly for the model organism Shewanella oneidensis MR‐1. Because flavin‐mediated electron transfer is important for Shewanella species, which can produce this electron shuttle endogenuously, we investigated the role of flavins in the performance of pure‐culture BESs with S. oneidensis MR‐1 with and without oxygen. We found that oxygen increases current production more than twofold under continuously fed conditions, but only modestly increases current production under batch‐fed conditions. We hypothesized that oxygen is more beneficial under continuously fed conditions because it allows S. oneidensis to grow and produce flavins at a faster rate, and thus lowers flavin washout. Our conclusions were supported by experiments with a flavin‐secretion deficient mutant of S. oneidensis. Biotechnol. Biotechnol. Bioeng. 2014;111: 692–699. © 2013 Wiley Periodicals, Inc.
Enhanced production of coenzyme Q10 by self‐regulating the engineered MEP pathway in Rhodobacter sphaeroides
Authors: Lu Wenqiang , Ye Lidan , Xu Haoming , Xie Wenping , Gu Jiali , Yu Hongwei 
Published: October 2013

ABSTRACTFine‐tuning the expression level of an engineered pathway is crucial for the metabolic engineering of a host toward a desired phenotype. However, most engineered hosts suffer from nonfunctional protein expression, metabolic imbalance, cellular burden or toxicity from intermediates when an engineered pathway is first introduced, which can decrease production of the desired product. To circumvent these obstacles, we developed a self‐regulation system utilizing the trc/tac promoter, LacIq protein and ribosomal binding sites (RBS). With the purpose of improving coenzyme Q10 (CoQ10) production by increasing the decaprenyl diphosphate supplement, enzymes DXS, DXR, IDI, and IspD were constitutively overexpressed under the control of the trc promoter in Rhodobacter sphaeroides. Then, a self‐regulation system combining a set of RBSs for adjusting the expression of the LacIq protein was applied to tune the expression of the four genes, resulting in improved CoQ10 production. Finally, another copy of the tac promoter with the UbiG gene (involved in the ubiquinone pathway of CoQ10 biosynthesis) was introduced into the engineered pathway. By optimizing the expression level of both the upstream and downstream pathway, CoQ10 production in the mutants was improved up to 93.34 mg/L (7.16 mg/g DCW), about twofold of the wild‐type (48.25 mg/L, 3.24 mg/g DCW). Biotechnol. Bioeng. 2014;111: 761–769. © 2013 Wiley Periodicals, Inc.
Ultra‐high‐performance liquid chromatography–tandem mass spectrometry for pharmacokinetics of bakuchiol in rats
Authors: Zhang Shuang‐Qing , Fan Yu‐Ming 
Published: October 2013

ABSTRACTPsoralea Corylifolia L. is a traditional Chinese medicine with many beneficial effects in medical therapies. Bakuchiol was the main active ingredient of Psoralea Corylifolia L., used for the treatment of various diseases and also as a natural food additive. A specific and reliable ultra‐high performance liquid chromatography–tandem mass spectrometry has been developed and fully validated for the quantification of bakuchiol in rat plasma. Chromatographic separation of bakuchiol and an internal standard, daidzein, was achieved on a Hypersil Gold C18 column with gradient elution that consisted of methanol and water at a flow rate of 0.2 mL/min. The compounds were detected at negative ionization mode using mass transition m/z 255.2 → 172.0 and 252.9 → 132.0 for bakuchiol and daidzein, respectively. Good linearity was obtained over the range of 2–1000 ng/mL and the lower limit of quantification was 2 ng/mL. The intra‐ and inter‐day accuracies ranged from 91.1 to 105.7% and precisions (relative standard deviations) were within 9.3%. Bakuchiol was found to be stable under three freeze–thaw cycles, short‐term temperature, post‐preparative and long‐term temperature conditions. The method was applied to a pharmacokinetic study of bakuchiol intravenously administered to rats at a dose of 5 mg/kg. Copyright © 2013 John Wiley & Sons, Ltd.
Studies on excretion kinetics of ten constituents in rat urine after oral administration of Shensong Yangxin Capsule by UPLC‐MS/MS
Authors: Liu Minyan , Li Song , Zhao Shaohua , Wang Hongtao , Wang Hairong , Tu Pengfei 
Published: October 2013

ABSTRACTA rapid and sensitive ultra‐high performance liquid chromatography–mass spectrometry (UPLC‐MS/MS) method was developed and validated for the quantification of 10 major active constituents in rat urine after oral administration of Shensong Yangxin Capsule (SSYX) using diazepam as an internal standard (IS). The urine samples were pretreated and extracted by solid‐phase extraction prior to UPLC. Chromatographic separation was achieved on a Waters C18 (2.1 × 50 mm, 1.7 µm) column using a gradient elution program with 0.1% formic acid aqueous solution and acetonitrile at a flow rate of 0.4 mL/min. Detection and quantitation were accomplished by a hybrid quadrupole mass spectrometer using electrospray ionization source and multiple reaction monitoring in the positive ionization mode. The mass transition ion‐pairs (m/z) for quantitation were all optimized and the total run time was 4.50 min. The specificity, linearity, accuracy, precision, recovery, matrix effect and stabilities were all validated for the analytes in urine samples. The validation results indicated that this method was simple, rapid, specific and reliable. The proposed method was successfully applied to investigate the urinary excretion kinetics of 10 compounds in rat after oral administration of SSYX. Copyright © 2013 John Wiley & Sons, Ltd.
Out of the Cold – the Rising Importance of Environmental Management in the Corporate Governance of Russian Oil and Gas Producers
Authors: Thurner Thomas , Proskuryakova Liliana Nikolaevna 
Published: October 2013

ABSTRACTOil and gas producers play a pivotal role in the Russian economy. The industry itself is very energy consuming and capable of producing major environmental damage. For a long time, however, innovative ways of production were low on their priority list, leading to heavily outdated equipment and hardware. Recently, Russian oil‐ and gas producers have kicked off major programs to catch up with their western counterparts. Until now, however, insights into the importance of environmental management of oil and gas producers are very limited. We studied the annual reports and environmental reports of the six most prominent industry actors between 2008 and 2010 and analyze their changing approaches to green management. Most companies start in 2009 to address their environmental activities in the statement of the CEO and chairmen. In 2010, the environmental activities have made it up to the list of top priorities in the companies. On an industry‐level, we find that management's own initiatives drive companies' adoption of greener production technologies and are much more influential than government regulation. In fact, we see that leading industry actors inform government regulation and thereby lift up the greening of production also in late followers. Green innovation either stems from international cooperation for industry leaders or out of in‐house knowledge generated through own R&D institutes. Copyright © 2013 John Wiley & Sons, Ltd and ERP Environment.
The Integration of Quality, Environmental and Health and Safety Management by Car Manufacturers – a Long‐Term Empirical Study
Authors: von Ahsen Anette 
Published: October 2013

ABSTRACTThe diversity of stakeholder requirements is currently a pivotal challenge for companies. Stakeholders expect companies to increasingly consider environmental and social aspects in their decisions. Thus, corporate goal systems are including not only qualitative and financial goals, but also environmental and social ones. Management systems for ensuring quality, environmental and occupational safety play an important role in achieving these objectives. Considering the interdependency between the different systems constitutes a central challenge. Much of the literature and the results from empirical studies suggest that the spatial application of integrated management systems is state of the art. Integrated management systems in particular are regarded as more effective and more efficient than separate and distinct management systems. However, the present long‐term study demonstrates that for car manufacturers in Germany these integration efforts are implemented in very different ways, and that some integration approaches are partially abandoned after a period of unsatisfactory implementation. Copyright © 2013 John Wiley & Sons, Ltd and ERP Environment
Using Social Cognitive Theory to Investigate Green Consumer Behavior
Authors: Lin Hsiu‐Yi , Hsu Meng‐Hsiang 
Published: October 2013

AbstractGreen consumer behavior can induce industries to develop green production methods and convert wasteful patterns of consumption into green consumption patterns. This study demonstrates that the practice of green consumption relies on the self‐sanction concept in individuals. The objective of this study was to develop a research model of green consumer behavior based on social cognitive theory. The results show that personal self‐concepts (the most significant of which is green consumption self‐efficacy), personal outcome expectation and social sanction all have a significant influence. On the other hand, the influences of the expected outcome of green consumer behavior, climate change and the mass media were not significant. Copyright © 2015 John Wiley & Sons, Ltd and ERP Environment.