bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer
Authors: Zhang Rongfu , Sahu Indra D. , Gibson Kaylee R. , Muhammad Nefertiti B. , Bali Avnika P. , Comer Raven G. , Liu Lishan , Craig Andrew F. , Mccarrick Robert M. , Dabney‐Smith Carole , Sanders Charles R. , Lorigan Gary A. 
Published: August 2015

AbstractMembrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane‐bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a 2H‐labeled d8‐Val overexpressed membrane protein in a membrane mimetic environment. The membrane‐bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α‐helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α‐helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α‐helical in a more native‐like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X‐ray crystallography and/or NMR spectroscopy.
SANIST: a rapid mass spectrometric SACI/ESI data acquisition and elaboration platform for verifying potential candidate biomarkers
Authors: Albini Adriana , Briga Daniela , Conti Matteo , Bruno Antonino , Farioli Daniela , Canali Sara , Sogno Ilaria , D'Ambrosio Gioacchino , Consonni Paolo , Noonan Douglas M. 
Published: August 2015

RationaleSurface‐Activated Chemical Ionization/Electrospray Ionization mass spectrometry (SACI/ESI‐MS) is a technique with high sensitivity and low noise that allows accurate biomarker discovery studies. We developed a dedicated SACI/ESI software, named SANIST, for both biomarker fingerprint data acquisition and as a diagnostic tool, using prostate cancer (PCa) as the disease of interest.MethodsLiquid chromatography (LC)/SACI/ESI‐MS technology was employed to detect a potential biomarker panel for PCa disease prediction. Serum from patients with histologically confirmed or negative prostate biopsies for PCa was employed. The biomarker data (m/z or Thompson value, retention time and extraction mass chromatogram peak area) were stored in an ascii database. SANIST software allowed identification of potential biomarkers. A Bayesian scoring algorithm developed in house allowed sample separation based on comparison with samples in the database.ResultsBiomarker candidates from the carnitine family were detected at significantly lower levels in patients showing histologically confirmed PCa. Using these biomarkers, the SANIST scoring algorithm allowed separation of patients with PCa from biopsy negative subjects with high accuracy and sensitivity.ConclusionsSANIST was able to rapidly identify and perform a preliminary evaluation of the potential diagnostic efficiency of potential biomarkers for PCa. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.
Improved radiocarbon analyses of modern human hair to determine the year‐of‐death by cross‐flow nanofiltered amino acids: common contaminants, implications for isotopic analysis, and recommendations
Authors: Santos Guaciara M. , De La Torre Hector A. Martinez , Boudin Mathieu , Bonafini Marco , Saverwyns Steven 
Published: August 2015

RationaleIn forensic investigation, radiocarbon (14C) measurements of human tissues (i.e., nails and hair) can help determine the year‐of‐death. However, the frequent use of cosmetics can bias hair 14C results as well as stable isotope values. Evidence shows that hair exogenous impurities percolate beyond the cuticle layer, and therefore conventional pretreatments are ineffective in removing them.MethodsWe conducted isotopic analysis (14C, δ13C, δ15N and C/N) of conventionally treated and cross‐flow nanofiltered amino acid (CFNAA)‐treated samples (scalp‐ and body‐hair) from a single female subject using fingernails as a reference. The subject studied frequently applies a permanent dark‐brown dye kit to her scalp‐hair and uses other care products for daily cleansing. We also performed pyrolysis‐gas chromatography/mass spectrometry (Py‐GC/MS) analyses of CFNAA‐treated scalp‐hair to identify contaminant remnants that could possibly interfere with isotopic analyses.ResultsThe conventionally treated scalp‐ and body‐hair showed 14C offsets of ~21‰ and ~9‰, respectively. These offsets confirm the contamination by petrochemicals in modern human hair. A single CFNAA extraction reduced those offsets by ~34%. No significant improvement was observed when sequential extractions were performed, as it appears that the procedure introduced some foreign contaminants. A chromatogram of the CFNAA scalp‐hair pyrolysis products showed the presence of petroleum and plant/animal compound residues, which can bias isotopic analyses.ConclusionsWe have demonstrated that CFNAA extractions can partially remove cosmetic contaminants embedded in human hair. We conclude that fingernails are still the best source of keratin protein for year‐of‐death determinations and isotopic analysis, with body‐hair and/or scalp‐hair coupled with CFNAA extraction a close second. Copyright © 2015 John Wiley & Sons, Ltd.
An open port sampling interface for liquid introduction atmospheric pressure ionization mass spectrometry
Authors: Van Berkel Gary J. , Kertesz Vilmos 
Published: August 2015

RATIONALEA simple method to introduce unprocessed samples into a solvent for rapid characterization by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The continuous flow, self‐cleaning open port sampling interface introduced here fills this void.METHODSThe open port sampling interface used a vertically aligned, co‐axial tube arrangement enabling solvent delivery to the sampling end of the device through the tubing annulus and solvent aspiration down the center tube and into the ionization source of the mass spectrometer via the commercial APCI emitter probe. The solvent delivery rate to the interface was set to exceed the aspiration rate, creating a continuous sampling interface along with a constant, self‐cleaning spillover of solvent from the top of the probe.RESULTSUsing the open port sampling interface with positive ion mode APCI and a hybrid quadrupole time‐of‐flight mass spectrometer, rapid, direct sampling and analysis possibilities are exemplified with plastics, ballpoint and felt tip ink pens, skin, and vegetable oils. These results demonstrated that the open port sampling interface could be used as a simple, versatile and self‐cleaning system to rapidly introduce multiple types of unprocessed, sometimes highly concentrated and complex, samples into a solvent flow stream for subsequent ionization and analysis by mass spectrometry. The basic setup presented here could be incorporated with any self‐aspirating liquid introduction ionization source (e.g., ESI, APCI, APPI, ICP, etc.) or any type of atmospheric pressure sampling‐ready mass spectrometer system.CONCLUSIONSThe open port sampling interface provides a means to introduce and quickly analyze unprocessed solid or liquid samples with the liquid introduction atmospheric pressure ionization source without fear of sampling interface or ionization source contamination. Copyright © 2015 John Wiley & Sons, Ltd.
Suppression of peptide ion dissociation under electron capture: role of backbone amide hydrogen
Authors: Wong P.‐S. Joyce , Chen Xiangfeng , Deng Liulin , Wang Ze , Li Wan , Elaine Wong Y. L. , Dominic Chan T.‐W. 
Published: August 2015

RationaleThe electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides.MethodsGlycine containing model polypeptides were used to probe the mechanism. Molecular‐mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.ResultsSignificant decreases in the intensities of the fragment ions were observed for the 23‐mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen‐bonding 'ladder' formed in the 23‐mer polypeptide, which was not found in the 15‐mer peptide. Substituting the normal amino acid residues by the corresponding N‐methylated amino acid residues in the model peptide, the suppression effect disappeared.ConclusionsOur results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation. Copyright © 2015 John Wiley & Sons, Ltd.
Compound‐specific δ13C analyses reveal sterol metabolic constraints in an aquatic invertebrate
Authors: Gergs René , Steinberger Nicole , Beck Birgit , Basen Timo , Yohannes Elizabeth , Schulz Ralf , Martin‐Creuzburg Dominik 
Published: August 2015

RationaleDietary sterol deficiencies can have severe life history consequences for consumers. Compound‐specific stable isotope analysis (CSIA) was applied to the exploration of the sterol metabolic constraints and bioconversion capacities of the amphipod Gammarus roeselii. Evaluating structural sterol requirements has great potential to improve our understanding of the ecological relevance of sterols as limiting nutrients.MethodsJuvenile G. roeselii were reared on food mixtures consisting of different ratios of the two algae Scenedesmus obliquus (cultivated with 13C‐labeled NaHCO3) and Nannochloropsis limnetica (unlabeled), which have been shown previously to differ in food quality. We measured the sterol content and composition using a gas chromatograph equipped with a flame ionization detector and the δ13C values of sterols using compound‐specific isotope ratio mass spectrometry to examine potential sterol‐mediated nutritional constraints of G. roeselii.ResultsIn the food mixtures, δ13C values of cholesterol, synthesized by N. limnetica, were −25‰ and those of the Δ7‐phytosterols, chondrillasterol and fungisterol, synthesized by S. obliquus, were 7 and 18‰, respectively. Although the cholesterol concentrations in G. roeselii decreased with increasing proportion of dietary S. obliquus, the δ13C values remained constant at −25‰. Lathosterol, which appeared in G. roeselii at high dietary proportions of S. obliquus, had a δ13C value of 35‰.ConclusionsWe provide evidence that the the Δ7‐phytosterols present in S. obliquus cannot be metabolized to cholesterol in G. roeselii, resulting in the accumulation of lathosterol in the animals and potentially in sterol‐limited growth. These findings emphasize the advantage of CSIA in revealing the physiological mechanisms associated with nutritional constraints. Copyright © 2015 John Wiley & Sons, Ltd.
A non‐instrument‐based method for the analysis of formalin‐fixed paraffin‐embedded human spinal cord via matrix‐assisted laser desorption/ionisation imaging mass spectrometry
Authors: O'Rourke Matthew B. , Djordjevic Steven P. , Padula Matthew P. 
Published: August 2015

RationaleThis paper, in conjunction with a work published earlier this year by O'Rourke et al., aims to provide a comprehensive set of protocols for the analysis of formalin‐fixed paraffin‐embedded (FFPE) tissue via matrix‐assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) in a low‐cost and highly repeatable and robust way, thereby allowing other research teams to begin their own IMS‐centered avenues of research.MethodsSamples of FFPE tissue were sectioned at 5 µm, water float mounted to specially prepared ITO glass slides and then dilipidated in a graded alcohol series. Tissue sections were then antigen retrieved under pressure in 20 mmol Tris‐HCl (pH 8.8), coated with trypsin and digested O/N at 37°C. Samples were then sublimated with matrix to a final coverage of 0.2 mg/cm2, recrystallised at 37°C with 50:50 acetonitrile (ACN)/0.1% trifluoroacetic acid (TFA) for 1 h and analysed with a MALDI TOF/TOF mass spectrometer.ResultsSerial sections were imaged, revealing little to no variation with regards to image quality and corresponding spectra. We have also attempted to describe the processes that govern the various aspects of this protocol with respect to each step necessary to ensure reproducibility.ConclusionsWe are confident that this protocol in conjunction with the work published earlier by O'Rourke et al. provides the basis for a repeatable and robust protocol for the analysis of tissues from various sources via MALDI‐IMS. The descriptions of key steps within allows for easy adoption of the protocol while allowing for desired modifications to be performed with minimal yet intuitive adjustment. Copyright © 2015 John Wiley & Sons, Ltd.
A systematic study of glycopeptide esterification for the semi‐quantitative determination of sialylation in antibodies
Authors: Gomes de Oliveira Andrey Giovanni , Roy Rini , Raymond Céline , Bodnar Edward D. , Tayi Venkata S. , Butler Michael , Durocher Yves , Perreault Hélène 
Published: August 2015

RationaleIn the expression of recombinant proteins, an important parameter to control or influence is their level of sialylation. Matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometric (MS) methods tend to either underestimate (positive mode) or overestimate (negative mode) the content of sialylated vs. neutral glycans in glycoproteins. Esterification methods have been developed for free sialylated glycans and sialylated Asn‐glycans, allowing these acidic groups to ionize with the same efficiency as neutral sugars.MethodsHere we describe a method which modifies glycopeptides by esterification. This simple procedure is applied to glycopeptides isolated from tryptic digests of monoclonal antibodies (mAbs), some highly sialylated. To better understand the effect of esterification on the peptide backbone, synthetic EEQYNSTYR was esterified and studied by tandem mass spectrometry (MS/MS). Acetamidation of EEQYNSTYR was also studied as some mAb samples had been overalkylated prior to tryptic digestion.ResultsAs a general trend, ethyl‐esterification or lactonization is observed for each sialic acid on glycoforms of EEQYNSTYR (the N‐glycosylated tryptic peptide of IgG Fc), depending on the branching position of the sialic acid (α2,3 or α2,6). Esterification also affects the carboxyl groups in the peptide, including the C‐terminal COOH.ConclusionsFor antibody analysis, MALDI‐MS ion abundances give a better semi‐quantitative estimate of sialylation levels for esterified than for unreacted glycopeptides. The method is simple to use and helps to differentiate the branching patterns of sialic acids in antibodies. Copyright © 2015 John Wiley & Sons, Ltd.
Low Carbon Innovation in China: From Overlooked Opportunities and Challenges to Transitions in Power Relations and Practices
Authors: Tyfield David , Ely Adrian , Geall Sam 
Published: August 2015

ABSTRACTThis paper explores environmental innovation in the largest emerging economy – China – and its potential for contributing to global transitions to low‐carbon, more sustainable patterns of development. It builds on earlier studies bringing alternative forms of low(er)‐technology, ‘below‐the‐radar', ‘disruptive' and/or social innovation into its analysis. In addition, however, the paper develops our understanding of low‐carbon innovation by paying particular attention to issues of changing power relations and social practices: theoretical issues that need attention in the literature generally but are notably absent when studying transitions in China. This shift in perspective allows four neglected questions to be introduced and, in each case, points to both opportunities and challenges to low‐carbon system transition that are overlooked by an orthodox focus on technological innovations alone. These are briefly illustrated by drawing on examples from three key domains of low‐carbon innovation: solar‐generated energy, electric urban mobility, and food and agriculture. © 2015 The Authors. Sustainable Development published by ERP Environment and John Wiley & Sons, Ltd
How do Public Demonstration Projects Promote Green‐Manufacturing Technologies? A Case Study from China
Authors: Zhou Yuan , Xu Guannan , Minshall Tim , Liu Peng 
Published: August 2015

ABSTRACTPublic demonstration projects are used to promote the upscaling of green‐manufacturing technologies in China, in order to expedite innovation ‘catch‐up’ and transitions to sustainable development. However, these projects are facing implementation challenges, because the relevant barriers are different from traditional demonstrations in new technological niches, when involving complex economic concerns and prolific small and medium enterprises (SMEs) as adopters. This paper, therefore, adopts a case‐based approach to investigate a specific example of a demonstration project in China to support the large‐scale diffusion of green technology and its pilot implementations. Through the case study, this paper reveals that these demonstrations face a different set of diffusion barriers in testing technologies and promoting learning. In addition, this case also shows that a new policy model may be needed in order to cope with these barriers, when emphasizing market‐oriented policies and non‐legislative actors as well as combining them with traditional mandatory measures. Copyright © 2015 John Wiley & Sons, Ltd and ERP Environment
Effects of spatial and temporal resolution of the turbulent inflow on wind turbine performance estimation
Authors: Rai Raj K. , Gopalan Harish , Naughton Jonathan W. 
Published: August 2015

AbstractThe effects of spatial and temporal resolution of wind inflows generated using large eddy simulations (LES) on the scales of turbulence present in the wind inflow, and the resulting changes in wind turbine performance were investigated for neutral atmospheric boundary layer conditions. Wind inflows with four different spatial resolutions and five different temporal resolutions were used to produce different turbine responses. An aero‐elastic code assessed the dynamic response of two wind turbines to the different inflows. Auto‐spectral density functions (ASDF) of turbine responses, such as blade deflection and bending moment, that are representative of the turbine response were used to assess the effect of the inflow. The results indicated that, as additional turbulence scales were resolved, the wind turbines showed a similar increased response that was evident in both the ASDF and variance of the different wind turbine performance parameters. As a result, the amount to which turbulence is resolved in the inflow, particularly using tools such as LES, will be important to consider when using these inflows for wind turbine design and performance prediction. Copyright © 2015 John Wiley & Sons, Ltd.
In fault ride through reactive current rise time requirements of various European grid codes—analysis based on a full‐converter wind turbine
Authors: Curzi Massimiliano , Sharma Ranjan , Martin Frank 
Published: August 2015

AbstractThe European transmission system operators specify grid codes to ensure a safe and reliable operation of the electrical power system, even during grid faults. Wind power plants have to comply with such specific requirements prior to installation and operation. Some of the requirements, however, are open to interpretation, especially because of lack of specification, and therefore, they pose technical challenges to full‐converter wind turbines. In fact, different interpretations leave it open to debate on whether a requirement can be fulfilled or not. The rise time requirement across some European grid codes is discussed in this paper. First the uncertainties in some transmission system operators' definitions of rise time, step response time and settling time are presented, and then a comparative analysis is performed among calculation methods, such as instantaneous reactive current in alpha‐beta reference frame, direct and quadrature reference frame and root mean square of the positive sequence component. The comparison results of both ideal cases and randomly selected measurements from actual full‐converter wind turbine field tests show that the rise time of the reactive current is significantly affected by the calculation methods. This effect in some cases can make the difference between fulfilling the requirement or not. As a result of that, it is highlighted in this paper the need for a common understanding of the rise time requirements between industry and system operators, based on clear technical fundamentals. Copyright © 2015 John Wiley & Sons, Ltd.
Ecological monitoring through harmonizing existing data: Lessons from the boreal avian modelling project
Authors: Barker Nicole K. S. , Fontaine Patricia C. , Cumming Steven G. , Stralberg Diana , Westwood Alana , Bayne Erin M. , Sólymos Péter , Schmiegelow Fiona K. A. , Song Samantha J. , Rugg David J. 
Published: August 2015

ABSTRACTTo accomplish the objectives of a long‐term ecological monitoring program (LTEM), repurposing research data collected by other researchers is an alternative to original data collection. The Boreal Avian Modelling (BAM) Project is a 10‐year‐old project that has integrated the data from >100 avian point‐count studies encompassing thousands of point‐count surveys, and harmonized across data sets to account for heterogeneity induced by methodological and other differences. The BAM project faced the classic data‐management challenges any LTEM must deal with, as well as special challenges involved with harmonizing so many disparate data sources. We created a data system consisting of 4 components: Archive (to preserve each contributor's data), Avian Database (harmonized point‐count data), Biophysical Database (spatially explicit environmental covariates), and Software Tools library (linking the other components and providing analysis capability). This system has allowed the project to answer many questions about boreal birds; we believe it to be successful enough to merit consideration for use in monitoring other taxa. We have learned a number of lessons that will guide the project as it moves forward. These include the importance of creating a data protocol, the critical importance of high‐quality metadata, and the need for a flexible design that accommodates changes in field techniques. One of the challenges the BAM team faced—gaining access to relevant data sets—may become easier with the increased expectation by journals and funding agencies that documenting and preserving research data be a standard part of scientific research. © 2015 The Wildlife Society.