bluuebunny/crossref_metadata_2025_split huggingface dataset:
The incidence of diabetes in atypical antipsychotic users differs according to agent—results from a multisite epidemiologic study
Authors: Yood Marianne Ulcickas , deLorenze Gerald , Quesenberry Charles P. , Oliveria Susan A. , Tsai Ai‐Lin , Willey Vincent J. , McQuade Robert , Newcomer John , L'Italien Gilbert 
Published: June 2009

AbstractPurposeThe purpose of this study was to examine the association between atypical antipsychotics, including the newer agents, aripiprazole and ziprasidone, and newly treated diabetes, using the largest post‐marketing cohort of patients exposed to these newer treatments that has been studied to date.MethodsIdentified two overlapping cohorts—a simple cohort (all antipsychotic users) and an inception cohort (new users of antipsychotics)—using automated data from three United States sites (60.4 million covered lives). Patients exposed to antipsychotics ≥ 45 days were identified and followed for incident diagnoses of treated diabetes. Data analysis accounted for drug switching and non‐consistent drug use.ResultsIn the 55 287‐member inception cohort, 357 cases of newly treated diabetes were identified. Compared with current use of typical antipsychotics, current users of aripiprazole (adjusted hazard ratio (aHR) 0.93, 95% confidence interval (CI) 0.50–1.76), quetiapine (aHR 1.04, 95%CI, 0.67–1.62), risperidone (aHR 0.85, 95%CI, 0.54–1.36) and ziprasidone (aHR 1.05, 95%CI, 0.54–2.08) had similar low risk of diabetes. Patients exposed to olanzapine had an increased risk of diabetes (aHR 1.71, 95%CI, 1.12–2.61), and although the effect estimate is imprecise, clozapine‐exposed patients had a trend towards an elevated hazard ratio (aHR 2.58, 95%CI, 0.76–8.80). Results for the simple cohort were similar.ConclusionsRelative to typical antipsychotics, aripiprazole, ziprasidone, risperidone and quetiapine were not associated with an increased risk of diabetes; olanzapine and clozapine were associated with an increased risk. This analysis constitutes the largest post‐marketing pharmacoepidemiologic study to date that includes the newer agents. Copyright © 2009 John Wiley & Sons, Ltd.
A sensitive magnetic bead method for the detection and identification of tyrosine phosphorylation in proteins by MALDI‐TOF/TOF MS
Authors: Condina Mark R. , Guthridge Mark A. , McColl Shaun R. , Hoffmann Peter 
Published: June 2009

AbstractPhosphorylation is one of the most important PTMs and is estimated to occur on 30% of the mammalian proteome. Its perturbed regulation has been implicated in many pathologies. The rarity of phosphotyrosine compared with phosphoserine or phosphothreonine is prompting the development of more sensitive approaches because proteomic technologies that are currently used to assess tyrosine phosphorylation in proteins are inadequate, identifying only a fraction of the predicted tyrosine phosphoproteome. Here we describe the development of a reproducible, high‐sensitivity methodology for the detection and mapping of phosphotyrosine residues by MS. The anti‐phosphotyrosine antibody 4G10 was coupled covalently to super para‐magnetic beads or by affinity to super para‐magnetic beads with protein G covalently attached. Using this approach, we successfully enriched phosphotyrosine peptides mixed with non‐phosphorylated peptides at a ratio of up to 1:200, enabling detection at a level representing the highest sensitivity reported for tyrosine phosphorylation. The beads were subsequently used to enrich tyrosine phosphopeptides from a digest of the in vitro‐phosphorylated recombinant β‐intracellular region of the granulocyte‐macrophage colony‐stimulating factor receptor, which was subsequently analysed by MALDI‐TOF/TOF MS. Our results define this methodology as a sensitive approach for tyrosine phosphoproteome analysis.
New changes in the plasma‐membrane‐associated proteome of rice roots under salt stress
Authors: Cheng Yanwei , Qi Yaocheng , Zhu Qian , Chen Xi , Wang Ning , Zhao Xin , Chen Haiyan , Cui Xiangju , Xu Langlai , Zhang Wei 
Published: June 2009

AbstractTo gain a better understanding of salt stress responses in plants, we used a proteomic approach to investigate changes in rice (Oryza sativa) root plasma‐membrane‐associated proteins following treatment with 150 mmol/L NaCl. With or without a 48 h salt treatment, plasma membrane fractions from root tip cells of a salt‐sensitive rice cultivar, Wuyunjing 8, were purified by PEG aqueous two‐phase partitioning, and plasma‐membrane‐associated proteins were separated by IEF/SDS‐PAGE using an optimized rehydration buffer. Comparative analysis of three independent biological replicates revealed that the expressions of 18 proteins changed by more than 1.5‐fold in response to salt stress. Of these proteins, nine were up‐regulated and nine were down‐regulated. MS analysis indicated that most of these membrane‐associated proteins are involved in important physiological processes such as membrane stabilization, ion homeostasis, and signal transduction. In addition, a new leucine‐rich‐repeat type receptor‐like protein kinase, OsRPK1, was identified as a salt‐responding protein. Immuno‐blots indicated that OsRPK1 is also induced by cold, drought, and abscisic acid. Using immuno‐histochemical techniques, we determined that the expression of OsRPK1 was localized in the plasma membrane of cortex cells in roots. The results suggest that different rice cultivars might have different salt stress response mechanisms.
The hemolymph proteome of the honeybee: Gel‐based or gel‐free?
Authors: Bogaerts Annelies , Baggerman Geert , Vierstraete Evy , Schoofs Liliane , Verleyen Peter 
Published: June 2009

AbstractThe honeybee has an invaluable economic impact and is a model for studying immunity, development and social behavior. The recent sequencing and annotation of the honeybee genome facilitates the study of its hemolymph, which reflects the physiological condition and mediates immune responses. We aimed at making a proteomic reference map of honeybee hemolymph and compared gel‐free and gel‐based techniques. One hundered and four 2‐DE spots corresponding to 62 different proteins were identified. Eight identical 2‐DLC experiments resulted in the identification of 32 unique proteins. One repeat was clearly not representative for the potential of the given 2‐DLC setup. Only 27% of the identified hemolymph proteins were found by both techniques. In addition, we found proteins of three different viruses which creates possibilities for biomarker design. Future hemolymph studies will benefit from this work.
Proteomic analysis on the temperature‐dependent complexes in Thermoanaerobacter tengcongensis
Authors: Meng Bo , Qian Zhong , Wei Fan , Wang Weiwei , Zhou Chuanqi , Wang Zhuowei , Wang Quanhui , Tong Wei , Wang Qian , Ma Yanhe , Xu Ningzhi , Liu Siqi 
Published: June 2009

AbstractIt is generally accepted that protein complexes play an active role in avoiding the protein degradation of the thermophiles. Thermoanaerobacter tengcongensis was cultured at three different temperatures (55, 75 and 80°C) and the extracts of protein complexes were prepared. Through blue native PAGE, the changes of the relative band volumes in response to different temperatures were semi‐quantitatively compared and six temperature‐dependent bands were obtained. These bands were excised, digested with trypsin and then analyzed with MS for the identification of protein components. With the combination of the proteins identified by LC MS/MS and MALDI TOF/TOF MS, a total of 92 unique proteins were ascertained in these complexes. Besides, some protein components were examined with Western blot, which gave us insights into the survival mechanism of thermophiles. These included (i) the composition of complex at 80°C was significantly different from that at the other two temperatures; (ii) HSPs presented in all temperature‐dependent complexes; (iii) several proteins associated with the functional pathways existed in the same complexes, indicating that the complex structure provided facility for the functional efficiency.
Identification and comparative analysis of the structural proteomes of ϕKZ and EL, two giant Pseudomonas aeruginosa bacteriophages
Authors: Lecoutere Elke , Ceyssens Pieter‐Jan , Miroshnikov Konstantin A. , Mesyanzhinov Vadim V. , Krylov Victor N. , Noben Jean‐Paul , Robben Johan , Hertveldt Kirsten , Volckaert Guido , Lavigne Rob 
Published: June 2009

AbstractGiant bacteriophages ϕKZ and EL of Pseudomonas aeruginosa contain 62 and 64 structural proteins, respectively, identified by ESI‐MS/MS on total virion particle proteins. These identifications verify gene predictions and delineate the genomic regions dedicated to phage assembly and capsid formation (30 proteins were identified from a tailless ϕKZ mutant). These data form the basis for future structural studies and provide insights into the relatedness of these large phages. The ϕKZ structural proteome strongly correlates to that of Pseudomonas chlororaphis bacteriophage 201ϕ2‐1. Phage EL is more distantly related, shown by its 26 non‐conserved structural proteins and the presence of genomic inversions.
Multiplexed LC‐MS/MS analysis of horse plasma proteins to study doping in sport
Authors: Barton Chris , Beck Paul , Kay Richard , Teale Phil , Roberts Jane 
Published: June 2009

AbstractThe development of protein biomarkers for the indirect detection of doping in horse is a potential solution to doping threats such as gene and protein doping. A method for biomarker candidate discovery in horse plasma is presented using targeted analysis of proteotypic peptides from horse proteins. These peptides were first identified in a novel list of the abundant proteins in horse plasma. To monitor these peptides, an LC‐MS/MS method using multiple reaction monitoring was developed to study the quantity of 49 proteins in horse plasma in a single run. The method was optimised and validated, and then applied to a population of race‐horses to study protein variance within a population. The method was finally applied to longitudinal time courses of horse plasma collected after administration of an anabolic steroid to demonstrate utility for hypothesis‐driven discovery of doping biomarker candidates.
Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis
Authors: Dumas Emilie , Desvaux Mickaël , Chambon Christophe , Hébraud Michel 
Published: June 2009

AbstractWhileListeria monocytogenesis responsible for listeriosis, it is also a saprophytic species with exceptional survival aptitudes. Secreted proteins are one of the main tools used by bacteria to interact with their environment. In order to take into account the biodiversity ofL. monocytogenesspecies, exoproteomic analysis was carried out on 12 representative strains. Following 2‐DE and MALDI‐TOF MS, a total of 151 spots were identified and corresponded to 60 non‐orthologous proteins. To categorize and analyze these proteomic data, a rational bioinformatic approach predicting final subcellular localization was carried out. Fifty‐two out of the 60 proteins identified (86.7%) were indeed predicted as localized in the extracellular milieu (gene ontology (GO): 0005576). Most of them (65.4%) were actually predicted as secretedviathe Sec translocon. Comparative analysis allowed for proteins found in all or only in a subset ofL. monocytogenesstrains to be defined. While the core exoproteome included most proteins related to bacterial virulence, cell wall biogenesis, as well as proteins secreted by unknown pathways, a slight variation in the protein members of these categories were observed and constituted the variant exoproteome. This investigation resulted in the first definition of the core and variant exoproteomes ofL. monocytogeneswhere corollaries on bacterial physiology are further discussed.
A novel fractionation method of the rough ER integral membrane proteins; Resident proteins versus exported proteins?
Authors: Sakai Kumiko , Hamanaka Ryoji , Yuki Hideo , Watanabe Makoto 
Published: June 2009

AbstractWe treated the high salt‐washed canine pancreatic rough ER (KRM) with 0.18% Triton X‐100, separated the extract from the residual membrane (0.18%Tx KRM), and processed the extract with SM‐2 beads to recover membrane proteins in proteoliposomes. To focus on integral membrane proteins, KRM, 0.18%Tx KRM and proteoliposomes were subjected to sodium carbonate treatment, and analyzed by 2‐D gel electrophoresis. Consequently we found that a distinct group of integral membrane protein of KRM preferentially extracted from the membrane and recovered in proteoliposomes did exist, while majority of KRM integral membrane proteins were fractionated in 0.18%Tx KRM, which retained the basic structure and functions of KRM. Protein identification showed that the former group was enriched with proteins exported from the ER and the latter group comprised mostly of ER resident proteins. This result will potentially affect the prevailing view of the ER membrane structure as well as protein sorting from the ER.
Application of quantitative immunoprecipitation combined with knockdown and cross‐linking to Chlamydomonas reveals the presence of vesicle‐inducing protein in plastids 1 in a common complex with chloroplast HSP90C
Authors: Heide Heinrich , Nordhues André , Drepper Friedel , Nick Sabine , Schulz‐Raffelt Miriam , Haehnel Wolfgang , Schroda Michael 
Published: June 2009

AbstractKnowledge of the interaction partners of a protein of interest may provide important information on its function. Common to currently available tools for the identification of protein–protein interactions, however, is their high rates of false positives. Only recently an assay was reported that allowed for the unequivocal identification of protein–protein interactions in mammalian cells in a single experiment. This assay, termed quantitative immunoprecipitation combined with knockdown (QUICK), combines RNAi, stable isotope labeling with amino acids in cell culture, immunoprecipitation, and quantitative MS. We are using the unicellular green alga Chlamydomonas reinhardtii to understand the roles of chaperones in chloroplast biogenesis. The goal of this work was to apply QUICK to Chlamydomonas for the identification of novel interaction partners of vesicle‐inducing protein in plastids 1 (VIPP1), a protein required for the biosynthesis/maintenance of thylakoid membranes and known substrate of chloroplast HSP70B. We report here a robust QUICK protocol for Chlamydomonas that has been improved (i) by introducing a cross‐linking step (‐X) to improve protein complex stability and (ii) by including a control for the correction of unequal immunoprecipitation and/or labeling efficiencies. Using QUICK and cross‐linking we could verify that HSP70B and CGE1 form a complex with VIPP1 and could also demonstrate that chloroplast HSP90C is part of this complex. Moreover, we could show that the chaperones interact with VIPP1 also in membrane fractions.
A rapid and simple procedure for the depletion of abundant storage proteins from legume seeds to advance proteome analysis: A case study using Glycine max
Authors: Krishnan Hari B. , Oehrle Nathan W. , Natarajan Savithiry S. 
Published: June 2009

Abstract2‐D analysis of plant proteomes containing thousands of proteins has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the non‐abundant proteins within seeds is difficult when 60–80% is storage proteins. Resolution can be improved through sample fractionation using separation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca2+ to precipitate soybean (Glycine max) seed storage globulins, glycinin and β‐conglycinin. This method removes 87±4% of the highly abundant seed proteins from the extract, allowing for 541 previously inconspicuous proteins present in soybean seed to be more detectable (volume increase of ≥50%) using fluorescent detection. Of those 541 enhanced spots, 197 increased more than 2.5‐fold when visualized with Coomassie. The majority of those spots were isolated and identified using peptide mass fingerprinting. Fractionation also provided detection of 63 new phosphorylated protein spots and enhanced the visibility of 15 phosphorylated protein spots, using 2‐D electrophoretic separation and an in‐gel phosphoprotein stain. Application of this methodology toward other legumes, such as peanut, bean, pea, alfalfa and others, also containing high amounts of storage proteins, was examined, and is reported here.
Integrated platform for manual and high‐throughput statistical validation of tandem mass spectra
Authors: Yu Kebing , Sabelli Anthony , DeKeukelaere Lisa , Park Richard , Sindi Suzanne , Gatsonis Constantine A. , Salomon Arthur 
Published: June 2009

AbstractAs proteomic data sets increase in size and complexity, the necessity for database‐centric software systems able to organize, compare, and visualize all the proteomic experiments in a lab grows. We recently developed an integrated platform called high‐throughput autonomous proteomic pipeline (HTAPP) for the automated acquisition and processing of quantitative proteomic data, and integration of proteomic results with existing external protein information resources within a lab‐based relational database called PeptideDepot. Here, we introduce the peptide validation software component of this system, which combines relational database‐integrated electronic manual spectral annotation in Java with a new software tool in the R programming language for the generation of logistic regression spectral models from user‐supplied validated data sets and flexible application of these user‐generated models in automated proteomic workflows. This logistic regression spectral model uses both variables computed directly from SEQUEST output in addition to deterministic variables based on expert manual validation criteria of spectral quality. In the case of linear quadrupole ion trap (LTQ) or LTQ‐FTICR LC/MS data, our logistic spectral model outperformed both XCorr (242% more peptides identified on average) and the X!Tandem E‐value (87% more peptides identified on average) at a 1% false discovery rate estimated by decoy database approach.
Oxalic acid‐mediated stress responses in Brassica napus L.
Authors: Liang Yue , Strelkov Stephen E. , Kav Nat N. V. 
Published: June 2009

AbstractOxalic acid (OA) occurs extensively in nature and plays diverse roles, especially in pathogenic processes involving various plant pathogens. However, proteome changes and modifications of signaling and oxidative network of plants in response to OA are not well understood. In order to investigate the responses of Brassica napus toward OA, a proteome analysis was conducted employing 2‐DE with MS/MS. A total of 37 proteins were identified as responding to OA stress, of which 13 were up‐regulated and 24 were down‐regulated. These proteins were categorized into several functional groups including protein processing, RNA processing, photosynthesis, signal transduction, stress response, and redox homeostasis. Investigation of the effect of OA on phytohormone signaling and oxidative responses revealed that jasmonic acid‐, ethylene‐, and abscisic acid‐mediated signaling pathways appear to increase at later time points, whereas those pathways mediated by salicylic acid appear to be suppressed. Moreover, the activities of the antioxidant enzymes catalase, peroxidase, superoxide dismutase and oxalic acid oxidase, but not NADPH oxidase, were suppressed by OA stress. Our findings are discussed within the context of the proposed role(s) of OA during infection by Sclerotinia sclerotiorum and subsequent disease progression.
Quantitation of glycogen synthase kinase‐3 sensitive proteins in neuronal membrane rafts
Authors: Thompson Andrew J. , Williamson Ritchie , Schofield Emma , Stephenson John , Hanger Diane , Anderton Brian 
Published: June 2009

AbstractWe report a quantitative proteomic study to investigate the changes induced in membrane rafts by the inhibition of glycogen synthase kinase‐3. Sensitive quantitation of membrane raft proteins using isobaric tagging chemistries was enabled by a novel hybrid proteomic method to isolate low‐microgram (10–30 μg) membrane raft protein preparations as unresolved bands in a low‐density acrylamide gel. Samples were in‐gel digested, differentially tagged and combined for 2‐D LC and quantitative MS. Analysis of hippocampal membrane preparations using this approach resulted in a sixfold increase in sensitivity and a threefold increase in the number of quantifiable proteins compared with parallel processing using a traditional in‐solution method. Quantitative analysis of membrane raft preparations from a human neuronal cell line treated with glycogen synthase kinase‐3 inhibitors SB415286 or lithium chloride, that have been reported to modulate processing of the Alzheimer amyloid precursor protein, identified several protein changes. These included decreases in lamin B1 and lamin B receptor, as well as increases in several endosome regulating rab proteins, rab5, rab7 and rab11 that have been implicated in processing of the amyloid precursor protein in Alzheimer's disease.
Mapping of the chaperone AcrH binding regions of translocators AopB and AopD and characterization of oligomeric and metastable AcrH‐AopB‐AopD complexes in the type III secretion system of Aeromonas hydrophila
Authors: Tan Yih Wan , Yu Hong Bing , Sivaraman J. , Leung Ka Yin , Mok Yu‐Keung 
Published: June 2009

AbstractIn the type III secretion system (T3SS) of Aeromonas hydrophila, AcrH acts as a chaperone for translocators AopB and AopD. AcrH forms a stable 1:1 monomeric complex with AopD, whereas the 1:1 AcrH‐AopB complex exists mainly as a metastable oligomeric form and only in minor amounts as a stable monomeric form. Limited protease digestion shows that these complexes contain highly exposed regions, thus allowing mapping of intact functional chaperone binding regions of AopB and AopD. AopD uses the transmembrane domain (DF1, residues 16–147) and the C‐terminal amphipathic helical domain (DF2, residues 242–296) whereas AopB uses a discrete region containing the transmembrane domain and the putative N‐terminal coiled coil domain (BF1, residues 33–264). Oligomerization of the AcrH‐AopB complex is mainly through the C‐terminal coiled coil domain of AopB, which is dispensable for chaperone binding. The three proteins, AcrH, AopB, and AopD, can be coexpressed to form an oligomeric and metastable complex. These three proteins are also oligomerized mainly through the C‐terminal domain of AopB. Formation of such an oligomeric and metastable complex may be important for the proper formation of translocon of correct topology and stoichiometry on the host membrane.
Kinetically trapped metastable intermediate of a disulfide‐deficient mutant of the starch‐binding domain of glucoamylase
Authors: Sugimoto Hayuki , Nakaura Miho , Nishimura Shigenori , Karita Shuichi , Miyake Hideo , Tanaka Akiyoshi 
Published: June 2009

AbstractRefolding of a thermally unfolded disulfide‐deficient mutant of the starch‐binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and 1H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half‐lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with β‐cyclodextrin as the native state, suggesting that the intermediate is highly‐ordered and native‐like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far‐UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off‐pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.