bluuebunny/crossref_metadata_2025_split huggingface dataset:
The analysis of heavy metals in Chinese herbal medicine by flow injection–mercury hydride system and graphite furnace atomic absorption spectrometry
Authors: Yuan Xudong , Ling Koh Hwee , Keung Chui Wai 
Published: April 2009

AbstractIntroduction Simple and robust atomic absorption spectrometry (AAS) analytical methods were developed to determine the contents of arsenic (As), lead (Pb) and mercury (Hg) contained in Chinese herbal medicine products or Chinese proprietary medicine.ObjectiveTo develop AAS analytical methods to determine the contents of the toxic heavy metals in herbal medicine, and thus monitor them according to the regulated content limits to ensure the quality and safety of herbal products.MethodologyA flow injection‐mercury hydride system technique was used for the quantitation of As and Hg, and a graphite furnace technique was used for the analysis of Pb. Limits of detection (LOD) for the three toxic heavy metals were found to be 0.3 ppb for As, 0.1 ppb for Pb and 0.5 ppb for Hg. Eight samples of ‘Yin Qiao Jie Du’ tablets available on the market were selected as the model herbal medicine for analysis.ConclusionThe developed analytical methods are sensitive enough to detect these heavy metals to meet regulated guidelines. No trace amounts of Hg were found in the test samples due to the fact that the Hg level is less than the LOD. However, variable amounts of As (135.0–5349.3 ppb) and Pb (22.5–968.3 ppb) were found in all products. Copyright © 2009 John Wiley & Sons, Ltd.
Comparison of the phenolic component profiles of skullcap (Scutellaria lateriflora) and germander (Teucrium canadense and T. chamaedrys), a potentially hepatotoxic adulterant
Authors: Lin Long‐Ze , Harnly James M. , Upton Roy 
Published: April 2009

AbstractIntroductionScutellaria lateriflora, commonly known as skullcap, is used as an ingredient in numerous herbal products. Unfortunately, it has occasionally been adulterated with Teucrium canadense or T. chamaedrys, commonly known as germander, which contains potentially hepatotoxic diterpenes. Chromatographic profiles of the phenolic components provide a means of distinguishing between these plants and enhancing public safety.ObjectiveTo develop a chromatographic method for the identification of Scutellaria lateriflora and two Teucrium species and to quantify the latter as adulterants.MethodologySamples were extracted with aqueous methanol and the extracts were analysed using a standardised LC‐DAD‐ESI/MS profiling method to obtain their phenolic profiles.ResultsSkullcap contained primarily flavonoids, while the major phenolic components of the two Teucrium species were the phenylethanoids, verbascoside and teucrioside. Using the phenylethanoids as markers, it was possible to clearly distinguish between the two genus and to determine 5% Teucrium mixed with Scutellaria using either ultraviolet absorption spectrometry or mass spectrometry in the total ion count mode. Using MS in the selective ion monitoring (SIM) mode, 1% Teucrium could be measured.ConclusionsThis study showed that chromatographic profiling was able to identify Scutellaria and Teucrium, separately and when mixed together. Copyright © 2009 John Wiley & Sons, Ltd.
Antioxidant diterpenoids from the roots of Salvia barrelieri
Authors: Kolak Ufuk , Kabouche Ahmed , Öztürk Mehmet , Kabouche Zahia , Topçu Gülaçtl , Ulubelen Ayhan 
Published: April 2009

AbstractIntroduction The phytochemical and biological studies carried out on Salvia species showed that their extracts and constituents have various biological activities.ObjectiveThe aim of this study was the isolation of diterpenoids from the roots of Salvia barrelieri Ettling and the determination of the antioxidant activity.MethodologyChromatographic methods were used for fractionation and isolation, respectively. Structure elucidation was established by spectroscopic methods. Five antioxidant assays were performed.ResultsThree new abietane diterpenoids barreliol, royleanone 12‐methyl ether and 7‐epi‐salviviridinol, and six known diterpenoids, with a known dammarane triterpenoid, pyxinol were isolated. The absolute stereochemistry of pyxinol was confirmed by X‐ray analysis.ConclusionTaxodione exhibited the highest antioxidant activity among the tested compounds. Copyright © 2009 John Wiley & Sons, Ltd.
Direct metabolic fingerprinting of commercial herbal tinctures by nuclear magnetic resonance spectroscopy and mass spectrometry
Authors: Politi Matteo , Zloh Mire , Pintado Manuela E. , Castro Paula M. L. , Heinrich Michael , Prieto Jose M. 
Published: April 2009

AbstractIntroductionTinctures are widely used liquid pharmaceutical preparations traditionally obtained by maceration of one or more medicinal plants in ethanol–water solutions. Such a process results in the extraction of virtually hundreds of structurally diverse compounds with different polarities. Owing to the large chemical diversity of the constituents present in the herbal tinctures, the analytical tools used for the quality control of tinctures are usually optimised only for the detection of single chemical entities or specific class of compounds.ObjectiveIn order to overcome the major limitations of the current methods used for analysis of tinctures, a new methodological approach based on NMR spectroscopy and MS spectrometry has been tested with different commercial tinctures.MethodologyDiffusion‐edited 1H‐NMR (1D DOSY) and 1H‐NMR with suppression of the ethanol and water signals have been applied here for the first time to the direct analysis of commercial herbal tinctures derived from Echinacea purpurea, Hypericum perforatum, Ginkgo biloba and Valeriana officinalis. The direct injection of the tinctures in the MS detector in order to obtain the corresponding metabolic profiles was also performed.ResultsUsing both NMR and MS methods it was possible, without evaporation or separation steps, to obtain a metabolic fingerprint able to distinguish between tinctures prepared with different plants. Batch‐to‐batch homogeneity, as well as degradation after the expiry date of a batch, was also investigated.ConclusionThe techniques proposed here represent fast and convenient direct analyses of medicinal herbal tinctures. Copyright © 2009 John Wiley & Sons, Ltd.
Identification of elicitor‐responsive proteins in rice leaves by a proteomic approach
Authors: Liao Ming , Li Yunfeng , Wang Zhenzhong 
Published: April 2009

AbstractExperiments were conducted to identify the differentially expressed proteins in rice (Oryza sativa L.) plants after treatment with the glycoprotein elicitor CSB I, purified from ZC13, a race of the rice blast fungus Magnaporthe grisea. The interactions of two near isogenic lines of rice, C101A51 and CO39, with ZC13 resulted in completely incompatible and compatible types, respectively. Proteins were extracted from rice leaves at 12 and 24 h after treatment with CSB I. Temporal changes in total proteins were examined using 2‐DE. Among more than 900 protein spots reproducibly detected on each gel, 11 were up‐regulated, three were down‐regulated and seven were newly induced during, at a minimum, one time point. Twenty‐one differentially expressed proteins were identified by linear ion trap quadrupole (LTQ)‐MS/MS. The identified proteins were classified into six categories based on their putative function reported: (i) defense proteins (PR‐10a, PR‐5 and putative salt‐induced protein), (ii) signal transduction (nucleoside diphosphate kinase and putative profilin), (iii) ROS (Mn‐SOD, Cu/Zn‐SOD, GST and CAT), (iv) programmed cell death (translationally controlled tumor protein), (v) molecule biosynthesis (putative ribosomal protein S5, putative ribosomal protein L12, putative translational elongation factor Tu and putative chaperonin 21 precursor) and (vi) metabolism (putative fructose‐bisphosphate aldolase class‐I, putative malate dehydrogenase, cytoplasmic malate dehydrogenase, putative acid phosphatase, putative transketolase1 and gamma hydroxybutyrate dehydrogenase‐like protein). All of these proteins (except Cu/Zn‐SOD, putative acid phosphatase and translationally controlled tumor protein) were induced faster and to a higher degree in C101A51 than in CO39. These data suggest that the incompatible rice line may possess a more sensitive recognition system that can identify and react to specific chemical, biological or physical triggers in a more efficient manner, thus eliciting an early and fast defense response.
Studying the effects of correlation on protein selection in proteomics data
Authors: Venkataramani Savita , Naik Dayanand N. 
Published: April 2009

AbstractRecently, Efron (2007) provided methods for assessing the effect of correlation on false discovery rate (FDR) in large‐scale testing problems in the context of microarray data. Although FDR procedure does not require independence of the tests, existence of correlation grossly under‐ or overestimates the number of critical genes. Here, we briefly review Efron's method and apply it to a relatively smaller spectrometry proteomics data. We show that even here the correlation can affect the FDR values and the number of proteins declared as critical.
Detergent addition to tryptic digests and ion mobility separation prior to MS/MS improves peptide yield and protein identification for in situ proteomic investigation of frozen and formalin‐fixed paraffin‐embedded adenocarcinoma tissue sections
Authors: Djidja Marie‐Claude , Francese Simona , Loadman Paul M. , Sutton Chris W. , Scriven Peter , Claude Emmanuelle , Snel Marten F. , Franck Julien , Salzet Michel , Clench Malcolm R. 
Published: April 2009

AbstractThe identification of proteins involved in tumour progression or which permit enhanced or novel therapeutic targeting is essential for cancer research. Direct MALDI analysis of tissue sections is rapidly demonstrating its potential for protein imaging and profiling in the investigation of a range of disease states including cancer. MALDI‐mass spectrometry imaging (MALDI‐MSI) has been used here for direct visualisation and in situ characterisation of proteins in breast tumour tissue section samples. Frozen MCF7 breast tumour xenograft and human formalin‐fixed paraffin‐embedded breast cancer tissue sections were used. An improved protocol for on‐tissue trypsin digestion is described incorporating the use of a detergent, which increases the yield of tryptic peptides for both fresh frozen and formalin‐fixed paraffin‐embedded tumour tissue sections. A novel approach combining MALDI‐MSI and ion mobility separation MALDI‐tandem mass spectrometry imaging for improving the detection of low‐abundance proteins that are difficult to detect by direct MALDI‐MSI analysis is described. In situ protein identification was carried out directly from the tissue section by MALDI‐MSI. Numerous protein signals were detected and some proteins including histone H3, H4 and Grp75 that were abundant in the tumour region were identified.
A comprehensive proteome map of the Haemophilus parasuis serovar 5
Authors: Zhou Mingguang , Zhang Anding , Guo Yi , Liao Yonghong , Chen Huanchun , Jin Meilin 
Published: April 2009

AbstractHaemophilus parasuis is the causative agent of Glässer's disease of pigs, a disease associated with fibrinous polyserositis, polyarthritis and meningitis. Systematic reference maps of outer membrane, intracellular and extracellular proteome fractions of the clinical isolate H. parasuis SH0165 were examined by 2‐DE coupled with MALDI‐TOF MS. A total of 539 proteins spots were successfully identified, corresponding to 317 different proteins that were classified into functional categories. The majority of these proteins were linked to housekeeping functions in amino acid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism and post‐translational modification, protein turnover and chaperones. A significant number of outer membrane proteins were identified, such as Wza, Omp2, Omp5, D15 and PalA, which were supposed to play important roles in basic physiology of H. parasuis. In addition, several virulence‐associated proteins involved in type I (TolC), type III (DsbA and DsbC) and type V (Autotransporter adhesins) secretion systems, and solute‐binding proteins participating in iron‐uptake systems were also identified in the present study.
Proteomic analysis of chicory root identifies proteins typically involved in cold acclimation
Authors: Degand Hervé , Faber Anne‐Marie , Dauchot Nicolas , Mingeot Dominique , Watillon Bernard , Cutsem Pierre Van , Morsomme Pierre , Boutry and Marc 
Published: April 2009

AbstractChicory (Cichorium intybus) roots contain high amounts of inulin, a fructose polymer used as a storage carbohydrate by the plant and as a human dietary and prebiotic compound. We performed 2‐D electrophoretic analysis of proteins from root material before the first freezing period. The proteins were digested with trypsin and the peptides analyzed by MS (MALDI‐TOF/TOF). From the 881 protein spots analyzed, 714 proteins corresponded to a database accession, 619 of which were classified into functional categories. Besides expected proteins (e.g. related to metabolism, energy, protein synthesis, or cell structure), other well‐represented categories were proteins related to folding and stability (49 spots), proteolysis (49 spots), and the stress response (67 spots). The importance of abiotic stress response was confirmed by the observation that 7 of the 21 most intense protein spots are known to be involved in cold acclimation. These results suggest a major effect of the low temperature period that preceded root harvesting.
Understanding rice plant resistance to the Brown Planthopper (Nilaparvata lugens): A proteomic approach
Authors: Wei Zhe , Hu Wei , Lin Qishan , Cheng Xiaoyan , Tong Mengjie , Zhu Lili , Chen Rongzhi , He Guangcun 
Published: April 2009

AbstractEngineering and breeding resistant plant varieties are the most effective and environmentally friendly ways to control agricultural pests and improve crop performance. However, the mechanism of plant resistance to pests is poorly understood. Here we used a quantitative mass‐spectrometry‐based proteomic approach for comparative analysis of expression profiles of proteins in rice leaf sheaths in responses to infestation by the brown planthopper (Nilaparvata lugens Stål, BPH), which is a serious rice crop pest. Proteins involved in multiple pathways showed significant changes in expression in response to BPH feeding, including jasmonic acid synthesis proteins, oxidative stress response proteins, beta‐glucanases, protein; kinases, clathrin protein, glycine cleavage system protein, photosynthesis proteins and aquaporins. The corresponding genes of eight important proteins were further analyzed by quantitative RT‐PCR. Proteomic and transcript responses that were related to wounding, oxidative and pathogen stress overlapped considerably between BPH‐resistant (carrying the resistance gene BPH15) and susceptible rice lines. In contrast, proteins and genes related to callose metabolism remained unchanged and glycine cleavage system protein was up‐regulated in the BPH‐resistant lines, indicating that they have an efficient and specific defense mechanism. Our results provide new information about the interaction between rice and the BPH.
RNF2 is the target for phosphorylation by the p38 MAPK and ERK signaling pathways
Authors: Rao Prema S. , Satelli Arun , Zhang Sheng , Srivastava Sanjay K. , Srivenugopal Kalkunte S. , Rao U. Subrahmanyeswara 
Published: April 2009

AbstractRNF2, a member of polycomb group (PcG) proteins, is involved in chromatin remodeling. However, mechanisms that regulate RNF2 function are unknown. To identify such mechanisms, RNF2 was expressed in HEK‐293 cells and analyzed by 2‐D electrophoresis. RNF2 was resolved into at least seven protein spots, migrating toward the lower pI from its expected pI of 6.38, suggesting that RNF2 undergoes post‐translational modifications. Western blotting indicated that majority of these RNF2 spots contained phosphoserine(s), which were completely dephosphorylated upon treatment with a phosphatase. SB203580, a specific inhibitor of p38 MAPK, inhibited RNF2 phosphorylation at one site. On the other hand, PD98059, an inhibitor of MEK1/2, inhibited majority of the phosphorylation events in RNF2. Mass spectrometry analysis identified that RNF2 expressed in Sf9 insect cells undergoes co‐translational excision of 1Met coupled to N‐acetylation of 2Ser, and phosphorylation of 41Ser. Interestingly, 41Ser is a predicted p38/MAPK phosphorylation site, consistent with the loss of phosphorylation induced by SB203580. Further analysis indicated that RNF2 phosphorylation differentially modulates the expression of transcription factors and histone 2B acetylation. These results provide first evidence for phosphorylation of RNF2, and suggest that the mitogen activated protein kinases including p38 MAPK and ERK1/2 regulate growth, stress response, differentiation and other cellular processes, through phosphorylation of RNF2.
High‐throughput generation of tagged stable cell lines for proteomic analysis
Authors: Torres Jorge Z. , Miller Julie J. , Jackson Peter K. 
Published: April 2009

AbstractWe present an optimized system for rapid generation of localization and affinity purification‐tagged mammalian stable cell lines that facilitates complex purification and interacting protein identification. The improved components of this method, including the flexibility of inducible expression, circumvent issues associated with toxicity, clonal selection, sample yields and time to data acquisition. We have applied this method to the study of cell‐cycle regulators and novel microtubule‐associated proteins.
Protein profile in hepatitis B virus replicating rat primary hepatocytes and HepG2 cells by iTRAQ‐coupled 2‐D LC‐MS/MS analysis: Insights on liver angiogenesis
Authors: Zhang Jianhua , Niu Dandan , Sui Jianjun , Ching Chi Bun , Chen Wei Ning 
Published: April 2009

AbstractHepatitis B virus (HBV) infection and in particular Hepatitis B Virus X Protein have been shown to modulate angiogenesis. However, a comprehensive and coordinated mechanism in the HBV‐induced angiogenesis remains to be established. In this study, transient transfection of replicative HBV genome was carried out in rat primary hepatocytes (RPHs) as well as HepG2 cells. Angiogenesis was assessed by tube formation assay. 2‐D LC‐MS/MS analysis was used to detect differentially expressed proteins in cells, supporting HBV replication compared with those transfected with the empty vector. A cell‐based HBV replication was established in both RPHs and HepG2 cells. HBV replication‐induced angiogenesis was indicated by tube formation of endothelial cells cultured in condition medium from RPHs or HepG2 cells supporting HBV replication. Enzymes associated with angiogenesis, namely fumarate hydratase and tryptophanyl‐tRNA synthetase, were identified by 2‐D LC‐MS/MS analysis in HBV replicating RPHs and HepG2 cells. Our results indicated that the application of quantitative proteomics based on iTRAQ can be an effective approach to evaluate the effects of HBV replication on liver angiogenesis. The angiogenesis‐associated proteins identified in our study may eventually lead to novel anti‐angiogenic hepatocellular carcinoma cancer therapy based on tumor vascular targeting or be the markers for hepatocellular carcinoma diagnosis.
Recent developments in the application of proteomics to the analysis of plant responses to heavy metals
Authors: Ahsan Nagib , Renaut Jenny , Komatsu Setsuko 
Published: April 2009

AbstractPollution of soils by heavy metals is an ever‐growing problem throughout the world, and is the result of human activities as well as geochemical weathering of rocks and other environmental causes such as volcanic eruptions, acid rain and continental dusts. Plants everywhere are continuously exposed to metal‐contaminated soils. The uptake of heavy metals not only constrains crop yields, but can also be a major hazard to the health of humans and to the entire ecosystem. Although analysis of gene expression at the mRNA level has enhanced our understanding of the response of plants to heavy metals, many questions regarding the functional translated portions of plant genomes under metal stress remain unanswered. Proteomics offers a new platform for studying complex biological functions involving large numbers and networks of proteins, and can serve as a key tool for revealing the molecular mechanisms that are involved in interactions between toxic metals and plant species. This review focuses on recent developments in the applications of proteomics to the analysis of the responses of plants to heavy metals; such studies provide a deeper understanding of protein responses and the interactions among the possible pathways that are involved in detoxification of toxic metals in plant cells. In addition, the challenges faced by proteomics in understanding the responses of plants to toxic metal are discussed, and some possible future strategies for meeting these challenges are proposed.
Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process
Authors: Wiltzius Jed J. W. , Sievers Stuart A. , Sawaya Michael R. , Eisenberg David 
Published: April 2009

AbstractIslet Amyloid Polypeptide (IAPP or amylin) is a peptide hormone produced and stored in the β‐islet cells of the pancreas along with insulin. IAPP readily forms amyloid fibrils in vitro, and the deposition of fibrillar IAPP has been correlated with the pathology of type II diabetes. The mechanism of the conversion that IAPP undergoes from soluble to fibrillar forms has been unclear. By chaperoning IAPP through fusion to maltose binding protein, we find that IAPP can adopt a α‐helical structure at residues 8–18 and 22–27 and that molecules of IAPP dimerize. Mutational analysis suggests that this dimerization is on the pathway to fibrillation. The structure suggests how IAPP may heterodimerize with insulin, which we confirmed by protein crosslinking. Taken together, these experiments suggest the helical dimerization of IAPP accelerates fibril formation and that insulin impedes fibrillation by blocking the IAPP dimerization interface.
Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4‐helix bundle proteins
Authors: Patel Shona C. , Bradley Luke H. , Jinadasa Sayuri P. , Hecht Michael H. 
Published: April 2009

AbstractTo probe the potential for enzymatic activity in unevolved amino acid sequence space, we created a combinatorial library of de novo 4‐helix bundle proteins. This collection of novel proteins can be considered an “artificial superfamily” of helical bundles. The superfamily of 102‐residue proteins was designed using binary patterning of polar and nonpolar residues, and expressed in Escherichia coli from a library of synthetic genes. Sequences from the library were screened for a range of biological functions including heme binding and peroxidase, esterase, and lipase activities. Proteins exhibiting these functions were purified and characterized biochemically. The majority of de novo proteins from this superfamily bound the heme cofactor, and a sizable fraction of the proteins showed activity significantly above background for at least one of the tested enzymatic activities. Moreover, several of the designed 4‐helix bundles proteins showed activity in all of the assays, thereby demonstrating the functional promiscuity of unevolved proteins. These studies reveal that de novo proteins—which have neither been designed for function, nor subjected to evolutionary pressure (either in vivo or in vitro)—can provide rudimentary activities and serve as a “feedstock” for evolution.