bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrasonic extraction and HPLC determination of anthraquinones, aloe‐emodine, emodine, rheine, chrysophanol and physcione, in roots of Polygoni multiflori
Authors: Jiao Yue , Zuo Yuegang
Published: April 2009

Introduction

Polygoni multiflori, one of traditional Chinese herbal medicines for the treatment of various diseases commonly associated with aging, is known to contain active anthraquinone ingredients. However, the content of the anthraquinones varies among P. multiflori samples with collection season and sites. Thus, simple, reliable and accurate analytical methods for determining of anthraquinones in P. multiflori products are needed for the quality control and pharmacological studies.

Objective

To develop an HPLC method for the simultaneous determination of five anthraquinones, aloe‐emodine, rheine, emodine, chrysophanol and physcione, in the roots of P. multiflori.

Methodology

Anthraquinones were extracted from the roots of P. multiflori using aqueous alcohol solutions or hot water under ultrasonication. Separation and quantitation of anthraquinones was accomplished using a reversed‐phase C18 column with the mobile phase of methanol–water–phosphoric acid (600:400:1), and the detection wavelength of 254 nm.

Results

Seventy per cent aqueous ethanol showed the highest extraction efficiency for anthraquinones from roots of P. multiflori when compared with four other extraction solvents tested. All calibration curves were linear over the concentration range tested with the square of correlation coefficients >0.999. The detection limits (S/N = 3) were 0.89, 1.1, 1.6, 1.7 and 2.0 ng for chrysophanol, aloe‐emodine, rheine, emodine and physcione, respectively. Emodine and physcione were found in the samples tested at concentrations of 0.341 and 0.197 mg/g, respectively.

Conclusion

The described HPLC methods are simple, accurate and selective techniques for separation and quantification of anthraquinones in roots of P. multiflori and other plant samples. Copyright © 2009 John Wiley & Sons, Ltd.
Identification of chrysanthenyl esters from the essential oil of Anthemis maritima L. investigated by GC/RI, GC‐MS (EI and CI) and 13C‐NMR spectroscopy: chemical composition and variability
Authors: Darriet Florent , Desjobert Jean‐Marie , Costa Jean , Muselli Alain
Published: April 2009

Introduction

Anthemis maritima L. (Asteraceae) is a wild plant growing in Corsica and Sardinia. No previous studies of the chemical composition of A. maritima essential oil have been found. The oil contains two series of cis‐ and trans‐chrysanthenyl esters for which the MS data are not present in available libraries and the 13C‐NMR data are not reported in the literature. The determination of these compounds is a challenging problem since some of these esters are present in low concentrations and they exhibit very similar EI‐MS.

Objective

To develop comprehensive strategies involving integrated techniques including CC, GC/RI, GC‐MS (EI and CI), 1H‐ and 13C‐NMR and hemi‐synthesis for the identification of both series of chrysanthenyl esters in A. maritima oils.

Methodology

Seventeen oil samples were prepared by hydrodistillation. A fine analysis of a pool of Corsican oils was conducted after repeated CC. A selected Sardinian oil was used as source of product for the hemi‐synthesis of chrysanthenyl esters. The identification of these compounds was based on joint information from GC‐MS (EI and CI), 13C‐NMR and hemi‐synthesis.

Results

Integrated analysis of Corsican and Sardinian oils allowed the identification of 124 components accounting for 83.3–91.6% of the total oil. With the aid of principal component analysis, oil samples could be divided in two groups. Among 16 chrysanthenyl esters identified, 12 were laboratory‐synthesised and their 13C‐NMR data are reported for the first time.

Conclusions

The study illustrates the contribution of integrated techniques for the characterisation of unusual essential oils. Copyright © 2009 John Wiley & Sons, Ltd.
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

Introduction

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.

Objective

To 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.

Methodology

A 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.

Conclusion

The 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

Introduction

Scutellaria 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.

Objective

To develop a chromatographic method for the identification of Scutellaria lateriflora and two Teucrium species and to quantify the latter as adulterants.

Methodology

Samples were extracted with aqueous methanol and the extracts were analysed using a standardised LC‐DAD‐ESI/MS profiling method to obtain their phenolic profiles.

Results

Skullcap 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.

Conclusions

This 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

Introduction

The phytochemical and biological studies carried out on Salvia species showed that their extracts and constituents have various biological activities.

Objective

The aim of this study was the isolation of diterpenoids from the roots of Salvia barrelieri Ettling and the determination of the antioxidant activity.

Methodology

Chromatographic methods were used for fractionation and isolation, respectively. Structure elucidation was established by spectroscopic methods. Five antioxidant assays were performed.

Results

Three 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.

Conclusion

Taxodione 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

Introduction

Tinctures 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.

Objective

In 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.

Methodology

Diffusion‐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.

Results

Using 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.

Conclusion

The 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

Experiments 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

Recently, 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

The 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

Haemophilus 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

Chicory (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

Engineering 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

RNF2, 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

We 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

Hepatitis 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

Pollution 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

Islet 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

To 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.
Mutations of key hydrophobic surface residues of 11β‐hydroxysteroid dehydrogenase type 1 increase solubility and monodispersity in a bacterial expression system
Authors: Lawson Alexander J. , Walker Elizabeth A. , White Scott A. , Dafforn Timothy R. , Stewart Paul M. , Ride Jonathan P.
Published: April 2009

11β‐Hydroxysteroid dehydrogenase type 1 (11β‐HSD1) is a key enzyme in the conversion of cortisone to the functional glucocorticoid hormone cortisol. This activation has been implicated in several human disorders, notably the metabolic syndrome where 11β‐HSD1 has been identified as a novel target for potential therapeutic drugs. Recent crystal structures have revealed the presence of a pronounced hydrophobic surface patch lying on two helices at the C‐terminus. The physiological significance of this region has been attributed to facilitating substrate access by allowing interactions with the endoplasmic reticulum membrane. Here, we report that single mutations that alter the hydrophobicity of this patch (I275E, L266E, F278E, and L279E in the human enzyme and I275E, Y266E, F278E, and L279E in the guinea pig enzyme) result in greatly increased yields of soluble protein on expression in E. coli. Kinetic analyses of both reductase and dehydrogenase reactions indicate that the F278E mutant has unaltered Km values for steroids and an unaltered or increased kcat. Analytical ultracentrifugation shows that this mutation also decreases aggregation of both the human and guinea pig enzymes, resulting in greater monodispersity. One of the mutants (guinea pig F278E) has proven easy to crystallize and has been shown to have a virtually identical structure to that previously reported for the wild‐type enzyme. The human F278E enzyme is shown to be a suitable background for analyzing the effects of naturally occurring mutations (R137C, K187N) on enzyme activity and stability. Hence, the F278E mutants should be useful for many future biochemical and biophysical studies of the enzyme.
L2′ loop is critical for caspase‐7 active site formation
Authors: Witkowski Witold A. , Hardy Jeanne A.
Published: April 2009

The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2′) from the other half of the dimer to bind substrate. In an inactive form, the two L2′ loops form a cross‐dimer hydrogen‐bond network over the dimer interface. Although the L2′ loop has been implicated as playing a central role in the formation of the active‐site loop bundle, its precise role in catalysis has not been shown. A detailed understanding of the active and inactive conformations is essential to control the caspase function. We have interrogated the contributions of the residues in the L2′ loop to catalytic function and enzyme stability. In wild‐type and all mutants, active‐site binding results in substantial stabilization of the complex. One mutation, P214A, is significantly destabilized in the ligand‐free conformation, but is as stable as wild type when bound to substrate, indicating that caspase‐7 rests in different conformations in the absence and presence of substrate. Residues K212 and I213 in the L2′ loop are shown to be essential for substrate‐binding and thus proper catalytic function of the caspase. In the crystal structure of I213A, the void created by side‐chain deletion is compensated for by rearrangement of tyrosine 211 to fill the void, suggesting that the requirements of substrate‐binding are sufficiently strong to induce the active conformation. Thus, although the L2′ loop makes no direct contacts with substrate, it is essential for buttressing the substrate‐binding groove and is central to native catalytic efficiency.
Daily consumption of Reliv Glucaffect™ for 8 weeks significantly lowered blood glucose and body weight in 50 subjects
Authors: Belcaro Gianni , Cesarone Maria , Silvia Errichi , Ledda Andrea , Stuard Stefano , G Vinciguerra , Dougall Mark , Cornelli Umberto , Hastings Carl , Schönlau Frank
Published: April 2009

A public change to healthier lifestyles with more physical activity and better nutrition, including caloric restriction, is required to address the obesity epidemic. Weight loss can be achieved by caloric restrictions; current research suggests that this may be achieved by consumption of slowly absorbed carbohydrates owing to the resulting prolonged satiety.

Our rationale was to prolong the satiety of overweight volunteers by supplementation with a proprietary formulation Glucaffect™ which delays absorption of carbohydrates. Glucaffect™ provides potent α‐glucosidase inhibitors of herbal source such Pycnogenol®, Madeglucyl™ and various others which obstruct absorption of carbohydrates, such as starch.

Fifty overweight subjects received either Glucaffect™ or an inactive control product for eight weeks. Consumption of Glucaffect™ was found to statistically significantly lower blood‐fasting glucose from baseline 145.3 mg/dL to 101.1 mg/dL (−30.4%) and Hba1c from 7.59% to 6.33% as compared to the control group where values decreased only marginally.

The weight and the body mass index (BMI) decreased significantly from an average of 88.5 kg (BMI 26.8 kg/m2) to 81.3 kg (BMI 24.5 kg/m2) as compared to the control group.

In conclusion, Glucaffect™ enabled subjects with metabolic syndrome to achieve healthy BMI and blood glucose levels. Glucaffect™ was well tolerated and no subject dropped out. Copyright © 2009 John Wiley & Sons, Ltd.
Development, Validation and Inspection of the Applicability Domain of QSPR Models for Physicochemical Properties of Polybrominated Diphenyl Ethers
Authors: Papa Ester , Kovarich Simona , Gramatica Paola
Published: April 2009

Polybrominated diphenyl ethers (PBDEs) are a group of brominated flame retardants (BFRs), which were widely used in a variety of consumer products. Because of evidences of toxicity effects on different organisms and humans, as well as the ubiquitary profile of these compounds, PBDEs are considered an emerging group of toxic and persistent organic pollutants. However, due to the small amount of experimental data available, still little is known about the properties of most of these chemicals. In this study several physicochemical properties, experimentally available for few PBDE congeners and hexabromobenzene (HBB), were investigated through a modelling approach based on quantitative structure–property relationships (QSPR). The OLS regression models, based on theoretical molecular descriptors, are calculated for Henry's law constant, melting point, subcooled liquid vapor pressure, water solubility, octanol‐air partition coefficient, and octanol‐water partition coefficient. These models can be useful to predict the big amount of missing data and to plan safer alternatives to dangerous BFRs. The innovative aspect of the proposed models, compared to those already published in the literature, is their development according to the OECD principles for regulatory acceptability of QSARs. This includes the validation for predictivity (both by internal and external statistical validation) and the inspection of the applicability domain.
Global or Local QSAR: Is There a Way Out?
Authors: Feher Miklos , Ewing Todd
Published: April 2009

We recently developed a global‐local fusion model for CYP450 predictions. This model has the advantages of both global and local models. The expected error of the model is also estimated that helps to qualify the reliability of the predictions. It is described how different potential errors in QSAR model generation and prediction were averted and how the method was applied in an industrial environment.
Standardization of the first‐trimester fetal cardiac examination using spatiotemporal image correlation with tomographic ultrasound and color Doppler imaging
Authors: Turan S. , Turan O. M. , Ty‐Torredes K. , Harman C. R. , Baschat A. A.
Published: April 2009

Objective

The challenges of the first‐trimester examination of the fetal heart may in part be overcome by technical advances in three‐dimensional (3D) ultrasound techniques. Our aim was to standardize the first‐trimester 3D imaging approach to the cardiac examination to provide the most consistent and accurate display of anatomy.

Methods

Low‐risk women with normal findings on first‐trimester screening at 11 to 13 + 6 weeks had cardiac ultrasound using the following sequence: (1) identification of the four‐chamber view; (2) four‐dimensional (4D) volume acquisition with spatiotemporal image correlation (STIC) and color Doppler imaging (angle = 20°, sweep 10 s); (3) offline, tomographic ultrasound imaging (TUI) analysis with standardized starting plane (four‐chamber view), slice number and thickness; (4) assessment of fetal cardiac anatomy (four‐chamber view, cardiac axis, size and symmetry, atrioventricular valves, great arteries and descending aorta) with and without color Doppler.

Results

107 consecutive women (age, 16–42 years, body mass index 17.2–50.2 kg/m2) were studied. A minimum of three 3D volumes were obtained for each patient, transabdominally in 91.6%. Fetal motion artifact required acquisition of more than three volumes in 20%. The median time for TUI offline analysis was 100 (range, 60–240) s. Individual anatomic landmarks were identified in 89.7–99.1%. Visualization of all structures in one panel was observed in 91 patients (85%).

Conclusion

Starting from a simple two‐dimensional cardiac landmark—the four‐chamber view—the standardized STIC‐TUI technique enables detailed segmental cardiac evaluation of the normal fetal heart in the first trimester. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Shape optimization of wind turbine blades
Authors: Xudong Wang , Shen Wen Zhong , Zhu Wei Jun , Sørensen Jens Nørkær , Jin Chen
Published: April 2009

This paper presents a design tool for optimizing wind turbine blades. The design model is based on an aerodynamic/aero‐elastic code that includes the structural dynamics of the blades and the Blade Element Momentum (BEM) theory. To model the main aero‐elastic behaviour of a real wind turbine, the code employs 11 basic degrees of freedom corresponding to 11 elastic structural equations. In the BEM theory, a refined tip loss correction model is used. The objective of the optimization model is to minimize the cost of energy which is calculated from the annual energy production and the cost of the rotor. The design variables used in the current study are the blade shape parameters, including chord, twist and relative thickness. To validate the implementation of the aerodynamic/aero‐elastic model, the computed aerodynamic results are compared to experimental data for the experimental rotor used in the European Commision‐sponsored project Model Experiments in Controlled Conditions, (MEXICO) and the computed aero‐elastic results are examined against the FLEX code for flow past the Tjæreborg 2 MW rotor. To illustrate the optimization technique, three wind turbine rotors of different sizes (the MEXICO 25 kW experimental rotor, the Tjæreborg 2 MW rotor and the NREL 5 MW virtual rotor) are applied. The results show that the optimization model can reduce the cost of energy of the original rotors, especially for the investigated 2 MW and 5 MW rotors. Copyright © 2009 John Wiley & Sons, Ltd.
Optimal positioning of wind turbines on Gökçeada using multi‐objective genetic algorithm
Authors: Şişbot Sedat , Turgut Özgü , Tunç Murat , Çamdalı Ünal
Published: April 2009

This paper addresses the problem of optimal placement of wind turbines in a farm on Gokçeada Island located at the north‐east of Aegean Sea bearing full potential of wind energy generation. A multi‐objective genetic algorithm approach is employed to obtain optimal placement of wind turbines by maximizing the power production capacity while constraining the budget of installed turbines. Considering the speed and direction history, wind with constant intensity from a single direction is used during optimization. This study is based on wake deficit model mainly because of its simplicity, accuracy and fast calculation time. The individuals of the Pareto optimal solution set are evaluated with respect to various criteria, and the best configurations are presented. In addition to best placement layouts, results include objective function values, total power output, cost and number of turbines for each configuration. Copyright © 2009 John Wiley & Sons, Ltd.
Sox2 and Oct‐3/4: a versatile pair of master regulators that orchestrate the self‐renewal and pluripotency of embryonic stem cells
Authors: Rizzino Angie
Published: April 2009

During the past 10 years, remarkable progress has been made in understanding the transcriptional mechanisms that control the biology of stem cells. Given the importance of stem cells in development, regenerative medicine, and cancer, it is no surprise that the pace of discovery continues to accelerate—paradigm‐shifting models proposed only a few years ago are quickly giving way to even more sophisticated models of regulation. This review summarizes some of the major advances made in delineating the roles of two transcription factors, Sox2 and Oct‐3/4, in stem cell biology. Additionally, unanswered questions related to their mechanisms of action are discussed. When viewed together, it is evident that Sox2 and Oct‐3/4 exhibit the major properties expected of master regulators. They are each essential for mammalian development, they help regulate the transcription of other genes that are essential for development, and they influence their own transcription by both positive and negative feedback loops. Moreover, small changes in the levels of either Sox2 or Oct‐3/4 trigger the differentiation of embryonic stem (ES) cells. Thus, each functions as a molecular rheostat to control the self‐renewal and pluripotency of ES cells. Overall, understanding how Sox2 and Oct‐3/4 function mechanistically will not only provide important insights into stem cells in general, but should also have a significant impact on our understanding of induced pluripotent stem (iPS) cells and, hence, the emerging field of regenerative medicine. Copyright © 2009 John Wiley & Sons, Inc.

This article is categorized under:

Developmental Biology > Stem Cell Biology and Regeneration
Kidney modeling and systems physiology
Authors: Randall Thomas S.
Published: April 2009

We present an overview of currently available resources in renal systems physiology and indicate directions for development toward the renal physiome. After a brief resumé of objectives, we summarize legacy‐modeling studies that can serve as the foundation for a more complete toolset. These include detailed models of practically all renal cell types and nephron segments and a variety of models of nephro‐vascular exchanges in the medulla, of renal hemodynamics, and studies of tubuloglomerular feedback and autoregulation. Recent detailed anatomical reconstructions have brought surprising new results to bear on classic unsolved problems. In parallel with the modeling environment, progress has been made toward the quantitative database and model repository resources that must accompany the modeling environment in order to attain the goal of an open‐ended, flexible, and collaborative infrastructure for renal systems biology, with an indication of prospects for integration with initiatives in the larger IUPS Physiome Project. Copyright © 2009 John Wiley & Sons, Inc.

This article is categorized under:

Models of Systems Properties and Processes > Cellular Models

Physiology > Mammalian Physiology in Health and Disease

Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models

Translational, Genomic, and Systems Medicine > Translational Medicine
Computational modeling of epithelial tissues
Authors: Smallwood Rod
Published: April 2009

There is an extensive literature on the computational modeling of epithelial tissues at all levels from subcellular to whole tissue. This review concentrates on behavior at the individual cell to whole tissue level, and particularly on organizational aspects, and provides an indication of where information from other areas, such as the modeling of angiogenesis, is relevant. The skin, and the lining of all of the body cavities (lung, gut, cervix, bladder etc) are epithelial tissues, which in a topological sense are the boundary between inside and outside the body. They are thin sheets of cells (usually of the order of 0.5 mm thick) without extracellular matrix, have a relatively simple structure, and contain few types of cells. They have important barrier, secretory and transport functions, which are essential for the maintenance of life, so homeostasis and wound healing are important aspects of the behavior of epithelial tissues. Carcinomas originate in epithelial tissues.

There are essentially two approaches to modeling tissues—to start at the level of the tissue (i.e., a length scale of the order of 1 mm) and develop generalized equations for behavior (a continuum approach); or to start at the level of the cell (i.e., a length scale of the order of 10 µm) and develop tissue behavior as an emergent property of cellular behavior (an individual‐based approach). As will be seen, these are not mutually exclusive approaches, and they come in a variety of flavors. Copyright © 2009 John Wiley & Sons, Inc.

This article is categorized under:

Analytical and Computational Methods > Computational Methods

Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models

Analytical and Computational Methods > Topological Methods

Translational, Genomic, and Systems Medicine > Translational Medicine
Networks and pathways in pigmentation, health, and disease
Authors: Baxter Laura L. , Loftus Stacie K. , Pavan William J.
Published: April 2009

Extensive studies of the biology of the pigment‐producing cell (melanocyte) have resulted in a wealth of knowledge regarding the genetics and developmental mechanisms governing skin and hair pigmentation. The ease of identification of altered pigment phenotypes, particularly in mouse coat color mutants, facilitated early use of the pigmentary system in mammalian genetics and development. In addition to the large collection of developmental genetics data, melanocytes are of interest because their malignancy results in melanoma, a highly aggressive and frequently fatal cancer that is increasing in Caucasian populations worldwide. The genetic programs regulating melanocyte development, function, and malignancy are highly complex and only partially understood. Current research in melanocyte development and pigmentation is revealing new genes important in these processes and additional functions for previously known individual components. A detailed understanding of all the components involved in melanocyte development and function, including interactions with neighboring cells and response to environmental stimuli, will be necessary to fully comprehend this complex system. The inherent characteristics of pigmentation biology as well as the resources available to researchers in the pigment cell community make melanocytes an ideal cell type for analysis using systems biology approaches. In this review, the study of melanocyte development and pigmentation is considered as a candidate for systems biology‐based analyses. Copyright © 2009 John Wiley & Sons, Inc.

This article is categorized under:

Developmental Biology > Lineages