bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of the venom from the fish eating coral snake Micrurus surinamensis: Novel toxins, their function and phylogeny
Authors: Olamendi‐Portugal Timoteo , Batista Cesar V. F. , Restano‐Cassulini Rita , Pando Victoria , Villa‐Hernandez Oscar , Zavaleta‐Martínez‐Vargas Alfonso , Salas‐Arruz Maria C. , de la Vega Ricardo C. Rodríguez , Becerril Baltazar , Possani Lourival D. 
Published: April 2008

AbstractThe protein composition of the soluble venom from the South American fish‐eating coral snake Micrurus surinamensis surinamensis, here abbreviated M. surinamensis, was separated by RP‐HPLC and 2‐DE, and their components were analyzed by automatic Edman degradation, MALDI‐TOF and ESI‐MS/MS. Approximately 100 different molecules were identified. Sixty‐two components possess molecular masses between 6 and 8 kDa, are basically charged molecules, among which are cytotoxins and neurotoxins lethal to fish (Brachidanios rerio). Six new toxins (abbreviated Ms1–Ms5 and Ms11) were fully sequenced. Amino acid sequences similar to the enzymes phospholipase A2 and amino acid oxidase were identified. Over 20 additional peptides were identified by sequencing minor components of the HPLC separation and from 2‐DE gels. A functional assessment of the physiological activity of the six toxins was also performed by patch clamp using muscular nicotinic acetylcholine receptor assays. Variable degrees of blockade were observed, most of them reversible. The structural and functional data obtained were used for phylogenetic analysis, providing information on some evolutionary aspects of the venom components of this snake. This contribution increases by a factor of two the total number of α‐neurotoxins sequenced from the Micrurus genus in currently available literature.
The 6th East Midlands Proteomics Workshop supported by the BSPR and BMSS 14 November 2007, Nottingham, UK
Authors: Layfield Robert , Matharoo‐Ball Balwir 
Published: April 2008

AbstractNow in its 6th year, the East Midlands Proteomics workshop held in November 2007 brought together over 200 scientists with a common interest in proteomic techniques and their application to complex biological and biomedical problems. For the first time, this meeting was jointly supported by the British Society for Proteome Research (BSPR) and British Mass Spectrometry Society (BMSS).
JunD mediates androgen‐induced oxidative stress in androgen dependent LNCaP human prostate cancer cells
Authors: Mehraein‐Ghomi Farideh , Lee Elyse , Church Dawn R. , Thompson Todd A. , Basu Hirak S. , Wilding George 
Published: April 2008

AbstractBACKGROUNDNumerous and compelling evidence shows that high level of reactive oxygen species (ROS) plays a key role in prostate cancer occurrence, recurrence and progression. The molecular mechanism of ROS overproduction in the prostate gland, however, remains mostly unknown. Unique AP‐1 transcription factor JunD has been shown to inhibit cell proliferation, promote differentiation and mediate stress responses in a variety of eukaryotic cells. We previously reported that androgen–androgen receptor induced ROS production in androgen‐dependent LNCaP human prostate cancer cells is associated with increased JunD level/AP‐1 transcriptional activity.METHODSLNCaP cells constitutively overexpressing a functionally inactive form of JunD (JunDΔTA) or stably transfected with JunD siRNA (siJunD) to suppress JunD protein expression were established. Overexpression of JunD in LNCaP cells using transient transfection method was applied to assess the induction of ROS production in LNCaP cells. DCF assay was used to measure the ROS concentrations in the transfected as well as non‐transfected control cells. RT‐PCR and Western blot analyses were used to confirm silencing or overexpression of JunD in the transfected cells.RESULTSIn the absence of androgen, LNCaP cells transiently transfected with a JunD overexpressing vector have relatively enhanced cellular ROS levels as compared to LNCaP cells transfected with a vector control. LNCaP cells that fail to express functional JunD (JunDΔTA or siJunD) do not exhibit any increase in ROS production in response to androgen.CONCLUSIONBased on these data, we conclude that JunD is an essential mediator of the androgen‐induced increase in ROS levels in LNCaP cells. Prostate 68:924–934, 2008. © 2008 Wiley‐Liss, Inc.
Restoration of PTEN expression alters the sensitivity of prostate cancer cells to EGFR inhibitors
Authors: Wu Z. , Gioeli D. , Conaway M. , Weber M. J. , Theodorescu D. 
Published: April 2008

AbstractIntroductionProstate cancer (CaP) progression from an androgen‐dependent to an androgen‐independent state is associated with overexpression of EGFR family members or activation of their downstream signaling pathways, such as PI3K‐Akt and MAPK. Although there are data implicating PI3K‐Akt or MAPK pathway activation with resistance to EGFR inhibitors in CaP, the potential cross‐talk between these pathways in response to EGFR or MAPK inhibitors remains to be examined.MethodsCross‐talk between PTEN and MAPK signaling and its effects on CaP cell sensitivity to EGFR or MAPK inhibitors were examined in a PTEN‐null C4‐2 CaP cell, pTetOn PTEN C4‐2, where PTEN expression was restored conditionally.ResultsExpression of PTEN in C4‐2 cells exposed to EGF or serum was associated with increased phospho‐ERK levels compared to cells without PTEN expression. Similar hypersensitivity of MAPK signaling was observed when cells were treated with a PI3K inhibitor LY294002. This enhanced sensitivity of MAPK signaling in PTEN‐expressing cells was associated with a growth stimulatory effect in response to EGF. Furthermore, EGFR inhibitors gefitinib and lapatinib abrogated hypersensitivity of MAPK signaling and cooperated with PTEN expression to inhibit cell growth in both monolayer and anchorage‐independent conditions. Similar cooperative growth inhibition was observed when cells were treated with the MEK inhibitor, CI1040, in combination with PTEN expression suggesting that inhibition of MAPK signaling could mediate the cooperation of EGFR inhibitors with PTEN expression.ConclusionsOur results suggest that signaling cross‐talk between the PI3K‐Akt and MAPK pathways occurs in CaP cells, highlighting the potential benefit of targeting both the PI3K‐Akt and MAPK pathways in CaP treatment. Prostate 68:935–944, 2008. © 2008 Wiley‐Liss, Inc.
Structural characterization and anti‐angiogenic properties of prostate‐specific antigen isoforms in seminal fluid
Authors: Mattsson Johanna M. , Valmu Leena , Laakkonen Pirjo , Stenman Ulf‐Håkan , Koistinen Hannu 
Published: April 2008

AbstractBACKGROUNDThe prostate produces high levels of prostate‐specific antigen (PSA), which has been shown to exert anti‐angiogenic properties and thus might slow down prostate tumor growth. It has been suggested that the protease activity of PSA is not needed for its anti‐angiogenic function. We have previously shown that seminal fluid contains both active and inactive, internally cleaved forms of PSA. The precise structural differences between these isoforms and their function are not known.METHODSTo elucidate the structures, we purified PSA from seminal fluid and separated it by anion‐exchange chromatography into six different isoforms, which were characterized by mass spectrometry. The anti‐angiogenic activity of these PSA‐isoforms was analyzed by human umbilical vein endothelial cell (HUVEC) tube formation assay.RESULTSThe enzymatically active PSA‐isoforms had an intact peptide moiety but could be separated into three isoforms based on differences in glycosylation. The major isoform contained PSA with a biantennary carbohydrate with terminal sialic acids on both antennae. The other active isoforms showed significant carbohydrate heterogeneity, containing one or no sialic acid. The inactive isoforms were internally cleaved at several different positions, but the fragments were held together by disulphide bonds. The enzymatic activity of PSA correlated with its inhibitory effect on the endothelial cell tube formation and the inhibition was dose‐dependent at physiological concentrations, whereas enzymatically inactive internally cleaved PSA‐isoforms had no effect.CONCLUSIONSOur results show that the anti‐angiogenic effect of PSA is based on its proteolytic activity. Prostate 68:945–954, 2008. © 2008 Wiley‐Liss, Inc.
Prediction of lymphatic invasion by peritumoral lymphatic vessel density in prostate biopsy cores
Authors: Kuroda Kenji , Horiguchi Akio , Asano Takako , Asano Tomohiko , Hayakawa Masamichi 
Published: April 2008

AbstractBACKGROUNDLymphatic invasion in radical prostatectomy specimens has been suggested to be an unfavorable prognostic factor in clinically localized prostate cancer. Lymphangiogenesis detected by antibodies specific for lymphatic endothelial cells has been associated with lymphatic invasion and lymph node metastasis in prostate cancer. This study was designed to examine whether lymphangiogenesis in prostate biopsy could predict lymphatic spread in radical prostatectomy specimens.METHODSParaffin‐embedded positive biopsy cores obtained from 99 patients who underwent radical prostatectomy at our institution were immunostained with D2‐40 monoclonal antibody, which specifically recognizes lymphatic endothelium. The association between lymphatic parameters in prostate biopsy and pathological parameters in radical prostatectomy specimens was analyzed.RESULTSPeritumoral and intratumoral lymphatic (ITL) vessels were observed in 90 (90.9%) and 23 cases (23.2%). Average and maximal peritumoral lymphatic vessel density (PTLD) and the presence of ITL in positive biopsy cores were significantly associated with positive biopsy core rates (P = 0.0015 for average PTLD, P < 0.0001 for maximal PTLD, and P = 0.0038 for ITL) and lymphatic vessel invasion (P < 0.0001 for average PTLD, P < 0.0001 for maximal PTLD, and P = 0.0322 for ITL). Among preoperative parameters, the biopsy Gleason score (P = 0.0092, HR = 6.108) and average PTLD (P = 0.0034, HR = 1.860) were significant predictors of lymphatic invasion in radical prostatectomy specimens in multivariate analysis.CONCLUSIONSPTLD in prostate biopsy specimens assessed by immunohistochemistry using D2‐40 antibody could be a useful parameter for predicting lymphatic spread of clinically localized prostate cancer. Prostate 68:1057–1063, 2008. © 2008 Wiley‐Liss, Inc.
Region‐specific role of water in collagen unwinding and assembly
Authors: Ravikumar Krishnakumar M. , Hwang Wonmuk 
Published: April 2008

AbstractConformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino‐poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30‐residue long collagen triple helices, including a structure that has a biologically relevant 9‐residue imino‐poor region from type III collagen (PDB ID: 1BKV). A torsional map approach was used to characterize the conformational motion of the molecule that differ between imino‐rich and imino‐poor regions. At temperatures 300 K and above, unwinding initiates at a common cleavage site, the glycine‐isoleucine bond in the imino‐poor region. This provides a linkage between previous observations that unwinding of the imino‐poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. We found that unwinding of the imino‐poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short‐lived in the imino‐poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 Å, in good agreement with the experimentally measured inter‐collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger‐scale lubrication layer mediating collagen self‐assembly. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Insights from the energetics of water binding at the domain‐ligand interface of the Src SH2 domain
Authors: Fabritiis Gianni De , Geroult Sebastien , Coveney Peter V. , Waksman Gabriel 
Published: April 2008

AbstractSH2 domains play important roles in signal transduction by binding phosphorylated tyrosine residues on cell surface receptors. In an effort to understand the mechanism of ligand binding and more specifically the role of water, we have designed a general computational protocol based on the potential of mean force to compute the thermodynamics of water molecules at the protein–ligand interface for two SH2 domain complexes of the Src kinase, those bound to the two peptides Ac‐PQpYEpYI‐NH2 and Ac‐PQpYIpYV‐NH2 where pY indicates a phosphotyrosine. These two peptides were chosen because they have similar binding affinities but very different entropic/enthalpic thermodynamic binding signatures, indicating different interactions with solvent. We find that the isoleucine to valine mutation at position +3 (the third amino acid C‐terminal to pY) in the ligand has only limited impact on the water structure. By contrast, the glutamic acid to isoleucine mutation at position +1 has a significant impact by not only abrogating a local hydrophilic binding site but, more importantly and surprisingly, inducing a favorable nonlocal entropic contribution from the water molecules around the phophorylated tyrosine at the +2 position. Our study demonstrates the validity of the method reported here for exploring the thermodynamic solvation landscape of protein–protein interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis
Authors: Vivan Ana Luiza , Caceres Rafael Andrade , Beltran Abrego Jose Ramon , Borges Júlio César , Neto João Ruggiero , Ramos Carlos H.I , de Azevedo Walter Filgueira , Basso Luiz Augusto , Santos Diógenes Santiago 
Published: April 2008

AbstractTuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure‐based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X‐ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT. A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT is stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Analysis of the structure of human apo‐S100B at low temperature indicates a unimodal conformational distribution is adopted by calcium‐free S100 proteins
Authors: Malik Shahid , Revington Matthew , Smith Steven P. , Shaw Gary S. 
Published: April 2008

AbstractS100B is one of the best‐characterized members of the calcium‐signaling S100 protein family. Most S100 proteins are dimeric, with each monomer containing two EF‐hand calcium‐binding sites (EF1, EF2). S100B and other S100 proteins respond to calcium increases in the cell by coordinating calcium and undergoing a conformational change that allows them to interact with a variety of cellular targets. Although several three dimensional structures of S100 proteins are available in the calcium‐free (apo‐) state it has been observed that these structures appear to adopt a wide range of conformations in the EF2 site with respect to the positioning of helix III, the helix that undergoes the most dramatic calcium‐induced conformational change. In this work, we have determined the structure of human apo‐S100B at 10°C to examine whether temperature might be responsible for these structural differences. Further, we have used this data, and other available apo‐S100 structures, to show that despite the range of interhelical angles adopted in the apo‐S100 structures, normal Gaussian distributions about the mean angles found in the structure of human apo‐S100B are observed. This finding, only obvious from the analysis of all available apo‐S100 proteins, provides direct structural evidence that helix III is a loosely packed helix. This is likely a necessary functional property of the S100 proteins that facilitates the calcium‐induced conformational change of helix III. In contrast, the calcium‐bound structures of the S100 proteins show significantly smaller variability in the interhelical angles. This shows that calcium binding to the S100 proteins causes not only a conformational change but results in a tighter distribution of helices within the EF2 calcium binding site required for target protein interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Evaluation of the environmental fate of thymol and phenethyl propionate in the laboratory
Authors: Hu Dingfei , Coats Joel 
Published: April 2008

AbstractBACKGROUND: The natural monoterpenoid pesticides thymol and phenethyl propionate (PEP) are used indoors and outdoors, but their fate in the environment has not been reported. In order better to understand their impact on the environment, water metabolism and soil metabolism studies were conducted with thymol and PEP at a concentration of 10 µg g−1 in water and in soil under laboratory conditions.RESULTS: Dissipation half‐lives of thymol and PEP were 16 and 5 days in water and 5 and 4 days in soil. 2‐Phenylethanol and 2‐(4‐hydroxyphenyl)ethanol were detected as primary degradation products of PEP. Over time, a considerable volatilization loss of thymol, but not of phenethyl propionate, was found in the 1 month study under the experimental conditions used. Less than 6% of thymol and PEP were detected as bound residues, and less than 3% were mineralized during the 30 day study.CONCLUSION: In order to maximize the pesticidal effect, more attention should be paid to the temperature for thymol than for PEP when they are being applied, owing to the high volatility of the former. Thymol and PEP pose low risks to the ecosystem because of their rapid dissipation and low bound residues in the environment. Copyright © 2008 Society of Chemical Industry
Long term exposure effect of a unique metabolic nutrition system containing a diverse group of phytochemicals on serum chemistry and genomic and non‐genomic changes in the liver of female B6C3F1 mice
Authors: Ray Sidhartha D. , Parmar Mayur , Syed Ismail , Rathod Jasmine , Zinkovsky Daniel , Bulku Elida , Gigliotti Joseph , Hackman Robert M. , Stohs Sidney J. 
Published: April 2008

AbstractThe nutritional value and therapeutic benefits coupled with presumed safety have heightened interest in the use of custom designed dietary supplements. Their use has increased substantially since the passage of the 1994 Dietary Supplement Health Education Act. However, few well‐controlled studies have been conducted to assess the safety and potential adverse effects of dietary supplements. MNSO (MNS Orange‐AdvoCare®) is a unique combination of vitamins, minerals, omega‐3 fatty acids and herbal extracts designed to provide a strong foundation of nutritional support, enhance thermogenesis, heighten energy levels and improve immune status. This investigation was designed to explore the safety and toxic effects, if any, of 12 months of continuous exposure to the ephedra and caffeine containing MNSO on serum chemistry and histopathology of seven vital target organs in female B6C3F1 mice. MNSO is enriched with extracts of citrus, Ephedra, Ginkgo, green tea and Ocimum. In this study, mice were fed control (‐MNSO) or MNSO (1×–10×, 1× = daily human dose) diets. Blood was collected from all groups including the control every 4 months for serum chemistry analysis (enzyme, lipid, carbohydrate, electrolyte profiles), and liver tissue was collected for tissue biochemistry and histopathology. Multiple biochemical parameters included: (i) determination of oxidative stress via lipid peroxidation and (ii) assessment of genomic integrity via DNA fragmentation. In addition, food consumption and body weight changes were also monitored biweekly. The data showed that 12 months ingestion of 10×‐MNSO did not significantly influence organ histopathology, alter the normal serum chemistry profile or any of the crucial tissue biochemistry. MNSO‐exposed animals were more active, consumed more food and were relatively leaner compared with the controls. This study indicates that a caffeine and ephedra containing metabolic nutrition system is non‐toxic and non‐hepatotoxic in mice at up to 10× the human consumption dose of ephedra. Copyright © 2008 John Wiley & Sons, Ltd.
Biphasic effects of Morus alba leaves green tea extract on mice in chronic forced swimming model
Authors: Sattayasai Jintana , Tiamkao Siriporn , Puapairoj Prapawadee 
Published: April 2008

AbstractIn this study, the effects of an aqueous extract of Morus alba leaves green tea (ME) on mouse behaviors (depression, anxiety, climbing activity and thermal response), muscle coordination and muscle strength were studied. Male IRC mice received a single intraperitoneal injection of either the ME, desipramine or diazepam. Thirty minutes after injection, the mice were tested in all experimental models. A significant antidepressant‐like effect could be detected in the animals receiving either 100 or 200 mg/kg ME. The effect of 200 mg/kg ME in decreasing the immobility time was comparable to 10 mg/kg desipramine. With higher dose (1000 mg/kg), a significant increase in immobility time could be observed. In the elevated plus maze, no increase in time in the open arm could be observed in mice treated with ME at either 100 or 200 mg/kg. However, high doses of ME (500 or 1000 mg/kg) decreased both time in the open arm and the number of entries in the maze. No change in thermal response could be seen in mice treated with ME at doses up to 500 mg/kg, however, at 1000 mg/kg, the response time to heat was increased significantly. The ME at either 500 or 1000 mg/kg also decreased muscle coordination, strength and climbing activity significantly when compared with the control. This study suggests that ME possesses an antidepressant‐ without an anxiolytic‐like effect, however, at high doses, the extract might show the sedative effect and alter other functions such as muscle strength, animal activity in the maze and pain response. Copyright © 2008 John Wiley & Sons, Ltd.