bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive proteomic and transcriptomic analysis reveals early induction of a protective anti‐oxidative stress response by low‐dose proteasome inhibition
Authors: Bieler Sven , Meiners Silke , Stangl Verena , Pohl Thomas , Stangl Karl 
Published: June 2009

AbstractEffective inhibition of the proteasome by high doses of proteasome inhibitors induces apoptotic cell death. In contrast, partial proteasome inhibition by low inhibitor doses mediates a protective cellular stress response. The early targets and mediators of these dose‐dependent effects of proteasome inhibitors are unknown. Primary human umbilical cord vein endothelial cells were treated with low and high doses of the proteasome inhibitor MG132 for 2 h. In a combined 2‐DE and MS approach, we identified more than 20 new targets of proteasome inhibition. These proteins are involved in cell cycle regulation, signaling, cytoskeletal rearrangement, and cellular stress response. Accompanying Affymetrix analysis revealed that these proteins are not regulated on the transcriptional level but are mainly stabilized by proteasome inhibition. The proteasome‐dependent accumulation of the anti‐oxidative sensor proteins DJ‐1, peroxiredoxin‐1 and ‐6 was accompanied by dose‐dependent induction of oxidative stress after 2 h of proteasome inhibition and contributed to the differential transcriptional stress response to low‐ and high‐dose proteasome inhibition: Whereas low‐dose proteasome inhibition induces a transcriptional profile reminiscent of a physiological stress response that preconditions and protects endothelial cells from oxidative stress, high inhibitor doses induce massive transcriptional dysregulation and pronounced oxidative stress triggering apoptosis.
Quantitative analysis of phosphopeptides in search of the disease biomarker from the hepatocellular carcinoma specimen
Authors: Lee Hyoung‐Joo , Na Keun , Kwon Min‐Seok , Kim Hoguen , Kim Kyoung Sik , Paik Young‐Ki 
Published: June 2009

AbstractReversible phosphorylation of proteins is the most common PTM in cell‐signaling pathways. Despite this, high‐throughput methods for the systematic detection, identification, and quantification of phosphorylated peptides have yet to be developed. In this paper, we describe the establishment of an efficient online titaniuim dioxide (TiO2)‐based 3‐D LC (strong cationic exchange/TiO2/C18)‐MS3‐linear ion trap system, which provides fully automatic and highly efficient identification of phosphorylation sites in complex peptide mixtures. Using this system, low‐abundance phosphopeptides were isolated from cell lines, plasma, and tissue of healthy and hepatocellular carcinoma (HCC) patients. Furthermore, the phosphorylation sites were identified and the differences in phosphorylation levels between healthy and HCC patient specimens were quantified by labeling the phosphopeptides with isotopic analogs of amino acids (stable isotope labeling with amino acids in cell culture for HepG2 cells) or water (HO for tissues and plasma). Two examples of potential HCC phospho‐biomarkers including plectin‐1(phopho‐Ser‐4253) and alpha‐HS‐glycoprotein (phospho‐Ser 138 and 312) were identified by this analysis. Our results suggest that this comprehensive TiO2‐based online‐3‐D LC‐MS3‐linear ion trap system with high‐throughput potential will be useful for the global profiling and quantification of the phosphoproteome and the identification of disease biomarkers.
Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry
Authors: de Souza Gustavo A. , Søfteland Tina , Koehler Christian J. , Thiede Bernd , Wiker Harald G. 
Published: June 2009

AbstractMycobacterium leprae has undergone extensive degenerative evolution, with a large number of pseudogenes. It is also the organism with the greatest divergence between gene annotations from independent institutes. Therefore, M. leprae is a good model to verify the currently predicted coding sequence regions between different annotations, to identify new ones and to investigate the expression of pseudogenes. We submitted a total extract of the bacteria isolated from Armadillo to Gel‐LC‐MS/MS using a linear quadrupole ion trap‐Orbitrap mass spectrometer. Spectra were analyzed using the Leproma (1614 genes and 1133 pseudogenes) and TIGR (5446 genes) databases and a database containing the full genome translation. We identified a total of 1046 proteins, including five proteins encoded by previously predicted pseudogenes, which upon closer inspection appeared to be proper genes. Only 11 of the additional annotations by TIGR were verified. We also identified six tryptic peptides from five proteins from regions not considered to be coding sequences, in addition to peptides from two unannotated gene candidates that overlap with other genes. Our data show that the Leproma annotation of M. leprae is quite accurate, and there were no peptide observations corresponding to true pseudogenes, except for a new gene candidate, overlapping with an essential enolase on the complementary strand.
2‐D DIGE analysis implicates cytoskeletal abnormalities in psychiatric disease
Authors: English Jane A. , Dicker Patrick , Föcking Melanie , Dunn Michael J. , Cotter David R. 
Published: June 2009

AbstractThe mechanisms underlying white matter changes in psychiatric disease are not known. We aimed to characterise the differential protein expression in deep white matter from the dorsolateral prefrontal cortex from 35 schizophrenia, 35 bipolar disorder, and 35 control subjects, from the Stanley Array Collection. We used 2‐D DIGE to profile for protein expression changes in the brain. We found 70 protein spots to be significantly differentially expressed between disease and control subjects (ANCOVA, p<0.05), 46 of which were subsequently identified by LC‐MS/MS. The proteins identified included novel disease candidates as well as proteins that have previously been reported as abnormal in schizophrenia, thus reinforcing their association with the disease. Furthermore, we confirmed the direction of change for three proteins using ELISA, namely neurofilament‐light, amphiphysin II, and Rab‐GDP‐α, in a subset of the Stanley Array Collection. In addition, altered expression of neurofilament‐light, amphiphysin II, and Rab‐GDP‐α was not observed in the cortex of mice chronically treated with haloperidol, making it less likely that these alterations are a consequence of neuroleptic medication. The data presented here strongly suggest disruption of the cytoskeleton and its associated signal transduction proteins in schizophrenia, and to a lesser extent in bipolar disorder.
Synaptic proteome changes in the superior frontal gyrus and occipital cortex of the alcoholic brain
Authors: Etheridge Naomi , Lewohl Joanne M. , Mayfield R. Dayne , Harris R. Adron , Dodd Peter R. 
Published: July 2009

AbstractCognitive deficits and behavioral changes that result from chronic alcohol abuse are a consequence of neuropathological changes that alter signal transmission through the neural network. To focus on the changes that occur at the point of connection between the neural network cells, synaptosomal preparations from post‐mortem human brain of six chronic alcoholics and six non‐alcoholic controls were compared using 2‐D differential in‐gel electrophoresis (DIGE). Functionally affected and spared regions (superior frontal gyrus, SFG, and occipital cortex, OC, respectively) were analyzed from both groups to further investigate the specific pathological response that alcoholism has on the brain. Forty‐nine proteins were differentially regulated between the SFG of alcoholics and the SFG of controls and 94 proteins were regulated in the OC with an overlap of 23 proteins. Additionally, the SFG was compared to the OC within each group (alcoholics or controls) to identify region‐specific differences. A selection was identified by MALDI‐TOF mass spectrometry revealing proteins involved in vesicle transport, metabolism, folding and trafficking, and signal transduction, all of which have the potential to influence synaptic activity. A number of proteins identified in this study have been previously related to alcoholism; however, the focus on synaptic proteins has also uncovered novel alcoholism‐affected proteins. Further exploration of these proteins will illuminate the mechanisms altering synaptic plasticity, and thus neuronal signaling and response, in the alcoholic brain.
Diazinon reduction and partitioning between water, sediment and vegetation in stormwater runoff mitigation through rice fields
Authors: Moore Matthew T , Kröger Robert , Cooper Charles M , Cullum Robert F , Smith, Sammie , Locke Martin A 
Published: July 2009

AbstractBACKGROUND: Contamination of surface waters by pesticides is a concern in the United States and around the world. Innovative mitigation strategies are needed to remediate this potential environmental contaminant. One potential solution is to divert pesticide‐laden drainage or surface water through agricultural rice fields. With a hydroperiod, hydrosoil and hydrophyte (rice), these systems serve essentially as a type of constructed wetland. In both summer and fall experiments, diazinon‐amended water was diverted through two rice ponds at the University of Mississippi Field Station. Likewise, a non‐vegetated control pond was amended with diazinon‐laden water. Water, sediment and plant samples were taken spatially and temporally to determine the distribution of diazinon within systems.RESULTS: Outflow diazinon concentrations decreased significantly (P < 0.05) from inflow in both vegetated ponds for both preharvest and post‐harvest experiments. Although sorption to rice plants was minimal in the overall mass distribution of diazinon (1–3%), temporal data indicated that diazinon concentrations reached the outflow sediment of the non‐vegetated control twice as fast as in either vegetated (rice) system. In both vegetated systems, sediment diazinon concentrations decreased (77 and 100%) from inflow to outflow, while a decrease of <2% was noted in the non‐vegetated control.CONCLUSIONS: Diversion of pesticide‐contaminated water through rice fields demonstrated potential as a low‐cost, environmentally efficient mitigation practice. Studies on these systems are continuing to evaluate the optimal chemical retention time for rice field mitigation, as well as diazinon transfer to rice grain seeds that may be used as a food source. Published in 2009 by John Wiley & Sons, Ltd.
Protective effects of a flavonoid‐rich extract of Hypericum perforatum L. against hydrogen peroxide‐induced apoptosis in PC12 cells
Authors: Zou Yan‐Ping , Lu Yan‐Hua , Wei Dong‐Zhi 
Published: July 2009

AbstractHypericum perforatum L. has been used traditionally as an antidepressant for the treatment of mild to moderate depression. In a previous study, a flavonoid‐rich extract of Hypericum perforatum L. (FEHP) was prepared and its antioxidant activity was determined by a series of models in vitro. In the present study, the protective effects of FEHP against hydrogen peroxide‐induced apoptosis in rat pheochromocytoma line PC12 cells were investigated by MTT assay, lactate dehydrogenase (LDH) release assay, flow cytometry analysis and DNA fragmentation assay. Following a 4 h exposure of PC12 cells to H2O2, a significant decrease in the cell viability and increased levels of LDH release were observed. However, pretreatment of PC12 cells with FEHP prior to H2O2 exposure elevated the cell viability, decreased the levels of LDH release and decreased the occurrence of apoptotic cells. Also, the intensity of H2O2‐induced DNA laddering was inhibited in a dose‐dependent fashion by a DNA fragmentation assay. These results suggested that FEHP possessed protective effects against H2O2‐induced apoptosis in PC12 cells and FEHP might be useful in the treatment of oxidative stress‐related neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. Copyright © 2009 John Wiley & Sons, Ltd.
Hesperidin suppressed proliferations of both Human breast cancer and androgen‐dependent prostate cancer cells
Authors: Lee Choong Jae , Wilson Leslie , Jordan Mary Ann , Nguyen Vy , Tang Jessica , Smiyun Gregory 
Published: July 2009

AbstractHesperidin, a flavonoid derived from citrus fruits, has been reported to show various biological effects including anticancer activity. This study investigated whether hesperidin affected the proliferation of MCF‐7 human breast cancer cells transfected with green fluorescent protein (GFP)/α‐tubulin (MCF‐7‐GFP‐Tubulin cells), androgen‐independent PC‐3 and DU‐145 prostate cancer cells, and androgen‐dependent LNCaP prostate cancer cells. The results were as follows. (1) Hesperidin inhibited the proliferation of MCF‐7‐GFP‐Tubulin cells, probably not through an antimitotic mechanism. (2) Hesperidin also inhibited both basal and testosterone‐induced proliferation of LNCaP cells. (3) However, hesperidin did not significantly affect the cell proliferation of two hormone‐independent prostate cancer cells, PC‐3 and DU‐145. It is concluded that hesperidin can inhibit the proliferation of breast cancer cells through mechanisms other than antimitosis and it is suggested that hesperidin be further investigated for the possible interaction with androgenic receptors and involvement in signaling pathway after receptor binding in prostate cancer cells through future research. Copyright © 2009 John Wiley & Sons, Ltd.
Protective effect of oleanolic acid on gentamicin induced nephrotoxicity in rats
Authors: Patil Chandragouda R. , Jadhav Ramchandra B. , Singh Pushparaj K. , Mundada Sneha , Patil Prabhakar R. 
Published: July 2009

AbstractOleanolic acid is a molecule of current therapeutic interest. In the present study, oleanolic acid isolated from the cuticular epithelium of Viscum articulatum Burm. f. (Viscaceae) was investigated for its protective effects on gentamicin‐induced renal damage in rats. Nephrotoxicity was induced in rats by intraperitoneal injection of gentamicin at a dose of 100 mg/kg/day for 8 days. The effect of Oleanolic acid administered orally at doses 40, 60 and 80 mg/kg/day was assessed biochemically by determination of albumin, urea and creatinine in serum and urine samples and also through histopathological examination of the kidneys.Oleanolic acid protected the rat kidneys from gentamicin‐induced nephrotoxicity as evident from a decrease in the serum and urine levels of creatinine, albumin and urea. Oleanolic acid also protected the rat kidneys from histological alterations induced by gentamicin and also improved the glomerular filtration rate. Compared with an earlier report on intraperitoneal administration of oleanolic acid in paracetamol‐induced nephrotoxicity in rats, the data show that orally administered oleanolic acid also exerted a nephroprotective effect even in the case of a nephrotoxicant such as gentamicin, which directly deteriorates the kidney function without prior metabolism. Copyright © 2009 John Wiley & Sons, Ltd.
Respondent‐driven sampling as Markov chain Monte Carlo
Authors: Goel Sharad , Salganik Matthew J. 
Published: July 2009

AbstractRespondent‐driven sampling (RDS) is a recently introduced, and now widely used, technique for estimating disease prevalence in hidden populations. RDS data are collected through a snowball mechanism, in which current sample members recruit future sample members. In this paper we present RDS as Markov chain Monte Carlo importance sampling, and we examine the effects of community structure and the recruitment procedure on the variance of RDS estimates. Past work has assumed that the variance of RDS estimates is primarily affected by segregation between healthy and infected individuals. We examine an illustrative model to show that this is not necessarily the case, and that bottlenecks anywhere in the networks can substantially affect estimates. We also show that variance is inflated by a common design feature in which the sample members are encouraged to recruit multiple future sample members. The paper concludes with suggestions for implementing and evaluating RDS studies. Copyright © 2009 John Wiley & Sons, Ltd.
Firm‐specific knowledge resources and competitive advantage: the roles of economic‐ and relationship‐based employee governance mechanisms
Authors: Wang Heli C. , He Jinyu , Mahoney Joseph T. 
Published: July 2009

AbstractThe resource‐based view of the firm emphasizes the role of firm‐specific resources, especially firm‐specific knowledge resources, in helping a firm to achieve sustainable competitive advantage. However, the deployment of firm‐specific knowledge often requires key employees to make specialized human capital investments that are not easily redeployable to other settings. Thus, in the absence of effective safeguards and trust building devices, employees with foresight may be reluctant to make such specialized investments. This study explores both economic‐ and relationship‐based governance mechanisms that might mitigate this underinvestment problem. Effective use of these governance mechanisms enables a firm to obtain greater performance from its efforts to deploy firm‐specific knowledge resources. Empirical results further support these key arguments. Copyright © 2009 John Wiley & Sons, Ltd.
Protein‐Based Nanomedicine Platforms for Drug Delivery
Authors: MaHam Aihui , Tang Zhiwen , Wu Hong , Wang Jun , Lin Yuehe 
Published: July 2009

AbstractProtein‐based nanomedicine platforms for drug delivery comprise naturally self‐assembled protein subunits of the same protein or a combination of proteins making up a complete system. They are ideal for drug‐delivery platforms due to their biocompatibility and biodegradability coupled with low toxicity. A variety of proteins have been used and characterized for drug‐delivery systems, including the ferritin/apoferritin protein cage, plant‐derived viral capsids, the small Heat shock protein (sHsp) cage, albumin, soy and whey protein, collagen, and gelatin. There are many different types and shapes that have been prepared to deliver drug molecules using protein‐based platforms, including various protein cages, microspheres, nanoparticles, hydrogels, films, minirods, and minipellets. The protein cage is the most newly developed biomaterial for drug delivery and therapeutic applications. The uniform size, multifunctionality, and biodegradability push it to the frontier of drug delivery. In this Review, the recent strategic development of drug delivery is discussed with emphasis on polymer‐based, especially protein‐based, nanomedicine platforms for drug delivery. The advantages and disadvantages are also discussed for each type of protein‐based drug‐delivery system.magnified image
A Self‐Assembled Protein Nanotube with High Aspect Ratio
Authors: Miranda Frederico F. , Iwasaki Kenji , Akashi Satoko , Sumitomo Koji , Kobayashi Mime , Yamashita Ichiro , Tame Jeremy R. H. , Heddle Jonathan G. 
Published: June 2009

AbstractProduction of a self‐assembled protein nanotube achieved through engineering of the 11mer ring protein trp RNA‐binding attenuation protein is described. The produced mutant protein is able to stack in solution to produce an extremely narrow, uniform nanotube apparently stabilized by a mixture of disulfide bonds and hydrophobic interactions. Assembly is reversible and the length of tube can potentially be controlled. Large quantities of hollow tubes 8.5 nm in overall diameter with lengths varying from 7 nm to over 1 µm are produced. The structure is analyzed using transmission electron microscopy, atomic force microscopy, mass spectrometry, and single‐particle analysis and it is found that component rings stack in a head‐to‐head fashion. The internal diameter of the tube is 2.5 nm, and the amino acid residues lining the central cavity can be mutated, raising the possibility that the tube can be filled with a variety of conducting or semiconducting materials.
Di‐ and Triazaphospholes as Ligands for Ruthenium(II) and Iridium(III) Complexes
Authors: Köhler Brigitte , Kammerer Susanne , Mayer Tobias , Neumann Bernd , Lorenz Ingo‐Peter 
Published: July 2009

AbstractThe reaction of the azaphospholes 5‐methyl‐2‐phenyl‐1,2,3‐diazaphospole (PDAP) and 2‐methyl‐2‐phenyl‐1,2,4,3‐triazaphospole (PTAP) with the dimers [LMCl2]2 (LM = η6‐C6Me6Ru, η5‐C5Me5Ir) of ruthenium(II) and iridium(III) only occurs in presence of nucleophiles such as EtOH or H2O leading to their metal‐coordination after cleavage of the dimers. [(η6‐C6Me6)RuCl2]2 reacts with PDAP and EtOH in the molar ratio 0.5:1:1 to give the phosphorus‐coordinated complex (η6‐C6Me6)RuCl2(P‐PDAP·EtOH) (1). In the case of [(η5‐C5Me5)IrCl2]2, the triazaphosphole PTAP was used in the presence of EtOH or H2O yielding the analogous products (η5‐C5Me5)IrCl2(P‐PTAP·EtOH) (2) or (η5‐C5Me5)IrCl2(P‐PTAP·H2O) (3). In 1–3, the former aromatic azaphosphole (σ2,λ3‐P) has been converted by 1,2 addition of EtOH or H2O to their P=C or P=N double bond with the nucleophiles EtO– and OH– bonded to phosphorus (σ3,λ3‐P). Complexes 1–3 with a piano‐stool configuration were characterized by elemental analysis, 31P NMR spectroscopy and single‐crystal X‐ray diffraction.
Evidence of divergent growth rates among populations of the lizard Anolis carolinensis based on experimental manipulations of egg size
Authors: Goodman Rachel M. 
Published: July 2009

AbstractGeographic variation in body size is of special interest because it affects nearly all aspects of an organism's life. I examined whether differences in body size among four populations of the green anole lizard, Anolis carolinensis, were attributable to maternal investment in egg size and/or growth rates of embryos and juveniles. Larger body size and larger egg size relative to female size in the northern part of the range have been documented in this species, and suggested to be adaptive responses to more extreme winters. The current study confirmed the trends in adult size and egg size in the north, but rejected the trend of larger egg size relative to body size in the south. To control for differences in maternal investment in egg size among populations, I performed yolk removals on eggs from two northern populations to produce comparably sized eggs relative to one southern population. This manipulation was designed to minimize the confounding effect of maternal investment in yolk, the primary energy reserves for eggs, so that intrinsic differences in embryonic growth due to metabolism could be investigated. I found that differences in juvenile and, potentially, embryonic growth rates existed among populations of A. carolinensis, both due to and independent of differences in egg size. Juveniles from the northernmost population were bigger not only due to larger egg size, but also due to faster juvenile growth and possibly differences in developmental stage of oviposition or conversion of egg mass to hatchling mass. Larger body size may hold a number of advantages in northern populations of this species, including starvation resistance through winters and better competitive access to food resources and warmer microhabitats.