bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome analysis of adipogenesis
Authors: Welsh Gavin I. , Griffiths Matthew R. , Webster Kenneth J. , Page Martin J. , Tavaré Jeremy M. 
Published: March 2004

AbstractAdipose tissue plays a crucial endocrine role in controlling whole body glucose homeostasis and insulin sensitivity. Given the substantial rise in obesity and obesity‐related diseases such as diabetes, it is important to understand the molecular basis of adipocyte differentiation and its control. Many studies have successfully exploited gene array technology to monitor changes in the profile of expressed genes during adipocyte differentiation, although this method only measures changes at the level of individual mRNA species. Using two‐dimensional polyacrylamide gel electrophoresis, high‐throughput image analysis, and candidate picking coupled with sequencing mass spectrometry, we have followed the changes in protein expression profile that occur during the differentiation of 3T3‐L1 fibroblasts into adipocytes in response to dexamethasone, isobutyl methyl xanthine and insulin, or to the PPARγ agonist, ciglitazone. Using this technique we have found alterations in the profile of over 2000 protein species during adipogenesis. Our studies reveal previously unknown alterations during adipogenesis in the expression or mobility (on sodium dodecyl sulfate‐polyacrylamide gel electrophoresis) of coactosin, which promotes actin filament destabilization, several signalling molecules, including RhoGDI‐1, RhoGDI‐2 and EHD1, and NEDD5 a protein involved in cytokinesis.
Modulation of androgen receptor‐dependent transcription by resveratrol and genistein in prostate cancer cells
Authors: Gao Shen , Liu Guo‐Zhen , Wang Zhengxin 
Published: March 2004

AbstractBACKGROUNDThe androgen receptor (AR) is a ligand‐activated transcription factor that mediates the biological responses of androgens in the prostate gland. This study focuses on the chemopreventive agents, resveratrol and genistein, on AR‐mediated transcription in prostate cancer cells.RESULTSWe found that resveratrol and genistein activated AR‐driven gene expression at low concentrations, whereas they repressed the AR‐dependent reporter gene activity at high concentrations. We determined that resveratrol and genistein induced AR‐driven gene expression by activating the Raf–MEK–ERK kinase pathway. The ERK1 kinase phosphorylated the AR on multiple sites in vitro, but this phosphorylation event did not contribute to the resveratrol‐induced AR transactivation.CONCLUSIONSIn vitro and in vivo studies have indicated that resveratrol and genistein are promising chemopreventive agents. Given the clear evidence that AR pathways are involved in the development and progression of prostate cancer, these data showed that the ability to modulate AR function would contribute the observed chemopreventive activity of resveratrol and genistein. © 2004 Wiley‐Liss, Inc.
Purification of the keratan sulfate proteoglycan expressed in prostatic secretory cells and its identification as lumican
Authors: Holland John W. , Meehan Katie L. , Redmond Sharon L. , Dawkins Hugh J.S. 
Published: March 2004

AbstractBACKGROUNDSecretory epithelial cells of human prostate contain a keratan sulfate proteoglycan (KSPG) associated with the prostatic secretory granules (PSGs). The proteoglycan has not been identified, but like the PSGs, it is lost in the early stages of malignant transformation.METHODSAnion exchange and affinity chromatography were used to purify KSPG from human prostate tissue. Enzymatic deglycosylation was used to remove keratan sulfate (KS). The core protein was isolated using 2D gel electrophoresis, digested in‐gel with trypsin, and identified by peptide mass fingerprinting (PMF).RESULTSThe purified proteoglycan was detected as a broad smear on Western blots with an apparent molecular weight of 65–95 kDa. The KS moiety was susceptible to digestion with keratanase II and peptide N‐glycosidase F defining it as highly sulfated and N‐linked to the core protein. The core protein was identified, following deglycosylation and PMF, as lumican and subsequently confirmed by Western blotting using an anti‐lumican antibody.CONCLUSIONSThe KSPG associated with PSGs in normal prostate epithelium is lumican. While the role of lumican in extracellular matrix is well established, its function in the prostate secretory process is not known. It's potential to facilitate packaging of polyamines in PSGs, to act as a tumor suppressor and to mark the early stages of malignant transformation warrant further investigation. © 2004 Wiley‐Liss, Inc.
Enhanced invasion of hormone refractory prostate cancer cells through hepatocyte growth factor (HGF) induction of urokinase‐type plasminogen activator (u‐PA)
Authors: Hall Christopher L. , Tsan Rachel , Mugnai Gabriele , Mazar Andrew , Radinsky Robert , Pettaway Curtis A. 
Published: March 2004

AbstractBACKGROUNDIncreased expression of the hepatocyte growth factor (HGF) receptor (MET) is associated with high‐grade prostatic adenocarcinoma and metastasis. However, the mechanism through which MET signaling contributes to prostate cancer (CaP) metastasis remains unclear.METHODSHuman PC‐3 CaP cells and in vivo selected, isogeneic variant cells of increasing metastatic potential (PC‐3M, PC‐3M‐Pro4, and PC‐3M‐LN4) were used to investigate the effect of HGF on CaP cell growth, protease production, and invasion. Cell‐free urokinase‐type plasminogen activator (u‐PA) expression and function following HGF treatment were analyzed by Western blot, ELISA, and casein/plasminogen zymography. In vitro invasion stimulated by HGF was measured using Matrigel‐coated invasion chambers.RESULTSBoth mRNA and functional protein for MET were detected in each of the CaP cell lines. HGF treatment (0–40 ng/ml) weakly increase proliferation, however, HGF induced soluble u‐PA protein and activity 3‐fold in the metastatic variant cells. HGF significantly stimulated the invasion of highly metastatic PC‐3M‐LN4 cells through Matrigel and treatment with specific urokinase receptor inhibitors diminished the HGF‐stimulated invasion in a dose‐dependent manner.CONCLUSIONSThese results demonstrate the biological significance of u‐PA up‐regulation in response to HGF in highly metastatic hormone refractory CaP cells. © 2004 Wiley‐Liss, Inc.
Combination therapy with vitamins C plus E inhibits survivin and human prostate cancer cell growth
Authors: Gunawardena Kushlani , Campbell L. David , Meikle A. Wayne 
Published: March 2004

AbstractBACKGROUNDWe postulated that combinations of C and E vitamins modulate the antioxidant network and blocks survivin gene expression in androgen‐responsive and non‐responsive human prostate cancer cell (HPCC) lines.METHODSALVA‐101 and DU‐145 cell growth and apoptosis were estimated using the Cell Titer 96 AQ and cell death detection ELISA. Reverse transcription‐polymerase chain reaction, Western blot and electrophoretic mobility shift assay were used to quantify survivin mRNA, protein, nuclear factor kappa B (NF‐κB), and activator protein‐1 (AP‐1).RESULTSAll the tested combinations of vitamins C and E (25–100 μM, 72 hr) reduced cell growth (4–83%). Vitamin C enhanced the growth suppressive effect of vitamin E. Apoptosis was enhanced (25–45%) (vitamins = 100 μM, 24 hr). Survivin mRNA was decreased (26–29%) (vitamins = 250 μM, 24 hr), and survivin protein was decreased (>90%) (vitamins = 100 μM, 72 hr). NF‐κB and AP‐1 activities were increased (vitamins = 100 μM, 24 hr).CONCLUSIONSThe combinations of vitamins C and E are potent inducers of apoptosis in HPCC and suppressers of surviving, an antiapoptotic factor. © 2004 Wiley‐Liss, Inc.
Upregulation and Nuclear Recruitment of HDAC1 in Hormone Refractory Prostate Cancer
Authors: Halkidou Kalipso , Gaughan Luke , Cook Susan , Leung Hing Y. , Neal David E. , Robson Craig N. 
Published: March 2004

AbstractBACKGROUNDHistone deacetylase 1 (HDAC1) is a co‐repressor involved in differentiation and proliferation control. It is upregulated in malignant compared to benign tissue, and targets a number of transcription factors including p53.METHODSBy immunohistochemistry, HDAC1 protein expression was investigated in human prostate specimens and the CWR22 mouse xenograft model. Flow cytometry and deconvolution immunofluorescence were also performed.RESULTSHDAC1 was upregulated in pre‐malignant and malignant lesions, with the highest increase in expression in hormone refractory (HR) cancer. Using the CWR22 xenograft model we showed androgen dependent regulation of HDAC1. HDAC1 overexpression led to a significant increase in proliferation and a shift towards the undifferentiated cytokeratin (CK) profile in a PC3M derivative clone constitutively expressing HDAC1.CONCLUSIONThis study underlines the importance of HDAC1 in cell proliferation and the development of prostate cancer (CaP) and proposes a mechanism for HDAC1 nuclear recruitment. HDAC1 may constitute a crucial therapeutic target particularly in the most lethal phase of androgen independence. © 2004 Wiley‐Liss, Inc.
Androgen responsiveness of Renilla luciferase reporter vectors is promoter, transgene, and cell line dependent
Authors: Mulholland David J. , Cox Michael , Read Jason , Rennie Paul , Nelson Colleen 
Published: March 2004

AbstractRenilla based reporters are frequently used as transfection controls for luciferase transcriptional reporter assays. However, recent evidence suggests that a commonly used reporter (HSV‐thymidine kinase driven Renilla) is responsive to androgen receptor (AR) and glucocorticoid receptors in the presence of the cognate ligands, dihydrotestosterone (DHT) and dexamethasone (DEX), respectively [1]. We further validate this important technical difficulty by illustrating that in LNCaP prostate cancer cells, spurious Renilla luciferase activity is a function of (a) the promoter driving Renilla expression, (b) the presence of co‐transfected transgenes, and (c) the androgen responsiveness of the cell line used. Using inhibitors of transcription and translation we showed that transcript interference or translational modulation is not a major means by which androgens affect Renilla luciferase activity. As luciferase reporter assays are a frequent means of studying transcriptional co‐regulation in the highly androgen dependent LNCaP cell line, our data serves as a cautionary note that alternative normalization techniques should be employed to avoid misinterpretation of data. © 2004 Wiley‐Liss, Inc.
Using the Triad Approach to expedite the acquisition of an Abbott district school site
Authors: Ellerbusch Fred , Mack James , Shim Jeong Seop 
Published: March 2004

AbstractThe Triad Approach was field‐tested to determine if characterization objectives could be met for a
brownfields property that had been identified as a future elementary school site. The new school is in response to
a New Jersey Supreme Court ruling (the Abbott decision) that directed the state of New Jersey to fund
school construction in poorer districts to expand physical facilities to relieve overcrowding. The Triad Approach
is promoted by the United States Environmental Protection Agency as a process that has the potential to improve
the timeliness and efficiency of site characterization, and the New Jersey Department of Environmental Protection
(NJDEP) recently issued a policy statement supporting its potential. Aggressive school construction
deadlines are contingent on property acquisitions that are relatively faster than the traditional investigatory
process. In addition, given the future sensitive population, the investigations must be thorough. This case study
is among the first studies to document the use of the Triad Approach for a future school site. The Triad Approach
was used to define site conditions for six areas of concern in a two‐month time frame (from the start
of the planning process to completed investigation). © 2004 Wiley Periodicals, Inc.
In Situ flushing of contaminated soils from a refinery: Organic compounds and metal removals
Authors: Iturbe Rosario , Flores Carlos , Chávez Claudia , Ramírez Adriana , Torres Luis G. 
Published: March 2004

AbstractThis article demonstrates the applicability of in situ flushing for the remediation of soil
contaminated with petroleum hydrocarbons at a Mexican refinery. The initial average total petroleum hydrocarbon
(TPH) concentration for the demonstration field test was 55,156 g/kg. After six weeks of
in situ flushing with alternate periods of water and water/surfactant, an average
concentration of 1,407 mg/kg was reached, achieving a total removal efficiency of 98 percent. At the end of
the process, no hydrocarbons such as diesel; gasoline; benzene, toluene, ethyl benzene, and xylene
(BTEX); or petroleum aromatic hydrocarbons (PAHs) were found. Iron washing achieved a
removal efficiency of 70 percent, and for vanadium, the removal efficiency was 94.4 percent. The volume of soil
treated was 41.6 m3 (38 m2), equivalent to 69.5 tons of soil. A rough
calculation of the process costs estimated a total cost of $104.20/m3
($114.00/m2). Our research indicates that there are a few studies demonstrating
in situ flushing experiences under field conditions where both organic (TPH, diesel, gasoline, PAHs,
BTEX) and metal (iron and vanadium) removals are reported. © 2004 Wiley Periodicals,
Inc.
Control of variable‐speed wind turbines by LPV gain scheduling
Authors: Bianchi F. D. , Mantz R. J. , Christiansen C. F. 
Published: March 2004

AbstractThis article considers gain‐scheduling control of variable‐speed wind energy conversion systems (WECS) in the context of linear parameter‐varying (LPV) systems. The typical problems of the classic gain‐scheduling techniques, such as stability guarantees, undesirable transient responses in the controller commutations and arduous design procedures, can be avoided with this new formulation. A model of a variable‐speed WECS expressed in LPV form and an optimal LPV gain‐scheduling control strategy are presented. Copyright © 2004 John Wiley & Sons, Ltd.
Power system frequency response from fixed speed and doubly fed induction generator‐based wind turbines
Authors: Holdsworth L. , Ekanayake J. B. , Jenkins N. 
Published: March 2004

AbstractThroughout Europe there is an increasing trend of connecting high penetrations of wind turbines to the transmission networks. This has resulted in transmission system operators revising their grid code documents for the connection of large wind farms. These specifications require large MW capacity wind farms to have the ability to assist in some of the power system control services currently carried out by conventional synchronous generation. These services include voltage and frequency control. It is now recognized that much of this new wind generation plant will use either fixed speed induction generator (FSIG)‐ or doubly fed induction generator (DFIG)‐based wind turbines. The addition of a control loop to synthesize inertia in the DFIG wind turbine using the power electronic control system has been described. The possibility of deloading wind turbines for frequency response using blade pitch angle control is discussed. A pitch control scheme to provide frequency response from FSIG and DFIG wind turbines is also described. A case study of an FSIG wind turbine with frequency response capabilities is investigated. Copyright © 2004 John Wiley & Sons, Ltd.
Power loss in the upper cut‐out wind speed interval
Authors: Kristensen L. , Højstrup J. , Rathmann O. 
Published: March 2004

AbstractTime series of mean wind speeds at several sites in Denmark have been used to estimate the power loss for wind turbines in the wind speed interval from where the operation has to stop at high winds to where a lower wind speed allows the operation to resume. For inland wind turbines the fractional loss is less than 0·25%. For offshore wind turbines it may be as high as about 1·5%. To facilitate the estimation of ‘dead zone’ power loss for offshore wind turbines, an engineering model for the sea surface state has been developed on the basis of a generalization of Charnock's roughness model and the geostrophic drag law. This model predicts the surface friction velocity and the surface roughness as functions of the geostrophic wind speed and the length of the water fetch. Copyright © 2004 John Wiley & Sons, Ltd.
Reactive oxygen species may influence the heat shock response and stress tolerance in the yeast Saccharomyces cerevisiae
Authors: Moraitis Christos , Curran Brendan P. G. 
Published: March 2004

AbstractModerate levels of reactive oxygen species (ROS) have been implicated as second messengers in a number of biochemical pathways, and in animal cells have been associated with the activation of the heat shock response (HSR). Here, using an intracellular probe, we demonstrate that differential accumulation of ROS in the yeast Saccharomyces cerevisiae is strongly associated with differential induction of an HS reporter gene over a range of heat shock temperatures. There was a good correlation between cellular ROS levels and the levels of HS‐induced reporter gene expression between 37 °C and 44 °C, both reaching maximal values at 41 °C. Furthermore, the addition of 150 µM H2O2 to the yeast cells during heat treatment resulted in a 3 °C decrease in the temperature required for maximal induction of the HS expression vector—an increased HS sensitivity that corresponded to a concomitant increase in ROS levels at these lower HS temperatures. Conversely, cells treated with 10 mM of the antioxidant ascorbic acid required a temperature that was 2 °C above that required in untreated controls for maximal induction of the HS expression vector. This decreased HS sensitivity corresponded to a decrease in ROS levels at these higher HS temperatures. Finally, cell viability assays reveal that intrinsic thermotolerance remains high in control cells despite concomitant decreases in HS‐reporter gene expression and ROS accumulation between 41 °C and 44 °C. We conclude that the sensitivity of the yeast HSR is strongly associated with ROS accumulation, and suggest that ROS‐mediated signalling ensures cooperation between the HS and the antioxidant responses. Copyright © 2004 John Wiley & Sons, Ltd.
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
Authors: Ma Hong-Wu , Zhao Xue-Ming , Yuan Ying-Jin , Zeng An-Ping 
Published: March 2004

Abstract
Motivation: Metabolic networks are organized in a modular, hierarchical manner. Methods for a rational decomposition of the metabolic network into relatively independent functional subsets are essential to better understand the modularity and organization principle of a large-scale, genome-wide network. Network decomposition is also necessary for functional analysis of metabolism by pathway analysis methods that are often hampered by the problem of combinatorial explosion due to the complexity of metabolic network. Decomposition methods proposed in literature are mainly based on the connection degree of metabolites. To obtain a more reasonable decomposition, the global connectivity structure of metabolic networks should be taken into account.
Results: In this work, we use a reaction graph representation of a metabolic network for the identification of its global connectivity structure and for decomposition. A bow-tie connectivity structure similar to that previously discovered for metabolite graph is found also to exist in the reaction graph. Based on this bow-tie structure, a new decomposition method is proposed, which uses a distance definition derived from the path length between two reactions. An hierarchical classification tree is first constructed from the distance matrix among the reactions in the giant strong component of the bow-tie structure. These reactions are then grouped into different subsets based on the hierarchical tree. Reactions in the IN and OUT subsets of the bow-tie structure are subsequently placed in the corresponding subsets according to a ‘majority rule’. Compared with the decomposition methods proposed in literature, ours is based on combined properties of the global network structure and local reaction connectivity rather than, primarily, on the connection degree of metabolites. The method is applied to decompose the metabolic network of Escherichia coli. Eleven subsets are obtained. More detailed investigations of the subsets show that reactions in the same subset are really functionally related. The rational decomposition of metabolic networks, and subsequent studies of the subsets, make it more amenable to understand the inherent organization and functionality of metabolic networks at the modular level.
Supplementary Information: http://genome.gbf.de/bioinformatics/
Normalization of single-channel DNA array data by principal component analysis
Authors: Stoyanova Radka , Querec Troy D. , Brown Truman R. , Patriotis Christos 
Published: March 2004

Abstract
Motivation: Detailed comparison and analysis of the output of DNA gene expression arrays from multiple samples require global normalization of the measured individual gene intensities from the different hybridizations. This is needed for accounting for variations in array preparation and sample hybridization conditions.
Results: Here, we present a simple, robust and accurate procedure for the global normalization of datasets generated with single-channel DNA arrays based on principal component analysis. The procedure makes minimal assumptions about the data and performs well in cases where other standard procedures produced biased estimates. It is also insensitive to data transformation, filtering (thresholding) and pre-screening.
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins
Authors: Guda Chittibabu , Fahy Eoin , Subramaniam Shankar 
Published: March 2004

Abstract
Motivation: Currently available methods for the prediction of subcellular location of mitochondrial proteins rely largely on the presence of mitochondrial targeting signals in the protein sequences. However, a large fraction of mitochondrial proteins lack such signals, making those tools ineffective for genome-scale prediction of mitochondria-targeted proteins. Here, we propose a method for genome-scale prediction of nucleus-encoded mitochondrial proteins. The new method, MITOPRED, is based on the Pfam domain occurrence patterns and the amino acid compositional differences between mitochondrial and non-mitochondrial proteins.
Results: MITOPRED could predict mitochondrial proteins with 100% specificity at a 44% sensitivity rate and with 67% specificity at 99% sensitivity. Additionally, it was sufficiently robust to predict mitochondrial proteins across different eukaryotic species with similar accuracy. Based on Matthews correlation coefficient measure, the prediction performance of MITOPRED is clearly superior (0.73) to those of the two popular methods TargetP (0.51) and PSORT (0.53). Using this method, we predicted the nucleus-encoded mitochondrial proteins from six complete genomes (three invertebrate, two vertebrate and one plant species) and estimated the total number in each genome. In human, our method estimated the existence of 1362 mitochondrial proteins corresponding to 4.8% of the total proteome.
Availability: MITOPRED program is freely accessible at http://mitopred.sdsc.edu. Source code is available on request from the authors.
Supplementary information: Training data sets are also available at http://mitopred.sdsc.edu