bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic analysis of cholangiocarcinoma cell line
Authors: Srisomsap Chantragan , Sawangareetrakul Phannee , Subhasitanont Pantipa , Panichakul Tasanee , Keeratichamroen Siriporn , Lirdprapamongkol Kriengsak , Chokchaichamnankit Daranee , Sirisinha Stitaya , Svasti Jisnuson
Published: March 2004

Cholangiocarcinoma (CCA), a malignant tumor derived from bile duct epithelium, occurs with a higher incidence in tropical countries, such as Thailand. Distinguishing CCA from hepatocellular carcinoma (HCC) of the liver often requires the use of histochemistry, so molecular markers for diagnosis and prognosis are still required. In this study, the two‐dimensional (2‐D) protein map of a Thai human bile duct epithelial carcinoma cell line (HuCCA‐1) has been compared to human hepatocellular carcinoma cell lines (HepG2 and HCC‐S102) and a human breast epithelial cancer cell line (MCF‐7). Our results show that HuCCA‐1 expressed a unique pattern of proteins. Forty‐three major proteins were identified by matching to the map of MCF‐7, and by matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) and electrospray ionization‐tandem MS (ESI‐MS/MS). Cytokeratins CK8 and CK18 were overexpressed in both HuCCA‐1 and HCC, while CK7 and CK19 were only expressed in HuCCA‐1. Four specific proteins with MW/pI 57.2/5.21 (U1, vimentin), 42.2/6.20 (U2), 43.2/6.20 (U3, EF‐TU), and 42.2/6.40 (U4, unidentified) were absent from HepG2. U2 showed high expression in HuCCA‐1, while U1 and U4 showed high expression in HCC‐S102. U2 could be separated in 2 proteins, U2/1 (α‐enolase) and U2/2 (not identified) by using IPG pH 4–7. Galectin‐3 showed high expression level in HuCCA‐1 by 1‐DE immunodetection, and gave only one spot with MW 32.9 kDa and pI 8.29 on 2‐DE immunoblotting, Thus, certain proteins, namely CK7, CK19, U2/2 and galectin‐3, may be good markers useful for differential diagnosis of cholangiocarcinoma compared to hepatocellular carcinoma.
Proteomic determination of metabolic enzymes of the amnion cell: Basis for a possible diagnostic tool?
Authors: Oh Ji‐eun , Fountoulakis Michael , Juranville Jean‐François , Rosner Margit , Hengstschlaeger Markus , Lubec Gert
Published: March 2004

Amniocentesis is a valuable and standard procedure for prenatal diagnosis of genetic or inborn errors of metabolism. Amnion cells are cultivated and chromosomes or proteins can be examined to provide molecular diagnosis. Mainly individual proteins are searched for based upon pedigrees and/or anamnesis. As inborn errors of metabolism involve a vast diversity of metabolic enzymes, we aimed to find a screening method for a large series of metabolic enzymes. Amnion cells were obtained from amniocentesis and subjected to proteomic analysis. We used two‐dimensional gel electrophoresis with in‐gel digestion followed by matrix‐assisted laser desorption/ionization‐time of flight analysis, to identify metabolic enzymes. Furthermore, we compared metabolic proteins in amnion cells from controls with those from Down Syndrome (DS). Enzymes involved in carbohydrate handling, amino acid handling, ­purine metabolism and intermediary metabolism as well as miscellaneous metabolic pathways were detected. Protein levels of several enzymes were significantly deranged in samples obtained from patients with DS. This approach, with the advantage of the concomitant determination of many enzyme proteins, may form the basis for future metabolic screens when amniocentesis is carried out.
A computational method for assessing peptide‐ identification reliability in tandem mass spectrometry analysis with SEQUEST
Authors: Razumovskaya Jane , Olman Victor , Xu Dong , Uberbacher Edward C. , VerBerkmoes Nathan C. , Hettich Robert L. , Xu Ying
Published: March 2004

High‐throughput protein identification in mass spectrometry is predominantly achieved by first identifying tryptic peptides by a database search and then by combining the peptide hits for protein identification. One of the popular tools used for the database search is SEQUEST. Peptide identification is carried out by selecting SEQUEST hits above a specified threshold, the value of which is typically chosen empirically in an attempt to separate true identifications from false ones. These SEQUEST scores are not normalized with respect to the composition, length and other parameters of the peptides. Furthermore, there is no rigorous reliability estimate assigned to the protein identifications derived from these scores. Hence, the interpretation of SEQUEST hits generally requires human involvement, making it difficult to scale up the identification process for genome‐scale applications. To overcome these limitations, we have developed a method, which combines a neural network and a statistical model, for normalizing SEQUEST scores, and also for providing a reliability estimate for each SEQUEST hit. This method improves the sensitivity and specificity of peptide identification compared to the standard filtering procedure used in the SEQUEST package, and provides a basis for estimating the reliability of protein identifications.
Transforming growth factor‐β1‐regulated proteins in human endothelial cells identified by two‐dimensional gel electrophoresis and mass spectrometry
Authors: Lomnytska Marta , Lukiyanchuk Vasyl , Hellman Ulf , Souchelnytskyi Serhiy
Published: March 2004

Transforming growth factor‐β (TGFβ) is a potent regulator of angiogenesis affecting proliferation, differentiation and migration of endothelial cells. The effect of TGFβ on endothelial cells depends on the origin of the cells and on the experimental conditions. Global analysis of TGFβ signalling is expected to unveil mechanisms of this variability and identify novel targets of the growth factor. Here, we report proteome profiling of human microvascular endothelial cells obtained from dermis, which were treated with TGFβ1 and compared to nontreated cells. We identified 54 proteins affected by TGFβ1 using two‐dimensional gel electrophoresis and peptide mass fingerprinting. Thirteen of the identified proteins are involved in various signalling processes. Seven proteins are involved in cytoskeleton rearrangements and six are involved in regulation of metabolism. Ten proteins were identical to predicted hypothetical proteins with no assigned functions. In agreement with the effect of TGFβ1 on components of the cytoskeleton, TGFβ1 induces actin cytoskeleton rearrangements. TGFβ1 also affected expression of E2F6, p57Kip2, G(q)α, hnRNP A1 and myosin light chain proteins as shown by immunoblotting. Down‐regulation of the transcriptional repressor E2F6 by TGFβ1 correlated with a weak growth‐inhibitory activity of TGFβ1 on HMVEC‐d cells. Twenty‐five of the identified proteins have not previously been described as being regulated by TGFβ1, providing new insights into TGFβ1 signalling in endothelial cells.
Mass spectrometric analysis of Plasmodium falciparum erythrocyte membrane protein‐1 variants expressed by placental malaria parasites
Authors: Fried Michal , Wendler Jason P. , Mutabingwa Theonest K. , Duffy Patrick E.
Published: March 2004

Surface proteins from Plasmodium falciparum are important malaria vaccine targets. However, the surface proteins previously identified are highly variant and difficult to study. We used tandem mass spectrometry to characterize the variant antigens (Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1)) expressed on the surface of malaria‐infected erythrocytes that bind to chondroitin sulfate A (CSA) in the placenta. Whereas PfEMP1 variants previously implicated as CSA ligands were detected, in unselected parasites four novel variants were detected in CSA‐binding or placental parasites but not in unselected parasites. These novel PfEMP1 variants require further study to confirm whether they play a role in placental malaria.
Identification of apoptotic tyrosine‐phosphorylated proteins after etoposide or retinoic acid treatment
Authors: Navakauskiene Ruta , Treigyte Grazina , Gineitis Arunas , Magnusson Karl‐Eric
Published: March 2004

A main shortcoming of using HL‐60 cells as a model of granulocyte‐macrophage differentiation is that some cells in the differentiating population undergo apoptosis. To address this issue, we have identified which tyrosine‐phosphorylated proteins are involved in apoptosis and differentiation, respectively. HL‐60 cells were induced specifically to undergo apoptosis with 68 μM etoposide, and to undergo granulocytic differentiation with 1 μM retinoic acid (RA). The corresponding two‐dimensional electrophoretic maps of tyrosine‐phosphorylated proteins from treated cells were compared. In the 8 h etoposide‐treated HL‐60 cell population, 83% of the cells were apoptotic. In the 120 h RA‐treated cells, 50% of the cells were apoptotic. Eighteen cytosolic and nuclear tyrosine‐phosphorylated proteins were found in both the 8 h etoposide‐ and the 120 h RA‐treated cells, but not in the proliferating HL‐60 cell population. Matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry analyses suggested that some of the proteins may be involved in signal transduction pathways (NFκB, GTP‐binding protein, protein disulfide isomerase, Cyclophilin A), others in cell transcriptional and translational control (hnRNP H, hnRNP L, Hsp60, Hp1, Hcc‐1, 26S proteasome beta‐subunit, ATP synthase beta‐chain), and a third group in cell cytoskeleton organization and receptor cycling (profilin, caveolin‐1). An understanding of signal transduction in apoptosis initiation by screening for tyrosine‐phosphorylated proteins associated with apoptosis may provide new targets for the treatment of leukemia.
Nonredundant mass spectrometry: A strategy to integrate mass spectrometry acquisition and analysis
Authors: Scherl Alexander , Francois Patrice , Converset Véronique , Bento Manuela , Burgess Jennifer A. , Sanchez Jean‐Charles , Hochstrasser Denis F. , Schrenzel Jacques , Corthals Garry L.
Published: March 2004

Protein identification using automated data‐dependent tandem mass spectrometry (MS/MS) is now a standard procedure. However, in many cases data‐dependent acquisition becomes redundant acquisition as many different peptides from the same protein are fragmented, whilst only a few are needed for unambiguous identification. To increase the quality of information but decrease the amount of information, a nonredundant MS (nrMS) strategy has been developed. With nrMS, data analysis is an integral part of the overall MS acquisition and analysis, and not an endpoint as typically performed. In this nrMS workflow a matrix assisted laser desorption/ionization‐time of flight‐time of flight (MALDI‐TOF/TOF) instrument is used. MS and restricted MS/MS data are searched and identified proteins are used to generate an “exclusion list”, after in silico digestion. Peptide fragmentation is then restricted to only the most intense ions not present in the exclusion list. This process is repeated until all peaks are accounted for or the sample is consumed. Compared to nanoLC‐MS/MS, nrMS yielded similar results for the analysis of six pooled two‐dimensional electrophoresis (2‐DE) spots. In comparison to standard data‐dependent MALDI‐MS/MS for sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) gel band analysis, nrMS dramatically increased the number of identified proteins. It was also found that this new workflow significantly increased sequence coverage by identifying unexpected peptides, which can result from post‐translational modifications.
Proteome analysis of adipogenesis
Authors: Welsh Gavin I. , Griffiths Matthew R. , Webster Kenneth J. , Page Martin J. , Tavaré Jeremy M.
Published: March 2004

Adipose 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

BACKGROUND

The 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.

RESULTS

We 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.

CONCLUSIONS

In 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

BACKGROUND

Secretory 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.

METHODS

Anion 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).

RESULTS

The 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.

CONCLUSIONS

The 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

BACKGROUND

Increased 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.

METHODS

Human 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.

RESULTS

Both 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.

CONCLUSIONS

These 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

BACKGROUND

We 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.

METHODS

ALVA‐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).

RESULTS

All 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).

CONCLUSIONS

The 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

BACKGROUND

Histone 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.

METHODS

By immunohistochemistry, HDAC1 protein expression was investigated in human prostate specimens and the CWR22 mouse xenograft model. Flow cytometry and deconvolution immunofluorescence were also performed.

RESULTS

HDAC1 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.

CONCLUSION

This 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

Renilla 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

The 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

This 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

This 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

Throughout 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

Time 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

Moderate 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.
WATER UPTAKE AND USE BY MORPHOLOGICALLY CONTRASTING MAIZE/PEA CULTIVARS IN SOLE AND INTERCROPS IN TEMPERATE CONDITIONS
Authors: KANTON R. A. L. , DENNETT M. D.
Published: March 2004

Growth and water use of sole crops and intercrops of morphologically contrasting maize and pea cultivars were measured in two years. The maize cultivars were Nancis with erectophile and Sophy with planophile leaves and the pea cultivars Maro a leafy pea and Princess a semi-leafless pea. In the first part of the season water use was lower for sole maize but intercrops and sole pea used similar amounts of water. By 90 days after sowing, when peas had matured, all crops had used similar amounts of water. Maize had slightly greater water use efficiency than peas. Cultivars Nancis and Princess tended to have greater water use efficiency than Sophy and Maro respectively. Intercrops produced more dry matter than sole crops and therefore had consistently greater water use efficiencies.
FARMERS' PERCEPTION OF THE STRIGA PROBLEM AND ITS CONTROL IN NORTHERN NIGERIA
Authors: EMECHEBE A. M. , ELLIS-JONES J. , SCHULZ S. , CHIKOYE D. , DOUTHWAITE B. , KUREH I. , TARAWALI G. , HUSSAINI M. A. , KORMAWA P. , SANNI A.
Published: March 2004

The parasitic angiosperms, Striga hermonthica and S. gesnerioides, obligate root parasites endemic in sub-Saharan Africa, constitute severe constraints to cereal and legume production in West and Central Africa. Over the years, a range of effective component technologies has been identified for Striga control in Africa. The potential of these technologies has been demonstrated under researcher-managed conditions. To promote farmer testing of the technologies, community workshops were conducted in 42 rural communities in Kaduna State, northern Nigeria. These revealed that agriculture was the main source of livelihood for most households. The three most important crops, maize, sorghum and pearl millet are attacked by S. hermonthica, regarded as the major constraint to crop production, often causing 70–100% crop loss. Farmers recognised two types of Striga damage (underground and aboveground), with greater damage being caused by underground Striga. Farmers attributed increasing incidence and severity of Striga damage to lack of capital, poor soil fertility, infestation of previously uninfested land by Striga seeds, and continuous cropping of host crops. The most widely used among the 15 existing Striga control techniques identified by the farmers were hoe weeding and hand pulling, application of inorganic fertilizer and manure, crop rotations, fallowing, and early planting. In assessing possible control measures farmers considered increased crop yield, reduced Striga reproduction and Striga emergence, greater crop vigour, and increased soil fertility as positive attributes. Negative attributes comprised increased labour requirement, higher costs, increased risk of crop damage or yield reduction, and lower quantity and quality of produce. Overall, a legume-cereal rotation was the most highly rated control option for S. hermonthica management evaluated by the farmers. The implications of these results are examined with respect to farmers' adoption and adaptation of Striga control options beyond the experimental plots.
Warming of the Arctic lower stratosphere by light absorbing particles
Authors: Baumgardner D. , Kok G. , Raga G.
Published: March 2004

Recent measurements of light absorbing particles in the Arctic lower stratosphere show significantly higher mass concentrations of black carbon than were measured in 1992. The difference is primarily a result of measurements with a more quantitative and accurate technique than was previously used. We attribute the large amount of light absorbing material to transport from lower latitude, tropospheric sources rather than increases in aircraft emissions. The calculated heating rate in this aerosol layer, as compared to an atmosphere consisting of only gases, increases by 12% during the winter. This is a result of light absorption by the particles and could perturb the altitude of the local tropopause and affect tropospheric/stratospheric exchange processes.
Disappearing Arctic sea ice reduces available water in the American west
Authors: Sewall Jacob O. , Sloan Lisa Cirbus
Published: March 2004

Recent decreases in Arctic sea ice cover and the probability of continued decreases have raised the question of how reduced Arctic sea ice cover will influence extrapolar climate. Using a fully coupled earth system model, we generate one possible future Arctic sea ice distribution. We use this “future” sea ice distribution and the corresponding sea surface temperatures (SSTs) to run a fixed SST and ice concentration experiment with the goal of determining direct climate responses to the reduction in Arctic sea ice that is projected to occur in the next 50 years. Our results indicate that future reductions in Arctic sea ice cover could significantly reduce available water in the American west and highlight the fact that the most severe impacts of future climate change will likely be at a regional scale.
Electric potential in the low‐Mach‐number quasi‐perpendicular collisionless shock ramp revisited
Authors: Gedalin M. , Balikhin M.
Published: March 2004

Knowledge of the details of the electric field inside the shock is essential forunderstanding ion and electron dynamics. Theoretical modeling of the electric field distribution in the whole structured profile of a quasi‐perpendicular collisionless high‐Mach‐number shock is a difficult problem. Ramp, however, is sufficiently narrow to be analyzed in a simple and efficient way. Behavior of the cross‐shock electric field inside the ramp of low‐Mach‐number shocks and high‐Mach‐number shocks has a number of features which can be considered as common for most shocks. We reconsider the distribution of the cross‐ramp electric potential in low‐Mach‐number shocks in close connection with the ion motion across the ramp. We derive the relation between the electric potential in the ramp and density of transmitted ions taking into account the narrowness of the ramp. The derivation is based on the ion equations of motion and does not require additional model assumptions. The relation is valid (at least as a good approximation) in a wide range of shock parameters and can be applied (with suitable corrections) to high‐Mach‐number shocks as well. If the ion and electron β are moderate, it is possible to establish a useful approximate relation of the potential to the magnetic field in the ramp. We suggest that using the derived relations may allow direct testing of the shock models by comparison of high‐resolution electric field measurements with measurements of ion density and magnetic field across the ramp. On the other hand, the ion and magnetic field measurements may complete the electric field measurements, when they are insufficient alone (e.g., only two components are measured).
On the propagation of low‐frequency fluctuations in the plasma sheet: 1. Cluster observations and magnetohydrodynamic analysis
Authors: Louarn P. , Fruit G. , Budnik E. , Sauvaud J. A. , Jacquey C. , Le Quéau D. , Rème H. , Lucek E. , Balogh A.
Published: March 2004

Low‐frequency pressure and magnetic oscillations observed by Cluster in the plasma sheet are investigated with the aim of determining if they are magnetohydrodynamic (MHD) eigenmodes. We analyze the plasma sheet crossing occurring on 22 August 2001, as the magnetosphere was first quiet and then active, and compare the observations with theoretical results concerning the MHD propagation in a Harris sheet. The theory shows that the eigenmodes have periods scaled by a characteristic time, τ, equal to the ratio between (1) the thickness of the sheet and (2) the sound speed. Using the Cluster 4 spacecraft, we estimate the sheet thickness and determine this characteristic time. It is compared with the typical periods of the fluctuations deduced from a wavelet analysis. During the quiet period, the fluctuations have periods larger than 100 s or 15τ. Discrete MHD eigenmodes with such periods would have wavelengths larger than the distance separating Cluster from Earth (18 RE). Thus they are very unlikely interpreted as freely propagating eigenmodes. However, fluctuations of shorter periods (∼20 s) are observed during and just after the substorm onset. We demonstrate that they are compatible with the fundamental MHD eigenmode (kink‐like mode) of the sheet, with a wavelength of ∼5–6 RE, their direction of propagation being not determined at this stage of the analysis. We thus conclude that freely propagating MHD eigenmodes observable by Cluster would have periods that hardly exceed a minute for typical plasma sheet parameters (thickness of 1 RE, temperature of a few keV).
Seasonal and interannual variability of satellite‐derived chlorophyll pigment, surface height, and temperature off Baja California
Authors: Espinosa‐Carreon T. Leticia , Strub P. T. , Beier Emilio , Ocampo‐Torres Francisco , Gaxiola‐Castro Gilberto
Published: March 2004

Mean fields, seasonal cycles, and interannual variability are examined for fields of satellite‐derived chlorophyll pigment concentrations (CHL), sea surface height (SSH), and sea surface temperature (SST) during 1997–2002. The analyses help to identify three dynamic regions: an upwelling zone next to the coast, the Ensenada Front in the north, and regions of repeated meanders and/or eddy variability west and southwest of Point Eugenia. High values of CHL are found in the upwelling zone, diminishing offshore. The exception is the area north of 31°N (the Ensenada Front), where higher CHL are found about 150 km offshore. South of 31°N, the long‐term mean dynamic topography decreases next to the coast, creating isopleths of height parallel to the coastline, consistent with southward geostrophic flow. North of 31°N the mean flow is toward the east, consistent with the presence of the Ensenada Front. The mean SST reveals a more north‐south gradient, reflecting latitudinal differences in surface heating due to solar radiation. Harmonic analyses and EOFs reveal the seasonal and interannual patterns, including the region of repeated eddy activity to the west and southwest of Point Eugenia. A maximum CHL occurs in spring in most of the inshore regions, reflecting the growth of phytoplankton in response to the seasonal maximum in upwelling‐favorable winds. SST and SSH anomalies are negative in the coastal upwelling zone in spring, also consistent with a response to the seasonal maximum in upwelling. When the seasonal cycle is removed, the strongest signal in the EOF time series is the response to the strong 1997–1998 El Niño, with a weaker signal representing La Niña (1998–1999) conditions. El Niño conditions consist of low chlorophyll, high SSH, and high SST, with opposite conditions during La Niña.
In situ aerosol profiles over the Southern Great Plains cloud and radiation test bed site: 2. Effects of mixing height on aerosol properties
Authors: Delle Monache Luca , Perry Kevin D. , Cederwall Richard T. , Ogren John A.
Published: March 2004

The goal of this study was to determine under what meteorological conditions, if any, measurements of aerosol properties made at the Earth's surface are representative of aerosol properties measured within the column of air above the surface. Specifically, this study uses instrumentation from the Atmospheric Radiation Measurement (ARM) Program's Southern Great Plains (SGP) site to determine how the observed mixing height (MH) and the degree of mixing affects the vertical variation of aerosol extensive and intensive properties. The MH was estimated by applying the Heffter [1980] technique with a critical lapse rate of 0.001 K m−1 to the available radiosonde data. This estimate was then used to determine whether each vertical aerosol profile flight leg from 59 flights was within or above the atmospheric boundary layer (ABL). Although the aerosol extensive properties, such as light absorption by particles σap, light scattering by particles σsp, and total extinction by particles σext measured within the ABL were highly correlated with the surface measurements (R2 = 0.74, 0.88, and 0.88, respectively), the airborne measurements of σap were systematically lower (slope = 0.77). By contrast, the σsp and σext regression line slopes were 0.99 and 1.00. The aerosol extensive properties measured above the ABL were poorly correlated with surface values and were almost an order of magnitude lower than the simultaneous measurements made within the ABL. Aerosol intensive properties such as the single‐scattering albedo ϖo, the hemispheric backscatter fraction b, and the Ångström exponent å exhibited a similar behavior (R2 = 0.74, 0.61, and 0.55, respectively) but had regression line slopes within the ABL of 0.88, 0.75, and 0.62, respectively. There were no statistically significant correlations between the intensive aerosol properties measured above the ABL and those measured at the surface. Limiting the analysis to well‐mixed days with near‐neutral static stability did not significantly improve the results. Thus the hypothesis that the best agreement between surface measurements and those within the ABL will occur when the atmosphere is well mixed was not supported by this data set.
Fast analysis of transient scattering from lossy inhomogeneous dielectric bodies
Authors: Shanker B. , Aygün K. , Michielssen E.
Published: March 2004

A time domain integral equation (TDIE)‐based approach for analyzing transient wave scattering from linear lossy media is proposed. The pertinent TDIEs are cast in terms of a “conduction current corrected flux density” and are solved using a marching‐on‐in‐time (MOT) scheme that incorporates a differential equation update algorithm for the aforementioned flux. The scheme is accelerated by the PWTD algorithm, and it is shown that the computational complexity and memory requirements of the resulting solver scales as (NtNs) and (Ns), where Nt and Ns denote the number of temporal and spatial degrees of freedom in the flux expansion, respectively. Numerical results that validate the accuracy and efficacy of the proposed method are presented.
Competitive and optimal control strategies for groundwater pumping by agricultural production units
Authors: Ibáñez Javier , Martínez Silvio , Martínez Jaime
Published: March 2004

A theoretical model of aquifer exploitation, where groundwater is devoted to agricultural production, is presented here. As new aspects with regard to other models found in literature, the model has explicit formulations for the number of production units and the natural discharge of the aquifer. It is specialized to competitive and optimal control strategies, and a comparison between steady states and trajectories under both strategies is made for ideal aquifers of very different dimensions. The commonly accepted conclusion of little differences between control and no control results to be expected in aquifers of a high “storage capacity” is confirmed for the area‐times‐storativity dimension but not for the vertical dimension of the aquifer, for which the conclusion could be quite the opposite. Sensitivity analyses are also carried out on both versions of the model where it is shown that a limitation to the entry of production units is the best instrument to improve important features regarding the competitive steady states and also to bring closer control and no control strategies.
Publishing in the Electronic World
Authors: Hornberger George , Lanzerotti Louis J.
Published: March 2004

The American Geophysical Union and many other scholarly publishers have made tremendous advances in creating a resilient and flexible electronic publishing environment that can assure access into the future no matter how the online world evolves. When AGU was preparing to become an online publisher, the Union formally recognized its archival obligation to the research community and made a firm commitment to the protection and adaptation of its electronic publications for future use. With advice from its Information Technology Committee, AGU established standards for file formats and software that would make it possible to meet this commitment.
Retinoblastoma protein functions as a molecular switch determining white versus brown adipocyte differentiation
Authors: Hansen Jacob B. , Jørgensen Claus , Petersen Rasmus K. , Hallenborg Philip , De Matteis Rita , Bøye Hans A. , Petrovic Natasa , Enerbäck Sven , Nedergaard Jan , Cinti Saverio , Riele Hein te , Kristiansen Karsten
Published: March 2004

Adipocyte precursor cells give raise to two major cell populations with different physiological roles: white and brown adipocytes. Here we demonstrate that the retinoblastoma protein (pRB) regulates white vs. brown adipocyte differentiation. Functional inactivation of pRB in wild-type mouse embryo fibroblasts (MEFs) and white preadipocytes by expression of simian virus 40 large T antigen results in the expression of the brown fat-specific uncoupling protein 1 (UCP-1) in the adipose state. Retinoblastoma gene-deficient (
Rb
–

/

–
) MEFs and stem cells, but not the corresponding wild-type cells, differentiate into adipocytes with a gene expression pattern and mitochondria content resembling brown adipose tissue. pRB-deficient MEFs exhibit an increased expression of the Forkhead transcription factor Foxc2 and its target gene cAMP-dependent protein kinase regulatory subunit RIα, resulting in increased cAMP sensitivity. Suppression of cAMP-dependent protein kinase activity in
Rb
–/–
MEFs blocked the brown adipocyte-like gene expression pattern without affecting differentiation
per se
. Immunohistochemical studies revealed that pRB is present in the nuclei of white but not brown adipocyte precursor cells at a developmental stage where both cell types begin to accumulate lipid and brown adipocytes express UCP-1. Furthermore, pRB rapidly undergoes phosphorylation upon cold-induced neodifferentiation and up-regulation of UCP-1 expression in brown adipose tissue. Finally, down-regulation of pRB expression accompanies transdifferentiation of white into brown adipocytes in response to β3-adrenergic receptor agonist treatment. We propose that pRB acts as a molecular switch determining white vs. brown adipogenesis, suggesting a previously uncharacterized function of this key cell cycle regulator in adipocyte lineage commitment and differentiation.