bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunohistochemical evaluation of pRb2/p130, VEGF, EZH2, p53, p16, p21waf‐1, p27, and PCNA in Barrett's esophagus
Authors: Merola Elettra , Mattioli Eliseo , Minimo Corrado , Zuo Weineng , Rabitti Carla , Cicala Michele , Caviglia Renato , Pollice Lucio , Gabbrielli Armando , Giordano Antonio , Claudio Pier Paolo
Published: January 2006

Control of the G1/S‐phase transition as well as angiogenic switch are two of the most studied mechanisms in cancer. The current study examined the correlation between the immunohistochemical expression of pRb2/p130, VEGF, EZH2, p53, p16, p21waf‐1, p27, and PCNA in Barrett's esophagus (BE). Overall, p53 showed a much higher expression in BE patients (up to 50%) than in controls (1–10%) (P < 0.005). Also p21 showed a downregulation in BE when compared to normal esophagus (70% of cells vs. 65%), but the difference did not show any statistical significance (P = 0.45). pRb2/p130 was detected in 80% of cells in normal controls, but showed positive in only 20% of cells in BE biopsies. Additionally, Rb2/p130 expression was inversely correlated to that of VEGF, EZH2, and PCNA (P < 0.0001, P = 0.0032, P < 0.001, respectively). p27 stained more intensely and in a widespread manner (70%) cells in normal esophageal tissues but about only 30% in BE samples (P < 0.001). Lastly, in accordance with other reports, we also found p16 expressed by immunohistochemistry at high levels in normal controls and at low levels in BE (P < 0.001). In conclusion, p16, p21, p27, and p53 staining confirmed previously published data. Interestingly, pRb2/p130 expression was found significantly decreased in metaplastic epithelium compared to normal controls and showed significant inverse correlation with the expression of other markers, such as VEGF, EZH2, and PCNA. These data, taken together, indicate that these molecular events occurring in Barrett's metaplasia (BM) may represent one of the many steps taking place during esophageal malignant progression such as impairment of cell‐cycle control, altered differentiation, and unbalanced angiogenesis. J. Cell. Physiol. 207: 512–519, 2006. © 2006 Wiley‐Liss, Inc.
Regulation of Ang2 release by PTEN/PI3‐kinase/Akt in lung microvascular endothelial cells
Authors: Tsigkos Stelios , Zhou Zongmin , Kotanidou Anastasia , Fulton David , Zakynthinos Spyros , Roussos Charis , Papapetropoulos Andreas
Published: January 2006

Angiopoietin‐2 (Ang2) is a Tie‐2 ligand that destabilizes vascular structures, allowing for neovascularization or vessel regression depending on local vascular endothelial cell growth factor (VEGF) concentrations. Although various stimuli have been shown to affect Ang2 expression, information on the underlying mechanisms involved in Ang2 production in endothelial cells (EC) is just beginning to emerge. In the present study, we have used adenovirus‐mediated gene transfer and pharmacological inhibitors to examine the role of the PTEN/PI3‐K/Akt pathway on Ang2 release. Inhibition of PI3‐kinase with wortmannin led to a stimulation of basal Ang2 release in EC, while overexpression of an active form of Akt reduced Ang2. In addition, adenovirus‐mediated gene transfer of the phosphatase PTEN stimulated Ang2 release. Incubation of the cells with Ang1, an agent that activates the PI3‐K/Akt pathway in EC, reduced Ang2 release. This effect of Ang1 could be prevented by wortmannin and LY‐294002 pretreatment. Similarly, in VEGF‐treated EC the increase in Ang2 production observed was greater in the presence of a PI3‐K inhibitor. Our observations that PTEN acts as a positive modulator of Ang2 release, while activation of the PI3‐K/Akt pathway downregulates Ang2, reveal an additional mechanism through which the PTEN/PI3‐K/Akt pathway could affect the angiogenic process. J. Cell. Physiol. 207: 506–511, 2006. © 2006 Wiley‐Liss, Inc.
Bone morphogenetic protein 4 mediates bile duct ligation induced liver fibrosis through activation of Smad1 and ERK1/2 in rat hepatic stellate cells
Authors: Fan Jianghong , Shen Hong , Sun Yu , Li Ping , Burczynski Frank , Namaka Mike , Gong Yuewen
Published: January 2006

Bone morphogenetic proteins (BMPs) are the important cytokine involving in cell differentiation especially in bone morphogenesis. Hepatic stellate cells (HSCs) undergo a trans‐differentiation during their activation after liver injury. Although it has been demonstrated that BMP2 and BMP4 significantly increased the abundance of smooth muscle alpha actin (α‐SMA) in cultured HSCs, the expression of BMPs has not been examined during the activation of HSCs. In current study, we documented the expression of BMP4 in bile duct ligation (BDL) rats and HSCs in culture. We have found that the expression of BMP4 was significantly elevated in the liver of BDL rats. The increase in BMP4 protein showed two peaks during 6 weeks after BDL. The expression and phosphorylation of Smad1, ERK1/2 and p38 were also elevated after BDL. Moreover, there was a gradual elevation of BMP4 mRNA abundance during 24 days' in vitro culture of HSCs. Furthermore, BMP4 stimulated phosphorylation of Smad1 and ERK1/2 in HSCs. In conclusion, BMP4 expression was significantly increased in the liver of BDL rats and HSCs in culture. These findings indicate that BMP4 may mediate HSC activation through activation of Smad1 and ERK1/2. J. Cell. Physiol. 207: 499–505, 2006. © 2006 Wiley‐Liss, Inc.
Assembly of nuclear matrix–bound protein complexes involved in non‐homologous end joining is induced by inhibition of DNA topoisomerase II
Authors: Kantidze Omar L. , Iarovaia Olga V. , Razin Sergey V.
Published: January 2006

Topoisomerases maintain the DNA structure by relieving the torsional stress and alleviating other topological problems occurring in DNA during transcription and replication. Topoisomerase II appears to have a close association with the family of proteins involved in the organization of chromatin in a series of loops on the proteinaceous chromosomal matrix. Beyond its physiological functions, topoisomerase II is the target for some of the most active anticancer drugs. Inhibition of the topoisomerase II function can result in DNA double‐strand breaks (DSBs) and, thus, lead to chromosomal translocations. The earliest event during DSB repair is phosphorylation of histone H2AX at S139 (so‐called γH2AX) which is believed to serve as a focal point for the assembly of repair proteins at the DSB. In this work, we have demonstrated the formation of γH2AX foci in two human cell lines ‐ K562 and HeLa ‐ after suppression of topoisomerase II activity with etoposide. Furthermore, these foci remained visible at nuclear matrices and colocalized with the major components of non‐homologous end joining (NHEJ) system of DSBs repair. Thus, inhibition of topoisomerase II activity triggers assembly of NHEJ complexes at the nuclear matrix. J. Cell. Physiol. © 2006 Wiley‐Liss, Inc.
Dynamic regulation and involvement of the heat shock transcriptional response in arsenic carcinogenesis
Authors: Khalil Sara , Luciano Jason , Chen Wenjun , Liu Alice Y.‐C.
Published: January 2006

The objective of this study is to better define induction of the heat shock response by arsenite, and to evaluation if induction of heat shock proteins (HSPs) contributes to the carcinogenic activity of arsenite. We show here that arsenite is a ubiquitous inducer of the heat shock response in mammalian cells: that it activated heat shock transcription factor 1 (HSF1) DNA‐binding activity, enhanced hsp 70 promoter, and induced hsp70mRNA and synthesis of HSP chaperones. Using a high throughput hsp70 promoter‐luciferase reporter assay, we observed a hormetic dose response where low concentrations of arsenite stimulated and high concentrations inhibited. Further, the response was time‐dependent such that with longer times of incubation, the dose response shifted to the left. The effect of arsenite in inducing the hsp 70‐luciferase reporter absolutely required a functional HSF1 as it was not observed in HSF1 minus cells but re‐instated by expression of HSF1. Consistent with the suggestion that arsenic targets vicinal cysteine‐SH, we showed that dithiothreitol blocked the effect of arsenite. Assays of cell viability and caspase showed that arsenite caused a dose‐dependent increase in cell death by activation of caspase 3/7 and pre‐induction of HSPs blunted these effects. Using anchorage independent cell growth as a late stage tumor promotion assay, we showed that low concentrations of arsenite had a growth promoting effect, which was enhanced by moderate heat shock. Our study provides evidence that induction of the heat shock response is a sensitive biomarker of arsenic exposure and that induction of HSPs likely contributes to the tumor promotion effect of arsenic. J. Cell. Physiol. 207: 562–569, 2006. © 2006 Wiley‐Liss, Inc.
Analysis of dystroglycan regulation and functions in mouse mammary epithelial cells and implications for mammary tumorigenesis
Authors: Sgambato A. , Di Salvatore M.A. , De Paola B. , Rettino A. , Faraglia B. , Boninsegna A. , Graziani C. , Camerini A. , Proietti G. , Cittadini A.
Published: January 2006

Abnormalities in the interactions of cells with the extracellular matrix (ECM) play an important role in the development and progression of many types of cancer and are a hallmark of malignant transformation. The dystroglycan (DG) complex is a transmembrane glycoprotein that forms a continuous link from the ECM to the actin cytoskeleton, providing structural integrity and perhaps transducing signal, in a manner similar to integrins. Deregulated expression of DG has been reported in a variety of human malignancies and related to tumor differentiation and aggressiveness. In breast cancer, reduced DG expression has been associated with patient survival and with loss of differentiation of tumor cells. Limited data are available on DG physiology in epithelial cells. In this study, we used the HC11 spontaneously immortalized murine mammary epithelial cells to study DG function(s) and regulation in normal cells. We found that expression of DG protein and mRNA is cell‐cycle and cell‐density regulated in these cells. Moreover, expression of both DG subunits increased upon lactogenic differentiation of the HC11 cells. The turnover of cell‐surface‐expressed DG was evaluated in the same cells and half‐life of DG subunits was evaluated to be about 12 h. DG‐specific small inhibitory RNAs were used to analyze the effects of a reduced expression of DG in these cells. Cells in which DG expression was suppressed were growth inhibited, accumulated in the S‐phase of the cell cycle, failed to undergo lactogenic differentiation, and displayed an increase in the percentage of apoptotic cells. Moreover, changes were observed in the expression and/or activity of several molecules involved in cell growth control. These results demonstrate that DG expression is tightly regulated in normal mammary epithelial cells and support the hypothesis that DG is involved in several functions other than structural integrity in these cells. This finding provides new insight into the roles played by DG in epithelial cell physiology and will contribute to our understanding of its involvement in the process of epithelial cell transformation. J. Cell. Physiol. 207: 520–529, 2006. © 2006 Wiley‐Liss, Inc.
ERK1/2 and p38 MAP kinase control MMP‐2, MT1‐MMP, and TIMP action and affect cell migration: A comparison between mesothelioma and mesothelial cells
Authors: Zhong Jun , Cornelsen Gencay Mikael M. , Bubendorf Lukas , Burgess Janette K. , Parson Holly , Robinson Bruce W.S. , Tamm Michael , Black Judith L. , Roth Michael
Published: January 2006

Pleural malignant mesothelioma is a locally aggressive tumor of mesothelial cell origin. In other tumor types high expression of matrix metalloproteinase (MMP)‐2, together with membrane‐type1‐MMP (MT1‐MMP), and low levels of the tissue inhibitor of MMP (TIMP)‐2 have been correlated with aggressive tumor progression and low survival rates. Therefore, we compared the expression and activation of these three factors and their regulation by two mesothelioma associated growth factors, platelet‐derived growth factor (PDGF)‐BB, and transforming growth factor (TGF)‐β1 in six human mesothelioma and one mesothelial cell line. Polymerase chain reaction (PCR), immnuoblotting, zymography, and small inhibitory RNAs (siRNA) were used to study gene expression, protein activation, and signal transduction. To proof the relevance of our in vitro data immunohistochemistry was performed in tissue sections. PDGF‐BB induced, while TGF‐β1 inhibited cell proliferation. PDGF‐BB was a chemoattractant for mesothelial cells, and its effect was increased in the presence of TGF‐β1. TGF‐β1 stimulated the de novo synthesis of pro‐MMP‐2 in both cell types. Pro‐MMP‐2 synthesis involved p38 MAP kinase. In cell culture and tissue sections only mesothelial cells expressed MT1‐MMP. Migration of mesothelioma cells was dependent on the presence of MT1‐MMP. Migration, but not proliferation of mesothelioma cells was inhibited by oleoyl‐N‐hydroxylamide, TIMP‐2, and siRNA for MT1‐MMP. Our data suggest that in mesothelioma cells the phosphorylation of p38 MAP kinase is deregulated and is involved in pro‐MMP‐2 expression. Mesothelioma progression depends on an interaction with mesothelial cells that provide MT1‐MMP necessary to activate pro‐MMP‐2 to facilitate migration through an extracellular matrix (ECM) layer. J. Cell. Physiol. 207: 540–552, 2006. © 2006 Wiley‐Liss, Inc.
Proteolytic activation of latent TGF‐β precedes caspase‐3 activation and enhances apoptotic death of lung epithelial cells
Authors: Solovyan Victor T. , Keski‐Oja Jorma
Published: January 2006

Transforming growth factors β (TGF‐βs) are multifunctional cytokines, which are secreted in latent forms in large latent TGF‐β complexes (LL‐TGF‐β) with subsequent deposition to the extracellular matrix (ECM). While a variety of mechanisms capable of activating latent TGF‐β in vitro have been described, the physiological conditions, which promote the activation of TGF‐β in vivo are poorly understood. Mink lung epithelial cells (Mv1Lu) are a widely used model for evaluation of the effects of exogenous TGF‐β both in transcriptional and growth inhibitor assays. We find here that apoptosis of Mv1Lu cells, induced either by staurosporine or serum deprivation, is accompanied by proteolytic processing of LL‐TGF‐β and the activation of endogenous TGF‐β. Activation of TGF‐β preceded caspase‐3 activation and was almost completely suppressed by the serine protease inhibitor, AEBSF. Both exogenous and endogenously activated TGF‐βs were able to enhance the apoptotic response of Mv1Lu cells leading to potentiation of cell death. Potentiation of cell death by activated TGF‐β was associated with downregulation of Akt and p38 MAPK, which were both activated at the initial stages of Mv1Lu apoptosis and were suppressed by exogenous TGF‐β. Pharmacological interruption of either phosphoinositide‐3‐kinase (PI‐3K)/Akt or p38 MAPK signaling by the specific inhibitors mimicked the effect of TGF‐β leading to potentiation of cell death. Current results suggest that proteolytic activation of endogenous TGF‐β is a component of the apoptotic response, capable of modulating the death of Mv1Lu cells by inhibition of both PI‐3K/Akt and p38 MAPK‐dependent survival pathways. J. Cell. Physiol. 207: 445–453, 2006. © 2006 Wiley‐Liss, Inc.
Non‐freezing points below zero induce low‐temperature breakdown of kiwifruit at harvest
Authors: Gerasopoulos Dimitrios , Chlioumis George , Sfakiotakis Evangelos
Published: January 2006

To induce low‐temperature breakdown (LTB) at harvest, a post‐storage disorder of kiwifruit, kiwifruit were exposed to −2 °C (a temperature determined to be above the freezing point), for 0 (control), 6, 12, 18, 24, 30, 36 and 42 h, followed by 5 days at 20 °C. Kiwifruit were also stored at −0.5 °C for 16 and 24 weeks plus 5 days at 20 °C. LTB incidence and severity were measured on the cut surfaces following slicing at the upper, middle and lower parts of each fruit subjected to −2 °C, whereas in stored fruit LTB incidence was measured following slicing at the middle part. Electrolyte leakage (ELL) was also determined. Exposure of fruit to −2 °C resulted in induction of LTB incidence and severity, which increased with the duration of exposure, particularly, on the upper fruit part. Maximum ELL during exposure at −2 °C for 36 h or during storage at −0.5 °C for 16 weeks was as high as 50% of that of the frozen fruit. Fruit exposed to −2 °C or stored at −0.5 °C had similar LTB symptoms but both differed from those observed in frozen fruit. LTB of fruit stored at −0.5 °C for 24 weeks was 27% and corresponded to LTB induced at harvest by exposure at −2 °C for 24 h. The results of this study confirm that LTB is inducible by low but not freezing temperatures at harvest and therefore it might be considered as the physiological basis towards the development of an LTB incidence index for harvested kiwifruit. Copyright © 2006 Society of Chemical Industry
Alternating repetition time balanced steady state free precession
Authors: Leupold J. , Hennig J. , Scheffler K.
Published: January 2006

A novel balanced SSFP technique for the separation or suppression of different resonance frequencies (e.g., fat suppression) is presented. The method is based on applying two alternating and different repetition times, TR1 and TR2. This RF scheme manipulates the sensitivity of balanced SSFP to off‐resonance effects by a modification of the frequency response profile. Starting from a general approach, an optimally broadened stopband within the frequency response function is designed. This is achieved with a TR2 being one third of TR1 and an RF‐pulse phase increment of 90°. With this approach TR2 is too short (∼1 ms) to switch imaging gradients and is only used to change the frequency sensitivity. Without a significant change of the spectral position of the stopband, TR1 can be varied over a range of values (∼2.5–4.5 ms) while TR2 and phase cycling is kept constant. On‐resonance spins show a magnetization behavior similar to balanced SSFP, but with maximal magnetization at flip angles about 10° lower than in balanced SSFP. The total scan time is increased by about 30% compared to conventional balanced SSFP. The new technique was applied on phantoms and volunteers to produce rapid, fat suppressed images. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Investigation of laser‐fired rear‐side recombination properties using an analytical model
Authors: Kray Daniel , Glunz Stefan
Published: January 2006

This paper presents the application of the analytical model for locally contacted rear sides recently published by Fischer to the determination of recombination losses of solar cells with fixed metallization fraction, but varying contact pitch. After the successful experimental validation of the model on oxide‐passivated solar cells with ohmic contacts, the model was used for a detailed investigation of rear sides prepared by the laser‐fired contacts (LFC) method. In this way the surface recombination velocity (SRV) at the very contact areas was extracted for a broad base doping range. The determined parameterization allows the calculation of the SRV of any LFC rear side concerning base doping and contact pitch. The excellent passivation quality of the alnealed oxide with LFC contacts is shown: on 1 (100) Ω cm FZ an effective SRV of only 35 (4·3) cm/s could be measured with 1000 µm contact pitch. Copyright © 2006 John Wiley & Sons, Ltd.
Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two‐dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis
Authors: Snijders Ambrosius P. L. , Walther Jasper , Peter Stefan , Kinnman Iris , de Vos Marjon G. J. , van de Werken Harmen J. G. , Brouns Stan J. J. , van der Oost John , Wright Phillip C.
Published: January 2006

In the last decade, an increasing number of sequenced archaeal genomes have become available, opening up the possibility for functional genomic analyses. Here, we reconstructed the central carbon metabolism in the hyperthermophilic crenarchaeon Sulfolobus solfataricus (glycolysis, gluconeogenesis and tricarboxylic acid cycle) on the basis of genomic, proteomic, transcriptomic and biochemical data. A 2‐DE reference map of S. solfataricus grown on glucose, consisting of 325 unique ORFs in 255 protein spots, was created to facilitate this study. The map was then used for a differential expression study based on 15N metabolic labelling (yeast extract + tryptone‐grown cells (YT) vs. glucose‐grown cells (G)). In addition, the expression ratio of the genes involved in carbon metabolism was studied using DNA microarrays. Surprisingly, only 3 and 14% of the genes and proteins, respectively, involved in central carbon metabolism showed a greater than two‐fold change in expression level. All results are discussed in the light of the current understanding of central carbon metabolism in S. solfataricus and will help to obtain a system‐wide understanding of this organism.
Proteomic analysis of beryllium‐induced genotoxicity in an Escherichia coli mutant model system
Authors: Taylor‐McCabe Kirsten J. , Wang Zaolin , Sauer Nancy N. , Marrone Babetta L.
Published: January 2006

Beryllium is the second lightest metal, has a high melting point and high strength‐to‐weight ratio, and is chemically stable. These unique chemical characteristics make beryllium metal an ideal choice as a component material for a wide variety of applications in aerospace, defense, nuclear weapons, and industry. However, inhalation of beryllium dust or fumes induces significant health effects, including chronic beryllium disease and lung cancer. In this study, the mutagenicity of beryllium sulfate (BeSO4) and the comutagenicity of beryllium with a known mutagen 1‐methyl‐3‐nitro‐1‐nitrosoguanidine (MNNG) were evaluated using a forward mutant detection system developed in Escherichia coli. In this system, BeSO4 was shown to be weakly mutagenic alone and significantly enhanced the mutagenicity of MNNG up to 3.5‐fold over MNNG alone. Based on these results a proteomic study was conducted to identify the proteins regulated by BeSO4. Using the techniques of 2‐DE and oMALDI‐TOF MS, we successfully identified 32 proteins being differentially regulated by beryllium and/or MNNG in the E. coli test system. This is the first study to describe the proteins regulated by beryllium in vitro, and the results suggest several potential pathways for the focus of further research into the mechanisms underlying beryllium‐induced genotoxicity.
The phosphate‐starvation response in Vibrio cholerae O1 and phoB mutant under proteomic analysis: Disclosing functions involved in adaptation, survival and virulence
Authors: von Krüger Wanda Maria Almeida , Santos Lery Leticia Miranda , Soares Marcia Regina , Saloum de Neves‐Manta Fernanda , Batista e Silva Celia Maria , da Costa Neves‐Ferreira Ana Gisele , Perales Jonas , Bisch Paulo Mascarello
Published: January 2006

A proteomic analysis of a wild‐type and of a phoB mutant showed that Vibrio cholerae expresses genes of two major regulons in response to phosphate starvation. The Pho regulon, expressed by the wild‐type, allowed the cells to adapt to the new environment. Induction of the general stress regulon was mainly observed in the phoB mutant as a strategy to resist stress and survive. Some functions of the adaptative and survival responses play roles in the pathogenicity of the bacteria. Among the members of the Pho regulon, we found a porin described as an important factor for the intestinal colonisation. Other functions not obviously related to phosphate metabolism, expressed preferentially by the wild‐type cells, have also been implicated in virulence. These findings might explain the lack of virulence of the phoB mutant. The Pho regulon picture of V. cholerae, however, will not be complete until minor members and membrane proteins are identified. Among the phosphate‐starvation induced genes we have found 13 hypothetical ones and for some of them functions have been assigned. The majority of the genes identified here have not been described before, thus they could be used to expand the proteomic reference map of V. cholerae El Tor.
Protein profiling the effects of in vitro hyperoxic exposure on fetal rabbit lung
Authors: Henschke Phillip , Vorum Henrik , Honoré Bent , Rice Gregory Edward
Published: January 2006

The aim of this study was to test the hypothesis that acute in vitro exposure of prematurely delivered fetal rabbit lungs to hyperoxic conditions will induce the expression of an adaptive cassette of proteins that mediates antioxidant and inflammatory processes. To test this hypothesis, ex situ fetal rabbit lung explants were prepared from New Zealand white rabbits delivered by cesarean section on day 29 of gestation and incubated under air (21% O2; 5% CO2) or hyperoxic (95% O2; 5% CO2) atmospheres. Total tissue protein was extracted following incubation and subjected to 2‐DE. Using this technique, 1500–2000 protein spots were resolved per gel. Treatment‐dependent, differentially expressed proteins were identified by image analysis (Melanie II) and MALDI‐TOF MS and MALDI‐MS/MS. The analysis identified 12 protein spots that were differentially expressed by 1.5‐fold or more (p<0.05) by exposure to hyperoxic conditions. Six of these differentially expressed proteins were identified as vimentin, annexin I, inorganic pyrophosphatase, prohibitin, an N‐terminal fragment of ATP synthase and heat shock protein 27. The data obtained are consistent with the roles of these proteins in mediating cellular response to oxidative stress and in regulating cell proliferation.
The tegument surface membranes of the human blood parasite Schistosoma mansoni: A proteomic analysis after differential extraction
Authors: Braschi Simon , Curwen Rachel S. , Ashton Peter D. , Verjovski‐Almeida Sergio , Wilson Alan
Published: January 2006

The blood fluke Schistosoma mansoni can live for years in the hepatic portal system of its human host and so must possess very effective mechanisms of immune evasion. The key to understanding how these operate lies in defining the molecular organisation of the exposed parasite surface. The adult worm is covered by a syncytial tegument, bounded externally by a plasma membrane and overlain by a laminate secretion, the membranocalyx. In order to determine the protein composition of this surface, the membranes were detached using a freeze/thaw technique and enriched by sucrose density gradient centrifugation. The resulting preparation was sequentially extracted with three reagents of increasing solubilising power. The extracts were separated by 2‐DE and their protein constituents were identified by MS/MS, yielding predominantly cytosolic, cytoskeletal and membrane‐associated proteins, respectively. After extraction, the final pellet containing membrane‐spanning proteins was processed by liquid chromatographic techniques before MS. Transporters for sugars, amino acids, ions and other solutes were found together with membrane enzymes and proteins concerned with membrane structure. The proteins identified were categorised by their function and putative location on the basis of their homology with annotated proteins in other organisms.
Comparison of the mechanisms of reactions of β‐lactams and β‐sultams, including their reactions with some serine enzymes
Authors: Page Michael I. , Tsang Wing Y. , Ahmed Naveed
Published: January 2006

The strain energy of the four‐membered ring of β‐lactams is not released in the transition state to lower the activation energy of reactions involving ring‐opening. The alkaline hydrolysis of N‐aroyl β‐lactams occurs with competitive exo‐ and endocyclic CN ring fission, the ratio of which varies with the aryl substituent. β‐Sultams are four‐membered cyclic sulfonamides and are about 103 fold more reactive than analogous β‐lactams. Nucleophiles usually attack N‐acylsulfonamides at the carbonyl centre resulting in CN bond fission, but the hydrolysis of N‐acyl β‐sultams occurs with SN fission and opening of the four‐membered ring. The 3‐oxo‐β‐sultams are a unique combination of both β‐lactams and β‐sultams and therefore are susceptible to nucleophilic attack at either the acyl or the sulfonyl centre, but they hydrolyse with exclusive SN bond fission. β‐Sultams are novel inhibitors of the serine enzymes elastase, transpeptidase and β‐lactamase due to sulfonylation of the active‐site serine residue. Structure–activity relationships are used to identify differences in transition‐state structures between β‐sultams as inhibitors and β‐lactams as substrates. Copyright © 2006 John Wiley & Sons, Ltd.
Emulsion atom transfer radical block copolymerization of 2‐ethylhexyl methacrylate and methyl methacrylate
Authors: Eslami Hormoz , Zhu Shiping
Published: January 2006

The emulsion atom transfer radical block copolymerization of 2‐ethylhexyl methacrylate (EHMA) and methyl methacrylate (MMA) was carried out with the bifunctional initiator 1,4‐butylene glycol di(2‐bromoisobutyrate). The system was mediated by copper bromide/4,4′‐dinonyl‐2,2′‐bipyridyl and stabilized by polyoxyethylene sorbitan monooleate. The effects of the initiator concentration and temperature profile on the polymerization kinetics and latex stability were systematically examined. Both EHMA homopolymerization and successive copolymerization with MMA proceeded in a living manner and gave good control over the polymer molecular weights. The polymer molecular weights increased linearly with the monomer conversion with polydispersities lower than 1.2. A low‐temperature prepolymerization step was found to be helpful in stabilizing the latex systems, whereas further polymerization at an elevated temperature ensured high conversion rates. The EHMA polymers were effective as macroinitiators for initiating the block polymerization of MMA. Triblock poly(methyl methacrylate–2‐ethylhexyl methacrylate–methyl methacrylate) samples with various block lengths were synthesized. The MMA and EHMA reactivity ratios determined by a nonlinear least‐square method were ∼0.903 and ∼0.930, respectively, at 70 °C. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1914–1925, 2006
Structural prediction of peptides binding to MHC class I molecules
Authors: Bui Huynh‐Hoa , Schiewe Alexandra J. , von Grafenstein Hermann , Haworth Ian S.
Published: January 2006

Peptide binding to class I major histocompatibility complex (MHCI) molecules is a key step in the immune response and the structural details of this interaction are of importance in the design of peptide vaccines. Algorithms based on primary sequence have had success in predicting potential antigenic peptides for MHCI, but such algorithms have limited accuracy and provide no structural information. Here, we present an algorithm, PePSSI (peptide‐MHC prediction of structure through solvated interfaces), for the prediction of peptide structure when bound to the MHCI molecule, HLA‐A2. The algorithm combines sampling of peptide backbone conformations and flexible movement of MHC side chains and is unique among other prediction algorithms in its incorporation of explicit water molecules at the peptide‐MHC interface. In an initial test of the algorithm, PePSSI was used to predict the conformation of eight peptides bound to HLA‐A2, for which X‐ray data are available. Comparison of the predicted and X‐ray conformations of these peptides gave RMSD values between 1.301 and 2.475 Å. Binding conformations of 266 peptides with known binding affinities for HLA‐A2 were then predicted using PePSSI. Structural analyses of these peptide‐HLA‐A2 conformations showed that peptide binding affinity is positively correlated with the number of peptide‐MHC contacts and negatively correlated with the number of interfacial water molecules. These results are consistent with the relatively hydrophobic binding nature of the HLA‐A2 peptide binding interface. In summary, PePSSI is capable of rapid and accurate prediction of peptide‐MHC binding conformations, which may in turn allow estimation of MHCI‐peptide binding affinity. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Conductance phenomena in microcrystalline cellulose
Authors: Nilsson M.
Published: January 2006

We have investigated the conduction phenomena in compacted tablets of cellulose with varying relative humidity (RH) with techniques such as Low Frequency Dielectric Spectroscopy (LFDS) and Transient Current (TC) at room temperature. Two exponential decaying regions in the transient current measurements indicate two ionic species contributing to the conduction mechanism. A high power‐law exponent of ∼9 for the conductance with moisture content has been found. The mobility initially decreases with RH up to monolayer coverage, and further water vapor increases the mobility, indicating a blocking of available positions for the charge carrier ions. When the amount of water molecules present in the tablet increases one order of magnitude, the number of charge carriers increases 5‐6 orders of magnitude, suggesting a transition from a power‐law increase to a linear effective medium theory for the conduction. The charge carrier dependence on RH suggests that a percolating network of water molecules adsorbed to 6‐OH units on the cellulose chain span through the sample. The conductivity mechanisms in cellulose are still not clear. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The intrinsic conductivity of nanosized semiconducting crystals
Authors: Huijbregts L. J. , Brom H. B. , Brokken‐Zijp J. C. M. , Michels M. A. J. , de Goeje M. , Yuan M.
Published: January 2006

We show how the dielectric response of powders of semiconducting nanocrystals can be used to extract the intrinsic conductivity of the nanocrystals. The method is applied to powders of nanocrystals of semiconductive aquocyanophthalocyaninatocobalt (III) (Phthalcon‐11), a promising filler material for conducting composites, and published data of silicon. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spreading resistance microscopy study of polyamidine thin films
Authors: Rentzsch R. , Ionov A. N. , Nikolaeva M. N. , Dunaevskii M. S.
Published: January 2006

We have observed that thin films of polyamidine may exhibit high conductivity in some locations on the polymer surface at low electrical field strength. The conductance which has been tested by spreading resistance mode of an atomic force microscope depended on the type of substrate. We consider that a critical density of charge inside the polymer is needed for its switching to the conductive state. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simulation of the phononless hopping in a Coulomb glass
Authors: Matulewski J. , Baranovskii S. D. , Thomas P.
Published: January 2006

The phononless hopping conductivity of a disordered system with localized states is studied in a broad range of frequencies by straightforward computer simulations taking into account Coulomb interactions. At sufficiently low temperatures, the conductivity is determined by the zero‐phonon absorption of the photon by pairs of states. The laser frequency dependence of the conductivity is examined and compared with the analytical model of Efros and Shklovskii and with recent experimental data obtained on Si:P. The range of parameters is determined, for which the conductivity dependence on photon energy best reproduces the experimental results. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magneto‐transport in ferromagnetic granular networks
Authors: Vilchik Hagai , Frydman Aviad , Berkovits Richard
Published: January 2006

Using numerical simulations and analytical calculations we have examined the transport properties of a ferromagnetic granular systems. We model this complex network system by an ensemble of ferromagnetic conducting grains randomly located on a 2D plain. Quite surprisingly, the magneto‐resistance of a complex network can be approximated by the magneto‐resistance of a single pair of ferromagnetic grains, although our simulations show that the transport trajectories change from a quasi‐1D path through the system to a percolation network through the larger grains as the number of grain in the system increases. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Generalized pair approximation in the description of the ac conductivity of a dense disordered array of quantum dots
Authors: Zvyagin I. P.
Published: January 2006

The frequency dependence of the hopping conductivity of dense arrays of semiconductor quantum dots of size $ \bar a $ substantially exceeding the edge‐to‐edge separation $ \bar w $ between the neighboring quantum dots is considered. It is shown that at low frequencies in a wide frequency range the conductivity obeys a fractional power law and its magnitude depends on the structural characteristics of the material. The possibility of the deviations from universality related to the material structure is discussed. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetoresistance and Hall effect of a 2DEG in GaAs/AlGaAs: electron interaction and ‘memory’ effects in the presence of a mixed disorder
Authors: Galaktionov E. A. , Savchenko A. K. , Ritchie D. A.
Published: January 2006

We have studied the corrections to the Drude conductivity and Hall constant of a high‐mobility twodimensional electron gas in a GaAs/AlGaAs heterostructure due to the electron‐electron interaction in the presence of a mixed disorder. A parabolic, negative, temperature‐dependent magnetoresistance (MR) and temperature‐dependent Hall constant are observed. We show that these effects can be explained in terms of the electron interaction theory and obtain the values of the Fermi‐liquid interaction parameter Fσo . In addition, a temperature independent, positive MR has been detected. This classical MR is also shown to be a consequence of the mixed disorder. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Disorder‐induced features of the transverse resistance in a Si‐MOSFET in the quantum Hall effect regime
Authors: Shlimak I. , Friedland K.‐J. , Ginodman V. , Kravchenko S.V.
Published: January 2006

We investigate two features of the transverse resistance Rxy in a Si‐MOSFET in the quantum Hall effect regime. The first, the “overshoot” phenomenon, is observed at filling factor ν = 3. In this case, when the magnetic field increases and the filling factor ν approaches ν = 3, Rxy overshoots its normal plateau value of 1/3(h /e 2). However, if magnetic field increases further, Rxy decreases to its normal value. This effect has been previously observed in other two‐dimensional systems, particularly, in a more perfect Si/SiGe heterostructure. Comparing the two Si systems, Si‐MOSFET and Si/SiGe, with similar electron density and different mobility clearly shows that the increase in disorder leads to significant enhancement of the overshoot. The second effect is reported here for the first time and is characteristic only of Si‐MOSFET. It was observed that when the filling factor approaches ν = 5, Rxy , which is already at the plateau of 1/4(h /e 2), abruptly decreases to 1/5(h /e 2) and then sharply returns to 1/4(h /e 2). This “deep” effect is more pronounced at higher electron concentration for which ν = 5 is achieved at stronger magnetic fields. The explanation is based on the assumption of the equality between the disorder–induced broadening of adjacent valley‐split Landau bands and the energy gap between them. In the narrow interval of magnetic fields near ν = 5, the gap increases sharply due to exchange enhancement of the valley splitting, which results in a corresponding drop in Rxy . (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interference quantum corrections in the low temperature microwave magnetoresistance of the nondegenerate Ge
Authors: Veinger A. I. , Zabrodskii A. G. , Tisnek T. V. , Goloshchapov S. I.
Published: January 2006

The first observation of low temperature magnetoresistance (MR) of interference nature in the case of a light doping is reported. This MR occurs in both n‐ and p‐type Ge samples in weak magnetic fields at frequency of 10 GHz and temperatures below 30 K. It is registered on the background of the classical MR effect associated with electrons in different valleys of n‐Ge and with different (heavy and light) holes of p‐Ge. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phononless inelastic transport through a disordered array of quantum wires
Authors: Chudnovskiy A. L.
Published: January 2006

Phononless plasmon assisted transport through a long disordered array of finite length quantum wires is investigated analytically. Generically strong electron plasmon interaction in quantum wires results in a qualitative change of the temperature dependence of thermally activated resistance in comparison to phonon assisted transport. At high temperatures, the thermally activated resistance is determined by the Luttinger liquid interaction parameter of the wires. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of a non‐uniform scattering potential on conductance fluctuations in a quantum wire
Authors: Horsell D. W. , Galaktionov E. A. , Savchenko A. K. , Kretinin A. V. , Ghosh A. , Beere H. E. , Ritchie D. A.
Published: January 2006

We investigate experimentally the fluctuations of the conductance of a high mobility quantum wire. We show that scattering of electrons is not evenly distributed across the wire. In the centre of the wire electrons propagate almost ballistically. However, when the electrons are forced into the boundaries of the wire diffusive scattering occurs. This is seen as a dramatic enhancement of the variance and characteristic period of the fluctuations at the field at which maximum boundary scattering is predicted. We compare our results with recent theories and construct an empirical model to describe the transport processes in the wire. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crossover from strong to weak localization in the split‐off impurity band in two‐dimensional p ‐GaAs/AlGaAs structures
Authors: Agrinskaya N. V. , Kozub V. I. , Poloskin D. V. , Chernyaev A. V. , Shamshur D. V.
Published: January 2006

A crossover from strongly localized behavior to weak localization (SL–WL) was observed in two‐dimensional modulation‐doped GaAs/Al0.3Ga0.7As structures as the impurity concentration increased. The low‐temperature dependence of the conductivity changed its character (from exponential to logarithmic) and the magnetoresistance changed its sign (from linear negative to root positive). For 2D structures, it is shown that this transition takes place in the impurity band separated from the valence band by the mobility gap whereas the effective mass in the impurity band is larger than in the valence band. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Scaling at the energy‐driven metal‐insulator transition and the thermoelectric power
Authors: Croy Alexander , Römer Rudolf A.
Published: January 2006

The electronic properties of disordered systems at the Anderson metal‐insulator transition (MIT) have been the subject of intense study for several decades. Thermoelectric properties at the MIT, such as thermopower and thermal conductivity, however, have been relatively neglected. Using the recursive Green's function method and the Chester‐Thellung‐Kubo‐Greenwood formalism, we calculate numerically the low temperature behaviour of all kinetic coefficients Lij . From these we can deduce for example the electrical conductivity ω and the thermopower S at finite temperatures. Here we present results for the case of completely coherent transport in cubic 3D systems. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Antiferromagnetic phase in doped semiconductors near the insulator–metal phase transition
Authors: Veinger A. I. , Zabrodskii A. G. , Tisnek T. V. , Goloshchapov S. I. , Mokhov E. N.
Published: January 2006

We show for n ‐type semiconductors, using Ge:As and 4H ‐SiC:N as examples, that the spin density measured by electron spin resonance (ESR) falls sharply near the insulator–metal (IM) transition. Two reasons might be responsible for this phenomenon: potential fluctuations with concentration of the electrons in local minima or local antiferromagnetic spin pairing (“spin glass”) in the insulating state just below the IM transition. In the investigated semiconductors manifestation of the latter is observed as a change from Curie to a Curie–Weiss behaviour with negative constant Θ. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Solution‐phase deuterium/hydrogen exchange at a specific residue using nozzle‐skimmer and electron capture dissociation mass spectrometry
Authors: Hagman Charlotte , Tsybin Yury O. , Håkansson Per
Published: January 2006

Information about protein conformation can be obtained with hydrogen/deuterium exchange (HDX) mass spectrometry. The isotopic solution‐phase exchange of specific amide hydrogen atoms can be followed using low‐vacuum nozzle‐skimmer collision‐induced dissociation (CID). In this study, the nozzle‐skimmer technique was complemented by electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The solution‐phase exchange at a specific residue is monitored by comparing isotopic distributions of two consecutive b‐ or c‐type ions. While nozzle‐skimmer fragmentation takes place in the low‐vacuum region of the mass spectrometer, ECD occurs at ultra‐high vacuum within the mass analyzer cell of the FTICR mass spectrometer. The dissociations take place at 10−4 and 10−9 mbar, respectively. Low‐vacuum nozzle‐skimmer fragmentation can result in intramolecular exchange between product ions and solvent molecules in the gas phase. Consequently, the solution‐phase information about protein or peptide conformation is lost. It was not possible to monitor isotopic solution‐phase exchange at the eighth residue in substance P, (Phe)8, with nozzle‐skimmer CID. By using the in‐cell ECD fragmentation method, the solution‐phase exchange at the (Phe)8 residue was preserved during mass spectrometric analysis. This result shows the complementary aspects of applying fragmentation at low and at high vacuum, when studying isotopic exchange in solution at specific residues using FTICRMS. Copyright © 2006 John Wiley & Sons, Ltd.
Monitoring enzyme‐catalyzed production of glucosamine‐6P by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry: a new enzymatic assay for glucosamine‐6P synthase
Authors: Maillard Ludovic T. , Guérineau Vincent , Badet‐Denisot Marie‐Ange , Badet Bernard , Laprévote Olivier , Durand Philippe
Published: January 2006

A matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) method for quantification of D‐glucosamine‐6P (GlcN‐6P) that allows the kinetic study of glucosamine‐6P synthase (Glms) is presented. The present report describes the optimization of the different steps of a new enzymatic assay for Glms based on in situ N‐acetylation of GlcN‐6P and MALDI‐TOFMS analysis using N‐(13C2)acetylglucosamine‐6P as internal standard. Since no isotopically substituted GlcN‐6P was available, the N‐(13C2)acetyl derivative, easily obtained from (13C4)‐acetic anhydride, was used as internal standard. Validation of the assay was achieved by measuring the fructose‐6P Michaelis constant, in full agreement with reported values, and by studying the inhibition properties of arabinose‐5P oxime. Copyright © 2006 John Wiley & Sons, Ltd.
Structural analysis of secondary ions by post‐source decay in time‐of‐flight secondary ion mass spectrometry
Authors: Touboul David , Brunelle Alain , Laprévote Olivier
Published: January 2006

Tandem mass spectrometry measurements have been achieved using time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) and a post source decay (PSD)‐like method. The performance of the method has been demonstrated on model molecules with well‐known fragmentation pathways. Several lipids have been fragmented including the phosphocholine ion, phosphatidylcholines, cholesterol and vitamin E. Pure samples were analyzed, and the results compared with those obtained with the same compounds on a quadrupole‐TOF hybrid mass spectrometer. Then, the structures of some lipids which are currently observed in the TOF‐SIMS imaging of mammalian tissue sections were verified. Copyright © 2006 John Wiley & Sons, Ltd.