bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct telomere length regulation in premalignant cervical and endometrial lesions: implications for the roles of telomeres in uterine carcinogenesis
Authors: Maida Y , Kyo S , Forsyth NR , Takakura M , Sakaguchi J , Mizumoto Y , Hashimoto M , Nakamura M , Nakao S , Inoue M 
Published: August 2006

AbstractMouse models show that progressive shortening of telomeres with ageing causes chromosomal instability, which can lead to the initiation of cancer. However, it is unclear what roles telomere shortening plays in human carcinogenesis. The present study has investigated the involvement of telomere dynamics in uterine carcinogenesis. Using telomere‐FISH (telo‐FISH) assays, telomere lengths in premalignant and malignant cervical and endometrial lesions were measured and compared with chromosomal arm loss or gain. Telo‐FISH signals were visualized with Cy3‐labelled telomere‐specific probes and presented as telomere intensity (TI). Early‐stage cervical intraepithelial neoplasias (CINs), especially CIN2, had significantly shorter telomeres than corresponding normal squamous epithelia (p = 0.019), together with increased rates of chromosomal arm loss/gain (p < 0.001). Cervical cancers had relatively short telomeres, but they also showed greater heterogeneity than other sampled tissues, including those with long telomeres. In contrast, there was no significant difference between the telomere length of normal endometrium and of endometrial hyperplasia and endometrial cancer. There was no significant difference in the rate of chromosomal arm loss/gain between normal endometrium and endometrial hyperplasia. These findings suggest that progressive shortening of telomeres occurs in CIN, in association with chromosomal instability, which may play critical roles in cervical carcinogenesis. In contrast, endometrial hyperplasias have relatively stable telomeres without widespread chromosome alteration, implying that endometrial carcinogenesis involves mechanisms distinct from those of cervical carcinogenesis, possibly including microsatellite instability. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Melt blending of polypropylene‐blend‐ polyamide 6‐blend‐organoclay systems
Authors: Su Quansheng , Feng Meng , Zhang Shimin , Jiang Jianming , Yang Mingshu 
Published: August 2006

AbstractThe melt blending of polypropylene‐blend‐polyamide 6‐blend‐organoclay (PP/PA6/organoclay) systems has been investigated using an internal mixer without any traditional compatibilizer. In the presence of organoclay, the melting of PA6 phase is accelerated and the dimension of the dispersed phase in the matrix is reduced. Transmission electron microscopy results reveal clay‐rich interface zones formed between the PA6 dispersed phase and the PP matrix in the PP/PA6/organoclay system. An interface blending approach has been designed to investigate the interface zones between the immiscible polymers, and the interface zones have been characterized by Fourier transform infrared and X‐ray photoelectron spectroscopy. In the presence of the organoclay, the PA6 component in interface zones is stable even after etching extraction with formic acid, suggesting a strong interaction takes place among PP, PA6 and the organoclay. Such clay‐rich interface zones act as a compatibilizer for the two immiscible polymers, resulting in a better dispersion of PA6 phase in PP matrix. Copyright © 2006 Society of Chemical Industry
A novel approach and protocol for discovering extremely low‐abundance proteins in serum
Authors: Tanaka Yoshinori , Akiyama Hideo , Kuroda Toshihiko , Jung Giman , Tanahashi Kazuhiro , Sugaya Hiroyuki , Utsumi Jun , Kawasaki Hiroshi , Hirano Hisashi 
Published: August 2006

AbstractThe proteomic analysis of serum (plasma) has been a major approach to determining biomarkers essential for early disease diagnoses and drug discoveries. The determination of these biomarkers, however, is analytically challenging since the dynamic concentration range of serum proteins/peptides is extremely wide (more than 10 orders of magnitude). Thus, the reduction in sample complexity prior to proteomic analyses is essential, particularly in analyzing low‐abundance protein biomarkers. Here, we demonstrate a novel approach to the proteomic analyses of human serum that uses an originally developed serum protein separation device and a sequentially linked 3‐D‐LC‐MS/MS system. Our hollow‐fiber‐membrane‐based serum pretreatment device can efficiently deplete high‐molecular weight proteins and concentrate low‐molecular weight proteins/peptides automatically within 1 h. Four independent analyses of healthy human sera pretreated using this unique device, followed by the 3‐D‐LC‐MS/MS successfully produced 12 000–13 000 MS/MS spectra and hit around 1800 proteins (>95% reliability) and 2300 proteins (>80% reliability). We believe that the unique serum pretreatment device and proteomic analysis protocol reported here could be a powerful tool for searching physiological biomarkers by its high throughput (3.7 days per one sample analysis) and high performance of finding low abundant proteins from serum or plasma samples.
Gene expression changes in human cells after exposure to mobile phone microwaves
Authors: Remondini Daniel , Nylund Reetta , Reivinen Jukka , Poulletier de Gannes Florence , Veyret Bernard , Lagroye Isabelle , Haro Emmanuelle , Trillo M. Angeles , Capri Miriam , Franceschi Claudio , Schlatterer Kathrin , Gminski Richard , Fitzner Rudolf , Tauber Rudolf , Schuderer Jurgen , Kuster Niels , Leszczynski Dariusz , Bersani Ferdinando , Maercker Christian 
Published: August 2006

AbstractPossible biological effects of mobile phone microwaves were investigated in vitro. In this study, which was part of the 5FP EU project REFLEX (Risk Evaluation of Potential Environmental Hazards From Low‐Energy Electromagnetic Field Exposure Using Sensitive in vitro Methods), six human cell types, immortalized cell lines and primary cells, were exposed to 900 and 1800 MHz. RNA was isolated from exposed and sham‐exposed cells and labeled for transcriptome analysis on whole‐genome cDNA arrays. The results were evaluated statistically using bioinformatics techniques and examined for biological relevance with the help of different databases. NB69 neuroblastoma cells, T lymphocytes, and CHME5 microglial cells did not show significant changes in gene expression. In EA.hy926 endothelial cells, U937 lymphoblastoma cells, and HL‐60 leukemia cells we found between 12 and 34 up‐ or down‐regulated genes. Analysis of the affected gene families does not point towards a stress response. However, following microwave exposure, some but not all human cells might react with an increase in expression of genes encoding ribosomal proteins and therefore up‐regulating the cellular metabolism.
Mobile phone radiation causes changes in gene and protein expression in human endothelial cell lines and the response seems to be genome‐ and proteome‐dependent
Authors: Nylund Reetta , Leszczynski Dariusz 
Published: August 2006

AbstractWe have examined in vitro cell response to mobile phone radiation (900 MHz GSM signal) using two variants of human endothelial cell line: EA.hy926 and EA.hy926v1. Gene expression changes were examined in three experiments using cDNA Expression Arrays and protein expression changes were examined in ten experiments using 2‐DE and PDQuest software. Obtained results show that gene and protein expression were altered, in both examined cell lines, in response to one hour mobile phone radiation exposure at an average specific absorption rate of 2.8 W/kg. However, the same genes and proteins were differently affected by the exposure in each of the cell lines. This suggests that the cell response to mobile phone radiation might be genome‐ and proteome‐dependent. Therefore, it is likely that different types of cells and from different species might respond differently to mobile phone radiation or might have different sensitivity to this weak stimulus. Our findings might also explain, at least in part, the origin of discrepancies in replication studies between different laboratories.
Proteomic analysis and comparison of the biopsy and autopsy specimen of human brain temporal lobe
Authors: He Sizhi , Wang Qingsong , He Jintang , Pu Hai , Yang Wei , Ji Jianguo 
Published: August 2006

AbstractThe proteomic study on human temporal lobe can help us to understand the physiological function of CNS in normal as well as in pathological state. Proteomic tools are potent for the assessment of protein stability post mortem. In this pilot study, the human temporal lobe biopsy specimen with chronic pharmacoresistant temporal lobe epilepsy (TLE) and autopsy specimen in control were separated by 2‐DE. Using MALDI‐TOF‐MS and MS/MS, 375 protein spots were identified which were the products of 267 genes. Six down‐regulated and 23 up‐regulated protein spots in the autopsy specimen were ascertained after the gel image analysis with the ImageMaster software. A number of proteins that include neurotransmitter metabolic and glycolytic enzymes, cytoprotective proteins and cytoskeleton were found decreased while the precursor of apolipoprotein A‐I increased in the TLE brain. We tried several methods to prepare the protein samples and found that DNase and RNase treatment, ultracentrifugation and Amersham clean‐up kit purification can improve gel separation quality. This work optimized the sample preparation method and constructed a primary protein database of human temporal lobe and found some proteins with remarkable level change probably involved in the post‐mortem process and chronic pharmacoresistant TLE pathogenesis.
Gel‐free analysis of the human brain proteome: Application of liquid chromatography and mass spectrometry on biopsy and autopsy samples
Authors: Dumont Debora , Noben Jean‐Paul , Verhaert Peter , Stinissen Piet , Robben Johan 
Published: August 2006

AbstractThis paper reports on the findings of the Biomedical Research Institute, as one of the participants in the pilot study of the HUPO Brain Proteome Project. A biopsy and autopsy study sample derived from human brain was distributed among the participants for proteomic analysis. In our laboratory, attention was focused on protein identification using the bottom‐up shotgun approach. Protein extracts derived from both samples were trypsinized and analyzed separately by 2‐D LC and MS. In a complementary approach, the tryptic digests were analyzed directly by LC‐ESI‐MS/MS and gas‐phase fractionation in the mass spectrometer. Taken together, both proteomic approaches in combination with a stringent evaluation process, resulted in the confident identification of 209 proteins in the human brain samples under investigation.
Peroxynitrite treatment in vitro disables catalytic activity of recombinant p38 MAPK
Authors: Webster Rose P. , Macha Stephen , Brockman Diane , Myatt Leslie 
Published: August 2006

AbstractProtein tyrosine nitration is a post‐translational modification occurring under conditions of oxidative stress in a number of diseases. The causative agent of tyrosine nitration is the potent prooxidant peroxynitrite that results from the interaction of nitric oxide and superoxide. We have previously demonstrated existence of nitrotyrosine in placenta from pregnancies complicated by preeclampsia, which suggested the possibility of the existence of nitrated proteins. Nitration of various proteins has been demonstrated to more commonly result in loss of protein function. Potential nitration of p38 MAPK, a critical signaling molecule has been suggested and also tentatively identified in certain in vivo systems. In this study we demonstrate for the first time nitration of recombinant p38 MAPK in vitro and an associated loss of its catalytic activity. LC‐MS data identified tyrosine residues Y132, Y245 and Y258 to be nitrated. Nitration of these specific residues was deduced from the 45.0‐Da change in mass that these residues exhibited that was consistent with the loss of a proton and addition of the nitro group.
Evaluation of 2‐DE protein patterns from pre‐ and postnatal stages of the mouse brain
Authors: Seefeldt Ingo , Nebrich Grit , Römer Irmgard , Mao Lei , Klose Joachim 
Published: August 2006

AbstractBrains of the mouse from three developmental stages, embryo day 16 (Ed16), postnatal stage one week (1W) and eight weeks (8W), were distributed to different laboratories for a collaborative proteome analysis (The Human Brain Proteome Project). As one of the laboratories involved in this project, we separated total protein extracts of the brains by large gel 2‐DE. From the 2‐DE protein patterns a section was evaluated for each of the three stages according to resolution, reproducibility and quantitative changes using an image analysis software. The evaluated pattern section was selected to allow comparisons of 2‐DE patterns between different laboratories on the basis of optimum separation. Changes in protein expression were analysed within two phases of development: Stage Ed16 versus stage 1W and stage 1W versus stage 8W. Out of the 200 protein spots evaluated 5–6% showed quantitative changes in the range of ≥30% between two stages. The relationship in the frequency of up‐ and down‐regulated protein spots differed between the two investigated phases. Most of the protein spots which showed altered expression between two stages were identified by MS. High quality in protein separation and evaluation is demonstrated.
Gaining knowledge from previously unexplained spectra‐application of the PTM‐Explorer software to detect PTM in HUPO BPP MS/MS data
Authors: Chamrad Daniel C. , Körting Gerhard , Schäfer Heike , Stephan Christian , Thiele Herbert , Apweiler Rolf , Meyer Helmut E. , Marcus Katrin , Blüggel Martin 
Published: August 2006

AbstractA novel software tool named PTM‐Explorer has been applied to LC‐MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM‐Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM‐Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM‐Explorer was evaluated on excellently manually characterized and evaluated LC‐MS/MS data sets from Alpha‐A‐Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.
A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies
Authors: Martens Lennart , Müller Michael , Stephan Christian , Hamacher Michael , Reidegeld Kai A. , Meyer Helmut E. , Blüggel Martin , Vandekerckhove Joël , Gevaert Kris , Apweiler Rolf 
Published: August 2006

AbstractThe pilot phase of the Brain Proteome Project (BPP), the Human Proteome Organization (HUPO) initiative that focuses on studies of the brain of both humans and mice, has now been completed. Participating laboratories studied the proteomes of two human samples derived from biopsy and autopsy as well as three mouse samples from various developmental stages. With the combined and centrally reprocessed data now available, a comparison in terms of protein identifications and project organization is made between the HUPO BPP pilot and three other proteomics studies: the HUPO Plasma Proteome Project (PPP) pilot, a proteome of human blood platelets and a recently published comprehensive mouse proteome. Finally, as any comparison between large‐scale proteomics datasets is decidedly non‐trivial, we also evaluate and discuss several ways to go about comparing such different result sets.
Detection of a hidden folding intermediate in the focal adhesion target domain: Implications for its function and folding
Authors: Zhou Zheng , Feng Hanqiao , Bai Yawen 
Published: August 2006

AbstractThe focal adhesion target (FAT) domain of focal adhesion kinase has a four‐helix bundle structure. Based on a hydrogen exchange‐constrained computer simulation study and some indirect experimental results, it has been suggested that a partially unfolded state of the FAT domain with the N‐terminal helix unfolded plays an important role in its biological function. Here, using a native‐state hydrogen exchange method, we directly detected an intermediate with the N‐terminal helix unfolded in a mutant (Y925E) of the FAT domain. In addition, kinetic folding studies on the FAT domain suggest that this intermediate exists on the native side of the rate‐limiting transition state for folding. These results provide more direct evidence of the existence of the proposed intermediate and help to understand the folding mechanism of small single domain proteins. Proteins 2006. © 2006 Wiley‐Liss, Inc.
High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: The role of histidine residues in modulating the strength of the root effect
Authors: Mazzarella Lelio , Vergara Alessandro , Vitagliano Luigi , Merlino Antonello , Bonomi Giovanna , Scala Sonia , Verde Cinzia , di Prisco Guido 
Published: August 2006

AbstractThe Root effect is a widespread property in fish hemoglobins (Hbs) that produces a drastic reduction of cooperativity and oxygen‐binding ability at acidic pH. Here, we report the high‐resolution structure of the deoxy form of Hb isolated from the Antarctic fish Trematomus bernacchii (HbTb) crystallized at pH 6.2 and 8.4. The structure at acidic pH has been previously determined at a moderate resolution (Ito et al., J Mol Biol 1995;250:648–658). Our results provide a clear picture of the events occurring upon the pH increase from 6.2 to 8.4, observed within a practically unchanged crystal environment. In particular, at pH 8.4, the interaspartic hydrogen bond at the α1β2 interface is partially broken, suggesting a pKa close to 8.4 for Asp95α. In addition, a detailed survey of the histidine modifications, caused by the change in pH, also indicates that at least three hot regions of the molecule are modified (Eβ helix, Cβ‐tail, CDα corner) and can be considered to be involved at various levels in the release of the Root protons. Most importantly, at the CDα corner, the break of the salt bridge Asp48α–His55α allows us to describe a detailed mechanism that transmits the modification from the CDα corner far to the α heme. More generally, the results shed light on the role played by the histidine residues in modulating the strength of the Root effect and also support the emerging idea that the structural determinants, at least for a part of the Root effect, are specific of each Hb endowed with this property. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Coherence control of electron spin currents in semiconductors
Authors: van Driel Henry M. , Sipe John E. , Smirl Arthur L. 
Published: August 2006

AbstractWe provide an overview of some of our recent work on the use of one color and two color optical techniques to generate and control electronic spin currents in semiconductors for which a spin–orbit interaction exists. The generation process relies on the quantum interference between different absorption pathways, such as that between single and two photon absorption or those involving different polarization states of a monochromatic beam. For different crystal orientations and/or beam polarizations it is possible to generate a spin current with or without an electric current, and an electrical current with or without a spin current. In our experiments, which are conducted either at 80 K or 295 K, we typically employ nominally 100 fs pulses centered near 1500 and 750 nm. The currents generated are quasi‐ballistic and the carriers typically move distances of ∼1–10 nm, determined by the momentum relaxation time, which is of the order of 100 fs. The transient characteristics of spin‐polarized electrical currents generated in strained GaAs at room temperature by ∼100 fs pulses is detected by the emitted THz radiation. Pure spin currents can be detected by taking advantage of the accumulation of up and down spins on opposite sides of tightly focused pump beams. The spin states are detected through differential transmission measurements of tightly focused right and left circularly polarized, near‐band‐edge probe pulses, delayed by several picoseconds from the pump pulses to allow carrier thermalization to occur. By spatial scanning across the differential spin profiles and determining the amplitude of the response we are able to translate this into nm spatial resolution of spin displacement. Finally, the ability to generate ballistic currents using purely optical techniques allows us to generate transverse Hall‐like currents, with transverse charge currents generated from pure spin currents and transverse spin currents generated from pure charge currents. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pure dephasing of carriers in quantum dots due to anharmonicity‐induced phonon scattering
Authors: Machnikowski Paweł 
Published: August 2006

AbstractAnharmonic coupling between phonon modes leads to scattering of phonons on the polaronic deformation around localized charges, which results in dephasing of charge states. This dephasing process is studied for an electron in a double‐dot structure and for an exciton in a quantum dot. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction between localized and delocalized surface plasmon polariton modes in a metallic photonic crystal
Authors: Christ A. , Zentgraf T. , Tikhodeev S. G. , Gippius N. A. , Martin O. J. F. , Kuhl J. , Giessen H. 
Published: August 2006

AbstractWe experimentally and theoretically study the controlled coupling between localized and delocalized surface plasmon modes supported by a multilayer metallic photonic crystal slab. The model system to visualize the interaction phenomena consists of a gold nanowire grating and a spatially separated homogeneous silver film. We show that plasmon‐plasmon coupling leads to drastic modification of the optical properties in dependence on the chosen geometrical parameters. Strong coupling and plasmon hybridization can be clearly observed. The numerical calculations reveal excellent agreement with the experiments. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Plasmon‐polariton transport in hybrid semiconductor–metal–nanoparticle structures with gain
Authors: Citrin D. S. , Backes T. D. 
Published: August 2006

AbstractPlasmon‐polariton transport in noble‐metal nanoparticle chains embedded in an optical‐gain medium are considered theoretically. We show that short‐wavelength modes can acquire gain to counter loss. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)