bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of in situ labeled cell surface proteins by mass spectrometry: Application to the membrane subproteome of human mammary epithelial cells
Authors: Chen Wan‐Nan U. , Yu Li‐Rong , Strittmatter Eric F. , Thrall Brian D. , Camp David G. , Smith Richard D. 
Published: August 2003

AbstractCharacterization of the surface exposed membrane subproteome of human mammary epithelial cells (strain 184 A1L5) implemented lysine specific in situ labeling of the proteins using sulfosuccinimidyl‐6‐(biotinamido)hexanoate, followed by enrichment of the biotinylated, tryptically digested peptides, and then liquid chromatography‐tandem mass spectrometry analysis of the labeled peptides. Probing the membrane subproteome in this manner yielded unambiguous identification of proteins situated on the cell surface. The method reported can be adapted to include stable isotope labeling of proteins for quantitation of changes occurring on the cell surface in response to specific perturbations.
A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease
Authors: Carrette Odile , Demalte Isabelle , Scherl Alexander , Yalkinoglu Oezkarn , Corthals Garry , Burkhard Pierre , Hochstrasser Denis F. , Sanchez Jean‐Charles 
Published: August 2003

AbstractThe diagnosis of Alzheimer's disease (AD), the most common form of dementia in the general population, usually relies upon the presence of typical clinical features and structural changes on brain magnetic resonance imaging. Over the last decade, a number of biological abnormalities have been reported in the cerebrospinal fluid (CSF) of AD patients, in particular altered levels of the tau protein and the 1‐42 fragment of the amyloid precursor protein. These, however, have not yet proved sensitive and specific enough to be included in the diagnostic criteria for AD, leaving plenty of room for the search of novel biomarkers. The present study describes the analysis of CSF polypeptides by a protein‐chip array technology called surface enhanced laser desorption/ionization‐time of flight‐mass spectrometry (SELDI‐TOF‐MS). Using this approach, we detected statistically significant quantitative differences (p < 0.05) regarding four overexpressed and one underexpressed polypeptides in the CSF of AD patients as compared to healthy controls. Four of them were further purified by strong anionic exchange chromatography (SAX) and identified by MS analysis as cystatin C, two β‐2‐microglobulin isoforms, an unknown 7.7 kDa polypeptide, and a 4.8 kDa VGF polypeptide. The combination of the five polypeptides for the diagnosis of AD allowed to classified six AD patients out of the nine included in this study and all the ten controls, which means in this small cohort that the specificity and sensitivity are 100% and 66%, respectively. This study, based on the protein‐chip array technology, demonstrates the presence in the CSF of novel potential biomarkers for AD, which may be used for the diagnosis and perhaps the assessment of the severity and progression of the disease.
Prefractionation techniques in proteome analysis
Authors: Righetti Pier Giorgio , Castagna Annalisa , Herbert Ben , Reymond Frederic , Rossier Joël S. 
Published: August 2003

AbstractThe present review deals with a number of prefractionation protocols in preparation for two‐dimensional map analysis, both in the fields of chromatography and in the field of electrophoresis. In the first case, Fountoulaki’s groups has reported just about any chromatographic procedure useful as a prefractionation step, including affinity, ion‐exchange, and reversed‐phase resins. As a result of the various enrichment steps, several hundred new species, previously undetected in unfractionated samples, could be revealed for the first time. Electrophoretic prefractionation protocols include all those electrokinetic methodologies which are performed in free solution, essentially all relying on isoelectric focusing steps. The devices here reviewed include multichamber apparatus, such as the multicompartment electrolyzer with Immobiline membranes, Off‐Gel electrophoresis in a multicup device and the Rotofor, an instrument also based on a multichamber system but exploiting the conventional technique of carrier‐ampholyte‐focusing. Other instruments of interest are the Octopus, a continuous‐flow device for isoelectric focusing in a upward flowing liquid curtain, and the Gradiflow, where different pI cuts are obtained by a multistep passage through two compartments buffered at different pH values. It is felt that this panoply of methods could offer a strong step forward in “mining below the tip of the iceberg” for detecting the “unseen proteome”.
OLAV: Towards high‐throughput tandem mass spectrometry data identification
Authors: Colinge Jacques , Masselot Alexandre , Giron Marc , Dessingy Thierry , Magnin Jérôme 
Published: August 2003

AbstractMass spectrometry combined with database searching has become the preferred method for identifying proteins in proteomics projects. Proteins are digested by one or several enzymes to obtain peptides, which are analyzed by mass spectrometry. We introduce a new family of scoring schemes, named OLAV, aimed at identifying peptides in a database from their tandem mass spectra. OLAV scoring schemes are based on signal detection theory, and exploit mass spectrometry information more extensively than previously existing schemes. We also introduce a new concept of structural matching that uses pattern detection methods to better separate true from false positives. We show the superiority of OLAV scoring schemes compared to MASCOT, a widely used identification program. We believe that this work introduces a new way of designing scoring schemes that are especially adapted to high‐throughput projects such as GeneProt large‐scale human plasma project, where it is impractical to check all identifications manually.
Preprocessing of tandem mass spectrometric data to support automatic protein identification
Authors: Gentzel Marc , Köcher Thomas , Ponnusamy Saravanan , Wilm Matthias 
Published: August 2003

AbstractLiquid chromatography tandem mass spectrometry is a major tool for identifying proteins. The fragment spectra of peptides can be interpreted automatically in conjunction with a sequence database search. With the development of powerful automatic search engines, research now focuses on optimizing the result returned from database searches. We present a series of preprocessing steps for fragment spectra to increase the accuracy and specificity of automatic database searches. After processing, the correct amino acid sequences from the database can be related better to the fragment spectra. This increases the sensitivity and reliability of protein identifications, especially with very large genomic databanks, and can be important for the systematic characterization of post‐translational modifications.
Mass spectrometric proteome analysis for profiling temperature‐dependent changes of protein expression in wild‐typeCaenorhabditis elegans
Authors: Mádi András , Mikkat Stefan , Ringel Bruno , Ulbrich Markus , Thiesen Hans‐Jürgen , Glocker Michael O. 
Published: August 2003

AbstractWe investigated the effect of cultivation temperatures on the protein expression levels in the fourth larval stage of the postembryonic development of wild‐typeCaenorhabditis elegansby mass spectrometric proteome analysis. From the 64 protein spots that were investigated, 5 spots were found reproducibly differently expressed when proteome maps derived from animals kept at 15°C and at 25°C, respectively, were compared. Spots of heat shock proteins HSP 70 (CE18679 or CE09682) and HSP 16 (CE14249) were present only in gels from protein extracts when worms were grown at 15°C. Spots of two metabolic enzymes, the isocitrate dehydrogenase (CE10345) and the aspartic proteinase (CE21681) were detected only in cultures grown at the lower temperature as well. A protein with still unknown function (CE05036) was present only in gels from worm samples grown at 25°C. We show for the first time by proteome analyses that cultivation of worms at the lowest temperature of the known physiological range (15°C) already triggers a (weak) stress response in wild‐type animals. This work led to the identification of “internal control proteins” in the wild‐type strain for further characterization of temperature‐sensitive strains using a proteomics approach.
Changes in protein expression profiles in bivalve molluscs (Chamaelea gallina) exposed to four model environmental pollutants
Authors: Rodríguez‐Ortega Manuel J. , Grøsvik Bjørn Einar , Rodríguez‐Ariza Antonio , Goksøyr Anders , López‐Barea Juan 
Published: August 2003

AbstractProteomics has been used in the clam Chamaelea gallina as a preliminary screening of changes in protein expression caused by pollutants, potentially useful as new biomarkers. Clams were exposed in water for seven days to four model contaminants, Aroclor 1254, copper(II), tributyltin (TBT), and arsenic(III), and cytosolic fractions were initially analyzed by two‐dimensional (2‐D) electrophoresis in 7 cm IPG strips (pH 4–7). On average, about 1000 spots were resolved and altered expression was qualitatively detected in 9–26 spots per treatment. Aroclor 1254, Cu(II) and As(III) had a mainly upregulating effect, in contrast to TBT. Altered protein expression was confirmed in 18 cm gels (at narrow pH ranges). The 15 spots more drastically altered were excised and analyzed by mass spectrometry (MS), and four proteins were identified. Aroclor 1254 and Cu(II) upregulated putative isoforms of tropomyosin and light chain of myosin. Actin was downregulated by Aroclor and Cu(II) but upregulated by TBT and As(III), while the opposite behavior was shown by a truncated actin form, homologous to the Drosophila act87E gene product. The exclusive identification of cytoskeletal proteins could reflect their relative abundance, their prevalence in databases in molluscs, or their role as major targets of pollutant‐related oxidative stress.
Exploitation of specific properties of trifluoroethanol for extraction and separation of membrane proteins
Authors: Deshusses Jacques M. P. , Burgess Jennifer A. , Scherl Alexander , Wenger Yvan , Walter Nadia , Converset Véronique , Paesano Salvo , Corthals Garry L. , Hochstrasser Denis F. , Sanchez Jean‐Charles 
Published: August 2003

AbstractHydrophobic proteins are difficult to analyze by two‐dimensional electrophoresis (2‐DE) because of their intrinsic tendency to self‐aggregate during the first dimension (isoelectric focusing, IEF) or the equilibration steps. This aggregation renders their redissolution for the second dimension uncertain and results in the reduction of the number and intensity of protein spots, and in undesirable vertical and horizontal streaks across gels. Trifluoroethanol (TFE) is traditionally used at high concentration to solubilize peptides and proteins for NMR studies. Depending upon its concentration, TFE strongly affects the three‐dimensional structure of proteins. We report here a phase separation system based on TFE/CHCl3, which is able to extract a number of intrinsic membrane proteins. The addition of TFE in the in‐gel sample rehydration buffer to improve membrane protein IEF separation is also presented. The procedure using urea, thiourea, and sulfobetaine as chaotropic agents was modified by the addition of TFE and removing of sulfobetaine at an optimized concentration in the solubilization medium used for the first dimension. When using membrane fractions isolated from Escherichia coli, the intensity and the number of spots detected from 2‐DE gels that used TFE in the solubilization medium were significantly increased. The majority of the proteins identified using peptide mass fingerprinting and tandem mass spectrometry (MS/MS) were intrinsic membrane proteins, proteins of beta barrel structure or transmembrane proteins.
Development of narrow immobilized pH gradients covering one pH unit for human seminal plasma proteomic analysis
Authors: Starita‐Geribaldi Mireille , Roux Françoise , Garin Jérôme , Chevallier Daniel , Fénichel Patrick , Pointis Georges 
Published: August 2003

AbstractMicropreparatively loaded two‐dimensional (2‐D) electrophoresis gels were used to identify human seminal plasma polypeptides by using narrow immobilized pH gradients (IPGs) covering one pH unit as first dimension. This investigation was restricted to IPG 4.5–5.5 and 5–6 because of the main spot distribution in the acidic part of the 2‐D map performed with IPG 3–10, a zone presumed to be rich in spermatogenic markers. Both highly expressed and minor spots of the 2‐D map were analyzed by matrix‐assisted laser desorption/ionization mass spectrometry and tandem mass spectroscopy analysis. Identification was obtained by a combination of mass spectrometry and database searching. Identified proteins were of different origin from the male genital tract and some proteolysis was observed. They appeared as either isolated molecules or isoforms. At the analytical level, narrow IPGs allowed a two‐fold increase in the number of spots, improved resolution of minor spots particularly in surrounding of highly expressed spots and sensitivity level. Some of these faint spots were differently expressed in azoospermic patients as compared to normospermic men. Therefore, zooming‐in on the proteome of human seminal plasma allowed more accurate differential expression analysis of impaired spermatogenesis associated markers.
Towards a phosphoproteome map of Corynebacterium glutamicum
Authors: Bendt Anne K. , Burkovski Andreas , Schaffer Steffen , Bott Michael , Farwick Mike , Hermann Thomas 
Published: August 2003

AbstractIn this study, the phosphoproteome of Corynebacterium glutamicum, an industrially important soil bacterium of the Corynebacterium/Mycobacterium/Nocardia (CMN) group of Gram‐positive bacteria, was investigated by two different detection methods: first, by in vivo radio‐labeling using [33P]‐phosphoric acid with subsequent autoradiography and second, by immunostaining with phosphoamino acid‐specific monoclonal antibodies. After two‐dimensional gel electrophoresis (2‐DE), around 60 [33P]‐labeled protein spots were visualized and around 90 antibody‐decorated protein spots detected; 31 of the protein spots were detected with both methods. By peptide mass fingerprinting, 41 different proteins were identified, namely 5‐enolpyruvylshikimate 3‐phosphate synthase, aconitase, acyl‐CoA carboxylase, acyl‐CoA synthetase, ATP (synthase α‐ and β‐chain), carbamoyl‐phosphate synthase, citrate synthase, cysteine synthase, DnaK, the elongation factors G, P, Ts and Tu, enolase, fructose bisphosphate aldolase, fumarase, Gap dehydrogenase, glutamine synthetase I, glycine hydroxymethyltransferase, GroEL2, GTPase, heat‐inducible transcriptional repressor DnaJ2, inorganic pyrophosphatase, isocitrate dehydrogenase, ketol‐acid reductoisomerase, lactate dehydrogenase, leucine‐tRNA ligase, lipoamide dehydrogenase, methionine synthase, O‐acetylhomoserine sulfhydrylase, pyruvate carboxylase, pyruvate kinase, pyruvate oxidase, ribosomal protein S1, RNA polymerase (β‐subunit), succinyl‐CoA:CoA transferase, transketolase and UDP‐N‐acetylmuramoyl‐L‐alanine ligase, besides a hypothetical 35k protein and a hypothetical glucose kinase. Both detection techniques were used to create a phosphoproteome map. Additionally, the influence of nitrogen deprivation on the phosphoproteome of C. glutamicum was investigated.
Psychometric properties of the Chinese version of the Mini‐Mental Adjustment to Cancer (MINI‐MAC) scale
Authors: Ho Samuel M.Y. , Kam Fung Wong , Chan Cecilia L.W. , Watson Maggie , Tsui Yenny K.Y. 
Published: August 2003

AbstractThe psychometric properties of a Chinese version of the Mini‐Mental Adjustment to Cancer scale (Mini‐MAC) were examined among 115 Chinese cancer patients in Hong Kong. The five subscales from the original Mini‐MAC (Anxious Preoccupation, Helpless–Hopeless, Fighting Spirit, Fatalism, Cognitive Avoidance) had acceptable internal reliabilities (Cronbach's α ranged from 0.65 to 0.88) and construct validities in our sample. Factor analysis suggested three factors: (1) Negative Emotion (α=0.91) contained items of the Anxious Preoccupation and the Helpless–Hopeless subscales of the original Mini‐MAC, (2) Positive Attitude (α=0.77) combined the Fighting Spirit and the Fatalism subscales of the original version, and (3) Cognitive Avoidance (α=0.65) which was identical to the Cognitive Avoidance subscale of the original Mini‐MAC. Construct validities of the novel factors were shown by their correlations with HADS Anxiety and Depression scores in the predicted directions. It was concluded that both the 5‐factor model from the original Mini‐MAC and the 3‐factor model from the present study were valid in Hong Kong Chinese cancer patients. The results were discussed in terms of the meaning of the original Mini‐MAC factors and cultural differences in coping functions between Chinese and UK cancer patients. Copyright © 2003 John Wiley & Sons, Ltd.
Lay understanding of terms used in cancer consultations
Authors: Chapman Kristina , Abraham Charles , Jenkins Valerie , Fallowfield Lesley 
Published: August 2003

AbstractThe study assessed lay understanding of terms used by doctors during cancer consultations.Terms and phrases were selected from 50‐videotaped consultations and included in a survey of 105 randomly selected people in a seaside resort. The questionnaire included scenarios containing potentially ambiguous diagnostic/prognostic terms, multiple‐choice, comprehension questions and figures on which to locate body organs that could be affected by cancer. Respondents also rated how confident they were about their answers.About half the sample understood euphemisms for the metastatic spread of cancer e.g. ‘seedlings’ and ‘spots in the liver’ (44 and 55% respectively). Sixty‐three per cent were aware that the term ‘metastasis’ meant that the cancer was spreading but only 52% understood that the phrase ‘the tumour is progressing’ was not good news. Yet respondents were fairly confident that they understood these terms. Knowledge of organ location varied. For example, 94% correctly identified the lungs but only 46% located the liver.The findings suggest that a substantial proportion of the lay public do not understand phrases often used in cancer consultations and that knowledge of basic anatomy cannot be assumed. Yet high confidence ratings indicate that asking if patients understand is likely to overestimate comprehension. Awareness of the unfamiliarity of the lay population with cancer‐related terms could prompt further explanation in cancer‐related consultations. Copyright © 2003 John Wiley & Sons, Ltd.
Audiotaped social comparison information for cancer patients undergoing radiotherapy: Differential effects of procedural, emotional and coping information
Authors: Bennenbroek Femke T.C. , Buunk Bram P. , Stiegelis Heidi E. , Hagedoorn Mariët , Sanderman Robbert , Van den Bergh Alfons C.M. , Botke Gerrit 
Published: August 2003

AbstractThe present study focused on the effects of social comparison information on subjective understanding of radiation therapy, validation of emotions, and self‐efficacy of cancer patients undergoing radiation therapy. The effects of three different audiotapes, containing different kinds of social comparison information, were examined. On the procedural tape a man and woman discussed their illness and radiation treatment, on the emotion tape they focused on the emotional aspects of these issues, and on the coping tape they focused on the way they had been coping. The effects of these tapes were measured on subjective understanding about radiation therapy, validation and recognition of emotions, self‐efficacy, and mood. The results indicate positive effects of the tapes, especially of the procedural and the coping tape. These audiotapes increased understanding of radiation therapy, self‐efficacy and the feeling of validation of emotions. Therefore, these tapes may be an important supplement to existing patient education information. Possible explanations and practical implications are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Cognitive‐existential group psychotherapy for women with primary breast cancer: A randomised controlled trial
Authors: Kissane David W. , Bloch Sidney , Smith Graeme C. , Miach Patricia , Clarke David M. , Ikin Jillian , Love Anthony , Ranieri Nadia , McKenzie Dean 
Published: August 2003

AbstractBackground. We conducted a randomised, controlled trial of cognitive‐existential group therapy (CEGT) for women with early stage breast cancer receiving adjuvant chemotherapy with the aim of improving mood and mental attitude to cancer.Methods. Women were randomised to 20 sessions of weekly group therapy plus 3 relaxation classes or to a control arm receiving 3 relaxation classes. Assessments, independently done at baseline, 6 and 12 months, included a structured psychiatric interview and validated questionnaires covering mood, attitudes to cancer, family relationships, and satisfaction with therapy.Results. Three hundred and three of 491 (62%) eligible patients participated over 3 years. Distress was high pre‐intervention: 10% were diagnosed as suffering from major depression, 27% from minor depression and 9% from anxiety disorders. On an intention‐to‐treat analysis, there was a trend for those receiving group therapy (n=154) to have reduced anxiety (p=0.05, 2‐sided) compared to controls (n=149). Women in group therapy also showed a trend towards improved family functioning compared to controls (p=0.07, 2‐sided). The women in the groups reported greater satisfaction with their therapy (p<0.001, 2‐sided), appreciating the support and citing better coping, self‐growth and increased knowledge about cancer and its treatment. They valued the CEGT therapy. Overall effect size for the group intervention was small (d=0.25), with cancer recurrence having a deleterious effect in three of the 19 therapy groups. Psychologists as a discipline achieved a moderate mean effect size (d=0.52).Conclusion. CEGT is a useful adjuvant psychological therapy for women with early stage breast cancer. Interaction effects between group members and therapists are relevant to outcome. Group‐as‐a‐whole effects are powerful, but the training and experience of the therapist is especially critical to an efficacious outcome. Copyright © 2003 John Wiley & Sons, Ltd.
The relationship of APOE genotype to neuropsychological performance in long‐term cancer survivors treated with standard dose chemotherapy
Authors: Ahles Tim A. , Saykin Andrew J. , Noll Walter W. , Furstenberg Charlotte T. , Guerin Stephen , Cole Bernard , Mott Leila A. 
Published: August 2003

AbstractPurpose: The primary purpose of this study was to compare the neuropsychological performance of long‐term survivors of breast cancer and lymphoma treated with standard dose chemotherapy who carried the ε4 allele of the Apolipoprotein E (APOE) gene to those who carry other APOE alleles.Patients and methods: Long‐term survivors (mean=8.8±4.3 years post‐treatment) of breast cancer (N=51, age=55.9±8.8) or lymphoma (N=29, age=55.8±11.6) who had been treated with standard‐dose chemotherapy completed a standardized battery of neuropsychological and psychological tests. Survivors were also classified into two groups based on the presence (N=17) or absence (N=63) of at least one ε4 allele of APOE.Results: Analysis of covariance, controlling for age, gender, education, diagnosis, and WRAT‐3 reading subtest (a proxy measure of baseline IQ), indicated that survivors with at least one ε4 allele scored significantly lower in the visual memory (p<0.03) and the spatial ability (p<0.05) domains and tended to score lower in the psychomotor functioning (p<0.08) domain as compared to survivors who did not carry an ε4 allele. No group differences were found on depression, anxiety, or fatigue.Conclusions: The results of this study provide preliminary support for the hypothesis that the ε4 allele of APOE may be a potential genetic marker for increased vulnerability to chemotherapy‐induced cognitive decline. Copyright © 2003 John Wiley & Sons, Ltd.