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PubMed2005

Proteomic analysis of cadmium-induced protein profile alterations from marine alga Nannochloropsis oculata.

Protein profile alterations following exposure to cadmium were examined in marine alga Nannochloropsis oculata through proteomic analysis. Alterations of the protein expression patterns following 10 muM cadmium treatment were analyzed on 2-dimensional gels. Out of 380 protein spots detected on 2-D gel using Coomassie staining, 11 spots were changed significantly following cadmium treatment. Because of the non-availability of molecular background information on this non-sequenced algal species, cross-species protein identification through ESI-Q-TOF MS/MS was used to identify altered proteins. Two newly induced proteins were identified as malate dehydrogenase orthologue and NADH dehydrogenase orthologue. One suppressed protein was identified to be glyceraldehydes 3-phosphate dehydrogenase A. Protein spot showing a 3-fold increase was identified as mitochondrial NADH: ubiquinone oxidoreductase orthologue. However, we could not find any matches in the database from ESI-Q-TOF MS/MS for the remaining seven proteins, thus only partial peptide sequences of these proteins were found.

Amino Acid Sequence↗

PubMed1993

Whole cell protein profiling of actinobacillus-like strains classified as taxon 2 and taxon 3 according to Bisgaard.

Thirty-nine strains representing all biovars established within the taxa 2 and 3 complex of Bisgaard and two strains belonging to the avian [P.] haemolytical[A.] salpingitidis complex were characterized by one-dimensional SDS-PAGE of cellular proteins. The protein patterns, which contained 40 to 45 discrete protein bands, were highly reproducible. Numerical analysis of the background protein patterns obtained resulted in six major and twelve minor groups (phena). Comparison of the phena defined by protein profiling with species/groups previously established by DNA: DNA hybridization, chemotyping and "biotyping" showed that the best correlation existed between DNA:DNA hybridization and "biotyping". A correlation between results obtained from DNA:DNA hybridization and protein profiling was not obtained. With a few exceptions, a connection was demonstrated between protein profiles and hosts from which the strains belonging to the respective phena originated.

Actinobacillus↗

PubMed2006

Multivariate analysis of protein profiles of metal hyperaccumulator Thlaspi caerulescens accessions.

Thlaspi caerulescens is increasingly acknowledged as one of the best models for studying metal hyperaccumulation in plants. In order to study the mechanisms underlying metal hyperaccumulation, we used proteomic profiling to identify differences in protein intensities among three T. caerulescens accessions with pronounced differences in tolerance, uptake and root to shoot translocation of Zn and Cd. Proteins were separated using two-dimensional electrophoresis and stained with SYPRO Orange. Intensity values and quality scores were obtained for each spot by using PDQuest software. Principal component analysis was used to test the separation of the protein profiles of the three plant accessions at various metal exposures, and to detect groups of proteins responsible for the differences. Spot sets representing individual proteins were analysed with the analysis of variance and non-parametric Kruskal-Wallis test. Clearest differences were seen among the Thlaspi accessions, while the effects of metal exposures were less pronounced. The 48 tentatively identified spots represent core metabolic functions (e.g. photosynthesis, nitrogen assimilation, carbohydrate metabolism) as well as putative signalling and regulatory functions. The possible roles of some of the proteins in heavy metal accumulation and tolerance are discussed.

Cadmium↗

PubMed1994

Biochemical properties and whole-cell protein profiles of group G streptococci isolated from dogs.

Whole-cell protein profiles obtained by SDS-PAGE were used in conjunction with physiological tests to differentiate strains of Streptococcus canis isolated from dogs. Fermentation of trehalose and lactose, aesculin hydrolysis together with production of beta-D-glucuronidase and alpha-D-galactosidase allowed the demonstration of nine different biotypes. However, visual analysis of the protein patterns and comparison by the coefficient of Dice showed minor differences in band patterns among strains. Only two different profiles were observed. Although a correlation between biotyping and protein profile has been found, this kind of analysis did not provide the basis for a typing method.

Animals↗

PubMed2005

High abundance protein profiling of cystic fibrosis lung epithelial cells.

Protein profiles of cultured cystic fibrosis (CF) lung epithelial cells were analyzed by two-dimensional gel electrophoresis and mass spectrometry (MS). The analysis gave rise to a protein map over the pI range of 4-7, and a molecular weight range of ca. 100-10 kDa. The map contains 194 identified proteins, which were detectable by silver stain. All silver stained features were identified by matrix-assisted laser desorption/ionization-time of flight MS of tryptic peptides. Some proteins were found to be represented by multiple features on the 2-D gel. Among the high abundance proteins identified were sets of proteins associated with inflammation, including the classical NFkappaB, p65 (RelA) and NFkappaB, p65 (RelB). We suggest that this composite atlas of the high abundance CF lung epithelial proteome will serve as a reference database for future studies of candidate CF drugs, validating different approaches to CFTR gene therapy, and analogous investigations of other types of human lung disorders.

Cell Culture Techniques↗

PubMed1996

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.

DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving homologous sequences, such as database searches and inferences on structure, function or phylogeny made from multiple alignments. A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix for one or more aligned sequences) against the three translation frames of a DNA strand, allowing frameshifting. The algorithm has been incorporated into a new package, WiseTools, for comparison of biological sequences. A protein profile can be compared against either a DNA sequence or a protein sequence. The program PairWise may be used interactively for alignment of any two sequence inputs. SearchWise can perform combinations of searches through DNA or protein databases by a protein profile or DNA sequence. Routine application of the programs has revealed a set of database entries with frameshifts caused by errors in sequence determination.

Algorithms↗

PubMed1990

Neonatal exposure to oestrogens alters the protein profiles and gene expression in the genital tract of adult male mice.

After neonatal administration of supraphysiological doses of oestradiol, the concentration of tissue proteins, in adult mice, was significantly reduced by 39, 45 and 56% in epididymis, vas deferens and seminal vesicle respectively. The protein profiles showed persistent alterations. In epididymis, 4 protein bands were differentially increased (14.4, 43 and 67 kDa) or reduced (24 kDa) in oestrogenized males. In vas deferens, 4 proteins were increased (14.4, 49,67 and 76 kDa) and one (34 kDa) virtually absent. In seminal vesicle, about 20 proteins of varying molecular weights (12-140 kDa) were differentially increased or decreased. Testosterone substitution, at adulthood, was unable to reverse these effects. Treatments with oestradiol during adult life induced persistent alterations in the protein profiles of the 3 organs but, in contrast to neonatal treatment, these alterations could be reversed by androgen therapy. A cDNA library has been constructed with RNA prepared from adult seminal vesicle and screened by differential hybridization. Neonatal oestrogenization strongly reduced the abundance of some mRNA species. Eleven recombinants containing putative oestrogen-sensitive sequences were isolated. Two of them, having an insert of about 500 base pairs, were used for dot-blot hybridization. Results showed that the two clones contained sequences which were differently regulated by androgens.

Aging↗

PubMed2004

Antibodies immobilized as arrays to profile protein post-translational modifications in mammalian cells.

Previously, we demonstrated that antibodies printed on a solid support were able to detect protein-protein interaction in mammalian cells. Here we further developed the antibody array system for detecting proteins with various post-translational modifications in mammalian cells. In this novel approach, immunoprecipitated proteins were labeled with fluorescent dye followed by incubation over antibody arrays. Targeted proteins, captured by the antibodies immobilized on PVDF membrane or glass slide, were detected by means of near infrared fluorescent scanner or fluorescent microscopy. To demonstrate the application of the antibody arrays in protein post-translational modifications, we profiled protein tyrosine phosphorylation, ubiquitination, and acetylation in mammalian cells under different conditions. Our results indicate that antibody array technology can provide a powerful means of profiling a large number of proteins with different post-translational modifications in cells.

3T3 Cells↗

PubMed1994

Outer membrane protein profiling to distinguish between Haemophilus aegyptius and non-capsulate Haemophilus influenzae biotype III.

Outer membrane protein profiling was used to assist in determining the identity of an isolate of Haemophilus spp. that was presumptively identified as non-capsulate Haemophilus influenzae biotype III. The possibility that this strain was in fact Haemophilus aegyptius was queried because of clinical information and the source of the isolate. Sodium dodecyl-sulphate polyacrylamide gel electrophoresis was used to establish the identity of the isolate as non-capsulate H. influenzae biotype III and no H. aegyptius. Generally, protein profiling compared very favourably with other standard tests for identifying H. aegyptius: the method was easily and rapidly performed and gave an unequivocal result.

Bacterial Outer Membrane Proteins↗

PubMed1992

[Studies of outer membrane protein profiles by SDS-PAGE for Campylobacter jejuni in an epidemiological investigation].

The characteristics of outer membrane protein profiles of 41 strains of Campylobacter jejuni from various sources by SDS-PAGE was studied. Seven and nine OMP patterns were differentiated respectively by the presence or absence of six outer membrane protein bands and by the number and size of the molecular weight of the major protein bands. Comparing the OMP patterns of the strains from human with those from animals, the authors inferred that chickens and other animals might be one of the sources for the human infection of Campylobacter jejuni in this district. A comparison between the OMP patterns of the strains from diarrheic children and those from healthy carriers suggested that the pathogenesis of Campylobacter jejuni be possibly associated with the outer membrane proteins. Using the techniques, the authors studied the infection of Campylobacter jejuni in a nursery. The result showed the infection was sporadic and of multi-sources, as evidenced by the multi-patterns of the outer membrane protein profiles. It also indicates that the person-to-person transmission plays a significant role in the infection of Campylobacter jejuni.

Animals↗

PubMed2006

Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions.

The responses of Populus euphratica Oliv. plants to soil water deficit were assessed by analyzing gene expression, protein profiles, and several plant performance criteria to understand the acclimation of plants to soil water deficit. Young, vegetatively propagated plants originating from an arid, saline field site were submitted to a gradually increasing water deficit for 4 weeks in a greenhouse and were allowed to recover for 10 d after full reirrigation. Time-dependent changes and intensity of the perturbations induced in shoot and root growth, xylem anatomy, gas exchange, and water status were recorded. The expression profiles of approximately 6,340 genes and of proteins and metabolites (pigments, soluble carbohydrates, and oxidative compounds) were also recorded in mature leaves and in roots (gene expression only) at four stress levels and after recovery. Drought successively induced shoot growth cessation, stomatal closure, moderate increases in oxidative stress-related compounds, loss of CO2 assimilation, and root growth reduction. These effects were almost fully reversible, indicating that acclimation was dominant over injury. The physiological responses were paralleled by fully reversible transcriptional changes, including only 1.5% of the genes on the array. Protein profiles displayed greater changes than transcript levels. Among the identified proteins for which expressed sequence tags were present on the array, no correlation was found between transcript and protein abundance. Acclimation to water deficit involves the regulation of different networks of genes in roots and shoots. Such diverse requirements for protecting and maintaining the function of different plant organs may render plant engineering or breeding toward improved drought tolerance more complex than previously anticipated.

Climate↗

PubMed1996

[Protein profile and iron deficiency: value of the study of the albumin-transferrin couple].

From a clinical standpoint, the search for iron deficiency is based upon serum ferritin. However, serumferritin values may be pathologic in other numerous pathological conditions such as inflammation, liver diseases, malignant hematologic disorders, hemolysis, etc. Proteic profile combines the analyze of proteins variations: protein results are converted in percent of normal values referenced for the technique used. It has been suggested that on the protein profile, an increase in serum transferrin level compared to a normal serum albumin level (DAT: difference albumin-transferrin), appears early in the course of iron deficiency. In order to know the value of a pathologic DAT > or = 28% in the diagnosis of iron deficiency, we prospectively studied 156 patients consecutively hospitalized in an internal medicine department. Iron deficiency was defined by a low serum ferritin level. Diagnosis performance (sensitivity, specificity, positive and negative predictive values) of different biologic markers of iron deficiency (serum iron, saturation of total iron-binding capacity, low mean erythrocyte volume) and DAT was compared to the performance of low serum ferritin values. With the exception of low serum ferritin (which have by definition a specificity and a positive predictive value of 100%), pathologic DAT appeared as the best index of iron deficiency with the highest sensitivity (67.4%), specificity (97.3%), positive predictive value (91.2%), negative predicitive value (87.7%) and diagnosis efficacy (sensitivity x specificity = 0.66). A pathologic DAT associated to a low serum ferritin level increased the diagnosis performance of both tests to 0.72. Diagnosis efficacy of DAT was not changed (0.66) in 83 patients with a confounding factor for serum ferritin analysis (inflammation, liver diseases, malignant hematologic disorders, hemolysis) when diagnosis efficacy of all other tests decreased. There was a negative correlation between serum ferritin level and DAT level (r = 0.55; P < 0.0001). In conclusion, an increase of serum transferrin of more than 28% compared to serum albumin on a proteic profile gives a significant benefit for the diagnosis of iron deficiency. This benefit increases when data of both DAT and serum ferritin are associated.

Anemia, Iron-Deficiency↗

PubMed1991

In vitro evaluation of ocular irritants using corneal protein profiles.

This report represents the first application of tissue isoelectric focusing to establish reference human and rabbit corneal protein profiles and to study the corneal response to ocular irritants. The methods developed in this study provide a direct, semiquantitative comparison of tissue-irritant interactions without the potential limitations of standard homogenization and extraction procedures. The in vitro exposure of corneal sections to acetic acid (1 and 4%) and ammonium hydroxide (0.25 and 2%) solutions resulted in selective modifications of tissue protein profiles which were evaluated by scanning densitometry. Direct comparison of the rabbit and human corneal protein changes induced by in vitro irritant action revealed a similar acid/base effect on a common rabbit and human corneal protein band (pI 8.1).

Animals↗

PubMed2005

Optimized normalization for antibody microarrays and application to serum-protein profiling.

The measurements of coordinated patterns of protein abundance using antibody microarrays could be used to gain insight into disease biology and to probe the use of combinations of proteins for disease classification. The correct use and interpretation of antibody microarray data requires proper normalization of the data, which has not yet been systematically studied. Therefore we undertook a study to determine the optimal normalization of data from antibody microarray profiling of proteins in human serum specimens. Forty-three serum samples collected from patients with pancreatic cancer and from control subjects were probed in triplicate on microarrays containing 48 different antibodies, using a direct labeling, two-color comparative fluorescence detection format. Seven different normalization methods representing major classes of normalization for antibody microarray data were compared by their effects on reproducibility, accuracy, and trends in the data set. Normalization with ELISA-determined concentrations of IgM resulted in the most accurate, reproducible, and reliable data. The other normalization methods were deficient in at least one of the criteria. Multiparametric classification of the samples based on the combined measurement of seven of the proteins demonstrated the potential for increased classification accuracy compared with the use of individual measurements. This study establishes reliable normalization for antibody microarray data, criteria for assessing normalization performance, and the capability of antibody microarrays for serum-protein profiling and multiparametric sample classification.

Adenocarcinoma↗

PubMed1984

[Evaluation of normal protein profile of the mixed saliva and serum by laser nephelometry].

The aim of this study was to produce a protein profile of both whole saliva saliva and serum in a normal population of adults of both sexes ranging from 18 to 35 years of age using laser nephelometry. Twelve proteins were titrated: IgA, IgG, IgM, C3c, C4, alpha 2-macroglobulin, alpha 1-antitrypsin, C-reactive protein, albumin, hapto-globulin, alpha 1-glycoprotein acid and transferrine. This study is an original attempt to define a normal protein profile in the healthy adult. The next stage will be to analyse the physiopathological variations of this profile in inflammed oral and dental diseases.

Adolescent↗

PubMed1986

Numerical analysis of normalized whole-cell protein profiles after sodium dodecyl sulphate-polyacrylamide gel electrophoresis.

A technique is described for mathematically normalizing whole-cell protein profiles after sodium dodecyl sulphate-polyacrylamide gel electrophoresis to obtain standardized absolute migration distances using two internal Mr standards. A soft laser scanning densitometer was used to measure protein band migration distances in wet, silver-stained gels. The normalized values were superior to the unnormalized migration distances and common RF values in reducing the inter- and intragel variability of the protein band positions. A procedure is described for clustering normalized bacterial protein profiles using a sample data set obtained from the type strains of four Legionella species.

Bacterial Proteins↗

PubMed2004

Differential protein profiling in renal-cell carcinoma.

Characterizing the alterations of protein expression in cancer cells can be very useful in providing insight into the changes in the functional pathways and thus the fundamental mechanisms of cancer development at the molecular level. In this study, we profiled protein expressions in eleven pairs of primary cell cultures derived from renal-cell carcinoma (RCC) tissues and patient-matched normal kidney tissues utilizing two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Together with the immunoblot analysis of proteins from the RCC tissues, the study also demonstrated that the alterations of protein expression observed in RCC primary cell cultures reflected those observed in the original RCC tissues. We analyzed the expression profiles and identified proteins differentially expressed in RCC primary cell cultures by 2-D PAGE and mass spectrometry (MS). We found sixteen proteins were overexpressed and seven proteins underexpressed in RCC. The deregulated expressions of proteins include those involved in metabolism, cellular morphology, heat shock response, cell growth, etc. Overexpression of three proteins, alphabeta-crystallin, manganese superoxide dismutase (MnSOD), and annexin IV, most commonly observed in primary RCC cell cultures, were also observed by immunoblot analysis of proteins from the RCC tissues from which the primary cell cultures were derived. Semi-quantitative reverse transcription (RT)-polymerase chain reaction (PCR) analysis revealed the direct correlation between deregulated gene expression and the corresponding protein abundance in two of the three most commonly upregulated proteins we found in RCC.

Annexin A4↗

PubMed2006

Multivariate analysis approach to the plasma protein profile of patients with advanced colorectal cancer.

The aim of the present study was to identify the pattern of plasma protein species of interest as markers of colorectal cancer (CRC). Using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), the plasma protein profile was determined in nine stage IV CRC patients (study group) and nine clean-colon healthy subjects (control group). Multivariate analysis methods were employed to identify distinctive disease patterns at protein spectrum. In the study and control groups, cluster analysis (CA) on the complete MALDI-MS spectra plasma protein profile showed a distinction between CRC patients and healthy subjects, thus allowing the identification of the most discriminating ionic species. Principal component analysis (PCA) and linear discriminant analysis (LDA) yielded similar grouping results. LDA with leave-one-out cross validation achieved a correct classification rate of 89% in both the patients and the healthy subjects.

Adenocarcinoma↗