Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Comparative proteomics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 793 records · Page 44Linked to original sources
PubMed2003

Proteomic studies of potential cerebrospinal fluid protein markers for Alzheimer's disease.

By comparing the cerebrospinal fluid (CSF) proteome between Alzheimer's disease (AD) patients and controls, it may be possible to identify proteins that play a role in the disease process and thus to study the pathogenesis of AD. Two-dimensional gel electrophoresis (2-DE), SYPRO Ruby staining and mass spectrometry were used for clinical screening of disease-influenced CSF proteins in AD patients compared to controls. In order to increase the detection of CSF proteins and to improve the separation of protein isoforms in a 2-D gel, micro-narrow range IPG strips were used. The levels of eight proteins and their isoforms, including apolipoprotein A1, apolipoprotein E, apolipoprotein J, beta-trace, retinol-binding protein, kininogen, alpha-1 antitrypsin, cell cycle progression 8 protein, and alpha-1beta glycoprotein were significantly altered in CSF of AD patients compared to controls. Furthermore, we also used liquid-phase IEF, as a prefractionation step, prior to 2-DE for comparison of CSF proteins between individual AD patients and controls. The levels of 37 proteins spots were altered in AD patients. One of the identified proteins, alpha-2-HS glycoprotein, has not previously been linked to AD. Our study shows that several glycoproteins are altered in AD.

Aged↗
PubMed2005

Peroxisomal proteomics, a new tool for risk assessment of peroxisome proliferating pollutants in the marine environment.

In an attempt to improve the detection of peroxisome proliferation as a biomarker in environmental pollution assessment, we have applied a novel approach based on peroxisomal proteomics. Peroxisomal proteins from digestive glands of mussels Mytilus galloprovincialis were analyzed using 2-DE and MS. We have generated a reference 2-DE map from samples obtained in a well-studied reference area and compared this with peroxisomal proteomes from other sequenced genomes. In addition, by comparing 2-DE maps from control samples with samples obtained in a polluted area, we have characterized the peroxisome proliferation expression pattern associated with exposure to a polluted environment. Over 100 spots were reproducibly resolved per 2-DE map; 55 differentially expressed spots were quantitatively detected and analyzed, and 14 of these showed an increase in protein expression of more than fourfold. Epoxide hydrolase, peroxisomal antioxidant enzyme, and sarcosine oxidase (SOX) have been identified by ESI MS/MS, and acyl-CoA oxidase, multifunctional protein, and Cu,Zn-superoxide dismutase were immunolocalized by Western blotting. Our results indicate that a peroxisomal protein pattern associated to marine pollutant exposure can be generated, and this approach may have a greater potential as biomarker than traditional, single-protein markers.

Animals↗
PubMed2025

The small nucleolar RNA NON-CODING RNA 1 negatively regulates drought tolerance in Arabidopsis thaliana.

Small nucleolar RNAs (snoRNAs) function in ribosome biogenesis, and many ribosome biogenesis-related genes were downregulated by osmotic stress, implying a negative role of snoRNAs in drought tolerance. A snoRNA, namely, the NON-CODING RNA 1 (NCR1) was studied for its roles in drought tolerance in Arabidopsis. In comparison with wild-type (WT) plants, the loss-of-function ncr1 mutant plants showed enhanced drought tolerance, which was restored in the NCR1-complemented plants, whereas the NCR1-overexpressing plants revealed a drought-sensitive phenotype. Physiological analyses revealed that the ncr1 plants had a higher leaf surface temperature, lower water loss rates, and improved cell membrane integrity compared with WT. Comparative leaf transcriptomics and proteomics suggested that wax biosynthesis, anthocyanin metabolism, and leaf senescence processes are regulated by NCR1 under both normal and water-deficit conditions. Under drought, an increase in wax and anthocyanin accumulations and a delay in leaf senescence in ncr1 plants, when compared with WT, supported the transcriptome and proteomics data. Additionally, the ncr1 plants exhibited higher abscisic acid (ABA) sensitivity and longer root hairs than WT. Collectively, our results suggest that NCR1 negatively regulates drought tolerance through modification of wax biosynthesis, anthocyanin accumulation, leaf senescence, cell membrane integrity, ABA responses, and root hair development.

Arabidopsis↗
PubMed2002

A comparative study on feature selection and classification methods using gene expression profiles and proteomic patterns.

Feature selection plays an important role in classification. We present a comparative study on six feature selection heuristics by applying them to two sets of data. The first set of data are gene expression profiles from Acute Lymphoblastic Leukemia (ALL) patients. The second set of data are proteomic patterns from ovarian cancer patients. Based on features chosen by these methods, error rates of several classification algorithms were obtained for analysis. Our results demonstrate the importance of feature selection in accurately classifying new samples.

Algorithms↗
PubMed2006

Protein and proteome phosphorylation stoichiometry analysis by element mass spectrometry.

Protein phosphorylation stoichiometry was assessed by two analytical strategies. Both are based on element mass spectrometry (ICPMS, inductively coupled plasma mass spectrometry) and simultaneous monitoring of (31)P and (34)S. One strategy employs a combination of 1D gel electrophoresis, in-gel digestion, and final microLC-ICPMS analysis (microLC = capillary liquid chromatography). The other strategy uses the combination of 1D gel electrophoresis, protein blotting, and imLA-ICPMS (imLA = imaging laser ablation). The two methods were evaluated with standard phosphoproteins and were applied to the analysis of the cytoplasmatic proteome of bacterial cells (Corynebacterium glutamicum) and eukaryotic cells (Mus musculus). The eukaryotic proteome was found to exhibit a significantly higher phosphorylation degree (approximately 0.8 mol of P/mol of protein) compared to the bacterial proteome (approximately 0.01 mol of P/mol of protein). Both analytical strategies revealed consistent quantitative results, with the microLC-ICPMS approach providing the higher sensitivity. In summary, two ICPMS-based methods for quantitative estimation of the phosphorylation degree of a cellular proteome are presented which access the native proteome state and do not require any type of label introduction or derivatization.

Phosphorylation↗
PubMed2005

A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes.

Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis are closely related species that share a similar genetic background but occupy different ecological niches. Virulence plasmids bearing genes coding for toxins, may explain, at least partly, this specialization. We have compared by 2-DE in the early stationary phase of growth the extracellular proteomes of three strains of these species that have lost their virulence plasmids. Proteins expected to be secreted or to belong to the cell wall or to the cytosol were found in the three proteomes. For the cell wall and cytosolic proteins located in the extracellular space, the three proteomes were similar. Cytosolic proteins included enolase, GroEL, PdhB, PdhD, SodA and others. Cell surface proteins were mainly autolysins, proteases, nucleotidases and OppAs. In contrast, the secreted proteins profiles of B. cereus and B. thuringiensis were quite different from that of B. anthracis. B. cereus and B. thuringiensis extracellular proteomes both contained large amounts of secreted degradative enzymes and toxins, including nine proteases, three phospholipases, two haemolysins and several enterotoxins. Most of the genes encoding these enzymes and toxins are controlled by the transcriptional activator PlcR. The extracellular proteome of the pXO1-, pXO2- B. anthracis 9131 strain contained only one secreted protein: the metalloprotease InhA1, also found in the proteomes of the two other strains and possibly involved in antibacterial peptide degradation.

Amino Acid Sequence↗
PubMed2004

Lateral roots affect the proteome of the primary root of maize (Zea mays L.).

Lateral roots are initiated from the pericycle cells of other types of roots and remain in contact with these roots throughout their life span. Although this physical contact has the potential to permit the exchange of signals, little is known about the flow of information from the lateral roots to the primary root. To begin to study these interactions the proteome of the primary root system of the maize (Zea mays L.) lrt1 mutant, which does not initiate lateral roots, was compared with the corresponding proteome of wild-type seedlings 9 days after germination. Approximately 150 soluble root proteins were resolved by two-dimensional electrophoresis and analyzed by MALDI-ToF mass spectrometry and database searching. The 96 most abundant proteins from a pH 4-7 gradient were analyzed; 67 proteins representing 47 different Genbank accessions were identified. Interestingly, 10 (15/150) of the detected proteins were preferentially expressed in lrt1 roots that lack lateral roots. Eight of these lrt1-specific proteins were identified and four are involved in lignin metabolism. This study demonstrates for the first time the influence of lateral roots on the proteome of the primary root system. To our knowledge this is the first study to demonstrate an interaction between two plant organs (viz., lateral and primary roots) at the level of the proteome.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2026

Cardiac mitochondrial proteome of lean, healthy Ossabaw minipigs with predisposition to metabolic syndrome versus that of Göttingen minipigs.

Ossabaw minipigs differ from other (mini)pig strains by their genetic predisposition to develop full metabolic syndrome and their nonresponsiveness to cardioprotective interventions, even before developing the diseased phenotype. Previous DNA sequencing data revealed differences in a cluster of mitochondrial protein-coding genes between Ossabaw and Göttingen minipigs-a large animal model without such a genetic predisposition and a responsiveness to cardioprotection. Alterations in mitochondrial protein composition affect mitochondrial function, and mitochondria play a crucial role in the development of metabolic syndrome and for cardioprotection. Therefore, we aimed to compare the cardiac mitochondrial proteome between lean Ossabaw minipigs with a healthy phenotype and Göttingen minipigs to gain initial insights into potential differences in mitochondrial protein composition and function. Cardiac mitochondria (left ventricular tissue) of both minipig strains (male/female pigs) were isolated, and the proteome was analyzed by liquid chromatography-tandem mass spectrometry. An unbiased, nonhypothesis-driven proteome analysis identified 97% overlap in the proteome. Among the 3% of differentially expressed proteins, 19 were related to mitochondrial metabolism, 8 to transcription and translation, 3 to small molecule transport, 2 to oxidative phosphorylation, and 1 to dynamics and surveillance. These small differences in protein composition were associated with an altered mitochondrial energy turnover-ATP production was reduced by 49% in Ossabaw compared with Göttingen minipig mitochondria. This proteome analysis provides a broader basis to understand how genetic alterations result in changes of the mitochondrial proteome and function, which might be relevant for the development and progression of metabolic syndrome and/or the primordial nonresponsiveness to cardioprotection in Ossabaw minipigs.NEW & NOTEWORTHY Our comprehensive cardiac mitochondrial proteome of Ossabaw and Göttingen minipigs is a valuable resource for cardiac biomedical research. Moreover, our proteome analysis provides a broader basis for understanding how genetic alterations result in changes of the mitochondrial proteome and support a mechanistic link between subtle, strain-specific mitochondrial proteomic signatures and altered mitochondrial energy turnover. These changes may be relevant for the development and progression of metabolic syndrome and/or primordial nonresponsiveness to cardioprotection in Ossabaw minipigs.

Animals↗
PubMed2026

High-Throughput Proteomic and Glycoproteomic Analyses in Benign Prostatic Hyperplasia.

Benign prostatic hyperplasia (BPH) is a disease affecting the majority of aging men; 90% of men develop histological BPH by the time they reach their eighties. BPH can lead to bothersome lower urinary tract symptoms (LUTS), which may reduce quality of life. Many patients fail current treatment options and may progress to surgical intervention. Furthermore, diagnosis is reliant on symptom questionnaires and the cause of LUTS can be difficult to distinguish. Currently, BPH can only be definitively diagnosed through histological analysis of prostate tissue, which is not the standard of care. The resulting lack of clinical tissue samples is a major limitation in investigating disease pathology. Improved understanding of disease development and progression, along with objective biomarkers of disease, is needed for BPH. This investigation uses mass spectrometry (MS)-based proteomics and glycoproteomics to compare healthy prostate tissue with prostate tissue affected by BPH to address this gap in knowledge. By integrating proteomics and glycoproteomics, we identified 206 proteins and 44 glycopeptides that were significantly altered between BPH and control samples. These findings provide deeper insight into disease-associated pathways and may facilitate the identification of clinically relevant targets for further investigation.

Male↗
PubMed2006

Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer.

Large-scale genomic and proteomic analysis has provided a wealth of information on biologically relevant systems, and the ability to analyze this information is crucial to uncovering important biological relationships. However, it has proven difficult to compare large datasets from different sources due to different gene and protein identifiers assigned by individual laboratories and database systems. Here, we describe the design of a fully automated blast program (BlastPro) that facilitates rapid comparison of large protein-protein, nucleotide--nucleotide, or nucleotide--protein datasets from numerous, independent studies. Using this system, we compared several published genomic and proteomic databases for proteins that are upregulated in highly motile, metastatic tumor cells. Analysis of five independent studies comprised of greater than 1 x 10(6) genomic sequences and greater than 1,000 proteins revealed that the cytoskeletal-associated protein alpha-actinin is increased at both the mRNA and protein level in metastatic breast, prostate, and skin cancer cells. Interestingly, spatial analysis of alpha-actinin expression revealed that it is amplified 8-fold in the leading pseudopodium compared to the cell body compartment of migrating cells. These findings indicate that amplification of alpha-actinin and its localization to the leading pseudopodium are potential biomarkers of cancer progression to a more metastatic phenotype. Together, our results demonstrate that the BlastPro system can be used to compare large genomic and proteomic datasets to reveal important biological relationships including those associated with cancer progression.

Actinin↗
PubMed2002

Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.

The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches. Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences. According to their altered synthesis patterns in response to DL-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes. However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis. The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp. The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG). On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins. A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp.

Bacillus subtilis↗
PubMed2004

Transcriptomic and proteomic analysis of a 14-3-3 gene-deficient yeast.

BMH1 and BMH2 encode Saccharomyces cerevisiae 14-3-3 homologues whose exact functions have remained unclear. The present work compares the transcriptomic and proteomic profiles of the wild type and a BMH1/2-deficient S. cerevisiae mutant (bmhDelta) using DNA microarrays and two-dimensional polyacrylamide gel electrophoresis. It is reported here that, although the global patterns of gene and protein expression are very similar between the two types of yeast cells, a subset of genes and proteins (a total of 220 genes) is significantly induced or reduced in the absence of Bmh1/2p. These genes include approximately 60 elements that could be linked to the reported phenotypes of the bmhDelta mutant (e.g., accumulation of glycogen and hypersensitivity to environmental stress) and/or could be the potential downstream targets of interacting partners of Bmh1/2p such as Msn2p and Rtg3p. Importantly, >30% of the identified genes (71 genes) were found to be associated with carbon (C) and nitrogen (N) metabolism and transport, thereby suggesting that Bmh1/2p may play a major role in the regulation of C/N-responsive cellular processes. This study presents the first comprehensive overview of the genes and proteins that are affected by the depletion of Bmh1/2p and extends the scope of knowledge of the regulatory roles of Bmh1/2p in S. cerevisiae.

14-3-3 Proteins↗
PubMed2006

GARBAN II: an integrative framework for extracting biological information from proteomic and genomic data.

Genomic and proteomic analyses generate a massive amount of data that requires specific bioinformatic tools for its management and interpretation. GARBAN II, developed from the previous GARBAN platform, provides an integrated framework to simultaneously analyse and compare multiple datasets from DNA microarrays and proteomic studies. The general architecture, gene classification and comparison, and graphical representation have been redesigned to ensure a user-friendly feature and to improve the capabilities and efficiency of this system. Additionally, GARBAN II has been extended with new applications to display networks of coexpressed genes and to integrate access to BioRag and MotifScanner so as to facilitate the holistic analysis of users' data.

Animals↗
PubMed2004

Comparative analysis of the Kekkon molecules, related members of the LIG superfamily.

Leucine-rich repeats (LRRs) and immunoglobulin (Ig) domains represent two of the most abundant sequence elements in metazoan proteomes. Despite this prevalence, comparatively few molecules containing both LRR and Ig (LIG) modules exist, and fewer still have been functionally defined. One LIG whose function has been investigated is the Drosophila protein Kekkon1 (Kek1). In vivo studies have demonstrated a role for Kek1 in Epidermal Growth Factor Receptor (EGFR) signaling and have suggested a role in neuronal pathfinding. Kek1 is the founding member of the Kek family, a group of six Drosophila transmembrane proteins that contain seven LRRs and a single Ig in their extracellular domains. While this arrangement of domains predicts a possible role as cell adhesion molecules (CAMs), to date little is known about the function or evolutionary relationship of these additional Kek molecules. Here we report that orthologs of Kek1, Kek2, Kek5, and Kek6 exist in the mosquito, Anopheles gambiae, and the honeybee, Apis mellifera, indicating that this family has been conserved for ~300 million years of evolutionary time. Comparative sequence analyses reveal remarkable identity among these orthologs, primarily in their extracellular regions. In contrast, the intracellular regions are more divergent, exhibiting only small pockets of conservation. In addition, we provide support for the general notion that these molecules may share common functions as CAMs, by demonstrating that Kek family members can form homotypic and heterotypic complexes.

Amino Acid Sequence↗
PubMed2003

Interplay of transcriptomics and proteomics.

Despite the obvious attractions of parallel profiling of transcripts and proteins on a global 'omic' scale, there are practical and biological differences involved in their application. Transcriptomics is now a robust, high-throughput, cost-effective technology capable of simultaneously quantifying tens of thousands of defined mRNA species in a miniaturized, automated format. Conversely, proteomic analysis is currently much more limited in breadth and depth of coverage owing to variations in protein abundance, hydrophobicity, stability, size and charge. Nevertheless, transcriptomic and proteomic data can be compared and contrasted provided the studies are carefully designed and interpreted. Differential splicing, post-translational modifications and data integration are among some of the future challenges to tackle.

Biotechnology↗
PubMed2006

Biomarkers in cardiovascular disease: integrating pathophysiology into clinical practice.

Biomarkers play an important role in the diagnosis, prognostic assessment, and management of patients with suspected acute coronary syndromes (ACS). Specific biomarkers identify different components of the pathophysiology of ACS: troponins are prototype markers of myocyte necrosis, natriuretic peptides reflect neurohormonal activation and hemodynamic stress, soluble CD40 ligand is an indicator of platelet activation, and C-reactive protein, myeloperoxidase, and monocyte chemoattractant protein-1 reflect various inflammatory processes. When combined, multiple biomarkers reflecting different pathophysiologic processes appear to enhance risk stratification, as compared with using individual markers alone. Advances in proteomic technology promise to identify additional novel biomarkers that facilitate diagnosis, risk stratification, and selection of therapies in ACS. In the future, it is hoped that multiple biomarker panels will form the basis of an individualized approach to the treatment of ACS, in which therapy is tailored to individual biomarker profiles.

Biomarkers↗