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At least 73 records · Page 4Linked to original sources
PubMed2005

Proteomic analysis of brain plasma membranes isolated by affinity two-phase partitioning.

A comprehensive analysis of plasma membrane proteins is essential to in-depth understanding of brain development, function, and diseases. Proteomics offers the potential to perform such a comprehensive analysis, yet it requires efficient protocols for the purification of the plasma membrane compartment. Here, we present a novel and efficient protocol for the separation and enrichment of brain plasma membrane proteins. It lasts only 4 h and is easy to perform. It highly enriches plasma membrane proteins and can be applied to small amounts of brain tissue, such as the cerebellum of a single rat, which was used in the present study. The protocol is based on affinity partitioning of microsomes in an aqueous two-phase system. Marker enzyme assays demonstrated a more than 12-fold enrichment of plasma membranes and a strong reduction of other compartments, such as mitochondria and the endoplasmic reticulum. 506 different proteins were identified when the enriched proteins underwent LC-MS/MS analysis subsequent to protein separation by SDS-PAGE. Using gene ontology, 146 proteins were assigned to a subcellular compartment. Ninety-three of those (64%) were membrane proteins, and 49 (34%) were plasma membrane proteins. A combined literature and database search for all 506 identified proteins revealed subcellular information on 472 proteins, of which 197 (42%) were plasma membrane proteins. These comprised numerous transporters, channels, and neurotransmitter receptors, e.g. the inward rectifying potassium channel Kir7.1 and the cerebellum-specific gamma-aminobutyric acid receptor GABRA6. Surface proteins involved in cell-cell contact and disease-related proteins were also identified. Six of the 146 assigned proteins were derived from mitochondrial membranes and 5 from membranes of the endoplasmic reticulum. Taken together, our protocol represents a simple, rapid, and reproducible tool for the proteomic characterization of brain plasma membranes. Because it conserves membrane structure and protein interactions, it is also suitable to enrich multimeric protein complexes from the plasma membrane for subsequent analysis.

Alkaline Phosphatase↗
PubMedDate not supplied

Detection of hypothetical proteins in human fetal perireticular nucleus.

There is a legion of hypothetical proteins (HP) in prokaryotic and eukaryotic proteomes and the aim of this study was to describe HP in the perireticular nucleus (PN), a key structure in human brain development. Tissue from four PNs was homogenized and extracted proteins were run on two-dimensional gel electrophoresis followed by in-gel digestion and mass spectrometrical identification of proteins. Several databases were used for obtaining bioinformatic information and searching for functional and structural domains. Five spots represented HP: KIAA0423 protein (Q9Y4F4), hypothetical protein KIAA0153 (Q14166), hypothetical protein DKFZp564A2416 (Q9NTW4), hypothetical protein DKFZp564H1122 (Q9H0W9), and hypothetical protein DKFZp564D1378 (Q9H0R4). These structures were predicted to serve in cell cycle, DNA-condensation, neurogenesis, or apoptosis. The existence of formerly HP proteins in the PN of human fetal brain is shown, thus extending knowledge of the brain proteome and proposing the method used as a suitable analytical tool for searching HP.

Apoptosis↗
PubMed2006

Proteome resolution by two-dimensional gel electrophoresis varies with the commercial source of IPG strips.

By facilitating reproducible first dimension separations, commercial immobilized pH gradient (IPG) strips enable high throughput and high-resolution proteomic analyses using two-dimensional gel electrophoresis (2DE). Amersham, Biorad, Invitrogen, and Sigma all market linear pH 3-10 IPG strips. We have applied optimized 2DE protocols with both membrane and soluble brain protein extracts to critically evaluate all four products. Resolved protein spots were quantitatively evaluated after carrying out these protocols using IPG strips from the four companies. Biorad and Amersham IPG strips resolved a high number of membrane and soluble proteins, respectively. Furthermore, Amersham IPG strips eluted the largest amount of protein into the second dimension gels and had the most protein remaining in the strip after 2DE. Biorad and Amersham IPG strips maintained a consistent linear pH 3-10 gradient, whereas those from Invitrogen appeared nonlinear or "compressed" within the central pH region. The gradient range within Sigma IPG strips appeared to be slightly less than pH 3-10, due to one extended pH unit within the gradient. Overall, all four commercially available IPG strips have the ability to resolve both membrane and soluble brain proteomes. The difference is that Amersham and Biorad do so more consistently and with better spot resolution. It appears that the physical/chemical nature of commercially available IPG strips can vary considerably, leading to marked differences in subsequent protein resolution in 2DE. These differences likely reflect variations in the uptake of proteins into the strips, and differences in the focusing and elution of proteins from the first to the second dimension. These differences would appear, in part, to underlie some inter-lab variations in the effective resolution of proteomes.

Animals↗
PubMed2004

Putative endogenous mediators of preconditioning-induced ischemic tolerance in rat brain identified by genomic and proteomic analysis.

In brain, a brief ischemic episode induces protection against a subsequent severe ischemic insult. This phenomenon is known as preconditioning-induced neural ischemic tolerance. An understanding of the molecular mechanisms leading to preconditioning helps in identifying potential therapeutic targets for preventing the post-stroke brain damage. The present study conducted the genomic and proteomic analysis of adult rat brain as a function of time following preconditioning induced by a 10-min transient middle cerebral artery (MCA) occlusion. GeneChip analysis showed induction of 40 putative neuroprotective transcripts between 3 to 72 h after preconditioning. These included heat-shock proteins, heme oxygenases, metallothioneins, signal transduction mediators, transcription factors, ion channels and apoptosis/plasticity-related transcripts. Real-time PCR confirmed the GeneChip data for the transcripts up-regulated after preconditioning. Two-dimensional gel electrophoresis combined with MALDI-TOF analysis showed increased expression of HSP70, HSP27, HSP90, guanylyl cyclase, muskelin, platelet activating factor receptor and beta-actin at 24 h after preconditioning. HSP70 protein induction after preconditioning was localized in the cortical pyramidal neurons. The infarct volume induced by focal ischemia (1-h MCA occlusion) was significantly smaller (by 38 +/- 7%, p < 0.05) in rats subjected to preconditioning 3 days before the insult. Preconditioning also prevented several gene expression changes induced by focal ischemia.

Animals↗
PubMed2001

Analysis of the proteomic profiling of brain tissue in Alzheimer's disease.

In proteome analysis, it is necessary to separate proteins as a first step prior to characterization. Thus, the overall performance of the analysis depends strongly on the separation tool, which is usually two-dimensional electrophoresis (2DE). We have utilized 2DE to begin characterization of the complex pathologic processes in Alzheimer's disease (AD). In the present study, we show how a reliable 2-DE database of brain proteins in Alzheimer's disease was created, improving reproducibility by using an immobilized pH gradient (IPG) for the first dimension gel electrophoresis. The recent progress in this field, and future prospects in this area are also discussed. Preparation of brain proteins into a suitable solubilized state enabled us to separate over 1000 well-defined protein spots in each 2-DE. A comparison of the density of the spots identified on the reference map between the AD and control group, showed that 5 protein spots were significantly increased, 28 spots were significantly decreased and 7 spots were specifically detected in AD. Two spots among those significantly increased and one spot among those significantly decreased were identified as GFAP related. It is hoped that comparative studies to identify, quantitate, and characterize the proteins differentially expressed in normal brain versus diseased brain will give insight into the mechanisms of pathogenesis and allow the development of a strategy to control both the etiology and course of the diseases.

Aged↗
PubMed2006

Blood-brain barrier genomics and proteomics: elucidating phenotype, identifying disease targets and enabling brain drug delivery.

The blood-brain barrier (BBB) regulates the passage of material between the bloodstream and the brain. Recent genomic and proteomic studies of the BBB have identified some of the unique molecular characteristics of this vascular bed, and have reinforced the concept that the BBB is heavily involved in brain function. Genomic and proteomic techniques have also been used to analyze the molecular events underlying diseases that have BBB involvement, such as multiple sclerosis, Alzheimer's disease, stroke and HIV-1 infection. It is expected that a better understanding of the complex mechanisms that link the BBB to neurological disease will ultimately lead to the development of innovative treatments.

Animals↗
PubMed2006

PRIDE: a public repository of protein and peptide identifications for the proteomics community.

PRIDE, the 'PRoteomics IDEntifications database' (http://www.ebi.ac.uk/pride) is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will typically be from specific species, tissues and sub-cellular locations, perhaps under specific disease conditions. Any post-translational modifications that have been identified on individual peptides can be described. These identifications may be annotated with supporting mass spectra. At the time of writing, PRIDE includes the full set of identifications as submitted by individual laboratories participating in the HUPO Plasma Proteome Project and a profile of the human platelet proteome submitted by the University of Ghent in Belgium. By late 2005 PRIDE is expected to contain the identifications and spectra generated by the HUPO Brain Proteome Project. Proteomics laboratories are encouraged to submit their identifications and spectra to PRIDE to support their manuscript submissions to proteomics journals. Data can be submitted in PRIDE XML format if identifications are included or mzData format if the submitter is depositing mass spectra without identifications. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an internet browser. PRIDE can be searched by experiment accession number, protein accession number, literature reference and sample parameters including species, tissue, sub-cellular location and disease state. Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML.

Databases, Protein↗
PubMed2003

Proteomic analysis of immunostained, laser-capture microdissected brain samples.

Proteomic analysis is often performed on homogenized preparations of whole tissues, which does not provide any information about relevant biochemical changes in specific cell types. Laser-capture microdissection (LCM) is a technique that is precise enough to dissect single cells within a tissue section. Phenotypically defined cells of interest may be visualized by immunostaining prior to microdissection. Previously published immunostaining protocols adapted to LCM require the use of very high antibody titers and very short incubation times. This raises the concern that low-abundance antigens would not be detected and that antisera would be rapidly depleted. In addition, protein recovery from samples was not evaluated in most of these studies. Here, we describe an optimized immunostaining method based on immunofluorescence. By comparing two-dimensional electrophoresis (2-DE) results obtained from immunostained LCM brain tissue samples to those obtained from unstained, manually dissected samples, we demonstrated that immunofluorescent staining gave comparable protein recovery and similar resolution of protein spots on 2-DE gels. Moreover, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry analysis of selected spots from gels derived from control and immunostained LCM samples revealed that the immunostaining process had minimal effect on protein identification. LCM of immunofluorescently labeled tissue sections is a practical and powerful method to perform proteomic studies on specifically defined cell groups.

Animals↗
PubMed1998

Proteomic changes associated with degeneration of myelin-forming cells in the central nervous system of c-myc transgenic mice.

Myelin is necessary for the conduction of high frequency and high velocity nerve impulses in the central nervous system of mammals, and severe neurological disturbances develop as a result of myelin loss. In this report, we have characterized changes in the brain proteomic profile of transgenic mice that develop a c-myc-induced degenerative disorder of myelin. Marked differences were seen in the accumulation of cytoskeletal proteins associated with the pathological condition fibrous gliosis in the optic nerves of affected animals, including upregulation of glial fibrillary acid protein and vimentin. In addition, the expression of several major myelin proteins, including five isoforms of myelin basic protein, four isoforms of cyclic nucleotide 3'-phosphodiesterase, and myelin-associated glycoprotein, was markedly reduced in the brains of c-myc transgenic mice as revealed by immunocytochemistry and by two-dimensional immunoblots. A number of novel proteomic disease marker candidates were revealed, which displayed pronounced changes in their expression profile. Sequence determination of these proteins and molecular cloning of their mRNAs will provide an opportunity to further evaluate their roles in the disease process.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2005

"Subcellular proteomics" of neuromelanin granules isolated from the human brain.

"Subcellular proteomics" is currently the most effective approach to characterize subcellular compartments. Based on the powerful combination of subcellular fractionation and protein identification by LC-MS/MS we were able for the first time to 1) isolate intact neuromelanin granules from the human brain and 2) establish the first protein profile of these granules. This compartment containing neuromelanin (NM) is primarily located in the primate's substantia nigra, one of the main brain regions that severely degenerates in Parkinson disease. We used mechanic tissue disaggregation, discontinuous sucrose gradient centrifugation, cell disruption, and organelle separation to isolate NM granules from human substantia nigra. Using transmission electron microscopy we demonstrated that the morphological characteristics of the isolated NM granules are similar to those described in human brain tissue. Fundamentally we found numerous proteins definitely demonstrating a close relationship of NM-containing granules with lysosomes or lysosome-related organelles originating from the endosome-lysosome lineage. Intriguingly we further revealed the presence of endoplasmic reticulum-derived chaperones, especially the transmembrane protein calnexin, which recently has been located in lysosome-related melanosomes and has been suggested to be a melanogenic chaperone.

Calnexin↗
PubMed2005

Proteomic analysis of parkin knockout mice: alterations in energy metabolism, protein handling and synaptic function.

Parkin knockout (KO) mice show behavioural and biochemical changes that reproduce some of the presymptomatic aspects of Parkinson's disease, in the absence of neuronal degeneration. To provide insight into the pathogenic mechanisms underlying the preclinical stages of parkin-related parkinsonism, we searched for possible changes in the brain proteome of parkin KO mice by means of fluorescence two-dimensional difference gel electrophoresis and mass spectrometry. We identified 87 proteins that differed in abundance between wild-type and parkin KO mice by at least 45%. A high proportion of these proteins were related to energy metabolism. The levels of several proteins involved in detoxification, stress-related chaperones and components of the ubiquitin-proteasome pathway were also altered. These differences might reflect adaptive mechanisms aimed at compensating for the presence of reactive oxygen species and the accumulation of damaged proteins in parkin KO mice. Furthermore, the up-regulation of several members of the membrane-associated guanylate kinase family of synaptic scaffold proteins and several septins, including the Parkin substrate cell division control related protein 1 (CDCRel-1), may contribute to the abnormalities in neurotransmitter release previously observed in parkin KO mice. This study provides clues into possible compensatory mechanisms that protect dopaminergic neurones from death in parkin KO mice and may help us understand the preclinical deficits observed in parkin-related parkinsonism.

Animals↗
PubMed2002

Proteomic analysis of the fetal brain.

We applied proteomic technologies to analyze the human fetal brain. Such an analysis could provide us with important information on the development of the early neuronal life in healthy and diseased states. The proteins from the cerebellum of control subjects were analyzed by two-dimensional electrophoresis and identified by matrix-assisted laser desorption/ionization-mass spectrometry on the basis of peptide mass fingerprinting, following in-gel digestion with trypsin. Approximately 3,000 spots, excised from three two-dimensional gels, were analyzed which resulted in the identification of about 1,700 proteins that were the products of 437 different genes. About half of them are enzyme subunits and are mainly localized in the cytosol and in mitochondria. The most frequently identified proteins in the various gels were heat shock proteins, house-keeping enzymes, such as ATP synthase chains, protein disulfide isomerase, and structural proteins, such as tubulin chains. Seven gene products were identified for the first time in the fetal brain. The other proteins had also been detected in other human samples which were analyzed in our laboratory. Most proteins were represented by multiple spots. In average, about 3-5 spots were detected per gene product. The fetal brain database includes proteins with important functions and also with unknown functions and represents today one of the largest two-dimensional databases for higher eukaryotic proteomes. It may be a useful tool in the investigation of protein changes in neurodegenerative diseases early in life.

Brain↗
PubMed2002

Alterations of stress related proteins in genetically altered mice revealed by two-dimensional differential in-gel electrophoresis analysis.

Transgenic, knockout and knockin mice are useful tools for linking specific genes with behaviour and other complex biological processes. However, complications arising due to compensatory changes, genetic background differences and other factors could lead to difficulty in interpreting the resulting changes in phenotype. We have used fluorescence two-dimensional differential in-gel electrophoresis in combination with matrix-assisted laser desorption/ionization-time of flight mass fingerprinting to investigate the possibility that distinct genetic alterations can lead to common protein expression changes in genetically modified mice. Brain proteomes were compared from two transgenic mouse strains (Tg2576 x TgPS1 and Tg2576), two knockout mouse strains (5-HT(7)R -/- and GABA(A)Ralpha5 -/-) and one knockin mouse strain (GABA(A)Ralpha1-H101R). Both of the transgenic models showed an isoform change in the heat shock 70 related protein, mortalin. The knockout and knockin models showed similar changes in mortalin expression along with an alteration of the anti-oxidant protein 2. The observed proteomic alterations indicate that stress-responsive protein pathways may be altered artefactually in all of the mouse models used in this study and highlights an area where caution is needed in interpreting proteomic changes in genetically modified mice.

Animals↗
PubMed2006

Protein biomarkers in a mouse model of extremes in trait anxiety.

Brain proteome analysis of mice selectively bred for either high or low anxiety-related behavior revealed quantitative and qualitative protein expression differences. The enzyme glyoxalase-I was consistently expressed to a higher extent in low anxiety as compared with high anxiety mice in several brain areas. The same phenotype-dependent difference was also found in red blood cells with normal and cross-mated animals showing intermediate expression profiles of glyoxalase-I. Another protein that showed a different mobility during two-dimensional gel electrophoresis was identified as enolase phosphatase. The presence of both protein markers in red or white blood cells, respectively, creates the opportunity to screen for their expression in clinical blood specimens from patients suffering from anxiety.

Amygdala↗
PubMed2003

Neuroprotective strategies in Parkinson's disease : an update on progress.

In spite of the extensive studies performed on postmortem substantia nigra from Parkinson's disease patients, the aetiology of the disease has not yet been established. Nevertheless, these studies have demonstrated that, at the time of death, a cascade of events had been initiated that may contribute to the demise of the melanin-containing nigro-striatal dopamine neurons. These events include increased levels of iron and monoamine oxidase (MAO)-B activity, oxidative stress, inflammatory processes, glutamatergic excitotoxicity, nitric oxide synthesis, abnormal protein folding and aggregation, reduced expression of trophic factors, depletion of endogenous antioxidants such as reduced glutathione, and altered calcium homeostasis. To a large extent, the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and 6-hydroxydopamine (6-OHDA) animal models of Parkinson's disease confirm these findings. Furthermore, neuroprotection can be afforded in these models with iron chelators, radical scavenger antioxidants, MAO-B inhibitors, glutamate antagonists, nitric oxide synthase inhibitors, calcium channel antagonists and trophic factors. Despite the success obtained with animal models, clinical neuroprotection is much more difficult to accomplish. Although the negative studies obtained with the MAO-B inhibitor selegiline (deprenyl) and the antioxidant tocopherol (vitamin E) may have resulted from an inappropriate choice of drug (selegiline) or an inadequate dose (tocopherol), the niggling problem that still remains is why these drugs, and others, do work in animals while they fail in the clinic. One reason for this may be related to the fact that in normal human brains the number of dopaminergic neurons falls by around 3-5% every decade, while in Parkinson's disease this decline is greater. Brain autopsy studies have shown that by the time the disease is identified, some 70-75% of the dopamine-containing neurons have been lost. More sensitive reliable methods and clinical correlative markers are required to discern between confoundable symptomatic effects versus a possible neuroprotective action of drugs, namely, the ability to delay or forestall disease progression by protecting or rescuing the remaining dopamine neurons or even restoring those that have been lost.A number of other possibilities for the clinical failure of potential neuroprotectants also exist. First, the animal models of Parkinson's disease may not be totally reflective of the disease and, therefore, the chemical pathologies established in the animal models may not cause, or contribute to, the progression of the disease clinically. Second, because of the series of events occurring in neurodegeneration and our ignorance about which of these factors constitutes the primary event in the pathogenic process, a single drug may not be adequate to induce neuroprotection and, as a consequence, use of a cocktail of drugs may be more appropriate. The latter concept receives support from recent complementary DNA (cDNA) microarray gene expression studies, which show the existence of a gene cascade of events occurring in the nigrostriatal pathway of MPTP, 6-OHDA and methamphetamine animal models of Parkinson's disease. Even with the advent of powerful new tools such as genomics, proteomics, brain imaging, gene replacement therapy and knockout animal models, the desired end result of neuroprotection is still beyond our current capability.

Animals↗
PubMed2005

Identification of nitrated proteins in the normal rat brain using a proteomics approach.

BACKGROUND: The nitration of tyrosine has been suggested to play a role in the pathogenesis of neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD) and Alzheimer's disease (AD). METHODS: In the present study, we identified four targets of protein nitration, T-complex polypeptide 1 alpha subunit (TCP-1), neurofilament L (NFL), glial fibrillary acidic protein (GFAP) and clathrin heavy chain (CHC), in the normal rat cortex using a proteomics approach. CONCLUSIONS: There have been no reports on these proteins being identified by proteomics as nitrated forms in the brain. For further study, we have to investigate alterations in these nitrated proteins during aging and in neurodegenerative disorders.

Amino Acid Sequence↗
PubMed2005

HUPO BPP Workshop on Mouse Models for Neurodegeneration--Choosing the right models.

The HUPO Brain Proteome Project met during the 4th Dutch Endo-Neuro-Psycho Meeting in Doorwerth, The Netherlands, on June 1, 2005, in order to discuss appropriate (mouse) models for neurodegenerative diseases as well as to conceptualise sophisticated proteomics analyses strategies. Here, the topics of the meeting are summarised.

Animals↗
PubMed2005

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

Computational Biology↗