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J C Sanchez

Publications and source records attributed to J C Sanchez.

At least 19 recordsLinked to original sources
PubMed2006

A comparison of optimal MIMO linear and nonlinear models for brain-machine interfaces.

The field of brain-machine interfaces requires the estimation of a mapping from spike trains collected in motor cortex areas to the hand kinematics of the behaving animal. This paper presents a systematic investigation of several linear (Wiener filter, LMS adaptive filters, gamma filter, subspace Wiener filters) and nonlinear models (time-delay neural network and local linear switching models) applied to datasets from two experiments in monkeys performing motor tasks (reaching for food and target hitting). Ensembles of 100-200 cortical neurons were simultaneously recorded in these experiments, and even larger neuronal samples are anticipated in the future. Due to the large size of the models (thousands of parameters), the major issue studied was the generalization performance. Every parameter of the models (not only the weights) was selected optimally using signal processing and machine learning techniques. The models were also compared statistically with respect to the Wiener filter as the baseline. Each of the optimization procedures produced improvements over that baseline for either one of the two datasets or both.

Action Potentials↗
PubMed2001

CSF detection of the 14-3-3 protein in unselected patients with dementia.

OBJECTIVE: To determine the usefulness of the 14-3-3 test in patients with dementia of various causes. BACKGROUND: Recent reports have suggested that the detection of the 14-3-3 protein in the CSF of patients with Creutzfeldt--Jakob disease is a highly sensitive and specific marker of the disease that might be used as a diagnostic criterion. We examined the validity of this test when applied to a cohort of unselected patients prospectively examined for an ongoing dementing process. METHODS: One hundred patients underwent an extensive neurologic examination for dementia, including a CSF 14-3-3 protein immunoblotting assay. Final clinical diagnoses were compared with the qualitative results of the test, and statistical measures of test validity were carried out. RESULTS: We found a positive test in 14 of 100 patients, only two of whom had definite Creutzfeldt--Jakob disease. Positive results were found in patients with various degenerative dementias, including AD (4), frontotemporal dementia (2), and dementia with Lewy body (1), and in patients with vascular dementia (1), carcinomatous meningitis (1), and anoxic encephalopathy (1). In two other positive patients, the dementia could not be confidently classified. Sensitivity, specificity, and negative predictive value were fairly good, but positive predictive value was poor. Similar results were found independently of the disease duration. There was no correlation between intensity nor pattern of the 14-3-3 protein expression and diagnosis. CONCLUSIONS: The 14-3-3 test is not valid for discriminating between Creutzfeldt--Jakob disease and non-Creutzfeldt--Jakob disease in unselected patients with dementia. Positive results are found in various degenerative and secondary, prion-unrelated dementias.

14-3-3 Proteins↗
PubMed2001

Proteomic dissection of dome formation in a mammary cell line: role of tropomyosin-5b and maspin.

In this work we extended the study of genes controlling the formation of specific differentiation structures called "domes" formed by the rat mammary adenocarcinoma cell line LA7 under the influence of DMSO. We have reported previously that an interferon-inducible gene, rat-8, and the beta-subunit of the epithelial sodium channel (ENaC) play a fundamental role in this process. Now, we used a proteomic approach to identify proteins differentially expressed either in DMSO-induced LA7 or in 106A10 cells. Two differentially expressed proteins were investigated. The first, tropomyosin-5b, strongly expressed in DMSO-induced LA7 cells, is needed for dome formation because its synthesis inhibition by the antisense RNA technology abolished domes. The second protein, maspin, strongly expressed in the uninduced 106A10 cell line, inhibits dome formation because 106A10 cells, transfected with rat8 cDNA (the function of which is required for the organization of these structures), acquired the ability to develop domes when cultured in presence of an antimaspin antibody. Dome formation in these cultures are accompanied by ENaC beta-subunit expression in the absence of DMSO. Therefore, dome formation requires the expression of tropomyosin-5b, in addition to the ENaC beta-subunit and the rat8 proteins, and is under the negative control of maspin.

Animals↗
PubMed2001

Peroxisomal bifunctional enzyme binds and activates the activation function-1 region of the peroxisome proliferator-activated receptor alpha.

The transcriptional activity of peroxisome proliferator-activated receptors (PPARs), and of nuclear hormone receptors in general, is subject to modulation by cofactors. However, most currently known co-activating proteins interact in a ligand-dependent manner with the C-terminal ligand-regulated activation function (AF)-2 domain of nuclear receptors. Since PPARalpha exhibits a strong constitutive transactivating function contained within an N-terminal AF-1 region, it can be speculated that a different set of cofactors might interact with this region of PPARs. An affinity purification approach was used to identify the peroxisomal enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (bifunctional enzyme, BFE) as a protein which strongly and specifically interacted with the N-terminal 92 amino acids of PPARalpha. Protein-protein interaction assays with the cloned BFE confirmed this interaction, which could be mapped to amino acids 307-514 of the BFE and the N-terminal 70 amino acids of PPARalpha. Moreover, transient transfection experiments in hepatoma cells revealed a 2.2-fold increase in the basal and ligand-stimulated transcriptional activity of PPARalpha in the presence of BFE. This stimulatory effect is preferentially observed for the PPARalpha isoform and it is significantly stronger (4.8-fold) in non-hepatic cells, which presumably express lower levels of endogenous BFE. Hence, the BFE represents the first known cofactor capable of activating the AF-1 domain of PPAR without requiring additional regions of this receptor. These data are compatible with a model whereby the PPAR-regulated BFE is able to modulate its own expression through an enhancement of the activity of PPARalpha, representing a novel peroxisomal-nuclear feed-forward regulatory loop.

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed2001

Assessing cerebrospinal fluid rhinorrhea: a two-dimensional electrophoresis approach.

Assessment of nasal cerebrospinal fluid (CSF) fistula commonly relies on the determination of CSF markers in an aqueous rhinorrhea, such as the beta2-transferrin immunofixation assay. While generally reliable, false positive and false negative results have been reported for most of the laboratory tests yet available. Based on the hypothesis that the simultaneous assessment of several CSF markers may yield an increased sensitivity and specificity, we used a proteomics, two-dimensional electrophoresis 2-DE based approach to study samples of nasal secretions obtained from 18 patients suspected of CSF rhinorrhea. Since CSF, nasal mucus and plasma may coexist in the nasal cavities, we first defined five specific markers for each of these biological fluids (transferrin, prostaglandin-D synthase, transthyretin, and two unknown trains of spots for CSF, immunoglobulin A (IgA) S-chain, lipocortin-1, lipocalin-1, prolactine-inducible protein and palatal lung nasal epithelium clone protein for mucus, haptoglobin alpha1/2- and beta-chains, fibrinogen alpha-, beta- and gamma-chains for plasma). Gels from the rhinorrhea patients were then compared to these 2-DE reference maps to determine the presence or absence of the defined markers, and clinical data were independently compared to the results of the 2-DE study. In all cases, the biological fluid(s) anticipated to be present in the nasal secretions based on clinical data were correctly identified by 2-DE. Moreover, an excellent correlation was found in nine patients who underwent extensive workup for suspected CSF rhinorrhea, since CSF was found by the 2-DE method in four patients in whom a CSF fistula was confirmed, whereas the test was negative in five patients in whom a CSF fistula was excluded. In the remaining patients, mucus, sometimes contamined with blood, was found to be the major component of the nasal secretions, confirming that clear mucus may mimick CSF rhinorrhea. These preliminary results suggest that a 2-DE-based multimarker approach is a valid, sensitive, and specific method to assess the presence of CSF in occult rhinorrhea.

Adult↗
PubMed2001

The mouse SWISS-2D PAGE database: a tool for proteomics study of diabetes and obesity.

A number of two-dimensional electrophoresis (2-DE) reference maps from mouse samples have been established and could be accessed through the internet. An up-to-date list can be found in WORLD-2D PAGE (http://www.expasy.ch/ch2d/2d- index.html), an index of 2-DE databases and services. None of them were established from mouse white and brown adipose tissues, pancreatic islets, liver nuclei and skeletal muscle. This publication describes the mouse SWISS-2D PAGE database. Proteins present in samples of mouse (C57BI/6J) liver, liver nuclei, muscle, white and brown adipose tissue and pancreatic islets are assembled and described in an accessible uniform format. SWISS-2D PAGE can be accessed through the World Wide Web (WWW) network on the ExPASy molecular biology server (http://www.expasy.ch/ ch2d/).

Animals↗
PubMed2001

New perspectives in the Escherichia coli proteome investigation.

Escherichia coli is a model organism for biochemical and biological studies as it is one of the best characterised prokaryote. Two-dimensional polyacrylamide gel electrophoresis, computer image analysis and different protein identification techniques gave rise, in 1995, to the Escherichia coli SWISS-2D PAGE database (http://www.expasy.ch/ch2d/). In the E. coli 3.5-10 SWISS-2D PAGE map, 40% of the E. coli proteome was displayed. The present study demonstrated that the use of narrow range pH gradients is able to potentially display up to a few copies of protein per E. coli cell. Moreover, the six new E. coli SWISS-2D PAGE maps (pH 4-5, 4.5-5.5, 5-6, 5.5-6.7, 6-9 and 6-11) presented here displayed altogether more than 70% of the entire E. coli proteome.

Databases, Protein↗
PubMed2001

Identification of ribosome-associated viral and cellular basic proteins during the course of infection with herpes simplex virus type 1.

Herpes simplex virus type 1 (HSV-1) infection induces severe alterations of the translational apparatus, including the phosphorylation of a few ribosomal proteins, and the progressive association of several nonribosomal proteins to ribosomes. Therefore, we hypothesized that ribosomes themselves could contribute to the HSV-1-induced translational control of host and viral gene expression. As a prerequisite to test this hypothesis, we undertook the identification of the nonribosomal proteins associated to the ribosomes during the course of HSV-1 infection. After separation by two-dimensional polyacrylamide gel electrophoresis of basic proteins extracted from the ribosomal fraction, the identification of unknown protein spots was carried out by N-terminal sequencing and peptide mass determination by mass spectrometry. This allowed us to identify HSV-1 VP19C and VP26 that associated to ribosomes with different kinetics. Another nonribosomal protein turned out to be the poly(A)-binding protein 1 (PAB1P). Newly synthesized PAB1P continued to associate to ribosomes all along infection.

Gene Expression Regulation, Viral↗
PubMed2001

Cellular distribution of translationally controlled tumor protein in rat and human testes.

In a recent proteomic study we identified 53 spermatogonial proteins among which was the translationally controlled tumor protein (TCTP). This is a protein previously reported as being implicated in proliferation events in normal and tumoral tissues that had never previously been seen in the testis. The present study was aimed at establishing the complete cellular distribution of TCTP and its transcript and the ontogenetic expression of this gene within the testis. Using an immunohistochemistry technique, an intense TCTP signal was detected in gonocytes (the prespermatogonia) in the fetal rat testis and in spermatogonia within adult human and neonatal and adult rat testes. Meiotic spermatocytes and postmeiotic haploid spermatids were also strongly immunostained in a stage-dependent manner in human and rat testes. In addition, different levels of TCTP expression were also observed in the testicular somatic cells, with strong expression in Leydig cells and peritubular cells, and weak expression in Sertoli cells. Western and Northern blot analyses confirmed the presence of TCTP at all ages studied, with higher levels of RNA expression at 9 and 20 d postpartum, when spermatogonia and primary spermatocytes represent the highest proportion of germ cells: it was also confirmed that TCTP is present in all populations of isolated testicular cells. A transcript of 0.85 kb corresponding to TCTP, was expressed at all ages studied. This transcript was found to be expressed strongly in spermatogonia, somewhat less in isolated Leydig, resident macrophage, peritubular and Sertoli cells, weakly in the primary spermatocytes but not at all in spermatids. Interestingly, in the latter, a different transcript of 1.1 kb was present. The same 1.1 kb transcript appeared in testis extracts from 35 days postpartum onwards, corresponding to an age when spermatids accumulate within the tubules. Of note is that resident macrophages were found to express both the 0.85 and the 1.1 kb transcripts. We conclude that the strong expression of TCTP in spermatogonia makes it highly likely that the protein plays a significant role in spermatogenesis.

Adult↗
PubMed2001

Contribution of proteomics to the molecular analysis of renal cell carcinoma with an emphasis on manganese superoxide dismutase.

Renal cell carcinoma (RCC) originates in the renal cortex. It accounts for 2-3 percent of all cancers occurring in adults and it is characterised by lack of early clinical manifestations, unpredictable outcome, and absence of effective treatment modalities except early surgery. RCC comprises a heterogeneous group of tumours with various molecular and cytogenetic abnormalities and different histological features as cell types and tumour architecture. Molecular genetic and proteomic tools led to the discovery of potential diagnostic prognostic and therapeutic biomarkers of RCC. In this review we discuss recent developments in understanding genotype-phenotype relationships, with attention to manganese superoxide dismutase, a mitochondrial enzyme related to the redox cycle which affects various regulatory functions of cells. The expression of this protein has been evaluated in numerous human tumour types including RCC, and post-translational modifications are being investigated.

Biomarkers, Tumor↗
PubMed2000

Proteomics: new perspectives, new biomedical opportunities.

Proteomics-based approaches, which examine the expressed proteins of a tissue or cell type, complement the genome initiatives and are increasingly being used to address biomedical questions. Proteins are the main functional output, and the genetic code cannot always indicate which proteins are expressed, in what quantity, and in what form. For example, post-translational modifications of proteins, such as phosphorylation or glycosylation, are very important in determining protein function. Similarly, the effects of environmental factors or multigenic processes such as ageing or disease cannot be assessed simply by examination of the genome alone. This review describes the underlying technology and illustrates several areas of biomedical research, ranging from pathogenesis of neurological disorders to drug and vaccine design, in which potential clinical applications are being explored.

Animals↗
PubMed2000

The 1999 SWISS-2DPAGE database update.

SWISS-2DPAGE (http://www.expasy.ch/ch2d/ ) is an annotated two-dimensional polyacrylamide gel electro-phoresis (2-DE) database established in 1993. The current release contains 24 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps have now 2824 identified spots, corresponding to 614 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence or any user-entered amino acids sequence. Last year improvements in the SWISS-2DPAGE database are as follows: three new maps have been created and several others have been updated; cross-references to newly built federated 2-DE databases have been added; new functions to access the data have been provided through the ExPASy proteomics server.

Animals↗
PubMed2000

The dynamic range of protein expression: a challenge for proteomic research.

Proteomic research, for its part, is benefiting enormously from the last decade of genomic research as we now have archived, annotated and audited sequence databases to correlate and query experimental data. While the two-dimensional electrophoresis (2-DE) gels are still a central part of proteomics, we reflect on the possibilities and realities of the current 2-DE technology with regard to displaying and analysing proteomes. Limitations of analysing whole cell/tissue lysates by 2-DE alone are discussed, and we investigate whether extremely narrow p/ranges (1 pH unit/25 cm) provide a solution to display comprehensive protein expression profiles. We are confronted with a challenging task: the dynamic range of protein expression. We believe that most of the existing technology is capable of displaying many more proteins than is currently achievable by integrating existing and new techniques to prefractionate samples prior to 2-DE display or analysis. The availability of a "proteomics toolbox", consisting of defined reagents, methods, and equipment, would assist a comprehensive analysis of defined biological systems.

Chemical Fractionation↗
PubMed2000

Proteomics meets cell biology: the establishment of subcellular proteomes.

Proteome research aims to unravel the biological complexity encoded by the genome. Due to the complexity of higher eukaryotic cells, single-step characterization of a proteome is likely to be difficult to achieve. However, advantage can be taken of the macromolecular architecture of a cell, e.g., subcellular compartments, organelles, macromolecular structures and multiprotein complexes, to establish subcellular proteomes. This review highlights recent developments in this area of proteomics, namely the establishment of two-dimensional electrophoresis (2-DE) reference maps of subcellular compartments and organelles as well as the characterization of macromolecular structures and multiprotein complexes using a proteomics approach.

Proteome↗
PubMed2000

The establishment of a human liver nuclei two-dimensional electrophoresis reference map.

This short communication describes the establishment of a two-dimensional electrophoresis (2-DE) reference map of nuclear proteins isolated from human liver. The human liver nuclei 2-DE reference map contains 1497 spots. In an initial identification study using peptide mass fingerprinting as a means of protein identification we were able to identify 26 spots corresponding to 15 different proteins. The human liver nuclei 2-DE reference map is now included in the SWISS-2DPAGE database, which can be accessed through the ExPASy server (http://www.expasy.ch/ch2d/).

Cell Nucleus↗
PubMed2000

Changes induced by oxygen in rat liver proteins identified by high-resolution two-dimensional gel electrophoresis.

Molecular oxygen (O2) regulates the expression of a variety of genes. Several of the proteins that respond to changes in oxygen concentration have been identified in a variety of cell lines. We extend these previous studies by analyzing the effect of oxygen on the entire protein expression profile of an intact organ using high-resolution two-dimensional gel electrophoresis. To this end, we used an isolated, in vitro perfused organ preparation to produce two groups of rat livers perfused with high (95% O2, 5% CO2) or low (95% N2, 5% CO2) oxygen concentrations. Using two-dimensional gel electrophoresis we compared the protein expression profiles of both groups of livers. Computer analysis of the files obtained after laser densitometry of the two-dimensional gels revealed two spots that were strongly up-regulated in high PO2 perfused livers compared with low PO2 perfused livers. These spots were analyzed by peptide mass fingerprinting analysis. These spots were identified as arginase 1 (liver-type arginase; EC 3.5.3.1) and mitochondrial enoyl-CoA hydratase 1 (EC 4.2.1.17). The possible role of these proteins in its new context of oxygen availability is discussed.

Animals↗