Data integration gets 'Sloppy'.
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Biology↗
Biomedical subjects
Romesh Stanislaus
Publications and source records attributed to Romesh Stanislaus.
N-acetyl-L-cysteine ameliorates the inflammatory disease process in experimental autoimmune encephalomyelitis in Lewis rats.
We report that N-acetyl-L-cysteine (NAC) treatment blocked induction of TNF-alpha, IL-1beta, IFN-gamma and iNOS in the CNS and attenuated clinical disease in the myelin basic protein induced model of experimental allergic encephalomyelitis (EAE) in Lewis rats. Infiltration of mononuclear cells into the CNS and induction of inflammatory cytokines and iNOS in multiple sclerosis (MS) and EAE have been implicated in subsequent disease progression and pathogenesis. To understand the mechanism of efficacy of NAC against EAE, we examined its effect on the production of cytokines and the infiltration of inflammatory cells into the CNS. NAC treatment attenuated the transmigration of mononuclear cells thereby lessening the neuroinflammatory disease. Splenocytes from NAC-treated EAE animals showed reduced IFN-gamma production, a Th1 cytokine and increased IL-10 production, an anti-inflammatory cytokine. Further, splenocytes from NAC-treated EAE animals also showed decreased nitrite production when stimulated in vitro by LPS. These observations indicate that NAC treatment may be of therapeutic value in MS against the inflammatory disease process associated with the infiltration of activated mononuclear cells into the CNS.
Journal Article↗
AGML Central: web based gel proteomic infrastructure.
SUMMARY: AGML Central is a web-based open-source public infrastructure for dissemination of two-dimensional Gel Electrophoresis (2-DE) proteomics data in AGML format (Annotated Gel Markup Language). It includes a growing collection of converters from proprietary formats such as those produced by PDQUEST (BioRad), PHORETIX 2-D (Nonlinear Dynamics) and Melanie (GenBio SA). The resulting unifying AGML formatted entry, with or without the raw gel images, is optionally stored in a database for future reference. AGML Central was developed to provide a common platform for data dissemination and development of 2-DE data analysis tools. This resource responds to an increasing use of AGML for 2-DE public source data representation which requires automated tools for conversion from proprietary formats. Conversion and short-term storage is made publicly available, permanent storage requires prior registering. A JAVA applet visualizer was developed to visualize the AGML data with cross-reference links. In order to facilitate automated access a SOAP web service is also included in the AGML Central infrastructure. AVAILABILITY: http://bioinformatics.musc.edu/agmlcentral.
Database Management Systems↗
Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics.
Although two-dimensional gel electrophoresis (2-DE) has long been a favorite experimental method to screen proteomes, its reproducibility is seldom analyzed with the assistance of quantitative error models. The lack of models of residual distributions that can be used to assign likelihood to differential expression reflects the difficulty in tackling the combined effect of variability in spot intensity and uncertain recognition of the same spot in different gels. In this report we have analyzed a series of four triplicate two-dimensional gels of chicken embryo heart samples at two distinct development stages to produce such a model of residual distribution. In order to achieve this reference error model, a nonparametric procedure for consistent spot intensity normalization had to be established, and is also reported here. In addition to variability in normalized intensity due to various sources, the residual variation between replicates was observed to be compounded by failure to identify the spot itself (gel alignment). The mixed effect is reflected by variably skewed bimodal density distributions of residuals. The extraction of a global error model that accommodated such distribution was achieved empirically by machine learning, specifically by bootstrapped artificial neural networks. The model described is being used to assign confidence values to observed variations in arbitrary 2-DE gels in order to quantify the degree of over-expression and under-expression of protein spots.
Animals↗
Prediction of urinary protein markers in lupus nephritis.
BACKGROUND: Lupus nephritis is divided into six classes and scored according to activity and chronicity indices based on histologic findings. Treatment differs based on the pathologic findings. Renal biopsy is currently the only way to accurately predict class and activity and chronicity indices. We propose to use patterns of abundance of urine proteins to identify class and disease indices. METHODS: Urine was collected from 20 consecutive patients immediately prior to biopsy for evaluation of lupus nephritis. The International Society of Nephrology/Renal Pathology Society (ISN/RPS) class of lupus nephritis, activity, and chronicity indices were determined by a renal pathologist. Proteins were separated by two-dimensional gel electrophoresis. Artificial neural networks were trained on normalized spot abundance values. RESULTS: Biopsy specimens were classified in the database according to ISN/RPS class, activity, and chronicity. Nine samples had characteristics of more than one class present. Receiver operating characteristic (ROC) curves of the trained networks demonstrated areas under the curve ranging from 0.85 to 0.95. The sensitivity and specificity for the ISN/RPS classes were class II 100%, 100%; III 86%, 100%; IV 100%, 92%; and V 92%, 50%. Activity and chronicity indices had r values of 0.77 and 0.87, respectively. A list of spots was obtained that provided diagnostic sensitivity to the analysis. CONCLUSION: We have identified a list of protein spots that can be used to develop a clinical assay to predict ISN/RPS class and chronicity for patients with lupus nephritis. An assay based on antibodies against these spots could eliminate the need for renal biopsy, allow frequent evaluation of disease status, and begin specific therapy for patients with lupus nephritis.
Adult↗
Impaired peroxisomal function in the central nervous system with inflammatory disease of experimental autoimmune encephalomyelitis animals and protection by lovastatin treatment.
Peroxisomes are ubiquitous subcellular organelles and abnormality in their biogenesis and specific gene defects leads to fatal demyelinating disorders. We report that neuroinflammatory disease in brain of experimental autoimmune encephalomyelitis (EAE) rats decreased the peroxisomal functions. Degradation of very long chain fatty acids decreased by 47% and resulted in its accumulation (C26:0, 40%). Decreased activity (66% of control) of dihydroxyacetonephosphate acyltransferase (DHAP-AT), first enzyme in plasmalogens biosynthesis, resulted in decreased levels of plasmalogens (16-30%). Catalase activity, a peroxisomal enzyme, was also reduced (37%). Gene microarray analysis of EAE spinal cord showed significant decrease in transcripts encoding peroxisomal proteins including catalase (folds 3.2; p<0.001) and DHAP-AT (folds 2.6; p<0.001). These changes were confirmed by quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis, suggesting that decrease of peroxisomal functions in the central nervous system will have negative consequences for myelin integrity and repair because these lipids are major constituents of myelin. However, lovastatin (a cholesterol lowering and anti-inflammatory drug) administered during EAE induction provided protection against loss/down-regulation of peroxisomal functions. Attenuation of induction of neuroinflammatory mediators by statins in cultured brain cells [J. Clin. Invest. 100 (1997) 2671-2679], and in central nervous system of EAE animals and thus the EAE disease [J. Neurosci. Res. 66 (2001) 155-162] and the studies described here indicate that inflammatory mediators have a marked negative effect on peroxisomal functions and thus on myelin assembly and that these effects can be prevented by treatment with statins. These observations are of importance because statins are presently being tested as therapeutic agents against a number of neuroinflammatory demyelinating diseases.
ATP-Binding Cassette Transporters↗
Regulation of gene expression associated with acute experimental autoimmune encephalomyelitis by Lovastatin.
The attenuation of experimental autoimmune encephalomyelitis (EAE) by Lovastatin (LOV) has now been well established. The present study was designed to explore the global effect of LOV treatment on expression of immune-related genes in lumbar spinal cord (LSC) during acute EAE by using Affymetrix DNA microarrays. LOV treatment demonstrated the limited infiltration of inflammatory cells into the LSC, and microarray analysis further validated those interpretations by demonstrating relatively less alteration in expression of immune response genes in LOV-treated EAE rats on peak clinical day and recovery vs. untreated EAE counterparts. There was significant change in expression of about 158 immune-related genes (including 127 genes reported earlier) in LOV-treated vs. untreated EAE (>1.5 or <-1.5 fold change; P </=.05), of which 140 genes were suppressed and only 18 genes were up-regulated. These altered genes encode for leukocyte-specific markers and receptors, histocompatibility complex, cytokines/receptors, chemokines/receptors, adhesion molecules, components of the complement cascade, cellular activation, and transcription factors and signal transduction-related molecules. Interestingly, T(H)2 phenotype cytokines such as interleukin-4, interleukin-10, and transforming growth factor-beta1 and transcription factors such as peroxisome proliferator-activated receptor (PPAR)-gamma were up-regulated in LSC by LOV treatment as further revealed by real-time PCR and immunoblotting. These findings indicate that PPARs may be mediating the antiinflammatory and immunomodulatory effects of LOV. Together, these findings provide new insight into the molecular events associated with the protection provided by statins during treatment of demyelinating diseases such as multiple sclerosis.
Animals↗
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.
BACKGROUND: Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data. RESULTS: In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG) as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML) schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here. CONCLUSION: The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at http://bioinformatics.musc.edu/agml. Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.
Computational Biology↗
Immunomodulation of experimental autoimmune encephalomyelitis in the Lewis rats by Lovastatin.
Previous studies have demonstrated the immunomodulatory potential of Lovastatin, a hydroxy methyl glutaryl-CoA reductase inhibitor, in lessening the clinical and histological manifestations in the neuroinflammatory animal model experimental autoimmune encephalomyelitis (EAE) (Neurosci. Lett., 269 (1999) 71, and J. Neurosci. Res., 66 (2001) 155). To determine the mechanism behind the observed amelioration of EAE by Lovastatin, we examined the cytokine profile of stimulated splenocytes from control, EAE and Lovastatin treated EAE rats. Splenocytes from Lovastatin-treated EAE rats showed decreased levels of interferon-gamma, a Th1 type cytokine, while interleukin (IL)-10, a Th2 type cytokine, was markedly increased as compared to untreated EAE animals. In addition, we also observed reduced levels of IL-6 and nitric oxide production in lipopolysaccharide-stimulated splenocytes isolated from Lovastatin-treated animals. This study documents for the first time that Lovastatin induces a bias towards Th2 cytokines ex vivo, and as a result may be of therapeutic value for cell-mediated diseases such as multiple sclerosis.
Animals↗