19 research outputs found
Protein Expression During Murine Thymus Differentiation
Driven by our long-standing interest in identifying proteins of the immune system and in
characterizing processes involved in lymphocyte differentiation, we studied protein expression
in biosynthetically labeled fetal and newborn thymus by 2D gel electrophoresis.
Autoradiographs of the gels were scanned with a densitometer and image analysis was
performed using the Kepler system. Calibrated polypeptide spot abundances (volumes)
were compared to assesses qualitative and quantitative changes of the spot volumes. Among
over 300 proteins evaluated at GD (gestation day) 13,15, and 17, there were sets of proteins
that increased and others that decreased in intensity. We could in addition recognize proteins
that were completely absent at GD 13 and/or 15 and that appeared thereafter to
gradually increase in intensity. Conversely, various polypeptide spots present at early stages
(at GD 13 and 15) disappear later (at GD 17 or at birth). Among the proteins that increase
in intensity prevail molecules with masses less than 35 kD, whereas a considerable portion
of those that decrease in intensity are characterized by masses above 60 kD. Spots reported
in this communication were not defined beyond tagging them with numbers, which is a
prerequisite to follow them up in the proteinpaedia developed in our laboratory. The next
step will be to retrieve the coding sequences from the existing partitioned cDNA library
(BW 5147) as well as from thymocyte subtraction libraries. We predict that among those
polypeptides with varying intensity, important regulatory proteins in thymus development
will be found
Internal standard-based analysis of microarray data2—Analysis of functional associations between HVE-genes
In this work we apply the Internal Standard-based analytical approach that we described in an earlier communication and here we demonstrate experimental results on functional associations among the hypervariably-expressed genes (HVE-genes). Our working assumption was that those genetic components, which initiate the disease, involve HVE-genes for which the level of expression is undistinguishable among healthy individuals and individuals with pathology. We show that analysis of the functional associations of the HVE-genes is indeed suitable to revealing disease-specific differences. We show also that another possible exploit of HVE-genes for characterization of pathological alterations is by using multivariate classification methods. This in turn offers important clues on naturally occurring dynamic processes in the organism and is further used for dynamic discrimination of groups of compared samples. We conclude that our approach can uncover principally new collective differences that cannot be discerned by individual gene analysi
Integrated Epigenetics of Human Breast Cancer: Synoptic Investigation of Targeted Genes, MicroRNAs and Proteins upon Demethylation Treatment
The contribution of aberrant DNA methylation in silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations are reversible, it became of interest to determine the effects of the 5-aza-2'-deoxycytidine (DAC) demethylation therapy in breast cancer at different molecular levels
Internal standard-based analysis of microarray data2—Analysis of functional associations between HVE-genes
In this work we apply the Internal Standard-based analytical approach that we described in an earlier communication and here we demonstrate experimental results on functional associations among the hypervariably-expressed genes (HVE-genes). Our working assumption was that those genetic components, which initiate the disease, involve HVE-genes for which the level of expression is undistinguishable among healthy individuals and individuals with pathology. We show that analysis of the functional associations of the HVE-genes is indeed suitable to revealing disease-specific differences. We show also that another possible exploit of HVE-genes for characterization of pathological alterations is by using multivariate classification methods. This in turn offers important clues on naturally occurring dynamic processes in the organism and is further used for dynamic discrimination of groups of compared samples. We conclude that our approach can uncover principally new collective differences that cannot be discerned by individual gene analysis
Proteomics in cardiovascular surgery
Proteomics describes, analogous to the term genomics, the study of the complete set of proteins present in a cell, organ, or organism at a given time. The genome tells us what could theoretically happen, whereas the proteome tells us what does happen. Therefore, a genomic-centered view of biologic processes is incomplete and does not describe what happens at the protein level. Proteomics is a relatively new methodology and is rapidly changing because of extensive advances in the underlying techniques. The core technologies of proteomics are 2-dimensional gel electrophoresis, liquid chromatography, and mass spectrometry. Proteomic approaches might help to close the gap between traditional pathophysiologic and more recent genomic studies, assisting our basic understanding of cardiovascular disease. The application of proteomics in cardiovascular medicine holds great promise. The analysis of tissue and plasma/serum specimens has the potential to provide unique information on the patient. Proteomics might therefore influence daily clinical practice, providing tools for diagnosis, defining the disease state, assessing of individual risk profiles, examining and/or screening of healthy relatives of patients, monitoring the course of the disease, determining the outcome, and setting up individual therapeutic strategies. Currently available clinical applications of proteomics are limited and focus mainly on cardiovascular biomarkers of chronic heart failure and myocardial ischemia. Larger clinical studies are required to test whether proteomics may have promising applications for clinical medicine. Cardiovascular surgeons should be aware of this increasingly pertinent and challenging field of science