Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions

Genome-scale microarray experiments for comparative analysis of gene expressions produce massive amounts of information. Traditional statistical approaches fail to achieve the required accuracy in sensitivity and specificity of the analysis. Since the problem can be resolved neither by increasing the number of replicates nor by manipulating thresholds, one needs a novel approach to the analysis. This article describes methods to improve the power of microarray analyses by defining internal standards to characterize features of the biological system being studied and the technological processes underlying the microarray experiments. Applying these methods, internal standards are identified and then the obtained parameters are used to define (i) genes that are distinct in their expression from background; (ii) genes that are differentially expressed; and finally (iii) genes that have similar dynamical behavio

Frequency analysis of cytolytic T cell precursors (CTL-P) generated in vivo during lethal rabies infection of mice. I. Distinction of CTL-P with different interleukin 2 sensitivity

The aim of this study was to determine the number and state of activity of cytolytic T lymphocytes (CTL) and their precursors (CTL-P) present in vivo during the early stages of viral infection. The local response to lethal infection with rabies virus was used as a model system that is not accessible to analysis by secondary activation in vitro. The local response to alloantigen served as a control. Experimental protocols were established that allow frequency estimates of in vivo antigen-triggered CTL-P. Data allow a distinction between CTL-P activated in vivo by alloantigen and viral antigen with respect to their different capacity to utilize T cell growth factors (inter-leukins). In vivo alloantigen-primed CTL-P generate, in vitro, an active effector progeny in the presence of interleukins of xenogeneic origin, whereas the majority of virus-specific CTL-P, in spite of considerable expansion in vivo, fail to generate CTL in vitro unless antigen is added

Quantitative Proteomics of Lymphocytes

Lymphocytes are the best-studied higher eukaryote cells. In this report, quantitative relationships of the protein components in resting cell, blast cell and plasma cell types are evaluated. The comparison of these cell types leads to the conclusion that resting cells synthesize about one-twentieth of the protein species as compared to blast cells. Blast cells seem to be metabolically the most robust lymphocyte type. Plasma cells are geared towards synthesis of one main product (antibody in B plasma cells), while most of the synthesis of other protein species (including those for housekeeping and repair) decreases as the messages decay. Although the data presented in this communication allow a meaningful comparison of three cell populations, they are far from providing a full picture. Both silver staining and radiofluorography depict only proteins of high or intermediate abundance. Silver staining misses most proteins present at <10 000 copies/cell, while radiofluorography misses all those proteins with slow turnover (and those with no methionine residue in their sequence). The detection of 1100 spots in the blast cell-related radiofluorograph includes visualization of some 97–99% of protein mass, but some 3900 polypeptide species in the remaining 1–3% of protein mass will pass undetected. This protein mass (0.7–2 pg) reflects some 2500–7500 copies of each of those 3900 polypeptide species that are present in the cell below the detection limit. The work emphasizes that full understanding of cellular function can be achieved only if quantitative aspects of cell inventory are considered

Improvements on Gabor Descriptor Retrieval for Patch Detection

The localization of object parts in the component-based object detection is among the main tasks to solve. This paper presents several improvements of the proposed local image descriptor based on Gabor wavelets. Including these descriptors in the desired application is an ambitious challenge if we take into account the high number of parameters. Determining of parameters can be very hard because of their infinite definition range. Defining the filters is done in two stages: a theoretical consideration narrows the domain and the cardinality of parameters; this is followed by adequate experiments to select the most characteristic descriptor for a target image patch. The descriptor is created from a given number of 2D Gabor filters chosen by the GentleBoost learning algorithm. Comparing the proposed descriptor to those found in the state of the art, we can conclude that the selected filters are adaptable to any target object. In contrast to this, the majority of filter-based descriptors have fixed values for the parameters that do not allow to be ductile to the given object. Parameters fine-tuning allows the descriptor to be general, and discriminative at the same time. The effect of the following experiments has been analyzed during the investigation: elimination of redundancy between the weak classifiers, using the LoG interest points in the detection process. Finally, we propose an acceleration algorithm in order to deter- mine the response map faster. By means of the descriptor, the response map is created, which accurately localizes the target object part and can easily be integrated in almost all detection systems

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

The Pl(A2) polymorphism of integrin beta(3) enhances outside-in signaling and adhesive functions.

Genetic factors are believed to influence the development of arterial thromboses. Because integrin alpha(IIb)beta(3) plays a crucial role in thrombus formation, we analyzed receptor adhesive properties using Chinese hamster ovary and human kidney embryonal 293 cells overexpressing the Pl(A1) or Pl(A2) polymorphic forms of alpha(IIb)beta(3). Soluble fibrinogen binding was no different between Pl(A1) and Pl(A2) cells, either in a resting state or when alpha(IIb)beta(3) was activated with anti-LIBS6. Pl(A1) and Pl(A2) cells bound equivalently to immobilized fibronectin. In contrast, significantly more Pl(A2) cells bound to immobilized fibrinogen in an alpha(IIb)beta(3)-dependent manner than did Pl(A1) cells. Disruption of the actin cytoskeleton by cytochalasin D abolished the increased binding of Pl(A2) cells. Compared with Pl(A1) cells, Pl(A2) cells exhibited a greater extent of polymerized actin and cell spreading, enhanced tyrosine phosphorylation of pp125(FAK), and greater fibrin clot retraction. These adhesion differences appear to depend on a signaling mechanism sensitive to receptor occupancy. Thus, the Pl(A2) polymorphism altered integrin-mediated functions of adhesion, spreading, actin cytoskeleton rearrangement, and clot retraction

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