ABSTRACT
Systemic lupus erythematosus (SLE) is an autoimmune disease in which polymorphisms within the human leukocyte antigen (HLA) region have been associated to its etiology. For this study, HLA-DQB1, DQA1, and DRB1 genes were typed by polymerase chain reaction-sequence-specific primer in 237 individuals, taken from 74 families, who had a member with SLE, and who had their residence in the western region of Mexico; as well as in 159 ethnically matched healthy volunteers taken from 32 families. Genotype and allele frequency analysis was performed in 74 SLE patients and 54 unrelated controls. Precise three-loci identification of independent haplotypes was performed in 48 patients and 54 controls by familial segregation. Genotype distribution at each loci was concordant with Hardy-Weinberg's equilibrium in the control group. In general, no genotype effect was observed in SLE patients. Allele distribution comparison showed in the SLE group a significant increase of HLA-DQA1*0102, DQB1*0402, and DRB1*15; whereas alleles HLA-DQB1*0303 and *0501 were significantly decreased. SLE patients showed haplotype DQB1*0602-DQA1-*0102-DRB1*15 increased. As expected, patients with SLE have a reduced haplotype genetic diversity. The associations found in this study are related to an ancestral haplotype that has been observed in SLE populations of different origins.
Subject(s)
Genes, MHC Class II , HLA-D Antigens/genetics , Lupus Erythematosus, Systemic/genetics , Lupus Erythematosus, Systemic/immunology , Adolescent , Adult , Aged , Alleles , Case-Control Studies , Female , Gene Frequency , Genotype , HLA-DQ Antigens/genetics , HLA-DQ alpha-Chains , HLA-DQ beta-Chains , HLA-DR Antigens/genetics , HLA-DRB1 Chains , Haplotypes , Humans , Male , Mexico , Middle AgedABSTRACT
Since its inception, the analysis of time-lapse video-images acquired during Ca2+ imaging experiments using fluorescence microscopy has been progressively optimized for achieving a high temporal resolution. In contrast, the spatial resolution of the acquired images is often compromised during analysis to varying degrees by the need to draw regions of interest (ROI). We developed a strategy to analyze images at the acquired spatial resolution-pixel-by-pixel, grouping all pixels based on criteria of interest (COI) in regard to their associated fluorescence values over time and visualizing the distributions of the pixel-groups detected in a pseudo-colored map. We applied this pixel-based COI-strategy to the analysis of relative intracellular free calcium levels (Ca(i)(2+)) in attached cultured embryonic hippocampal cells under baseline and experimental conditions designed to evaluate the contribution of extracellular Ca2+ (Ca(e)(2+)) to baseline Ca(i)(2+) levels. We discovered distinct groups of Ca(e)(2+)-dependent Ca(i)(2+) regulation patterns emergent during the earliest phases of hippocampal cell differentiation, which were not limited to inter-cell differences. Thus, pixel-based COI-analysis of time-lapse images can be used to disclose distinct patterns of Ca(e)(2+)-dependent Ca(i)(2+) levels and their corresponding subcellular distributions in developing hippocampal cells. Such a strategy should be useful in studying the emergence and distribution of Ca(i)(2+) signaling at subcellular levels of resolution using fluorescence microscopy.
Subject(s)
Calcium/metabolism , Hippocampus/metabolism , Image Processing, Computer-Assisted/methods , Microscopy, Fluorescence/methods , Aniline Compounds/metabolism , Animals , Caffeine/pharmacology , Cells, Cultured , Central Nervous System Stimulants/pharmacology , Demography , Embryo, Mammalian , Embryo, Nonmammalian , Fluorescent Dyes/metabolism , Hippocampus/cytology , Hippocampus/embryology , Image Processing, Computer-Assisted/instrumentation , Microscopy, Fluorescence/instrumentation , Signal Processing, Computer-Assisted/instrumentation , Time , Time Factors , Xanthenes/metabolismABSTRACT
DNA microarrays are valuable but expensive tools for expression profiling of cells, tissues, and organs. The design of custom microarrays leads to cost reduction without necessarily compromising their biological value. Here we present a strategy for designing custom cDNA microarrays and constructed a microarray for mouse immunology research (ImmunoChip). The strategy used interrogates expressed sequence tag databases available in the public domain but overcomes many of the problems encountered. Immunologically relevant clusters were selected based on the expression of expressed sequence tags in relevant libraries. Selected clusters were organized in modules, and the best representative clones were identified. When tested, this microarray was found to have minimal clone identity errors or phage contamination and identified molecular signatures of lymphoid cell lines. Our proposed design of custom microarrays avoids probe redundancy, allows the organization of the chip to optimize chip production, and reduces microarray production costs. The strategy described is also useful for the design of oligonucleotide microarrays.
