K-ary clustering with optimal leaf ordering for gene expression data.
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MOTIVATION: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical clustering allows a user to view relationships in scales ranging from single genes to large sets of genes, while at the same time providing a global view of the expression data. However, hierarchical clustering is very sensitive to noise, it usually lacks of a method to actually identify distinct clusters, and produces a large number of possible leaf orderings of the hierarchical clustering tree. In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree. RESULTS: We present an algorithm that efficiently constructs a k-ary tree, where each node can have up to k children, and then optimally orders the leaves of that tree. By combining k clusters at each step our algorithm becomes more robust against noise and missing values. By optimally ordering the leaves of the resulting tree we maintain the pairwise relationships that appear in the original method, without sacrificing the robustness. Our k-ary construction algorithm runs in O(n(3)) regardless of k and our ordering algorithm runs in O(4(k)n(3)). We present several examples that show that our k-ary clustering algorithm achieves results that are superior to the binary tree results in both global presentation and cluster identification. AVAILABILITY: We have implemented the above algorithms in C++ on the Linux operating system. (+info)
Neurotrophins and the immune system.
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The neurotrophins are a family of polypeptide growth factors that are essential for the development and maintenance of the vertebrate nervous system. In recent years, data have emerged indicating that neurotrophins could have a broader role than their name might suggest. In particular, the putative role of NGF and its receptor TrkA in immune system homeostasis has become a much studied topic, whereas information on the other neurotrophins is scarce in this regard. This paper reviews what is known about the expression and possible functions of neurotrophins and their receptors in different immune tissues and cells, as well as recent data obtained from studies of transgenic mice in our laboratory. Results from studies to date support the idea that neurotrophins may regulate some immune functions. They also play an important role in the development of the thymus and in the survival of thymocytes. (+info)
Activation of the c-myb locus is insufficient for the rapid induction of disseminated avian B-cell lymphoma.
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We have previously reported that infection of 9- to 13-day-old chicken embryos with RAV-1 results in rapid development of a novel B-cell lymphoma in which proviral insertion has activated expression of the c-myb gene (E. Pizer and E. H. Humphries, J. Virol. 63:1630-1640, 1989). The biological properties of these B-cell lymphomas are distinct from those associated with the B-cell lymphomas that develop following avian leukosis virus proviral insertion within the c-myc locus. In an extension of this study, more than 200 chickens, infected as 10- to 11-day-old embryos, were examined for development of lymphomas that possess disrupted c-myb loci. Fourteen percent developed disseminated B-cell lymphoma. In the majority of these tumors, the RAV-1 provirus had inserted between the first and second exons that code for p75c-myb. However, insertions between the second and third exons and between the third and fourth exons were also detected. In situ analysis of myb protein expression in tumor tissue revealed morphological features suggesting that the tumor originates in the bursa. Within the bursa, the lymphoma appeared to spread from follicle to follicle without compromising the structural integrity of the organ. Tumor masses in liver demonstrated heterogeneous levels of myb protein suggestive of biologically distinct subpopulations. In contrast to the morbidity data, immunohistological analysis of bursae from 4- to 6-week-old chickens at risk of developing lymphomas bearing altered c-myb loci revealed lesions expressing elevated levels of myb in 16 of 19 birds. The activated myb lymphoma displayed very poor capacity to proliferate outside its original host. Only 1 of 33 in vivo transfers of tumor to recipient hosts established a transplantable tumor. None of the primary tumor tissue nor the transplantable tumor exhibited the capacity for in vitro proliferation. Similar experimental manipulation has yielded in vitro lines established from avian B-cell lymphomas expressing elevated levels of c-myc or v-rel. The dependence on embryonic infection for development of activated-myb lymphoma suggests a requirement for a specific target cell in which c-myb is activated by proviral insertion. It is likely, moreover, that continued tumor development requires elevated expression of myb proteins within a specific cell population in a restricted stage of differentiation. (+info)
a1/EBP: a leucine zipper protein that binds CCAAT/enhancer elements in the avian leukosis virus long terminal repeat enhancer.
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Avian leukosis virus (ALV) induces bursal lymphoma in chickens after integration of proviral long terminal repeat (LTR) enhancer sequences next to the c-myc proto-oncogene. Labile LTR-binding proteins appear to be essential for c-myc hyperexpression, since both LTR-enhanced transcription and the activities of LTR-binding proteins are specifically decreased after inhibition of protein synthesis (A. Ruddell, M. Linial, W. Schubach, and M. Groudine, J. Virol. 62:2728-2735, 1988). This lability is restricted to hematopoietic cells from ALV-susceptible chicken strains, suggesting that the labile proteins play an important role in lymphomagenesis. The major labile activity binding to the a1 LTR region (A. Ruddell, M. Linial, and M. Groudine, Mol. Cell. Biol. 12:5660-5668, 1989) was purified from bursal lymphoma cells by conventional and oligonucleotide affinity chromatography, yielding three proteins of 35, 40, and 42 kDa. More than one of these species binds the a1 LTR region, as judged by gel shift analysis. A gene encoding an a1-binding protein (designated a1/EBP) was cloned by screening a bursal lymphoma cDNA library for fusion proteins binding the a1 LTR site. DNase I footprinting and gel shift assays indicate that the a1/EBP fusion protein binds multiple LTR CCAAT/enhancer elements in a pattern similar to that of the purified B-cell protein. DNA sequence analysis shows that this 2.2-kb cDNA encodes a 209-amino-acid open reading frame containing carboxy-terminal basic and leucine zipper motifs, indicating that a1/EBP encodes a novel member of the leucine zipper family of transcription factors. (+info)
Subclinical infectious bursal disease in an integrated broiler production operation.
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A field study was designed to determine the prevalence of subclinical infectious bursal disease (IBD) in broiler chickens from a commercial poultry company. Bursae of Fabricius (BF) from two vaccinated and three nonvaccinated broiler flocks were evaluated histologically, and antibody profiles of these broiler and matched parent breeder flocks were established. Lesions of IBD, including lymphoid necrosis, stromal edema, and infiltrates of heterophils and macrophages, were first detected in BF at 24 days of age in both vaccinated and nonvaccinated chickens. At 41 days, all BF had lesions characteristic of IBD, including severe lymphoid depletion, proliferation of epithelial cells, and mild fibroplasia. Although mean maternal antibody levels (measured by enzyme-linked immunosorbent assay) in broilers were apparently protective through day 12, IBD antibodies decreased to nonprotective levels (below 1,000) by day 16 or 20. Titers began to increase by day 28 or 32 because of field exposure. Sentinel birds, placed with broiler flocks, also developed IBD antibody titers. Broiler breeders had low and nonuniform antibody titers. Prevalence of field IBD exposure was high, and existing vaccination programs were not effective. (+info)
Chicken BAFF--a highly conserved cytokine that mediates B cell survival.
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Members of the tumor necrosis factor (TNF) family play key roles in the regulation of inflammation, immune responses and tissue homeostasis. Here we describe the identification of the chicken homologue of mammalian B cell activating factor of the TNF family (BAFF/BLyS). By searching a chicken EST database we identified two overlapping cDNA clones that code for the entire open reading frame of chicken BAFF (chBAFF), which contains a predicted transmembrane domain and a putative furin protease cleavage site like its mammalian counterparts. The amino acid identity between soluble chicken and human BAFF is 76%, considerably higher than for most other known cytokines. The chBAFF gene is most strongly expressed in the bursa of Fabricius. Soluble recombinant chBAFF produced by human 293T cells interacted with the mammalian cell-surface receptors TACI, BCMA and BAFF-R. It bound to chicken B cells, but not to other lymphocytes, and it promoted the survival of splenic chicken B cells in culture. Furthermore, bacterially expressed chBAFF induced the selective expansion of B cells in the spleen and cecal tonsils when administered to young chicks. Our results suggest that like its mammalian counterpart, chBAFF plays an important role in survival and/or proliferation of chicken B cells. (+info)
Viability of preserved Cryptosporidium baileyi oocysts.
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The present study was undertaken to determine the viability and infectivity of oocysts of Cryptosporidium baileyi that had been stored from 1 to 40 months at 4 degrees C preserved in 2.5% potassium dichromate solution. Oocysts of C. baileyi were purified from the feces of experimentally infected chickens using discontinuous sucrose gradients. Subsequently, the purified oocysts were suspended in 2.5% potassium dichromate solution at a concentration of 1 x 10(7) organism/ml, and their viabilities were assessed by nucleic acid staining, histologic examination, and infectivity to 2-day-old chickens. All chickens inoculated with oocysts that had been stored for 1-18 months developed patent infections, while chickens infected with older oocysts remained uninfected. Between 5.8% and 82.2% of the oocysts, stored at 4 degrees C in 2.5% potassium dichromate solution, were found to be viable, as determined by nucleic acid staining. Parasite colonization in the bursa of Fabricius was detected in the microvillus border of bursal epithelium. The finding that C. baileyi oocysts remain infective to chickens for at least 18 months offers important time-saving advantages to investigators who frequently require large numbers of oocysts. (+info)
The cytoplasmic domain of Ig alpha is necessary and sufficient to support efficient early B cell development.
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The B cell receptor complex (BcR) is essential for normal B lymphocyte function, and surface BcR expression is a crucial checkpoint in B cell development. However, functional requirements for chains of the BcR during development remain controversial. We have used retroviral gene transfer to introduce components of the BcR into chicken B cell precursors during embryonic development. A chimeric heterodimer, in which the cytoplasmic domains of chicken Igalpha and Igbeta are expressed by fusion with the extracellular and transmembrane domains of murine CD8alpha and CD8beta, respectively, targeted the cytoplasmic domains of the BcR to the cell surface in the absence of extracellular BcR domains. Expression of this chimeric heterodimer supported all early stages of embryo B cell development: bursal colonization, clonal expansion, and induction of repertoire diversification by gene conversion. Expression of the cytoplasmic domain of Igalpha, in the absence of the cytoplasmic domain of Igbeta, was not only necessary, but sufficient to support B cell development as efficiently as the endogenous BcR. In contrast, expression of the cytoplasmic domain of Igbeta in the absence of the cytoplasmic domain of Igalpha failed to support B cell development. The ability of the cytoplasmic domain of Igalpha to support early B cell development required a functional Igalpha immunoreceptor tyrosine-based activation motif. These results support a model in which expression of surface IgM following productive V(D)J recombination in developing B cell precursors serves to chaperone the cytoplasmic domain of Igalpha to the B cell surface, thereby initiating subsequent stages of development. (+info)