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Asthma is one of the foremost contributors to morbidity and mortality in industrialized countries. Our objective was to characterize the acute response to allergen and to identify potentially novel molecular targets for pharmacological intervention in asthma. We therefore designed a study to identify genes whose regulation was altered following ovalbumin (OVA) challenge in the presence and absence of treatment with glucocorticoids in BALBc mice. RNA was isolated from lungs for gene profiling from 8-week-old sensitized mice, 3 and 18 hours post OVA challenge on days 1, 4, and 7 of aerosol challenge. Taqman (real time RT-PCR) analysis of marker genes indicative of Th2 (IL-4, IL-13), eosinophil (RANTES, eotaxin), Th1macrophage (IFN?) and epithelial cell (MUC5AC) phenotypes were used to characterize responses to allergen challenge. Histological evaluation of lungs from additional challenged animals revealed inflammatory infiltrates on days 4 and 7, but not on day 1 post challenge. We postulate that expression of IL-4, IL-13 and other genes by OVA at day 1 probably reflects activation of resident cells, whereas the fivefold increase in the number of regulated genes at day 7 reflects the contribution of recruited cells. Of the regulated genes, only a subset was counter-regulated by dexamethasone treatment. Although regulated genes included genes in many protein families, herein we report regulation of two proteases whose role in response to OVA challenge has not been characterized. This model will be used to generate disease hypotheses for which may play an important role in initiating disease pathology in this model.

A supervised classification scheme for analyzing microarray expression data, based on the k-nearest-neighbor method coupled to noise-reduction filters, has been used to find genes involved in the osteogenic pathway of the mouse C2C12 cell line studied here as a model for in vivo osteogenesis. The scheme uses as input a training set embodying expert biological knowledge, and provides internal estimates of its own misclassification errors, which furthermore enables systematic optimization of the classifier parameters. On the basis of the C2C12-generated expression data set with 34,130 expression profiles across 2 time courses, each comprised of 6 points, and a training set containing known members of the osteogenic, myoblastic, and adipocytic pathways, 176 new genes in addition to 28 originally in the training set are selected as relevant to osteogenesis. For this selection, the estimated sensitivity is 42% and the posterior false-positive rate (fraction of candidates that are spurious) is 12%. The corresponding sensitivity and false-positive rate for detection of myoblastic genes are 9% and 31%, respectively, and only 4% and approximately 100%, respectively, for adipocytic genes, in accordance with an experimental design that predominantly stimulated the osteogenic pathway. Validation of this selection is provided by examining expression of the genes in an independent biological assay involving mouse calvaria (skull bone) primary cell cultures, in which a large fraction of the 176 genes are seen to be strongly regulated, as well as by case-by-case analysis of the genes on the basis of expert domain knowledge. The methodology should be generalizable to any situation in which enough a priori biological knowledge exists to define a training set.

The signal recognition particle (SRP)-mediated transport of proteins across mammalian endoplasmic reticulum requires GTP in a capacity distinct from polypeptide elongation. We defined the role of GTP by a molecular characterization of translocation intermediates that accumulate after incubation of SRP-ribosome complexes with microsomal membranes. SRP receptor-catalyzed displacement of SRP from ribosomes was GTP-dependent both with intact membranes and with the purified SRP receptor. GTP-specific binding was localized to the α subunit of the receptor by photoaffinity labeling and by probing nitrocellulose blots of the receptor with GTP. Analysis of the α subunit of the SRP receptor revealed amino acid sequences that are similar to guanine ribonucleotide binding site consensus sequence elements.

Bone marrow contains a rare population of mesenchymal stem cells (MSCs) capable of giving rise to multiple mesodermal tissues including bone, cartilage, tendon, muscle, and fat. The cell surface antigen recognized by monoclonal antibody SB‐10 is expressed on human MSCs but is lost during their developmental progression into differentiated phenotypes. Here we report on the immunopurification of the SB‐10 antigen and its identification as activated leukocyte‐cell adhesion molecule (ALCAM). Mass spectrometry establishes that the molecular mass of ALCAM is 80,303 ± 193 Da and that it possesses 17,763 ± 237 Da of N‐linked oligosaccharide substituents. Molecular cloning of a full‐length cDNA from a MSC expression library demonstrates nucleotide sequence identity with ALCAM. We also identified ALCAM homologs in rat, rabbit, and canine MSCs, each of which is over 90% identical to human ALCAM in their peptide sequence. The addition of antibody SB‐10 Fabfragments to human MSCs undergoing osteogenic differentiation in vitro accelerated the process, thereby implicating a role for ALCAM during bone morphogenesis and adding ALCAM to the group of cell adhesion molecules involved in osteogenesis. Together, these results provide evidence that ALCAM plays a critical role in the differentiation of mesenchymal tissues in multiple species across the phylogenetic tree.