Biomedical subjects

Michael G Walker

Publications and source records attributed to Michael G Walker.

21 records · Page 2Linked to original sources

PubMed2002

Z39Ig is co-expressed with activated macrophage genes.

Z39Ig is a recently-identified gene with immunoglobulin-like domains whose function is unknown. We examined expression of Z39Ig in 1432 human cDNA libraries, and found it primarily in synovium of patients with rheumatoid arthritis, in placenta, and in lung. We analyzed its co-expression pattern using the Guilt-by-Association (GBA) algorithm, and found that it is most similar in expression to early genes in the classical complement system (C1qA, C1qB, C1qC, C1r, and C1 inhibitor), MHC class II genes (HLA-DR alpha, HLA-DR beta 1, and HLA-DP alpha 1), Fc receptors (Fc gamma RIIa and Fc epsilon R1), lysosomal protein (LAPTm5), tissue transglutaminase, and macrophage receptors (MARCO and CD163/M130). The sequence and expression data suggest that Z39Ig is a cell surface receptor, expressed in activated macrophages, and linked with the classical complement system, most likely in phagocytosis preceding antigen presentation. Knowledge of this gene may contribute to better understanding of the role of complement and activated macrophages in rheumatoid arthritis and systemic lupus.

Algorithms↗

PubMed2002

SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size.

MOTIVATION: Searches for near exact sequence matches are performed frequently in large-scale sequencing projects and in comparative genomics. The time and cost of performing these large-scale sequence-similarity searches is prohibitive using even the fastest of the extant algorithms. Faster algorithms are desired. RESULTS: We have developed an algorithm, called SST (Sequence Search Tree), that searches a database of DNA sequences for near-exact matches, in time proportional to the logarithm of the database size n. In SST, we partition each sequence into fragments of fixed length called 'windows' using multiple offsets. Each window is mapped into a vector of dimension 4(k) which contains the frequency of occurrence of its component k-tuples, with k a parameter typically in the range 4-6. Then we create a tree-structured index of the windows in vector space, with tree-structured vector quantization (TSVQ). We identify the nearest neighbors of a query sequence by partitioning the query into windows and searching the tree-structured index for nearest-neighbor windows in the database. When the tree is balanced this yields an O(logn) complexity for the search. This complexity was observed in our computations. SST is most effective for applications in which the target sequences show a high degree of similarity to the query sequence, such as assembling shotgun sequences or matching ESTs to genomic sequence. The algorithm is also an effective filtration method. Specifically, it can be used as a preprocessing step for other search methods to reduce the complexity of searching one large database against another. For the problem of identifying overlapping fragments in the assembly of 120 000 fragments from a 1.5 megabase genomic sequence, SST is 15 times faster than BLAST when we consider both building and searching the tree. For searching alone (i.e. after building the tree index), SST 27 times faster than BLAST. AVAILABILITY: Request from the authors.

Algorithms↗

PubMedDate not supplied

The role of transforming growth factor beta1 in the vascular system.

The transforming growth factor beta (TGFbeta) family of cytokines exert pleiotropic effects upon a wide variety of cell types. TGFbeta1 has been demonstrated to be of fundamental importance in the development, physiology and pathology of the vascular system. As the role of TGFbeta1 in these processes becomes clearer, influencing its activity for therapeutic benefit is now beginning to be investigated. This review presents an overview of the role of TGFbeta1 in the vasculature. The cellular and extracellular biology of the TGFbeta family is first addressed, followed by an overview of the function of TGFbeta1 during vascular development, atherogenesis, hypertension, and vessel injury.

Animals↗