Biomedical subjects

K Lindauer

Publications and source records attributed to K Lindauer.

5 recordsLinked to original sources

PubMed2001

Analysis of cellular adhesion by microarray expression profiling.

Microarrays of oligonucleotides or cDNAs can be used to establish the expression profiles of numerous genes in a single experiment. We have established a microarray platform to identify genes in a number of different pathological conditions, particularly those with an inflammation component. This platform utilised the output of an eosinophil sequencing project in which 1069 sequences were identified that were not represented in the public domain. An eosinophil model cell line, AML14.3D10, was used to investigate cell adhesion. The transcription profile of adhered and non-adhered AML 14.3D10 cells was shown to be both technically and biologically reproducible. A number of genes were found differentially expressed in the adhered vs. non-adhered populations. In the adhered population, the expression of these genes was restricted compared to brain, lung, kidney and especially bone marrow. However, the differentially regulated genes were not among those genes most restricted to eosinophils. We discuss the implications of transcription profiling on gene annotation and its potential utility for the identification of targets for drug intervention.

Base Sequence↗

PubMed2001

Prediction of the structure of human Janus kinase 2 (JAK2) comprising the two carboxy-terminal domains reveals a mechanism for autoregulation.

The structure of human Janus kinase 2 (JAK2) comprising the two C-terminal domains (JH1 and JH2) was predicted by application of homology modelling techniques. JH1 and JH2 represent the tyrosine kinase and tyrosine kinase-like domains, respectively, and are crucial for function and regulation of the protein. A comparison between the structures of the two domains is made and structural differences are highlighted. Prediction of the relative orientation of JH1 and JH2 was aided by a newly developed method for the detection of correlated amino acid mutations. Analysis of the interactions between the two domains led to a model for the regulatory effect of JH2 on JH1. The predictions are consistent with available experimental data on JAK2 or related proteins and provide an explanation for inhibition of JH1 tyrosine kinase activity by the adjacent JH2 domain.

Amino Acid Sequence↗

PubMed2001

Microarray analysis of eosinophils reveals a number of candidate survival and apoptosis genes.

The increase in eosinophils at the site of antigen challenge has been used as evidence to suggest that this cell type plays a role in the pathophysiology of asthma. Aberrant production of several different cytokines, particularly interleukin (IL)-5, has been shown to result in eosinophilia. IL-5 influences the development and maturation of eosinophils in a number of different ways. Of note is the ability of IL-5 to act as a survival factor for eosinophils specifically inhibiting apoptosis. The precise mechanism by which IL-5 exerts its effect remains obscure. We used microarray technologies to investigate the changes in the messenger RNA expression profile of eosinophils after treatment with IL-5. Using the Affymetrix Hu6800 chip, a total of 80 genes were observed to be regulated by 2-fold or greater. Many of the genes previously identified as regulated by IL-5 were regulated in our microarray experiments. Of the 73 genes found to be upregulated, many were shown to play a role in adhesion, migration, activation, or survival of eosinophils or hematopoietic cells, whereas the function of others was unknown. To facilitate the identification of genes that govern the apoptosis and survivability of eosinophils, we used an alternative cellular model, TF1.8 cells, whose survival was also dependent on IL-5. Comparison of these models identified four genes, Pim-1, DSP-5 (hVH3, B23), CD24, and SLP-76, whose regulation was similarly coordinated in both systems. Identification of Pim-1 and SLP-76 as regulated by IL-5 led us to suggest a direct role for these proteins in the IL-5 signaling pathway in eosinophils. The tissue distribution of these genes demonstrated that Pim-1 and SLP-76 were relatively restricted to the eosinophil compared with their expression in brain, bone marrow, kidney, liver, and lung. By contrast, DSP-5 and CD24 were confirmed as ubiquitous in their expression by microarray.

Adaptor Proteins, Signal Transducing↗

PubMed1996

HBexplore--a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules.

The program HBexplore is a new tool for identifying and analysing H-bonding patterns in biological macromolecules. It selects all potential H-bonds according to geometrical criteria. The H-bond table can then be subjected to further automatic or interactive analysis tools. These tools include the calculation of mean values and distributions of geometrical H-bond parameters for parts of a single structure, for complete single structures and for structure sets, the classification of each H-bond according to the participation of backbone, side chain or base, ligand and water parts of nucleic acids or proteins, identification of Watson-Crick nucleotide pairs and of H-bonded pairs of equal nucleotides, the calculation of the mean number of H-bonds per residue, and of the fraction of potential donor and acceptor atoms involved in H-bonds. HBexplore further generates automatically a H-bond residue interaction table. This table lists for all residues of the structure the other residues, ligands or water molecules directly connected via a H-bond. By means of a binary tree search algorithm, this table is then converted into a H-bond cluster table. Clusters are understood here as an uninterrupted network of H-bonded residues. For nucleic acids, secondary structures and tertiary interactions are automatically derived from the H-bonding pattern. HBexplore is applied to two example RNA structures: a pseudoknot and a hairpin. It provides a comprehensive listing of individual H-bonds and statistical information for larger structure sets. In addition, it can identify interesting new H-bond motifs. One example is a pentanucleotide base-base H-bond interaction motif in the RNA pseudoknot. HBexplore is intended to contribute both to the elucidation of general principles of the architecture of biological macromolecules, and to the prediction and refinement of single structures.

Algorithms↗

PubMed1995

Molecular cloning, functional expression and pharmacological characterization of the human metabotropic glutamate receptor type 2.

A cDNA encoding the human metabotropic glutamate receptor type 2 (hmGluR2) was isolated from human brain cDNA libraries by cross-hybridization with rat mGluR2 probes. The deduced amino acid sequence of the human mGluR2 receptor consists of 872 residues and shows a sequence identity of 97% to the amino acid sequence of rat mGluR2. Northern blot analyses showed that hmGluR2 is widely expressed in different regions of the adult brain as well as in fetal human brain. Genomic Southern blotting localized the mGluR2 gene to human chromosome 3. Chinese hamster ovary (CHO) cells stably transfected with the cloned hmGluR2 cDNA exhibit agonist induced depression of forskolin-stimulated cAMP accumulation. A direct comparison of CHO cells stably expressing human and rat mGluR2 with five agonists revealed the same rank order of potency [(2S,3S,4S)-alpha-(carboxycyclopropyl)-glycine >> (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid = L-glutamate >> quisqualate = L-2-amino-4-phosphonobutyric acid] and similar EC50 values for both homologous receptors. (R,S)-alpha-methyl-4-carboxyphenylglycine, a reported antagonist at some mGluR subtypes, reduced the depression of forskolin-induced cAMP accumulation by (1S,3R)-ACPD in both human and rat mGluR2.

Amino Acid Sequence↗