Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray

Background  

Unravelling the path from genotype to phenotype, as it is influenced by an organism's environment, is one of the central goals in biology. Gene expression profiling by means of microarrays has become very prominent in this endeavour, although resources exist only for relatively few model systems. As genomics has matured into a comparative research program, expression profiling now also provides a powerful tool for non-traditional model systems to elucidate the molecular basis of complex traits.     

Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria

The identification of mycobacteria is essential because tuberculosis (TB) and mycobacteriosis are clinically indistinguishable and require different therapeutic regimens. The traditional phenotypic method is time consuming and may last up to 60 days. Indeed, rapid, affordable, specific and easy-to-perform identification methods are needed. We have previously described a polymerase chain reaction-based method called a mycobacteria mobility shift assay (MMSA) that was designed for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) species identification. The aim of this study was to assess the MMSA for the identification of MTC and NTM clinical isolates and to compare its performance with that of the PRA-hsp65 method. A total of 204 clinical isolates (102 NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing fragments of the 16S rRNA and hsp65 genes. Both methods correctly identified all MTC isolates. Among the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement was observed for the 94 NTM isolates identified by both methods. The MMSA provided correct identification for 96.8% of the NTM isolates compared with 94.7% for PRA-hsp65. The MMSA is a suitable auxiliary method for routine use for the rapid identification of mycobacteria.     

Clustering cancer gene expression data: a comparative study

Background  

The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context.     

Was Hopkins right? Influence of larval and early adult experience on the olfactory response in the granary weevil Sitophilus granarius (Coleoptera,Curculionidae)

Abstract The induction of olfactory preferences by larval and early adult experience for odour from wheat or maize grain was examined for the granary weevil Sitophilus granarius L. in a static four-chamber olfactometer. Weevils were reared on either wheat or maize grain and received different early adult experience. It turned out that weevils that were reared in wheat and isolated as pupae from the kernels preferred wheat odour in the olfactometer when they emerged without any odour or in the presence of maize odour. Weevils that emerged in the presence of wheat odour preferred both wheat and maize odour. When weevils emerged normally as adults from the wheat kernel in which they developed, maize odour was avoided. In contrast, for weevils that were reared in maize no preferences were found in most experiments. Only weevils that emerged in the presence of wheat odour preferred the maize odour over the controls. These results demonstrate that host-selection behaviour in S. granarius weevil is shaped by experience according to the Hopkins host-selection principle or the chemical legacy hypothesis and the neo-Hopkins principle.     

Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin

An intronless gene encoding a protein of 592 amino acid residues with similarity to 70-kDa heat shock proteins (HSP70s) has been cloned and sequenced from the amitochondrial protist Encephalitozoon cuniculi (phylum Microsporidia). Southern blot analyses show the presence of a single gene copy located on chromosome XI. The encoded protein exhibits an N-terminal hydrophobic leader sequence and two motifs shared by proteobacterial and mitochondrially expressed HSP70 homologs. Phylogenetic analysis using maximum likelihood and evolutionary distances place the E. cuniculi sequence in the cluster of mitochondrially expressed HSP70s, with a higher evolutionary rate than those of homologous sequences. Similar results were obtained after cloning a fragment of the homologous gene in the closely related species E. hellem. The presence of a nuclear targeting signal-like sequence supports a role of the Encephalitozoon HSP70 as a molecular chaperone of nuclear proteins. No evidence for cytosolic or endoplasmic reticulum forms of HSP70 was obtained through PCR amplification. These data suggest that Encephalitozoon species have evolved from an ancestor bearing mitochondria, which is in disagreement with the postulated presymbiotic origin of Microsporidia. The specific role and intracellular localization of the mitochondrial HSP70-like protein remain to be elucidated.      

T-cell leukemias of adulthood]

9 adult patients suffering from different forms of T-cell-malignancies were investigated: 4 patients with T-ALL; 1-T-ALL-CLL mixed form (prolymphocytic); 2 T-CLL; 2 Sézary-syndrome. The clinical peculiarities of the different forms of leukemias were compared: involvement of lymph nodes and spleen, of the central nervous system and the skin was frequent; in contrast to the findings in Sézary-syndrome, bone marrow infiltration was prominent. Light and electron microscopic morphology of the malignant cells are described. In all cases a strong activity of acid phosphatase was demonstrated, in one patient prominent deposits of glycogen. The T-cell-quality of the respective malignant cell population as well as the B-T-cell distribution of the remaining "normal" lymphocytes were shown by the following cell markers: demonstration of T-cell-antigen, resp. membrane immunoglobulins with the aid of specific heterologous antisera conjugated with peroxidase, 125iodine or fluoresceine; complement consumtion or cytotoxicity with such antisera; spontaneous rosette formation with sheep red cells or with acrylic acid beads. Usually, there was a good coincidence in results obtained with the different markers. In two patients, however, T-cells demonstrated by anti-T-globulin were not able to form T-rosettes. Responsiveness of the malignant T-cells and also of the remaining "normal" blood lymphocytes to different mitogens usually was depressed, immunoglobulin levels in the blood mostly were normal. Taking all findings into consideration, T-cell-leukemias of the adult represent a special group of hematological malignancies; the different subgroups show similarities; transitional forms occur.