The Evolution of the Tetrapod Middle Ear in the Rhipidistian-Amphibian Transition

From a survey ot the structure of the skull in rhipidistianfishes and early labylinthodont Amphibia and of the mechanismof hearing in these two groups, an account of the evolutionof the tetrapod middle ear is presented. The overall modificationof the otic region of the skull during the rhipidistian-amphibiantransition is analyzed in terms of changes in different organsystems in response to different selective pressures (affecting,for example, the feeding, respiratory, and locomotory mechanisms).These changes are seen to occur in a completely integrated pattern.Considerations of the different requirements for sound receptionunder water and in air, in connection with this correlated progressionof evolutionary change in the otic region of the head, revealthe manner in which the hyomandibular, spiracular diverticulum,and operculum of rhipidistian fishes became modified to formthe stapes, the tympanic cavity, and the outer portion of thetympanum, respectively, of tetrapods.     

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.     

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.     

Root xylem transport of amino acids in the root hemiparasitic shrub Olax phyllanthi (Labill) R.Br. (Olacaceaea) and its multiple hosts

The amino acid compositions of the root xylem saps of Olax phyllanthi and a range of its common hosts were examined in native coastal heath in Western Australia and in pot cultures of Olax reliant on single hosts. When hosts specializing in the xylem transport of one major solute (asparagine, glutamine, histidine, arginine or proline) were exploited, the endophytic tissue of haustoria and the xylem sap of Olax showed much lower proportions of this than of other solutes, suggesting pronounced metabolic transformation prior to xylem loading by the parasite. However, the xylem sap of Olax did partly reflect the compositions of its hosts; for example, djenkolic acid and pipecolic acid were present when Olax was parasitic on species of Acacia, and levels of citrulline and aspartic acid were higher than normal when it exploited hosts transporting large amounts of these compounds. Back-flow of S-ethenyl cysteine, a novel amino acid specific to Olax, was observed to another root hemiparasite (Exocarpos sparteus) in native habitat and to certain non-parasitic hosts in water-stressed pot cultures. Haustoria exhibited high levels of glutamine synthetase but showed appreciable in vivo nitrate reductase activity only when on hosts with high xylem levels of nitrate.     

Glutamine Synthetase Isoenzymes of Striga hermonthica and other Angiosperm Root Parasites

The occurrence of multiple forms of glutamine synthetase inStriga hermonthica and other angiosperm root parasites was investigated.The facultative chlorophyllous parasite Melampyrum arvense exhibitedtwo isoenzymes in leaf tissue, the cytosolic component (GS₁)comprised less than 30% of total glutamine synthetase. In contrastGS₁ was the major component (<70%) in photosynthetic tissueof Striga hermonthica and S. gesnerioides. Only a single isoenzyme(GS₁) was detectable in the achlorophyllous root parasites Orobancheand Lathraea and in non-photosynthetic tissue of S. gesnerioides.The kinetic and physical properties of GS₁ and GS₂ of theseangiosperm parasites were similar to those of the isoenzymesin other non-parasitic angiosperms. Key words: Glutamine synthetase, Angiosperms, Root parasites     

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.