Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022)

Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022(T) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Vulcanisaeta distributa type strain (IC-017)

Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea project.     

Identification of Protein-Tyrosine Phosphatases in Archaea

Protein-tyrosine dephosphorylation is a major mechanism in cellular regulation. A large number of protein-tyrosine phosphatases is known from Eukarya, and more recently bacterial homologues have also been identified. By employing conserved sequence patterns from both eukaryotic and bacterial protein-tyrosine phosphatases, we have identified three homologous sequences in two of the four complete archaeal genomes. Two hypothetical open reading frames in the genome of Methanococcus jannaschii (MJ0215 and MJECL20) and one in the genome of Pyrococcus horikoshii (PH1732) clearly bear all the conserved residues of this family. No homologues were found in the genomes of Archaeoglobus fulgidus and Methanobacterium thermoautotrophicum. This is the first report of protein-tyrosine phosphatase sequences in Archaea. Received: 29 April 1998 / Accepted: 27 November 1998     

Living polypeptides

Block copolypeptides, which combine the self-assembly of block copolymers and the highly ordered 3D structures of proteins, are potential candidates for novel supramolecular structures and biotech applications, such as biosensors, tissue engineering, and selective drug delivery. The synthesis of model block copolypeptides through living nucleophilic/basic polymerization of alpha-amino acid N-carboxyanhydrides (NCAs) has been a challenge for more than fifty years, most probably due to traces of impurities in the system. This problem has been overcome, using high vacuum techniques in order to create and maintain the conditions necessary for the living polymerization of NCAs with primary amines. This method is a general one and opens avenues leading to novel, well-defined polypeptides with various architectures.     

On the mechanism of thrombin-induced angiogenesis: involvement of alphavbeta3-integrin

Thrombin has been reported to be a potent angiogenic factor both in vitro and in vivo, and many of the cellular effects of thrombin may contribute to activation of angiogenesis. In this report we show that thrombin-treatment of human endothelial cells increases mRNA and protein levels of alphavbeta3-integrin. This thrombin-mediated effect is specific, dose dependent, and requires the catalytic site of thrombin. In addition, thrombin interacts with alphavbeta3 as demonstrated by direct binding of alphavbeta3 protein to immobilized thrombin. This interaction of thrombin with alphavbeta3-integrin, which is an angiogenic marker in vascular tissue, is of functional significance. Immobilized thrombin promotes endothelial cells attachment, migration, and survival. Antibody to alphavbeta3 or a specific peptide antagonist to alphavbeta3 can abolish all these alphavbeta3-mediated effects. Furthermore, in the chick chorioallantoic membrane system, the antagonist peptide to alphavbeta3 diminishes both basal and the thrombin-induced angiogenesis. These results support the pivotal role of thrombin in activation of endothelial cells and angiogenesis and may be related to the clinical observation of neovascularization within thrombi.     

Ultra high-resolution fMRI in monkeys with implanted RF coils

Spatiotemporally resolved functional MRI (fMRI) in animals can reveal how wide-spread neural networks are organized and accompanying electrophysiological recordings can show how small neural assemblies contribute to this organization. Here we present a novel technique that yields high-resolution structural and functional images of the monkey brain with small, tissue-compatible, intraosteally implantable radiofrequency coils. Voxel sizes as small as 0.0113 microl with high signal-to-noise and contrast-to-noise ratios were obtained, revealing both structural and functional cortical architecture in great detail. Up to a certain point, contrast sensitivity increased with decreasing voxel size, probably because of the decreased partial volume effects. Spatial specificity was demonstrated by the lamina-specific activation in experiments comparing responses to moving and flickering stimuli. The implications of this technique for combined fMRI/electrophysiology experiments and its limitations in terms of spatial coverage are discussed.     

Field parasitism of Ceratitis capitata larvae by Aganaspis daci in Chios, Greece

High parasitism rates were recorded in the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) in pupae derived from field infested figs, on the Greek island of Chios in 1999 and 2000. Adult parasitoids were identified as Aganaspis daci (Weld) (Hymenoptera:Eucoilidae), previously known as Trybliographa daci (Weld). Approximately 45%of C. capitata pupae yielded adultparasitoid in both years and the totalmortality of pupae due to the parasitoid was62–65%. Development of male A. daci at25°C, reared on 3rd instar larvaeof C. capitata, was shorter than that of the female (34 and 37 days respectively). Average adultmale longevity was 4–5 days longer than female(16–17 to 11–12 days, respectively) and almostidentical in wild and F₁ parasitoids ofboth sexes. We suggest that A. daci maybe an efficient form of biological control ofC. capitata in the Mediterranean regionand probably in other areas.     

Beyond 100 genomes

By the end of 2002, we witnessed the landmark submission of the 100th complete genome sequence in the databases. An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments.