Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T))

The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. baltica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacterium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 protein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.     

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.     

Monkeys match the number of voices they hear to the number of faces they see

Convergent evidence demonstrates that adult humans possess numerical representations that are independent of language [1, 2, 3, 4, 5 and 6]. Human infants and nonhuman animals can also make purely numerical discriminations, implicating both developmental and evolutionary bases for adult humans' language-independent representations of number [7 and 8]. Recent evidence suggests that the nonverbal representations of number held by human adults are not constrained by the sensory modality in which they were perceived [9]. Previous studies, however, have yielded conflicting results concerning whether the number representations held by nonhuman animals and human infants are tied to the modality in which they were established [10, 11, 12, 13, 14 and 15]. Here, we report that untrained monkeys preferentially looked at a dynamic video display depicting the number of conspecifics that matched the number of vocalizations they heard. These findings suggest that number representations held by monkeys, like those held by adult humans, are unfettered by stimulus modality.     

Discrimination between Francisella tularensis and Francisella-Like Endosymbionts when Screening Ticks by PCR

The presence of Francisella-like endosymbionts in tick species known to transmit tularemia poses a potential diagnostic problem for laboratories that screen tick samples by PCR for Francisella tularensis. Tick samples initially considered positive for F. tularensis based on standard 16S rRNA gene PCR were found to be positive only for Francisella-like endosymbionts using a multitarget F. tularensis TaqMan assay (ISFtu2, tul4, and iglC) and 16S rRNA gene sequencing. Specificity of PCR-based diagnostics for F. tularensis should be carefully evaluated with appropriate specimen types prior to diagnostic use.     

Medfly populations differ in diel and age patterns of sexual signalling

Insect populations may differ in several life history traits, including behavioural ones such as sexual signalling. We tested whether male Mediterranean fruit fly (medlfy), Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), populations obtained from geographically isolated areas exhibit differences in quantitative and qualitative aspects of male sexual signalling. Male sexual signalling was studied in four medfly populations (originating from Brazil, Portugal, Kenya, and Greece) under identical laboratory conditions (25 °C, 60% r.h., and L14:D10). The four populations had been reared for one generation in the laboratory. Sexual signalling was studied in the F₁ progeny that were fed one of two diets (yeast hydrolysate plus sugar or sugar only). On both diets, the four populations differed significantly in the progress of maturity (indicated by the average number of males exhibiting sexual signalling) and in the quantity of signalling after attaining maturity. Yeast availability significantly increased sexual signalling; however, it had a different impact on the quantity of signalling in the different populations. A bi-modal pattern of sexual signalling, with one peak at approximately 08:00–09:00 hours and the second at approximately 13:00–14:00 hours, was recorded for all populations and diets. However, quantitative differences among the populations within the 'sexually active' period of the day resulted in significant differences in the daily pattern of sexual signalling. The significance of these findings for understanding adaptations of geographically isolated medfly populations to different ecosystems, as well as its practical importance for the application of the sterile insect technique against C. capitata , is discussed.     

Molecular phylogeny and historical biogeography of the Anatolian lizard Apathya (Squamata,Lacertidae)

Apathya is a lacertid genus occurring mainly in south-east Turkey and its adjacent regions (part of Iran and Iraq). So far two morphological species have been attributed to the genus; A. cappadocica (with five subspecies, A. c. cappadocica, A. c. muhtari, A. c. schmidtlerorum, A. c. urmiana and A. c. wolteri) and A. yassujica. The first species occupies most of the genus’ distribution range, while A. yassujica is endemic of the Zagros Mountains. Here, we explored Apathya’s taxonomy and investigated the evolutionary history of the species by employing phylogenetic and phylogeographic approaches and using both mitochondrial (mtDNA) and nuclear markers. The phylogenetic relationships and the genetic distances retrieved, revealed that Apathya is a highly variable genus, which parallels its high morphological variation. Such levels of morphological and genetic differentiation often exceed those between species of other Lacertini genera that are already treated as full species, suggesting the necessity for a taxonomic revision of Apathya. The phylogeographical scenario emerging from the genetic data suggests that the present distribution of the genus was determined by a combination of dispersal and vicariance events between Anatolia and Southwest Asia dating back to the Miocene and continuing up to the Pleistocene. Key geological events for the understanding of the phylogeography of the genus are the movement of the Arabian plate that led to the configuration of Middle East (orogenesis of the mountain ranges of Turkey and Iran) and the formation of Anatolian Diagonal.     

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.