Complete genome sequence of Oceanithermus profundus type strain (506)

Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

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.     

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.     

Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: kinetic and crystallographic studies

In an attempt to identify a new lead molecule that would enable the design of inhibitors with enhanced affinity for glycogen phosphorylase (GP), beta-D-glucopyranosyl bismethoxyphosphoramidate (phosphoramidate), a glucosyl phosphate analogue, was tested for inhibition of the enzyme. Kinetic experiments showed that the compound was a weak competitive inhibitor of rabbit muscle GPb (with respect to alpha-D-glucose-1-phosphate (Glc-1-P)) with a Ki value of 5.9 (+/-0.1) mM. In order to elucidate the structural basis of inhibition, we determined the structure of GPb complexed with the phosphoramidate at 1.83 A resolution. The complex structure reveals that the inhibitor binds at the catalytic site and induces significant conformational changes in the vicinity of this site. In particular, the 280s loop (residues 282-287) shifts 0.4-4.3 A (main-chain atoms) to accommodate the phosphoramidate, but these conformational changes do not lead to increased contacts between the inhibitor and the protein that would improve ligand binding.     

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.     

Evaluation of synthetic female attractants against Ceratitis capitata (Diptera: Tephritidae) in sticky coated spheres and McPhail type traps

In field experiments conducted in a citrus orchard in Chios, Greece, we tested the efficacy of yellow, sticky, plastic, hollow spheres baited with long-lasting dispensers of the food attractants ammonium acetate, 1,4-diaminobutane (putrescine), and trimethylamine (FA-3) to capture adults of the Mediterranean fruit fly, Ceratitis capitato (Wiedemann) (Diptera: Tephritidae). Yellow spheres (7.5 cm in diameter) baited internally or externally with FA-3 were approximately 30 and approximately 12 times more attractive for females and males respectively than unbaited spheres. However, they were approximately 3 times less attractive for both sexes than plastic McPhail type traps baited with the same attractants and provided with water and a drop of a surfactant in their bases (wet traps), and only 1.5 and 2.8 times less attractive for females and males, respectively, than likewise-baited McPhail type traps provided with a killing agent (dimethyl dichlorovinyl phosphate) but not water in their bases (dry trap). Baited spheres were more C. capitata female selective than either wet or dry McPhail traps. The importance of these findings in developing lure and kill devices for the Mediterranean fruit fly is discussed.     

A data-mining approach for multiple structural alignment of proteins

Comparing the 3D structures of proteins is an important but computationally hard problem in bioinformatics. In this paper, we propose studying the problem when much less information or assumptions are available. We model the structural alignment of proteins as a combinatorial problem. In the problem, each protein is simply a set of points in the 3D space, without sequence order information, and the objective is to discover all large enough alignments for any subset of the input. We propose a data-mining approach for this problem. We first perform geometric hashing of the structures such that points with similar locations in the 3D space are hashed into the same bin in the hash table. The novelty is that we consider each bin as a coincidence group and mine for frequent patterns, which is a well-studied technique in data mining. We observe that these frequent patterns are already potentially large alignments. Then a simple heuristic is used to extend the alignments if possible. We implemented the algorithm and tested it using real protein structures. The results were compared with existing tools. They showed that the algorithm is capable of finding conserved substructures that do not preserve sequence order, especially those existing in protein interfaces. The algorithm can also identify conserved substructures of functionally similar structures within a mixture with dissimilar ones. The running time of the program was smaller or comparable to that of the existing tools.