Involvement of the AtoS-AtoC signal transduction system in poly-(R)-3-hydroxybutyrate biosynthesis in Escherichia coli

The AtoS–AtoC signal transduction system in E. coli, which induces the atoDAEB operon for the growth of E. coli in short-chain fatty acids, can positively modulate the levels of poly-(R)-3-hydroxybutyrate (cPHB) biosynthesis, a biopolymer with many physiological roles in E. coli. Increased amounts of cPHB were synthesized in E. coli upon exposure of the cells to acetoacetate, the inducer of the AtoS–AtoC two-component system. While E. coli that overproduce both components of the signal transduction system synthesize higher quantities of cPHB (1.5–4.5 fold), those that overproduce either AtoS or AtoC alone do not display such a phenotype. Lack of enhanced cPHB production was also observed in cells overexpressing AtoS and phosphorylation-impaired AtoC mutants. The results were not affected by the nature of the carbon source used, i.e., glucose, acetate or acetoacetate. An E. coli strain with a deletion in the atoS–atoC locus (ΔatoSC) synthesized lower amounts of cPHB compared to wild-type cells. When the ΔatoSC strain was transformed with a plasmid carrying a 6.4-kb fragment encoding the AtoS–AtoC system, cPHB biosynthesis was restored to the level of the atoSC⁺ cells. Introduction of a multicopy plasmid carrying a functional atoDAEB operon, but not one with a promoterless operon, resulted in increased cPHB synthesis only in atoSC⁺ cells in the presence of acetoacetate. These results indicate that the presence of both a functional AtoS–AtoC two-component signal transduction system and a functional atoDAEB operon is critical for the enhanced cPHB biosynthesis in E. coli.     

Antiinflammatory and immunosuppressive activity of sialostatin L, a salivary cystatin from the tick Ixodes scapularis

Here we report the ability of the tick Ixodes scapularis, the main vector of Lyme disease in the United States, to actively and specifically affect the host proteolytic activity in the sites of infestation through the release of a cystatin constituent of its saliva. The cystatin presence in the saliva was verified both biochemically and immunologically. We named the protein sialostatin L because of its inhibitory action against cathepsin L. We also show that the proteases it targets, although limited in number, have a prominent role in the proteolytic cascades that take place in the extracellular and intracellular environment. As a result, sialostatin L displays an antiinflammatory role and inhibits proliferation of cytotoxic T lymphocytes. Beyond unraveling another component accounting for the properties of tick saliva, contributing to feeding success and pathogen transmission, we describe a novel tool for studying the role of papain-like proteases in diverse biologic phenomena and a protein with numerous potential pharmaceutical applications.     

Breeding bird assemblages of eastern Mediterranean shrublands: composition, organisation and patterns of diversity

The patterns of α-diversity and the structure and organisation of breeding bird assemblages were studied in four vegetation stages (characteristic of Mediterranean shrublands) on an eastern Mediterranean island (Crete, Greece): low phrygana, tall phrygana, low maquis and tall maquis. Phrygana differed significantly from maquis, in regard to the community metrics, composition and the homogeneity of bird assemblages. Moreover, detrended correspondence analysis ordered the census plots along a continuum of increasing vegetation height. On the other hand, within-maquis differences were few, while no significant differences were found within phrygana stages. Based upon the observed patterns, we recognise three vegetation groups: (1) phrygana, with low α-diversity and abundance and homogenous bird assemblages; (2) low maquis with relatively high α-diversity and heterogenous bird assemblages; and (3) tall maquis with relatively high α-diversity and heterogenous assemblages in which “woodland” bird species contribution is prominent.     

Viscous flow simulation in a stenosis model using discrete particle dynamics: a comparison between DPD and CFD

Flow and stresses induced by blood flow acting on the blood cellular constituents can be represented to a certain extent by a continuum mechanics approach down to the order of the?μm level. However, the molecular effects of, e.g., adhesion/aggregation bonds of blood clotting can be on the order of nm. The coupling of the disparate length and timescales between such molecular levels and macroscopic transport represents a major computational challenge. To address this challenge, a multiscale numerical approach based on discrete particle dynamics (DPD) methodology derived from molecular dynamics (MD) principles is proposed. The feasibility of the approach was firstly tested for its ability to simulate viscous flow conditions. Simulations were conducted in low Reynolds numbers flows (Re = 25–33) through constricted tubes representing blood vessels with various degrees of stenosis. Multiple discrete particles interacting with each other were simulated, with 1.24–1.36 million particles representing the flow domain and 0.4 million particles representing the vessel wall. The computation was carried out on the massive parallel supercomputer NY BlueGene/L employing NAMD-a parallel MD package for high performance computing (HPC). Typical recirculation zones were formed distal to the stenoses. The velocity profiles and recirculation zones were in excellent agreement with computational fluid dynamics (CFD) 3D Navier–Stokes viscous fluid flow simulations and with classic numerical and experimental results by YC Fung in constricted tubes. This feasibility analysis demonstrates the potential of a methodology that widely departs from a continuum approach to simulate multiscale phenomena such as flow induced blood clotting.     

An audio–visual nest monitoring system for the study and manipulation of siblicide in bearded vultures <Emphasis Type="Italic">Gypaetus barbatus</Emphasis> on the island of Crete (Greece)

We describe here an automated surveillance system that was installed in a bearded vulture (Gypaetus barbatus) nest in Crete during 2003–2006 with the aim of studying siblicide in this species. The system caused only minimal levels of disturbance to the birds and was capable of operating autonomously for more than 1 week. It comprised (1) a nest monitoring subsystem (camera, microphone, battery with a charge controller and a transmitter together with an antenna), which was supported by a solar panel, and (2) a recording subsystem (antenna receiver, video signal controller and a remote controlled PC through a GSM modem) that compressed the audio–video signal and provided real time monitoring. Two-egg clutches with a 7-day laying and hatching interval were recorded while hatching asynchrony was also determined through an analysis of the bioacoustic data. Food delivery rate and number of feeds to the first chick increased after the hatching of its sibling although not significantly so. Of the aggressive interactions recorded, 98% were initiated by the dominant chick and resulted in an average of 246 ± 157 peckings per day. Supplementary feeding did not produce any significant correlation between feeding rate and sibling aggression. The second chick survived 5 days and died as a result of starvation accelerated by sibling aggression. Intervention measures aimed at increasing the survival chance of the second chick should be undertaken when the latter is 1–2 days old.     

Outcome prediction based on microarray analysis: a critical perspective on methods

Background  

Information extraction from microarrays has not yet been widely used in diagnostic or prognostic decision-support systems, due to the diversity of results produced by the available techniques, their instability on different data sets and the inability to relate statistical significance with biological relevance. Thus, there is an urgent need to address the statistical framework of microarray analysis and identify its drawbacks and limitations, which will enable us to thoroughly compare methodologies under the same experimental set-up and associate results with confidence intervals meaningful to clinicians. In this study we consider gene-selection algorithms with the aim to reveal inefficiencies in performance evaluation and address aspects that can reduce uncertainty in algorithmic validation.     

Blood as a reactive species generator and redox status regulator during exercise

The exact origin of reactive species and oxidative damage detected in blood is largely unknown. Blood interacts with all organs and tissues and, consequently, with many possible sources of reactive species. In addition, a multitude of oxidizable substrates are already in blood. A muscle-centric approach is frequently adopted to explain reactive species generation, which obscures the possibility that sources of reactive species and oxidative damage other than skeletal muscle may be also at work during exercise. Plasma and blood cells can autonomously produce significant amounts of reactive species at rest and during exercise. The major reactive species generators located in blood during exercise may be erythrocytes (mainly due to their quantity) and leukocytes (mainly due to their drastic activation during exercise). Therefore, it is plausible to assume that oxidative stress/damage measured frequently in blood after exercise or any other experimental intervention derives, at least in part, from the blood.