Metabolic requirements for entry of DNA inBranhamella catarrhalis

Summary Although requirements for transformation inBranhamella catarrhalis are quite complex, DNA synthesis does not appear to be one of these needs, as indicated by the inability of nalidixic acid to interefere with transformation. Exogeneous sources of energy, such as cAMP and cGMP, also failed to enhance frequency, suggesting cells may actively engage in energy production to achieve uptake of DNA, or lack a transport mechanism for these compounds.     

A zone of non-proliferating cells at a lineage restriction boundary in Drosophila

The use of X-ray-induced mitotic recombination to genetically mark individual cells and their descendants during development has led to the discovery of lineage restriction boundaries in Drosophila imaginal disks, dividing the disks into areas called compartments. Clones of cells initiated after a given developmental stage are unable to grow across these boundaries, even if provided with a growth rate advantage over the remaining cells. It has been suggested that cells within compartments are distinguished by the differential activation of selector genes and that the lineage restrictions are maintained by adhesivity differences between the cells in different compartments, but other mechanisms have not been ruled out. Recently a discrete population of cells with unusual permeability properties has been described along an intersegmental lineage restriction boundary in Oncopeltus, suggesting that a lineage restriction could be maintained by a zone of cells which present a barrier to clone growth. Here we demonstrate by autoradiography the presence of a narrow zone of non-proliferating cells (ZNC) coincident with the presumptive wing margin in the Drosophila wing disk, and suggest that this could account for the observed lineage restriction between presumptive dorsal and ventral surfaces of the wing. As the anterior/posterior compartment boundary does not coincide with a ZNC, the results indicate that different lineage boundaries may be maintained by different mechanisms.     

Distinct molecular mechanism for initiating TRAF6 signalling

Tumour-necrosis factor (TNF) receptor-associated factor 6 (TRAF6) is the only TRAF family member that participates in signal transduction of both the TNF receptor (TNFR) superfamily and the interleukin-1 receptor (IL-1R)/Toll-like receptor (TLR) superfamily; it is important for adaptive immunity, innate immunity and bone homeostasis. Here we report crystal structures of TRAF6, alone and in complex with TRAF6-binding peptides from CD40 and TRANCE-R (also known as RANK), members of the TNFR superfamily, to gain insight into the mechanism by which TRAF6 mediates several signalling cascades. A 40 degrees difference in the directions of the bound peptides in TRAF6 and TRAF2 shows that there are marked structural differences between receptor recognition by TRAF6 and other TRAFs. The structural determinant of the petide TRAF6 interaction reveals a Pro-X-Glu-X-X-(aromatic/acidic residue) TRAF6-binding motif, which is present not only in CD40 and TRANCE-R but also in the three IRAK adapter kinases for IL-1R/TLR signalling. Cell-permeable peptides with the TRAF6-binding motif inhibit TRAF6 signalling, which indicates their potential as therapeutic modulators. Our studies identify a universal mechanism by which TRAF6 regulates several signalling cascades in adaptive immunity, innate immunity and bone homeostasis.     

Functional genomic hypothesis generation and experimentation by a robot scientist

The question of whether it is possible to automate the scientific process is of both great theoretical interest and increasing practical importance because, in many scientific areas, data are being generated much faster than they can be effectively analysed. We describe a physically implemented robotic system that applies techniques from artificial intelligence to carry out cycles of scientific experimentation. The system automatically originates hypotheses to explain observations, devises experiments to test these hypotheses, physically runs the experiments using a laboratory robot, interprets the results to falsify hypotheses inconsistent with the data, and then repeats the cycle. Here we apply the system to the determination of gene function using deletion mutants of yeast (Saccharomyces cerevisiae) and auxotrophic growth experiments. We built and tested a detailed logical model (involving genes, proteins and metabolites) of the aromatic amino acid synthesis pathway. In biological experiments that automatically reconstruct parts of this model, we show that an intelligent experiment selection strategy is competitive with human performance and significantly outperforms, with a cost decrease of 3-fold and 100-fold (respectively), both cheapest and random-experiment selection.     

DNA overwinds when stretched

DNA is often modelled as an isotropic rod, but its chiral structure suggests the possible importance of anisotropic mechanical properties, including coupling between twisting and stretching degrees of freedom. Simple physical intuition predicts that DNA should unwind under tension, as it is pulled towards a denatured structure. We used rotor bead tracking to directly measure twist-stretch coupling in single DNA molecules. Here we show that for small distortions, contrary to intuition, DNA overwinds under tension, reaching a maximum twist at a tension of approximately 30 pN. As tension is increased above this critical value, the DNA begins to unwind. The observed twist-stretch coupling predicts that DNA should also lengthen when overwound under constant tension, an effect that we quantitatively confirm. We present a simple model that explains these unusual mechanical properties, and also suggests a possible origin for the anomalously large torsional rigidity of DNA. Our results have implications for the action of DNA-binding proteins that must stretch and twist DNA to compensate for variability in the lengths of their binding sites. The requisite coupled DNA distortions are favoured by the intrinsic mechanical properties of the double helix reported here.     

Metabolic requirements for entry of DNA in Branhamella catarrhalis.

Although requirements for transformation in Branhamella catarrhalis are quite complex, DNA synthesis does not appear to be one of these needs, as indicated by the inability of nalidixic acid to interefere with transformation. Exogenous sources of energy, such as cAMP and cGMP also failed to enhance frequency, suggesting cells may actively engage in energy production to achieve uptake of DNA, or lack a transport mechanism for these compounds.     

SYSTEMIC PATHOLOGIES OF CONFRONTATION： DIAGNOSING SECURITY DISRUPTION

The world post-9/11 is characterised by uncertainty, fear and suspicion. Psychological confrontations amplified by the mass media have even come to dominate physical engagements between warring parties. Drama theory provides a powerful framework for understanding these interactions in much the way that game theory was able to support strategy making by autonomous players in a less inter-connected era. A model of the ‘normal’ process leading to dramatic resolution is an essential feature of the drama theory approach and is described here. However this process can be derailed or fail in many ways. This paper reviews many of these systemic pathologies and illustrates some of them through consideration of three high-profile cases. The conclusion is that it is important to recognise and possibly to use pathological behavior as an element of a character’s interaction strategy.