Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

WZW-like Action for Heterotic String Field Theory

We complete the construction of the Neveu-Schwarz sector of heterotic string field theory begun in hep-th/0406212 by giving a closed-form expression for the action and gauge transformations. Just as the Wess-Zumino-Witten (WZW) action for open superstring field theory can be constructed from pure-gauge fields in bosonic open string field theory, our heterotic string field theory action is constructed from pure-gauge fields in bosonic closed string field theory. The construction involves a simple alternative form of the WZW action which is consistent with the algebraic structures of closed string field theory.Comment: 22 pages, no figures, LaTeX2

Nematoda - free living

The list was compiled by Guy De Smet, a non-specialist, who was assisted by nematologists Magda Vincx, Ann Vanreusel, Sandra Vanhove, Jan Vanaverbeke and Maaike Steyaert. Dr. F. Riemann gave useful advice for the genus Daptonema. The classification in the list is based upon Lorenzen (1979, 1994). Information on the geographic distribution in the list is based upon Gerlach and Riemann (1973, 1974), Platt and Warwick (1983, 1988) and Warwick et al. (1998).ReferencesLorenzen, S. Entwürf eines Phylogenetischen Systems der Freilebenden Nematoden, Kiel, 1979.Lorenzen, S. The Phylogenetic Systematics of Freeliving Nematodes, The Ray Society, 1994.Gerlach, S. A. and Riemann, F. The Bremerhaven Checklist of Aquatic Nematodes. Veröffentlichungen des Instituts für Meeresforschung in Bremerhaven, Supplement 4, (Heft 1 1973, Heft 2 1974).Platt, H. M. and Warwick, R. M. Free-living Marine Nematodes (Part I British Enoplids) Synopses of the British Fauna (New series) No. 28, 1983.Platt, H. M. and Warwick, R. M. Free-living Marine Nematodes (Part II British Chromadorids) Synopses of the British Fauna (New series) No. 38, 1988.Warwick, R. M., Platt, H. M. and Somerfield, P. J. Free-living Marine Nematodes (Part III Monhysterids) Synopses of the British Fauna (New series) No. 53, 1998.</ul

Layer charge instability in unbalanced bilayer systems in the quantum Hall regime

Measurements in GaAs hole bilayers with unequal layer densities reveal a pronounced magneto-resistance hysteresis at the magnetic field positions where either the majority or minority layer is at Landau level filling factor one. At a fixed field in the hysteretic regions, the resistance exhibits an unusual time dependence, consisting of random, bidirectional jumps followed by slow relaxations. These anomalies are apparently caused by instabilities in the charge distribution of the two layers.Comment: 4 pages, 4 figure

Spinor classification of the Weyl tensor in five dimensions

We investigate the spinor classification of the Weyl tensor in five dimensions due to De Smet. We show that a previously overlooked reality condition reduces the number of possible types in the classification. We classify all vacuum solutions belonging to the most special algebraic type. The connection between this spinor and the tensor classification due to Coley, Milson, Pravda and Pravdov\'a is investigated and the relation between most of the types in each of the classifications is given. We show that the black ring is algebraically general in the spinor classification.Comment: 40 page

Rolling Closed String Tachyons and the Big Crunch

We study the low-energy effective field equations that couple gravity, the dilaton, and the bulk closed string tachyon of bosonic closed string theory. We establish that whenever the tachyon induces the rolling process, the string metric remains fixed while the dilaton rolls to strong coupling. For negative definite potentials we show that this results in an Einstein metric that crunches the universe in finite time. This behavior is shown to be rather generic even if the potentials are not negative definite. The solutions are reminiscent of those in the collapse stage of a cyclic universe cosmology where scalar field potentials with negative energies play a central role.Comment: 13 pages, 2 figures, LaTeX. Replaced version: one reference adde