Integrated Calendar

Cell motility is based on the dynamics of active polymer gels and other macromolecules. The physical state of these dynamic components, and cellular matter in general, is controlled by complex protein and genetic networks. We propose to classify participating molecules into three categories. First, there are the basic structural proteins. Second, the physical state of these structural proteins is set by regulating proteins, which constitute the control parameters of the system. Together, structural and regulating proteins build cellular modules exhibiting distinct dynamic phases and phase transitions. Third, these modules are interlinked by a signaling network determining the functional state of the cell. However, the topology of the ensuing dynamic phase diagram is independent of cellular signaling. In contrast, phase trajectories are set by the signaling network. I discuss examples of such dynamic phases and phase transitions found in cell spreading of mouse embryonic fibroblasts and wing disk cells of drosophila melanogaster, as well as the slime mold physarum polycephalum. Remarkably, there is universal behavior in these evolutionary distant species.

We have performed a direct calculation of Witten index I in N = 1,2,3
supersymmetric Yang-Mills Chern-Simons (SYMCS) 3d theories.
We do it in the framework of Born-Oppenheimer (BO) approach by putting the
system into a small spatial box and studying the effective Hamiltonian
depending on the zero field harmonics. At the tree level, our results
coincide with the results obtained by Witten back in 1999, but there is
a difference in the way the loop effects are implemented. In Witten's
approach, one has only take into account the fermion loops, which bring
about a negative shift of the (chosen positive at the tree level)
Chern-Simons coupling k. As a result, the index vanishes and supersymmetry
is broken at small k. In the effective BO Hamiltonian framework, fermion,
gluon and ghost loops contribute on an equal footing. Fermion loop
contribution to the effective Hamiltonian can be evaluated exactly, and
their effect amounts to the negative shift k -> k - h/2 for N =1 and
k -> k - h for N = 2,3 in the tree-level formulae for the index (h
being the adjoint Kasimir eigenvalue). In our approach, the shift k -> k + h
brought about by the gluon loops also affects the index. Since the total
shift of k is positive or zero, Witten index appears to be nonzero at nonzero
k, and supersymmetry is not broken.
We briefly discuss possible reasons for such disagreement

After reviewing the construction of a superfluid phase of
gauge theories with a gravity dual, I will discuss some of its
features: its speed of sound and its interaction with a heavy quark.
I will argue that, as opposed to superfluid helium, these features
indicate that the low lying excitations of the theory behave like
massless quasi-particles.

Abstract

Regulatory RNA has been discovered in all three domains of life. However, transcriptional units that give rise to non-coding RNAs (ncRNAs) or cis-acting antisense RNAs (asRNAs) are not identified during normal genome annotation, and in phototrophic bacteria only a small number of such RNAs have been described so far. We have used 5 different methods for the identification of novel non-coding and antisense RNAs in various cyanobacteria, with a focus on model cyanobacteria. The reliability of computational predictions for the detection of ncRNAs and asRNAs in Synechocystis sp. PCC 6803 and for marine Synechococcus species was scrutinized in microarrays, complemented by deep sequencing of the small RNA population and validated by extensive Northern and 5' RACE analyses (1-4). The total number of classical trans-acting ncRNAs in Synechocystis sp. PCC 6803 reaches several hundred different transcripts, the number of antisense RNAs is even more than 1000. Thus, non-coding RNAs play a much more important role in this model organism and probably also in most other bacteria. Although clear-cut functions have been established only for very few of these RNAs so far (5), there isl evidence for cyanobacterial ncRNAs acting against invading phages, controlling the expression of key photosynthetic genes, or serving as signals for RNA maturation, processing and degradation.

(1) Axmann et al. (2005), Genome Biol. 6, R73: 1-16.
(2) Steglich et al. (2008), PLoS Genetics 4 (8) e10000173.
(3) Voss et al. (2009), BMC Genomics 10, 123.
(4) Georg et al. (2009), Mol. Sys. Biol. 5, 305.
(5) Duehring et al. (2006) Proc. Natl. Acad. Sci. USA 103, 7054-7058