Integrated Calendar

They are out there, they are detectable and they are crucial theoretically. De-tection of highly eccentric (e>~ 0.99) extra-solar gas-giants with periastron
of a few stellar radii may answer the question of how hot Jupiters get so close to their host star. Detection of early high energy emission (soft X-ray to gam-ma-rays) at the onset of Supernovae will allow us to measure key properties of the exploding star, including its pre-explosion radius and the blast
wave velocity.

We explore the possibility of controlling rotational and torsional dynamics of rigid and non-rigid molecules with strong, non-resonant laser pulses and demonstrate that transient laser-induced alignment and torsional alignment depends on the nuclear spin of the molecule.
Consequently, nuclear spin isomers can be manipulated selectively by a sequence of time-delayed laser pulses. In particular, in non-rigid molecular, torsion can be induced selectively by a sequence of two pulses with different polarization direction.

Ultrashort complementary DNA and RNA oligomers, down to 6 base pairs in length, are found to exhibit nematic and columnar liquid crystal phases, even though such duplexes lack the shape anisotropy required for liquid crystal orientational ordering. These phases are produced whenever fragments of double helices display some - even weak - end-to-end attractive interactions promoting living polymerization into longer polydisperse anisotropic rod-shaped aggregates, which can order. This is the case for self-complementary sequences that, upon hybridizing, form duplexes interacting via the stacking of the terminal nucleobases. This is also the case when duplexes have unpaired overhangs that mutually interact through full or partial pairing. Further mechanisms of self-assembly are active in mixtures of oligonucleotides and flexible polymers of different nature and in random pools of oligomeric sequences. These systems phase separate into a liquid crystal phase rich in well-formed duplexes coexisting with an isotropic phase formed by polymers, single strands and highly defected duplexes. In this way, through a combination of multiple effects, including depletion-type forces and non-equilibrium DNA pairing, the system spontaneously selects well-paired sequences, which are spatially segregated. The result is an efficient spontaneous piling of DNA duplexes in which the terminals of the oligonucleotides are held in physical contact by the collective behavior, a condition favorable for their non-enzymatic ligation.
REFERENCES
Nakata M, Zanchetta G, Chapman BD, Jones CD, Cross JO, Pindak R, Bellini T, Clark NA (2007) Living Polymerization and Liquid Crystal Condensation of 6-20 Base Pair DNA Duplexes. Science 318: 1276-1279
Zanchetta G, Nakata M, Bellini T, Clark NA (2008) Physical Polymerization and Liquid Crystal Crystallization of RNA Oligomers. J. Am. Chem. Soc. 130: 12864-12865
Zanchetta G, Nakata M, Buscaglia M, Clark NA, Bellini T (2008) Liquid Crystal Ordering of DNA and RNA Oligomers with Partially Overlapping Sequences. J. Phys.: Condensed Matter. 28: 494214
Zanchetta G, Nakata M, Buscaglia M, Bellini T, Clark NA (2008) Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers. Proc. Nat. Acad. Sci. 105: 1111-1117
Zanchetta G, Giavazzi F, Nakata M, Buscaglia M, Cerbino R, Clark NA, Bellini T (2010) Right-handed double-helix ultrashort DNA yields chiral nematic phases with both right- and left-handed director twist. Proc. Nat. Acad. Sci. 107: 17497-17502
Bellini T, Zanchetta G, Fraccia T, Cerbino R, Tsai E, Smith GP, Moran MJ, Walba DM, Clark NA, Liquid Crystal Ordering as Evidence for the Structured Self-Assembly of Random-Sequence DNA Oligomers, Proc. Nat. Acad. Sci (to be published)

Bioinformatics Workshop Series 2011-2012

Analysing Affymetrix microarray data using Partek: From raw data to biological knowledge
In the workshop we will learn how to analyze Affymetrix microarray data using the software Partek.
The tutorial will illustrate how to import the data and to do exploratory analysis using PCA and hierarchical clustering.
We will also learn to generate lists of differentially expressed genes and cluster them.