A proteome database of human primary T helper cells

We have established the first public database of human primary T helper cell proteome using two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight-mass spectrometry. For the database, CD4+ human T cells were activated with anti-CD3+anti-CD28 antibodies and metabolically labeled with [35S]methionine for 24 h. Cells were lysed and proteins were separated by 2-DE. About 1500 protein spots were detected in the resulting 2-DE gels with silver staining, and 2000 spots with autoradiography. We have identified 91 proteins from the 2-DE gels using peptide mass fingerprinting, and annotated them to our database. The identified proteins are also linked to SWISS-PROTand NCBI protein databases. Our database is available via the Internet at http://www3.btk.utu.fi:8080/Genomics/Proteomics/Database.     

Transition from a two-dimensional superfluid to a one-dimensional Mott insulator

A two-dimensional system of atoms in an anisotropic optical lattice is studied theoretically. If the system is finite in one direction, it is shown to exhibit a transition between a two-dimensional superfluid and a one-dimensional Mott insulating chain of superfluid tubes. Monte Carlo simulations are consistent with the expectation that the phase transition is of Kosterlitz-Thouless type. The effect of the transition on experimental time-of-flight images is discussed.     

Chemical Synthesis, 3D Structure,and ASIC Binding Site of the Toxin Mambalgin‐2

Mambalgins are a novel class of snake venom components that exert potent analgesic effects mediated through the inhibition of acid‐sensing ion channels (ASICs). The 57‐residue polypeptide mambalgin‐2 (Ma‐2) was synthesized by using a combination of solid‐phase peptide synthesis and native chemical ligation. The structure of the synthetic toxin, determined using homonuclear NMR, revealed an unusual three‐finger toxin fold reminiscent of functionally unrelated snake toxins. Electrophysiological analysis of Ma‐2 on wild‐type and mutant ASIC1a receptors allowed us to identify α‐helix 5, which borders on the functionally critical acidic pocket of the channel, as a major part of the Ma‐2 binding site. This region is also crucial for the interaction of ASIC1a with the spider toxin PcTx1, thus suggesting that the binding sites for these toxins substantially overlap. This work lays the foundation for structure–activity relationship (SAR) studies and further development of this promising analgesic peptide.     

Enantioselective synthetic thalidomide receptors based upon DNA binding motifs

A series of molecularly imprinted polymer (MIP) synthetic receptors selective for the sedative thalidomide (5) have been designed and synthesized based upon the functional monomer 9-(2'-methacryloyloxyethyl)adenine (2). (1)H-NMR studies were used to establish the existence of DNA-like binding interactions between 2 and the template (5). A series of ethylene glycol dimethacrylate cross-linked copolymers was synthesized using either 2 or methacrylic acid, or a combination of these functional monomers. Zonal HPLC studies demonstrated enantioselectivity (alpha = 2.11) and ligand selectivity which could be attributed to the interaction of 2 with the imide moiety of 5. Compound 2 provided a more significant contribution to the binding of 5 than methacrylic acid, though a combination of these two functional monomers resulted in improved enantioselectivity. Frontal chromatographic and batch binding studies confirmed the observed differences in affinity of the imprinted and reference polymers for the template.     

Schur Q-polynomials, multiple hypergeometric series and enumeration of marked shifted tableaux

We study Schur Q-polynomials evaluated on a geometric progression, or equivalently q-enumeration of marked shifted tableaux, seeking explicit formulas that remain regular at q=1. We obtain several such expressions as multiple basic hypergeometric series, and as determinants and pfaffians of continuous q-ultraspherical or continuous q-Jacobi polynomials. As special cases, we obtain simple closed formulas for staircase-type partitions.     

An ab initio molecular dynamics study of iron phases at high pressure and temperature

The crystal structure of iron, the major component of the Earth's inner core (IC), is unknown for the IC high pressure (P; 3.3-3.6 Mbar) and temperature (T; 5000-7000 K). There is mounting evidence that the hexagonal close-packed (hcp) phase of iron, stable at the high P of the IC and a low T, might be unstable under the IC conditions due to the impact of high T and impurities. Experiments at the IC P and T are difficult and do not provide a conclusive answer as regards the iron stability at the pressure of the IC and temperatures close to the iron melting curve. Recent theory provides contradictory results regarding the nature of the stable Fe phase. We investigated the possibility of body-centered cubic (bcc) phase stabilization at the P and T in the vicinity of the Fe melting curve by using ab initio molecular dynamics. Thermodynamic calculations, relying on the model of uncorrelated harmonic oscillators, provide nearly identical free energies within the error bars of our calculations. However, direct simulation of iron crystallization demonstrates that liquid iron freezes in the bcc structure at the P of the IC and T = 6000 K. All attempts to grow the hcp phase from the liquid failed. The mechanism of bcc stabilization is explained. This resolves most of the earlier confusion.     

Molecular dynamics simulation of zirconia melting

The melting point for the tetragonal and cubic phases of zirconia (ZrO₂) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over the tetragonal phase at high temperatures, ReaxFF also gives approximately the correct melting point, around 2900 K, whereas the Lewis-Catlow estimate is above 6000 K.