Cell fates as high-dimensional attractor states of a complex gene regulatory network

Cells in multicellular organisms switch between distinct cell fates, such as proliferation or differentiation into specialized cell types. Genome-wide gene regulatory networks govern this behavior. Theoretical studies of complex networks suggest that they can exhibit ordered (stable) dynamics, raising the possibility that cell fates may represent high-dimensional attractor states. We used gene expression profiling to show that trajectories of neutrophil differentiation converge to a common state from different directions of a 2773-dimensional gene expression state space, providing the first experimental evidence for a high-dimensional stable attractor that represents a distinct cellular phenotype.     

The coherent scattering function of the reptation model: Simulations compared to theory

We present results of Monte Carlo simulations measuring the coherent structure function of a chain moving through an ordered lattice of fixed topological obstacles. Our computer experiments use chains up to 320 beads and cover a large range of wave vectors and a time range exceeding the reptation time. For additional information we also measured the coherent structure function of internal pieces of the chain. We compare our results i) to the predictions of the primitive chain model, ii) to an approximate form resulting from Rouse motion in a coiled tube, and iii) to our recent evaluation of the full reptation model. i) The primitive chain model can fit the data for times , where T ₂ is the Rouse time of the chain. Besides some phenomenological amplitude factor this fit involves the reptation time T ₃ as a second fit parameter. For the chain lengths measured, the asymptotic behavior is not attained. ii) The model of Rouse motion in a tube, which we have criticized before on theoretical grounds, is shown to fail also on the purely phenomenological level. iii) Our evaluation of the full reptation model yields an excellent fit to the data for both total chains and internal pieces and for all wave vectors and all times, provided specific micro-structure effects of the MC dynamics are negligible. Such micro-structure effects show up for wave vectors of the order of the inverse segment size and enforce the introduction of some phenomenological, wave-vector-dependent prefactor. For the dynamics of the total chain our data analysis based on the full reptation model shows the importance of tube length fluctuations. Universal (Rouse-type) internal relaxation, however, is unimportant. It can be observed only in the form of the diffusive motion of a short central subchain in the tube. Finally, we present a fit formula which in a large range of wave vectors and chain lengths reproduces the numerical results of our theory for the scattering from the total chain.Received: 9 July 2003, Published online: 11 November 2003PACS: 83.10.Kn Reptation and tube theories - 82.35.Lr Physical properties of polymers - 83.10.Rs Computer simulation of molecular and particle dynamics     

Density functional theory calculations of nuclear quadrupole coupling constants with calibrated 14N quadrupole moments

Density functional calculations of the electric field gradient tensor at the nitrogen nucleus in 13 test molecules, containing 14 nitrogen sites, have been performed using the linear combination of Gaussian-type orbital Kohn-Sham density functional theory (LCGTO-KSDFT) approach. Local and gradient corrected functionals were used for all-electron calculations. All the molecular structures were optimized at their respective levels of theory with extended basis sets. Calibrated ¹⁴N nuclear quadrupole moments were obtained through a fitting procedure between calculated electric field gradients and experimental nuclear quadrupole coupling constants of the test set of molecules for each basis set and functional considered. With these calibrated ¹⁴N nuclear quadrupole moments, the nuclear quadrupole coupling constants of the following selected systems were determined: fluoromethylisonitrile, pyridine, pyrrole, imadazole, pyrazole, 1,8-bis(dimethyl-amino)naphthalene, cyclotetramethylenetetranitramine, cocaine and heroin.     

Exploring the MRCI method for calculating interaction energies: application to the HeNe potential curve

A multi-reference configuration interaction (MRCI) method is described, which is devised for the calculation of interaction energies of van der Waals complexes and applied to calculating the HeNe potential energy curve. The MRCI calculations make use of a generalized Pople-correction in order to account for the lack of size consistency. The orbital space is partitioned into three subspaces: the first active space (AS1), which contains the strongly occupied orbitals; the second active space (AS2), which contains the main intra-correlating orbitals; and the external space (ES). It is shown that, to keep the error below ± 0.2 K in the excitation scheme and the active orbital space it is sufficient to include only σ-orbitals in AS2 and to use an excitation scheme (labelled Qq-MRCI) that encompasses only up to quadruply excited configurations. The final active orbital space (AS2) turned out to be 2s(He), 2pσ(He), 3s(Ne), 3σ(Ne) and 3dσ(Ne). Other MRCI variants, in which most or all quadruply excited configurations were deleted from the CI expansion (Qt- and Tt-MRCI), were found to be inadequate. Using the Qq-MRCI scheme together with a 197-orbital ‘interaction optimized’ basis set (IO197), the MRCI interaction energy at R = 5.7 _a0 was calculated to be -21.12K. The corresponding values at the MP4 and CCSD(T) levels of theory are -20.06 K and -20.99 K, respectively, indicating that the MP4 method is inappropriate for highly accurate calculations on this system. Fitting the calculated data using a generalized Morse function, including an additional C₆/R⁶ term to account for a correct long-range behaviour of the potential, the MRCI well depth was calculated to be -21.16K at R_eq = 5.73a ₀. The MRCI and CCSD(T) potentials have the same quality and are found to be in good agreement with the Hartree-Fock dispersion (HFD-B) potential of Keil, M., Danielson, L. J., and Dunlop, P. J., 1991, J. Chem. Phys., 94, 296. It is concluded that, for basis IO197, the CCSD(T) method is sufficiently accurate for calculating the HeNe interaction. To recover the small, missing contributions (a few tenths of a Kelvin), MRCI should be used.     

LIGHT PROMOTION OF SEED GERMINATION IN Datura ferox IS MEDIATED BY A HIGHLY STABLE POOL OF PHYTOCHROME

Abstract— The duration of the far-red light-absorbing form of phytochrome (Pfr) of the photoreceptor pool involved in the control of seed germination was investigated for Datura ferox seeds. These seeds require both Pfr and alternating temperatures (20/30°C) to germinate. After 24 h imbibition (25°C), the seeds received pretreatment-light pulses providing different phytochrome photoequilibria (Pfr/P), followed by a 24 h dark incubation (25°C), and test-light pulses providing different Pfr/P immediately prior to transfer to alternating temperatures. Germination increased with increasing Pfr/P provided by the test-light pulses, but was unaffected by the pretreatment-light pulses. This suggests that phytochrome synthesis, phytochrome degradation and phytochrome-mediated changes in response to phytochrome were negligible. In other experiments, red light-pretreatment pulses were followed by dark incubations (25°C) of different duration before transfer to alternating temperatures. The proportion of Pfr remaining after the 25°C incubation period was estimated by comparing germination rates with those of seeds that received test-light pulses of known calculated Pfr/P immediately prior to the start of the cycles of alternating temperatures. More than 80% of the Pfr established by a Pfr/P= 0.87 light pulse was present and active even after 48 h dark incubation at 25°C. Surprisingly, when a pretreatmentlight pulse providing a Pfr/P= 0.70 was given, the reduction in [Pfr] was significantly faster.
Germination of Datura ferox seeds is under the control of a highly stable (type II like) phytochrome pool. Apparently, this pool follows Pfr dark reversion to the red light-absorbing form, the times to reach half the original Pfr pool being > 96 h or <14 h after light pulses providing Pfr/P= 0.87 or 0.70, respectively.     

La0.789Yb0.20Ho0.001Tm0.01F3纳米立方体的溶剂热合成及白色上转换发光性质

采用溶剂热方法制备了La0.789Yb0.20Ho0.001Tm0.01F3纳米立方体,并利用粉末X射线衍射仪、透射电子显微镜和X射线能谱仪表征了其组成、结构和形貌,用荧光分光光度计测量了样品的室温上转换发射光谱,结果表明,样品具有红、绿和蓝色3个发射带,其辐射跃迁分别归属于Tm3+的1G4→3H6(蓝色)和1G4→3...     

THE PROTONATION OF A RETINYL SCHIFF BASE

The hydrogen bonding-protonation equilibrium for retinyl Schiff base/propionic acid or 3-chloropropionic acid systems was examined by Fourier transform infrared spectroscopy in non polar solutions at temperatures ranging from 25 degrees C to about -150 degrees C. The spectra give evidence for the gradual increase in the degree of protonation as temperature is lowered. The bearing of this on applying low temperature spectroscopic results to physiological conditions in rhodopsin research is discussed.     

Linear dynamical systems with integer constraints

We study properties of dynamic discrete-time linear systemswith the input or the state constrained to have integer components.The reachability of input-constrained systems is investigated,and consistency conditions for state-constrained systems aregiven.     

The numerical solution of Stokes flow in a domain with re-entrant boundaries by the boundary element method

Numerical solutions are presented for two-dimensional low Reynolds number flow in a rotating tank with stationary barriers. The boundary element method is employed, assuming straight panels and quadratic source distribution. The feasibility of repositioning the nodes as a way to minimize the error is explored. A stretching parameter places smaller elements near the re-entrant regions. Elementary error analysis shows uniform improvement in the solution with stretching. The changing eddy pattern for different numbers and sizes of the barriers is compared with experimental results.