Bio-logic: gene expression and the laws of combinatorial logic

Original article can be found at: http://www.mitpressjournals.org/ Copyright MIT Press DOI: 10.1162/artl.2008.14.1.121At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection and multiplexing is performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This paper presents a systematic investigation into the effect of TF binding dependencies on the predicted regulatory function of this “bio-logic”. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each other’s affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: 1) the laws of combinatorial logic hold only for systems with independently binding TFs; 2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and 3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be more robustly controlled than that of single TF or (quasi-) logical multi-TF systems. Keywords: Transcription regulation, Genetic regulatory networks, Enzyme kinetics, Combinatorial logic, Non-Boolean continuous logic, Modelling.Peer reviewe

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin.

Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in chromosome dynamics and genome stability. However, our current understanding of 3D genome organization does not include PCH domains because of technical challenges associated with repetitive sequences enriched in PCH genomic regions. We investigated the 3D architecture of Drosophila melanogaster PCH domains and their spatial associations with the euchromatic genome by developing a novel analysis method that incorporates genome-wide Hi-C reads originating from PCH DNA. Combined with cytogenetic analysis, we reveal a hierarchical organization of the PCH domains into distinct territories. Strikingly, H3K9me2-enriched regions embedded in the euchromatic genome show prevalent 3D interactions with the PCH domain. These spatial contacts require H3K9me2 enrichment, are likely mediated by liquid-liquid phase separation, and may influence organismal fitness. Our findings have important implications for how PCH architecture influences the function and evolution of both repetitive heterochromatin and the gene-rich euchromatin

Observations of Reduced Electron Gyroscale Fluctuations in National Spherical Torus Experiment H-Mode Plasmas with Large E X B Flow Shear

Electron gyroscale fluctuation measurements in National Spherical Torus Experiment H-mode plasmas with large toroidal rotation reveal fluctuations consistent with electron temperature gradient (ETG) turbulence. Large toroidal rotation in National Spherical Torus Experiment plasmas with neutral beam injection generates ExB flow shear rates comparable to ETG linear growth rates. Enhanced fluctuations occur when the electron temperature gradient is marginally stable with respect to the ETG linear critical gradient. Fluctuation amplitudes decrease when the ExB flow shear rate exceeds ETG linear growth rates. The observations indicate that ExB flow shear can be an effective suppression mechanism for ETG turbulence.X1129sciescopu

Angle-resolved photoemission study of insulating and metallic Cu-O chains in PrBa2_2Cu3_3O7_7 and PrBa2_2Cu4_4O8_8

We compare the angle-resolved photoemission spectra of the hole-doped Cu-O chains in PrBa$_2$Cu$_3$O$_7$ (Pr123) and in PrBa$_2$Cu$_4$O$_8$ (Pr124). While, in Pr123, a dispersive feature from the chain takes a band maximum at $k_b$ (momentum along the chain) $\sim$ $\pi/4$ and loses its spectral weight around the Fermi level, it reaches the Fermi level at $k_b$ $\sim$ $\pi/4$ in Pr124. Although the chains in Pr123 and Pr124 are approximately 1/4-filled, they show contrasting behaviors: While the chains in Pr123 have an instability to charge ordering, those in Pr124 avoid it and show an interesting spectral feature of a metallic coupled-chain system.Comment: 4 pages, 5 figures, to be published in PR

Collective and independent-particle motion in two-electron artificial atoms

Investigations of the exactly solvable excitation spectra of two-electron quantum dots with a parabolic confinement, for different values of the parameter R_W expressing the relative magnitudes of the interelectron repulsion and the zero-point kinetic energy of the confined electrons, reveal for large R_W a remarkably well-developed ro-vibrational spectrum associated with formation of a linear trimeric rigid molecule composed of the two electrons and the infinitely heavy confining dot. This spectrum transforms to one characteristic of a "floppy" molecule for smaller values of R_W. The conditional probability distribution calculated for the exact two-electron wave functions allows for the identification of the ro-vibrational excitations as rotations and stretching/bending vibrations, and provides direct evidence pertaining to the formation of such molecules.Comment: Published version. Latex/Revtex, 5 pages with 2 postscript figures embedded in the text. For related papers, see http://www.prism.gatech.edu/~ph274c

Pressure-induced phase transition of Bi2Te3 into the bcc structure

The pressure-induced phase transition of bismuth telluride, Bi2Te3, has been studied by synchrotron x-ray diffraction measurements at room temperature using a diamond-anvil cell (DAC) with loading pressures up to 29.8 GPa. We found a high-pressure body-centered cubic (bcc) phase in Bi2Te3 at 25.2 GPa, which is denoted as phase IV, and this phase apperars above 14.5 GPa. Upon releasing the pressure from 29.8 GPa, the diffraction pattern changes with pressure hysteresis. The original rhombohedral phase is recovered at 2.43 GPa. The bcc structure can explain the phase IV peaks. We assumed that the structural model of phase IV is analogous to a substitutional binary alloy; the Bi and Te atoms are distributed in the bcc-lattice sites with space group Im-3m. The results of Rietveld analysis based on this model agree well with both the experimental data and calculated results. Therefore, the structure of phase IV in Bi2Te3 can be explained by a solid solution with a bcc lattice in the Bi-Te (60 atomic% tellurium) binary system.Comment: 12 pages, 5 figure

Two-subband electron transport in nonideal quantum wells

Electron transport in nonideal quantum wells (QW) with large-scale variations of energy levels is studied when two subbands are occupied. Although the mean fluctuations of these two levels are screened by the in-plane redistribution of electrons, the energies of both levels remain nonuniform over the plane. The effect of random inhomogeneities on the classical transport is studied within the framework of a local response approach for weak disorder. Both short-range and small-angle scattering mechanisms are considered. Magnetotransport characteristics and the modulation of the effective conductivity by transverse voltage are evaluated for different kinds of confinement potentials (hard wall QW, parabolic QW, and stepped QW).Comment: 10 pages, 6 figure

Stabilization of electron-scale turbulence by electron density gradient in national spherical torus experiment

Theory and experiments have shown that electron temperature gradient (ETG) turbulence on the electron gyro-scale, k⊥ρe ≲ 1, can be responsible for anomalous electron thermal transport in NSTX. Electron scale (high-k) turbulence is diagnosed in NSTX with a high-k microwave scattering system [D. R. Smith et al., Rev. Sci. Instrum. 79, 123501 (2008)]. Here we report on stabilization effects of the electron density gradient on electron-scale density fluctuations in a set of neutral beam injection heated H-mode plasmas. We found that the absence of high-k density fluctuations from measurements is correlated with large equilibrium density gradient, which is shown to be consistent with linear stabilization of ETG modes due to the density gradient using the analytical ETG linear threshold in F. Jenko et al. [Phys. Plasmas 8, 4096 (2001)] and linear gyrokinetic simulations with GS2 [M. Kotschenreuther et al., Comput. Phys. Commun. 88, 128 (1995)]. We also found that the observed power of electron-scale turbulence (when it exists) is anti-correlated with the equilibrium density gradient, suggesting density gradient as a nonlinear stabilizing mechanism. Higher density gradients give rise to lower values of the plasma frame frequency, calculated based on the Doppler shift of the measured density fluctuations. Linear gyrokinetic simulations show that higher values of the electron density gradient reduce the value of the real frequency, in agreement with experimental observation. Nonlinear electron-scale gyrokinetic simulations show that high electron density gradient reduces electron heat flux and stiffness, and increases the ETG nonlinear threshold, consistent with experimental observations.United States. Department of Energy (ontract No. DE-AC02- 09CH11466)United States. Department of Energy. Office of Science (Contract No. DE-AC02-05CH11231

DNA topoisomerases participate in fragility of the oncogene RET

Fragile site breakage was previously shown to result in rearrangement of the RET oncogene, resembling the rearrangements found in thyroid cancer. Common fragile sites are specific regions of the genome with a high susceptibility to DNA breakage under conditions that partially inhibit DNA replication, and often coincide with genes deleted, amplified, or rearranged in cancer. While a substantial amount of work has been performed investigating DNA repair and cell cycle checkpoint proteins vital for maintaining stability at fragile sites, little is known about the initial events leading to DNA breakage at these sites. The purpose of this study was to investigate these initial events through the detection of aphidicolin (APH)-induced DNA breakage within the RET oncogene, in which 144 APHinduced DNA breakpoints were mapped on the nucleotide level in human thyroid cells within intron 11 of RET, the breakpoint cluster region found in patients. These breakpoints were located at or near DNA topoisomerase I and/or II predicted cleavage sites, as well as at DNA secondary structural features recognized and preferentially cleaved by DNA topoisomerases I and II. Co-treatment of thyroid cells with APH and the topoisomerase catalytic inhibitors, betulinic acid and merbarone, significantly decreased APH-induced fragile site breakage within RET intron 11 and within the common fragile site FRA3B. These data demonstrate that DNA topoisomerases I and II are involved in initiating APH-induced common fragile site breakage at RET, and may engage the recognition of DNA secondary structures formed during perturbed DNA replication

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

Anthrax is a globally important animal disease and zoonosis. Despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. Here we show that the dynamics of an anthrax-causing agent, Bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. Using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of death for a broad range of mammalian hosts. We predict that this pathogen will accelerate the decline and possibly result in the extirpation of local chimpanzee (Pan troglodytes verus) populations. We present the epidemiology of a cryptic pathogen and show that its presence has important implications for conservation