Balancing noise and plasticity in eukaryotic gene expression

Coupling the control of expression stochasticity (noise) to the ability of expression change (plasticity) can alter gene function and influence adaptation. A number of factors, such as transcription re-initiation, strong chromatin regulation or genome neighboring organization, underlie this coupling. However, these factors do not necessarily combine in equivalent ways and strengths in all genes. Can we identify then alternative architectures that modulate in distinct ways the linkage of noise and plasticity? Here we first show that strong chromatin regulation, commonly viewed as a source of coupling, can lead to plasticity without noise. The nature of this regulation is relevant too, with plastic but noiseless genes being subjected to general activators whereas plastic and noisy genes experience more specific repression. Contrarily, in genes exhibiting poor transcriptional control, it is translational efficiency what separates noise from plasticity, a pattern related to transcript length. This additionally implies that genome neighboring organization -as modifier- appears only effective in highly plastic genes. In this class, we confirm bidirectional promoters (bipromoters) as a configuration capable to reduce coupling by abating noise but also reveal an important trade-off, since bipromoters also decrease plasticity. This presents ultimately a paradox between intergenic distances and modulation, with short intergenic distances both associated and disassociated to noise at different plasticity levels. Balancing the coupling among different types of expression variability appears as a potential shaping force of genome regulation and organization. This is reflected in the use of different control strategies at genes with different sets of functional constraints

Balancing noise and plasticity in gene expression

Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational mechanisms are the ones separating noise from plasticity in low-plastic genes, a pattern associated with the simplicity of their expression regulation. Neighboring genome architecture as modifier appears then only effective in highly plastic genes. This poses ultimately an interesting paradox between intergenic distances and modulation, with short intergenic distances both associated and not associated with noise at different plasticity levels. Balancing the coupling among different types of expression variability appears thus as a potential shaping force of genome architecture and regulation

Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated

Isolated factorizations and their applications in simplicial affine semigroups

We introduce the concept of isolated factorizations of an element of a commutative monoid and study its properties. We give several bounds for the number of isolated factorizations of simplicial affine semigroups and numerical semigroups. We also generalize $\alpha$-rectangular numerical semigroups to the context of simplicial affine semigroups and study their isolated factorizations. As a consequence of our results, we characterize those complete intersection simplicial affine semigroups with only one Betti minimal element in several ways. Moreover, we define Betti sorted and Betti divisible simplicial affine semigroups and characterize them in terms of gluings and their minimal presentations. Finally, we determine all the Betti divisible numerical semigroups, which turn out to be those numerical semigroups that are free for any arrangement of their minimal generators