Extending the dynamic range of transcription factor action by translational regulation

A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other transcription factors. Intuitively, each mRNA molecule acts as an independent sensor of the TF concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this new scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.Comment: 14 pages, 5 figure

Back-reaction of perturbation wave packets on gray solitons

Within the Bogoliubov-de Gennes linearization theory of quantum or classical perturbations around a background solution to the one-dimensional nonlinear Schr\"odinger equation, we study the back-reaction of wave packet perturbations on a gray soliton background. From our recently published exact solutions, we determine that a wave packet effectively jumps ahead as it passes through a soliton, emerging with a wavelength-dependent forward translation in comparison to its motion in absence of the soliton. From this and from the full theory's exact momentum conservation, we deduce that post-Bogoliubov back-reaction must include a commensurate forward advance by the soliton itself. We quantify this effect with a simple theory, and confirm that it agrees with full numerical solution of the classical nonlinear Schr\"odinger equation. We briefly discuss the implications of this effect for quantum behavior of solitons in quasi-condensed dilute gases at finite temperature.Comment: 12 pages, 2 figure

Capturing coevolutionary signals in repeat proteins

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural ensembles. Here we introduce a statistical coupling analysis for repeat proteins -- natural systems for which the identification of domains remains challenging. We show that the inherent translational symmetry of repeat protein sequences introduces a strong bias in the pair correlations at precisely the length scale of the repeat-unit. Equalizing for this bias reveals true co-evolutionary signals from which local native-contacts can be identified. Importantly, parameter values obtained for all other interactions are not significantly affected by the equalization. We quantify the robustness of the procedure and assign confidence levels to the interactions, identifying the minimum number of sequences needed to extract evolutionary information in several repeat protein families. The overall procedure can be used to reconstruct the interactions at long distances, identifying the characteristics of the strongest couplings in each family, and can be applied to any system that appears translationally symmetric

A mesoscopic ring as a XNOR gate: An exact result

We describe XNOR gate response in a mesoscopic ring threaded by a magnetic flux $\phi$. The ring is attached symmetrically to two semi-infinite one-dimensional metallic electrodes and two gate voltages, viz, $V_a$ and $V_b$, are applied in one arm of the ring which are treated as the inputs of the XNOR gate. The calculations are based on the tight-binding model and the Green's function method, which numerically compute the conductance-energy and current-voltage characteristics as functions of the ring-to-electrode coupling strength, magnetic flux and gate voltages. Our theoretical study shows that, for a particular value of $\phi$ ($=\phi_0/2$) ($\phi_0=ch/e$, the elementary flux-quantum), a high output current (1) (in the logical sense) appears if both the two inputs to the gate are the same, while if one but not both inputs are high (1), a low output current (0) results. It clearly exhibits the XNOR gate behavior and this aspect may be utilized in designing an electronic logic gate.Comment: 8 pages, 5 figure

Control of quantum interference in molecular junctions: Understanding the origin of Fano and anti- resonances

We investigate within a coarse-grained model the conditions leading to the appearance of Fano resonances or anti-resonances in the conductance spectrum of a generic molecular junction with a side group (T-junction). By introducing a simple graphical representation (parabolic diagram), we can easily visualize the relation between the different electronic parameters determining the regimes where Fano resonances or anti-resonances in the low-energy conductance spectrum can be expected. The results obtained within the coarse-grained model are validated using density-functional based quantum transport calculations in realistic T-shaped molecular junctions.Comment: 5 pages, 5 figure

Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves

Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody's amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems

Corporate Culture and Its Connection with External and Internal Public Relations

The main aim of this article is to present the influence of corporate culture on company's stakeholders. This paper signalises the tendency in corporate communication with its internal and external publics. It is focused on two issues: corporate social responsibility and employer branding. Those two categories are consequences of corporate culture model.Głównym celem artykułu jest zaprezentowanie wpływu jaki wywiera charakter kultury korporacyjnej na związanych z przedsiębiorstwem interesariuszy (stakeholders). W artykule zasygnalizowane zostały główne tendencje wyznaczające charakter komunikacji między organizacją a jej wewnętrznym i zewnętrznym otoczeniem. Tekst koncentruje się na dwóch kwestiach: społecznej odpowiedzialności przedsiębiorstwa (corporate social responsibilty) i budowanie wizerunku pracodawcy (employer branding), które zaprezentowane zostały jako efekty określonego modelu kultury organizacyjnej