A quantitative comparison of sRNA-based and protein-based gene regulation

Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare and contrast sRNAs with conventional transcription factors (TFs) to better understand the advantages of each form of regulation. In particular, we calculate the steady-state behavior, noise properties, frequency-dependent gain (amplification), and dynamical response to large input signals of both forms of regulation. While the mean steady-state behavior of sRNA-regulated proteins exhibits a distinctive tunable threshold-linear behavior, our analysis shows that transcriptional bursting leads to significantly higher intrinsic noise in sRNA-based regulation than in TF-based regulation in a large range of expression levels and limits the ability of sRNAs to perform quantitative signaling. Nonetheless, we find that sRNAs are better than TFs at filtering noise in input signals. Additionally, we find that sRNAs allow cells to respond rapidly to large changes in input signals. These features suggest a niche for sRNAs in allowing cells to transition quickly yet reliably between distinct states. This functional niche is consistent with the widespread appearance of sRNAs in stress-response and quasi-developmental networks in prokaryotes.Comment: 26 pages, 8 figures; accepted for publication in Molecular Systems Biolog

Functional central limit theorems for vicious walkers

We consider the diffusion scaling limit of the vicious walker model that is a system of nonintersecting random walks. We prove a functional central limit theorem for the model and derive two types of nonintersecting Brownian motions, in which the nonintersecting condition is imposed in a finite time interval $(0,T]$ for the first type and in an infinite time interval $(0,\infty)$ for the second type, respectively. The limit process of the first type is a temporally inhomogeneous diffusion, and that of the second type is a temporally homogeneous diffusion that is identified with a Dyson's model of Brownian motions studied in the random matrix theory. We show that these two types of processes are related to each other by a multi-dimensional generalization of Imhof's relation, whose original form relates the Brownian meander and the three-dimensional Bessel process. We also study the vicious walkers with wall restriction and prove a functional central limit theorem in the diffusion scaling limit.Comment: AMS-LaTeX, 20 pages, 2 figures, v6: minor corrections made for publicatio

Influence of subretinal fluid in advanced stage retinopathy of prematurity on proangiogenic response and cell proliferation

Purpose The clinical phenotype of advanced stage retinopathy of prematurity (ROP, stages 4 and 5) cannot be replicated in an animal model. To dissect the molecular events that can lead up to advanced ROP, we examined subretinal fluid (SRF) and surgically dissected retrolental membranes from patients with advanced ROP to evaluate its influences on cell proliferation, angiogenic properties, and macrophage polarity. Methods: We compared our findings to SRF collected from patients with uncomplicated rhegmatogenous retinal detachment (RD) without proliferative vitreoretinopathy and surgically dissected epiretinal membrane from eyes with macular pucker. All subretinal fluid samples were equalized for protein. The angiogenic potential of SRF from ROP eyes was measured using a combination of capillary cord formation in a fibrin clot assay, and its proliferative effect was tested with a DNA synthesis of human retinal microvascular endothelial cells. Findings were compared with SRF collected from participants with uncomplicated rhegmatogenous RD without proliferative vitreoretinopathy. The ability of SRF to induce nitric oxide production was measured in vitro using murine J774A.1 macrophages. Cytokine profiles of SRF from ROP and RD eyes were measured using a multienzyme-linked immunosorbent assay (ELISA). Fluorescent immunohistochemistry of retrolental membranes from ROP was performed to detect the presence of leukocytes and the composition of tissue macrophages using markers for M1 and M2 differentiation. Results: The cytokine composition in SRF revealed that in ROP, not only were several proangiogenic factors were preferentially elevated but also the profile of proinflammatory factors was also increased compared to the RD eyes. SRF from ROP eyes supported cell proliferation and endothelial cord formation while SRF from RD eyes had inhibitory effects. SRF from eyes with ROP but not RD robustly induced nitric oxide production in macrophages. Furthermore, fluorescent immunostaining revealed a preponderance of M1 over M2 macrophages in retrolental fibrous membranes from ROP eyes. The cytokine profile and biologic properties of SRF in ROP promote a proangiogenic environment, which supports the maintenance and proliferation of fibrous membranes associated with advanced stages of ROP. In contrast, SRF from RD eyes exhibits a suppressive environment for endothelial cell proliferation and angiogenesis. Conclusions: Our investigation demonstrates that the microenvironment in advanced ROP eyes is proangiogenic and proinflammatory. These findings suggest that management of advanced ROP should not be limited to the surgical removal of the fibrovascular membranes and antiangiogenic therapy but also directed to anti-inflammatory therapy and to promote M2 activation over M1 activity

Quantum Effects in Coulomb Blockade

We review the quantum interference effects in a system of interacting electrons confined to a quantum dot. The review starts with a description of an isolated quantum dot. We discuss the status of the Random Matrix theory (RMT) of the one-electron states in the dot, present the universal form of the interaction Hamiltonian compatible with the RMT, and derive the leading corrections to the universal interaction Hamiltonian. Next, we discuss a theoretical description of a dot connected to leads via point contacts. Having established the theoretical framework to describe such an open system, we discuss its transport and thermodynamic properties. We review the evolution of the transport properties with the increase of the contact conductances from small values to values $\sim e^2/\pi\hbar$. In the discussion of transport, the emphasis is put on mesoscopic fluctuations and the Kondo effect in the conductance.Comment: 169 pages, 28 figures; several references and footnotes are added, and noticed typos correcte

Review of auxetic materials for sports applications: expanding options in comfort and protection

Following high profile, life changing long term mental illnesses and fatalities in sports such as skiing, cricket and American football-sports injuries feature regularly in national and international news. A mismatch between equipment certification tests, user expectations and infield falls and collisions is thought to affect risk perception, increasing the prevalence and severity of injuries. Auxetic foams, structures and textiles have been suggested for application to sporting goods, particularly protective equipment, due to their unique form-fitting deformation and curvature, high energy absorption and high indentation resistance. The purpose of this critical review is to communicate how auxetics could be useful to sports equipment (with a focus on injury prevention), and clearly lay out the steps required to realise their expected benefits. Initial overviews of auxetic materials and sporting protective equipment are followed by a description of common auxetic materials and structures, and how to produce them in foams, textiles and Additively Manufactured structures. Beneficial characteristics, limitations and commercial prospects are discussed, leading to a consideration of possible further work required to realise potential uses (such as in personal protective equipment and highly conformable garments)

Angiotensin-(1-7) and angiotensin-(1-9): function in cardiac and vascular remodeling

The renin angiotensin system (RAS) is integral to cardiovascular physiology, however, dysregulation of this system largely contributes to the pathophysiology of cardiovascular disease (CVD). It is well established that angiotensin II (Ang II), the main effector of the RAS, engages the angiotensin type 1 receptor and promotes cell growth, proliferation, migration and oxidative stress, all processes which contribute to remodeling of the heart and vasculature, ultimately leading to the development and progression of various CVDs including heart failure and atherosclerosis. The counter-regulatory axis of the RAS, which is centered on the actions of angiotensin converting enzyme 2 (ACE2) and the resultant production of angiotensin-(1-7) (Ang-(1-7) from Ang II, antagonizes the actions of Ang II via the receptor Mas, thereby providing a protective role in CVD. More recently, another ACE2 metabolite, Ang-(1-9), has been reported to be a biologically active peptide within the counter-regulatory axis of the RAS. This review will discuss the role of the counter-regulatory RAS peptides, Ang-(1-7) and Ang-(1-9) in the cardiovascular system, with a focus on their effects in remodeling of the heart and vasculature

On the critical nature of plastic flow: one and two dimensional models

Steady state plastic flows have been compared to developed turbulence because the two phenomena share the inherent complexity of particle trajectories, the scale free spatial patterns and the power law statistics of fluctuations. The origin of the apparently chaotic and at the same time highly correlated microscopic response in plasticity remains hidden behind conventional engineering models which are based on smooth fitting functions. To regain access to fluctuations, we study in this paper a minimal mesoscopic model whose goal is to elucidate the origin of scale free behavior in plasticity. We limit our description to fcc type crystals and leave out both temperature and rate effects. We provide simple illustrations of the fact that complexity in rate independent athermal plastic flows is due to marginal stability of the underlying elastic system. Our conclusions are based on a reduction of an over-damped visco-elasticity problem for a system with a rugged elastic energy landscape to an integer valued automaton. We start with an overdamped one dimensional model and show that it reproduces the main macroscopic phenomenology of rate independent plastic behavior but falls short of generating self similar structure of fluctuations. We then provide evidence that a two dimensional model is already adequate for describing power law statistics of avalanches and fractal character of dislocation patterning. In addition to capturing experimentally measured critical exponents, the proposed minimal model shows finite size scaling collapse and generates realistic shape functions in the scaling laws.Comment: 72 pages, 40 Figures, International Journal of Engineering Science for the special issue in honor of Victor Berdichevsky, 201