Nucleosome-mediated cooperativity between transcription factors

Cooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated cooperativity is mathematically identical to the Monod-Wyman-Changeux (MWC) model of cooperativity in hemoglobin. This surprising parallel provides deep insights, with parallels between heterotropic regulation of hemoglobin (e.g. Bohr effect) and roles of nucleosome-positioning sequences and chromatin modifications in gene regulation. Characterized mechanism is consistent with numerous experimental results, allows substantial flexibility in and modularity of CRRs, and provides a rationale for a broad range of genomic and evolutionary observations. Striking parallels between cooperativity in hemoglobin and in transcription regulation point at a new design principle that may be used in range of biological systems

Statistical-mechanical lattice models for protein-DNA binding in chromatin

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J. Phys.: Cond. Mat

Distributed Cooperative Localization in Wireless Sensor Networks without NLOS Identification

In this paper, a 2-stage robust distributed algorithm is proposed for cooperative sensor network localization using time of arrival (TOA) data without identification of non-line of sight (NLOS) links. In the first stage, to overcome the effect of outliers, a convex relaxation of the Huber loss function is applied so that by using iterative optimization techniques, good estimates of the true sensor locations can be obtained. In the second stage, the original (non-relaxed) Huber cost function is further optimized to obtain refined location estimates based on those obtained in the first stage. In both stages, a simple gradient descent technique is used to carry out the optimization. Through simulations and real data analysis, it is shown that the proposed convex relaxation generally achieves a lower root mean squared error (RMSE) compared to other convex relaxation techniques in the literature. Also by doing the second stage, the position estimates are improved and we can achieve an RMSE close to that of the other distributed algorithms which know \textit{a priori} which links are in NLOS.Comment: Accepted in WPNC 201

Cooperative behavior of quantum dipole emitters coupled to a zero-index nanoscale waveguide

We study cooperative behavior of quantum dipole emitters coupled to a rectangular waveguide with dielectric core and silver cladding. We investigate cooperative emission and inter-emitter entanglement generation phenomena for emitters whose resonant frequencies are near the frequency cutoff of the waveguide, where the waveguide effectively behaves as zero-index metamaterial. We show that coupling emitters to a zero-index waveguide allows one to relax the constraint on precision positioning of emitters for observing inter-emitter entanglement generation and extend the spatial scale at which the superradiance can be observed

An Assessment on the Use of Stationary Vehicles as a Support to Cooperative Positioning

In this paper, we consider the use of stationary vehicles as tools to enhance the localisation capabilities of moving vehicles in a VANET. We examine the idea in terms of its potential benefits, technical requirements, algorithmic design and experimental evaluation. Simulation results are given to illustrate the efficacy of the technique.Comment: This version of the paper is an updated version of the initial submission, where some initial comments of reviewers have been taken into accoun

SOAR (Support Office for Aerogeophysical Research) Annual Report 1994/1995

The Support Office for Aerogeophysical Research (SOAR) was a facility of the National Science Foundation's Office of Polar Programs whose mission is to make airborne geophysical observations available to the broad research community of geology, glaciology and other sciences. The central office of the SOAR facility is located in Austin, Texas within the University of Texas Institute for Geophysics. Other institutions with significant responsibilities are the Lamont­ Doherty Earth Observatory of Columbia University and the Geophysics Branch of the U.S . Geological Survey. This report summarizes the goals and accomplishments of the SOAR facility during 1994/1995 and plans for the next year.National Science Foundation's Office of Polar ProgramsInstitute for Geophysic

WiFi-based PCL for monitoring private airfields

In this article, the potential exploitation of WiFi-based PCL systems is investigated with reference to a real-world civil application in which these sensors are expected to nicely complement the existing technologies adopted for monitoring purposes, especially when operating against noncooperative targets. In particular, we consider the monitoring application of small private airstrips or airfields. With this terminology, we refer to open areas designated for the takeoff and landing of small aircrafts that, unlike an airport, have generally short and possibly unpaved runways (e.g., grass, dirt, sand, or gravel surfaces) and do not necessarily have terminals. More important, such areas usually are devoid of conventional technologies, equipment, or procedures adopted to guarantee safety and security in large aerodromes.There exist a huge number of small, privately owned, and unlicensed airfields around the world. Private aircraft owners mainly use these “airports” for recreational, single-person, or private flights for small groups and training flight purposes. In addition, residential airparks have proliferated in recent years, especially inthe United States, Canada, and South Africa. A residential airpark, or “fly-in community,” features common airstrips where homes with attached hangars allow owners to taxi from their hangar to a shared runway. In many cases, roads are dual use for both cars and planes.In such scenarios, the possibility to employ low-cost, compact, nonintrusive, and nontransmitting sensors as a way to improve safety and security with limited impact on the airstrips' users would be of great potential interest. To this purpose, WiFi-based passive radar sensors appear to be good candidates [23]. Therefore, we investigate their application against typical operative conditions experienced in the scenarios described earlier. The aim is to assess the capability to detect, localize, and track authorized and unauthorized targets that can be occupying the runway and the surrounding areas