Distributed classifier based on genetically engineered bacterial cell cultures

We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a master population of cells with randomized synthetic biosensor circuits that have a broad range of sensitivities towards chemical signals of interest that form the input vectors subject to classification. The randomized sensitivities are achieved by constructing a library of synthetic gene circuits with randomized control sequences (e.g. ribosome-binding sites) in the front element. The training procedure consists in re-shaping of the master population in such a way that it collectively responds to the "positive" patterns of input signals by producing above-threshold output (e.g. fluorescent signal), and below-threshold output in case of the "negative" patterns. The population re-shaping is achieved by presenting sequential examples and pruning the population using either graded selection/counterselection or by fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of experimental implementation of such system computationally using a realistic model of the synthetic sensing gene circuits.Comment: 31 pages, 9 figure

Anapole Moment and Other Constraints on the Strangeness Conserving Hadronic Weak Interaction

Standard analyses of low-energy NN and nuclear parity-violating observables have been based on a pi-, rho-, and omega-exchange model capable of describing all five independent s-p partial waves. Here a parallel analysis is performed for the one-body, exchange-current, and nuclear polarization contributions to the anapole moments of 133Cs and 205Tl. The resulting constraints are not consistent, though there remains some degree of uncertainty in the nuclear structure analysis of the atomic moments.Comment: Revtex, 10 pages, 1 figur

Monomeric Bistability and the Role of Autoloops in Gene Regulation

Genetic toggle switches are widespread in gene regulatory networks (GRN). Bistability, namely the ability to choose among two different stable states, is an essential feature of switching and memory devices. Cells have many regulatory circuits able to provide bistability that endow a cell with efficient and reliable switching between different physiological modes of operation. It is often assumed that negative feedbacks with cooperative binding (i.e. the formation of dimers or multimers) are a prerequisite for bistability. Here we analyze the relation between bistability in GRN under monomeric regulation and the role of autoloops under a deterministic setting. Using a simple geometric argument, we show analytically that bistability can also emerge without multimeric regulation, provided that at least one regulatory autoloop is present

Pertambangan di Kawasan Konservasi: Permasalahan Regulasi dan Koordinasi

Informasi dan klaim tentang berlangsungnya kegiatan pertambangan di hutan konservasi dapat dengan mudah kita jumpai. Salah satunya, Komisi Pemberantasan Korupsi (KPK) dalam presentasi tentang koordinasi dan supervisi pengelolaan mineral dan batu bara di 19 provinsi pada akhir 2014, menyatakan bahwa izin pertambangan di kawasan hutan konservasi mencapai 1,37 juta hektar (KPK, 2014)

Comments on Non-Commutative Phenomenology

It is natural to ask whether non-commutative geometry plays a role in four dimensional physics. By performing explicit computations in various toy models, we show that quantum effects lead to violations of Lorentz invariance at the level of operators of dimension three or four. The resulting constraints are very stringent.Comment: Correction of an error in the U(1) and U(N) calculation leads to stronger limits than those given previously Clarifying comments and reference adde

Dynamically Driven Renormalization Group Applied to Sandpile Models

The general framework for the renormalization group analysis of self-organized critical sandpile models is formulated. The usual real space renormalization scheme for lattice models when applied to nonequilibrium dynamical models must be supplemented by feedback relations coming from the stationarity conditions. On the basis of these ideas the Dynamically Driven Renormalization Group is applied to describe the boundary and bulk critical behavior of sandpile models. A detailed description of the branching nature of sandpile avalanches is given in terms of the generating functions of the underlying branching process.Comment: 18 RevTeX pages, 5 figure

The Off-diagonal Goldberger-Treiman Relation and Its Discrepancy

We study the off-diagonal Goldberger-Treiman relation (ODGTR) and its discrepancy (ODGTD) in the N, Delta, pi sector through O(p^2) using heavy baryon chiral perturbation theory. To this order, the ODGTD and axial vector N to Delta transition radius are determined solely by low energy constants. Loop corrections appear at O(p^4). For low-energy constants of natural size, the ODGTD would represent a ~ 2% correction to the ODGTR. We discuss the implications of the ODGTR and ODGTD for lattice and quark model calculations of the transition form factors and for parity-violating electroexcitation of the Delta.Comment: 11 pages, 1 eps figur

Boolean network model predicts cell cycle sequence of fission yeast

A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully reproduces the known sequence of regulatory activity patterns along the cell cycle of the living cell. Contrary to existing differential equation models, no parameters enter the model except the structure of the regulatory circuitry. The dynamical properties of the model indicate that the biological dynamical sequence is robustly implemented in the regulatory network, with the biological stationary state G1 corresponding to the dominant attractor in state space, and with the biological regulatory sequence being a strongly attractive trajectory. Comparing the fission yeast cell-cycle model to a similar model of the corresponding network in S. cerevisiae, a remarkable difference in circuitry, as well as dynamics is observed. While the latter operates in a strongly damped mode, driven by external excitation, the S. pombe network represents an auto-excited system with external damping.Comment: 10 pages, 3 figure

Parity-Violating Interaction Effects I: the Longitudinal Asymmetry in pp Elastic Scattering

The proton-proton parity-violating longitudinal asymmetry is calculated in the lab-energy range 0--350 MeV, using a number of different, latest-generation strong-interaction potentials--Argonne V18, Bonn-2000, and Nijmegen-I--in combination with a weak-interaction potential consisting of rho- and omega-meson exchanges--the model known as DDH. The complete scattering problem in the presence of parity-conserving, including Coulomb, and parity-violating potentials is solved in both configuration- and momentum-space. The predicted parity-violating asymmetries are found to be only weakly dependent upon the input strong-interaction potential adopted in the calculation. Values for the rho- and omega-meson weak coupling constants $h^{pp}_\rho$ and $h^{pp}_\omega$ are determined by reproducing the measured asymmetries at 13.6 MeV, 45 MeV, and 221 MeV.Comment: 24 pages, 8 figures, submitted to Physical Review

Gateway vectors for efficient artificial gene assembly in vitro and expression in yeast Saccharomyces cerevisiae

Peer reviewedPublisher PD