Optimizing information flow in small genetic networks. I

In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable randomness of individual molecular events. Here we explore how cells can maximize their control power in the presence of these physical limits; formally, we solve the theoretical problem of maximizing the information transferred from inputs to outputs when the number of available molecules is held fixed. We start with the simplest version of the problem, in which a single transcription factor protein controls the readout of one or more genes by binding to DNA. We further simplify by assuming that this regulatory network operates in steady state, that the noise is small relative to the available dynamic range, and that the target genes do not interact. Even in this simple limit, we find a surprisingly rich set of optimal solutions. Importantly, for each locally optimal regulatory network, all parameters are determined once the physical constraints on the number of available molecules are specified. Although we are solving an over--simplified version of the problem facing real cells, we see parallels between the structure of these optimal solutions and the behavior of actual genetic regulatory networks. Subsequent papers will discuss more complete versions of the problem

Optimizing information flow in small genetic networks. II: Feed forward interactions

Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes. As the concentration of the transcription factor varies, the target genes thus undergo correlated changes, and this redundancy limits the ability of the cell to transmit information about input signals. We explore how interactions among the target genes can reduce this redundancy and optimize information transmission. Our discussion builds on recent work [Tkacik et al, Phys Rev E 80, 031920 (2009)], and there are connections to much earlier work on the role of lateral inhibition in enhancing the efficiency of information transmission in neural circuits; for simplicity we consider here the case where the interactions have a feed forward structure, with no loops. Even with this limitation, the networks that optimize information transmission have a structure reminiscent of the networks found in real biological systems

Creating a Culture of Voting in Direct and Generalist Practice: Training Field Instructors

Social workers have an ethical responsibility to be engaged in policy change, regardless of their practice area or specialization. Voter engagement and the importance of political power through voting is often overlooked in the literature as a valid and important component of social work practice. Creating a culture of nonpartisan voter engagement in practice settings can help empower individuals who have been historically and intentionally disenfranchised from our electoral system. Training for field instructors, faculty, and field staff is a key aspect of voter engagement in social work education. Unfortunately, social work education is unlikely to include substantive content on voter engagement or its connection to social work practice and impact. This article presents one component of a model for integrating voter engagement into social work education: the provision of training for field instructors on nonpartisan voter engagement at two universities over two years. Evaluation findings suggest that pre-existing levels of political efficacy affect the reaction of field instructors to nonpartisan voter engagement training. Furthermore, findings indicate that field instructors who receive voter engagement training are more likely to serve as resources for their students and to consider voter engagement as part of their own practice. We offer evidence on the important role field educators can play in the success of the larger national effort to integrate voter engagement in social work education. Increasing awareness of what social workers, nonprofit, and public agencies are allowed--or even required--to do is a critical first step

Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states

Jaynes' information theory formalism of statistical mechanics is applied to the stationary states of open, non-equilibrium systems. The key result is the construction of the probability distribution for the underlying microscopic phase space trajectories. Three consequences of this result are then derived : the fluctuation theorem, the principle of maximum entropy production, and the emergence of self-organized criticality for flux-driven systems in the slowly-driven limit. The accumulating empirical evidence for these results lends support to Jaynes' formalism as a common predictive framework for equilibrium and non-equilibrium statistical mechanics.Comment: 21 pages, 0 figures, minor modifications, version to appear in J. Phys. A. (2003

Sleep apnea predicts distinct alterations in glucose homeostasis and biomarkers in obese adults with normal and impaired glucose metabolism

<p>Abstract</p> <p>Background</p> <p>Notwithstanding previous studies supporting independent associations between obstructive sleep apnea (OSA) and prevalence of diabetes, the underlying pathogenesis of impaired glucose regulation in OSA remains unclear. We explored mechanisms linking OSA with prediabetes/diabetes and associated biomarker profiles. We hypothesized that OSA is associated with distinct alterations in glucose homeostasis and biomarker profiles in subjects with normal (NGM) and impaired glucose metabolism (IGM).</p> <p>Methods</p> <p>Forty-five severely obese adults (36 women) without certain comorbidities/medications underwent anthropometric measurements, polysomnography, and blood tests. We measured fasting serum glucose, insulin, selected cytokines, and calculated homeostasis model assessment estimates of insulin sensitivity (HOMA-IS) and pancreatic beta-cell function (HOMA-B).</p> <p>Results</p> <p>Both increases in apnea-hypopnea index (AHI) and the presence of prediabetes/diabetes were associated with reductions in HOMA-IS in the entire cohort even after adjustment for sex, race, age, and BMI (<it>P </it>= 0.003). In subjects with NGM (n = 30), OSA severity was associated with significantly increased HOMA-B (a trend towards decreased HOMA-IS) independent of sex and adiposity. OSA-related oxyhemoglobin desaturations correlated with TNF-α (r=-0.76; <it>P </it>= 0.001) in women with NGM and with IL-6 (rho=-0.55; <it>P </it>= 0.035) in women with IGM (n = 15) matched individually for age, adiposity, and AHI.</p> <p>Conclusions</p> <p>OSA is independently associated with altered glucose homeostasis and increased basal beta-cell function in severely obese adults with NGM. The findings suggest that moderate to severe OSA imposes an excessive functional demand on pancreatic beta-cells, which may lead to their exhaustion and impaired secretory capacity over time. The two distinct biomarker profiles linking sleep apnea with NGM and IGM via TNF-α and IL-6 have been discerned in our study to suggest that sleep apnea and particularly nocturnal oxyhemoglobin desaturations are associated with chronic metabolic fluxes and specific cytokine stressors that reflect links between sleep apnea and glucose metabolism. The study may help illuminate potential mechanisms for glucose dysregulation in OSA, and resolve some controversy over the associations of OSA with TNF-α and IL-6 in previous studies.</p

Novel Methodology for Creating Macaque Retinas with Sortable Photoreceptors and Ganglion Cells

Purpose: The ability to generate macaque retinas with sortable cell populations would be of great benefit to both basic and translational studies of the primate retina. The purpose of our study was therefore to develop methods to achieve this goal by selectively labeling, in life, photoreceptors (PRs) and retinal ganglion cells (RGCs) with separate fluorescent markers. Methods: Labeling of macaque (Macaca fascicularis) PRs and RGCs was accomplished by subretinal delivery of AAV5-hGRK1-GFP, and retrograde transport of micro-ruby™ from the lateral geniculate nucleus, respectively. Retinas were anatomically separated into different regions. Dissociation conditions were optimized, and cells from each region underwent fluorescent activated cell sorting (FACS). Expression of retinal cell type- specific genes was assessed by quantitative real-time PCR to characterize isolated cell populations. Results: We show that macaque PRs and RGCs can be simultaneously labeled in-life and enriched populations isolated by FACS. Recovery from different retinal regions indicated efficient isolation/enrichment for PRs and RGCs, with the macula being particularly amendable to this technique. Conclusions: The methods and materials presented here allow for the identification of novel reagents designed to target retinal ganglion cells and/or photoreceptors in a species that is phylogenetically and anatomically similar to human. These techniques will enable screening of intravitreally- delivered AAV capsid libraries for variants with increased tropism for PRs and/or RGCs and the evaluation of vector tropism and/or cellular promoter activity of gene therapy vectors in a clinically relevant species

Implementing a rapid fetal exome sequencing service: What do parents and health professionals think?

OBJECTIVES: Prenatal exome sequencing (pES) for the diagnosis of fetal abnormalities is being introduced more widely in clinical practice. Here we explore parents' and professionals' views and experiences of pES, to identify perceived benefits, concerns, and support needs. METHODS: Semi-structured interviews were conducted with 11 parents and 20 health professionals (fetal medicine and clinical genetics) with experience of rapid pES prior to implementation in the English National Health Service. Interviews were transcribed verbatim and analysed thematically. RESULTS: Parents and professionals were largely positive about pES, emphasising clinical and psychosocial benefits of a timely, definitive diagnosis in pregnancy. Concerns included parental anxiety related to the timing of pES results or uncertain findings, a need for guidelines for case selection and reporting, and ensuring sufficient capacity for counselling, phenotyping and variant interpretation. Professionals were concerned non-genetics professionals may not be equipped to counsel parents on the complexities of pES. CONCLUSION: These findings highlight important issues for clinical implementation of pES. Expert counselling is required to enable parents to make informed decisions during a stressful time. To achieve this, professionals need further education and training, and fetal medicine and genetics services must work closely together to ensure parental understanding and appropriate support

First-principles study of (BiScO3){1-x}-(PbTiO3){x} piezoelectric alloys

We report a first-principles study of a class of (BiScO3)_{1-x}-(PbTiO3)_x (BS-PT) alloys recently proposed by Eitel et al. as promising materials for piezoelectric actuator applications. We show that (i) BS-PT displays very large structural distortions and polarizations at the morphotropic phase boundary (MPB) (we obtain a c/a of ~1.05-1.08 and P_tet of ~1.1 C/m^2); (ii) the ferroelectric and piezoelectric properties of BS-PT are dominated by the onset of hybridization between Bi/Pb-6p and O-2p orbitals, a mechanism that is enhanced upon substitution of Pb by Bi; and (iii) the piezoelectric responses of BS-PT and Pb(Zr_{1-x}Ti_x)O3 (PZT) at the MPB are comparable, at least as far as the computed values of the piezoelectric coefficient d_15 are concerned. While our results are generally consistent with experiment, they also suggest that certain intrinsic properties of BS-PT may be even better than has been indicated by experiments to date. We also discuss results for PZT that demonstrate the prominent role played by Pb displacements in its piezoelectric properties.Comment: 6 pages, with 3 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/ji_bi/index.htm

Invasive Species Terminology: Standardizing for Stakeholder Education

The excessive number of terms associated with invasive species, and their often incorrect usage, hinders stakeholder education about the threats of invasive species. Here we introduce seven terms (native, nonnative, introduced, established, invasive, nuisance, and range change) that are applicable across invasive taxa, understandable, typically interpreted correctly, and useful for describing most situations regarding invasive species. We also list six terms to avoid (native invasive, invasive exotic, invasive weed, alien, foreign, and nonindigenous) that create confusion via their misuse and misinterpretation. The terms we propose will increase understanding, thereby promoting behavior changes aimed at limiting the negative impacts of invasive species