A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes

The study of eukaryotic gene transcription depends on methods to discover distal cis-acting control sequences. Comparative bioinformatics is one powerful strategy to reveal these domains, but still requires conventional wet-bench techniques to elucidate their specificity and function. The DNase I hypersensitivity assay (DHA) is also a method to identify regulatory domains, but can also suggest their function. Technically however, the classical DHA is constrained to mapping gene loci in small increments of ∼20 kb. This limitation hinders efficient and comprehensive analysis of distal gene regions. Here, we report an improved method termed mega-DHA that extends the range of existing DHAs to facilitate assaying intervals that approach 100 kb. We demonstrate its feasibility for efficient analysis of single-copy genes within a large and complex genome by assaying 230 kb of the human ADAMTS14-perforin-paladin gene cluster in four experiments. The results identify distinct networks of regulatory domains specific to expression of perforin and its two neighboring genes

Neuronal morphologies built for reliable physiology in a rhythmic motor circuit

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in eLife 8 (2019): e41728. doi: 10.7554/eLife.41728.It is often assumed that highly-branched neuronal structures perform compartmentalized computations. However, previously we showed that the Gastric Mill (GM) neuron in the crustacean stomatogastric ganglion (STG) operates like a single electrotonic compartment, despite having thousands of branch points and total cable length >10 mm (Otopalik et al., 2017a; 2017b). Here we show that compact electrotonic architecture is generalizable to other STG neuron types, and that these neurons present direction-insensitive, linear voltage integration, suggesting they pool synaptic inputs across their neuronal structures. We also show, using simulations of 720 cable models spanning a broad range of geometries and passive properties, that compact electrotonus, linear integration, and directional insensitivity in STG neurons arise from their neurite geometries (diameters tapering from 10-20 µm to < 2 µm at their terminal tips). A broad parameter search reveals multiple morphological and biophysical solutions for achieving different degrees of passive electrotonic decrement and computational strategies in the absence of active properties.We thank Jennifer Bestman for assistance in spinning disk and confocal microscopy; the Marine Resources Center at the Marine Biological Laboratories for acquiring and maintaining animals; Louie Kerr at the Central Microscopy Facility; Dana Mock-Munoz de Luna for administrative support; Kam-ran Kodhakhah, Heather Rhodes, and the 2017 Grass Fellows for their support and feedback; and lastly, Edward Dougherty at the Brandeis University Confocal Imaging Lab for support and microscope maintenance. This study was funded by the Grass Foundation and NINDS awards to F31NS092126 to AO and R35NS097343 to EM

Athletic training students in the college/ university setting and the scope of clinical education

Context: Athletic training education programs must provide the proper type and amount of clinical supervision in order for athletic training students to obtain appropriate clinical education and to meet Board of Certification examination requirements. Objective: To assess athletic training students' perceptions of the type and amount of clinical supervision received during clinical education. Design: Cross-sectional design. Setting: 124 CAAHEP-accredited NCAA institutions. Patients or other participants: We obtained a national stratified random sample (by National Athletic Trainers' Association district) of undergraduate athletic training students from 61 Commission on Accreditation of Allied Health Education Programs-accredited athletic training education programs. A total of 851 athletic training students participated in the study. Main outcome measure(s): Differences among athletic training students with first-aider/provider qualifications, student supervision during moderate-risk and increased-risk sports, program/institutional characteristics, type and amount of clinical supervision, and students' academic level and mean percentage of time spent in different types of clinical supervision. Results: A total of 276 (32.4%) of the students reported that they supplied medical care and athletic training-related coverage beyond that of a first aider/provider. Athletic training students stating that they traveled with teams without supervision numbered 342 (40.2%). A significant difference was noted between the amount of supervision reported by sophomore and senior students ( P < .01). Conclusions: Athletic training students do not seem to be receiving appropriate clinical supervision and are often acting outside the scope of clinical education

A prototypical model for tensional wrinkling in thin sheets

The buckling and wrinkling of thin films has recently seen a surge of interest among physicists, biologists, mathematicians and engineers. This has been triggered by the growing interest in developing technologies at ever decreasing scales and the resulting necessity to control the mechanics of tiny structures, as well as by the realization that morphogenetic processes, such as the tissue-shaping instabilities occurring in animal epithelia or plant leaves, often emerge from mechanical instabilities of cell sheets. While the most basic buckling instability of uniaxially compressed plates was understood by Euler more than 200 years ago, recent experiments on nanometrically thin (ultrathin) films have shown significant deviations from predictions of standard buckling theory. Motivated by this puzzle, we introduce here a theoretical model that allows for a systematic analysis of wrinkling in sheets far from their instability threshold. We focus on the simplest extension of Euler buckling that exhibits wrinkles of finite length - a sheet under axisymmetric tensile loads. This geometry, whose first study is attributed to Lam´e, allows us to construct\ud a phase diagram that demonstrates the dramatic variation of wrinkling patterns from near-threshold to far-from-threshold conditions. Theoretical arguments and comparison to experiments show that for thin sheets the far-from-threshold regime is expected to emerge under extremely small compressive loads, emphasizing the relevance of our analysis for nanomechanics applications

Variational Two Fermion Wave Equations in QED: Muonium Like Systems

We consider a reformulation of QED in which covariant Green functions are used to solve for the electromagnetic field in terms of the fermion fields. The resulting modified Hamiltonian contains the photon propagator directly. A simple Fock-state variational trial function is used to derive relativistic two-fermion equations variationally from the expectation value of the Hamiltonian of the field theory. The interaction kernel of the equation is shown to be, in essence, the invariant M-matrix in lowest order. Solutions of the two-body equations are presented for muonium like system for small coupling strengths. The results compare well with the observed muonium spectrum, as well as that for hydrogen and muonic hydrogen. Anomalous magnetic moment effects are discussed

Runx3 and T-box proteins cooperate to establish the transcriptional program of effector CTLs

Activation of naive CD8+ T cells with antigen induces their differentiation into effector cytolytic T lymphocytes (CTLs). CTLs lyse infected or aberrant target cells by exocytosis of lytic granules containing the pore-forming protein perforin and a family of proteases termed granzymes. We show that effector CTL differentiation occurs in two sequential phases in vitro, characterized by early induction of T-bet and late induction of Eomesodermin (Eomes), T-box transcription factors that regulate the early and late phases of interferon (IFN) γ expression, respectively. In addition, we demonstrate a critical role for the transcription factor Runx3 in CTL differentiation. Runx3 regulates Eomes expression as well as expression of three cardinal markers of the effector CTL program: IFN-γ, perforin, and granzyme B. Our data point to the existence of an elaborate transcriptional network in which Runx3 initially induces and then cooperates with T-box transcription factors to regulate gene transcription in differentiating CTLs

Viscoelastic response of contractile filament bundles

The actin cytoskeleton of adherent tissue cells often condenses into filament bundles contracted by myosin motors, so-called stress fibers, which play a crucial role in the mechanical interaction of cells with their environment. Stress fibers are usually attached to their environment at the endpoints, but possibly also along their whole length. We introduce a theoretical model for such contractile filament bundles which combines passive viscoelasticity with active contractility. The model equations are solved analytically for two different types of boundary conditions. A free boundary corresponds to stress fiber contraction dynamics after laser surgery and results in good agreement with experimental data. Imposing cyclic varying boundary forces allows us to calculate the complex modulus of a single stress fiber.Comment: Revtex with 24 pages, 7 Postscript figures included, accepted for publication in Phys. Rev.