Low cost production of 3D-printed devices and electrostimulation chambers for the culture of primary neurons
Contributors: Joanna D. Wardyn, Chris Sanderson, Laura E. Swan, Massimiliano Stagi
... The analysis of primary neurons is a basic requirement for many areas of neurobiology. However, the range of commercial systems available for culturing primary neurons is functionally limiting, and the expense of these devices is a barrier to both exploratory and large-scale studies. This is especially relevant as primary neurons often require unusual geometries and specialised coatings for optimum growth. Fortunately, the recent revolution in 3D printing offers the possibility to generate customised devices, which can support neuronal growth and constrain neurons in defined paths, thereby enabling many aspects of neuronal physiology to be studied with relative ease. In this article, we provide a detailed description of the system hardware and software required to produce affordable 3D-printed culture devices, which are also compatible with live-cell imaging. In addition, we also describe how to use these devices to grow and stimulate neurons within geometrically constrained compartments and provide examples to illustrate the practical utility and potential that these protocols offer for many aspects of experimental neurobiology.
Contributors: Kelly S. Subramanian, Rose C. Dziedzic, Hallie N. Nelson, Mary E. Stern, Vincent R. Roggero, Cornelius Bondzi, Lizabeth A. Allison
... The thyroid hormone receptor (TR) undergoes nucleocytoplasmic shuttling and regulates target genes involved in metabolism and development. Previously, we showed that TR follows a CRM1/calreticulin-mediated nuclear export pathway. However, two lines of evidence suggest TR also follows another pathway: export is only partially blocked by leptomycin B (LMB), a CRM1-specific inhibitor; and we identified nuclear export signals in TR that are LMB-resistant. To determine whether other exportins are involved in TR shuttling, we used RNA interference and fluorescence recovery after photobleaching shuttling assays in transfected cells. Knockdown of exportins 4, 5, and 7 altered TR shuttling dynamics, and when exportins 5 and 7 were overexpressed, TR distribution shifted toward the cytosol. To further assess the effects of exportin overexpression, we examined transactivation of a TR-responsive reporter gene. Our data indicate that multiple exportins influence TR localization, highlighting a fine balance of nuclear import, retention, and export that modulates TR function.
Contributors: Anastasiia Aleksandrova, Andras Czirok, Edina Kosa, Oleksandr Galkin, Tracey J. Cheuvront, Brenda J. Rongish
... Formation of the muscular layer of the heart, the myocardium, involves the medial movement of bilateral progenitor fields; driven primarily by shortening of the endoderm during foregut formation. Using a combination of time-lapse imaging, microsurgical perturbations and computational modeling, we show that the speed of the medial-ward movement of the myocardial progenitors is similar, but not identical to that of the adjacent endoderm. Further, the extracellular matrix microenvironment separating the two germ layers also moves with the myocardium, indicating that collective tissue motion and not cell migration drives tubular heart assembly. Importantly, as myocardial cells approach the midline, they perform distinct anterior-directed movements relative to the endoderm. Based on the analysis of microincision experiments and computational models, we propose two characteristic, autonomous morphogenetic activities within the early myocardium: 1) an active contraction of the medial portion of the heart field and 2) curling- the tendency of the unconstrained myocardial tissue to form a spherical surface with a concave ventral side. In the intact embryo, these deformations are constrained by the endoderm and the adjacent mesoderm, nevertheless the corresponding mechanical stresses contribute to the proper positioning of myocardial primordia.
Contributors: Jihyun Irizarry, Angelike Stathopoulos
... The thisbe (ths) gene encodes a Drosophila fibroblast growth factor (FGF), and mutant females are viable but sterile suggesting a link between FGF signaling and fertility. Ovaries exhibit abnormal morphology including lack of epithelial sheaths and muscle tissues that surround ovarioles. Here we investigated how FGF influences Drosophila ovary morphogenesis and identified several roles. Heartless (Htl) FGF receptor was found to be expressed within somatic cells at the larval and pupal stages, and phenotypes were uncovered using RNAi. Differentiation of terminal filament cells was affected, but this effect did not alter the ovariole number. In addition, proliferation of epithelial sheath progenitors, the apical cells, was decreased in both htl and ths mutants, while ectopic expression of the Ths ligand led to these cells' over-proliferation suggesting that FGF signaling supports ovarian muscle sheath formation by controlling apical cell number in the developing gonad. Additionally, live imaging of adult ovaries was used to show that htl RNAi mutants, hypomorphic mutants in which epithelial sheaths are present, exhibit abnormal muscle contractions. Collectively, our results demonstrate that proper formation of ovarian muscle tissues is regulated by FGF signaling in the larval and pupal stages through control of apical cell proliferation and is required to support fertility.
Genome-wide analysis of the zebrafish Klf family identifies two genes important for erythroid maturation
Contributors: Yuanyuan Xue, Shuai Gao, Feng Liu
... Krüppel-like transcription factors (Klfs), each of which contains a CACCC-box binding domain, have been investigated in a variety of developmental processes, such as angiogenesis, neurogenesis and somatic-cell reprogramming. However, the function and molecular mechanism by which the Klf family acts during developmental hematopoiesis remain elusive. Here, we report identification of 24 Klf family genes in zebrafish using bioinformatics. Gene expression profiling shows that 6 of these genes are expressed in blood and/or vascular endothelial cells during embryogenesis. Loss of function of 2 factors (klf3 or klf6a) leads to a decreased number of mature erythrocytes. Molecular studies indicate that both Klf3 and Klf6a are essential for erythroid cell differentiation and maturation but that these two proteins function in distinct manners. We find that Klf3 inhibits the expression of ferric-chelate reductase 1b (frrs1b), thereby promoting the maturation of erythroid cells, whereas Klf6a controls the erythroid cell cycle by negatively regulating cdkn1a expression to determine the rate of red blood cell proliferation. Taken together, our study provides a global view of the Klf family members that contribute to hematopoiesis in zebrafish and sheds new light on the function and molecular mechanism by which Klf3 and Klf6a act during erythropoiesis in vertebrates.
Resource - Automated Identification and Localization of Hematopoietic Stem Cells in 3D Intravital Microscopy Data
Contributors: Reema A. Khorshed, Edwin D. Hawkins, Delfim Duarte, Mark K. Scott, Olufolake A. Akinduro, Narges M. Rashidi, Martin Spitaler, Cristina Lo Celso
... Measuring three-dimensional (3D) localization of hematopoietic stem cells (HSCs) within the bone marrow microenvironment using intravital microscopy is a rapidly expanding research theme. This approach holds the key to understanding the detail of HSC-niche interactions, which are critical for appropriate stem cell function. Due to the complex tissue architecture of the bone marrow and to the progressive introduction of scattering and signal loss at increasing imaging depths, there is no ready-made software to handle efficient segmentation and unbiased analysis of the data. To address this, we developed an automated image analysis tool that simplifies and standardizes the biological interpretation of 3D HSC microenvironment images. The algorithm identifies HSCs and measures their localization relative to surrounding osteoblast cells and bone collagen. We demonstrate here the effectiveness, consistency, and accuracy of the proposed approach compared to current manual analysis and its wider applicability to analyze other 3D bone marrow components.
Macrophages engulf endothelial cell membrane particles preceding pupillary membrane capillary regression
Contributors: Ross A. Poché, Chih-Wei Hsu, Melissa L. McElwee, Alan R. Burns, Mary E. Dickinson
... Programmed capillary regression and remodeling are essential developmental processes. However, the cellular and molecular mechanisms that regulate vessel regression are only the beginning to be understood. Here, using in vivo, dynamic, confocal imaging of mouse transgenic reporters as well as static confocal and electron microscopy, we studied the embryonic development and postnatal regression of the transient mouse pupillary membrane (PM) vasculature. This approach allowed us to directly observe the precise temporal sequence of cellular events preceding and during the elimination of the PM from the mouse eye. Imaging of Tcf/Lef-H2B::GFP Wnt-reporter mice uncovered that, unlike the hyaloid vasculature of the posterior eye, a PM endothelial cell (EC) Wnt/β-catenin response is unlikely to be part of the regression mechanism. Live imaging of EC and macrophage dynamics revealed highly active Csf1r-GFP+ macrophages making direct contact with the Flk1-myr::mCherry+ vessel surface and with membrane protrusions or filopodia extending from the ECs. Flk1-myr::mCherry+ EC membrane particles were observed on and around ECs as well as within macrophages. Electron microscopy studies confirmed that they were in phagosomes within macrophages, indicating that the macrophages engulfed the membrane particles. Interestingly, EC plasma membrane uptake by PM macrophages did not correlate with apoptosis and was found shortly after vessel formation at mid-gestation stages in the embryo; long before vessel regression begins during postnatal development. Additionally, genetic ablation of macrophages showed that EC membrane particles were still shed in the absence of macrophages suggesting that macrophages do not induce the formation or release of EC microparticles. These studies have uncovered a novel event during programmed capillary regression in which resident macrophages scavenge endothelial cell microparticles released from the PM vessels. This finding suggests that there may be an initial disruption in vessel homeostasis embryonically as the PM forms that may underlie its ultimate regression postnatally.
Case report - 50 years to diagnosis: Autosomal dominant tubular aggregate myopathy caused by a novel STIM1 mutation
Contributors: Maggie C. Walter, Martina Rossius, Manuela Zitzelsberger, Matthias Vorgerd, Wolfgang Müller-Felber, Birgit Ertl-Wagner, Yaxin Zhang, Heinrich Brinkmeier, Jan Senderek, Benedikt Schoser
... Tubular aggregates in human muscle biopsies have been reported to occur in a variety of acquired and hereditary neuromuscular conditions since 1964. Recently mutations in the gene encoding the main calcium sensor in the sarcoplasmic reticulum, stromal interaction molecule 1 (STIM1), have been identified as a cause of autosomal dominant tubular aggregate myopathy. We studied a German family with tubular aggregate myopathy and defined cellular consequences of altered STIM1 function. Both patients in our family had early progressive myopathy with proximal paresis of arm and leg muscles, scapular winging, ventilatory failure, joint contractures and external ophthalmoplegia. One patient had a well-documented disease course over 50 years. Sequencing of the STIM1 gene revealed a previously unreported missense mutation (c.242G>A; p.Gly81Asp) located in the first calcium binding EF domain. Functional characterization of the new STIM1 mutation by calcium imaging revealed that calcium influx was significantly increased in primary myoblasts of the index patient compared to controls pointing at a severe alteration of intracellular calcium homeostasis. This new family widens the spectrum of STIM1-associated myopathies to a more severe phenotype.
OpenCL parallel integration of ordinary differential equations: Applications in computational dynamics
Contributors: Marcos Rodríguez, Fernando Blesa, Roberto Barrio
... In many physical problems the use of numerical simulations presents the only path to obtain insight into the behavior and evolution of the system of interest. GPU, CPU and MIC technologies are frequently employed for simulations on computational dynamics and we present results comparing different schemes for the numerical integration of ordinary differential systems (ODEs) in these architectures. The use of adapted methods with low memory storage (Low storage Runge–Kutta methods) gives good results for low precision studies, whereas the Taylor series method provides a powerful technique for high precision. We show how the computation of several dynamics indicators, such as a fast chaos indicator (FLI) or a phase shift indicator in small neuron networks (Central Pattern Generators), can be efficiently computed on these architectures by means of the numerical ODE methods executed through OpenCL. This high computational time reduction allows real-time simulations or generating video media.
Hydrogen oxidation reaction on Pd(111) electrode in alkaline media: Ab-initio DFT study of OH effects
Contributors: Javed Mazher, Faisal A. Al-Odail
... OH effects on the hydrogen oxidation reaction, during a metallic surface electrocatalysis, have been studied by using density functional theory (DFT) based first principles methods. The hydrogen reaction is carried out on Pd(111) surface with the help of Tafel’s hydrogen adsorption and Volmer’s alkaline reactions. Both the reactions are investigated in detail by performing Broyden–Fletcher–Goldfarb–Shanno (BFGS) type structural relaxation analysis. Relative changes in structural free energies, hydrogen adsorption, water formation parameters and electronic structure of atomic orbitals corresponding to the palladium surface and adsorbent atoms are studied during the reaction. A significant change in local density of states of s-, p-, and d-band states of the involved entities is obtained in respect to before- and after-water-formation circumstances. Spectral variations in the local density of states (LDOS) are discussed vis-à-vis the HOR, hydrogen adsorption and validation of the presence of water.