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https://www.readbyqxmd.com/read/28805224/molecular-dynamics-based-strength-estimates-of-beta-solenoid-proteins
#1
Amanda Parker, Krishnakumar Ravikumar, Daniel Cox
The use of beta solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their mechanical strengths, we can efficiently design the proteins for specific functions. We present a study of the mechanical properties of seven beta solenoid proteins using GROMACS molecular dynamics software to produce force/torque-displacement data, implement umbrella sampling of bending/twisting trajectories, produce Potentials of Mean Force (PMFs), extract effective spring constants, and calculate rigidities for two bending and two twisting directions for each protein...
August 14, 2017: Soft Matter
https://www.readbyqxmd.com/read/28801909/promoter-activation-with-electromagnetism
#2
Abraham O Rodríguez-De la Fuente, J Antonio Heredia-Rojas, Juan M Alcocer-González, Laura E Rodríguez-Flores, Cristina Rodríguez-Padilla, Reyes S Taméz-Guerra
Gene expression can be modified by physical factors, such as heat, electricity and magnetic fields , and several types of ionizing and non-ionizing radiation. Promoter activation with extremely low-frequency electromagnetic fields is possible with an appropriate promoter, containing electromagnetic field response elements. Here, we describe how to examine promoter activation with extremely low-frequency electromagnetic fields, and we provide a step-by-step guide to the assembly of a solenoid suitable for promoter activation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28796645/on-the-use-of-particle-filters-for-electromagnetic-tracking-in-high-dose-rate-brachytherapy
#3
Theresa Ida Götz, Godehard Lahmer, Tobias Brandt, Karoline Kallis, Vratislav Strnad, Christoph Bert, Bernhard Hensel, Ana Maria Tome, Elmar W Lang
Modern radiotherapy of female breat cancers often employ high dose rate Brachytherapy, where a radioactive source is moved inside catheters, implanted in the female breast, according to a prescribed treatment plan. Source localization relative to the patient's anatomy is determined with solenoid sensors whose spatial positions are measured with an electromagnetic tracking system. Precise sensor dwell position determination is of utmost importance to assure irradiation of the cancerous tissue according to the treatment plan...
August 10, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28792846/nanodosimetric-simulation-of-direct-ion-induced-dna-damage-using-different-chromatin-geometry-models
#4
N T Henthorn, J W Warmenhoven, M Sotiropoulos, R I Mackay, K J Kirkby, M J Merchant
Monte Carlo based simulation has proven useful in investigating the effect of proton-induced DNA damage and the processes through which this damage occurs. Clustering of ionizations within a small volume can be related to DNA damage through the principles of nanodosimetry. For simulation, it is standard to construct a small volume of water and determine spatial clusters. More recently, realistic DNA geometries have been used, tracking energy depositions within DNA backbone volumes. Traditionally a chromatin fiber is built within the simulation and identically replicated throughout a cell nucleus, representing the cell in interphase...
August 9, 2017: Radiation Research
https://www.readbyqxmd.com/read/28789542/intracavity-faraday-modulation-spectroscopy-infamos-a-tool-for-radical-detection
#5
Michele Gianella, Tomas H P Pinto, Xia Wu, Grant A D Ritchie
We present the intra-cavity Faraday modulation spectroscopy technique, whereby optical feedback cavity-enhanced spectroscopy is coupled with Faraday modulation spectroscopy to greatly enhance the interaction path length of a laser beam with a paramagnetic sample in a magnetic field. We describe a first prototype based upon a cw quantum cascade laser targeting a selection of fundamental rovibrational R-branch transitions of nitric oxide (1890 cm(-1)), consisting of a linear cavity (finesse F=6300) and a water-cooled solenoid...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28767037/cryo-em-structure-of-the-saga-and-nua4-coactivator-subunit-tra1-at-3-7-angstrom-resolution
#6
Luis Miguel Diaz-Santin, Natasha Lukoyanova, Emir Aciyan, Alan Cm Cheung
Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Saccharomyces cerevsisae Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair...
August 2, 2017: ELife
https://www.readbyqxmd.com/read/28731757/phase-locking-the-spin-precession-in-a-storage-ring
#7
N Hempelmann, V Hejny, J Pretz, E Stephenson, W Augustyniak, Z Bagdasarian, M Bai, L Barion, M Berz, S Chekmenev, G Ciullo, S Dymov, F-J Etzkorn, D Eversmann, M Gaisser, R Gebel, K Grigoryev, D Grzonka, G Guidoboni, T Hanraths, D Heberling, J Hetzel, F Hinder, A Kacharava, V Kamerdzhiev, I Keshelashvili, I Koop, A Kulikov, A Lehrach, P Lenisa, N Lomidze, B Lorentz, P Maanen, G Macharashvili, A Magiera, D Mchedlishvili, S Mey, F Müller, A Nass, N N Nikolaev, A Pesce, D Prasuhn, F Rathmann, M Rosenthal, A Saleev, V Schmidt, Y Semertzidis, V Shmakova, A Silenko, J Slim, H Soltner, A Stahl, R Stassen, H Stockhorst, H Ströher, M Tabidze, G Tagliente, R Talman, P Thörngren Engblom, F Trinkel, Yu Uzikov, Yu Valdau, E Valetov, A Vassiliev, C Weidemann, A Wrońska, P Wüstner, P Zuprański, M Żurek
This Letter reports the successful use of feedback from a spin polarization measurement to the revolution frequency of a 0.97  GeV/c bunched and polarized deuteron beam in the Cooler Synchrotron (COSY) storage ring in order to control both the precession rate (≈121  kHz) and the phase of the horizontal polarization component. Real time synchronization with a radio frequency (rf) solenoid made possible the rotation of the polarization out of the horizontal plane, yielding a demonstration of the feedback method to manipulate the polarization...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28706244/predicting-magnetostimulation-thresholds-in-the-peripheral-nervous-system-using-realistic-body-models
#8
Mathias Davids, Bastien Guérin, Matthias Malzacher, Lothar R Schad, Lawrence L Wald
Rapid switching of applied magnetic fields in the kilohertz frequency range in the human body induces electric fields powerful enough to cause Peripheral Nerve Stimulation (PNS). PNS has become one of the main constraints on the use of high gradient fields for fast imaging with the latest MRI gradient technology. In recent MRI gradients, the applied fields are powerful enough that PNS limits their application in fast imaging sequences like echo-planar imaging. Application of Magnetic Particle Imaging (MPI) to humans is similarly PNS constrained...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28691351/structures-of-designed-armadillo-repeat-proteins-binding-to-peptides-fused-to-globular-domains
#9
Simon Hansen, Jonathan D Kiefer, Chaithanya Madhurantakam, Peer R E Mittl, Andreas Plückthun
Designed armadillo repeat proteins (dArmRP) are α-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D...
July 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28685470/construction-of-0-15-tesla-overhauser-enhanced-mri
#10
Yuumi Tokunaga, Motonao Nakao, Tatsuya Naganuma, Kazuhiro Ichikawa
Overhauser enhanced MRI (OMRI) is one of the free radical imaging technologies and has been used in biomedical research such as for partial oxygen measurements in tumor, and redox status in acute oxidative diseases. The external magnetic field of OMRI is frequently in the range of 5-10 mTesla to ensure microwave penetration into small animals, and the S/N ratio is limited. In this study, a 0.15 Tesla OMRI was constructed and tested to improve the S/N ratio for a small sample, or skin measurement. Specification of the main magnet was as follows: 0...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28673961/understanding-the-molecular-differential-recognition-of-muramyl-peptide-ligands-by-lrr-domains-of-human-nod-receptors
#11
Sukhithasri Vijayrajratnam, Anju Choorakottayil Pushkaran, Aathira Balakrishnan, Anil Kumar Vasudevan, Raja Biswas, Chethampadi Gopi Mohan
Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso-diaminopimelic acid (mesoDAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and the hNOD2-LRR to understand the mechanism of differential recognition of muramyl peptide ligands by hNOD receptors...
July 27, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28663553/functional-and-dynamic-polymerization-of-the-als-linked-protein-tdp-43-antagonizes-its-pathologic-aggregation
#12
Tariq Afroz, Eva-Maria Hock, Patrick Ernst, Chiara Foglieni, Melanie Jambeau, Larissa A B Gilhespy, Florent Laferriere, Zuzanna Maniecka, Andreas Plückthun, Peer Mittl, Paolo Paganetti, Frédéric H T Allain, Magdalini Polymenidou
TDP-43 is a primarily nuclear RNA-binding protein, whose abnormal phosphorylation and cytoplasmic aggregation characterizes affected neurons in patients with amyotrophic lateral sclerosis and frontotemporal dementia. Here, we report that physiological nuclear TDP-43 in mouse and human brain forms homo-oligomers that are resistant to cellular stress. Physiological TDP-43 oligomerization is mediated by its N-terminal domain, which can adopt dynamic, solenoid-like structures, as revealed by a 2.1 Å crystal structure in combination with nuclear magnetic resonance spectroscopy and electron microscopy...
June 29, 2017: Nature Communications
https://www.readbyqxmd.com/read/28660676/manipulator-driven-selection-of-semi-active-mr-visible-markers
#13
Junmo An, Andrew G Webb, Dipan J Shah, Karen Chin, Nikolaos V Tsekos
BACKGROUND: A method for the identification of semi-active fiducial magnetic resonance (MR) markers is presented based on selectively optically tuning and detuning them. METHODS: Four inductively coupled solenoid coils with photoresistors were connected to light sources. A microcontroller timed the optical tuning/detuning of coils and image collection. The markers were tested on an MR manipulator linking the microcontroller to the manipulator control to visibly select the marker subset according to the actuated joint...
June 29, 2017: International Journal of Medical Robotics + Computer Assisted Surgery: MRCAS
https://www.readbyqxmd.com/read/28653338/a-method-for-detailed-movement-pattern-analysis-of-tadpole-startle-response
#14
Kasra Zarei, Karen L Elliott, Sanam Zarei, Bernd Fritzsch, James H J Buchholz
Prolonged space flight, specifically microgravity, presents a problem for space exploration. Animal models with altered connections of the vestibular ear, and thus altered gravity sensation, would allow the examination of the effects of microgravity and how various countermeasures can establish normal function. We describe an experimental apparatus to monitor the effects of ear manipulations to generate asymmetric gravity input on the tadpole escape response. To perform the movement pattern analysis, an imaging apparatus was developed that uses a high-speed camera to obtain time-resolved, high-resolution images of tadpole movements...
June 27, 2017: Journal of the Experimental Analysis of Behavior
https://www.readbyqxmd.com/read/28651199/aberration-corrected-stem-by-means-of-diffraction-gratings
#15
Martin Linck, Peter A Ercius, Jordan S Pierce, Benjamin J McMorran
In the past 15 years, the advent of aberration correction technology in electron microscopy has enabled materials analysis on the atomic scale. This is made possible by precise arrangements of multipole electrodes and magnetic solenoids to compensate the aberrations inherent to any focusing element of an electron microscope. Here, we describe an alternative method to correct for the spherical aberration of the objective lens in scanning transmission electron microscopy (STEM) using a passive, nanofabricated diffractive optical element...
June 12, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28633885/characteristics-of-paraspinal-muscle-spindle-response-to-mechanically-assisted-spinal-manipulation-a-preliminary-report
#16
William R Reed, Joel G Pickar, Randall S Sozio, Michael A K Liebschner, Joshua W Little, Maruti R Gudavalli
OBJECTIVES: The purpose of this preliminary study is to determine muscle spindle response characteristics related to the use of 2 solenoid powered clinical mechanically assisted manipulation (MAM) devices. METHODS: L6 muscle spindle afferents with receptive fields in paraspinal muscles were isolated in 6 cats. Neural recordings were made during L7 MAM thrusts using the Activator V (Activator Methods Int. Ltd., Phoenix, AZ) and/or Pulstar (Sense Technology Inc., Pittsburgh, PA) devices at their 3 lowest force settings...
June 17, 2017: Journal of Manipulative and Physiological Therapeutics
https://www.readbyqxmd.com/read/28622656/a-combined-experimental-setup-for-op-and-odnmr
#17
Erika L Sesti, Matthew M Willmering, Zayd L Ma, Dustin D Wheeler, Mark S Conradi, Sophia E Hayes
Instrumentation for optically-pumped and optically-detected nuclear magnetic resonance (OPNMR and ODNMR) has been developed and implemented as a single experimental apparatus to study semiconductors such as GaAs and CdTe. These two measurement schemes use many of the same components for experiments. Here we describe, in two parts, the apparatus that can record such measurements and give examples of representative data. In Part 1, the radio-frequency probe and low-temperature cryostat are described, including single-channel and two-channel static cryogenic probes that both incorporate a modified solenoid coil that permits better optical access...
June 7, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28622586/outerwear-through-the-ages-evolutionary-cell-biology-of-vesicle-coats
#18
REVIEW
Joel B Dacks, Margaret S Robinson
Vesicular transport was key to the evolution of eukaryotes, and is essential for eukaryotic life today. All modern eukaryotes have a set of vesicle coat proteins, which couple cargo selection to vesicle budding in the secretory and endocytic pathways. Although these coats share common features (e.g. recruitment via small GTPases, β-propeller-α-solenoid proteins acting as scaffolds), the relationships between them are not always clear. Structural studies on the coats themselves, comparative genomics and cell biology in diverse eukaryotes, and the recent discovery of the Asgard archaea and their 'eukaryotic signature proteins' are helping us to piece together how coats may have evolved during the prokaryote-to-eukaryote transition...
June 13, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28607928/extremely-low-frequency-electromagnetic-fields-affect-myogenic-processes-in-c2c12-myoblasts-role-of-gap-junction-mediated-intercellular-communication
#19
Caterina Morabito, Nathalie Steimberg, Francesca Rovetta, Jennifer Boniotti, Simone Guarnieri, Giovanna Mazzoleni, Maria A Mariggiò
Extremely low-frequency electromagnetic fields (ELF-EMFs) can interact with biological systems. Although they are successfully used as therapeutic agents in physiatrics and rehabilitative practice, they might represent environmental pollutants and pose a risk to human health. Due to the lack of evidence of their mechanism of action, the effects of ELF-EMFs on differentiation processes in skeletal muscle were investigated. C2C12 myoblasts were exposed to ELF-EMFs generated by a solenoid. The effects of ELF-EMFs on cell viability and on growth and differentiation rates were studied using colorimetric and vital dye assays, cytomorphology, and molecular analysis of MyoD and myogenin expression, respectively...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28575120/structural-basis-for-5-ets-recognition-by-utp4-at-the-early-stages-of-ribosome-biogenesis
#20
Fabiola R Calviño, Markus Kornprobst, Géza Schermann, Fabienne Birkle, Klemens Wild, Tamas Fischer, Ed Hurt, Yasar Luqman Ahmed, Irmgard Sinning
Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The 'U three protein' (UTP) complexes and snoRNP particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5'-end of the pre-ribosomal RNA (5'-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2...
2017: PloS One
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