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https://www.readbyqxmd.com/read/28228471/novel-layers-of-rna-polymerase-iii-control-affecting-trna-gene-transcription-in-eukaryotes
#1
REVIEW
Ewa Leśniewska, Magdalena Boguta
RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28228173/optimization-of-vascular-casting-for-three-dimensional-fluorescence-cryo-imaging-of-collateral-vessels-in-the-ischemic-rat-hindlimb
#2
Janina C V Schwarz, Monique G J T B van Lier, Erik N T P Bakker, Judith de Vos, Jos A E Spaan, Ed VanBavel, Maria Siebes
Development of collateral vessels, arteriogenesis, may protect against tissue ischemia, however, quantitative data on this process remain scarce. We have developed a technique for replicating the entire arterial network of ischemic rat hindlimbs in three dimensions (3D) based on vascular casting and automated sequential cryo-imaging. Various dilutions of Batson's No. 17 with methyl methacrylate were evaluated in healthy rats, with further protocol optimization in ischemic rats. Penetration of the resin into the vascular network greatly depended on dilution; the total length of casted vessels below 75 µm was 13-fold higher at 50% dilution compared with the 10% dilution...
February 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28228169/characterization-of-sulfur-and-nanostructured-sulfur-battery-cathodes-in-electron-microscopy-without-sublimation-artifacts
#3
Barnaby D A Levin, Michael J Zachman, Jörg G Werner, Ritu Sahore, Kayla X Nguyen, Yimo Han, Baoquan Xie, Lin Ma, Lynden A Archer, Emmanuel P Giannelis, Ulrich Wiesner, Lena F Kourkoutis, David A Muller
Lithium sulfur (Li-S) batteries have the potential to provide higher energy storage density at lower cost than conventional lithium ion batteries. A key challenge for Li-S batteries is the loss of sulfur to the electrolyte during cycling. This loss can be mitigated by sequestering the sulfur in nanostructured carbon-sulfur composites. The nanoscale characterization of the sulfur distribution within these complex nanostructured electrodes is normally performed by electron microscopy, but sulfur sublimates and redistributes in the high-vacuum conditions of conventional electron microscopes...
February 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28227855/simultaneous-reconstruction-and-segmentation-with-the-mumford-shah-functional-for-electron-tomography
#4
Li Shen, Eric Todd Quinto, Shiqiang Wang, Ming Jiang, Li Shen, Eric Todd Quinto, Shiqiang Wang, Ming Jiang, Ming Jiang, Eric Todd Quinto, Shiqiang Wang, Li Shen
Electron micrography (EM) is an important method for determining the three-dimensional (3D) structure of macromolecular complexes and biological specimens. But there are several limitations such as poor signal-to-noise, limitation on range of tilt angles and sub-region subject to electron exposure, unintentional movements of the specimen, with EM systems that make the reconstruction procedure a severely ill-posed problem. A different choice of reconstruction method may lead to different results and create different additional artifacts in reconstructed images...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227385/statistical-characterization-of-ensembles-of-symmetric-virus-particles-3-d-stochastic-signal-reconstruction-from-electron-microscope-images
#5
Nan Xu, Peter C Doerschuk, Nan Xu, Peter C Doerschuk, Nan Xu, Peter C Doerschuk
Stochastic models of nano-biomachines have been studied by 3-D reconstruction from cryo electron microscopy images in recent years. The image data is the projection of many heterogeneous instances of the object under study (e.g., a virus). Initial reconstruction algorithms require different instances of the object, while still heterogeneous, to have the same symmetry. This paper presents a maximum likelihood reconstruction approach which allows each object to lack symmetry while constraining the statistics of the ensemble of objects to have symmetry...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28223502/cryo-em-structure-of-the-replisome-reveals-multiple-interactions-coordinating-dna-synthesis
#6
Arkadiusz W Kulczyk, Arne Moeller, Peter Meyer, Piotr Sliz, Charles C Richardson
We present a structure of the ∼650-kDa functional replisome of bacteriophage T7 assembled on DNA resembling a replication fork. A structure of the complex consisting of six domains of DNA helicase, five domains of RNA primase, two DNA polymerases, and two thioredoxin (processivity factor) molecules was determined by single-particle cryo-electron microscopy. The two molecules of DNA polymerase adopt a different spatial arrangement at the replication fork, reflecting their roles in leading- and lagging-strand synthesis...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28218750/quaternary-contact-in-the-initial-interaction-of-cd4-with-the-hiv-1-envelope-trimer
#7
Qingbo Liu, Priyamvada Acharya, Michael A Dolan, Peng Zhang, Christina Guzzo, Jacky Lu, Alice Kwon, Deepali Gururani, Huiyi Miao, Tatsiana Bylund, Gwo-Yu Chuang, Aliaksandr Druz, Tongqing Zhou, William J Rice, Christoph Wigge, Bridget Carragher, Clinton S Potter, Peter D Kwong, Paolo Lusso
Binding of the gp120 envelope (Env) glycoprotein to the CD4 receptor is the first step in the HIV-1 infectious cycle. Although the CD4-binding site has been extensively characterized, the initial receptor interaction has been difficult to study because of major CD4-induced structural rearrangements. Here we used cryogenic electron microscopy (cryo-EM) to visualize the initial contact of CD4 with the HIV-1 Env trimer at 6.8-Å resolution. A single CD4 molecule is embraced by a quaternary HIV-1-Env surface formed by coalescence of the previously defined CD4-contact region with a second CD4-binding site (CD4-BS2) in the inner domain of a neighboring gp120 protomer...
February 20, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28218252/dissecting-the-molecular-organization-of-the-translocon-associated-protein-complex
#8
Stefan Pfeffer, Johanna Dudek, Miroslava Schaffer, Bobby G Ng, Sahradha Albert, Jürgen M Plitzko, Wolfgang Baumeister, Richard Zimmermann, Hudson H Freeze, Benjamin D Engel, Friedrich Förster
In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients...
February 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28217785/surfactant-free-microemulsions-of-1-butyl-3-methylimidazolium-hexafluorophosphate-propylamine-nitrate-and-water
#9
Jie Xu, Huanhuan Deng, Yunlei Fu, Yuquan Chen, Jing Zhang, Wanguo Hou
Generally, surfactants (or amphiphiles) are believed to be necessary components of microemulsions. However, it has been demonstrated that, in the absence of traditional surfactants, microemulsions can also form from a ternary system of two immiscible fluids (i.e., oil and water phases) and an amphi-solvent, but the current understanding of such surfactant-free microemulsions (SFMEs) is very limited. Herein, we report an SFME consisting of the hydrophobic ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate (bmimPF6), the protic IL propylamine nitrate (PAN), and water, in which bmimPF6 and PAN are used as the oil phase and the amphi-solvent, respectively...
February 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28217720/a-graph-partitioning-approach-to-simultaneous-angular-reconstitution
#10
Gabi Pragier, Ido Greenberg, Xiuyuan Cheng, Yoel Shkolnisky
One of the primary challenges in single particle reconstruction with cryo-electron microscopy is to find a three-dimensional model of a molecule using its noisy two-dimensional projection-images. As the imaging orientations of the projection-images are unknown, we suggest a common-lines-based method to simultaneously estimate the imaging orientations of all images that is independent of the distribution of the orientations. Since the relative orientation of each pair of images may only be estimated up to a two-way handedness ambiguity, we suggest an efficient procedure to consistently assign the same handedness to all relative orientations...
September 2016: IEEE Transactions on Computational Imaging
https://www.readbyqxmd.com/read/28216551/microscopic-characterization-of-the-brazilian-giant-samba-virus
#11
Jason R Schrad, Eric J Young, Jônatas S Abrahão, Juliana R Cortines, Kristin N Parent
Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts...
February 14, 2017: Viruses
https://www.readbyqxmd.com/read/28216515/particular-morphology-of-inferior-pulmonary-veins-and-difficulty-of-cryoballoon-ablation-in-patients-with-paroxysmal-atrial-fibrillation
#12
Ryobun Yasuoka, Takashi Kurita, Yasuhito Kotake, Naotaka Hashiguchi, Koichiro Motoki, Kazuhiro Kobuke, Yoshitaka Iwanaga, Shunichi Miyazaki
BACKGROUND: The CRYO-Japan PMS study indicated that cryoballoon ablation (Cryo-Abl) has a lower acute success rate of pulmonary vein isolation (PVI) for the right and left inferior PVs (RIPV and LIPV, respectively) than for the superior PVs. This study aimed to determine if the orientation and position of the inferior PVs are related to the difficulty of acute success of PVI.Methods and Results:We investigated 30 consecutive patients who underwent Cryo-Abl. A "difficult PV" was defined as the requirement for >2 cooling applications and/or touch-up ablation to achieve PVI...
February 17, 2017: Circulation Journal: Official Journal of the Japanese Circulation Society
https://www.readbyqxmd.com/read/28213539/critical-concentration-of-lecithin-enhances-the-antimicrobial-activity-of-eugenol-against-escherichia-coli
#13
Haoshu Zhang, Edward G Dudley, P Michael Davidson, Federico Harte
Lecithin is a natural emulsifier used in a wide range of food and non-food applications to improve physical stability with no known bioactive effects. In this study, the effect of lecithin on the antimicrobial performance of a constant eugenol concentration was tested against three Escherichia coli strains (C600, 0.1229, and O157:H7 strain ATCC 700728). This was the first study focusing on lecithin at concentrations below those commonly used in foods to improve the stability of oil in water emulsions (≤ 10mg/100ml)...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213018/pathogen-biofilm-formation-on-cantaloupe-surface-and-its-impact-on-the-antibacterial-effect-of-lauroyl-arginate-ethyl
#14
Yezhi Fu, Amanda J Deering, Arun K Bhunia, Yuan Yao
Pathogen biofilm at fruit surface may pose a particular risk to food safety. In this study, the biofilms of Listeria monocytogenes V7 and Salmonella enterica serovar Typhimurium ATCC 13311 on cantaloupe fruit surface were visualized, and the resistance of biofilms against lauroyl arginate ethyl (LAE, an antibacterial compound) was evaluated. Each bacterium was inoculated on isolated cantaloupe rind surfaces at 10(5)-10(6) CFU/cm(2) and after incubation for 2, 12, 24, and 48 h, the surfaces were imaged using cryo-scanning electron microscopy (Cryo-SEM)...
June 2017: Food Microbiology
https://www.readbyqxmd.com/read/28212379/distribution-and-abundance-of-key-vectors-of-rift-valley-fever-and-other-arboviruses-in-two-ecologically-distinct-counties-in-kenya
#15
Rosemary Sang, Samwel Arum, Edith Chepkorir, Gladys Mosomtai, Caroline Tigoi, Faith Sigei, Olivia Wesula Lwande, Tobias Landmann, Hippolyte Affognon, Clas Ahlm, Magnus Evander
BACKGROUND: Rift Valley fever (RVF) is a mosquito-borne viral zoonosis of ruminants and humans that causes outbreaks in Africa and the Arabian Peninsula with significant public health and economic consequences. Humans become infected through mosquito bites and contact with infected livestock. The virus is maintained between outbreaks through vertically infected eggs of the primary vectors of Aedes species which emerge following rains with extensive flooding. Infected female mosquitoes initiate transmission among nearby animals, which amplifies virus, thereby infecting more mosquitoes and moving the virus beyond the initial point of emergence...
February 17, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28209059/phase-behavior-of-aqueous-suspension-of-laponite-new-insights-with-microscopic-evidence
#16
Shweta Jatav, Yogesh M Joshi
Investigating microstructure of suspensions with particles having anisotropic shape that share complex interactions is a challenging task leading to competing claims. This work investigates phase behavior of one such system: aqueous Laponite suspension, which is highly contested in the literature, using rheological and microscopic tools. Remarkably, we observe that over a broad range of Laponite (1.4 to 4 weight %) and salt concentrations (0 to 7 mM), the system overwhelmingly demonstrates all the rheological characteristics of the sol-gel transition leading to a percolated network...
February 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28202257/radiofrequency-catheter-ablation-of-atrioventricular-node-reentrant-tachycardia-in-children-with-limited-fluoroscopy
#17
Moshe Swissa, Einat Birk, Tamir Dagan, Sody Abby Naimer, Michal Fogelman, Tom Einbinder, Elchanan Bruckheimer, Rami Fogelman
BACKGROUND: Limited fluoroscopy cryo-ablation using a 3D electro-anatomical system (3DS) has been used for AVNRT in children. We aimed to facilitate a fluoroscopy limited approach of RF ablation of AVNRT in children. METHODS: A retrospective study was performed of procedure parameters in children undergoing RF ablation of AVNRT in 75 consecutive children (June 2011 to November 2013 - Group A) using standard fluoroscopy techniques compared to those of 64 consecutive children (December 2013 to May 2015 - Group B), using a fluoroscopy limited approach with 3DS...
January 31, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28198180/engineering-recombinant-virus-like-nanoparticles-from-plants-for-cellular-delivery
#18
Lou Brillault, Philippe V Jutras, Noor Dashti, Eva C Thuenemann, Garry Morgan, George P Lomonossoff, Michael J Landsberg, Frank Sainsbury
Understanding capsid assembly following recombinant expression of viral structural proteins is critical to the design and modification of virus-like nanoparticles for biomedical and nanotechnology applications. Here, we use plant-based transient expression of the Bluetongue virus (BTV) structural proteins, VP3 and VP7, to obtain high yields of empty and green fluorescent protein (GFP)-encapsidating core-like particles (CLPs) from leaves. Single-particle cryo-electron microscopy of both types of particles revealed considerable differences in CLP structure compared to the crystal structure of infection-derived CLPs; in contrast, the two recombinant CLPs have an identical external structure...
February 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/28195421/protein-c-recognition-by-ion-coordinated-imprinted-monolithic-cryogels
#19
Binnaz Demirci, Nilay Bereli, Sevgi Aslıyüce, Gözde Baydemir, Adil Denizli
The protein C imprinted monolithic cryogel was synthesized using 2-hydroxyethyl methacrylate by redox cryo-polymerization method. The prepared monolithic cryogel was characterized by Fourier transform infrared spectroscopy, swelling test, surface area measurements and scanning electron microscopy. The non-imprinted cryogel was prepared as well for control. Adsorption of protein C from aqueous solutions was investigated in a continuous mode and several parameters affecting adsorption performance were optimized...
February 14, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28191458/structural-study-of-heterogeneous-biological-samples-by-cryoelectron-microscopy-and-image-processing
#20
REVIEW
H E White, A Ignatiou, D K Clare, E V Orlova
In living organisms, biological macromolecules are intrinsically flexible and naturally exist in multiple conformations. Modern electron microscopy, especially at liquid nitrogen temperatures (cryo-EM), is able to visualise biocomplexes in nearly native conditions and in multiple conformational states. The advances made during the last decade in electronic technology and software development have led to the revelation of structural variations in complexes and also improved the resolution of EM structures. Nowadays, structural studies based on single particle analysis (SPA) suggests several approaches for the separation of different conformational states and therefore disclosure of the mechanisms for functioning of complexes...
2017: BioMed Research International
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