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Cryo tubes

Ricardo C Guerrero-Ferreira, Mario Hupfeld, Sergey Nazarov, Nicholas Mi Taylor, Mikhail M Shneider, Jagan M Obbineni, Martin J Loessner, Takashi Ishikawa, Jochen Klumpp, Petr G Leiman
Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of Listeria bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography...
January 2, 2019: EMBO Journal
Young-Jun Park, Kaitlyn D Lacourse, Christian Cambillau, Frank DiMaio, Joseph D Mougous, David Veesler
Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG...
December 19, 2018: Nature Communications
Efrat Ziv, David Attia, Gleb Vasilyev, Orit Mendelson, Eyal Zussman, Rachel Yerushalmi-Rozen
Dispersion of carbon nanotubes in solutions of polyvinyl-alcohol is required for solution casting of composite materials with improved interfacial adhesion where chains adsorbed on the nanotubes serve in the dual role of dispersant and compatible "connector" to the polyvinyl-alcohol matrix. Yet polyvinyl-alcohol is known to induce coagulation of nanotubes in aqueous solutions and thus far, it has not been used for dispersing pristine nanotubes. Here, we report that non-fully hydrolyzed (80-90%) polyvinyl-alcohol can be used for the preparation of stable, surfactant-free, dispersions of multi-wall carbon nanotubes in ethanol-water mixtures (of at least 50 vol% ethanol)...
November 15, 2018: Soft Matter
Mariia Novikova, Lucas J Adams, Juan Fontana, Anna T Gres, Muthukumar Balasubramaniam, Dennis C Winkler, Sagar B Kudchodkar, Ferri Soheilian, Stefan G Sarafianos, Alasdair C Steven, Eric O Freed
Late in the HIV-1 replication cycle, the viral structural protein Gag is targeted to virus assembly sites at the plasma membrane of infected cells. The capsid (CA) domain of Gag plays a critical role in the formation of the hexameric Gag lattice in the immature virion, and, during particle release, CA is cleaved from the Gag precursor by the viral protease and forms the conical core of the mature virion. A highly conserved Pro-Pro-Ile-Pro (PPIP) motif (CA residues 122 to 125) [PPIP(122-125)] in a loop connecting CA helices 6 and 7 resides at a 3-fold axis formed by neighboring hexamers in the immature Gag lattice...
October 16, 2018: MBio
Yassine Cherrak, Chiara Rapisarda, Riccardo Pellarin, Guillaume Bouvier, Benjamin Bardiaux, Fabrice Allain, Christian Malosse, Martial Rey, Julia Chamot-Rooke, Eric Cascales, Rémi Fronzes, Eric Durand
To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate...
October 15, 2018: Nature Microbiology
Nicholas M Matsumoto, René P M Lafleur, Xianwen Lou, Kuo-Chih Shih, Sjors P W Wijnands, Clément Guibert, Johannes W A M van Rosendaal, Ilja K Voets, Anja R A Palmans, Yao Lin, E W Meijer
In biology, polymorphism is a well-known phenomenon by which a discrete biomacromolecule can adopt multiple specific conformations in response to its environment. The controlled incorporation of polymorphism into noncovalent aqueous assemblies of synthetic small molecules is an important step toward the development of bioinspired responsive materials. Herein, we report on a family of carboxylic acid functionalized water-soluble benzene-1,3,5-tricarboxamides (BTAs) that self-assemble in water to form one-dimensional fibers, membranes, and hollow nanotubes...
October 17, 2018: Journal of the American Chemical Society
Guibo Rao, Yan Fu, Na Li, Jiayi Yin, Jie Zhang, Manli Wang, Zhihong Hu, Sheng Cao
Viruses with filamentous morphologies, such as tobacco mosaic virus (TMV) and M13 bacteriophage, have long been studied as multivalent nanoscaffolds for loading functional motifs. Structural assembly of the capsid proteins (CPs) of filamentous viruses often requires the presence of DNA or RNA molecules, which has limited their applications. Here, we describe a strategy for controllable assembly of flexible bio-nanotubes consisting of Escherichia coli expressed CP of baculovirus Helicoverpa armigera nucleopolyhedrovirus (HearNPV) in vitro...
August 1, 2018: ACS Applied Materials & Interfaces
R Plašil, P Dohnal, Á Kálosi, Š Roučka, D Shapko, S Rednyk, R Johnsen, J Glosík
A cryogenic stationary afterglow apparatus equipped with a near-infrared cavity-ring-down-spectrometer (Cryo-SA-CRDS) for studies of electron-ion recombination processes in the plasma at temperatures 30-300 K has been designed, constructed, tested, and put into operation. The plasma is generated in a sapphire discharge tube that is contained in a microwave cavity. The cavity and the tube are attached to the second stage of the cold head of the cryocooler system, and they are inserted to an UHV chamber with mirrors for CRDS and vacuum windows on both ends of the tube...
June 2018: Review of Scientific Instruments
Diane G Edmondson, Bo Hu, Steven J Norris
Investigation of Treponema pallidum subsp. pallidum , the spirochete that causes syphilis, has been hindered by an inability to culture the organism continuously in vitro despite more than a century of effort. In this study, long-term logarithmic multiplication of T. pallidum was attained through subculture every 6 to 7 days and periodic feeding using a modified medium ( T. pallidum culture medium 2 [TpCM-2]) with a previously described microaerobic, rabbit epithelial cell coincubation system. Currently, cultures have maintained continuous growth for over 6 months with full retention of viability as measured by motility and rabbit infectivity...
June 26, 2018: MBio
Jan Huebinger, Markus Grabenbauer
Reduction or complete prevention of ice crystal formation during freezing of biological specimens is mandatory for two important biological applications: (1) cryopreservation of living cells or tissues for long-term storage, and (2) cryo-fixation for ultrastructural investigations by electron microscopy. Here, a protocol that is fast, easy-to-use, and suitable for both cryo-fixation and cryopreservation is described. Samples are rapidly cooled in tightly sealed metal tubes of high thermal diffusivity and then plunged into a liquid cryogen...
June 2018: Current Protocols in Cell Biology
Nicole Morikawa, Nicole Laferriere, Sylvia Koo, Sidney Johnson, Russell Woo, Devin Puapong
PURPOSE: The Nuss procedure for surgical correction of pectus excavatum often causes severe postoperative pain. Cryoanalgesia of intercostal nerves is an alternative modality for pain control. We describe our modification of the cryoICE™ probe that allows for nerve ablation through the ipsilateral chest along with early results utilizing this technique. METHODS: To allow for ipsilateral nerve ablation, a 20-French chest tube was cut and secured to the cryoICE probe, thus providing insulation for the malleable end of the probe...
September 2018: Journal of Laparoendoscopic & Advanced Surgical Techniques. Part A
Reginald McNulty, Giovanni Cardone, Eddie B Gilcrease, Timothy S Baker, Sherwood R Casjens, John E Johnson
Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the mature virion upon DNA release are not fully understood. We used cryogenic electron microscopy to obtain what is, to our knowledge, the first asymmetric reconstruction of mature bacteriophage P22 after double-stranded DNA has been extruded from the capsid-a state representative of one step during viral infection...
March 27, 2018: Biophysical Journal
Maria Valentina Dinu, Ionel Adrian Dinu, Maria Marinela Lazar, Ecaterina Stela Dragan
An original strategy is proposed here to design chitosan-based ion-imprinted cryo-composites (II-CCs) with pre-organized recognition sites and tailored porous structure by combining ion-imprinting and ice-templating techniques. The cryo-composites showed a tube-like porous morphology with interconnected parallel micro-channels, the distance between the channel walls being around 15 μm. Both the entrapment of a natural zeolite and the presence of carboxylate groups, generated by partial hydrolysis of amide moieties, led to II-CCs with controlled swelling ratios (25-40 g/g, depending on pH) and enhanced overall chelating efficiency (260 mg Cu2+ /g composite)...
April 15, 2018: Carbohydrate Polymers
Nadia El Harane, Anaïs Kervadec, Valérie Bellamy, Laetitia Pidial, Hany J Neametalla, Marie-Cécile Perier, Bruna Lima Correa, Léa Thiébault, Nicolas Cagnard, Angéline Duché, Camille Brunaud, Mathilde Lemitre, Jeanne Gauthier, Alexandra T Bourdillon, Marc P Renault, Yeranuhi Hovhannisyan, Solenne Paiva, Alexandre R Colas, Onnik Agbulut, Albert Hagège, Jean-Sébastien Silvestre, Philippe Menasché, Nisa K E Renault
Aims: We have shown that extracellular vesicles (EVs) secreted by embryonic stem cell-derived cardiovascular progenitor cells (Pg) recapitulate the therapeutic effects of their parent cells in a mouse model of chronic heart failure (CHF). Our objectives are to investigate whether EV released by more readily available cell sources are therapeutic, whether their effectiveness is influenced by the differentiation state of the secreting cell, and through which mechanisms they act. Methods and results: The total EV secreted by human induced pluripotent stem cell-derived cardiovascular progenitors (iPSC-Pg) and human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) were isolated by ultracentrifugation and characterized by Nanoparticle Tracking Analysis, western blot, and cryo-electron microscopy...
May 21, 2018: European Heart Journal
Sergey Nazarov, Johannes P Schneider, Maximilian Brackmann, Kenneth N Goldie, Henning Stahlberg, Marek Basler
The bacterial Type VI secretion system (T6SS) assembles from three major parts: a membrane complex that spans inner and outer membranes, a baseplate, and a sheath-tube polymer. The baseplate assembles around a tip complex with associated effectors and connects to the membrane complex by TssK. The baseplate assembly initiates sheath-tube polymerization, which in some organisms requires TssA. Here, we analyzed both ends of isolated non-contractile Vibrio cholerae sheaths by cryo-electron microscopy. Our analysis suggests that the baseplate, solved to an average 8...
February 15, 2018: EMBO Journal
Galia T Debelouchina, Tom W Muir
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion...
January 2017: Quarterly Reviews of Biophysics
Charles-Adrien Arnaud, Grégory Effantin, Corinne Vivès, Sylvain Engilberge, Maria Bacia, Pascale Boulanger, Eric Girard, Guy Schoehn, Cécile Breyton
The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin)...
December 5, 2017: Nature Communications
Mingzhang Wang, Caitlin M Quinn, Juan R Perilla, Huilan Zhang, Randall Shirra, Guangjin Hou, In-Ja Byeon, Christopher L Suiter, Sherimay Ablan, Emiko Urano, Theodore J Nitz, Christopher Aiken, Eric O Freed, Peijun Zhang, Klaus Schulten, Angela M Gronenborn, Tatyana Polenova
Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of the C-terminal region of CA and the peptide SP1 (CA-SP1), which represents an intermediate during maturation of the HIV-1 virus. By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA-SP1 tubes assembled in vitro, which represent the features of an intermediate assembly state during maturation, the SP1 peptide exists in a dynamic helix-coil equilibrium, and that the addition of the maturation inhibitors Bevirimat and DFH-055 causes stabilization of a helical form of SP1...
November 24, 2017: Nature Communications
Minki Lee, Hosub Lim, Jinkee Lee
Plants transport water from roots to leaves via xylem through transpiration, which is an evaporation process that occurs at the leaves. During transpiration, suction pressure is generated by the porous structure of mesophyll cells in the leaves. Here, we fabricate artificial leaf consisting of micro and nano hierarchy structures similar to the mesophyll cells and veins of a leaf using cryo-gel method. We show that the microchannels in agarose gel greatly decrease the flow resistance in dye diffusion and permeability experiments...
November 7, 2017: Scientific Reports
Tohnyui Ndinyanka Fabrice, Andres Kaech, Gery Barmettler, Christof Eichenberger, J Paul Knox, Ueli Grossniklaus, Christoph Ringli
BACKGROUND: The pollen tube (PT) serves as a model system for investigating plant cell growth and morphogenesis. Ultrastructural studies are indispensable to complement data from physiological and genetic analyses, yet an effective method is lacking for PTs of the model plant Arabidopsis thaliana. METHODS: Here, we present reliable approaches for ultrastructural studies of Arabidopsis PTs, as well as an efficient technique for immunogold detection of cell wall epitopes...
October 27, 2017: BMC Plant Biology
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