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Peter Jo, Manuel Nietert, Linda Gusky, Julia Kitz, Lena C Conradi, Annegret Müller-Dornieden, Philipp Schüler, Hendrik A Wolff, Josef Rüschoff, Philipp Ströbel, Marian Grade, Torsten Liersch, Tim Beißbarth, Michael B Ghadimi, Ulrich Sax, Jochen Gaedcke
Translational research relies on high-quality biospecimens. In patients with rectal cancer treated preoperatively with radiochemotherapy tissue based analyses are challenging. To assess quality challenges we analyzed tissue samples taken over the last years in a multicenter setting. We retrospectively evaluated overall 197 patients of the CAO/ARO/AIO-94- and 04-trial with locally advanced rectal cancer that were biopsied preoperatively at the University Medical Center Goettingen as well as in 10 cooperating hospitals in Germany...
October 18, 2016: Scientific Reports
Athanasios Ch Mitropoulos, Evangelos P Favvas, Konstantinos L Stefanopoulos, Etienne F Vansant
Everett's theorem-6 of the domain theory was examined by conducting adsorption in situ with small angle x-ray scattering (SAXS) supplemented by the contrast matching technique. The study focuses on the spectrum differences of a point to which the system arrives from different scanning paths. It is noted that according to this theorem at a common point the system has similar macroscopic properties. Furthermore it was examined the memory string of the system. We concluded that opposite to theorem-6: a) at a common point the system can reach in a finite (not an infinite) number of ways, b) a correction for the thickness of the adsorbed film prior to capillary condensation is necessary, and c) the scattering curves although at high-Q values coincide, at low-Q values are different indicating different microscopic states...
2016: PloS One
Emre Brookes, Patrice Vachette, Mattia Rocco, Javier Pérez
Size-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data. However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy. The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, Pérez, Cardinali, Profumo, Vachette & Rocco (2013 ▸)...
October 1, 2016: Journal of Applied Crystallography
Christopher D Putnam
The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q(2) transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters...
October 1, 2016: Journal of Applied Crystallography
Tahereh Javaheri, Zahra Kazemi, Jan Pencik, Ha Tt Pham, Maximilian Kauer, Rahil Noorizadeh, Barbara Sax, Harini Nivarthi, Michaela Schlederer, Barbara Maurer, Maximillian Hofbauer, Dave Nt Aryee, Marc Wiedner, Eleni M Tomazou, Malcolm Logan, Christine Hartmann, Jan P Tuckermann, Lukas Kenner, Mario Mikula, Helmut Dolznig, Aykut Üren, Günther H Richter, Florian Grebien, Heinrich Kovar, Richard Moriggl
Ewing sarcoma (ES) is the second most frequent childhood bone cancer driven by the EWS/FLI1 (EF) fusion protein. Genetically defined ES models are needed to understand how EF expression changes bone precursor cell differentiation, how ES arises and through which mechanisms of inhibition it can be targeted. We used mesenchymal Prx1-directed conditional EF expression in mice to study bone development and to establish a reliable sarcoma model. EF expression arrested early chondrocyte and osteoblast differentiation due to changed signaling pathways such as hedgehog, WNT or growth factor signaling...
October 13, 2016: Cell Death & Disease
Manuel M Neidhardt, Manpreet Wolfrum, Stuart Beardsworth, Tobias Wöhrle, Wolfgang Frey, Angelika Baro, Cosima Stubenrauch, Frank Giesselmann, Sabine Laschat
Synthetic strategies were developed to prepare l-tyrosine-based ionic liquid crystals with structural variations at the carboxylic and phenolic OH groups as well as the amino functionality. Salt metathesis additionally led to counterion variation. The liquid-crystalline properties were investigated by differential scanning calorimetry (DSC), polarizing optical microscopy (POM) and X-ray diffraction (WAXS, SAXS). The symmetrical ILC chlorides bearing the same alkyl chain at both the ester and ether but either an acyclic or cyclic guanidinium group displayed enantiotropic SmA2 mesophases with phase widths of 31-88 K irrespective of the head group...
October 13, 2016: Chemistry: a European Journal
Carmine D'Aniello, Maria G Vitale, Azzurra Farnesi, Lorenzo Calvetti, Maria M Laterza, Carla Cavaliere, Chiara Della Pepa, Vincenza Conteduca, Anna Crispo, Ferdinando De Vita, Francesco Grillone, Enrico Ricevuto, Michele De Tursi, Rocco De Vivo, Marilena Di Napoli, Sabrina C Cecere, Gelsomina Iovane, Alfonso Amore, Raffaele Piscitelli, Giuseppe Quarto, Salvatore Pisconti, Gennaro Ciliberto, Piera Maiolino, Paolo Muto, Sisto Perdonà, Massimiliano Berretta, Emanuele Naglieri, Luca Galli, Giacomo Cartenì, Ugo De Giorgi, Sandro Pignata, Gaetano Facchini, Sabrina Rossetti
Axitinib is an oral angiogenesis inhibitor, currently approved for treatment of metastatic renal cell carcinoma (mRCC) after failure of prior treatment with Sunitinib or cytokine. The present study is an Italian Multi-Institutional Retrospective Analysis that evaluated the outcomes of Axitinib, in second-line treatment of mRCC. The medical records of 62 patients treated with Axitinib, were retrospectively reviewed. The Progression Free Survival (PFS), the Overall Survival (OS), the Objective Response Rate (ORR), the Disease Control Rate (DCR), and the safety profile of axitinib and sunitinib-axitinib sequence, were the primary endpoint...
2016: Frontiers in Pharmacology
Suneale Banerji, William Lawrance, Clive Metcalfe, David C Briggs, Akira Yamauchi, Omer Dushek, P Anton Van Der Merwe, Anthony J Day, David G Jackson
The lymphatic vessel endothelial receptor LYVE-1 is implicated in uptake of hyaluronan (HA) and trafficking of leucocytes to draining lymph nodes. Yet LYVE-1 has only weak affinity for hyaluronan, and depends on receptor clustering and higher-order ligand organisation for durable binding in lymphatic endothelium. An unusual feature of LYVE-1 not found in other HA receptors is the potential to form disulfide-linked homodimers. However their influence on function has not been investigated. Here we show LYVE-1 homodimers are the predominant configuration in lymphatic endothelium in vitro and in vivo and formation requires solely the unpaired cysteine residue C201 within the membrane-proximal domain, yielding a 15 fold higher HA binding affinity and ~ 70 fold slower off-rate than monomer...
October 12, 2016: Journal of Biological Chemistry
Ursula Schulze-Gahmen, Ignacia Echeverria, Goran Stjepanovic, Yun Bai, Huasong Lu, Dina Schneidman-Duhovny, Jennifer A Doudna, Qiang Zhou, Andrej Sali, James H Hurley
HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn(2+)-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop...
October 12, 2016: ELife
Niki Baccile, Anne-Sophie Cuvier, Sylvain Prévost, Christian V Stevens, Elisabeth Delbeke, Jan Berton, Wim Soetaert, Inge N A Van Bogaert, Sophie Roelants
A set of four structurally related glycolipids are described: two of them have one glucose unit connected to either stearic or oleic acid, and two other ones have a diglucose headgroup (sophorose) similarly connected to either stearic or oleic acid. The self-assembly properties of these compounds, poorly known, are important to know due to their use in various fields of application from cleaning to cosmetics to medical. At basic pH, they all form mainly small micellar aggregates. At acidic pH, the oleic and stearic derivatives of the monoglucose form, respectively, vesicles and bilayer, while the same derivatives of the sophorose headgroup form micelles and twisted ribbons...
October 12, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Luigi Martino, Louise Holland, Evangelos Christodoulou, Simone Kunzelmann, Diego Esposito, Katrin Rittinger
NOD-like receptors represent an important class of germline-encoded pattern recognition receptors that play key roles in the regulation of inflammatory signalling pathways. They function as danger sensors and initiate inflammatory responses and the production of cytokines. Since NLR malfunction results in chronic inflammation and auto-immune diseases, there is a great interest in understanding how they work on a molecular level. To date, a lot of insight into the biological functions of NLRs is available but biophysical and structural studies have been hampered by the difficulty to produce soluble and stable recombinant NLR proteins...
2016: PloS One
Theyencheri Narayanan, Dhammika Weerakkody, Alexander G Karabadzhak, Michael Anderson, Oleg A Andreev, Yana K Reshetnyak
The pH (Low) Insertion Peptides (pHLIP® peptides) find application in studies of membrane-associated folding, since spontaneous insertion of these peptides is conveniently triggered by varying pH. Also, pHLIP® peptides have medical utility, since they can target acidic diseased tissues, such as tumors, and deliver therapeutic cargo molecules across membrane or target nanoparticles to cancer cells. Here we employed small angle X-ray scattering (SAXS) to investigate WT pHLIP® peptide oligomeric state in solution at high concentrations and monitor changes in liposome structure upon peptide insertion into bilayer...
October 11, 2016: Journal of Physical Chemistry. B
Juyeong Kim, Matthew R Jones, Zihao Ou, Qian Chen
We use liquid phase transmission electron microscopy (LP-TEM) to characterize the structure and dynamics of a solution-phase superlattice assembled from gold nanoprisms at the single particle level. The lamellar structure of the superlattice, determined by a balance of inter-prism interactions, is maintained and resolved under low-dose imaging conditions typically reserved for biomolecular imaging. In this dose range, we capture dynamic structural changes in the superlattice in real time, where contraction and smaller steady-state lattice constants are observed at higher electron dose rates...
October 10, 2016: ACS Nano
Xiaoyan Tan, Xiaoxi Li, Ling Chen, Fengwei Xie
This study compared the solubility of starch (G50) and microcrystalline cellulose (MCC) in an ionic liquid (IL), 1-ethyl-3-methylimidazolium acetate ([Emim][OAc]), at different temperatures. From SAXS and WAXS analysis, polysaccharides could be totally dissolved in [Emim][OAc]. Fourier-transform infrared (FTIR) spectra showed a similar dissolution mechanism for starch and MCC, which was related to the formation of hydrogen bonds between polysaccharide hydroxyls and acetic anions, causing the breakage of the hydrogen bonding network of the polysaccharide...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Pablo Gonzalez Rodriguez, Huiyu Yuan, Karin J H van den Nieuwenhuijzen, Walter Lette, Dik J Schipper, Johan E Ten Elshof
The intercalation of different primary n-alkylamines in the structure of a layered titanate of the lepidocrocite type (H1.07Ti1.73O4) for application in high temperature solid lubrication is reported. The intercalation process of the amines was explored by means of in-situ small angle X-ray scattering (SAXS), with variations in alkyl chain length (3 - 12 carbon atoms) and the ratio amine : titanate. The intercalation process was found to be completed within 5 min after mixing of the precursors in water at 80 °C...
October 7, 2016: ACS Applied Materials & Interfaces
Christine C Kathrein, Christian Pester, Markus Ruppel, Maike Jung, Marc Zimmermann, Alexander Böker
Time- and temperature-resolved in situ birefringence measurements were applied to analyze the effect of nanoparticles on the electric field-induced alignment of a microphase separated solution of poly(styrene)-block-poly(isoprene) in toluene. Through the incorporation of isoprene-confined CdSe quantum dots the reorientation behavior is altered. Particle loading lowers the order-disorder transition temperature, and increases the defect density, favoring nucleation and growth as an alignment mechanism over rotation of grains...
October 12, 2016: Soft Matter
Leïla Zerkoune, Sylviane Lesieur, Jean-Luc Putaux, Luc Choisnard, Annabelle Gèze, Denis Wouessidjewe, Borislav Angelov, Corinne Vebert-Nardin, James Doutch, Angelina Angelova
Soft mesoporous hierarchically structured particles were created by the self-assembly of an amphiphilic deep cavitand cyclodextrin βCD-nC10 (degree of substitution n = 7.3), with a nanocavity grafted by multiple alkyl (C10) chains on the secondary face of the βCD macrocycle through enzymatic biotransesterification, and the nonlamellar lipid monoolein (MO). The effect of the non-ionic dispersing agent polysorbate 80 (P80) on the liquid crystalline organization of the nanocarriers and their stability was studied in the context of vesicle-to-cubosome transition...
September 13, 2016: Soft Matter
Viviane Lutz-Bueno, Jianguo Zhao, Raffaele Mezzenga, Thomas Pfohl, Peter Fischer, Marianne Liebi
The determination of in situ structural information of soft matter under flow is challenging, as it depends on many factors, such as temperature, concentration, confinement, channel geometry, and type of imposed flow. Here, we combine microfluidics and scanning small-angle X-ray scattering (scanning-SAXS) to create a two-dimensional spatially resolved map, which represents quantitatively the variation of molecular properties under flow. As application examples, mappings of confined amyloid fibrils and wormlike micelles under flow into various channel geometries are compared...
October 5, 2016: Lab on a Chip
Cy M Jeffries, Melissa A Graewert, Clément E Blanchet, David B Langley, Andrew E Whitten, Dmitri I Svergun
Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume, including the solvent and buffer components, as well as the macromolecules of interest. To obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample...
November 2016: Nature Protocols
Jin Seob Kim, Bijan Afsari, Gregory S Chirikjian
Cryo-electron microscopy (EM) and small angle X-ray scattering (SAXS) are two different data acquisition modalities often used to glean information about the structure of large biomolecular complexes in their native states. A SAXS experiment is generally considered fast and easy but unveils the structure at very low resolution, whereas a cryo-EM experiment needs more extensive preparation and postacquisition computation to yield a three-dimensional (3D) density map at higher resolution. In certain applications, we may need to verify whether the data acquired in the SAXS and cryo-EM experiments correspond to the same structure (e...
October 6, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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