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Structure resolution

Riccardo Gottardi, Uwe Hansen, Roberto Raiteri, Marko Loparic, Marcel Düggelin, Daniel Mathys, Niklaus F Friederich, Peter Bruckner, Martin Stolz
Cartilage matrix is a composite of discrete, but interacting suprastructures, i.e. cartilage fibers with microfibrillar or network-like aggregates and penetrating extrafibrillar proteoglycan matrix. The biomechanical function of the proteoglycan matrix and the collagen fibers are to absorb compressive and tensional loads, respectively. Here, we are focusing on the suprastructural organization of collagen fibrils and the degradation process of their hierarchical organized fiber architecture studied at high resolution at the authentic location within cartilage...
2016: PloS One
Blanka Bucsella, Antoine Fornage, Catherine Le Denmat, Franka Kálmán
In biotechnological processes the intracellular level of nucleotides and nucleotide sugars have a direct impact on the post-translational modification (glycosylation) of the therapeutic protein products and on the exopolysaccharide pattern of the cells. Thus, they are precursors and also key components in the production of glycoproteins and glycolipids. All four nucleotides (at different phosphorylation stages) and their natural sugar derivatives coexist in biological samples. Their relative ratios depend on the actual conditions under which the cells are grown...
October 2016: Chimia
Florian Albrecht, Felix Bischoff, Wilhelm Auwärter, Johannes V Barth, Jascha Repp
In recent years atomic force microscopy (AFM) at highest resolution was widely applied to mostly planar molecules, while its application towards exploring species with structural flexibility and a distinct 3D-character remains a challenge. Herein, the scope of non-contact AFM is widened by investigating subtle conformational differences occurring in the well-studied reference systems 2H-TPP and Cu-TPP on Cu(111). Different saddle-shape conformations of both species can be recognized in conventional constant-height AFM images...
October 25, 2016: Nano Letters
Mattia Riccardo Monaco, Daniele Fazzi, Nobuya Tsuji, Markus Leutzsch, Saihu Liao, Walter Thiel, Benjamin List
The heterodimerizing self-assembly between a phosphoric acid catalyst and a carboxylic acid has recently been established as a new activation mode in Brønsted acid catalysis. In this article, we present a comprehensive mechanistic investigation on this activation principle, which eventually led to its elucidation. Detailed studies are reported, including computational investigations on the supramolecular heterodimer, kinetic studies on the catalytic cycle, and a thorough analysis of transition states by DFT calculations for the rationalization of the catalyst structure-selectivity relationship...
October 25, 2016: Journal of the American Chemical Society
Jorge Regueiro, Noelia Negreira, Marc H G Berntssen
Ion mobility spectrometry allows for the measurement of the collision cross section (CCS), which provides information about the shape of an ionic molecule in the gas phase. While the hyphenation of travelling-wave ion mobility spectrometry (TWIMS) with high-resolution quadrupole time-of-flight mass spectrometry (QTOFMS) has been mainly used for structural elucidation purposes, its potential for fast screening of small molecules in complex samples has not yet been thoroughly evaluated. The current work explores the capabilities of ultra-high performance liquid chromatography (UHPLC) coupled to a new design TWIMS-QTOFMS for the screening and identification of a large set of pesticides in complex salmon feed matrices...
October 25, 2016: Analytical Chemistry
Dian Su, Carl K Ng, Mehraban Khosraviani, Shang-Fan Yu, Ely Cosino, Surinder Kaur, Keyang Xu
Affinity capture liquid chromatography-mass spectrometry (LC-MS) intact antibody assay has been widely used for direct drug-to-antibody ratio (DAR) and catabolite characterization of antibody-drug conjugates (ADCs). However, the intact mass spectra of new ADCs, which incorporate new types of linkers and/or payloads other than maytansines and auristatins, are more complex than those examined previously. The current method has showed some limitations in elucidating certain structural modifications. Herein, we report an alternative analytical approach for ADCs, such as THIOMABTM antibody-drug conjugates (TDCs), where the linker-drugs are site-specifically conjugated in the Fab region...
October 25, 2016: Analytical Chemistry
H Li, C L Lv, C S Yang, D F Wei, K W Chen, S W Li, Z J Zhang
BACKGROUND AND PURPOSE: SORL1 rs1699102 is associated with the risk of late-onset Alzheimer's disease. However, the effects of this single nucleotide polymorphism on cognition and brain structure during normal aging are unclear. This study aimed to examine the effects of the rs1699102 polymorphism on age-related cognitive decline and cortical gray matter reduction in the Chinese Han population. METHODS: A total of 780 non-demented adults completed a battery of neuropsychological tests...
October 25, 2016: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
K M Meiburger, S Y Nam, E Chung, L J Suggs, S Y Emelianov, F Molinari
Blood vessels are the only system to provide nutrients and oxygen to every part of the body. Many diseases can have significant effects on blood vessel formation, so that the vascular network can be a cue to assess malicious tumor and ischemic tissues. Various imaging techniques can visualize blood vessel structure, but their applications are often constrained by either expensive costs, contrast agents, ionizing radiations, or a combination of the above. Photoacoustic imaging combines the high-contrast and spectroscopic-based specificity of optical imaging with the high spatial resolution of ultrasound imaging, and image contrast depends on optical absorption...
November 21, 2016: Physics in Medicine and Biology
Benjamin A Thomas, Vesna Cuplov, Alexandre Bousse, Adriana Mendes, Kris Thielemans, Brian F Hutton, Kjell Erlandsson
Positron emission tomography (PET) images are degraded by a phenomenon known as the partial volume effect (PVE). Approaches have been developed to reduce PVEs, typically through the utilisation of structural information provided by other imaging modalities such as MRI or CT. These methods, known as partial volume correction (PVC) techniques, reduce PVEs by compensating for the effects of the scanner resolution, thereby improving the quantitative accuracy. The PETPVC toolbox described in this paper comprises a suite of methods, both classic and more recent approaches, for the purposes of applying PVC to PET data...
November 21, 2016: Physics in Medicine and Biology
Biswaranjan Mohanty, Martin L Williams, Bradley C Doak, Mansha Vazirani, Olga Ilyichova, Geqing Wang, Wolfgang Bermel, Jamie S Simpson, David K Chalmers, Glenn F King, Mehdi Mobli, Martin J Scanlon
We describe a general approach to determine the binding pose of small molecules in weakly bound protein-ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of Ile, Leu, Val, Ala and Thr methyl groups using triple resonance scalar correlation data...
October 24, 2016: Journal of Biomolecular NMR
J Schnaidt, S Beckord, A K Engstfeld, J Klein, S Brimaud, R J Behm
We describe the construction and discuss the performance of a novel combined ultrahigh vacuum (UHV)-electrochemistry set-up, allowing the controlled preparation and structural characterization of complex nanostructured electrode surfaces by high resolution scanning tunnelling microscopy (STM) under UHV conditions on the one hand and, after electrode transfer under clean conditions, electrochemical measurements under continuous, controlled electrolyte mass transport conditions on the other. Electrochemical measurements can be coupled with online product detection, either using an additional collector electrode or by differential electrochemical mass spectrometry (DEMS)...
October 25, 2016: Physical Chemistry Chemical Physics: PCCP
Liqiang Ren, Di Wu, Yuhua Li, Bin Zheng, Yong Chen, Kai Yang, Hong Liu
This study presents a practical alignment method for X-ray spectral measurement in a rotating gantry based micro-computed tomography (micro-CT) system using three-dimensional (3D) printing technology. In order to facilitate the spectrometer placement inside the gantry, supporting structures including a cover and a stand were dedicatedly designed and printed using a 3D printer. According to the relative position between the spectrometer and the stand, the upright projection of the spectrometer collimator onto the stand was determined and then marked by a tungsten pinhole...
June 2016: Biomedical Physics & Engineering Express
Akiko Takashima, Naoki Takeshita, Toshihiko Kinoshita
A 41-year old pregnant woman underwent amniocentesis to conduct a conventional karyotyping analysis; the analysis reported an abnormal karyotype: 46, XY, add(9)(p24). Chromosomal microarray analysis (CMA) is utilized in prenatal diagnoses. A single nucleotide polymorphism microarray revealed a male fetus with balanced chromosomal translocations on 9p and balanced chromosomal rearrangements, but another chromosomal abnormality was detected. The fetus had microduplication. The child was born as a phenotypically normal male...
August 8, 2016: Clinics and Practice
Ana Sánchez Azofra, Trilokesh D Kidambi, Rita J Jeremy, Peggy Conrad, Amie Blanco, Megan Myers, James Barkovich, Jonathan P Terdiman
BACKGROUND: Familial adenomatous polyposis (FAP) is an autosomal dominant hereditary colon cancer syndrome caused by mutations in adenomatous polyposis coli (APC) with both colonic and extra-colonic manifestations. Case reports have noted an association with FAP and intellectual disability and animal studies have shown that APC is implicated in neural development and function, but no studies have investigated neuropsychological, behavioral, or structural brain characteristics of patients with FAP...
2016: Hereditary Cancer in Clinical Practice
Anjali Garg, Nivas Balasubramaniyam, Rocco Lafaro, Robert Timmermans, Wilbert S Aronow, Howard A Cooper, Julio A Panza
We report a contained rupture of a right coronary sinus of Valsalva aneurysm, in which repair resulted in symptomatic improvement. Patients often present with symptoms secondary to rupture of the sinus of Valsalva aneurysm into one of the cardiac chambers, or secondary to the compression of adjacent structures. Whereas sinus of Valsalva aneurysms and their rupture are well reported in the literature, contained ruptures have been described only rarely. In those cases, symptoms often arose from compression of adjacent structures...
October 2016: Texas Heart Institute Journal
D Grinfeld, I Kopaev, M Skoblin, M Monastyrskiy, A Makarov, S Alimpiev
A variational 3D approach to the problem of simulating stationary distributions of ions in the radiofrequency low-vacuum ion traps with regard to Coulomb interaction and collisions of ions with buffer gas molecules is proposed. The software developed in the course of this work is employed to study the structure of stationary ion ensembles in the radiofrequency ion traps of various types. The effect of high-frequency and constant voltages, space-charge density, and buffer gas temperature on the formation of stationary distributions in the radiofrequency ion traps and their limiting capacitance is investigated...
October 6, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
William A Cantara, Erik D Olson, Karin Musier-Forsyth
In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist...
October 21, 2016: Methods: a Companion to Methods in Enzymology
Jörg Peter Pfannmöller, Marvin Greiner, Mukund Balasubramanian, Martin Lotze
The fingertip somatotopy in BA1 and BA3b of monkeys exhibits characteristic differences with a more discrete separation of the body parts in BA3b and a continuous orientation column like structure in BA1. We present evidence for similar differences in the human somatotopy using BOLD fMRI for the investigations. Though the variability between the individual maps was large, we found a group wide somatotopic representation in BA3b and BA1. The variability due to anatomical differences was small in our sample. This was demonstrated by comparing exact shortest distances in the individual brains and after nonlinear normalization to the group space template, for the removal of the individual anatomical variability...
October 21, 2016: Neuroscience
Chang Chen, Ariane Wohlfarth, Hui Xu, Dan Su, Xin Wang, Hongliang Jiang, Yulin Feng, Mingshe Zhu
A novel analytical workflow was developed and applied for the detection and identification of unknown xenobiotics in biological samples. High-resolution mass spectrometry (HRMS)-based data-independent MS(E) acquisition was employed to record full scan MS and fragment spectral datasets of test and control samples. Then, an untargeted data-mining technique, background subtraction, was utilized to find xenobiotics present only in test samples. Structural elucidation of the detected xenobiotics was accomplished by database search, spectral interpretation, and/or comparison with reference standards...
November 9, 2016: Analytica Chimica Acta
Vinoth Wigneswaran, Kristian Fog Nielsen, Claus Sternberg, Peter Ruhdal Jensen, Anders Folkesson, Lars Jelsbak
BACKGROUND: Although a transition toward sustainable production of chemicals is needed, the physiochemical properties of certain biochemicals such as biosurfactants make them challenging to produce in conventional bioreactor systems. Alternative production platforms such as surface-attached biofilm populations could potentially overcome these challenges. Rhamnolipids are a group of biosurfactants highly relevant for industrial applications. However, they are mainly produced by the opportunistic pathogen Pseudomonas aeruginosa using hydrophobic substrates such as plant oils...
October 24, 2016: Microbial Cell Factories
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