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https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#1
Teresa Pankert, Thibaud Jegou, Maïwen Caudron-Herger, Karsten Rippe
Nuclear RNAs emerge as important factors to orchestrate the dynamic organization of the nucleus into functional subcompartments. By tethering RNAs to distinct genomic loci, the RNA-dependent chromatin changes can be dissected by fluorescence microscopic analysis. Here we describe how this approach is implemented in mammalian cells. It involves two high-affinity protein-nucleic acid interactions that can established with number of different protein domains and DNA and RNA sequences. A prototypic system is described here in detail: It consists of the binding of MS2 bacteriophage coat protein to its RNA recognition sequence and the interaction between the bacterial LacI repressor protein to its target lacO operator DNA sequences...
February 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28210246/prospects-of-in-vivo-incorporation-of-non-canonical-amino-acids-for-the-chemical-diversification-of-antimicrobial-peptides
#2
Tobias Baumann, Jessica H Nickling, Maike Bartholomae, Andrius Buivydas, Oscar P Kuipers, Nediljko Budisa
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28196481/nuctools-analysis-of-chromatin-feature-occupancy-profiles-from-high-throughput-sequencing-data
#3
Yevhen Vainshtein, Karsten Rippe, Vladimir B Teif
BACKGROUND: Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28195477/enzymatic-n-and-c-protection-in-cyanobactin-ripp-natural-products
#4
Debosmita Sardar, Yue Hao, Zhenjian Lin, Maho Morita, Satish K Nair, Eric W Schmidt
Recent innovations in peptide natural product biosynthesis reveal a surprising wealth of previously uncharacterized biochemical reactions that have potential applications in synthetic biology. Among these, the cyanobactins are noteworthy because these peptides are protected at their N- and C-termini by macrocyclization. Here, we use a novel bifunctional enzyme AgeMTPT to protect linear peptides by attaching prenyl and methyl groups at their free N- and C-termini. Using this peptide protectase in combination with other modular biosynthetic enzymes, we describe the total synthesis of the natural product aeruginosamide B and the biosynthesis of linear cyanobactin natural products...
February 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28165449/dissection-of-goadsporin-biosynthesis-by-in-vitro-reconstitution-leading-to-designer-analogues-expressed-in-vivo
#5
Taro Ozaki, Kona Yamashita, Yuki Goto, Morito Shimomura, Shohei Hayashi, Shumpei Asamizu, Yoshinori Sugai, Haruo Ikeda, Hiroaki Suga, Hiroyasu Onaka
Goadsporin (GS) is a member of ribosomally synthesized and post-translationally modified peptides (RiPPs), containing an N-terminal acetyl moiety, six azoles and two dehydroalanines in the peptidic main chain. Although the enzymes involved in GS biosynthesis have been defined, the principle of how the respective enzymes control the specific modifications remains elusive. Here we report a one-pot synthesis of GS using the enzymes reconstituted in the 'flexible' in vitro translation system, referred to as the FIT-GS system...
February 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28165313/colonoscopic-and-histologic-features-of-rectal-masses-in-dogs-82-cases-1995-2012
#6
Krista N Adamovich-Rippe, Philipp D Mayhew, Stanley L Marks, Laura E Selmic, William T N Culp, Angela M Youello, Jeffrey J Runge, David E Holt, Philip H Kass, John R Peauroi
OBJECTIVE To evaluate colonoscopic and histologic features of rectal masses in dogs. DESIGN Retrospective case series. ANIMALS 82 client-owned dogs with rectal masses that underwent colonoscopy. PROCEDURES Medical records of dogs with rectal masses that underwent colonoscopy were reviewed. History, signalment, clinical signs, results of physical examination, diagnostic imaging findings, and results of colonoscopy (including complications) were recorded. When available, tissue samples obtained during colonoscopy and by means of surgical biopsy were reviewed by a single board-certified pathologist...
February 15, 2017: Journal of the American Veterinary Medical Association
https://www.readbyqxmd.com/read/28135077/mechanistic-understanding-of-lanthipeptide-biosynthetic-enzymes
#7
Lindsay M Repka, Jonathan R Chekan, Satish K Nair, Wilfred A van der Donk
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that display a wide variety of biological activities, from antimicrobial to antiallodynic. Lanthipeptides that display antimicrobial activity are called lantibiotics. The post-translational modification reactions of lanthipeptides include dehydration of Ser and Thr residues to dehydroalanine and dehydrobutyrine, a transformation that is carried out in three unique ways in different classes of lanthipeptides. In a cyclization process, Cys residues then attack the dehydrated residues to generate the lanthionine and methyllanthionine thioether cross-linked amino acids from which lanthipeptides derive their name...
January 30, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28131315/retrieving-chromatin-patterns-from-deep-sequencing-data-using-correlation-functions
#8
Jana Molitor, Jan-Philipp Mallm, Karsten Rippe, Fabian Erdel
Epigenetic modifications and other chromatin features partition the genome on multiple length scales. They define chromatin domains with distinct biological functions that come in sizes ranging from single modified DNA bases to several megabases in the case of heterochromatic histone modifications. Due to chromatin folding, domains that are well separated along the linear nucleosome chain can form long-range interactions in three-dimensional space. It has now become a routine task to map epigenetic marks and chromatin structure by deep sequencing methods...
February 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28117558/microstructured-blood-vessel-surrogates-reveal-structural-tropism-of-motile-malaria-parasites
#9
Mendi J Muthinja, Johanna Ripp, Janina K Hellmann, Tamas Haraszti, Noa Dahan, Leandro Lemgruber, Anna Battista, Lucas Schütz, Oliver T Fackler, Ulrich S Schwarz, Joachim P Spatz, Friedrich Frischknecht
Plasmodium sporozoites, the highly motile forms of the malaria parasite, are transmitted naturally by mosquitoes and traverse the skin to find, associate with, and enter blood capillaries. Research aimed at understanding how sporozoites select blood vessels is hampered by the lack of a suitable experimental system. Arrays of uniform cylindrical pillars can be used to study small cells moving in controlled environments. Here, an array system displaying a variety of pillars with different diameters and shapes is developed in order to investigate how Plasmodium sporozoites associate to the pillars as blood vessel surrogates...
January 24, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28077628/the-creatininase-homolog-mfte-from-mycobacterium-smegmatis-catalyzes-a-peptide-cleavage-reaction-in-the-biosynthesis-of-a-novel-ripp
#10
Nathan A Bruender, Vahe Bandarian
Most ribosomally-synthesized and post-translationally modified peptide (RiPP) natural products are processed by tailoring enzymes to create complex natural products that are still recognizably peptide-based. However, some tailoring enzymes dismantle the peptide en route to synthesis of small molecules. The biosynthesis of a small-molecule natural product of as yet unknown structure, mycofactocin, is thought to be synthesized in this way, via the mft gene cluster found in many strains of Mycobacteria. This cluster harbors at least six genes, which appear to be conserved across species...
January 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28059275/development-and-characterization-of-high-suppression-and-high-%C3%A3-tendue-narrowband-spectral-filters
#11
Adam Kinos, Qian Li, Lars Rippe, Stefan Kröll
The present work addresses critical issues in constructing high suppression, narrowband spectral filters in rare-earth-ion-doped crystals, mainly targeting the application of ultrasound optical tomography but is also applicable for areas such as quantum memories, self-filtering of laser frequencies, and other applications relying on high absorption in rare-earth-ion-doped crystals. The polarization of light transmitted through a highly absorbing crystal is experimentally analyzed. Additionally, an existing wave propagation method is used to simulate beam propagation through a spectral hole to study the high étendue requirements of ultrasound optical tomography...
December 20, 2016: Applied Optics
https://www.readbyqxmd.com/read/28057678/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#12
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28051889/race-ethnicity-in-medical-education-an-analysis-of-a-question-bank-for-step-1-of-the-united-states-medical-licensing-examination
#13
Kelsey Ripp, Lundy Braun
: Phenomenon: There is growing concern over racial/ethnic bias in clinical care, yet how best to reduce bias remains challenging, in part because the sources of bias in medical education are poorly understood. One possible source is the routinized use of race/ethnicity in lectures, assessment, and preparatory materials, including question banks for licensing examinations. Because students worldwide use question banks to prepare for the United States Medical Licensing Examination, we examined how race/ethnicity was used in one of the most commonly recommended question banks...
January 4, 2017: Teaching and Learning in Medicine
https://www.readbyqxmd.com/read/28009976/ammosamides-unveil-novel-biosynthetic-machinery
#14
Dominic A Colosimo, John B MacMillan
In this issue of Cell Chemical Biology, Jordan and Moore (2016) present a thorough biosynthetic analysis of ammosamides, a bacterial natural product. The work highlights the previously unknown overlap between two natural products families: pyrroloquinoline alkaloids and ribosomally synthesized posttranslationally modified peptides (RiPPs).
December 22, 2016: Cell Chemical Biology
https://www.readbyqxmd.com/read/28005705/denervation-of-the-distal-renal-arterial-branches-vs-conventional-main-renal-artery-treatment-a-randomized-controlled-trial-for-treatment-of-resistant-hypertension
#15
Stanislav E Pekarskiy, Andrei E Baev, Victor F Mordovin, Galina V Semke, Tatyana M Ripp, Alla U Falkovskaya, Valeria A Lichikaki, Ekaterina S Sitkova, Irina V Zubanova, Sergei V Popov
BACKGROUND: Effective treatment of uncontrolled hypertension using catheter-based percutaneous renal denervation may depend strongly on the anatomic strategy applied when delivering therapy. We hypothesized that concentering renal denervation treatment in the distal region of the artery would improve clinical response. METHODS AND RESULTS: We conducted a single-center, double-blind, randomized, controlled, and parallel group study (ClinicalTrials.gov NCT02667912)...
February 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/27998080/structure-of-the-lasso-peptide-isopeptidase-identifies-a-topology-for-processing-threaded-substrates
#16
Jonathan R Chekan, Joseph D Koos, Chuhan Zong, Mikhail O Maksimov, A James Link, Satish K Nair
Lasso peptides are a class of bioactive ribosomally synthesized and post-translationally modified peptides (RiPPs), with a threaded knot structure that is formed by an isopeptide bond attaching the N-terminus of the peptide to a side chain carboxylate. Some lasso peptide biosynthetic clusters harbor an enzyme that specifically hydrolyzes the isopeptide bond to yield the linear peptide. We describe here the 2.4 Å resolution structure of a lasso peptide isopeptidase revealing a topologically novel didomain architecture consisting of an open β-propeller appended to an α/β hydrolase domain...
December 21, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27974597/what-is-the-appropriate-upper-limit-for-added-sugars-consumption
#17
James M Rippe, John L Sievenpiper, Kim-Anne Lê, John S White, Roger Clemens, Theodore J Angelopoulos
Dramatic increases in obesity and diabetes have occurred worldwide over the past 30 years. Some investigators have suggested that these increases may be due, in part, to increased added sugars consumption. Several scientific organizations, including the World Health Organization, the Scientific Advisory Council on Nutrition, the Dietary Guidelines Advisory Committee 2015, and the American Heart Association, have recommended significant restrictions on upper limits of sugars consumption. In this review, the scientific evidence related to sugars consumption and its putative link to various chronic conditions such as obesity, diabetes, heart disease, nonalcoholic fatty liver disease, and the metabolic syndrome is examined...
January 2017: Nutrition Reviews
https://www.readbyqxmd.com/read/27966282/enzyme-from-an-uncultivated-sponge-bacterium-catalyzes-s-methylation-in-a-ribosomal-peptide
#18
Maximilian Helf, Aurelia Jud, Jörn Piel
Amino acid modifications are essential for the structural diversity and bioactivity of ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs). A particularly large and virtually untapped pool of unusual RiPPs and associated modifying enzymes is provided by uncultivated bacteria. An example is the chemically rich sponge symbiont 'Candidatus Entotheonella factor' that produces the hypermodified polytheonamides of the poorly studied proteusin RiPP family. In addition to the polytheonamide genes, 'E...
December 14, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27934015/the-b12-radical-sam-enzyme-poyc-catalyzes-valine-c%C3%AE-methylation-during-polytheonamide-biosynthesis
#19
Aubérie Parent, Alain Guillot, Alhosna Benjdia, Gwladys Chartier, Jérôme Leprince, Olivier Berteau
Genomic and metagenomic investigations have recently led to the delineation of a novel class of natural products called ribosomally synthesized and post-translationally modified peptides (RiPPs). RiPPs are ubiquitous among living organisms and include pharmaceutically relevant compounds such as antibiotics and toxins. A prominent example is polytheonamide A, which exhibits numerous post-translational modifications, some of which were unknown in ribosomal peptides until recently. Among these post-translational modifications, C-methylations have been proposed to be catalyzed by two putative radical S-adenosylmethionine (rSAM) enzymes, PoyB and PoyC...
December 7, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27933322/silicone-disclosing-material-used-after-ceramic-surface-treatment-reduces-bond-strength
#20
Sara Fraga, Sara Cioccari Oliveira, Gabriel Kalil Rocha Pereira, Pieter Beekman, Marília Pivetta Rippe, Cornelis J Kleverlaan
PURPOSE: To evaluate the effect of a silicone disclosing procedure performed at different timepoints on the shear bond strength (SBS) of cements (self-adhesive composite cement, self-etch composite cement, resin-reinforced glass-ionomer cement) to different substrates (zirconia, lithium disilicate, bovine dentin). MATERIALS AND METHODS: The substrate/cement combinations were assigned to two groups (n = 15) according to the timepoint, at which the vinyl polyether silicone disclosing agent was applied: after (experimental groups, EXP) or before (control groups, CTRL) specific micromechanical treatments of the substrate surface...
December 8, 2016: Journal of Adhesive Dentistry
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