keyword
MENU ▼
Read by QxMD icon Read
search

Ripps

keyword
https://www.readbyqxmd.com/read/29321523/integrative-genomic-and-transcriptomic-analysis-of-leiomyosarcoma
#1
Priya Chudasama, Sadaf S Mughal, Mathijs A Sanders, Daniel Hübschmann, Inn Chung, Katharina I Deeg, Siao-Han Wong, Sophie Rabe, Mario Hlevnjak, Marc Zapatka, Aurélie Ernst, Kortine Kleinheinz, Matthias Schlesner, Lina Sieverling, Barbara Klink, Evelin Schröck, Remco M Hoogenboezem, Bernd Kasper, Christoph E Heilig, Gerlinde Egerer, Stephan Wolf, Christof von Kalle, Roland Eils, Albrecht Stenzinger, Wilko Weichert, Hanno Glimm, Stefan Gröschel, Hans-Georg Kopp, Georg Omlor, Burkhard Lehner, Sebastian Bauer, Simon Schimmack, Alexis Ulrich, Gunhild Mechtersheimer, Karsten Rippe, Benedikt Brors, Barbara Hutter, Marcus Renner, Peter Hohenberger, Claudia Scholl, Stefan Fröhling
Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic options. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown. Here we show, using whole-exome and transcriptome sequencing, that LMS tumors are characterized by substantial mutational heterogeneity, near-universal inactivation of TP53 and RB1, widespread DNA copy number alterations including chromothripsis, and frequent whole-genome duplication. Furthermore, we detect alternative telomere lengthening in 78% of cases and identify recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing insight into the genetic basis of this mechanism...
January 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/29316156/tailored-environments-to-study-motile-cells-and-pathogens
#2
REVIEW
Julianne Mendi Muthinja, Johanna Ripp, Timothy Krüger, Andrea Imle, Tamás Haraszti, Oliver T Fackler, Joachim P Spatz, Markus Engstler, Friedrich Frischknecht
Motile cells and pathogens migrate in complex environments and yet are mostly studied on simple 2D substrates. In order to mimic the diverse environments of motile cells a set of assays including substrates of defined elasticity, microfluidics, micropatterns, organotypic cultures and 3D gels have been developed. We briefly introduce these and then focus on the use of micro-patterned pillar arrays, which help to bridge the gap between 2D and 3D. These structures are made from polydimethylsiloxane, a moldable plastic and their use has revealed new insights into mechanoperception in Caenorhabditis elegans, gliding motility of Plasmodium, swimming of trypanosomes and nuclear stability in cancer cells...
January 7, 2018: Cellular Microbiology
https://www.readbyqxmd.com/read/29246964/first-person-anne-rademacher
#3
(no author information available yet)
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Anne Rademacher is the first author on 'Real-time observation of light-controlled transcription in living cells', published in Journal of Cell Science. Anne is a PhD student in the laboratory of Karsten Rippe at the German Cancer Research Center and the Bioquant institute, Heidelberg, Germany, investigating the transcriptional silencing and activation of heterochromatin by using optogenetic tools and other microscopy methods...
December 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29246867/a-roadmap-for-research-on-resident-well-being
#4
Mariah A Quinn, Hasan Bazari, Jonathan Ripp, Lauren Block, Katherine C Chretien, Ethan D Fried, Richard E Leiter, Amber T Pincavage, Brielle Spataro, Mickey Trockel, Colin P West
No abstract text is available yet for this article.
December 12, 2017: American Journal of Medicine
https://www.readbyqxmd.com/read/29236899/mechanical-behavior-of-yttria-stabilized-tetragonal-zirconia-polycrystal-effects-of-different-aging-regimens
#5
Luís Felipe Guilardi, Gabriel Kalil Rocha Pereira, Vinícius Felipe Wandscher, Marília Pivetta Rippe, Luiz Felipe Valandro
This study aimed to characterize and compare the effect of different aging regimens on surface characteristic (topography and roughness), structural stability (phase transformation) and mechanical performance (Weibull analysis) of a Y-TZP ceramic. Discs (15 × 1.2 mm; VITA In-Ceram YZ) were prepared according to ISO 6872-2015 for biaxial flexural strength testing and randomly assigned into five groups (n = 30): as-sintered, no aging treatment (CTRL); 20 h in autoclave at 134°C, 2 bar pressure (AUT); intermittent mechanical loading at 20 Hz/106 load pulses (MechLoad); AUT followed by MechLoad (AUT+MechLoad); and storage in distilled water at 37°C, for 1 year (STO)...
December 7, 2017: Brazilian Oral Research
https://www.readbyqxmd.com/read/29217510/loss-of-vascular-myogenic-tone-in-mir-143-145-knockout-mice-is-associated-with-hypertension-induced-vascular-lesions-in-small-mesenteric-arteries
#6
Johan Holmberg, Anirban Bhattachariya, Azra Alajbegovic, Catarina Rippe, Mari Ekman, Diana Dahan, Tran Thi Hien, Thomas Boettger, Thomas Braun, Karl Swärd, Per Hellstrand, Sebastian Albinsson
OBJECTIVE: Pressure-induced myogenic tone is involved in autoregulation of local blood flow and confers protection against excessive pressure levels in small arteries and capillaries. Myogenic tone is dependent on smooth muscle microRNAs (miRNAs), but the identity of these miRNAs is unclear. Furthermore, the consequences of altered myogenic tone for hypertension-induced damage to small arteries are not well understood. APPROACH AND RESULTS: The importance of smooth muscle-enriched microRNAs, miR-143/145, for myogenic tone was evaluated in miR-143/145 knockout mice...
December 7, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29214529/a-rapid-and-reagent-free-bioassay-for-the-detection-of-dioxin-like-compounds-and-other-aryl-hydrocarbon-receptor-ahr-agonists-using-autobioluminescent-yeast
#7
Tingting Xu, Anna Young, Enolia Marr, Gary Sayler, Steven Ripp, Dan Close
An autonomously bioluminescent Saccharomyces cerevisiae BLYAhS bioreporter was developed in this study for the simple and rapid detection of dioxin-like compounds (DLCs) and aryl hydrocarbon receptor (AhR) agonists. This recombinant yeast reporter was based on a synthetic bacterial luciferase reporter gene cassette (lux) that can produce the luciferase as well as the enzymes capable of self-synthesizing the requisite substrates for bioluminescent production from endogenous cellular metabolites. As a result, bioluminescent signal production is generated continuously and autonomously without cell lysis or exogenous reagent addition...
December 6, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29211045/co-cultured-continuously-bioluminescent-human-cells-as-bioreporters-for-the-detection-of-prodrug-therapeutic-impact-pre-and-post-metabolism
#8
Tingting Xu, Michael Conway, Ashley Frank, Steven Ripp, Gary Sayler, Dan Close
Modern drug discovery workflows require assay systems capable of replicating the complex interactions of multiple tissue types, but that can still function under high throughput conditions. In this work, we evaluate the use of substrate-free autobioluminescence in human cell lines to support the performance of these assays with reduced economical and logistical restrictions relative to substrate-requiring bioluminescent reporter systems. The use of autobioluminescence was found to support assay functionality similar to existing luciferase reporter targets...
December 6, 2017: Sensors
https://www.readbyqxmd.com/read/29207500/enrichment-of-circular-code-motifs-in-the-genes-of-the-yeast-saccharomyces-cerevisiae
#9
Christian J Michel, Viviane Nguefack Ngoune, Olivier Poch, Raymond Ripp, Julie D Thompson
A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches...
December 3, 2017: Life
https://www.readbyqxmd.com/read/29206037/macroamidine-formation-in-bottromycins-is-catalyzed-by-a-divergent-ycao-enzyme
#10
Laura Franz, Sebastian Adam, Javier Santos-Aberturas, Andrew W Truman, Jesko Koehnke
The YcaO superfamily of proteins catalyzes the phosphorylation of peptide backbone amide bonds, which leads to the formation of azolines and azoles in ribosomally synthesized and post-translationally modified peptides (RiPPs). Bottromycins are RiPPs with potent antimicrobial activity, and their biosynthetic pathway contains two divergent, stand-alone YcaO enzymes, IpoC and PurCD. From an untargeted metabolomics approach, it had been suggested that PurCD acts with a partner protein to form the 12-membered macroamidine unique to bottromycins...
December 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29200283/in-vitro-biosynthetic-studies-of-bottromycin-expand-the-enzymatic-capabilities-of-the-ycao-superfamily
#11
Christopher J Schwalen, Graham A Hudson, Simone Kosol, Nilkamal Mahanta, Gregory L Challis, Douglas A Mitchell
The bottromycins belong to the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Bottromycins exhibit unique structural features, including a hallmark macrolactamidine ring and thiazole heterocycle for which divergent members of the YcaO superfamily have been biosynthetically implicated. Here we report the in vitro reconstitution of two YcaO proteins, BmbD and BmbE, responsible for the ATP-dependent cyclodehydration reactions that yield thiazoline- and macrolactamidine-functionalized products, respectively...
December 4, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29187964/population-structure-and-connectivity-of-the-mountainous-star-coral-orbicella-faveolata-throughout-the-wider-caribbean-region
#12
John P Rippe, Mikhail V Matz, Elizabeth A Green, Mónica Medina, Nida Z Khawaja, Thanapat Pongwarin, Jorge H Pinzón C, Karl D Castillo, Sarah W Davies
As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29167789/radical-sam-enzymes-in-the-biosynthesis-of-ribosomally-synthesized-and-post-translationally-modified-peptides-ripps
#13
REVIEW
Alhosna Benjdia, Clémence Balty, Olivier Berteau
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29138389/phage-display-and-selection-of-lanthipeptides-on-the-carboxy-terminus-of-the-gene-3-minor-coat-protein
#14
Johannes H Urban, Markus A Moosmeier, Tobias Aumüller, Marcus Thein, Tjibbe Bosma, Rick Rink, Katharina Groth, Moritz Zulley, Katja Siegers, Kathrin Tissot, Gert N Moll, Josef Prassler
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an emerging class of natural products with drug-like properties. To fully exploit the potential of RiPPs as peptide drug candidates, tools for their systematic engineering are required. Here we report the engineering of lanthipeptides, a subclass of RiPPs characterized by multiple thioether cycles that are enzymatically introduced in a regio- and stereospecific manner, by phage display. This was achieved by heterologous co-expression of linear lanthipeptide precursors fused to the widely neglected C-terminus of the bacteriophage M13 minor coat protein pIII, rather than the conventionally used N-terminus, along with the modifying enzymes from distantly related bacteria...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29122982/real-time-observation-of-light-controlled-transcription-in-living-cells
#15
Anne Rademacher, Fabian Erdel, Jorge Trojanowski, Sabrina Schumacher, Karsten Rippe
Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 minutes after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light...
November 9, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29112329/in-vitro-and-in-vivo-investigation-of-potential-for-complex-cyp3a-interaction-for-pf-00251802-dagrocorat-a-novel-dissociated-agonist-of-the-glucocorticoid-receptor
#16
Sharon L Ripp, Arnab Mukherjee, Heather Eng, Thomas Stock, Dona Fleishaker, Tina Checchio, Brinda Tammara
The dissociated agonists of the glucocorticoid receptor are a novel class of agents in clinical development for rheumatoid arthritis. PF-04171327 (fosdagrocorat) is a phosphate ester prodrug of PF-00251802 (dagrocorat), a selective high-affinity partial agonist of the glucocorticoid receptor, which is further metabolized to PF-04015475. This study evaluated the cytochrome P450 (CYP)-mediated drug-drug interaction (DDI) potential of PF-00251802 and PF-04015475 in vitro and used model-based prediction approaches to estimate clinical impact...
November 7, 2017: Clinical Pharmacology in Drug Development
https://www.readbyqxmd.com/read/29095134/training-in-urban-medicine-and-public-health-preparing-physicians-to-address-urban-health-care-needs
#17
Cynthia Haq, Melissa Lemke, Michelle Buelow, Marjorie Stearns, Christine Ripp, Patrick McBride
BACKGROUND: Wisconsin is facing significant physician shortages. The University of Wisconsin School of Medicine and Public Health (UWSMPH) launched Training in Urban Medicine and Public Health (TRIUMPH) to recruit and prepare medical students to serve people living within urban Health Professional Shortage Areas. METHODS: Students are selected based on their commitment to improve health equity for urban populations. They complete clinical rotations, core curriculum, and community projects in Milwaukee, Wisconsin...
December 2016: WMJ: Official Publication of the State Medical Society of Wisconsin
https://www.readbyqxmd.com/read/29094593/correction-to-radical-s-adenosylmethionine-enzymes-involved-in-ripp-biosynthesis
#18
Nilkamal Mahanta, Graham A Hudson, Douglas A Mitchell
No abstract text is available yet for this article.
November 2, 2017: Biochemistry
https://www.readbyqxmd.com/read/29082082/analysis-of-the-potential-for-non-invasive-imaging-of-oxygenation-at-heart-depth-using-ultrasound-optical-tomography-uot-or-photo-acoustic-tomography-pat
#19
Andreas Walther, Lars Rippe, Lihong V Wang, Stefan Andersson-Engels, Stefan Kröll
Despite the important medical implications, it is currently an open task to find optical non-invasive techniques that can image deep organs in humans. Addressing this, photo-acoustic tomography (PAT) has received a great deal of attention in the past decade, owing to favorable properties like high contrast and high spatial resolution. However, even with optimal components PAT cannot penetrate beyond a few centimeters, which still presents an important limitation of the technique. Here, we calculate the absorption contrast levels for PAT and for ultrasound optical tomography (UOT) and compare them to their relevant noise sources as a function of imaging depth...
October 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/29074949/erratum-dnmt-and-hdac-inhibitors-induce-cryptic-transcription-start-sites-encoded-in-long-terminal-repeats
#20
David Brocks, Christopher R Schmidt, Michael Daskalakis, Hyo Sik Jang, Nakul M Shah, Daofeng Li, Jing Li, Bo Zhang, Yiran Hou, Sara Laudato, Daniel B Lipka, Johanna Schott, Holger Bierhoff, Yassen Assenov, Monika Helf, Alzbeta Ressnerova, Md Saiful Islam, Anders M Lindroth, Simon Haas, Marieke Essers, Charles D Imbusch, Benedikt Brors, Ina Oehme, Olaf Witt, Michael Lübbert, Jan-Philipp Mallm, Karsten Rippe, Rainer Will, Dieter Weichenhan, Georg Stoecklin, Clarissa Gerhäuser, Christopher C Oakes, Ting Wang, Christoph Plass
This corrects the article DOI: 10.1038/ng.3889.
October 27, 2017: Nature Genetics
keyword
keyword
103349
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"