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https://www.readbyqxmd.com/read/30289602/using-microarray-based-subtyping-methods-for-breast-cancer-in-the-era-of-high-throughput-rna-sequencing
#1
Christina Bligaard Pedersen, Finn Cilius Nielsen, Maria Rossing, Lars Rønn Olsen
Breast cancer is a highly heterogeneous disease that can be classified into multiple subtypes based on the tumor transcriptome. Most of the subtyping schemes used in clinics today are derived from analyses of microarray data from thousands of different tumors together with clinical data for the patients from which the tumors were isolated. However, RNA sequencing is gradually replacing microarrays as the preferred transcriptomics platform, and although transcript abundances measured by the two different technologies are largely compatible, subtyping methods developed for probe-based microarray data are incompatible with RNA sequencing as input data...
October 5, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/30198896/crystal-structure-of-the-acinetobacter-baumannii-outer-membrane-protein-omp33
#2
Javier Abellón-Ruiz, Michael Zahn, Arnaud Baslé, Bert van den Berg
Acinetobacter baumannii is becoming a major threat to human health due to its multidrug resistance. This is owing in a large part to the low permeability of its outer membrane (OM), which prevents high internal antibiotic concentrations and makes antibiotic-resistance mechanisms more effective. To exploit OM channels as potential delivery vehicles for future antibiotics, structural information is required. One abundant OM protein in A. baumannii is Omp33. This protein has been reported to be important for the in vivo fitness and virulence of A...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30100337/ectopic-basl-reveals-tissue-cell-polarity-throughout-leaf-development-in-arabidopsis-thaliana
#3
Catherine Mansfield, Jacob L Newman, Tjelvar S G Olsson, Matthew Hartley, Jordi Chan, Enrico Coen
Tissue-wide polarity fields, in which cell polarity is coordinated across the tissue, have been described for planar organs such as the Drosophila wing and are considered important for coordinating growth and differentiation [1]. In planar plant organs, such as leaves, polarity fields have been identified for subgroups of cells, such as stomatal lineages [2], trichomes [3, 4], serrations [5], or early developmental stages [6]. Here, we show that ectopic induction of the stomatal protein BASL (BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE) reveals a tissue-wide epidermal polarity field in leaves throughout development...
August 20, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/30083357/loss-or-duplication-of-key-regulatory-genes-coincides-with-environmental-adaptation-of-the-stomatal-complex-in-nymphaea-colorata-and-kalanchoe-laxiflora
#4
Meizhi Xu, Fei Chen, Shilian Qi, Liangsheng Zhang, Shuang Wu
The stomatal complex is critical for gas and water exchange between plants and the atmosphere. Originating over 400 million years ago, the structure of the stomata has evolved to facilitate the adaptation of plants to various environments. Although the molecular mechanism of stomatal development in Arabidopsis has been widely studied, the evolution of stomatal structure and its molecular regulators in different species remains to be answered. In this study, we examined stomatal development and the orthologues of Arabidopsis stomatal genes in a basal angiosperm plant, Nymphaea colorata , and a member of the eudicot CAM family, Kalanchoe laxiflora , which represent the adaptation to aquatic and drought environments, respectively...
2018: Horticulture Research
https://www.readbyqxmd.com/read/29975378/directed-ortho-c-h-borylation-catalyzed-using-cp-rh-iii-nhc-complexes
#5
Jompol Thongpaen, Thibault E Schmid, Loic Toupet, Vincent Dorcet, Marc Mauduit, Olivier Baslé
Cp*Rh(NHC) complexes with bulky chiral bidentate NHC-carboxylate ligands were efficiently synthesized and fully characterized including solid-state structures. These unprecedented rhodium(iii) complexes demonstrated high selectivity in pyridine-directed ortho-C-H borylation of arenes under mild conditions.
July 19, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29657131/unusual-constriction-zones-in-the-major-porins-ompu-and-ompt-from-vibrio-cholerae
#6
Monisha Pathania, Silvia Acosta-Gutierrez, Satya Pratyusha Bhamidimarri, Arnaud Baslé, Mathias Winterhalter, Matteo Ceccarelli, Bert van den Berg
The outer membranes (OM) of many Gram-negative bacteria contain general porins, which form nonspecific, large-diameter channels for the diffusional uptake of small molecules required for cell growth and function. While the porins of Enterobacteriaceae (e.g., E. coli OmpF and OmpC) have been extensively characterized structurally and biochemically, much less is known about their counterparts in Vibrionaceae. Vibrio cholerae, the causative agent of cholera, has two major porins, OmpU and OmpT, for which no structural information is available despite their importance for the bacterium...
May 1, 2018: Structure
https://www.readbyqxmd.com/read/29568346/validating-and-enabling-phosphoglycerate-dehydrogenase-phgdh-as-a-target-for-fragment-based-drug-discovery-in-phgdh-amplified-breast-cancer
#7
Judith E Unterlass, Arnaud Baslé, Timothy J Blackburn, Julie Tucker, Céline Cano, Martin E M Noble, Nicola J Curtin
3-Phosphoglycerate dehydrogenase (PHGDH) has recently been identified as an attractive target in cancer therapy as it links upregulated glycolytic flux to increased biomass production in cancer cells. PHGDH catalyses the first step in the serine synthesis pathway and thus diverts glycolytic flux into serine synthesis. We have used siRNA-mediated suppression of PHGDH expression to show that PHGDH is a potential therapeutic target in PHGDH -amplified breast cancer. Knockdown caused reduced proliferation in the PHGDH -amplified cell line MDA-MB-468, whereas breast cancer cells with low PHGDH expression or with elevated PHGDH expression in the absence of genomic amplification were not affected...
March 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29516467/from-learning-beliefs-to-achievement-among-chinese-immigrant-and-european-american-preschool-children
#8
Jin Li, Yoko Yamamoto, Jamison M Kinnane, Bree C Shugarts, Clarence K K Ho
Little research exists on how immigrant children develop their beliefs about school learning (BASLs) in their home and host cultures. We examined the BASLs and achievement children of Chinese immigrants' (CCI) and European American (EA) children. We followed longitudinally 120 middle-class children from age 4 to 5, balanced for gender. Children heard two story beginnings depicting a child eager to attend school and another not. Children completed the stories and were tested for math and literacy achievement...
March 7, 2018: Child Development
https://www.readbyqxmd.com/read/29411780/corrigendum-complex-pectin-metabolism-by-gut-bacteria-reveals-novel-catalytic-functions
#9
Didier Ndeh, Artur Rogowski, Alan Cartmell, Ana S Luis, Arnaud Baslé, Joseph Gray, Immacolata Venditto, Jonathon Briggs, Xiaoyang Zhang, Aurore Labourel, Nicolas Terrapon, Fanny Buffetto, Sergey Nepogodiev, Yao Xiao, Robert A Field, Yanping Zhu, Malcolm A O'Neill, Breeanna R Urbanowicz, William S York, Gideon J Davies, D Wade Abbott, Marie-Christine Ralet, Eric C Martens, Bernard Henrissat, Harry J Gilbert
This corrects the article DOI: 10.1038/nature21725.
August 31, 2017: Nature
https://www.readbyqxmd.com/read/29365216/insight-into-metal-removal-from-peptides-that-sequester-copper-for-methane-oxidation
#10
Arnaud Baslé, Abdelnasser El Ghazouani, Jaeick Lee, Christopher Dennison
Methanobactins (Mbns) are modified peptides that sequester copper (Cu) methanotrophs use to oxidize methane. Limited structural information is available for this class of natural products, as is an understanding of how cells are able to utilize Mbn-bound Cu. The crystal structure of Methylosinus sporium NR3K CuI -Mbn provides further information about the structural diversity of Mbns and the first insight into their Cu-release mechanism. Nitrogen ligands from oxazolone and pyrazinediol rings chelate CuI along with adjacent coordinating sulfurs from thioamides...
March 26, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29335469/structural-basis-for-chitin-acquisition-by-marine-vibrio-species
#11
Anuwat Aunkham, Michael Zahn, Anusha Kesireddy, Karunakar Reddy Pothula, Albert Schulte, Arnaud Baslé, Ulrich Kleinekathöfer, Wipa Suginta, Bert van den Berg
Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world's oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29287266/stability-of-infliximab-solutions-in-different-temperature-and-dilution-conditions
#12
COMPARATIVE STUDY
Nicolas Tokhadze, Philip Chennell, Yoann Le Basle, Valerie Sautou
Infliximab is a monoclonal antibody widely used for the treatment of inflammatory diseases. Over the past few years, many studies have assessed that monoclonal antibodies are prone to aggregation under stress conditions. The aim of this study was to investigate the stability of solutions of an infliximab biosimilar (Inflectra® ) at different concentrations (0.4, 2 and 10 mg/mL). These solutions were separately submitted to three temperature conditions that are likely to happen during the drug dispensing system: -20 °C, 5 °C and 25 °C...
February 20, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29262655/structural-insights-into-the-enzymatic-activity-and-potential-substrate-promiscuity-of-human-3-phosphoglycerate-dehydrogenase-phgdh
#13
Judith E Unterlass, Robert J Wood, Arnaud Baslé, Julie Tucker, Céline Cano, Martin M E Noble, Nicola J Curtin
Cancer cells reprogram their metabolism and energy production to sustain increased growth, enable metastasis and overcome resistance to cancer treatments. Although primary roles for many metabolic proteins have been identified, some are promiscuous in regards to the reaction they catalyze. To efficiently target these enzymes, a good understanding of their enzymatic function and structure, as well as knowledge regarding any substrate or catalytic promiscuity is required. Here we focus on the characterization of human 3-phosphoglycerate dehydrogenase (PHGDH)...
November 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/29255254/dietary-pectic-glycans-are-degraded-by-coordinated-enzyme-pathways-in-human-colonic-bacteroides
#14
Ana S Luis, Jonathon Briggs, Xiaoyang Zhang, Benjamin Farnell, Didier Ndeh, Aurore Labourel, Arnaud Baslé, Alan Cartmell, Nicolas Terrapon, Katherine Stott, Elisabeth C Lowe, Richard McLean, Kaitlyn Shearer, Julia Schückel, Immacolata Venditto, Marie-Christine Ralet, Bernard Henrissat, Eric C Martens, Steven C Mosimann, D Wade Abbott, Harry J Gilbert
The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood...
February 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29165717/crystal-structure-of-nucb-a-biofilm-degrading-endonuclease
#15
Arnaud Baslé, Lorraine Hewitt, Alan Koh, Heather K Lamb, Paul Thompson, J Grant Burgess, Michael J Hall, Alastair R Hawkins, Heath Murray, Richard J Lewis
Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site...
January 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122851/guidelines-on-the-management-of-abnormal-liver-blood-tests
#16
Philip N Newsome, Rob Cramb, Suzanne M Davison, John F Dillon, Mark Foulerton, Edmund M Godfrey, Richard Hall, Ulrike Harrower, Mark Hudson, Andrew Langford, Anne Mackie, Robert Mitchell-Thain, Karen Sennett, Nicholas C Sheron, Julia Verne, Martine Walmsley, Andrew Yeoman
These updated guidelines on the management of abnormal liver blood tests have been commissioned by the Clinical Services and Standards Committee (CSSC) of the British Society of Gastroenterology (BSG) under the auspices of the liver section of the BSG. The original guidelines, which this document supersedes, were written in 2000 and have undergone extensive revision by members of the Guidelines Development Group (GDG). The GDG comprises representatives from patient/carer groups (British Liver Trust, Liver4life, PBC Foundation and PSC Support), elected members of the BSG liver section (including representatives from Scotland and Wales), British Association for the Study of the Liver (BASL), Specialist Advisory Committee in Clinical Biochemistry/Royal College of Pathology and Association for Clinical Biochemistry, British Society of Paediatric Gastroenterology, Hepatology and Nutrition (BSPGHAN), Public Health England (implementation and screening), Royal College of General Practice, British Society of Gastrointestinal and Abdominal Radiologists (BSGAR) and Society of Acute Medicine...
January 2018: Gut
https://www.readbyqxmd.com/read/29038444/structural-basis-for-maintenance-of-bacterial-outer-membrane-lipid-asymmetry
#17
Javier Abellón-Ruiz, Shreyas S Kaptan, Arnaud Baslé, Beatrice Claudi, Dirk Bumann, Ulrich Kleinekathöfer, Bert van den Berg
The Gram-negative bacterial outer membrane (OM) is a unique bilayer that forms an efficient permeation barrier to protect the cell from noxious compounds 1 , 2 . The defining characteristic of the OM is lipid asymmetry, with phospholipids comprising the inner leaflet and lipopolysaccharides comprising the outer leaflet 1-3 . This asymmetry is maintained by the Mla pathway, a six-component system that is widespread in Gram-negative bacteria and is thought to mediate retrograde transport of misplaced phospholipids from the outer leaflet of the OM to the cytoplasmic membrane 4 ...
December 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28960539/target-highlights-from-the-first-post-psi-casp-experiment-casp12-may-august-2016
#18
Andriy Kryshtafovych, Reinhard Albrecht, Arnaud Baslé, Pedro Bule, Alessandro T Caputo, Ana Luisa Carvalho, Kinlin L Chao, Ron Diskin, Krzysztof Fidelis, Carlos M G A Fontes, Folmer Fredslund, Harry J Gilbert, Celia W Goulding, Marcus D Hartmann, Christopher S Hayes, Osnat Herzberg, Johan C Hill, Andrzej Joachimiak, Gert-Wieland Kohring, Roman I Koning, Leila Lo Leggio, Marco Mangiagalli, Karolina Michalska, John Moult, Shabir Najmudin, Marco Nardini, Valentina Nardone, Didier Ndeh, Thanh-Hong Nguyen, Guido Pintacuda, Sandra Postel, Mark J van Raaij, Pietro Roversi, Amir Shimon, Abhimanyu K Singh, Eric J Sundberg, Kaspars Tars, Nicole Zitzmann, Torsten Schwede
The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.
March 2018: Proteins
https://www.readbyqxmd.com/read/28908231/mental-hygiene-as-an-academic-discipline-at-the-university-of-basle
#19
C M Senn-Dürck
No abstract text is available yet for this article.
1950: Mental Health
https://www.readbyqxmd.com/read/28672083/bleaching-earths-as-powerful-additives-for-ru-catalyzed-self-metathesis-of-non-refined-methyl-oleate-at-pilot-scale
#20
Jessica Allard, Idriss Curbet, Guillaume Chollet, Fabien Tripoteau, Sophie Sambou, Frédéric Caijo, Yann Raoul, Christophe Crévisy, Olivier Baslé, Marc Mauduit
A practical and cost-effective ruthenium-catalyzed self-metathesis of non-refined methyl oleate (85 %) derived from very high oleic sunflower oils was demonstrated at pilot scale using a robust and kg-scale commercially available SIPr-M71 pre-catalyst. The simple addition of 1 wt % bleaching earths (Tonsil 110FF) to a thermally pretreated oil could efficiently prevent catalyst deactivation. Remarkably, without the need for filtration, the catalytic system was able to achieve a turnover number (TON) of more than 744 000 at a catalyst loading of only 1 ppm...
September 18, 2017: Chemistry: a European Journal
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