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https://www.readbyqxmd.com/read/29019686/virtual-exploration-of-the-ring-systems-chemical-universe
#1
Ricardo Visini, Josep Arus-Pous, Mahendra Awale, Jean-Louis Reymond
Here we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916,130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms, and GDB4c3D containing the corresponding 6,555,929 stereoisomers...
October 11, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28965845/the-immune-signaling-adaptor-lat-contributes-to-the-neuroanatomical-phenotype-of-16p11-2-bp2-bp3-cnvs
#2
Maria Nicla Loviglio, Thomas Arbogast, Aia Elise Jønch, Stephan C Collins, Konstantin Popadin, Camille S Bonnet, Giuliana Giannuzzi, Anne M Maillard, Sébastien Jacquemont, Binnaz Yalcin, Nicholas Katsanis, Christelle Golzio, Alexandre Reymond
Copy-number changes in 16p11.2 contribute significantly to neuropsychiatric traits. Besides the 600 kb BP4-BP5 CNV found in 0.5%-1% of individuals with autism spectrum disorders and schizophrenia and whose rearrangement causes reciprocal defects in head size and body weight, a second distal 220 kb BP2-BP3 CNV is likewise a potent driver of neuropsychiatric, anatomical, and metabolic pathologies. These two CNVs are engaged in complex reciprocal chromatin looping, intimating a functional relationship between genes in these regions that might be relevant to pathomechanism...
October 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28963451/cnv-association-meta-analysis-in-191-161-european-adults-reveals-new-loci-associated-with-anthropometric-traits
#3
Aurélien Macé, Marcus A Tuke, Patrick Deelen, Kati Kristiansson, Hannele Mattsson, Margit Nõukas, Yadav Sapkota, Ursula Schick, Eleonora Porcu, Sina Rüeger, Aaron F McDaid, David Porteous, Thomas W Winkler, Erika Salvi, Nick Shrine, Xueping Liu, Wei Q Ang, Weihua Zhang, Mary F Feitosa, Cristina Venturini, Peter J van der Most, Anders Rosengren, Andrew R Wood, Robin N Beaumont, Samuel E Jones, Katherine S Ruth, Hanieh Yaghootkar, Jessica Tyrrell, Aki S Havulinna, Harmen Boers, Reedik Mägi, Jennifer Kriebel, Martina Müller-Nurasyid, Markus Perola, Markku Nieminen, Marja-Liisa Lokki, Mika Kähönen, Jorma S Viikari, Frank Geller, Jari Lahti, Aarno Palotie, Päivikki Koponen, Annamari Lundqvist, Harri Rissanen, Erwin P Bottinger, Saima Afaq, Mary K Wojczynski, Petra Lenzini, Ilja M Nolte, Thomas Sparsø, Nicole Schupf, Kaare Christensen, Thomas T Perls, Anne B Newman, Thomas Werge, Harold Snieder, Timothy D Spector, John C Chambers, Seppo Koskinen, Mads Melbye, Olli T Raitakari, Terho Lehtimäki, Martin D Tobin, Louise V Wain, Juha Sinisalo, Annette Peters, Thomas Meitinger, Nicholas G Martin, Naomi R Wray, Grant W Montgomery, Sarah E Medland, Morris A Swertz, Erkki Vartiainen, Katja Borodulin, Satu Männistö, Anna Murray, Murielle Bochud, Sébastien Jacquemont, Fernando Rivadeneira, Thomas F Hansen, Albertine J Oldehinkel, Massimo Mangino, Michael A Province, Panos Deloukas, Jaspal S Kooner, Rachel M Freathy, Craig Pennell, Bjarke Feenstra, David P Strachan, Guillaume Lettre, Joel Hirschhorn, Daniele Cusi, Iris M Heid, Caroline Hayward, Katrin Männik, Jacques S Beckmann, Ruth J F Loos, Dale R Nyholt, Andres Metspalu, Johan G Eriksson, Michael N Weedon, Veikko Salomaa, Lude Franke, Alexandre Reymond, Timothy M Frayling, Zoltán Kutalik
There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations at 1q21.1, 3q29, 7q11.23, 11p14.2, and 18q21.32 and confirms two known loci at 16p11.2 and 22q11.21, implicating at least one anthropometric trait. The discovered CNVs are recurrent and rare (0.01-0.2%), with large effects on height (>2...
September 29, 2017: Nature Communications
https://www.readbyqxmd.com/read/28941184/frontiers-in-medicinal-chemistry-2017-in-bern-switzerland
#4
Daniel Probst, Marc Heitz, Marion Poirier, Bee Ha Gan, Clémence Delalande, Jean-Louis Reymond
Sharing capital ideas: The 2017 Frontiers in Medicinal Chemistry (FiMC) conference, organized jointly by the German Chemical Society, the German Pharmaceutical Society, and the Swiss Chemical Society, was held at the Department of Chemistry and Biochemistry of the University of Bern in February 2017. Herein we summarize the many conference highlights, and look forward to the next FiMC meeting, to be held in Jena (Germany) in March 2018.
September 22, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28941028/luciferases-with-tunable-emission-wavelengths
#5
Julien Hiblot, Qiuliyang Yu, Marina D B Sabbadini, Luc Reymond, Lin Xue, Alberto Schena, Olivier Sallin, Nicholas Hill, Rudolf Griss, Kai Johnsson
We introduce luciferases whose emission maxima can be tuned to different wavelengths by chemical labeling. The luciferases are chimeras of NanoLuc with either SNAP-tag or HaloTag7. Labeling of the self-labeling tag with a fluorophore shifts the emission maximum of NanoLuc to that of the fluorophore. Luciferases with tunable colors have applications as reporter genes, for the construction of biosensors and in bioimaging.
September 22, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28925919/computational-design-of-environmental-sensors-for-the-potent-opioid-fentanyl
#6
Matthew J Bick, Per J Greisen, Kevin J Morey, Mauricio S Antunes, David La, Banumathi Sankaran, Luc Reymond, Kai Johnsson, June I Medford, David Baker
We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability...
September 19, 2017: ELife
https://www.readbyqxmd.com/read/28919192/magnetic-resonance-index-of-activity-maria-and-clermont-score-are-highly-and-equally-effective-mri-indices-in-detecting-mucosal-healing-in-crohn-s-disease
#7
Anthony Buisson, Bruno Pereira, Marion Goutte, Maud Reymond, Christophe Allimant, Hélène Obritin-Guilhen, Gilles Bommelaer, Constance Hordonneau
BACKGROUND: Magnetic resonance index of activity (MaRIA) and Clermont score are currently the two main MRI indices that have been validated compared to endoscopy in Crohn's disease (CD). AIMS: To compare the accuracy of MaRIA and Clermont score in assessing CD mucosal healing. METHODS: Fourty-four CD patients underwent prospectively and consecutively MRI and colonoscopy. RESULTS: Considering 207 segments, MaRIA>7 and Clermont score>8...
August 31, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28813151/medicinal-and-biological-chemistry-mbc-library-an-efficient-source-of-new-hits
#8
Víctor Sebastián-Pérez, Carlos Roca, Mahendra Awale, Jean-Louis Reymond, Ana Martinez, Carmen Gil, Nuria E Campillo
Identification of new hits is one of the biggest challenges in drug discovery. Creating a library of well-characterized drug-like compounds is a key step in this process. Our group has developed an in-house chemical library called the Medicinal and Biological Chemistry (MBC) library. This collection has been successfully used to start several medicinal chemistry programs and developed in an accumulation of more than 30 years of experience in drug design and discovery of new drugs for unmet diseases. It contains over 1000 compounds, mainly heterocyclic scaffolds...
September 25, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28748955/bayesian-association-scan-reveals-loci-associated-with-human-lifespan-and-linked-biomarkers
#9
Aaron F McDaid, Peter K Joshi, Eleonora Porcu, Andrea Komljenovic, Hao Li, Vincenzo Sorrentino, Maria Litovchenko, Roel P J Bevers, Sina Rüeger, Alexandre Reymond, Murielle Bochud, Bart Deplancke, Robert W Williams, Marc Robinson-Rechavi, Fred Paccaud, Valentin Rousson, Johan Auwerx, James F Wilson, Zoltán Kutalik
The enormous variation in human lifespan is in part due to a myriad of sequence variants, only a few of which have been revealed to date. Since many life-shortening events are related to diseases, we developed a Mendelian randomization-based method combining 58 disease-related GWA studies to derive longevity priors for all HapMap SNPs. A Bayesian association scan, informed by these priors, for parental age of death in the UK Biobank study (n=116,279) revealed 16 independent SNPs with significant Bayes factor at a 5% false discovery rate (FDR)...
July 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28716054/combined-biotic-stresses-trigger-similar-transcriptomic-responses-but-contrasting-resistance-against-a-chewing-herbivore-in-brassica-nigra
#10
Christelle Bonnet, Steve Lassueur, Camille Ponzio, Rieta Gols, Marcel Dicke, Philippe Reymond
BACKGROUND: In nature, plants are frequently exposed to simultaneous biotic stresses that activate distinct and often antagonistic defense signaling pathways. How plants integrate this information and whether they prioritize one stress over the other is not well understood. RESULTS: We investigated the transcriptome signature of the wild annual crucifer, Brassica nigra, in response to eggs and caterpillars of Pieris brassicae butterflies, Brevicoryne brassicae aphids and the bacterial phytopathogen Xanthomonas campestris pv...
July 17, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28683118/reef-calcifiers-are-adapted-to-episodic-heat-stress-but-vulnerable-to-sustained-warming
#11
Marleen Stuhr, Claire E Reymond, Vera Rieder, Pamela Hallock, Jörg Rahnenführer, Hildegard Westphal, Michal Kucera
Shallow marine ecosystems naturally experience fluctuating physicochemical conditions across spatial and temporal scales. Widespread coral-bleaching events, induced by prolonged heat stress, highlight the importance of how the duration and frequency of thermal stress influence the adaptive physiology of photosymbiotic calcifiers. Large benthic foraminifera harboring algal endosymbionts are major tropical carbonate producers and bioindicators of ecosystem health. Like corals, they are sensitive to thermal stress and bleach at temperatures temporarily occurring in their natural habitat and projected to happen more frequently...
2017: PloS One
https://www.readbyqxmd.com/read/28586473/exome-sequencing-identifies-two-variants-of-the-alkylglycerol-monooxygenase-gene-as-a-cause-of-relapses-in-visceral-leishmaniasis-in-children-in-sudan
#12
Sandrine Marquet, Bruno Bucheton, Camille Reymond, Laurent Argiro, Sayda Hassan El-Safi, Musa Mohamed Kheir, Jean-Pierre Desvignes, Christophe Béroud, Adil Mergani, Awad Hammad, Alain J Dessein
Background: Visceral leishmaniasis (kala-azar, KA) is the most severe form of leishmaniasis, characterized by fever, weight loss, hepatosplenomegaly, and lymphadenopathy. During an outbreak of KA in Babar El Fugara (Sudan), 5.7% of cured patients displayed relapses, with familial clustering in half the cases. Methods: We performed whole-exome sequencing on 10 relapsing individuals and 11 controls from 5 nuclear families. Results: Rare homozygous and compound-heterozygous nonsense (c...
July 1, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28575298/chemo-enzymatic-synthesis-of-lipid-linked-glcnac2man5-oligosaccharides-using-recombinant-alg1-alg2-and-alg11-proteins
#13
Ana S Ramírez, Jérémy Boilevin, Chia-Wei Lin, Bee Ha Gan, Daniel Janser, Markus Aebi, Tamis Darbre, Jean-Louis Reymond, Kaspar P Locher
The biosynthesis of eukaryotic lipid-linked oligosaccharides (LLOs) that act as donor substrates in eukaryotic protein N-glycosylation starts on the cytoplasmic side of the endoplasmic reticulum and includes the sequential addition of five mannose units to dolichol-pyrophosphate-GlcNAc2. These reactions are catalyzed by the Alg1, Alg2 and Alg11 gene products and yield Dol-PP-GlcNAc2Man5, an LLO intermediate that is subsequently flipped to the lumen of the endoplasmic reticulum. While the purification of active Alg1 has previously been described, Alg11 and Alg2 have been mostly studied in vivo...
June 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/28503804/neural-correlates-of-visuomotor-adjustments-during-scaling-of-human-finger-movements
#14
Johannes Brand, Lars Michels, Romy Bakker, Marie-Claude Hepp-Reymond, Daniel Kiper, Manfred Morari, Kynan Eng
Visually guided finger movements include online feedback of current effector position to guide target approach. This visual feedback may be scaled or otherwise distorted by unpredictable perturbations. Although adjustments to visual feedback scaling have been studied before, the underlying brain activation differences between upscaling (visual feedback larger than real movement) and downscaling (feedback smaller than real movement) are currently unknown. Brain activation differences between upscaling and downscaling might be expected because within-trial adjustments during upscaling require corrective backwards accelerations, whereas correcting for downscaling requires forward accelerations...
May 15, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28496997/a-new-split-hand-foot-malformation-with-long-bone-deficiency-familial-case
#15
Carmela Fusco, Pasquelena De Nittis, Ali Abdullah Alfaiz, Maria Teresa Pellico, Bartolomeo Augello, Natascia Malerba, Leopoldo Zelante, Alexandre Reymond, Giuseppe Merla
Split hand/foot malformation with long bone deficiency (SHFLD) is a congenital limb anomaly where hands and/or feet cleft and syndactyly are associated with long bone defects, usually involving the tibia. Previously published data reported that 17p13.3 chromosomal duplication, including the BHLHA9 gene, has been associated with the distinct entity, termed SHFLD3 (OMIM 612576), inherited as an autosomal dominant trait. Here, we present a family with three members affected by SHFLD harboring BHLHA9 duplication...
June 2017: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/28455184/arabidopsis-glucosinolates-trigger-a-contrasting-transcriptomic-response-in-a-generalist-and-a-specialist-herbivore
#16
COMPARATIVE STUDY
Fabian Schweizer, Hanna Heidel-Fischer, Heiko Vogel, Philippe Reymond
Phytophagous insects have to deal with toxic defense compounds from their host plants. Although it is known that insects have evolved genes and mechanisms to detoxify plant allochemicals, how specialist and generalist precisely respond to specific secondary metabolites at the molecular level is less understood. Here we studied the larval performance and transcriptome of the generalist moth Heliothis virescens and the specialist butterfly Pieris brassicae feeding on Arabidopsis thaliana genotypes with different glucosinolate (GS) levels...
June 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28446340/peptide-dendrimer-lipid-conjugates-as-dna-and-sirna-transfection-reagents-role-of-charge-distribution-across-generations
#17
Marc Heitz, Albert Kwok, Gabriela A Eggimann, Florian Hollfelder, Tamis Darbre, Jean-Louis Reymond
Transfection reagents are used to deliver DNA and siRNA into cells to achieve genetic manipulations, and may ultimately enable nonviral gene therapy. Progress in transfection reagents is limited by the fact that such reagents cannot be easily optimized due to their polymeric nature and/or difficult synthesis. We have developed a new class of well-defined and easily modifiable transfection reagents in the form of peptide dendrimers. These dendrimers self-assemble with DNA or siRNA and lipofectin to form nanoparticles which efficiently enter mammalian cells and liberate their nucleic acid cargo...
April 26, 2017: Chimia
https://www.readbyqxmd.com/read/28437462/correction-virtual-hand-feedback-reduces-reaction-time-in-an-interactive-finger-reaching-task
#18
Johannes Brand, Marco Piccirelli, Marie-Claude Hepp-Reymond, Manfred Morari, Lars Michels, Kynan Eng
[This corrects the article DOI: 10.1371/journal.pone.0154807.].
2017: PloS One
https://www.readbyqxmd.com/read/28375006/fragment-database-fdb-17
#19
Ricardo Visini, Mahendra Awale, Jean-Louis Reymond
To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragmentlike molecules evenly covering a broad value range for molecular size, polarity, and stereochemical complexity...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28351929/genetic-heterogeneity-in-therapy-na%C3%A3-ve-synchronous-primary-breast-cancers-and-their-metastases
#20
Charlotte K Y Ng, Francois-Clement Bidard, Salvatore Piscuoglio, Felipe C Geyer, Raymond S Lim, Ino de Bruijn, Ronglai Shen, Fresia Pareja, Samuel H Berman, Lu Wang, Jean-Yves Pierga, Anne Vincent-Salomon, Agnes Viale, Larry Norton, Brigitte Sigal, Britta Weigelt, Paul Cottu, Jorge S Reis-Filho
Purpose: Paired primary breast cancers and metachronous metastases after adjuvant treatment are reported to differ in their clonal composition and genetic alterations, but it is unclear whether these differences stem from the selective pressures of the metastatic process, the systemic therapies, or both. We sought to define the repertoire of genetic alterations in breast cancer patients with de novo metastatic disease who had not received local or systemic therapy.Experimental Design: Up to two anatomically distinct core biopsies of primary breast cancers and synchronous distant metastases from nine patients who presented with metastatic disease were subjected to high-depth whole-exome sequencing...
March 28, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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