ALBERT

Description: Article Clouds play a pivotal role in the energy and mass balance of the Greenland ice sheet, thereby affecting its contribution to global sea-level rise. Here, using a combination of observations and model simulations, the authors show that clouds enhance Greenland ice sheet meltwater runoff by more than 30%. Nature Communications doi: 10.1038/ncomms10266 Authors: K. Van Tricht, S. Lhermitte, J. T. M. Lenaerts, I. V. Gorodetskaya, T. S. L’Ecuyer, B. Noël, M. R. van den Broeke, D. D. Turner, N. P. M. van Lipzig

Description: Treatment of renal calculi is highly dependent on the chemical composition of the stone in question, which is difficult to determine using standard imaging techniques. The objective of this study is to evaluate the potential of scatter-sensitive X-ray dark-field radiography to differentiate between the most common types of kidney stones in clinical practice. Here, we examine the absorption-to-scattering ratio of 118 extracted kidney stones with a laboratory Talbot-Lau Interferometer. Depending on their chemical composition, microscopic growth structure and morphology the various types of kidney stones show strongly varying, partially opposite contrasts in absorption and dark-field imaging. By assessing the microscopic calculi morphology with high resolution micro-computed tomography measurements, we illustrate the dependence of dark-field signal strength on the respective stone type. Finally, we utilize X-ray dark-field radiography as a non-invasive, highly sensitive (100%) and specific (97%) tool for the differentiation of calcium oxalate, uric acid and mixed types of stones, while additionally improving the detectability of radio-lucent calculi. We prove clinical feasibility of the here proposed method by accurately classifying renal stones, embedded within a fresh pig kidney, using dose-compatible measurements and a quick and simple visual inspection. Scientific Reports 5 doi: 10.1038/srep09527

Description: Besides the overall mass density, strength of trabecular bone depends significantly on its microstructure. However, due to dose constraints in medical CT imaging, it is impossible to gain sufficient information about very fine bone structures in vivo on the micrometer scale. Here we show that a recently developed method of X-ray vector radiography (XVR), an imaging method which uses X-ray scattering information to form an image, allows predictions on the bone microstructure without the explicit need to spatially resolve even individual trabeculae in the bone. We investigated thick human femoral bone samples and compared state-of-the-art μCT data with XVR imaging. A model is presented which proves that XVR imaging yields information directly correlated with the trabecular microstructure. This opens up possibilities of using XVR as a tool to help early diagnosis of bone diseases, such as osteoporosis. Scientific Reports 4 doi: 10.1038/srep03695

Description: We present the results of high-resolution VLBI (very long baseline interferometry) observations at 1.6 and 4.9 GHz of the radio-loud Seyfert galaxy, Mrk 6. These observations are able to detect a compact radio core in this galaxy for the first time. The core has an inverted spectral index ($\alpha ^{1.6}_{4.9}$ = +1.0 ± 0.2) and a brightness temperature of 1 10 8  K. Three distinct radio components, which resemble jet elements and/or hotspots, are also detected. The position angles of these elongated jet elements point not only to a curved jet in Mrk 6, but also towards a connection between the AGN and the kpc-scale radio lobes/bubbles in this galaxy. Firmer constraints on the star formation rate provided by new Herschel observations (SFR 〈 0.8 M  yr –1 ) make the starburst-wind-powered bubble scenario implausible. From plasma speeds, obtained via prior Chandra X-ray observations, and ram pressure balance arguments for the interstellar medium and radio bubbles, the north–south bubbles are expected to take 7.5 10 6 yr to form, and the east–west bubbles 1.4 10 6  yr. We suggest that the jet axis has changed at least once in Mrk 6 within the last 10 7 yr. A comparison of the nuclear radio-loudness of Mrk 6 and a small sample of Seyfert galaxies with a subset of low-luminosity FR I radio galaxies reveals a continuum in radio properties.

Description: Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaillon, Olivier -- Bouhouche, Khaled -- Gout, Jean-Francois -- Aury, Jean-Marc -- Noel, Benjamin -- Saudemont, Baptiste -- Nowacki, Mariusz -- Serrano, Vincent -- Porcel, Betina M -- Segurens, Beatrice -- Le Mouel, Anne -- Lepere, Gersende -- Schachter, Vincent -- Betermier, Mireille -- Cohen, Jean -- Wincker, Patrick -- Sperling, Linda -- Duret, Laurent -- Meyer, Eric -- England -- Nature. 2008 Jan 17;451(7176):359-62. doi: 10.1038/nature06495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genoscope (CEA), 2 rue Gaston Cremieux CP5706, 91057 Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202663" target="_blank"〉PubMed〈/a〉

Description: Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Henriet, Simon -- Mungpakdee, Sutada -- Aury, Jean-Marc -- Da Silva, Corinne -- Brinkmann, Henner -- Mikhaleva, Jana -- Olsen, Lisbeth Charlotte -- Jubin, Claire -- Canestro, Cristian -- Bouquet, Jean-Marie -- Danks, Gemma -- Poulain, Julie -- Campsteijn, Coen -- Adamski, Marcin -- Cross, Ismael -- Yadetie, Fekadu -- Muffato, Matthieu -- Louis, Alexandra -- Butcher, Stephen -- Tsagkogeorga, Georgia -- Konrad, Anke -- Singh, Sarabdeep -- Jensen, Marit Flo -- Huynh Cong, Evelyne -- Eikeseth-Otteraa, Helen -- Noel, Benjamin -- Anthouard, Veronique -- Porcel, Betina M -- Kachouri-Lafond, Rym -- Nishino, Atsuo -- Ugolini, Matteo -- Chourrout, Pascal -- Nishida, Hiroki -- Aasland, Rein -- Huzurbazar, Snehalata -- Westhof, Eric -- Delsuc, Frederic -- Lehrach, Hans -- Reinhardt, Richard -- Weissenbach, Jean -- Roy, Scott W -- Artiguenave, Francois -- Postlethwait, John H -- Manak, J Robert -- Thompson, Eric M -- Jaillon, Olivier -- Du Pasquier, Louis -- Boudinot, Pierre -- Liberles, David A -- Volff, Jean-Nicolas -- Philippe, Herve -- Lenhard, Boris -- Roest Crollius, Hugues -- Wincker, Patrick -- Chourrout, Daniel -- Z01 LM000073-12/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Institut de Genomique, Genoscope, Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097902" target="_blank"〉PubMed〈/a〉

Description: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Carretero-Paulet, Lorenzo -- Dereeper, Alexis -- Droc, Gaetan -- Guyot, Romain -- Pietrella, Marco -- Zheng, Chunfang -- Alberti, Adriana -- Anthony, Francois -- Aprea, Giuseppe -- Aury, Jean-Marc -- Bento, Pascal -- Bernard, Maria -- Bocs, Stephanie -- Campa, Claudine -- Cenci, Alberto -- Combes, Marie-Christine -- Crouzillat, Dominique -- Da Silva, Corinne -- Daddiego, Loretta -- De Bellis, Fabien -- Dussert, Stephane -- Garsmeur, Olivier -- Gayraud, Thomas -- Guignon, Valentin -- Jahn, Katharina -- Jamilloux, Veronique -- Joet, Thierry -- Labadie, Karine -- Lan, Tianying -- Leclercq, Julie -- Lepelley, Maud -- Leroy, Thierry -- Li, Lei-Ting -- Librado, Pablo -- Lopez, Loredana -- Munoz, Adriana -- Noel, Benjamin -- Pallavicini, Alberto -- Perrotta, Gaetano -- Poncet, Valerie -- Pot, David -- Priyono -- Rigoreau, Michel -- Rouard, Mathieu -- Rozas, Julio -- Tranchant-Dubreuil, Christine -- VanBuren, Robert -- Zhang, Qiong -- Andrade, Alan C -- Argout, Xavier -- Bertrand, Benoit -- de Kochko, Alexandre -- Graziosi, Giorgio -- Henry, Robert J -- Jayarama -- Ming, Ray -- Nagai, Chifumi -- Rounsley, Steve -- Sankoff, David -- Giuliano, Giovanni -- Albert, Victor A -- Wincker, Patrick -- Lashermes, Philippe -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. ; CIRAD, UMR Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales (AGAP), F-34398 Montpellier, France. ; IRD, UMR Diversite Adaptation et Developpement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Nestle Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oe, BP 49716, 37097 Tours Cedex 2, France. ; ENEA Trisaia Research Center, 75026 Rotondella, Italy. ; Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universitat Bielefeld, Universitatsstrasse 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultat, Universitat Bielefeld, 33594 Bielefeld, Germany. ; Institut National de la Recherche Agronomique (INRA), Unite de Recherches en Genomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China. ; Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Departament de Genetica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain. ; Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia. ; Laboratorio de Genetica Molecular, Nucleo de Biotecnologia (NTBio), Embrapa Recursos Geneticos e Biotecnologia, Final Av. W/5 Norte, Parque Estacao Biologia, Brasilia-DF 70770-917, Brazil. ; CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia. ; Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India. ; Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA. ; BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25190796" target="_blank"〉PubMed〈/a〉