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1687 Publications visible to you, out of a total of 1687
Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Abstract (Expand)

High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short … regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. However, new long-read sequencing technologies such as the Pacific Biosciences platform may provide sufficiently large sequence lengths to overcome the poor phylogenetic resolution of short amplicons. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain a ~4500 bp region of the eukaryotic rDNA operon spanning most of the small (18S) and large subunit (28S) ribosomal RNA genes. The CCS reads were first treated with a novel curation workflow that generated 650 high-quality OTUs containing the physically linked 18S and 28S regions of the long amplicons. In order to assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based and phylogenetic placement-based methods using shorter reads. The taxonomically-annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing to accurately derive the evolutionary origin of environmental diversity. A total of 1019 sequences were included, of which a majority (58%) corresponded to the new long environmental CCS reads. Comparisons to the 18S-only region of our amplicons revealed that the combined 18S-28S genes globally increased the phylogenetic resolution, recovering specific groupings otherwise missing. The long-reads also allowed to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Altogether, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.

Authors: Mahwash Jamy, Rachel Foster, Pierre Barbera, Lucas Czech, Alexey Kozlov, Alexandros Stamatakis, David Baß, Fabien Burki

Date Published: 5th May 2019

Publication Type: Journal

Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning

Abstract

Not specified

Authors: Ivo Baar, Lukas Hubner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel

Date Published: 1st May 2019

Publication Type: Proceedings

Exploring the sensitivity of gravitational wave detectors to neutron star physics

Abstract

Not specified

Authors: Denis Martynov, Haixing Miao, Huan Yang, Francisco Hernandez Vivanco, Eric Thrane, Rory Smith, Paul Lasky, William E. East, Rana Adhikari, Andreas Bauswein, Aidan Brooks, Yanbei Chen, Thomas Corbitt, Andreas Freise, Hartmut Grote, Yuri Levin, Chunnong Zhao, Alberto Vecchio

Date Published: 1st May 2019

Publication Type: Journal

Hydrodynamical simulations and similarity relations for eruptive mass-loss from massive stars

Abstract

Not specified

Authors: Stanley P Owocki, Ryosuke Hirai, Philipp Podsiadlowski, Fabian R N Schneider

Date Published: 1st May 2019

Publication Type: Journal

Catching Element Formation In The Act ; The Case for a New MeV Gamma-Ray Mission: Radionuclide Astronomy in the 2020s

Abstract

Not specified

Authors: Frank Timmes, Chris Fryer, Frank Timmes, Aimee L. Hungerford, Aaron Couture, Fred Adams, Wako Aoki, Almudena Arcones, David Arnett, Katie Auchettl, Melina Avila, Carles Badenes, Eddie Baron, Andreas Bauswein, John Beacom, Jeff Blackmon, Stéphane Blondin, Peter Bloser, Steve Boggs, Alan Boss, Terri Brandt, Eduardo Bravo, Ed Brown, Peter Brown, Steve Bruenn, Carl Budtz-Jørgensen, Eric Burns, Alan Calder, Regina Caputo, Art Champagne, Roger Chevalier, Alessandro Chieffi, Kelly Chipps, David Cinabro, Ondrea Clarkson, Don Clayton, Alain Coc, Devin Connolly, Charlie Conroy, Benoit Côté, Sean Couch, Nicolas Dauphas, Richard James deBoer, Catherine Deibel, Pavel Denisenkov, Steve Desch, Luc Dessart, Roland Diehl, Carolyn Doherty, Inma Domı́nguez, Subo Dong, Vikram Dwarkadas, Doreen Fan, Brian Fields, Carl Fields, Alex Filippenko, Robert Fisher, Francois Foucart, Claes Fransson, Carla Fröhlich, George Fuller, Brad Gibson, Viktoriya Giryanskaya, Joachim Görres, Stéphane Goriely, Sergei Grebenev, Brian Grefenstette, Evan Grohs, James Guillochon, Alice Harpole, Chelsea Harris, J. Austin Harris, Fiona Harrison, Dieter Hartmann, Masa-aki Hashimoto, Alexander Heger, Margarita Hernanz, Falk Herwig, Raphael Hirschi, Raphael William Hix, Peter Höflich, Robert Hoffman, Cole Holcomb, Eric Hsiao, Christian Iliadis, Agnieszka Janiuk, Thomas Janka, Anders Jerkstrand, Lucas Johns, Samuel Jones, Jordi José, Toshitaka Kajino, Amanda Karakas, Platon Karpov, Dan Kasen, Carolyn Kierans, Marc Kippen, Oleg Korobkin, Chiaki Kobayashi, Cecilia Kozma, Saha Krot, Pawan Kumar, Irfan Kuvvetli, Alison Laird, (John) Martin Laming, Josefin Larsson, John Lattanzio, James Lattimer, Mark Leising, Annika Lennarz, Eric Lentz, Marco Limongi, Jonas Lippuner, Eli Livne, Nicole Lloyd-Ronning, Richard Longland, Laura A. Lopez, Maria Lugaro, Alexander Lutovinov, Kristin Madsen, Chris Malone, Francesca Matteucci, Julie McEnery, Zach Meisel, Bronson Messer, Brian Metzger, Bradley Meyer, Georges Meynet, Anthony Mezzacappa, Jonah Miller, Richard Miller, Peter Milne, Wendell Misch, Lee Mitchell, Philipp Mösta, Yuko Motizuki, Bernhard Müller, Matthew Mumpower, Jeremiah Murphy, Shigehiro Nagataki, Ehud Nakar, Ken’ichi Nomoto, Peter Nugent, Filomena Nunes, Brian O’Shea, Uwe Oberlack, Steven Pain, Lucas Parker, Albino Perego, Marco Pignatari, Gabriel Martı́nez Pinedo, Tomasz Plewa, Dovi Poznanski, William Priedhorsky, Boris Pritychenko, David Radice, Enrico Ramirez-Ruiz, Thomas Rauscher, Sanjay Reddy, Ernst Rehm, Rene Reifarth, Debra Richman, Paul Ricker, Nabin Rijal, Luke Roberts, Friedrich Röpke, Stephan Rosswog, Ashley J. Ruiter, Chris Ruiz, Daniel Wolf Savin, Hendrik Schatz, Dieter Schneider, Josiah Schwab, Ivo Seitenzahl, Ken Shen, Thomas Siegert, Stuart Sim, David Smith, Karl Smith, Michael Smith, Jesper Sollerman, Trevor Sprouse, Artemis Spyrou, Sumner Starrfield, Andrew Steiner, Andrew W. Strong, Tuguldur Sukhbold, Nick Suntzeff, Rebecca Surman, Toru Tanimori, Lih-Sin The, Friedrich-Karl Thielemann, Alexey Tolstov, Nozomu Tominaga, John Tomsick, Dean Townsley, Pelagia Tsintari, Sergey Tsygankov, David Vartanyan, Tonia Venters, Tom Vestrand, Jacco Vink, Roni Waldman, Lifang Wang, Xilu Wang, MacKenzie Warren, Christopher West, J. Craig Wheeler, Michael Wiescher, Christoph Winkler, Lisa Winter, Bill Wolf, Richard Woolf, Stan Woosley, Jin Wu, Chris Wrede, Shoichi Yamada, Patrick Young, Remco Zegers, Michael Zingale, Simon Portegies Zwart

Date Published: 1st May 2019

Publication Type: Journal

Molecular Dynamics Simulations of Molecules in Uniform Flow

Abstract (Expand)

Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of … flow on molecules, we present uniform-flow molecular dynamics simulations at atomic level. The pull module of the GRoningen MAchine for Chemical Simulations package was extended to be able to force-group atoms within a defined layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules. We monitored the density of the whole system to establish the conditions under which the simulated flow is well-behaved. A maximal velocity of 1.3 m/s can be generated if a pull slice of 8 nm is used, and high velocities would require larger pull slices to still maintain a stable density. As expected, the target velocity increases linearly with the total external force applied. Finally, we suggest an appropriate setup to stretch a protein by uniform flow, in which protein extensions depend on the flow conditions. Our implementation provides an efficient computational tool to investigate the effect of the flow at the molecular level.

Authors: Ana M. Herrera-Rodríguez, Vedran Miletić, Camilo Aponte-Santamaría, Frauke Gräter

Date Published: 1st May 2019

Publication Type: Journal

How Do Stars Form? Open Questions on the Stellar Initial Mass Function

Abstract

Not specified

Authors: Daniela Calzetti, Nate Bastian, Charlie Conroy, Bruce G. Elmegreen, John S. Gallagher, Mark Krumholz, Selma E. de Mink, Stella S. Offner, Elena Sabbi, Fabian R. N. Schneider, Aida Wofford, Rosemary F. G. Wyse

Date Published: 1st May 2019

Publication Type: Journal

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