Skip to main content
Table of Contents

April 2018

Aminoacyl tRNA synthetases implement the genetic code and reflect the earliest episode of life. These enzymes are responsible for loading tRNA molecules with the correct amino acid. Two protein superfamilies of aminoacyl tRNA synthetases emerged, each responsible for ten amino acids. The delicate balance between these superfamilies is manifested in two structural motifs: the Backbone Brackets and the Arginine Tweezers. Aminoacyl tRNA synthetases constitute a reflexive system where each superfamily cannot exist without its counterpart. Both motifs support a popular hypothesis, which states that prototypic aminoacyl tRNA synthetases were once coded on complementary strands of the same gene. Kaiser et al.

Image Credit: Alexander Eisold


Ten simple rules for responsible referencing

Bart Penders

New computational approaches to understanding molecular protein function

Jacquelyn S. Fetrow, Patricia C. Babbitt

Education Articles

Eleven quick tips for finding research data

Kathleen Gregory, Siri Jodha Khalsa, William K. Michener, Fotis E. Psomopoulos, Anita de Waard, Mingfang Wu

Ten quick tips for teaching programming

Neil C. C. Brown, Greg Wilson


Automated plant species identification—Trends and future directions

Jana Wäldchen, Michael Rzanny, Marco Seeland, Patrick Mäder

Research Articles

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level

Małgorzata Kardyńska, Anna Paszek, Jarosław Śmieja, David Spiller, Wiesława Widłak, Michael R. H. White, Pawel Paszek, Marek Kimmel

Automated evaluation of quaternary structures from protein crystals

Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte

Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape

David R. J. Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadœuf, Emmanuel Jacquot, Gaël Thébaud

Related Articles

Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics

Kevin J. Flynn, David O. F. Skibinski, Christian Lindemann

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack Jr.

Material and shape perception based on two types of intensity gradient information

Masataka Sawayama, Shin'ya Nishida

Organization of the core respiratory network: Insights from optogenetic and modeling studies

Jessica Ausborn, Hidehiko Koizumi, William H. Barnett, Tibin T. John, Ruli Zhang, Yaroslav I. Molkov, Jeffrey C. Smith, Ilya A. Rybak

Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition

Catherine M. Byrne, Soren Gantt, Daniel Coombs

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

Vasyl V. Mykuliak, Alexander William M. Haining, Magdaléna von Essen, Armando del Río Hernández, Vesa P. Hytönen

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning

Ji-Sung Kim, Xin Gao, Andrey Rzhetsky

Personalizing physical exercise in a computational model of fuel homeostasis

Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti, Filippo Castiglione

Rational metareasoning and the plasticity of cognitive control

Falk Lieder, Amitai Shenhav, Sebastian Musslick, Thomas L. Griffiths

Switchable slow cellular conductances determine robustness and tunability of network states

Guillaume Drion, Julie Dethier, Alessio Franci, Rodolphe Sepulchre

Identifying robust hysteresis in networks

Tomáš Gedeon, Bree Cummins, Shaun Harker, Konstantin Mischaikow

Black-boxing and cause-effect power

William Marshall, Larissa Albantakis, Giulio Tononi

Correcting for batch effects in case-control microbiome studies

Sean M. Gibbons, Claire Duvallet, Eric J. Alm

A machine learning based framework to identify and classify long terminal repeat retrotransposons

Leander Schietgat, Celine Vens, Ricardo Cerri, Carlos N. Fischer, Eduardo Costa, Jan Ramon, Claudia M. A. Carareto, Hendrik Blockeel

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

Sneha Mitra, Anushua Biswas, Leelavati Narlikar

Exploiting glycan topography for computational design of Env glycoprotein antigenicity

Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B. Karsten, Todd J. Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L. Brass, Michael Tiemeyer, Michael Seaman, John R. Mascola, Lance Wells, Douglas A. Lauffenburger, Galit Alter

Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse

Reuben M. Buckley, R. Daniel Kortschak, David L. Adelson

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

Benjamin Schott, Manuel Traub, Cornelia Schlagenhauf, Masanari Takamiya, Thomas Antritter, Andreas Bartschat, Katharina Löffler, Denis Blessing, Jens C. Otte, Andrei Y. Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Johannes Stegmaier

Compositional clustering in task structure learning

Nicholas T. Franklin, Michael J. Frank

Decision making improves sperm chemotaxis in the presence of noise

Justus A. Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M. Friedrich

Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer

Itziar Irurzun-Arana, Alvaro Janda, Sergio Ardanza-Trevijano, Iñaki F. Trocóniz

Bayesian reconstruction of transmission within outbreaks using genomic variants

Nicola De Maio, Colin J. Worby, Daniel J. Wilson, Nicole Stoesser

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Geoffrey D. Hannigan, Melissa B. Duhaime, Danai Koutra, Patrick D. Schloss

Propagating annotations of molecular networks using in silico fragmentation

Ricardo R. da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein

A computational model of shared fine-scale structure in the human connectome

J. Swaroop Guntupalli, Ma Feilong, James V. Haxby

On the role of extrinsic noise in microRNA-mediated bimodal gene expression

Marco Del Giudice, Stefano Bo, Silvia Grigolon, Carla Bosia

A modelling approach for exploring muscle dynamics during cyclic contractions

Stephanie A. Ross, Nilima Nigam, James M. Wakeling

Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations

Russell B. Davidson, Josie Hendrix, Brian J. Geiss, Martin McCullagh

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde

Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms

Ricardo Martínez-García, Carey D. Nadell, Raimo Hartmann, Knut Drescher, Juan A. Bonachela

Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly

Juan Francisco Viso, Patricia Belelli, Matías Machado, Humberto González, Sergio Pantano, María Julia Amundarain, Fernando Zamarreño, Maria Marta Branda, Diego M. A. Guérin, Marcelo D. Costabel

A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability

Bronac Flanagan, Liam McDaid, John Wade, KongFatt Wong-Lin, Jim Harkin

Origins of scale invariance in vocalization sequences and speech

Fatemeh Khatami, Markus Wöhr, Heather L. Read, Monty A. Escabí

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W. Myers, Moritz Kreysing

Principles that govern competition or co-existence in Rho-GTPase driven polarization

Jian-Geng Chiou, Samuel A. Ramirez, Timothy C. Elston, Thomas P. Witelski, David G. Schaeffer, Daniel J. Lew

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G. Barrett, Peter H. Thrall

Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey

Robin Mills, Hanno Hildenbrandt, Graham K. Taylor, Charlotte K. Hemelrijk

Interactions of spatial strategies producing generalization gradient and blocking: A computational approach

Laurent Dollé, Ricardo Chavarriaga, Agnès Guillot, Mehdi Khamassi

Toward a theory of coactivation patterns in excitable neural networks

Arnaud Messé, Marc-Thorsten Hütt, Claus C. Hilgetag

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction

Wolfgang Giese, Gregor Milicic, Andreas Schröder, Edda Klipp

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

Huanan Zhang, Catherine A. A. Lee, Zhuliu Li, John R. Garbe, Cindy R. Eide, Raphael Petegrosso, Rui Kuang, Jakub Tolar

Need for speed: An optimized gridding approach for spatially explicit disease simulations

Stefan Sellman, Kimberly Tsao, Michael J. Tildesley, Peter Brommesson, Colleen T. Webb, Uno Wennergren, Matt J. Keeling, Tom Lindström

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin

Annie M. Westerlund, Lucie Delemotte

A probabilistic, distributed, recursive mechanism for decision-making in the brain

Javier A. Caballero, Mark D. Humphries, Kevin N. Gurney