Articles

Proteogenomics analysis of CUG codon translation in the human pathogen Candida albicans

Yeasts of the CTG-clade lineage, which includes the human-infecting Candida albicans, Candida parapsilosis and Candida tropicalis species, are characterized by an altered genetic code. Instead of translating CUG ...

Authors: Stefanie Mühlhausen, Hans Dieter Schmitt, Uwe Plessmann, Peter Mienkus, Pia Sternisek, Thorsten Perl, Michael Weig, Henning Urlaub, Oliver Bader and Martin Kollmar

Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation

The evolutionary history of cell types provides insights into how morphological and functional complexity arose during animal evolution. Photoreceptor cell types are particularly broadly distributed throughout...

Authors: Jonathan E. Valencia, Roberto Feuda, Dan O. Mellott, Robert D. Burke and Isabelle S. Peter

Daily rhythms in gene expression of the human parasite Schistosoma mansoni

The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimi...

Authors: Kate A. Rawlinson, Adam J. Reid, Zhigang Lu, Patrick Driguez, Anna Wawer, Avril Coghlan, Geetha Sankaranarayanan, Sarah K. Buddenborg, Carmen Diaz Soria, Catherine McCarthy, Nancy Holroyd, Mandy Sanders, Karl F. Hoffmann, David Wilcockson, Gabriel Rinaldi and Matthew Berriman

Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain

Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of g...

Authors: Emily J. Shields, Masato Sorida, Lihong Sheng, Bogdan Sieriebriennikov, Long Ding and Roberto Bonasio

Monkeying around with venom: an increased resistance to α-neurotoxins supports an evolutionary arms race between Afro-Asian primates and sympatric cobras

Snakes and primates have a multi-layered coevolutionary history as predators, prey, and competitors with each other. Previous work has explored the Snake Detection Theory (SDT), which focuses on the role of sn...

Authors: Richard J. Harris, K. Anne-Isola Nekaris and Bryan G. Fry

Flexible and stretchable polymer optical fibers for chronic brain and vagus nerve optogenetic stimulations in free-behaving animals

Although electrical stimulation of the peripheral and central nervous systems has attracted much attention owing to its potential therapeutic effects on neuropsychiatric diseases, its non-cell-type-specific ac...

Authors: Yi Cao, Suwan Pan, Mengying Yan, Chongyang Sun, Jianyu Huang, Cheng Zhong, Liping Wang and Lu Yi

Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum

The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered...

Authors: Ingrid Škodová-Sveráková, Kristína Záhonová, Valéria Juricová, Maksym Danchenko, Martin Moos, Peter Baráth, Galina Prokopchuk, Anzhelika Butenko, Veronika Lukáčová, Lenka Kohútová, Barbora Bučková, Aleš Horák, Drahomíra Faktorová, Anton Horváth, Petr Šimek and Julius Lukeš

Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning

Prokaryotic viruses, which infect bacteria and archaea, are the most abundant and diverse biological entities in the biosphere. To understand their regulatory roles in various ecosystems and to harness the pot...

Authors: Jiayu Shang and Yanni Sun

Chlorophyll fluorescence as a light signal enhances iron uptake by the marine diatom Phaeodactylum tricornutum under high-cell density conditions

Diatoms usually dominate phytoplankton blooms in open oceans, exhibiting extremely high population densities. Although the iron uptake rate of diatoms largely determines the magnitude and longevity of diatom b...

Authors: Xuehua Liu, Xiujun Xie, Shan Gao, Lepu Wang, Lu Zhou, Yao Liu, Qiang Hu, Wenhui Gu and Guangce Wang

Functional analyses of phosphatidylserine/PI(4)P exchangers with diverse lipid species and membrane contexts reveal unanticipated rules on lipid transfer

Lipid species are accurately distributed in the eukaryotic cell so that organelle and plasma membranes have an adequate lipid composition to support numerous cellular functions. In the plasma membrane, a preci...

Authors: Souade Ikhlef, Nicolas-Frédéric Lipp, Vanessa Delfosse, Nicolas Fuggetta, William Bourguet, Maud Magdeleine and Guillaume Drin

Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

The main function of telomerase is at the telomeres but under adverse conditions telomerase can bind to internal regions causing deleterious effects as observed in cancer cells.

Authors: Satyaprakash Pandey, Mona Hajikazemi, Theresa Zacheja, Stephanie Schalbetter, Jonathan Baxter, Victor Guryev, Andreas Hofmann, Dieter W. Heermann, Stefan A. Juranek and Katrin Paeschke

Adipoclast: a multinucleated fat-eating macrophage

Cell membrane fusion and multinucleation in macrophages are associated with physiologic homeostasis as well as disease. Osteoclasts are multinucleated macrophages that resorb bone through increased metabolic a...

Authors: Antoni Olona, Subhankar Mukhopadhyay, Charlotte Hateley, Fernando O. Martinez, Siamon Gordon and Jacques Behmoaras

Selection shapes the landscape of functional variation in wild house mice

Through human-aided dispersal over the last ~ 10,000 years, house mice (Mus musculus) have recently colonized diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantag...

Authors: Raman Akinyanju Lawal, Uma P. Arora and Beth L. Dumont

Formation of nuclear condensates by the Mediator complex subunit Med15 in mammalian cells

The Mediator complex is an evolutionarily conserved multi-subunit protein complex that plays major roles in transcriptional activation and is essential for cell growth, proliferation, and differentiation. Rece...

Authors: Yuanyuan Shi, Jian Chen, Wei-Jie Zeng, Miao Li, Wenxue Zhao, Xing-Ding Zhang and Jie Yao

Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals

Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set o...

Authors: Anabella P. Trigila, Francisco Pisciottano and Lucía F. Franchini

Circulating miRNA repertoire as a biomarker of metabolic and reproductive states in rainbow trout

Circulating miRNAs (c-miRNAs) are found in most, if not all, biological fluids and are becoming well-established non-invasive biomarkers of many human pathologies. However, their features in non-pathological c...

Authors: Emilie Cardona, Cervin Guyomar, Thomas Desvignes, Jérôme Montfort, Samia Guendouz, John H. Postlethwait, Sandrine Skiba-Cassy and Julien Bobe

Tube-dwelling in early animals exemplified by Cambrian scalidophoran worms

The radiation of ecdysozoans (moulting animals) during the Cambrian gave rise to panarthropods and various groups of worms including scalidophorans, which played an important role in the elaboration of early m...

Authors: Deng Wang, Jean Vannier, Cédric Aria, Jie Sun and Jian Han

An HSP90 cochaperone Ids2 maintains the stability of mitochondrial DNA and ATP synthase

Proteostasis unbalance and mitochondrial dysfunction are two hallmarks of aging. While the chaperone folds and activates its clients, it is the cochaperone that determines the specificity of the clients. Ids2 ...

Authors: Pei-Heng Jiang, Chen-Yan Hou and Shu-Chun Teng

The transposable element-rich genome of the cereal pest Sitophilus oryzae

The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosym...

Authors: Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, Federica Calevro, Patrick Callaerts, Théo Chancy, Hubert Charles, Stefano Colella, André Da Silva Barbosa…

Long-term dynamics of the human oral microbiome during clinical disease progression

Oral microbiome dysbiosis is linked to overt inflammation of tooth-supporting tissues, leading to periodontitis, an oral condition that can cause tooth and bone loss. Microbiome dysbiosis has been described as...

Authors: Ana Duran-Pinedo, Jose Solbiati, Flavia Teles, Ricardo Teles, Yanping Zang and Jorge Frias-Lopez

Publisher Correction to: Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers

Authors: Debashree Tagore, Farhang Aghakhanian, Rakesh Naidu, Maude E. Phipps and Analabha Basu

Author Correction to: A novel theory of Asian elephant high-frequency squeak production

Authors: Veronika C. Beeck, Gunnar Heilmann, Michael Kerscher and Angela S. Stoeger

Zinc antagonizes iron-regulation of tyrosine hydroxylase activity and dopamine production in Drosophila melanogaster

Dopamine (DA) is a neurotransmitter that plays roles in movement, cognition, attention, and reward responses, and deficient DA signaling is associated with the progression of a number of neurological diseases,...

Authors: Guiran Xiao, Mengran Zhao, Zhihua Liu, Fan Du and Bing Zhou

Publisher Correction to: An increase of phosphatidylcholines in follicular fluid implies attenuation of embryo quality on day 3 post-fertilization

Authors: Ju Wang, Wei Zheng, Shuoping Zhang, Keqiang Yan, Miao Jin, Huiling Hu, Zhen Ma, Fei Gong, Guangxiu Lu, Yan Ren, Liang Lin, Ge Lin, Liang Hu and Siqi Liu

Characterisation of the enzyme transport path between shipworms and their bacterial symbionts

Shipworms are marine xylophagus bivalve molluscs, which can live on a diet solely of wood due to their ability to produce plant cell wall-degrading enzymes. Bacterial carbohydrate-active enzymes (CAZymes), syn...

Authors: Giovanna Pesante, Federico Sabbadin, Luisa Elias, Clare Steele-King, J. Reuben Shipway, Adam A. Dowle, Yi Li, Marta Busse-Wicher, Paul Dupree, Katrin Besser, Simon M. Cragg, Neil C. Bruce and Simon J. McQueen-Mason

Plastid phylogenomic insights into relationships of all flowering plant families

Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full...

Authors: Hong-Tao Li, Yang Luo, Lu Gan, Peng-Fei Ma, Lian-Ming Gao, Jun-Bo Yang, Jie Cai, Matthew A. Gitzendanner, Peter W. Fritsch, Ting Zhang, Jian-Jun Jin, Chun-Xia Zeng, Hong Wang, Wen-Bin Yu, Rong Zhang, Michelle van der Bank…

Stage-specific expression of an odorant receptor underlies olfactory behavioral plasticity in Spodoptera littoralis larvae

The detection of environmental cues and signals via the sensory system directs behavioral choices in diverse organisms. Insect larvae rely on input from the chemosensory system, mainly olfaction, for locating ...

Authors: Santosh V. Revadi, Vito Antonio Giannuzzi, Valeria Rossi, Gert Martin Hunger, Lucie Conchou, Gabriele Rondoni, Eric Conti, Peter Anderson, William B. Walker, Emmanuelle Jacquin-Joly, Fotini Koutroumpa and Paul G. Becher

Monophyletic blowflies revealed by phylogenomics

Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet,...

Authors: Liping Yan, Thomas Pape, Karen Meusemann, Sujatha Narayanan Kutty, Rudolf Meier, Keith M. Bayless and Dong Zhang

MIEF1/2 orchestrate mitochondrial dynamics through direct engagement with both the fission and fusion machineries

Mitochondrial dynamics is the result of a dynamic balance between fusion and fission events, which are driven via a set of mitochondria-shaping proteins. These proteins are generally considered to be binary co...

Authors: Rong Yu, Tong Liu, Shao-Bo Jin, Maria Ankarcrona, Urban Lendahl, Monica Nistér and Jian Zhao

The mitochondrially-localized nucleoside diphosphate kinase D (NME4) is a novel metastasis suppressor

Mitochondrial nucleoside diphosphate kinase (NDPK-D, NME4, NM23-H4) is a multifunctional enzyme mainly localized in the intermembrane space, bound to the inner membrane.

Authors: Marie-Lise Lacombe, Frederic Lamarche, Olivier De Wever, Teresita Padilla-Benavides, Alyssa Carlson, Imran Khan, Anda Huna, Sophie Vacher, Claire Calmel, Céline Desbourdes, Cécile Cottet-Rousselle, Isabelle Hininger-Favier, Stéphane Attia, Béatrice Nawrocki-Raby, Joël Raingeaud, Christelle Machon…

Channel nuclear pore protein 54 directs sexual differentiation and neuronal wiring of female reproductive behaviors in Drosophila

Female reproductive behaviors and physiology change profoundly after mating. The control of pregnancy-associated changes in physiology and behaviors are largely hard-wired into the brain to guarantee reproduct...

Authors: Mohanakarthik P. Nallasivan, Irmgard U. Haussmann, Alberto Civetta and Matthias Soller

PACmn for improved optogenetic control of intracellular cAMP

Cyclic adenosine monophosphate (cAMP) is a ubiquitous second messenger that transduces extracellular signals in virtually all eukaryotic cells. The soluble Beggiatoa photoactivatable adenylyl cyclase (bPAC) rapid...

Authors: Shang Yang, Oana M. Constantin, Divya Sachidanandan, Hannes Hofmann, Tobias C. Kunz, Vera Kozjak-Pavlovic, Thomas G. Oertner, Georg Nagel, Robert J. Kittel, Christine E. Gee and Shiqiang Gao

Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

Cell-free DNA (cfDNA), which is extracellular DNA present in the circulating plasma and other body fluids, is currently investigated as a minimally invasive, highly informative biomarker. While nucleosome-size...

Authors: Osamu Hisano, Takashi Ito and Fumihito Miura

The evolution of pelvic canal shape and rotational birth in humans

The human foetus typically needs to rotate when passing through the tight birth canal because of the complex shape of the pelvis. In most women, the upper part, or inlet, of the birth canal has a round or medi...

Authors: Ekaterina Stansfield, Barbara Fischer, Nicole D. S. Grunstra, Maria Villa Pouca and Philipp Mitteroecker

Taxonomy-aware, sequence similarity ranking reliably predicts phage–host relationships

Characterizing phage–host interactions is critical to understanding the ecological role of both partners and effective isolation of phage therapeuticals. Unfortunately, experimental methods for studying these ...

Authors: Andrzej Zielezinski, Jakub Barylski and Wojciech M. Karlowski

Krüppel-homolog 1 exerts anti-metamorphic and vitellogenic functions in insects via phosphorylation-mediated recruitment of specific cofactors

The zinc-finger transcription factor Krüppel-homolog 1 (Kr-h1) exerts a dual regulatory role during insect development by preventing precocious larval/nymphal metamorphosis and in stimulating aspects of adult ...

Authors: Zhongxia Wu, Libin Yang, Huihui Li and Shutang Zhou

Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria

Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both a parasitic and free-living generation. During the parasit...

Authors: Ivan N. Chavez, Taylor M. Brown, Adrien Assié, Astra S. Bryant, Buck S. Samuel and Elissa A. Hallem

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance...

Authors: Saskia Pfrengle, Judith Neukamm, Meriam Guellil, Marcel Keller, Martyna Molak, Charlotte Avanzi, Alena Kushniarevich, Núria Montes, Gunnar U. Neumann, Ella Reiter, Rezeda I. Tukhbatova, Nataliya Y. Berezina, Alexandra P. Buzhilova, Dmitry S. Korobov, Stian Suppersberger Hamre, Vitor M. J. Matos…

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching

Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history an...

Authors: Tobias Mourier, Denise Anete Madureira de Alvarenga, Abhinav Kaushik, Anielle de Pina-Costa, Olga Douvropoulou, Qingtian Guan, Francisco J. Guzmán-Vega, Sarah Forrester, Filipe Vieira Santos de Abreu, Cesare Bianco Júnior, Julio Cesar de Souza Junior, Silvia Bahadian Moreira, Zelinda Maria Braga Hirano, Alcides Pissinatti, Maria de Fátima Ferreira-da-Cruz, Ricardo Lourenço de Oliveira…

A human iPSC-derived inducible neuronal model of Niemann-Pick disease, type C1

Niemann-Pick disease, type C (NPC) is a childhood-onset, lethal, neurodegenerative disorder caused by autosomal recessive mutations in the genes NPC1 or NPC2 and characterized by impaired cholesterol homeostasis,...

Authors: Anika V. Prabhu, Insung Kang, Raffaella De Pace, Christopher A. Wassif, Hideji Fujiwara, Pamela Kell, Xuntian Jiang, Daniel S. Ory, Juan S. Bonifacino, Michael E. Ward and Forbes D. Porter

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-...

Authors: Amrita Srivathsan, Leshon Lee, Kazutaka Katoh, Emily Hartop, Sujatha Narayanan Kutty, Johnathan Wong, Darren Yeo and Rudolf Meier

Publisher Correction to: An economical and highly adaptable optogenetics system for individual and population-level manipulation of Caenorhabditis elegans

Authors: M. Koopman, L. Janssen and E. A. A. Nollen

Neuroligin-1 mediates presynaptic maturation through brain-derived neurotrophic factor signaling

Maturation is a process that allows synapses to acquire full functionality, optimizing their activity to diverse neural circuits, and defects in synaptic maturation may contribute to neurodevelopmental disorde...

Authors: Andonia Petkova-Tuffy, Nina Gödecke, Julio Viotti, Martin Korte and Thomas Dresbach

Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila

How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, ...

Authors: Yun Wang, Franz Baumdicker, Paul Schweiger, Sven Kuenzel and Fabian Staubach

Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many org...

Authors: Ni-Chiao Tsai, Tzu-Shu Hsu, Shang-Che Kuo, Chung-Ting Kao, Tzu-Huan Hung, Da-Gin Lin, Chung-Shu Yeh, Chia-Chen Chu, Jeng-Shane Lin, Hsin-Hung Lin, Chia-Ying Ko, Tien-Hsien Chang, Jung-Chen Su and Ying-Chung Jimmy Lin

Control of vein-forming, striped gene expression by auxin signaling

Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals,...

Authors: Anmol Krishna, Jason Gardiner, Tyler J. Donner and Enrico Scarpella

Self-organising human gonads generated by a Matrigel-based gradient system

Advances in three-dimensional culture technologies have led to progression in systems used to model the gonadal microenvironment in vitro. Despite demonstrating basic functionality, tissue organisation is ofte...

Authors: Elizabeth Oliver, João Pedro Alves-Lopes, Femke Harteveld, Rod T. Mitchell, Elisabet Åkesson, Olle Söder and Jan-Bernd Stukenborg

Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species

Glossina species (tsetse flies), the sole vectors of African trypanosomes, maintained along their long evolutionary history a unique reproductive strategy, adenotrophic viviparity. Viviparity reduces their reprod...

Authors: Grazia Savini, Francesca Scolari, Lino Ometto, Omar Rota-Stabelli, Davide Carraretto, Ludvik M. Gomulski, Giuliano Gasperi, Adly M. M. Abd-Alla, Serap Aksoy, Geoffrey M. Attardo and Anna R. Malacrida

Species co-occurrence and management intensity modulate habitat preferences of forest birds

Species co-occurrences can have profound effects on the habitat use of species, and therefore habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organizat...

Authors: Marco Basile, Thomas Asbeck, João M. Cordeiro Pereira, Grzegorz Mikusiński and Ilse Storch

Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Authors: Sarah Farhat, Phuong Le, Ehsan Kayal, Benjamin Noel, Estelle Bigeard, Erwan Corre, Florian Maumus, Isabelle Florent, Adriana Alberti, Jean-Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne Da Silva, Benjamin Istace, Karine Labadie, Dominique Marie…