Articles

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on ...

Authors: Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps…

Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

The binding of HIV-1 Envelope glycoproteins (Env) to host receptor CD4 exposes vulnerable conserved epitopes within the co-receptor binding site (CoRBS) which are required for the engagement of either CCR5 or ...

Authors: William D. Tolbert, Rebekah Sherburn, Neelakshi Gohain, Shilei Ding, Robin Flinko, Chiara Orlandi, Krishanu Ray, Andrés Finzi, George K. Lewis and Marzena Pazgier

Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus

Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia) oryzae—the causal agent of ...

Authors: Sergio M. Latorre, C. Sarai Reyes-Avila, Angus Malmgren, Joe Win, Sophien Kamoun and Hernán A. Burbano

FAM20B-catalyzed glycosaminoglycans control murine tooth number by restricting FGFR2b signaling

The formation of supernumerary teeth is an excellent model for studying the molecular mechanisms that control stem/progenitor cell homeostasis needed to generate a renewable source of replacement cells and tis...

Authors: Jingyi Wu, Ye Tian, Lu Han, Chao Liu, Tianyu Sun, Ling Li, Yanlei Yu, Bikash Lamichhane, Rena N. D’Souza, Sarah E. Millar, Robb Krumlauf, David M. Ornitz, Jian Q. Feng, Ophir Klein, Hu Zhao, Fuming Zhang…

Wonky whales: the evolution of cranial asymmetry in cetaceans

Unlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earlies...

Authors: Ellen J. Coombs, Julien Clavel, Travis Park, Morgan Churchill and Anjali Goswami

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns

Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in huma...

Authors: Yang Zhou, Shuli Liu, Yan Hu, Lingzhao Fang, Yahui Gao, Han Xia, Steven G. Schroeder, Benjamin D. Rosen, Erin E. Connor, Cong-jun Li, Ransom L. Baldwin, John B. Cole, Curtis P. Van Tassell, Liguo Yang, Li Ma and George E. Liu

The roles of hybridization and habitat fragmentation in the evolution of Brazil’s enigmatic longwing butterflies, Heliconius nattereri and H. hermathena

Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been stro...

Authors: Darli Massardo, Nicholas W. VanKuren, Sumitha Nallu, Renato R. Ramos, Pedro G. Ribeiro, Karina L. Silva-Brandão, Marcelo M. Brandão, Marília B. Lion, André V. L. Freitas, Márcio Z. Cardoso and Marcus R. Kronforst

Temporospatial shifts within commercial laboratory mouse gut microbiota impact experimental reproducibility

Experimental reproducibility in mouse models is impacted by both genetics and environment. The generation of reproducible data is critical for the biomedical enterprise and has become a major concern for the s...

Authors: Rabindra K. Mandal, Joshua E. Denny, Morgan L. Waide, Qingsheng Li, Neal Bhutiani, Charles D. Anderson, Becca V. Baby, Venkatakrishna R. Jala, Nejat K. Egilmez and Nathan W. Schmidt

TDP-43 prevents retrotransposon activation in the Drosophila motor system through regulation of Dicer-2 activity

Mutations in the small RNA-binding protein TDP-43 lead to the formation of insoluble cytoplasmic aggregates that have been associated with the onset and progression of amyotrophic lateral sclerosis (ALS), a ne...

Authors: Giulia Romano, Raffaella Klima and Fabian Feiguin

AIMTOR, a BRET biosensor for live imaging, reveals subcellular mTOR signaling and dysfunctions

mTOR signaling is an essential nutrient and energetic sensing pathway. Here we describe AIMTOR, a sensitive genetically encoded BRET (Bioluminescent Resonance Energy Transfer) biosensor to study mTOR activity ...

Authors: Nathalie Bouquier, Enora Moutin, Lionel A. Tintignac, Amandine Reverbel, Elodie Jublanc, Michael Sinnreich, Yan Chastagnier, Julien Averous, Pierre Fafournoux, Chiara Verpelli, Tobias Boeckers, Gilles Carnac, Julie Perroy and Vincent Ollendorff

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in live...

Authors: Shuli Liu, Ying Yu, Shengli Zhang, John B. Cole, Albert Tenesa, Ting Wang, Tara G. McDaneld, Li Ma, George E. Liu and Lingzhao Fang

Real-time tracking of stem cell viability, proliferation, and differentiation with autonomous bioluminescence imaging

Luminescent reporter proteins are vital tools for visualizing cells and cellular activity. Among the current toolbox of bioluminescent systems, only bacterial luciferase has genetically defined luciferase and ...

Authors: Michael Conway, Tingting Xu, Andrew Kirkpatrick, Steven Ripp, Gary Sayler and Dan Close

Relationship between oxygen consumption and neuronal activity in a defined neural circuit

Neuronal computations related to sensory and motor activity along with the maintenance of spike discharge, synaptic transmission, and associated housekeeping are energetically demanding. The most efficient met...

Authors: Suzan Özugur, Lars Kunz and Hans Straka

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is h...

Authors: Pedro Almeida, Estelle Proux-Wera, Allison Churcher, Lucile Soler, Jacques Dainat, Pascal Pucholt, Jessica Nordlund, Tom Martin, Ann-Christin Rönnberg-Wästljung, Björn Nystedt, Sofia Berlin and Judith E. Mank

The evolution of the Puf superfamily of proteins across the tree of eukaryotes

Eukaryotic gene expression is controlled by a number of RNA-binding proteins (RBP), such as the proteins from the Puf (Pumilio and FBF) superfamily (PufSF). These proteins bind to RNA via multiple Puf repeat d...

Authors: Vladimíra Najdrová, Courtney W. Stairs, Martina Vinopalová, Luboš Voleman and Pavel Doležal

Phosphatidic acid-dependent localization and basal de-phosphorylation of RA-GEFs regulate lymphocyte trafficking

Lymphocytes circulate between peripheral lymphoid tissues via blood and lymphatic systems, and chemokine-induced migration is important in trafficking lymphocytes to distant sites. The small GTPase Rap1 is imp...

Authors: Sayaka Ishihara, Tsuyoshi Sato, Guangwei Du, Daniele Guardavaccaro, Akihiko Nakajima, Satoshi Sawai, Tohru Kataoka and Koko Katagiri

The evolutionarily conserved ESRE stress response network is activated by ROS and mitochondrial damage

Mitochondrial dysfunction causes or contributes to a wide variety of pathologies, including neurodegenerative diseases, cancer, metabolic diseases, and aging. Cells actively surveil a number of mitochondrial r...

Authors: Elissa Tjahjono, Aidan P. McAnena and Natalia V. Kirienko

A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice

Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may p...

Authors: Fengli Zhao, Yuexing Wang, Jianshu Zheng, Yanling Wen, Minghao Qu, Shujing Kang, Shigang Wu, Xiaojuan Deng, Kai Hong, Sanfeng Li, Xing Qin, Zhichao Wu, Xiaobo Wang, Cheng Ai, Alun Li, Longjun Zeng…

The merger that made us

Authors: Buzz Baum and David A. Baum

New targeted approaches for epigenetic age predictions

Age-associated DNA methylation changes provide a promising biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinu...

Authors: Yang Han, Julia Franzen, Thomas Stiehl, Michael Gobs, Chao-Chung Kuo, Miloš Nikolić, Jan Hapala, Barbara Elisabeth Koop, Klaus Strathmann, Stefanie Ritz-Timme and Wolfgang Wagner

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity

Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine ty...

Authors: Timothy P. Driscoll, Victoria I. Verhoeve, Joseph J. Gillespie, J. Spencer Johnston, Mark L. Guillotte, Kristen E. Rennoll-Bankert, M. Sayeedur Rahman, Darren Hagen, Christine G. Elsik, Kevin R. Macaluso and Abdu F. Azad

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and th...

Authors: Alexander L. Jaffe, Cindy J. Castelle, Paula B. Matheus Carnevali, Simonetta Gribaldo and Jillian F. Banfield

Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants

Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid...

Authors: Zhichao Xu, Xiangdong Pu, Ranran Gao, Olivia Costantina Demurtas, Steven J. Fleck, Michaela Richter, Chunnian He, Aijia Ji, Wei Sun, Jianqiang Kong, Kaizhi Hu, Fengming Ren, Jiejie Song, Zhe Wang, Ting Gao, Chao Xiong…

Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning

The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of ...

Authors: Yanhong Zhong, Carlos Herrera-Úbeda, Jordi Garcia-Fernàndez, Guang Li and Peter W. H. Holland

Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

Acetyl-CoA is a key molecule in all organisms, implicated in several metabolic pathways as well as in transcriptional regulation and post-translational modification. The human pathogen Toxoplasma gondii possesses...

Authors: Joachim Kloehn, Rebecca D. Oppenheim, Ghizal Siddiqui, Pieter-Jan De Bock, Sunil Kumar Dogga, Yohann Coute, Mohamed-Ali Hakimi, Darren J. Creek and Dominique Soldati-Favre

Stimulus-specific behavioral responses of zebrafish to a large range of odors exhibit individual variability

Odor-driven behaviors such as feeding, mating, and predator avoidance are crucial for animal survival. The neural pathways processing these behaviors have been well characterized in a number of species, and in...

Authors: Florence Kermen, Lea Darnet, Christoph Wiest, Fabrizio Palumbo, Jack Bechert, Ozge Uslu and Emre Yaksi

DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system

CRISPR-Cas systems, which provide adaptive immunity against foreign nucleic acids in prokaryotes, can serve as useful molecular tools for multiple applications in genome engineering. Diverse CRISPR-Cas systems...

Authors: Donata Tuminauskaite, Danguole Norkunaite, Marija Fiodorovaite, Sarunas Tumas, Inga Songailiene, Giedre Tamulaitiene and Tomas Sinkunas

A mutation that blocks integrin α₄β₇ activation prevents adaptive immune-mediated colitis without increasing susceptibility to innate colitis

β₇ integrins are responsible for the efficient recruitment of lymphocytes from the blood and their retention in gut-associated lymphoid tissues. Integrin α₄β₇ binds MAdCAM-1, mediating rolling adhesion of lymphoc...

Authors: Hailong Zhang, Yajuan Zheng, Youdong Pan, Changdong Lin, Shihui Wang, Zhanjun Yan, Ling Lu, Gaoxiang Ge, Jinsong Li, Yi Arial Zeng and Jianfeng Chen

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

Parkinson’s disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their f...

Authors: Federico Baldini, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger and Ines Thiele

The replication machinery of LUCA: common origin of DNA replication and transcription

Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal repl...

Authors: Eugene V. Koonin, Mart Krupovic, Sonoko Ishino and Yoshizumi Ishino

A tissue level atlas of the healthy human virome

Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and huma...

Authors: Ryuichi Kumata, Jumpei Ito, Kenta Takahashi, Tadaki Suzuki and Kei Sato

Intramembrane proteolysis of an extracellular serine protease, epithin/PRSS14, enables its intracellular nuclear function

Epithin/PRSS14, a type II transmembrane serine protease, is an emerging target of cancer therapy because of its critical roles in tumor progression and metastasis. In many circumstances, the protease, through ...

Authors: Youngkyung Cho, Sang Bum Kim, Jiyoon Kim, An Vuong Quynh Pham, Min Ji Yoon, Jeong Hwan Park, Ki-Tae Hwang, Dongeun Park, Yongcheol Cho, Moon Gyo Kim and Chungho Kim

Unraveling the molecular interactions involved in phase separation of glucocorticoid receptor

Functional compartmentalization has emerged as an important factor modulating the kinetics and specificity of biochemical reactions in the nucleus, including those involved in transcriptional regulation. The g...

Authors: Martin Stortz, Adali Pecci, Diego M. Presman and Valeria Levi

Deficits in coordinated neuronal activity and network topology are striatal hallmarks in Huntington’s disease

Network alterations underlying neurodegenerative diseases often precede symptoms and functional deficits. Thus, their early identification is central for improved prognosis. In Huntington’s disease (HD), the c...

Authors: S. Fernández-García, J. G. Orlandi, G. A. García-Díaz Barriga, M. J. Rodríguez, M. Masana, J. Soriano and J. Alberch

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution

Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD w...

Authors: Dick Roelofs, Arthur Zwaenepoel, Tom Sistermans, Joey Nap, Andries A. Kampfraath, Yves Van de Peer, Jacintha Ellers and Ken Kraaijeveld

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions

Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis ...

Authors: Timothy G. Stephens, Raúl A. González-Pech, Yuanyuan Cheng, Amin R. Mohamed, David W. Burt, Debashish Bhattacharya, Mark A. Ragan and Cheong Xin Chan

Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans

The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ...

Authors: Marco Sazzini, Paolo Abondio, Stefania Sarno, Guido Alberto Gnecchi-Ruscone, Matteo Ragno, Cristina Giuliani, Sara De Fanti, Claudia Ojeda-Granados, Alessio Boattini, Julien Marquis, Armand Valsesia, Jerome Carayol, Frederic Raymond, Chiara Pirazzini, Elena Marasco, Alberto Ferrarini…

Using a chimeric respiratory chain and EPR spectroscopy to determine the origin of semiquinone species previously assigned to mitochondrial complex I

For decades, semiquinone intermediates have been suggested to play an essential role in catalysis by one of the most enigmatic proton-pumping enzymes, respiratory complex I, and different mechanisms have been ...

Authors: John J. Wright, Justin G. Fedor, Judy Hirst and Maxie M. Roessler

NetConfer: a web application for comparative analysis of multiple biological networks

Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need f...

Authors: Sunil Nagpal, Krishanu Das Baksi, Bhusan K. Kuntal and Sharmila S. Mande

Tropomyosin 1 genetically constrains in vitro hematopoiesis

Identifying causal variants and genes from human genetic studies of hematopoietic traits is important to enumerate basic regulatory mechanisms underlying these traits, and could ultimately augment translationa...

Authors: Christopher Stephen Thom, Chintan D Jobaliya, Kimberly Lorenz, Jean Ann Maguire, Alyssa Gagne, Paul Gadue, Deborah L French and Benjamin Franklin Voight

Modeling confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations

The discovery of CRISPR-based gene editing and its application to homing-based gene drive systems has been greeted with excitement, for its potential to control mosquito-borne diseases on a wide scale, and con...

Authors: Héctor M. Sánchez C., Jared B. Bennett, Sean L. Wu, Gordana Rašić, Omar S. Akbari and John M. Marshall

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary tr...

Authors: Matteo De Chiara, Anne Friedrich, Benjamin Barré, Michael Breitenbach, Joseph Schacherer and Gianni Liti

Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

Opportunistic yeast pathogens of the genus Candida are an important medical problem. Candida albicans, the most prevalent Candida species, is a natural commensal of humans that can adopt a pathogenic behavior. Th...

Authors: Verónica Mixão and Toni Gabaldón

Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31

Genome-wide association studies (GWAS) have uncovered many genetic risk loci for psoriasis, yet many remain uncharacterised in terms of the causal gene and their biological mechanism in disease. This is largel...

Authors: Helen Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony Adamson, Christopher Taylor, James Ding, Vasanthi Priyadarshini Gaddi, Yao Fu, Patrick Gaffney, Gisela Orozco…

An automated aquatic rack system for rearing marine invertebrates

One hundred years ago, marine organisms were the dominant systems for the study of developmental biology. The challenges in rearing these organisms outside of a marine setting ultimately contributed to a shift...

Authors: Jonathan Q. Henry, Maryna P. Lesoway and Kimberly J. Perry

Direct evidence for transport of RNA from the mouse brain to the germline and offspring

The traditional concept that heritability occurs exclusively from the transfer of germline-restricted genetics is being challenged by the increasing accumulation of evidence confirming the existence of experie...

Authors: Elizabeth A. O’Brien, Kathleen S. Ensbey, Bryan W. Day, Paul A. Baldock and Guy Barry

Microtubule self-organisation during seed germination in Arabidopsis

Upon water uptake and release of seed dormancy, embryonic plant cells expand, while being mechanically constrained by the seed coat. Cortical microtubules (CMTs) are key players of cell elongation in plants: t...

Authors: Huifang Yan, Nicole Chaumont, Jean François Gilles, Susanne Bolte, Olivier Hamant and Christophe Bailly

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC ne...

Authors: Alfonso Soler-Bistué, Sebastián Aguilar-Pierlé, Marc Garcia-Garcerá, Marie-Eve Val, Odile Sismeiro, Hugo Varet, Rodrigo Sieira, Evelyne Krin, Ole Skovgaard, Diego J. Comerci, Eduardo P. C. Rocha and Didier Mazel

Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation

Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclea...

Authors: Markus Grosch, Sebastian Ittermann, Ejona Rusha, Tobias Greisle, Chaido Ori, Dong-Jiunn Jeffery Truong, Adam C. O’Neill, Anna Pertek, Gil Gregor Westmeyer and Micha Drukker

Integrating evolutionarily novel horns within the deeply conserved insect head

How novel traits integrate within ancient trait complexes without compromising ancestral functions is a foundational challenge in evo-devo. The insect head represents an ancient body region patterned by a deep...

Authors: David M. Linz and Armin P. Moczek