Articles

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida

Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species ca...

Authors: Courtney W. Stairs, Anna Kokla, Ásgeir Ástvaldsson, Jon Jerlström-Hultqvist, Staffan Svärd and Thijs J. G. Ettema

The golden death bacillus Chryseobacterium nematophagum is a novel matrix digesting pathogen of nematodes

Nematodes represent important pathogens of humans and farmed animals and cause significant health and economic impacts. The control of nematodes is primarily carried out by applying a limited number of anthelm...

Authors: Antony P. Page, Mark Roberts, Marie-Anne Félix, Derek Pickard, Andrew Page and William Weir

Q&A: modern crop breeding for future food security

Farmers around the world have recently experienced significant crop losses due to severe heat and drought. Such extreme weather events and the need to feed a rapidly growing population have raised concerns for...

Authors: Kai P. Voss-Fels, Andreas Stahl and Lee T. Hickey

Open questions: how to get developmental biology into shape?

Recent technical advances have provided unprecedented insights into the selective deployment of the genome in developing organisms, but how such differential gene expression is used to sculpt the complex shape...

Authors: Timothy E. Saunders and Philip W. Ingham

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa

Metazoan lineages exhibit a wide range of regenerative capabilities that vary among developmental stage and tissue type. The most robust regenerative abilities are apparent in the phyla Cnidaria, Platyhelminth...

Authors: Gregory A. Cary, Andrew Wolff, Olga Zueva, Joseph Pattinato and Veronica F. Hinman

Role of self-organising myddosome oligomers in inflammatory signalling by Toll-like receptors

A paper published in BMC Biology characterises biophysically oligomeric and filamentous structures formed spontaneously by the Toll-like receptor signalling adaptor MyD88. Naturally occurring mutants of MyD88 tha...

Authors: Nicholas J. Gay

Identification of functional long non-coding RNAs in C. elegans

Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 years ago. The last decade of research has seen a tremendous increase in...

Authors: Alper Akay, David Jordan, Isabela Cunha Navarro, Tomasz Wrzesinski, Chris P. Ponting, Eric A. Miska and Wilfried Haerty

Circadian oscillator proteins across the kingdoms of life: structural aspects

Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock componen...

Authors: Reena Saini, Mariusz Jaskolski and Seth J. Davis

A role for actomyosin contractility in Notch signaling

Notch-Delta signaling functions across a wide array of animal systems to break symmetry in a sheet of undifferentiated cells and generate cells with different fates, a process known as lateral inhibition. Unli...

Authors: Ginger L. Hunter, Li He, Norbert Perrimon, Guillaume Charras, Edward Giniger and Buzz Baum

Transcriptome, proteome and draft genome of Euglena gracilis

Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gr...

Authors: ThankGod E. Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis O’Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson Obado, Sara Silva-Pereira, Andrew P. Jackson, Damien P. Devos…

Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis

CRISPR-Cas12a (formerly Cpf1) is an RNA-guided endonuclease with distinct features that have expanded genome editing capabilities. Cas12a-mediated genome editing is temperature sensitive in plants, but a lack ...

Authors: Aimee A. Malzahn, Xu Tang, Keunsub Lee, Qiurong Ren, Simon Sretenovic, Yingxiao Zhang, Hongqiao Chen, Minjeong Kang, Yu Bao, Xuelian Zheng, Kejun Deng, Tao Zhang, Valeria Salcedo, Kan Wang, Yong Zhang and Yiping Qi

Inclusive fitness benefits mitigate costs of cuckoldry to socially paired males

In socially monogamous species, reproduction is not always confined to paired males and females. Extra-pair males commonly also reproduce with paired females, which is traditionally thought to be costly to the...

Authors: Aneesh P. H. Bose, Jonathan M. Henshaw, Holger Zimmermann, Karoline Fritzsche and Kristina M. Sefc

Thawing out frozen metabolic accidents

Photosynthesis and nitrogen fixation became evolutionarily immutable as “frozen metabolic accidents” because multiple interactions between the proteins and protein complexes involved led to their co-evolution ...

Authors: Dario Leister

A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis

The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), especially those that are multidrug resistant poses a serious threat to global tuberculosis control. However, the mechanism underlying ...

Authors: Lianhua Qin, Jie Wang, Junmei Lu, Hua Yang, Ruijuan Zheng, Zhonghua Liu, Xiaochen Huang, Yonghong Feng, Zhongyi Hu and Baoxue Ge

The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish

Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chrom...

Authors: Lisui Bao, Changxu Tian, Shikai Liu, Yu Zhang, Ahmed Elaswad, Zihao Yuan, Karim Khalil, Fanyue Sun, Yujia Yang, Tao Zhou, Ning Li, Suxu Tan, Qifan Zeng, Yang Liu, Yueru Li, Yun Li…

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate localization to specific sub-cellular compartments. RNA localization is critical for many different ce...

Authors: Sarah A. Middleton, James Eberwine and Junhyong Kim

Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas

Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two we...

Authors: Viola Grugni, Alessandro Raveane, Linda Ongaro, Vincenza Battaglia, Beniamino Trombetta, Giulia Colombo, Marco Rosario Capodiferro, Anna Olivieri, Alessandro Achilli, Ugo A. Perego, Jorge Motta, Maribel Tribaldos, Scott R. Woodward, Luca Ferretti, Fulvio Cruciani, Antonio Torroni…

In vivo genome and base editing of a human PCSK9 knock-in hypercholesterolemic mouse model

Plasma concentration of low-density lipoprotein (LDL) cholesterol is a well-established risk factor for cardiovascular disease. Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9), which regula...

Authors: Alba Carreras, Luna Simona Pane, Roberto Nitsch, Katja Madeyski-Bengtson, Michelle Porritt, Pinar Akcakaya, Amir Taheri-Ghahfarokhi, Elke Ericson, Mikael Bjursell, Marta Perez-Alcazar, Frank Seeliger, Magnus Althage, Ralph Knöll, Ryan Hicks, Lorenz M. Mayr, Rosie Perkins…

A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples

Current mesoscale 3D imaging techniques are limited to transparent or cleared samples or require the use of X-rays. This is a severe limitation for many research areas, as the 3D color surface morphology of op...

Authors: Axelle Kerstens, Nikky Corthout, Benjamin Pavie, Zengjin Huang, Frank Vernaillen, Greetje Vande Velde and Sebastian Munck

Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells

Cultured human cells are pivotal models to study human gene functions, but introducing complete loss of function in diploid or aneuploid cells has been a challenge. The recently developed CRISPR/Cas9-mediated ...

Authors: Chenzi Zhang, Xiangjun He, Yvonne K. Kwok, Feng Wang, Junyi Xue, Hui Zhao, Kin Wah Suen, Chi Chiu Wang, Jianwei Ren, George G. Chen, Paul B. S. Lai, Jiangchao Li, Yin Xia, Andrew M. Chan, Wai-Yee Chan and Bo Feng

BE-FLARE: a fluorescent reporter of base editing activity reveals editing characteristics of APOBEC3A and APOBEC3B

Base Editing is a precise genome editing method that uses a deaminase-Cas9 fusion protein to mutate cytidine to thymidine in target DNA in situ without the generation of a double-strand break. However, the eff...

Authors: Matthew A. Coelho, Songyuan Li, Luna Simona Pane, Mike Firth, Giovanni Ciotta, Jonathan D. Wrigley, Maria Emanuela Cuomo, Marcello Maresca and Benjamin J. M. Taylor

Pathological mutations differentially affect the self-assembly and polymerisation of the innate immune system signalling adaptor molecule MyD88

Higher-order self-assembly of proteins, or “prion-like” polymerisation, is now emerging as a simple and robust mechanism for signal amplification, in particular within the innate immune system, where the recog...

Authors: Ailís O’Carroll, Brieuc Chauvin, James W. P. Brown, Ava Meagher, Joanne Coyle, Jurgen Schill, Akshay Bhumkhar, Dominic J. B. Hunter, Thomas Ve, Bostjan Kobe, Emma Sierecki and Yann Gambin

Biological clock function is linked to proactive and reactive personality types

Many physiological processes in our body are controlled by the biological clock and show circadian rhythmicity. It is generally accepted that a robust rhythm is a prerequisite for optimal functioning and that ...

Authors: Christian Tudorache, Hans Slabbekoorn, Yuri Robbers, Eline Hin, Johanna H. Meijer, Herman P. Spaink and Marcel J. M. Schaaf

Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways

The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway activated by disruption of proteostasis in the mitochondria. This pathway has been proposed to influence lifespan, with studie...

Authors: Ziyun Wu, Megan M. Senchuk, Dylan J. Dues, Benjamin K. Johnson, Jason F. Cooper, Leira Lew, Emily Machiela, Claire E. Schaar, Heather DeJonge, T. Keith Blackwell and Jeremy M. Van Raamsdonk

Tackling waste in publishing through portable peer review

Authors: Graham P. Bell and Mirna Kvajo

Trait heritability in major transitions

Increases in biological complexity and the origins of life’s hierarchical organization are described by the “major transitions” framework. A crucial component of this paradigm is that after the transition in c...

Authors: Matthew D. Herron, Seyed A. Zamani-Dahaj and William C. Ratcliff

Two-component cyclase opsins of green algae are ATP-dependent and light-inhibited guanylyl cyclases

The green algae Chlamydomonas reinhardtii and Volvox carteri are important models for studying light perception and response, expressing many different photoreceptors. More than 10 opsins were reported in C. rein...

Authors: Yuehui Tian, Shiqiang Gao, Eva Laura von der Heyde, Armin Hallmann and Georg Nagel

Detecting neural assemblies in calcium imaging data

Activity in populations of neurons often takes the form of assemblies, where specific groups of neurons tend to activate at the same time. However, in calcium imaging data, reliably identifying these assemblie...

Authors: Jan Mölter, Lilach Avitan and Geoffrey J. Goodhill

Genome of tiny predator with big appetite

The capture and enslavement of eukaryotic algae by unicellular predators to acquire photosynthesis was a major driving force in early eukaryotic diversification. A genome presented in BMC Biology provides a glimp...

Authors: Geoffrey Ian McFadden

Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids

The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cy...

Authors: Ugo Cenci, Shannon J. Sibbald, Bruce A. Curtis, Ryoma Kamikawa, Laura Eme, Daniel Moog, Bernard Henrissat, Eric Maréchal, Malika Chabi, Christophe Djemiel, Andrew J. Roger, Eunsoo Kim and John M. Archibald

Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells

Mammalian cells are flexible and can rapidly change shape when they contract, adhere, or migrate. The nucleus must be stiff enough to withstand cytoskeletal forces, but flexible enough to remodel as the cell c...

Authors: Elsie C. Jacobson, Jo K. Perry, David S. Long, Ada L. Olins, Donald E. Olins, Bryon E. Wright, Mark H. Vickers and Justin M. O’Sullivan

Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria

Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases...

Authors: Markéta Petrů, Jeremy Wideman, Kristoffer Moore, Felicity Alcock, Tracy Palmer and Pavel Doležal

Precise A•T to G•C base editing in the zebrafish genome

Base editors are a class of genome editing tools with the ability to efficiently induce point mutations in genomic DNA, without inducing double-strand breaks or relying on homology-direct repair as in other su...

Authors: Wei Qin, Xiaochan Lu, Yunxing Liu, Haipeng Bai, Song Li and Shuo Lin

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

Characterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of ...

Authors: Xinyi Yang and Martin Vingron

Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida

Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embe...

Authors: Sunjoo Joo, Ming Hsiu Wang, Gary Lui, Jenny Lee, Andrew Barnas, Eunsoo Kim, Sebastian Sudek, Alexandra Z. Worden and Jae-Hyeok Lee

Host-parasite interactions: an interview with Emily Troemel

Emily Troemel is a Professor at the University of California San Diego, where her lab uses Caenorhabditis elegans to study host–pathogen interactions and the shaping of the immune response. In this interview, Emi...

Authors: Emily Troemel

Dissecting the forces that shape crops: an interview with Ryohei Terauchi

Ryohei Terauchi is a Professor at Kyoto University and a Group Leader at the Iwate Biotechnology Research Center, Japan, studying the evolution of crops and their pathogens. In this interview, Ryohei describes...

Authors: Ryohei Terauchi

Open questions: why should we care about ER-phagy and ER remodelling?

The endoplasmic reticulum (ER) is one of the most complex organelles in the eukaryotic cell. Recent findings suggest that a process called ER-phagy plays a major role in maintaining the ER’s shape and function.

Authors: Ivan Dikic

When a physicist wanders into biology…: an interview with KC Huang

Kerwyn Casey (“KC”) Huang is an Associate Professor at Stanford University, studying the physical nature of biological systems and the underpinnings of fundamental processes such as cell shape determination, c...

Authors: Kerwyn Casey Huang

Open questions: why are babies rarely born with cancer?

Childhood cancer is fundamentally a disease of dysregulated development. Why does it rarely occur during the fetal period, a time of enormous growth and development?

Authors: Michelle Monje

Communicating through scents: an interview with Jane Hurst

Jane Hurst is a William Prescott Professor of Animal Science at the University of Liverpool, UK, studying scent communication in mammals and its role in behaviours. In this interview, Jane discusses how scents...

Authors: Jane Hurst

On microbes, aging and the worm: an interview with David Weinkove

David Weinkove is an associate professor at Durham University, UK, studying host–microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiolog...

Authors: David Weinkove

Horizons in evolutionary genomics: an interview with David Ferrier

David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis o...

Authors: David E. K. Ferrier

From bacterial genomics to clinical epidemiology: an interview with Bill Hanage

Bill Hanage is an Associate Professor of Epidemiology at Harvard School of Public Health, where he studies fundamental and applied epidemiology using genomic and evolutionary methods. Bill spoke to us about th...

Authors: William P. Hanage

Systems biology of meristems: an interview with Teva Vernoux

Teva Vernoux is a plant developmental biologist and holds positions as the Director of the Institute for Reproduction and Development of Plants at ENS de Lyon, and as a Research Director at Centre National de ...

Authors: Teva Vernoux

Evolving eukaryotes: an interview with Joel Dacks

Joel Dacks is an Associate Professor and Canada Research Chair in Evolutionary Cell Biology at the University of Alberta, a Scientific Associate at the Natural History Museum (London), and the current Presiden...

Authors: Joel B. Dacks

Startling responses of zebrafish: an interview with Harold Burgess

Harold Burgess is a Senior Investigator at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), part of the National Institutes of Health. Work in his lab combines genetic ...

Authors: Harold A. Burgess

Evolutionary development and morphological modifications of the brain: an interview with Angelika Stollewerk

Angelika Stollewerk is a Reader at Queen Mary University of London, where her lab uses a diverse range of species to study the evolution of the arthropod nervous system. Angelika spoke to us about social spide...

Authors: Angelika Stollewerk

Open questions: what are the genes underlying antagonistic coevolution?

Although the idea of coevolution was first presented 150 years ago, we still only vaguely understand the genetic basis of its workings. Identifying the genes responsible for coevolutionary interactions would e...

Authors: Dieter Ebert

Open questions: respiratory chain supercomplexes—why are they there and what do they do?

In the mitochondrial inner membrane the respiratory enzymes associate to form supramolecular assemblies known as supercomplexes. The existence of supercomplexes is now widely accepted—but what functional or st...

Authors: Judy Hirst