Articles

Inferring cancer dependencies on metabolic genes from large-scale genetic screens

Cancer cells reprogram their metabolism to survive and propagate. Thus, targeting metabolic rewiring in tumors is a promising therapeutic strategy. Genome-wide RNAi and CRISPR screens are powerful tools for id...

Authors: Shoval Lagziel, Won Dong Lee and Tomer Shlomi

Cell size sensing—a one-dimensional solution for a three-dimensional problem?

Individual cell types have characteristic sizes, suggesting that size sensing mechanisms may coordinate transcription, translation, and metabolism with cell growth rates. Two types of size-sensing mechanisms h...

Authors: Ida Rishal and Mike Fainzilber

Mechanisms of tethering and cargo transfer during epididymosome-sperm interactions

The mammalian epididymis is responsible for the provision of a highly specialized environment in which spermatozoa acquire functional maturity and are subsequently stored in preparation for ejaculation. Making...

Authors: Wei Zhou, Simone J. Stanger, Amanda L. Anderson, Ilana R. Bernstein, Geoffry N. De Iuliis, Adam McCluskey, Eileen A. McLaughlin, Matthew D. Dun and Brett Nixon

In vivo assembly and trafficking of olfactory Ionotropic Receptors

Ionotropic receptors (IRs) are a large, divergent subfamily of ionotropic glutamate receptors (iGluRs) that are expressed in diverse peripheral sensory neurons and function in olfaction, taste, hygrosensation ...

Authors: Liliane Abuin, Lucia L. Prieto-Godino, Haiyun Pan, Craig Gutierrez, Lan Huang, Rongsheng Jin and Richard Benton

Derivation of adult canine intestinal organoids for translational research in gastroenterology

Large animal models, such as the dog, are increasingly being used for studying diseases including gastrointestinal (GI) disorders. Dogs share similar environmental, genomic, anatomical, and intestinal physiolo...

Authors: Lawrance Chandra, Dana C. Borcherding, Dawn Kingsbury, Todd Atherly, Yoko M. Ambrosini, Agnes Bourgois-Mochel, Wang Yuan, Michael Kimber, Yijun Qi, Qun Wang, Michael Wannemuehler, N. Matthew Ellinwood, Elizabeth Snella, Martin Martin, Melissa Skala, David Meyerholz…

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons

Epigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, i...

Authors: Pavan Agrawal, Phuong Chung, Ulrike Heberlein and Clement Kent

Correction to: Q&A: insulin secretion and type 2 diabetes: why do β-cells fail?

Upon publication of the original article [1], the authors noticed that they had accidently omitted to acknowledge funding from the European Research Council.

Authors: James Cantley and Frances M. Ashcroft

Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes

Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as...

Authors: Vanessa R. Marcelino, Michelle Wille, Aeron C. Hurt, Daniel González-Acuña, Marcel Klaassen, Timothy E. Schlub, John-Sebastian Eden, Mang Shi, Jonathan R. Iredell, Tania C. Sorrell and Edward C. Holmes

Selective processing of all rotational and translational optic flow directions in the zebrafish pretectum and tectum

The processing of optic flow in the pretectum/accessory optic system allows animals to stabilize retinal images by executing compensatory optokinetic and optomotor behavior. The success of this behavior depend...

Authors: Kun Wang, Julian Hinz, Väinö Haikala, Dierk F. Reiff and Aristides B. Arrenberg

The genome of the giant Nomura’s jellyfish sheds light on the early evolution of active predation

Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The...

Authors: Hak-Min Kim, Jessica A. Weber, Nayoung Lee, Seung Gu Park, Yun Sung Cho, Youngjune Bhak, Nayun Lee, Yeonsu Jeon, Sungwon Jeon, Victor Luria, Amir Karger, Marc W. Kirschner, Ye Jin Jo, Seonock Woo, Kyoungsoon Shin, Oksung Chung…

Modelling the potential of genetic control of malaria mosquitoes at national scale

The persistence of malaria in large parts of sub-Saharan Africa has motivated the development of novel tools to complement existing control programmes, including gene-drive technologies to modify mosquito vect...

Authors: Ace R. North, Austin Burt and H. Charles J. Godfray

Be the change you seek in science

Few would argue that science is better done in silos, with no transparency or sharing of methods and resources. Yet scientists and scientific stakeholders (e.g., academic institutions, funding agencies, journa...

Authors: Michael P. Milham and Arno Klein

Correction to: SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis

Upon publication of the original article [1], the authors noticed that they omitted Additional file 16: Table S10 from the Additional file list. Additional file 16: Table S10 can be found attached to this Corr...

Authors: Zhibo Cui, Aizi Tong, Yiqiong Huo, Zhiqiang Yan, Wenqi Yang, Xianli Yang and Xiao-Xue Wang

A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits

The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and...

Authors: Basten L. Snoek, Rita J. M. Volkers, Harm Nijveen, Carola Petersen, Philipp Dirksen, Mark G. Sterken, Rania Nakad, Joost A. G. Riksen, Philip Rosenstiel, Jana J. Stastna, Bart P. Braeckman, Simon C. Harvey, Hinrich Schulenburg and Jan E. Kammenga

GSK-3β protects fetal oocytes from premature death via modulating TAp63 expression in mice

Female mammals have a limited reproductive lifespan determined by the size of the primordial follicle pool established perinatally. Over two thirds of fetal oocytes are abolished via programmed cell death duri...

Authors: Jia Wen, Hao Yan, Meina He, Tuo Zhang, Xinyi Mu, Haibin Wang, Hua Zhang, Guoliang Xia and Chao Wang

Mesencephalic origin of the inferior lobe in zebrafish

Although the overall brain organization is shared in vertebrates, there are significant differences within subregions among different groups, notably between Sarcopterygii (lobe-finned fish) and Actinopterygii...

Authors: Solal Bloch, Manon Thomas, Ingrid Colin, Sonya Galant, Elodie Machado, Pierre Affaticati, Arnim Jenett and Kei Yamamoto

Correction to: Detecting neural assemblies in calcium imaging data

Upon publication of the original article, [1], the authors noticed that the first authors’ affiliation contained an error.

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

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations

Microbial communities are susceptible to the public goods dilemma, whereby individuals can gain an advantage within a group by utilizing, but not sharing the cost of producing, public goods. In bacteria, the d...

Authors: Kelei Zhao, Linjie Liu, Xiaojie Chen, Ting Huang, Lianming Du, Jiafu Lin, Yang Yuan, Yingshun Zhou, Bisong Yue, Kun Wei and Yiwen Chu

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