Articles

Blind free-living kiwi offer a unique window into the ecology and evolution of vertebrate vision

The first report of multiple, blind, wild birds in good health suggests vision is not necessary for the survival of kiwi.

Authors: Bret A. Moore, Joanne R. Paul-Murphy, Alan J. D. Tennyson and Christopher J. Murphy

Antibiotic resistance: it’s bad, but why isn’t it worse?

Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements. Nevertheless, despite long histories of antibiotic ...

Authors: Nicholas Waglechner and Gerard D. Wright

Q&A: Morphological insights into evolution

In this question and answer article we discuss how evolution shapes morphology (the shape and pattern of our bodies) but also how learning about morphology, and specifically how that morphology arises during d...

Authors: Neal Anthwal and Abigail S. Tucker

Q&A: The brain under a mesoscope: the forest and the trees

Neurons relevant to a particular behavior are often widely dispersed across the brain. To record activity in groups of individual neurons that might be distributed across large distances, neuroscientists and o...

Authors: Nicholas James Sofroniew

How driving endonuclease genes can be used to combat pests and disease vectors

Driving endonuclease genes (DEGs) spread through a population by a non-Mendelian mechanism. In a heterozygote, the protein encoded by a DEG causes a double-strand break in the homologous chromosome opposite to...

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

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

Similar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Ski-interacting protein (SKIP), a splicing factor, is essential for circadian clo...

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

Thioester-containing proteins regulate the Toll pathway and play a role in Drosophila defence against microbial pathogens and parasitoid wasps

Members of the thioester-containing protein (TEP) family contribute to host defence in both insects and mammals. However, their role in the immune response of Drosophila is elusive. In this study, we address the ...

Authors: Anna Dostálová, Samuel Rommelaere, Mickael Poidevin and Bruno Lemaitre

Dosage-sensitive genes in evolution and disease

For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typic...

Authors: Alan M. Rice and Aoife McLysaght

Q&A: Where did the Neanderthals go?

Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2–3% Neanderthal DNA. However, it is still hotly debated why the Neandert...

Authors: Kelley Harris and Rasmus Nielsen

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, ...

Authors: D. J. Lightfoot, D. E. Jarvis, T. Ramaraj, R. Lee, E. N. Jellen and P. J. Maughan

Blob-ology and biology of cryo-EM: an interview with Helen Saibil

Helen Saibil is Bernal Professor of Structural Biology at Birkbeck, University of London. After undergraduate work at McGill University, Canada, Helen moved to London for her PhD at Kings College. After stints...

Authors: Helen R. Saibil

Ribosome signatures aid bacterial translation initiation site identification

While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory...

Authors: Adam Giess, Veronique Jonckheere, Elvis Ndah, Katarzyna Chyżyńska, Petra Van Damme and Eivind Valen

A widespread family of polymorphic toxins encoded by temperate phages

Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to distinct families that share common features in terms of domain organization. PTs are found in all major bacterial clades, including m...

Authors: Anne Jamet, Marie Touchon, Bruno Ribeiro-Gonçalves, João André Carriço, Alain Charbit, Xavier Nassif, Mario Ramirez and Eduardo P. C. Rocha

Distinct unfolded protein responses mitigate or mediate effects of nonlethal deprivation of C. elegans sleep in different tissues

Disrupting sleep during development leads to lasting deficits in chordates and arthropods. To address lasting impacts of sleep deprivation in Caenorhabditis elegans, we established a nonlethal deprivation protoco...

Authors: Jarred Sanders, Monika Scholz, Ilaria Merutka and David Biron

Erratum to: Charged residues next to transmembrane regions revisited: “Positive-inside rule” is complemented by the “negative inside depletion/outside enrichment rule”

Authors: James Alexander Baker, Wing-Cheong Wong, Birgit Eisenhaber, Jim Warwicker and Frank Eisenhaber

Biological function in the twilight zone of sequence conservation

Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast ‘twilight zone’ in which sequence subject to transient or lower cons...

Authors: Chris P. Ponting

Multiple essential functions of Plasmodium falciparum actin-1 during malaria blood-stage development

The phylum Apicomplexa includes intracellular parasites causing immense global disease burden, the deadliest of them being the human malaria parasite Plasmodium falciparum, which invades and replicates within ery...

Authors: Sujaan Das, Leandro Lemgruber, Chwen L. Tay, Jake Baum and Markus Meissner

Erratum to: Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

Authors: S. L. Pearce, D. F. Clarke, P. D. East, S. Elfekih, K. H. J. Gordon, L. S. Jermiin, A. McGaughran, J. G. Oakeshott, A. Papanicolaou, O. P. Perera, R. V. Rane, S. Richards, W. T. Tay, T. K. Walsh, A. Anderson, C. J. Anderson…

Examining non-LTR retrotransposons in the context of the evolving primate brain

Researchers have long sought to understand the genetic basis of the cognitive differences between primates, with particular focus on the human brain. Although all mutational types have worked in concert with e...

Authors: Sara B. Linker, Maria C. Marchetto, Iñigo Narvaiza, Ahmet M. Denli and Fred H. Gage

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. a...

Authors: S. L. Pearce, D. F. Clarke, P. D. East, S. Elfekih, K. H. J. Gordon, L. S. Jermiin, A. McGaughran, J. G. Oakeshott, A. Papanikolaou, O. P. Perera, R. V. Rane, S. Richards, W. T. Tay, T. K. Walsh, A. Anderson, C. J. Anderson…

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplic...

Authors: Evelyn E. Schwager, Prashant P. Sharma, Thomas Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, HarshaVardhan Doddapaneni, Shannon Dugan, Cornelius Eibner…

Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization

Biological mineral formation (biomineralization) proceeds in specialized compartments often bounded by a lipid bilayer membrane. Currently, the role of membranes in biomineralization is hardly understood.

Authors: Alexander Kotzsch, Philip Gröger, Damian Pawolski, Paul H. H. Bomans, Nico A. J. M. Sommerdijk, Michael Schlierf and Nils Kröger

Charged residues next to transmembrane regions revisited: “Positive-inside rule” is complemented by the “negative inside depletion/outside enrichment rule”

Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane’s hydrophobicity and...

Authors: James Alexander Baker, Wing-Cheong Wong, Birgit Eisenhaber, Jim Warwicker and Frank Eisenhaber

Q&A: What is human language, when did it evolve and why should we care?

Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign ‘language’ i...

Authors: Mark Pagel

C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility

In addition to DNA, gametes contribute epigenetic information in the form of histones and non-coding RNA. Epigenetic programs often respond to stressful environmental conditions and provide a heritable history...

Authors: Wendy L. Johnston, Aldis Krizus, Arun K. Ramani, Wade Dunham, Ji Young Youn, Andrew G. Fraser, Anne-Claude Gingras and James W. Dennis

Peto’s Paradox: how has evolution solved the problem of cancer prevention?

The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-hu...

Authors: Marc Tollis, Amy M. Boddy and Carlo C. Maley

Life behind the wall: sensing mechanical cues in plants

There is increasing evidence that all cells sense mechanical forces in order to perform their functions. In animals, mechanotransduction has been studied during the establishment of cell polarity, fate, and di...

Authors: Olivier Hamant and Elizabeth S. Haswell

Q&A: using Patch-seq to profile single cells

Individual neurons vary widely in terms of their gene expression, morphology, and electrophysiological properties. While many techniques exist to study single-cell variability along one or two of these dimensi...

Authors: Cathryn R. Cadwell, Rickard Sandberg, Xiaolong Jiang and Andreas S. Tolias

Nanobodies raised against monomeric ɑ-synuclein inhibit fibril formation and destabilize toxic oligomeric species

The aggregation of the protein ɑ-synuclein (ɑS) underlies a range of increasingly common neurodegenerative disorders including Parkinson’s disease. One widely explored therapeutic strategy for these conditions...

Authors: Marija Iljina, Liu Hong, Mathew H. Horrocks, Marthe H. Ludtmann, Minee L. Choi, Craig D. Hughes, Francesco S. Ruggeri, Tim Guilliams, Alexander K. Buell, Ji-Eun Lee, Sonia Gandhi, Steven F. Lee, Clare E. Bryant, Michele Vendruscolo, Tuomas P. J. Knowles, Christopher M. Dobson…

Olfactory coding from the periphery to higher brain centers in the Drosophila brain

Odor information is processed through multiple receptor-glomerular channels in the first order olfactory center, the antennal lobe (AL), then reformatted into higher brain centers and eventually perceived by t...

Authors: Yoichi Seki, Hany K. M. Dweck, Jürgen Rybak, Dieter Wicher, Silke Sachse and Bill S. Hansson

Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues

Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed ...

Authors: Rohan Bythell-Douglas, Carl J. Rothfels, Dennis W. D. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, David C. Nelson and Tom Bennett

Tissue macrophages: heterogeneity and functions

Macrophages are present in all vertebrate tissues, from mid-gestation throughout life, constituting a widely dispersed organ system. They promote homeostasis by responding to internal and external changes with...

Authors: Siamon Gordon and Annette Plüddemann

Mov10 suppresses retroelements and regulates neuronal development and function in the developing brain

Moloney leukemia virus 10 (Mov10) is an RNA helicase that mediates access of the RNA-induced silencing complex to messenger RNAs (mRNAs). Until now, its role as an RNA helicase and as a regulator of retrotrans...

Authors: Geena Skariah, Joseph Seimetz, Miles Norsworthy, Monica C. Lannom, Phillip J. Kenny, Mohamed Elrakhawy, Craig Forsthoefel, Jenny Drnevich, Auinash Kalsotra and Stephanie Ceman

Non-model model organisms

Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but moder...

Authors: James J. Russell, Julie A. Theriot, Pranidhi Sood, Wallace F. Marshall, Laura F. Landweber, Lillian Fritz-Laylin, Jessica K. Polka, Snezhana Oliferenko, Therese Gerbich, Amy Gladfelter, James Umen, Magdalena Bezanilla, Madeline A. Lancaster, Shuonan He, Matthew C. Gibson, Bob Goldstein…

Organelle acidification: an ancient cellular leak detector

Intracellular membrane-bounded organelles of eukaryotic cells transiently contact the extracellular environment during endocytosis and secretion. Such contacts must be precisely timed to prevent leakage of car...

Authors: Mukund Thattai

Q&A: Expansion microscopy

Expansion microscopy (ExM) is a recently invented technology that uses swellable charged polymers, synthesized densely and with appropriate topology throughout a preserved biological specimen, to physically ma...

Authors: Ruixuan Gao, Shoh M. Asano and Edward S. Boyden

Who needs registered reports?

Registered Reports, an article format initiated to help promote transparency and reproducibility in the preclinical and social sciences, are spreading into the biological literature. The format is now offered by

Authors: Miranda Robertson

Dynamics of transcriptional (re)-programming of syncytial nuclei in developing muscles

A stereotyped array of body wall muscles enables precision and stereotypy of animal movements. In Drosophila, each syncytial muscle forms via fusion of one founder cell (FC) with multiple fusion competent myoblas...

Authors: Laetitia Bataillé, Hadi Boukhatmi, Jean-Louis Frendo and Alain Vincent

Open questions: completing the parts list and finding the integrating signals

One of the great revelations of post-genomic biology has been the extent to which essential functions and mechanisms are conserved across vast phylogenetic distances. Because of this, we can look to the fruit ...

Authors: Aurelio A. Teleman and Norbert Perrimon

Matriptase zymogen supports epithelial development, homeostasis and regeneration

Matriptase is a membrane serine protease essential for epithelial development, homeostasis, and regeneration, as well as a central orchestrator of pathogenic pericellular signaling in the context of inflammato...

Authors: Stine Friis, Daniel Tadeo, Sylvain M. Le-Gall, Henrik Jessen Jürgensen, Katiuchia Uzzun Sales, Eric Camerer and Thomas H. Bugge

Differential DARC/ACKR1 expression distinguishes venular from non-venular endothelial cells in murine tissues

Intravascular leukocyte recruitment in most vertebrate tissues is restricted to postcapillary and collecting venules, whereas capillaries and arterioles usually support little or no leukocyte adhesion. This se...

Authors: Aude Thiriot, Carolina Perdomo, Guiying Cheng, Igor Novitzky-Basso, Sara McArdle, Jamie K. Kishimoto, Olga Barreiro, Irina Mazo, Robinson Triboulet, Klaus Ley, Antal Rot and Ulrich H. von Andrian

Cell fixation and preservation for droplet-based single-cell transcriptomics

Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting ste...

Authors: Jonathan Alles, Nikos Karaiskos, Samantha D. Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier, Robert Zinzen, Christine Kocks and Nikolaus Rajewsky

Open Questions: We don’t really know anything, do we? Open questions in sensory biology

Senses connect organisms to both the world and to each other, yet there is much we don’t know about them. Using examples drawn primarily from the author’s subfield of vision research, this article discusses fi...

Authors: Sönke Johnsen

Optogenetic interrogation reveals separable G-protein-dependent and -independent signalling linking G-protein-coupled receptors to the circadian oscillator

Endogenous circadian oscillators distributed across the mammalian body are synchronised among themselves and with external time via a variety of signalling molecules, some of which interact with G-protein-coup...

Authors: Helena J. Bailes, Nina Milosavljevic, Ling-Yu Zhuang, Elliot J. Gerrard, Tomoki Nishiguchi, Takeaki Ozawa and Robert J. Lucas

OptiMouse: a comprehensive open source program for reliable detection and analysis of mouse body and nose positions

Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions...

Authors: Yoram Ben-Shaul

Knowing where the nose is

Improvements in imaging technology and the development of powerful machine learning algorithms are revolutionizing the study of animal behavior in the laboratory. These innovations promise to reveal both globa...

Authors: Winthrop F. Gillis and Sandeep R. Datta

Heterosis as a consequence of regulatory incompatibility

The merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. Heterosis is typically viewed as the opposit...

Authors: Rebecca H. Herbst, Dana Bar-Zvi, Sharon Reikhav, Ilya Soifer, Michal Breker, Ghil Jona, Eyal Shimoni, Maya Schuldiner, Avraham A. Levy and Naama Barkai

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors

Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tro...

Authors: Edouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, Temur Yunusov, Kévin Floch and Sebastian Schornack

NO_Xious gases and the unpredictability of emerging plant pathogens under climate change

Emerging pathogens of crops threaten food security and are increasingly problematic due to intensive agriculture and high volumes of trade and transport in plants and plant products. The ability to predict pat...

Authors: Helen N. Fones and Sarah J. Gurr

Can a biologist fix a smartphone?—Just hack it!

Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encode...

Authors: Sophien Kamoun