Articles

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

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

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

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

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

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

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

From plant immunity to food security: an interview with Ksenia Krasileva

Ksenia Krasileva is an Assistant Professor at UC Berkeley, studying innate immunity in plants. Ksenia’s work combines plant genomics and plant-microbe interactions with new technologies, spanning basic studies...

Authors: Ksenia Krasileva

15 years of BMC Biology

Authors: Christian Matheou, Graham P. Bell, Penelope Austin, Vitor Sousa and Mirna Kvajo

Studying the microbiome and its complexities: an interview with Alan Walker

Alan Walker is a Senior Lecturer at the University of Aberdeen, UK, studying the intestinal microbiota and its interactions with the host’s diet. In this interview, Alan discusses his research interests, earli...

Authors: Alan W. Walker

Unraveling rain forest biodiversity: an interview with Thomas Couvreur

Thomas Couvreur is a researcher and botanist at the Institut de Recherche pour le Développement (IRD), based in Montpellier, France, studying tropical biosystems. He is using diverse approaches—from taxonomy, ...

Authors: Thomas L. P. Couvreur

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Correction to: The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches

Reinvestigation of the raw data revealed an unfortunate error in Ugelvig et al. 2008 [1].

Authors: Line V. Ugelvig, Falko P. Drijfhout, Daniel J. C. Kronauer, Jacobus J. Boomsma, Jes S. Pedersen and Sylvia Cremer

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA pres...

Authors: Cesare de Filippo, Matthias Meyer and Kay Prüfer

Microtubule polyglutamylation and acetylation drive microtubule dynamics critical for platelet formation

Upon maturation in the bone marrow, polyploid megakaryocytes elongate very long and thin cytoplasmic branches called proplatelets. Proplatelets enter the sinusoids blood vessels in which platelets are ultimate...

Authors: Juliette van Dijk, Guillaume Bompard, Julien Cau, Shinji Kunishima, Gabriel Rabeharivelo, Julio Mateos-Langerak, Chantal Cazevieille, Patricia Cavelier, Brigitte Boizet-Bonhoure, Claude Delsert and Nathalie Morin

Open questions: knowing who’s who in multicellular animals is not always as simple as we imagine

The ability of certain tumor cells of mammals and molluscs to spread from the original host to others reopens the question of distinguishing self from non-self. It is part of a wider phenomenon of cellular par...

Authors: Robin A. Weiss

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage

High throughput methods for profiling the transcriptomes of single cells have recently emerged as transformative approaches for large-scale population surveys of cellular diversity in heterogeneous primary tis...

Authors: Aparna Bhaduri, Tomasz J Nowakowski, Alex A Pollen and Arnold R Kriegstein

Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Developmental physiology is very sensitive to nutrient availability. For instance, in the nematode Caenorhabditis elegans, newly hatched L1-stage larvae require food to initiate postembryonic development. In addi...

Authors: Rebecca E. W. Kaplan, Amy K. Webster, Rojin Chitrakar, Joseph A. Dent and L. Ryan Baugh

UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

H3.3 is an ancient and conserved H3 variant and plays essential roles in transcriptional regulation. HIRA complex, which is composed of HIRA, UBN1 or UBN2, and Cabin1, is a H3.3 specific chaperone complex. How...

Authors: Chaoyang Xiong, Zengqi Wen, Juan Yu, Jun Chen, Chao-Pei Liu, Xiaodong Zhang, Ping Chen, Rui-Ming Xu and Guohong Li

VOPP1 promotes breast tumorigenesis by interacting with the tumor suppressor WWOX

The WW domain-containing oxidoreductase (WWOX) gene, frequently altered in breast cancer, encodes a tumor suppressor whose function is mediated through its interactions with cancer-related proteins, such as the p...

Authors: Florian Bonin, Karim Taouis, Paula Azorin, Ambre Petitalot, Zakia Tariq, Sebastien Nola, Nadège Bouteille, Sandrine Tury, Sophie Vacher, Ivan Bièche, Khadija Ait Rais, Gaelle Pierron, Laetitia Fuhrmann, Anne Vincent-Salomon, Etienne Formstecher, Jacques Camonis…

Cell type-specific expression profiling unravels the development and evolution of stinging cells in sea anemone

Cnidocytes are specialized cells that define the phylum Cnidaria. They possess an “explosive” organelle called cnidocyst that is important for prey capture and anti-predator defense. An extraordinary morpholog...

Authors: Kartik Sunagar, Yaara Y Columbus-Shenkar, Arie Fridrich, Nadya Gutkovich, Reuven Aharoni and Yehu Moran

Synaptic coupling of inner ear sensory cells is controlled by brevican-based extracellular matrix baskets resembling perineuronal nets

Perineuronal nets (PNNs) are specialized aggregations of extracellular matrix (ECM) molecules surrounding specific neurons in the central nervous system (CNS). PNNs are supposed to control synaptic transmissio...

Authors: Mandy Sonntag, Maren Blosa, Sophie Schmidt, Katja Reimann, Kerstin Blum, Tobias Eckrich, Gudrun Seeger, Dietmar Hecker, Bernhard Schick, Thomas Arendt, Jutta Engel and Markus Morawski

Brevican “nets” voltage-gated calcium channels at the hair cell ribbon synapse

During hearing in mammals, “sensorineural” inner hair cells convert sound wave-generated mechanical input into electrical activity, resulting in glutamate release onto type I spiral ganglion neurons (SGNs) at ...

Authors: Thomas M. Coate and Katherine Conant

Loss of males from mixed-sex societies in termites

Sexual reproduction is the norm in almost all animal species, and in many advanced animal societies, both males and females participate in social activities. To date, the complete loss of males from advanced s...

Authors: Toshihisa Yashiro, Nathan Lo, Kazuya Kobayashi, Tomonari Nozaki, Taro Fuchikawa, Nobuaki Mizumoto, Yusuke Namba and Kenji Matsuura

The disposable male— the ultimate emancipation of females?

Sexual reproduction is costly compared to asexual reproduction, in particular because males generally contribute little to offspring. Research published today in BMC Biology shows that some populations of a termi...

Authors: Duur K. Aanen