Articles

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

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

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

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

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

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

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

Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells

The hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA. The histone variants H3.3 and H2A.Z...

Authors: Yan Wang, Haizhen Long, Juan Yu, Liping Dong, Michel Wassef, Baowen Zhuo, Xia Li, Jicheng Zhao, Min Wang, Cuifang Liu, Zengqi Wen, Luyuan Chang, Ping Chen, Qian-fei Wang, Xueqing Xu, Raphael Margueron…

Open questions: CRISPR biology

CRISPR-Cas systems, the purveyors of adaptive immunity in archaea and bacteria and sources of the new generation of genome engineering tools, have been studied in exquisite molecular detail. However, when it c...

Authors: Eugene V. Koonin

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

Defining the mechanisms that establish and regulate the transmission of epigenetic information from parent to offspring is critical for understanding disease heredity. Currently, the molecular pathways that re...

Authors: Jessica M. Stringer, Samuel C. Forster, Zhipeng Qu, Lexie Prokopuk, Moira K. O’Bryan, David K. Gardner, Stefan J. White, David Adelson and Patrick S. Western

The piRNA pathway responds to environmental signals to establish intergenerational adaptation to stress

piRNAs have a constitutive role in genome defence by silencing transposable elements in the germline. In the nematode Caenorhabditis elegans, piRNAs also induce epigenetic silencing of transgenes, which can be ma...

Authors: Tony Belicard, Pree Jareosettasin and Peter Sarkies

Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Two of the most widely cultivated rice strains are Oryza sativa indica and O. sativa japonica, and understanding the genetic basis of their agronomic traits is of importance for crop production. These two species...

Authors: Xiukun Li, Lian Wu, Jiahong Wang, Jian Sun, Xiuhong Xia, Xin Geng, Xuhong Wang, Zhengjin Xu and Quan Xu

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumen...

Authors: P. J. Fabre, M. Leleu, B. Mascrez, Q. Lo Giudice, J. Cobb and D. Duboule

Parkinson’s disease-linked Parkin mutations impair glutamatergic signaling in hippocampal neurons

Parkinson’s disease (PD)-associated E3 ubiquitin ligase Parkin is enriched at glutamatergic synapses, where it ubiquitinates multiple substrates, suggesting that its mutation/loss-of-function could contribute ...

Authors: Mei Zhu, Giuseppe P. Cortese and Clarissa L. Waites

Q&A: Array tomography

Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures in extremely fine structural and molecular detail...

Authors: Stephen J Smith

Ontogenetic and phylogenetic simplification during white stripe evolution in clownfishes

Biologists have long been fascinated by the striking diversity of complex color patterns in tropical reef fishes. However, the origins and evolution of this diversity are still poorly understood. Disentangling...

Authors: Pauline Salis, Natacha Roux, Olivier Soulat, David Lecchini, Vincent Laudet and Bruno Frédérich

Microdomain formation is a general property of bacterial membrane proteins and induces heterogeneity of diffusion patterns

Proteins within the cytoplasmic membrane display distinct localization patterns and arrangements. While multiple models exist describing the dynamics of membrane proteins, to date, there have been few systemat...

Authors: Daniella Lucena, Marco Mauri, Felix Schmidt, Bruno Eckhardt and Peter L. Graumann

Open questions: How many genes do we have?

Seventeen years after the initial publication of the human genome, we still haven’t found all of our genes. The answer turns out to be more complex than anyone had imagined when the Human Genome Project began.

Authors: Steven L. Salzberg

Horizons in the evolution of aging

Between the 1930s and 50s, evolutionary biologists developed a successful theory of why organisms age, firmly rooted in population genetic principles. By the 1980s the evolution of aging had a secure experimen...

Authors: Thomas Flatt and Linda Partridge

Targeting the Tie2–α_vβ₃ integrin axis with bi-specific reagents for the inhibition of angiogenesis

Increased activity of the receptor tyrosine kinase Tie2 has been implicated in the promotion of pathological angiogenesis. This activity is mainly mediated through angiopoietin (Ang)1- and Ang2-dependent activ...

Authors: Tomer Shlamkovich, Lidan Aharon, Dana Koslawsky, Yulia Einav and Niv Papo

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors an...

Authors: Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado, David A. Velázquez-Ramírez, Socorro Gama-Castro, Víctor H. Tierrafría, Stephen J. W. Busby, Patricia Aquino, Xin Fang, Bernhard O. Palsson, James E. Galagan and Julio Collado-Vides

Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor

Division of labor between reproductive queens and workers that perform brood care is a hallmark of insect societies. However, studies of the molecular basis of this fundamental dichotomy are limited by the fac...

Authors: Romain Libbrecht, Peter R. Oxley and Daniel J. C. Kronauer

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and th...

Authors: Joanna Koszela, Nhan T. Pham, David Evans, Stefan Mann, Irene Perez-Pi, Steven Shave, Derek F. J. Ceccarelli, Frank Sicheri, Mike Tyers and Manfred Auer

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts. TADs contribu...

Authors: Jan Krefting, Miguel A. Andrade-Navarro and Jonas Ibn-Salem

Attention decouples action potentials from the phase of local field potentials in macaque visual cortical area MT

The timing of action potentials (“spikes”) of cortical neurons has been shown to be aligned to the phase of low-frequency (< 10 Hz) local field potentials (LFPs) in several cortical areas. However, across the ...

Authors: Moein Esghaei, Mohammad Reza Daliri and Stefan Treue

Structural and functional characterization of protein–lipid interactions of the Salmonella typhimurium melibiose transporter MelB

Membrane lipids play critical roles in the structure and function of membrane-embedded transporters. Salmonella typhimurium MelB (MelB_St) is a symporter coupling melibiose translocation with a cation (Na⁺, Li⁺, o...

Authors: Parameswaran Hariharan, Elena Tikhonova, João Medeiros-Silva, Aike Jeucken, Mikhail V. Bogdanov, William Dowhan, Jos F. Brouwers, Markus Weingarth and Lan Guan

A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk

Helicobacter pylori are stomach-dwelling bacteria that are present in about 50% of the global population. Infection is asymptomatic in most cases, but it has been associated with gastritis, gastric ulcers and gas...

Authors: Elvire Berthenet, Koji Yahara, Kaisa Thorell, Ben Pascoe, Guillaume Meric, Jane M. Mikhail, Lars Engstrand, Helena Enroth, Alain Burette, Francis Megraud, Christine Varon, John C Atherton, Sinead Smith, Thomas S. Wilkinson, Matthew D. Hitchings, Daniel Falush…

Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging

Mammals display a wide range of variation in their lifespan. Investigating the molecular networks that distinguish long- from short-lived species has proven useful to identify determinants of longevity. Here, ...

Authors: Ivonne Heinze, Martin Bens, Enrico Calzia, Susanne Holtze, Oleksandr Dakhovnik, Arne Sahm, Joanna M. Kirkpatrick, Karol Szafranski, Natalie Romanov, Sai Nagender Sama, Kerstin Holzer, Stephan Singer, Maria Ermolaeva, Matthias Platzer, Thomas Hildebrandt and Alessandro Ori

Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Naked mole-rats (NMRs) are eusocially organized in colonies. Although breeders carry the additional metabolic load of reproduction, they are extremely long-lived and remain fertile throughout their lifespan. T...

Authors: Martin Bens, Karol Szafranski, Susanne Holtze, Arne Sahm, Marco Groth, Hans A. Kestler, Thomas B. Hildebrandt and Matthias Platzer

Additive contributions of melanopsin and both cone types provide broadband sensitivity to mouse pupil control

Intrinsically photosensitive retinal ganglion cells (ipRGCs) drive an array of non-image-forming (NIF) visual responses including circadian photoentrainment and the pupil light reflex. ipRGCs integrate extrins...

Authors: Edward A. Hayter and Timothy M. Brown

The different axes of the mammalian mitochondrial unfolded protein response

Mitochondria are sensitive to numerous environmental stresses, which can lead to activation of mitochondrial stress responses (MSRs). Of particular recent interest has been the mitochondrial unfolded protein r...

Authors: Christian Münch

Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates

The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and ...

Authors: Geneviève Arsenault-Labrecque, Humira Sonah, Amandine Lebreton, Caroline Labbé, Geneviève Marchand, Allen Xue, François Belzile, Brian J. Knaus, Niklaus J. Grünwald and Richard R. Bélanger

A gene regulatory network underlying the formation of pre-placodal ectoderm in Xenopus laevis

The neural plate border ectoderm gives rise to key developmental structures during embryogenesis, including the neural crest and the preplacodal ectoderm. Many sensory organs and ganglia of vertebrates develop...

Authors: Santosh Kumar Maharana and Gerhard Schlosser

Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat

Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypi...

Authors: Parvathy Krishnan, Lukas Meile, Clémence Plissonneau, Xin Ma, Fanny E. Hartmann, Daniel Croll, Bruce A. McDonald and Andrea Sánchez-Vallet

Structural complexity of the co-chaperone SGTA: a conserved C-terminal region is implicated in dimerization and substrate quality control

Protein quality control mechanisms are essential for cell health and involve delivery of proteins to specific cellular compartments for recycling or degradation. In particular, stray hydrophobic proteins are c...

Authors: Santiago Martínez-Lumbreras, Ewelina M. Krysztofinska, Arjun Thapaliya, Alessandro Spilotros, Dijana Matak-Vinkovic, Enrico Salvadori, Peristera Roboti, Yvonne Nyathi, Janina H. Muench, Maxie M. Roessler, Dmitri I. Svergun, Stephen High and Rivka L. Isaacson

Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir

RNA-guided CRISPR/Cas9 systems can be designed to mutate or excise the integrated HIV genome from latently infected cells and have therefore been proposed as a curative approach for HIV. However, most studies ...

Authors: Pavitra Roychoudhury, Harshana De Silva Feelixge, Daniel Reeves, Bryan T. Mayer, Daniel Stone, Joshua T. Schiffer and Keith R. Jerome

FlashFry: a fast and flexible tool for large-scale CRISPR target design

Genome-wide knockout studies, noncoding deletion scans, and other large-scale studies require a simple and lightweight framework that can quickly discover and score thousands of candidate CRISPR guides targeti...

Authors: Aaron McKenna and Jay Shendure

CDC42 controls the activation of primordial follicles by regulating PI3K signaling in mouse oocytes

In mammalian females, progressive activation of dormant primordial follicles in adulthood is crucial for the maintenance of the reproductive lifespan. Misregulated activation of primordial follicles leads to v...

Authors: Hao Yan, Jiawei Zhang, Jia Wen, Yibo Wang, Wanbao Niu, Zhen Teng, Tongtong Zhao, Yanli Dai, Yan Zhang, Chao Wang, Yingying Qin, Guoliang Xia and Hua Zhang

Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

The phenotypes of sperm are generally believed to be under the control of the diploid genotype of the male producing them rather than their own haploid genotypes, because developing spermatids share cytoplasm ...

Authors: Richard Borowsky, Alissa Luk, Xinjian He and Rebecca S. Kim

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the...

Authors: Amanda L. Pendleton, Feichen Shen, Angela M. Taravella, Sarah Emery, Krishna R. Veeramah, Adam R. Boyko and Jeffrey M. Kidd