Articles

Single-cell alternative polyadenylation analysis delineates GABAergic neuron types

Alternative polyadenylation (APA) is emerging as an important mechanism in the post-transcriptional regulation of gene expression across eukaryotic species. Recent studies have shown that APA plays key roles i...

Authors: Yang Yang, Anirban Paul, Thao Nguyen Bach, Z. Josh Huang and Michael Q. Zhang

Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organ...

Authors: Yupeng Geng, Yabin Guan, La Qiong, Shugang Lu, Miao An, M. James C. Crabbe, Ji Qi, Fangqing Zhao, Qin Qiao and Ticao Zhang

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causin...

Authors: Emily K. Herman, Alex Greninger, Mark van der Giezen, Michael L. Ginger, Inmaculada Ramirez-Macias, Haylea C. Miller, Matthew J. Morgan, Anastasios D. Tsaousis, Katrina Velle, Romana Vargová, Kristína Záhonová, Sebastian Rodrigo Najle, Georgina MacIntyre, Norbert Muller, Mattias Wittwer, Denise C. Zysset-Burri…

Disruption of left-right axis specification in Ciona induces molecular, cellular, and functional defects in asymmetric brain structures

Left-right asymmetries are a common feature of metazoans and can be found in a number of organs including the nervous system. These asymmetries are particularly pronounced in the simple central nervous system ...

Authors: Matthew J. Kourakis, Michaela Bostwick, Amanda Zabriskie and William C. Smith

Innate antiviral defense demonstrates high energetic efficiency in a bony fish

Viruses can impose energetic demands on organisms they infect, in part by hosts mounting resistance. Recognizing that oxygen uptake reliably indicates steady-state energy consumption in all vertebrates, we com...

Authors: Mark P. Polinski, Yangfan Zhang, Phillip R. Morrison, Gary D. Marty, Colin J. Brauner, Anthony P. Farrell and Kyle A. Garver

Author Correction to: Association of Bacteroides acidifaciens relative abundance with high-fibre diet-associated radiosensitisation

Authors: Chee Kin Then, Salome Paillas, Xuedan Wang, Alix Hampson and Anne E. Kiltie

An engineered genetic circuit for lactose intolerance alleviation

Lactose malabsorption occurs in around 68% of the world’s population, causing lactose intolerance (LI) symptoms, such as abdominal pain, bloating, and diarrhea. To alleviate LI, previous studies have mainly fo...

Authors: Mingyue Cheng, Zhangyu Cheng, Yiyan Yu, Wangjie Liu, Ruihao Li, Zhenyi Guo, Jiyue Qin, Zhi Zeng, Lin Di, Yufeng Mo, Chunxiu Pan, Yuanhao Liang, Jinman Li, Yigang Tong, Yunjun Yan, Yi Zhan…

LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images

Quantitative imaging of epithelial tissues requires bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common preprocessing step consists of projecting the ac...

Authors: Sébastien Herbert, Léo Valon, Laure Mancini, Nicolas Dray, Paolo Caldarelli, Jérôme Gros, Elric Esposito, Spencer L. Shorte, Laure Bally-Cuif, Nathalie Aulner, Romain Levayer and Jean-Yves Tinevez

Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

Cerebellar neurogenesis involves the generation of large numbers of cerebellar granule neurons (GNs) throughout development of the cerebellum, a process that involves tight regulation of proliferation and diff...

Authors: Wenqin Luo, Guan Ning Lin, Weichen Song, Yu Zhang, Huadong Lai, Man Zhang, Juju Miao, Xiaomu Cheng, Yongjie Wang, Wang Li, Wenxiang Wei, Wei-Qiang Gao, Ru Yang and Jia Wang

Exposure to ethanol leads to midfacial hypoplasia in a zebrafish model of FASD via indirect interactions with the Shh pathway

Gene-environment interactions are likely to underlie most human birth defects. The most common known environmental contributor to birth defects is prenatal alcohol exposure. Fetal alcohol spectrum disorders (F...

Authors: Alfire Sidik, Groves Dixon, Desire M. Buckley, Hannah G. Kirby, Shuge Sun and Johann K. Eberhart

Do all mice smell the same? Chemosensory cues from inbred and wild mouse strains elicit stereotypic sensory representations in the accessory olfactory bulb

For many animals, chemosensory cues are vital for social and defensive interactions and are primarily detected and processed by the vomeronasal system (VNS). These cues are often inherently associated with eth...

Authors: Rohini Bansal, Maximilian Nagel, Romana Stopkova, Yizhak Sofer, Tali Kimchi, Pavel Stopka, Marc Spehr and Yoram Ben-Shaul

OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation

Oligodendrocytes, responsible for axon ensheathment, are critical for central nervous system (CNS) development, function, and diseases. OLIG2 is an important transcription factor (TF) that acts during oligoden...

Authors: Haichao Wei, Xiaomin Dong, Yanan You, Bo Hai, Raquel Cuevas-Diaz Duran, Xizi Wu, Natasha Kharas and Jia Qian Wu

Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems

Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. V...

Authors: Jie-Yin Chen, Dan-Dan Zhang, Jin-Qun Huang, Ran Li, Dan Wang, Jian Song, Krishna D. Puri, Lin Yang, Zhi-Qiang Kong, Bang-Zhuo Tong, Jun-Jiao Li, Yu-Shan Huang, Ivan Simko, Steven J. Klosterman, Xiao-Feng Dai and Krishna V. Subbarao

α2β1 integrins spatially restrict Cdc42 activity to stabilise adherens junctions

Keratinocytes form the main protective barrier in the skin to separate the underlying tissue from the external environment. In order to maintain this barrier, keratinocytes form robust junctions between neighb...

Authors: Jake D. Howden, Magdalene Michael, Willow Hight-Warburton and Maddy Parsons

Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs

Targeted installation of designer chemical moieties on biopolymers provides an orthogonal means for their visualisation, manipulation and sequence analysis. Although high-throughput RNA sequencing is a widely ...

Authors: Milda Mickutė, Kotryna Kvederavičiūtė, Aleksandr Osipenko, Raminta Mineikaitė, Saulius Klimašauskas and Giedrius Vilkaitis

The adaptive benefit of evolved increases in hemoglobin-O₂ affinity is contingent on tissue O₂ diffusing capacity in high-altitude deer mice

Complex organismal traits are often the result of multiple interacting genes and sub-organismal phenotypes, but how these interactions shape the evolutionary trajectories of adaptive traits is poorly understoo...

Authors: Oliver H. Wearing, Catherine M. Ivy, Natalia Gutiérrez-Pinto, Jonathan P. Velotta, Shane C. Campbell-Staton, Chandrasekhar Natarajan, Zachary A. Cheviron, Jay F. Storz and Graham R. Scott

Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation

Proper placentation, including trophoblast differentiation and function, is essential for the health and well-being of both the mother and baby throughout pregnancy. Placental abnormalities that occur during t...

Authors: Jimi L. Rosenkrantz, Jessica E. Gaffney, Victoria H. J. Roberts, Lucia Carbone and Shawn L. Chavez

Author Correction to: Mixotrophic chemosynthesis in a deep-sea anemone from hydrothermal vents in the Pescadero Basin, Gulf of California

Authors: Shana K. Goffredi, Cambrie Motooka, David A. Fike, Luciana C. Gusmão, Ekin Tilic, Greg W. Rouse and Estefanía Rodríguez

Publisher Correction to: MATISSE: a method for improved single cell segmentation in imaging mass cytometry

Authors: Matthijs J. D. Baars, Neeraj Sinha, Mojtaba Amini, Annelies Pieterman-Bos, Stephanie van Dam, Maroussia M. P. Ganpat, Miangela M. Laclé, Bas Oldenburg and Yvonne Vercoulen

A novel theory of Asian elephant high-frequency squeak production

Anatomical and cognitive adaptations to overcome morpho-mechanical limitations of laryngeal sound production, where body size and the related vocal apparatus dimensions determine the fundamental frequency, inc...

Authors: Veronika C. Beeck, Gunnar Heilmann, Michael Kerscher and Angela S. Stoeger

Doxorubicin induces an alarmin-like TLR4-dependent autocrine/paracrine action of Nucleophosmin in human cardiac mesenchymal progenitor cells

Doxorubicin (Dox) is an anti-cancer anthracycline drug that causes double-stranded DNA breaks. It is highly effective against several types of tumours; however, it also has adverse effects on regenerative popu...

Authors: Sara Beji, Marco D’Agostino, Elisa Gambini, Sara Sileno, Alessandro Scopece, Maria Cristina Vinci, Giuseppina Milano, Guido Melillo, Monica Napolitano, Giulio Pompilio, Maurizio C. Capogrossi, Daniele Avitabile and Alessandra Magenta

Fruit bats adjust their foraging strategies to urban environments to diversify their diet

Urbanization is one of the most influential processes on our globe, putting a great number of species under threat. Some species learn to cope with urbanization, and a few even benefit from it, but we are only...

Authors: Katya Egert-Berg, Michal Handel, Aya Goldshtein, Ofri Eitan, Ivailo Borissov and Yossi Yovel

Divergent camptothecin biosynthetic pathway in Ophiorrhiza pumila

The anticancer drug camptothecin (CPT), first isolated from Camptotheca acuminata, was subsequently discovered in unrelated plants, including Ophiorrhiza pumila. Unlike known monoterpene indole alkaloids, CPT in

Authors: Mengquan Yang, Qiang Wang, Yining Liu, Xiaolong Hao, Can Wang, Yuchen Liang, Jianbo Chen, Youli Xiao and Guoyin Kai

Large-scale genomic analysis reveals the genetic cost of chicken domestication

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbree...

Authors: Ming-Shan Wang, Jin-Jin Zhang, Xing Guo, Ming Li, Rachel Meyer, Hidayat Ashari, Zhu-Qing Zheng, Sheng Wang, Min-Sheng Peng, Yu Jiang, Mukesh Thakur, Chatmongkon Suwannapoom, Ali Esmailizadeh, Nalini Yasoda Hirimuthugoda, Moch Syamsul Arifin Zein, Szilvia Kusza…

The Wnt-specific astacin proteinase HAS-7 restricts head organizer formation in Hydra

The Hydra head organizer acts as a signaling center that initiates and maintains the primary body axis in steady state polyps and during budding or regeneration. Wnt/beta-Catenin signaling functions as a primary ...

Authors: Berenice Ziegler, Irene Yiallouros, Benjamin Trageser, Sumit Kumar, Moritz Mercker, Svenja Kling, Maike Fath, Uwe Warnken, Martina Schnölzer, Thomas W. Holstein, Markus Hartl, Anna Marciniak-Czochra, Jörg Stetefeld, Walter Stöcker and Suat Özbek

Publisher Correction to: Loss of splicing factor IK impairs normal skeletal muscle development

Authors: Hye In Ka, Hyemin Seo, Youngsook Choi, Joohee Kim, Mina Cho, Seok-Yong Choi, Sujeong Park, Sora Han, Jinsu An, Hak Suk Chung, Young Yang and Min Jung Kim

Membrane recruitment of Atg8 by Hfl1 facilitates turnover of vacuolar membrane proteins in yeast cells approaching stationary phase

The vacuole/lysosome is the final destination of autophagic pathways, but can also itself be degraded in whole or in part by selective macroautophagic or microautophagic processes. Diverse molecular mechanisms...

Authors: Cheng-Wen He, Xue-Fei Cui, Shao-Jie Ma, Qin Xu, Yan-Peng Ran, Wei-Zhi Chen, Jun-Xi Mu, Hui Li, Jing Zhu, Qingqiu Gong and Zhiping Xie

The amygdala modulates prepulse inhibition of the auditory startle reflex through excitatory inputs to the caudal pontine reticular nucleus

Sensorimotor gating is a fundamental pre-attentive process that is defined as the inhibition of a motor response by a sensory event. Sensorimotor gating, commonly measured using the prepulse inhibition (PPI) o...

Authors: Jose Carlos Cano, Wanyun Huang and Karine Fénelon

Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

Many of genome features which could help unravel the often complex post-speciation evolution of closely related species are obscured because of their location in chromosomal regions difficult to accurately cha...

Authors: Zhaoen Yang, Xiaoyang Ge, Weinan Li, Yuying Jin, Lisen Liu, Wei Hu, Fuyan Liu, Yanli Chen, Shaoliang Peng and Fuguang Li

Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity

Sexual dimorphism in immunity is believed to reflect sex differences in reproductive strategies and trade-offs between competing life history demands. Sexual selection can have major effects on mating rates an...

Authors: Basabi Bagchi, Quentin Corbel, Imroze Khan, Ellen Payne, Devshuvam Banerji, Johanna Liljestrand-Rönn, Ivain Martinossi-Allibert, Julian Baur, Ahmed Sayadi, Elina Immonen, Göran Arnqvist, Irene Söderhäll and David Berger

Boundaries potentiate polycomb response element-mediated silencing

Epigenetic memory plays a critical role in the establishment and maintenance of cell identities in multicellular organisms. Polycomb and trithorax group (PcG and TrxG) proteins are responsible for epigenetic m...

Authors: Maksim Erokhin, Fedor Gorbenko, Dmitry Lomaev, Marina Yu Mazina, Anna Mikhailova, Azat K. Garaev, Aleksander Parshikov, Nadezhda E. Vorobyeva, Pavel Georgiev, Paul Schedl and Darya Chetverina

Single-cell transcriptomics reveals the effect of PD-L1/TGF-β blockade on the tumor microenvironment

The anti-tumor activity of anti-PD-1/PD-L1 therapies correlates with T cell infiltration in tumors. Thus, a major goal in oncology is to find strategies that enhance T cell infiltration and efficacy of anti-PD...

Authors: Yoong Wearn Lim, Garry L. Coles, Savreet K. Sandhu, David S. Johnson, Adam S. Adler and Erica L. Stone

Honeybee communication during collective defence is shaped by predation

Social insect colonies routinely face large vertebrate predators, against which they need to mount a collective defence. To do so, honeybees use an alarm pheromone that recruits nearby bees into mass stinging ...

Authors: Andrea López-Incera, Morgane Nouvian, Katja Ried, Thomas Müller and Hans J. Briegel

The epigenetic regulator G9a attenuates stress-induced resistance and metabolic transcriptional programs across different stressors and species

Resistance and tolerance are two coexisting defense strategies for fighting infections. Resistance is mediated by signaling pathways that induce transcriptional activation of resistance factors that directly e...

Authors: Human Riahi, Michaela Fenckova, Kayla J. Goruk, Annette Schenck and Jamie M. Kramer

A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration

Multicellular organisms are characterized by a wide diversity of forms and complexity despite a restricted set of key molecules and mechanisms at the base of organismal development. Development combines three ...

Authors: Somya Mani and Tsvi Tlusty

The dorsoanterior brain of adult amphioxus shares similarities in expression profile and neuronal composition with the vertebrate telencephalon

The evolutionary origin of the telencephalon, the most anterior part of the vertebrate brain, remains obscure. Since no obvious counterpart to the telencephalon has yet been identified in invertebrate chordate...

Authors: Èlia Benito-Gutiérrez, Giacomo Gattoni, Manuel Stemmer, Silvia D. Rohr, Laura N. Schuhmacher, Jocelyn Tang, Aleksandra Marconi, Gáspár Jékely and Detlev Arendt

An epilepsy-causing mutation leads to co-translational misfolding of the Kv7.2 channel

The amino acid sequence of proteins generally carries all the necessary information for acquisition of native conformations, but the vectorial nature of translation can additionally determine the folding outco...

Authors: Janire Urrutia, Alejandra Aguado, Carolina Gomis-Perez, Arantza Muguruza-Montero, Oscar R. Ballesteros, Jiaren Zhang, Eider Nuñez, Covadonga Malo, Hee Jung Chung, Aritz Leonardo, Aitor Bergara and Alvaro Villarroel

Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans

The majority of the human genome is transcribed in the form of long non-coding (lnc) RNAs. While these transcripts have attracted considerable interest, their molecular mechanisms of function and biological si...

Authors: Huifen Cao, Dongyang Xu, Ye Cai, Xueer Han, Lu Tang, Fan Gao, Yao Qi, DingDing Cai, Huifang Wang, Maxim Ri, Denis Antonets, Yuri Vyatkin, Yue Chen, Xiang You, Fang Wang, Estelle Nicolas…

Characterization of a novel type of carbonic anhydrase that acts without metal cofactors

Carbonic anhydrases (CAs) are universal metalloenzymes that catalyze the reversible conversion of carbon dioxide (CO₂) and bicarbonate (HCO₃^-). They are involved in various biological processes, including pH cont...

Authors: Yoshihisa Hirakawa, Miki Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, Masafumi Taira, Kazushi Kinbara and Toshiya Senda

Characterization of the dynamics and variability of neuronal subtype responses during growth, degrowth, and regeneration of Nematostella vectensis

The ability to regenerate body parts is a feature of metazoan organisms and the focus of intense research aiming to understand its basis. A number of mechanisms involved in regeneration, such as proliferation ...

Authors: Jamie A. Havrilak, Layla Al-Shaer, Noor Baban, Nesli Akinci and Michael J. Layden

Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans

The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitocho...

Authors: Kristína Záhonová, Gordon Lax, Savar D. Sinha, Guy Leonard, Thomas A. Richards, Julius Lukeš and Jeremy G. Wideman

Parental energy-sensing pathways control intergenerational offspring sex determination in the nematode Auanema freiburgensis

Environmental stimuli experienced by the parental generation influence the phenotype of subsequent generations (Demoinet et al., Proc Natl Acad Sci U S A 114:E2689-E2698, 2017; Burton et al., Nat Cell Biol 19:...

Authors: Pedro Robles, Anisa Turner, Giusy Zuco, Sally Adams, Panagiota Paganopolou, Michael Winton, Beth Hill, Vikas Kache, Christine Bateson and Andre Pires-daSilva

Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter

Adenosine triphosphate (ATP) is the main energy carrier in living organisms, critical for metabolism and essential physiological processes. In humans, abnormal regulation of energy levels (ATP concentration) a...

Authors: Yijie Deng, Douglas Raymond Beahm, Steven Ionov and Rahul Sarpeshkar

Apoptosis is not conserved in plants as revealed by critical examination of a model for plant apoptosis-like cell death

Animals and plants diverged over one billion years ago and evolved unique mechanisms for many cellular processes, including cell death. One of the most well-studied cell death programmes in animals, apoptosis,...

Authors: Elena A. Minina, Adrian N. Dauphinee, Florentine Ballhaus, Vladimir Gogvadze, Andrei P. Smertenko and Peter V. Bozhkov

MATISSE: a method for improved single cell segmentation in imaging mass cytometry

Visualizing and quantifying cellular heterogeneity is of central importance to study tissue complexity, development, and physiology and has a vital role in understanding pathologies. Mass spectrometry-based me...

Authors: Matthijs J. D. Baars, Neeraj Sinha, Mojtaba Amini, Annelies Pieterman-Bos, Stephanie van Dam, Maroussia M. P. Ganpat, Miangela M. Laclé, Bas Oldenburg and Yvonne Vercoulen

NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP

Mitochondrial respiration is organized in a series of enzyme complexes in turn forming dynamic supercomplexes. In Saccharomyces cerevisiae (baker’s yeast), Cox13 (CoxVIa in mammals) is a conserved peripheral subu...

Authors: Shu Zhou, Pontus Pettersson, Markus L. Björck, Hannah Dawitz, Peter Brzezinski, Lena Mäler and Pia Ädelroth

An agent-based model clarifies the importance of functional and developmental integration in shaping brain evolution

Vertebrate brain structure is characterised not only by relative consistency in scaling between components, but also by many examples of divergence from these general trends.. Alternative hypotheses explain th...

Authors: Shahar Avin, Adrian Currie and Stephen H. Montgomery

The CAT-SIR is out of the bag: tumors prefer host rather than dietary nutrients

The extent to which tumors acquire nutrients from dietary sources as opposed to from the breakdown of host tissues is not known. In this issue of BMC Biology, Holland et al. report an approach where food sourc...

Authors: Keene L. Abbott and Matthew G. Vander Heiden

Natural abundance isotope ratios to differentiate sources of carbon used during tumor growth in vivo

Radioactive or stable isotopic labeling of metabolites is a strategy that is routinely used to map the cellular fate of a selected labeled metabolite after it is added to cell culture or to the circulation of ...

Authors: Petter Holland, William M. Hagopian, A. Hope Jahren and Tor Erik Rusten

TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

Target of Rapamycin Complex 1 (TORC1) is a highly conserved eukaryotic protein complex that couples the presence of growth factors and nutrients in the environment with cellular proliferation. TORC1 is primari...

Authors: Mohammad Alfatah, Jin Huei Wong, Vidhya Gomathi Krishnan, Yong Cheow Lee, Quan Feng Sin, Corinna Jie Hui Goh, Kiat Whye Kong, Wei Ting Lee, Jacqueline Lewis, Shawn Hoon and Prakash Arumugam