Articles

MIEF1/2 orchestrate mitochondrial dynamics through direct engagement with both the fission and fusion machineries

Mitochondrial dynamics is the result of a dynamic balance between fusion and fission events, which are driven via a set of mitochondria-shaping proteins. These proteins are generally considered to be binary co...

Authors: Rong Yu, Tong Liu, Shao-Bo Jin, Maria Ankarcrona, Urban Lendahl, Monica Nistér and Jian Zhao

The mitochondrially-localized nucleoside diphosphate kinase D (NME4) is a novel metastasis suppressor

Mitochondrial nucleoside diphosphate kinase (NDPK-D, NME4, NM23-H4) is a multifunctional enzyme mainly localized in the intermembrane space, bound to the inner membrane.

Authors: Marie-Lise Lacombe, Frederic Lamarche, Olivier De Wever, Teresita Padilla-Benavides, Alyssa Carlson, Imran Khan, Anda Huna, Sophie Vacher, Claire Calmel, Céline Desbourdes, Cécile Cottet-Rousselle, Isabelle Hininger-Favier, Stéphane Attia, Béatrice Nawrocki-Raby, Joël Raingeaud, Christelle Machon…

Channel nuclear pore protein 54 directs sexual differentiation and neuronal wiring of female reproductive behaviors in Drosophila

Female reproductive behaviors and physiology change profoundly after mating. The control of pregnancy-associated changes in physiology and behaviors are largely hard-wired into the brain to guarantee reproduct...

Authors: Mohanakarthik P. Nallasivan, Irmgard U. Haussmann, Alberto Civetta and Matthias Soller

PACmn for improved optogenetic control of intracellular cAMP

Cyclic adenosine monophosphate (cAMP) is a ubiquitous second messenger that transduces extracellular signals in virtually all eukaryotic cells. The soluble Beggiatoa photoactivatable adenylyl cyclase (bPAC) rapid...

Authors: Shang Yang, Oana M. Constantin, Divya Sachidanandan, Hannes Hofmann, Tobias C. Kunz, Vera Kozjak-Pavlovic, Thomas G. Oertner, Georg Nagel, Robert J. Kittel, Christine E. Gee and Shiqiang Gao

Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

Cell-free DNA (cfDNA), which is extracellular DNA present in the circulating plasma and other body fluids, is currently investigated as a minimally invasive, highly informative biomarker. While nucleosome-size...

Authors: Osamu Hisano, Takashi Ito and Fumihito Miura

The evolution of pelvic canal shape and rotational birth in humans

The human foetus typically needs to rotate when passing through the tight birth canal because of the complex shape of the pelvis. In most women, the upper part, or inlet, of the birth canal has a round or medi...

Authors: Ekaterina Stansfield, Barbara Fischer, Nicole D. S. Grunstra, Maria Villa Pouca and Philipp Mitteroecker

Taxonomy-aware, sequence similarity ranking reliably predicts phage–host relationships

Characterizing phage–host interactions is critical to understanding the ecological role of both partners and effective isolation of phage therapeuticals. Unfortunately, experimental methods for studying these ...

Authors: Andrzej Zielezinski, Jakub Barylski and Wojciech M. Karlowski

Krüppel-homolog 1 exerts anti-metamorphic and vitellogenic functions in insects via phosphorylation-mediated recruitment of specific cofactors

The zinc-finger transcription factor Krüppel-homolog 1 (Kr-h1) exerts a dual regulatory role during insect development by preventing precocious larval/nymphal metamorphosis and in stimulating aspects of adult ...

Authors: Zhongxia Wu, Libin Yang, Huihui Li and Shutang Zhou

Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria

Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both a parasitic and free-living generation. During the parasit...

Authors: Ivan N. Chavez, Taylor M. Brown, Adrien Assié, Astra S. Bryant, Buck S. Samuel and Elissa A. Hallem

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance...

Authors: Saskia Pfrengle, Judith Neukamm, Meriam Guellil, Marcel Keller, Martyna Molak, Charlotte Avanzi, Alena Kushniarevich, Núria Montes, Gunnar U. Neumann, Ella Reiter, Rezeda I. Tukhbatova, Nataliya Y. Berezina, Alexandra P. Buzhilova, Dmitry S. Korobov, Stian Suppersberger Hamre, Vitor M. J. Matos…

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching

Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history an...

Authors: Tobias Mourier, Denise Anete Madureira de Alvarenga, Abhinav Kaushik, Anielle de Pina-Costa, Olga Douvropoulou, Qingtian Guan, Francisco J. Guzmán-Vega, Sarah Forrester, Filipe Vieira Santos de Abreu, Cesare Bianco Júnior, Julio Cesar de Souza Junior, Silvia Bahadian Moreira, Zelinda Maria Braga Hirano, Alcides Pissinatti, Maria de Fátima Ferreira-da-Cruz, Ricardo Lourenço de Oliveira…

A human iPSC-derived inducible neuronal model of Niemann-Pick disease, type C1

Niemann-Pick disease, type C (NPC) is a childhood-onset, lethal, neurodegenerative disorder caused by autosomal recessive mutations in the genes NPC1 or NPC2 and characterized by impaired cholesterol homeostasis,...

Authors: Anika V. Prabhu, Insung Kang, Raffaella De Pace, Christopher A. Wassif, Hideji Fujiwara, Pamela Kell, Xuntian Jiang, Daniel S. Ory, Juan S. Bonifacino, Michael E. Ward and Forbes D. Porter

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-...

Authors: Amrita Srivathsan, Leshon Lee, Kazutaka Katoh, Emily Hartop, Sujatha Narayanan Kutty, Johnathan Wong, Darren Yeo and Rudolf Meier

Publisher Correction to: An economical and highly adaptable optogenetics system for individual and population-level manipulation of Caenorhabditis elegans

Authors: M. Koopman, L. Janssen and E. A. A. Nollen

Neuroligin-1 mediates presynaptic maturation through brain-derived neurotrophic factor signaling

Maturation is a process that allows synapses to acquire full functionality, optimizing their activity to diverse neural circuits, and defects in synaptic maturation may contribute to neurodevelopmental disorde...

Authors: Andonia Petkova-Tuffy, Nina Gödecke, Julio Viotti, Martin Korte and Thomas Dresbach

Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila

How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, ...

Authors: Yun Wang, Franz Baumdicker, Paul Schweiger, Sven Kuenzel and Fabian Staubach

Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many org...

Authors: Ni-Chiao Tsai, Tzu-Shu Hsu, Shang-Che Kuo, Chung-Ting Kao, Tzu-Huan Hung, Da-Gin Lin, Chung-Shu Yeh, Chia-Chen Chu, Jeng-Shane Lin, Hsin-Hung Lin, Chia-Ying Ko, Tien-Hsien Chang, Jung-Chen Su and Ying-Chung Jimmy Lin

Control of vein-forming, striped gene expression by auxin signaling

Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals,...

Authors: Anmol Krishna, Jason Gardiner, Tyler J. Donner and Enrico Scarpella

Self-organising human gonads generated by a Matrigel-based gradient system

Advances in three-dimensional culture technologies have led to progression in systems used to model the gonadal microenvironment in vitro. Despite demonstrating basic functionality, tissue organisation is ofte...

Authors: Elizabeth Oliver, João Pedro Alves-Lopes, Femke Harteveld, Rod T. Mitchell, Elisabet Åkesson, Olle Söder and Jan-Bernd Stukenborg

Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species

Glossina species (tsetse flies), the sole vectors of African trypanosomes, maintained along their long evolutionary history a unique reproductive strategy, adenotrophic viviparity. Viviparity reduces their reprod...

Authors: Grazia Savini, Francesca Scolari, Lino Ometto, Omar Rota-Stabelli, Davide Carraretto, Ludvik M. Gomulski, Giuliano Gasperi, Adly M. M. Abd-Alla, Serap Aksoy, Geoffrey M. Attardo and Anna R. Malacrida

Species co-occurrence and management intensity modulate habitat preferences of forest birds

Species co-occurrences can have profound effects on the habitat use of species, and therefore habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organizat...

Authors: Marco Basile, Thomas Asbeck, João M. Cordeiro Pereira, Grzegorz Mikusiński and Ilse Storch

Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Authors: Sarah Farhat, Phuong Le, Ehsan Kayal, Benjamin Noel, Estelle Bigeard, Erwan Corre, Florian Maumus, Isabelle Florent, Adriana Alberti, Jean-Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne Da Silva, Benjamin Istace, Karine Labadie, Dominique Marie…

Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability

Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variabili...

Authors: Guillaume Le Goc, Julie Lafaye, Sophia Karpenko, Volker Bormuth, Raphaël Candelier and Georges Debrégeas

Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model

Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of ...

Authors: Hanako Ono, Yasuhito Arai, Eisaku Furukawa, Daichi Narushima, Tetsuya Matsuura, Hiromi Nakamura, Daisuke Shiokawa, Momoko Nagai, Toshio Imai, Koshi Mimori, Koji Okamoto, Yoshitaka Hippo, Tatsuhiro Shibata and Mamoru Kato

Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous s...

Authors: C. P. Stelzer, J. Blommaert, A. M. Waldvogel, M. Pichler, B. Hecox-Lea and D. B. Mark Welch

Insights into the evolutionary origin of the pineal color discrimination mechanism from the river lamprey

Pineal-related organs in cyclostomes, teleosts, amphibians, and reptiles exhibit color opponency, generating antagonistic neural responses to different wavelengths of light and thereby sensory information abou...

Authors: Seiji Wada, Emi Kawano-Yamashita, Tomohiro Sugihara, Satoshi Tamotsu, Mitsumasa Koyanagi and Akihisa Terakita

Competition-based screening helps to secure the evolutionary stability of a defensive microbiome

The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, ...

Authors: Sarah F. Worsley, Tabitha M. Innocent, Neil A. Holmes, Mahmoud M. Al-Bassam, Morten Schiøtt, Barrie Wilkinson, J. Colin Murrell, Jacobus J. Boomsma, Douglas W. Yu and Matthew I. Hutchings

Lepidoptera demonstrate the relevance of Murray’s Law to circulatory systems with tidal flow

Murray’s Law, which describes the branching architecture of bifurcating tubes, predicts the morphology of vessels in many amniotes and plants. Here, we use insects to explore the universality of Murray’s Law a...

Authors: Sandra R. Schachat, C. Kevin Boyce, Jonathan L. Payne and David Lentink

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation

Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms o...

Authors: Jana Sperschneider, Ashley W. Jones, Jamila Nasim, Bo Xu, Silke Jacques, Chengcheng Zhong, Narayana M. Upadhyaya, Rohit Mago, Yiheng Hu, Melania Figueroa, Karam B. Singh, Eric A. Stone, Benjamin Schwessinger, Ming-Bo Wang, Jennifer M. Taylor and Peter N. Dodds

Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

The world’s fast disappearing mangrove forests have low plant diversity and are often assumed to also have a species-poor insect fauna. We here compare the tropical arthropod fauna across a freshwater swamp an...

Authors: Darren Yeo, Amrita Srivathsan, Jayanthi Puniamoorthy, Foo Maosheng, Patrick Grootaert, Lena Chan, Benoit Guénard, Claas Damken, Rodzay A. Wahab, Ang Yuchen and Rudolf Meier

Caenorhabditis elegans exhibits positive gravitaxis

Gravity plays an important role in most life forms on Earth. Yet, a complete molecular understanding of sensing and responding to gravity is lacking. While there are anatomical differences among animals, there...

Authors: Wei-Long Chen, Hungtang Ko, Han-Sheng Chuang, David M. Raizen and Haim H. Bau

Single-cell analysis at the protein level delineates intracellular signaling dynamic during hematopoiesis

Hematopoietic stem and progenitor cell (HSPC) subsets in mice have previously been studied using cell surface markers, and more recently single-cell technologies. The recent revolution of single-cell analysis ...

Authors: Jinheng Wang, Chenggong Tu, Hui Zhang, Yongliang Huo, Eline Menu and Jinbao Liu

An increase of phosphatidylcholines in follicular fluid implies attenuation of embryo quality on day 3 post-fertilization

Although oocyte quality is the dominant factor determining embryo quality, few studies have been conducted to evaluate embryo quality based on the metabolites related to the oocyte. With quantification of the ...

Authors: Ju Wang, Wei Zheng, Shuoping Zhang, Keqiang Yan, Miao Jin, Huiling Hu, Zhen Ma, Fei Gong, Guangxiu Lu, Yan Ren, Liang Lin, Ge Lin, Liang Hu and Siqi Liu

Pathologic tau conformer ensembles induce dynamic, liquid-liquid phase separation events at the nuclear envelope

The microtubule-associated protein tau forms aggregates in different neurodegenerative diseases called tauopathies. Prior work has shown that a single P301L mutation in tau gene, MAPT, can promote alternative tau...

Authors: Sang-Gyun Kang, Zhuang Zhuang Han, Nathalie Daude, Emily McNamara, Serene Wohlgemuth, Laura Molina-Porcel, Jiri G. Safar, Sue-Ann Mok and David Westaway

Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis

Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Functions of the noncodi...

Authors: Hemakumar M. Reddy, Rupa Bhattacharya, Shrish Tiwari, Kankadeb Mishra, Pranatharthi Annapurna, Zeenath Jehan, Nissankararao Mary Praveena, Jomini Liza Alex, Vishnu M. Dhople, Lalji Singh, Mahadevan Sivaramakrishnan, Anurag Chaturvedi, Nandini Rangaraj, Thomas Michael Shiju, Badanapuram Sreedevi, Sachin Kumar…

Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep

Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Me...

Authors: Bingru Zhao, Hanpeng Luo, Junmin He, Xixia Huang, Siqian Chen, Xuefeng Fu, Weidan Zeng, Yuezhen Tian, Shuli Liu, Cong-jun Li, George E. Liu, Lingzhao Fang, Shengli Zhang and Kechuan Tian

Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection

The biophysics of an organism span multiple scales from subcellular to organismal and include processes characterized by spatial properties, such as the diffusion of molecules, cell migration, and flow of intr...

Authors: T. J. Sego, Josua O. Aponte-Serrano, Juliano F. Gianlupi and James A. Glazier

Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins

QconCATs are quantitative concatamers for proteomic applications that yield stoichiometric quantities of sets of stable isotope-labelled internal standards. However, changing a QconCAT design, for example, to ...

Authors: James Johnson, Victoria M. Harman, Catarina Franco, Edward Emmott, Nichola Rockliffe, Yaqi Sun, Lu-Ning Liu, Ayako Takemori, Nobuaki Takemori and Robert J. Beynon

ACBD3 modulates KDEL receptor interaction with PKA for its trafficking via tubulovesicular carrier

KDEL receptor helps establish cellular equilibrium in the early secretory pathway by recycling leaked ER-chaperones to the ER during secretion of newly synthesized proteins. Studies have also shown that KDEL r...

Authors: Xihua Yue, Yi Qian, Lianhui Zhu, Bopil Gim, Mengjing Bao, Jie Jia, Shuaiyang Jing, Yijing Wang, Chuanting Tan, Francesca Bottanelli, Pascal Ziltener, Sunkyu Choi, Piliang Hao and Intaek Lee

Inheritance of the reduced mitochondria of Giardia intestinalis is coupled to the flagellar maturation cycle

The presence of mitochondria is a distinguishing feature between prokaryotic and eukaryotic cells. It is currently accepted that the evolutionary origin of mitochondria coincided with the formation of eukaryot...

Authors: Pavla Tůmová, Luboš Voleman, Andreas Klingl, Eva Nohýnková, Gerhard Wanner and Pavel Doležal

A pair of long intergenic non-coding RNA LINC00887 variants act antagonistically to control Carbonic Anhydrase IX transcription upon hypoxia in tongue squamous carcinoma progression

Long noncoding RNAs (lncRNAs) are important regulators in tumor progression. However, their biological functions and underlying mechanisms in hypoxia adaptation remain largely unclear.

Authors: Tao Shen, Wangxiao Xia, Sainan Min, Zixuan Yang, Lehua Cheng, Wei Wang, Qianxi Zhan, Fanghong Shao, Xuehan Zhang, Zhiyu Wang, Yan Zhang, Guodong Shen, Huafeng Zhang, Li-Ling Wu, Guang-Yan Yu, Qing-Peng Kong…

Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis

Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct ef...

Authors: Nazreen F. Hadjirin, Eric L. Miller, Gemma G. R. Murray, Phung L. K. Yen, Ho D. Phuc, Thomas M. Wileman, Juan Hernandez-Garcia, Susanna M. Williamson, Julian Parkhill, Duncan J. Maskell, Rui Zhou, Nahuel Fittipaldi, Marcelo Gottschalk, A. W. ( Dan) Tucker, Ngo Thi Hoa, John J. Welch…

Urban bat pups take after their mothers and are bolder and faster learners than rural pups

Urbanization is rapidly changing our planet and animals that live in urban environments must quickly adjust their behavior. One of the most prevalent behavioral characteristics of urban dwelling animals is an ...

Authors: Lee Harten, Nesim Gonceer, Michal Handel, Orit Dash, H. Bobby Fokidis and Yossi Yovel

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species

The identification of open chromatin regions and transcription factor binding sites (TFBs) is an important step in understanding the regulation of gene expression in diverse species. ATAC-seq is a technique us...

Authors: Lianggang Huang, Xuejie Li, Liangbo Dong, Bin Wang and Li Pan

Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

A number of cellular processes have evolved in metazoans that increase the proteome repertoire in relation to the genome, such as alternative splicing and translation recoding. Another such process, translatio...

Authors: Yunpo Zhao, Bo Gustav Lindberg, Shiva Seyedoleslami Esfahani, Xiongzhuo Tang, Stefano Piazza and Ylva Engström

The ATPase SRCAP is associated with the mitotic apparatus, uncovering novel molecular aspects of Floating-Harbor syndrome

A variety of human genetic diseases is known to be caused by mutations in genes encoding chromatin factors and epigenetic regulators, such as DNA or histone modifying enzymes and members of ATP-dependent chrom...

Authors: Giovanni Messina, Yuri Prozzillo, Francesca Delle Monache, Maria Virginia Santopietro, Maria Teresa Atterrato and Patrizio Dimitri

Transcription-dependent confined diffusion of enzymes within subcellular spaces of the bacterial cytoplasm

Knowledge on the localization and mobility of enzymes inside bacterial cells is scarce, but important for understanding spatial regulation of metabolism. The four central enzymes (Rib enzymes) of the riboflavi...

Authors: Daniel A. O. Rotter, Christoph Heger, Luis M. Oviedo-Bocanegra and Peter L. Graumann

Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

Speed and trajectory of locomotion are the characteristic traits of individual species. Locomotion kinematics may have been shaped during evolution towards increased survival in the habitats of each species. A...

Authors: Yuji Matsuo, Akinao Nose and Hiroshi Kohsaka

Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular di...

Authors: Charles Ross Lindsey, Frank Rosenzweig and Matthew D. Herron

Asymmetric expansions of FT and TFL1 lineages characterize differential evolution of the EuPEBP family in the major angiosperm lineages

In flowering plants, precise timing of the floral transition is crucial to maximize chances of reproductive success, and as such, this process has been intensively studied. FLOWERING LOCUS T (FT) and TERMINAL ...

Authors: Tom Bennett and Laura E. Dixon