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  • Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
    BMC Biol. (IF 6.765) Pub Date : 2020-09-19
    Jialin Liu; Michael Frochaux; Vincent Gardeux; Bart Deplancke; Marc Robinson-Rechavi

    The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum. Hypotheses to explain this hourglass pattern have focused on purifying the selection of gene regulation. Here, we propose an alternative—genes are regulated

  • Genetic modifiers ameliorate endocytic and neuromuscular defects in a model of spinal muscular atrophy
    BMC Biol. (IF 6.765) Pub Date : 2020-09-16
    Melissa B. Walsh; Eva Janzen; Emily Wingrove; Seyyedmohsen Hosseinibarkooie; Natalia Rodriguez Muela; Lance Davidow; Maria Dimitriadi; Erika M. Norabuena; Lee L. Rubin; Brunhilde Wirth; Anne C. Hart

    Understanding the genetic modifiers of neurodegenerative diseases can provide insight into the mechanisms underlying these disorders. Here, we examine the relationship between the motor neuron disease spinal muscular atrophy (SMA), which is caused by reduced levels of the survival of motor neuron (SMN) protein, and the actin-bundling protein Plastin 3 (PLS3). Increased PLS3 levels suppress symptoms

  • A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems
    BMC Biol. (IF 6.765) Pub Date : 2020-09-16
    Motoki Kayama; Jun-Feng Chen; Takashi Nakada; Yoshiki Nishimura; Toshiharu Shikanai; Tomonori Azuma; Hideaki Miyashita; Shinichi Takaichi; Yuichiro Kashiyama; Ryoma Kamikawa

    Plastid electron transport systems are essential not only for photosynthesis but also for dissipating excess reducing power and sinking excess electrons generated by various redox reactions. Although numerous organisms with plastids have lost their photoautotrophic lifestyles, there is a spectrum of known functions of remnant plastids in non-photosynthetic algal/plant lineages; some of non-photosynthetic

  • Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome
    BMC Biol. (IF 6.765) Pub Date : 2020-09-16
    Lena Constantin; Rebecca E. Poulsen; Leandro A. Scholz; Itia A. Favre-Bulle; Michael A. Taylor; Biao Sun; Geoffrey J. Goodhill; Gilles C. Vanwalleghem; Ethan K. Scott

    Loss or disrupted expression of the FMR1 gene causes fragile X syndrome (FXS), the most common monogenetic form of autism in humans. Although disruptions in sensory processing are core traits of FXS and autism, the neural underpinnings of these phenotypes are poorly understood. Using calcium imaging to record from the entire brain at cellular resolution, we investigated neuronal responses to visual

  • Independent glial subtypes delay development and extend healthy lifespan upon reduced insulin-PI3K signalling
    BMC Biol. (IF 6.765) Pub Date : 2020-09-14
    Nathaniel S. Woodling; Arjunan Rajasingam; Lucy J. Minkley; Alberto Rizzo; Linda Partridge

    The increasing age of global populations highlights the urgent need to understand the biological underpinnings of ageing. To this end, inhibition of the insulin/insulin-like signalling (IIS) pathway can extend healthy lifespan in diverse animal species, but with trade-offs including delayed development. It is possible that distinct cell types underlie effects on development and ageing; cell-type-specific

  • A molecular insight into the dissociable regulation of associative learning and motivation by the synaptic protein neuroligin-1
    BMC Biol. (IF 6.765) Pub Date : 2020-09-14
    Jiaqi Luo; Jessica M. Tan; Jess Nithianantharajah

    In a changing environment, a challenge for the brain is to flexibly guide adaptive behavior towards survival. Complex behavior and the underlying neural computations emerge from the structural components of the brain across many levels: circuits, cells, and ultimately the signaling complex of proteins at synapses. In line with this logic, dynamic modification of synaptic strength or synaptic plasticity

  • Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
    BMC Biol. (IF 6.765) Pub Date : 2020-09-11
    Claude Rispe; Fabrice Legeai; Paul D. Nabity; Rosa Fernández; Arinder K. Arora; Patrice Baa-Puyoulet; Celeste R. Banfill; Leticia Bao; Miquel Barberà; Maryem Bouallègue; Anthony Bretaudeau; Jennifer A. Brisson; Federica Calevro; Pierre Capy; Olivier Catrice; Thomas Chertemps; Carole Couture; Laurent Delière; Angela E. Douglas; Keith Dufault-Thompson; Paula Escuer; Honglin Feng; Astrid Forneck; Toni

    An amendment to this paper has been published and can be accessed via the original article.

  • Mechanical force-induced morphology changes in a human fungal pathogen
    BMC Biol. (IF 6.765) Pub Date : 2020-09-11
    Charles Puerner; Nino Kukhaleishvili; Darren Thomson; Sebastien Schaub; Xavier Noblin; Agnese Seminara; Martine Bassilana; Robert A. Arkowitz

    The initial step of a number of human or plant fungal infections requires active penetration of host tissue. For example, active penetration of intestinal epithelia by Candida albicans is critical for dissemination from the gut into the bloodstream. However, little is known about how this fungal pathogen copes with resistive forces upon host cell invasion. In the present study, we have used PDMS micro-fabrication

  • Some like it hot: population-specific adaptations in venom production to abiotic stressors in a widely distributed cnidarian
    BMC Biol. (IF 6.765) Pub Date : 2020-09-09
    Maria Y. Sachkova; Jason Macrander; Joachim M. Surm; Reuven Aharoni; Shelcie S. Menard-Harvey; Amy Klock; Whitney B. Leach; Adam M. Reitzel; Yehu Moran

    In cnidarians, antagonistic interactions with predators and prey are mediated by their venom, whose synthesis may be metabolically expensive. The potentially high cost of venom production has been hypothesized to drive population-specific variation in venom expression due to differences in abiotic conditions. However, the effects of environmental factors on venom production have been rarely demonstrated

  • Novel developmental bases for the evolution of hypobranchial muscles in vertebrates
    BMC Biol. (IF 6.765) Pub Date : 2020-09-09
    Rie Kusakabe; Shinnosuke Higuchi; Masako Tanaka; Mitsutaka Kadota; Osamu Nishimura; Shigeru Kuratani

    Vertebrates are characterized by possession of hypobranchial muscles (HBMs). Cyclostomes, or modern jawless vertebrates, possess a rudimentary and superficial HBM lateral to the pharynx, whereas the HBM in jawed vertebrates is internalized and anteroposteriorly specified. Precursor cells of the HBM, marked by expression of Lbx1, originate from somites and undergo extensive migration before becoming

  • Call order within vocal sequences of meerkats contains temporary contextual and individual information
    BMC Biol. (IF 6.765) Pub Date : 2020-09-09
    Ramona Rauber; Bart Kranstauber; Marta B. Manser

    The ability to recombine smaller units to produce infinite structures of higher-order phrases is unique to human language, yet evidence of animals to combine multiple acoustic units into meaningful combinations increases constantly. Despite increasing evidence for meaningful call combinations across contexts, little attention has been paid to the potential role of temporal variation of call type composition

  • Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress responses
    BMC Biol. (IF 6.765) Pub Date : 2020-09-08
    Katherine E. Larrimore; Natalia S. Barattin-Voynova; David W. Reid; Davis T. W. Ng

    The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport, and degradation within a cell. Failure to maintain proteostasis is associated with aging and disease, leading to concerted efforts to study how the network responds to various proteotoxic stresses. This is often accomplished using ectopic overexpression of well-characterized, model misfolded protein

  • Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression
    BMC Biol. (IF 6.765) Pub Date : 2020-09-07
    Soulafa Mamlouk; Tincy Simon; Laura Tomás; David C. Wedge; Alexander Arnold; Andrea Menne; David Horst; David Capper; Markus Morkel; David Posada; Christine Sers; Hendrik Bläker

    Colorectal cancer (CRC) development is generally accepted as a sequential process, with genetic mutations determining phenotypic tumor progression. However, matching genetic profiles with histological transition requires the analyses of temporal samples from the same patient at key stages of progression. Here, we compared the genetic profiles of 34 early carcinomas with their respective adenomatous

  • CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of rRNA
    BMC Biol. (IF 6.765) Pub Date : 2020-09-04
    Yun Wang; Chenchun Weng; Xiangyang Chen; Xufei Zhou; Xinya Huang; Yonghong Yan; Chengming Zhu

    Modification of RNAs, particularly at the terminals, is critical for various essential cell processes; for example, uridylation is implicated in tumorigenesis, proliferation, stem cell maintenance, and immune defense against viruses and retrotransposons. Ribosomal RNAs can be regulated by antisense ribosomal siRNAs (risiRNAs), which downregulate pre-rRNAs through the nuclear RNAi pathway in Caenorhabditis

  • LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data
    BMC Biol. (IF 6.765) Pub Date : 2020-09-03
    Benedict Hew; Qiao Wen Tan; William Goh; Jonathan Wei Xiong Ng; Marek Mutwil

    Bacterial resistance to antibiotics is a growing health problem that is projected to cause more deaths than cancer by 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the structurally conserved bacterial ribosomes, factors involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental

  • Machine-learning strategies for testing patterns of morphological variation in small samples: sexual dimorphism in gray wolf (Canis lupus) crania
    BMC Biol. (IF 6.765) Pub Date : 2020-09-03
    Norman MacLeod; Liora Kolska Horwitz

    Studies of mammalian sexual dimorphism have traditionally involved the measurement of selected dimensions of particular skeletal elements and use of single data-analysis procedures. Consequently, such studies have been limited by a variety of both practical and conceptual constraints. To compare and contrast what might be gained from a more exploratory, multifactorial approach to the quantitative assessment

  • Modified nucleic acids: replication, evolution, and next-generation therapeutics.
    BMC Biol. (IF 6.765) Pub Date : 2020-09-02
    Karen Duffy,Sebastian Arangundy-Franklin,Philipp Holliger

    Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are

  • Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-31
    Zhiquan Liu,Siyu Chen,Huanhuan Shan,Yingqi Jia,Mao Chen,Yuning Song,Liangxue Lai,Zhanjun Li

    Cytidine base editors (CBEs), composed of a cytidine deaminase fused to Cas9 nickase (nCas9), enable efficient C-to-T conversion in various organisms. However, current base editors can induce unwanted bystander C-to-T conversions when multiple Cs are present in the ~ 5-nucleotide activity window of cytidine deaminase, which negatively affects their precision. Here, we develop a new base editor which

  • Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-31
    Ashwin Nair,Kiran Sankar Chatterjee,Vikram Jha,Ranabir Das,P V Shivaprasad

    To successfully invade new hosts, plant viruses must break host resistance and be competent to move within and between plant cells. As a means, viral proteins known as pathogenicity determinants have evolved to coordinate a network of protein interactions. The βC1 protein encoded by specific geminiviral satellites acts as a key pathogenicity determinant for this disease-causing family of plant viruses

  • Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-31
    Arnaud Lavergne,Estefania Tarifeño-Saldivia,Justine Pirson,Anne-Sophie Reuter,Lydie Flasse,Isabelle Manfroid,Marianne L Voz,Bernard Peers

    Endocrine cells of the zebrafish digestive system play an important role in regulating metabolism and include pancreatic endocrine cells (PECs) clustered in the islets of Langerhans and the enteroendocrine cells (EECs) scattered in the intestinal epithelium. Despite EECs and PECs are being located in distinct organs, their differentiation involves shared molecular mechanisms and transcription factors

  • 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-28
    Judith Neukamm,Saskia Pfrengle,Martyna Molak,Alexander Seitz,Michael Francken,Partick Eppenberger,Charlotte Avanzi,Ella Reiter,Christian Urban,Beatrix Welte,Philipp W Stockhammer,Barbara Teßmann,Alexander Herbig,Katerina Harvati,Kay Nieselt,Johannes Krause,Verena J Schuenemann

    Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still

  • Excess diacylglycerol at the endoplasmic reticulum disrupts endomembrane homeostasis and autophagy.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-28
    Dan Li,Shu-Gao Yang,Cheng-Wen He,Zheng-Tan Zhang,Yongheng Liang,Hui Li,Jing Zhu,Xiong Su,Qingqiu Gong,Zhiping Xie

    When stressed, eukaryotic cells produce triacylglycerol (TAG) to store nutrients and mobilize autophagy to combat internal damage. We and others previously reported that in yeast, elimination of TAG synthesizing enzymes inhibits autophagy under nitrogen starvation, yet the underlying mechanism has remained elusive. Here, we show that disruption of TAG synthesis led to diacylglycerol (DAG) accumulation

  • Machine learning approaches identify male body size as the most accurate predictor of species richness.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-28
    Klemen Čandek,Urška Pristovšek Čandek,Matjaž Kuntner

    A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness –the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward

  • Nutritional status impacts dengue virus infection in mice.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-27
    Christina Chuong,Tyler A Bates,Shamima Akter,Stephen R Werre,Tanya LeRoith,James Weger-Lucarelli

    Dengue virus (DENV) is estimated to infect 390 million people annually. However, few host factors that alter disease severity are known. Malnutrition, defined as both over- and undernutrition, is a growing problem worldwide and has long been linked to dengue disease severity by epidemiological and anecdotal observations. Accordingly, we sought to establish a mouse model to assess the impact of nutritional

  • Extreme mobility of the world's largest flying mammals creates key challenges for management and conservation.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-21
    Justin A Welbergen,Jessica Meade,Hume E Field,Daniel Edson,Lee McMichael,Luke P Shoo,Jenny Praszczalek,Craig Smith,John M Martin

    Effective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. Flying-foxes (Pteropus spp.) are large bats that forage by night on floral resources and rest by day in arboreal roosts that may contain colonies of many thousands of individuals. They are the

  • Using spatial genetics to quantify mosquito dispersal for control programs.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-20
    Igor Filipović,Hapuarachchige Chanditha Hapuarachchi,Wei-Ping Tien,Muhammad Aliff Bin Abdul Razak,Caleb Lee,Cheong Huat Tan,Gregor J Devine,Gordana Rašić

    Hundreds of millions of people get a mosquito-borne disease every year and nearly one million die. Transmission of these infections is primarily tackled through the control of mosquito vectors. The accurate quantification of mosquito dispersal is critical for the design and optimization of vector control programs, yet the measurement of dispersal using traditional mark-release-recapture (MRR) methods

  • Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-19
    Matthew J Robertson,Katarzyna Kent,Nathan Tharp,Kaori Nozawa,Laura Dean,Michelle Mathew,Sandra L Grimm,Zhifeng Yu,Christine Légaré,Yoshitaka Fujihara,Masahito Ikawa,Robert Sullivan,Cristian Coarfa,Martin M Matzuk,Thomas X Garcia

    The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, understanding male reproductive physiology is limited by incomplete information on the genes expressed in reproductive tissues, and no contraceptive

  • Association of Bacteroides acidifaciens relative abundance with high-fibre diet-associated radiosensitisation.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-19
    Chee Kin Then,Salome Paillas,Xuedan Wang,Alix Hampson,Anne E Kiltie

    Patients with pelvic malignancies often receive radiosensitising chemotherapy with radiotherapy to improve survival; however, this is at the expense of increased normal tissue toxicity, particularly in elderly patients. Here, we explore if an alternative, low-cost, and non-toxic approach can achieve radiosensitisation in mice transplanted with human bladder cancer cells. Other investigators have shown

  • Reengineering anthrax toxin protective antigen for improved receptor-specific protein delivery.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-13
    Lukas Becker,Wouter P R Verdurmen,Andreas Plückthun

    To increase the size of the druggable proteome, it would be highly desirable to devise efficient methods to translocate designed binding proteins to the cytosol, as they could specifically target flat and hydrophobic protein-protein interfaces. If this could be done in a manner dependent on a cell surface receptor, two layers of specificity would be obtained: one for the cell type and the other for

  • The role of vegetative cell fusions in the development and asexual reproduction of the wheat fungal pathogen Zymoseptoria tritici.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-11
    Carolina Sardinha Francisco,Maria Manuela Zwyssig,Javier Palma-Guerrero

    The ability of fungal cells to undergo cell-to-cell communication and anastomosis, the process of vegetative hyphal fusion, allows them to maximize their overall fitness. Previous studies in a number of fungal species have identified the requirement of several signaling pathways for anastomosis, including the so far best characterized soft (So) gene, and the MAPK pathway components MAK-1 and MAK-2

  • Modelling the suppression of a malaria vector using a CRISPR-Cas9 gene drive to reduce female fertility.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-11
    Ace R North,Austin Burt,H Charles J Godfray

    Gene drives based on CRISPR-Cas9 technology are increasingly being considered as tools for reducing the capacity of mosquito populations to transmit malaria, and one of the most promising options is driving endonuclease genes that reduce the fertility of female mosquitoes. In particular, there is much interest in constructs that target the conserved mosquito doublesex (dsx) gene such that the emergence

  • Genome-wide pQTL analysis of protein expression regulatory networks in the human liver.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-10
    Bing He,Jian Shi,Xinwen Wang,Hui Jiang,Hao-Jie Zhu

    Previous expression quantitative trait loci (eQTL) studies have identified thousands of genetic variants to be associated with gene expression at the mRNA level in the human liver. However, protein expression often correlates poorly with mRNA levels. Thus, protein quantitative trait loci (pQTL) study is required to identify genetic variants that regulate protein expression in human livers. We conducted

  • The C-terminal region of the oxidoreductase MIA40 stabilizes its cytosolic precursor during mitochondrial import.
    BMC Biol. (IF 6.765) Pub Date : 2020-08-06
    Lena Maria Murschall,Anne Gerhards,Thomas MacVicar,Esra Peker,Lidwina Hasberg,Stephan Wawra,Thomas Langer,Jan Riemer

    The mitochondrial intermembrane space (IMS) is home to proteins fulfilling numerous essential cellular processes, particularly in metabolism and mitochondrial function. All IMS proteins are nuclear encoded and synthesized in the cytosol and must therefore be correctly targeted and transported to the IMS, either through mitochondrial targeting sequences or conserved cysteines and the mitochondrial disulfide

  • Impact of COVID-19 on early career scientists: an optimistic guide for the future.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-30
    Christina M Termini,David Traver

    Nationally mandated social distancing efforts have been implemented throughout the world during the COVID-19 pandemic to support the health and safety of the public. In response to the pandemic, research institutions have enacted strict changes to permitted research operations, requiring scientists to abide by social distancing guidelines in the laboratory, facility closures, and ramped down laboratory

  • Genetic background mutations drive neural circuit hyperconnectivity in a fragile X syndrome model.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-30
    Tyler Kennedy,David Rinker,Kendal Broadie

    Neural circuits are initially assembled during development when neurons synapse with potential partners and later refined as appropriate connections stabilize into mature synapses while inappropriate contacts are eliminated. Disruptions to this synaptogenic process impair connectivity optimization and can cause neurodevelopmental disorders. Intellectual disability (ID) and autism spectrum disorder

  • A simple threat-detection strategy in mice.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-29
    Xing Yang,Qingqing Liu,Jinling Zhong,Ru Song,Lin Zhang,Liping Wang

    Avoiding danger and accessing environmental resources are two fundamental, yet conflicting, survival instincts across species. To maintain a balance between these instincts, animals must efficiently distinguish approaching threats from low-threat cues. However, little is known about the key visual features that animals use to promptly detect such imminent danger and thus facilitate an immediate and

  • Correction to: Improving the usability and comprehensiveness of microbial databases.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-28
    Caitlin Loeffler,Aaron Karlsberg,Lana S Martin,Eleazar Eskin,David Koslicki,Serghei Mangul

    An amendment to this paper has been published and can be accessed via the original article.

  • Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-24
    Fabrice Legeai,Bernardo F Santos,Stéphanie Robin,Anthony Bretaudeau,Rebecca B Dikow,Claire Lemaitre,Véronique Jouan,Marc Ravallec,Jean-Michel Drezen,Denis Tagu,Frédéric Baudat,Gabor Gyapay,Xin Zhou,Shanlin Liu,Bruce A Webb,Seán G Brady,Anne-Nathalie Volkoff

    Polydnaviruses (PDVs) are mutualistic endogenous viruses inoculated by some lineages of parasitoid wasps into their hosts, where they facilitate successful wasp development. PDVs include the ichnoviruses and bracoviruses that originate from independent viral acquisitions in ichneumonid and braconid wasps respectively. PDV genomes are fully incorporated into the wasp genomes and consist of (1) genes

  • The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-23
    Claude Rispe,Fabrice Legeai,Paul D Nabity,Rosa Fernández,Arinder K Arora,Patrice Baa-Puyoulet,Celeste R Banfill,Leticia Bao,Miquel Barberà,Maryem Bouallègue,Anthony Bretaudeau,Jennifer A Brisson,Federica Calevro,Pierre Capy,Olivier Catrice,Thomas Chertemps,Carole Couture,Laurent Delière,Angela E Douglas,Keith Dufault-Thompson,Paula Escuer,Honglin Feng,Astrid Forneck,Toni Gabaldón,Roderic Guigó,Frédérique

    Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the

  • Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-21
    William D Tolbert,Rebekah Sherburn,Neelakshi Gohain,Shilei Ding,Robin Flinko,Chiara Orlandi,Krishanu Ray,Andrés Finzi,George K Lewis,Marzena Pazgier

    The binding of HIV-1 Envelope glycoproteins (Env) to host receptor CD4 exposes vulnerable conserved epitopes within the co-receptor binding site (CoRBS) which are required for the engagement of either CCR5 or CXCR4 co-receptor to allow HIV-1 entry. Antibodies against this region have been implicated in the protection against HIV acquisition in non-human primate (NHP) challenge studies and found to

  • Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-16
    Sergio M Latorre,C Sarai Reyes-Avila,Angus Malmgren,Joe Win,Sophien Kamoun,Hernán A Burbano

    Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia) oryzae—the causal agent of blast disease of cereals— is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat, and other cereals. Although M. oryzae is a

  • FAM20B-catalyzed glycosaminoglycans control murine tooth number by restricting FGFR2b signaling.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-14
    Jingyi Wu,Ye Tian,Lu Han,Chao Liu,Tianyu Sun,Ling Li,Yanlei Yu,Bikash Lamichhane,Rena N D'Souza,Sarah E Millar,Robb Krumlauf,David M Ornitz,Jian Q Feng,Ophir Klein,Hu Zhao,Fuming Zhang,Robert J Linhardt,Xiaofang Wang

    The formation of supernumerary teeth is an excellent model for studying the molecular mechanisms that control stem/progenitor cell homeostasis needed to generate a renewable source of replacement cells and tissues. Although multiple growth factors and transcriptional factors have been associated with supernumerary tooth formation, the regulatory inputs of extracellular matrix in this regenerative process

  • Wonky whales: the evolution of cranial asymmetry in cetaceans.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-10
    Ellen J Coombs,Julien Clavel,Travis Park,Morgan Churchill,Anjali Goswami

    Unlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earliest diverging odontocetes. Early cetaceans (whales, dolphins, and porpoises) such as archaeocetes, namely the protocetids and basilosaurids, have asymmetric rostra, but it is unclear when nasofacial

  • Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-06
    Yang Zhou,Shuli Liu,Yan Hu,Lingzhao Fang,Yahui Gao,Han Xia,Steven G Schroeder,Benjamin D Rosen,Erin E Connor,Cong-Jun Li,Ransom L Baldwin,John B Cole,Curtis P Van Tassell,Liguo Yang,Li Ma,George E Liu

    Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data

  • The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Darli Massardo,Nicholas W VanKuren,Sumitha Nallu,Renato R Ramos,Pedro G Ribeiro,Karina L Silva-Brandão,Marcelo M Brandão,Marília B Lion,André V L Freitas,Márcio Z Cardoso,Marcus R Kronforst

    Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been strongly influenced by hybridization, which has created new species and allowed sharing of color patterning alleles between mimetic species pairs. While these processes have frequently been observed

  • Temporospatial shifts within commercial laboratory mouse gut microbiota impact experimental reproducibility.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Rabindra K Mandal,Joshua E Denny,Morgan L Waide,Qingsheng Li,Neal Bhutiani,Charles D Anderson,Becca V Baby,Venkatakrishna R Jala,Nejat K Egilmez,Nathan W Schmidt

    Experimental reproducibility in mouse models is impacted by both genetics and environment. The generation of reproducible data is critical for the biomedical enterprise and has become a major concern for the scientific community and funding agencies alike. Among the factors that impact reproducibility in experimental mouse models is the variable composition of the microbiota in mice supplied by different

  • TDP-43 prevents retrotransposon activation in the Drosophila motor system through regulation of Dicer-2 activity.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Giulia Romano,Raffaella Klima,Fabian Feiguin

    Mutations in the small RNA-binding protein TDP-43 lead to the formation of insoluble cytoplasmic aggregates that have been associated with the onset and progression of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder affecting homeostasis of the motor system which is also characterized by aberrant expression of retrotransposable elements (RTEs). Although the TDP-43 function was shown

  • AIMTOR, a BRET biosensor for live imaging, reveals subcellular mTOR signaling and dysfunctions.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Nathalie Bouquier,Enora Moutin,Lionel A Tintignac,Amandine Reverbel,Elodie Jublanc,Michael Sinnreich,Yan Chastagnier,Julien Averous,Pierre Fafournoux,Chiara Verpelli,Tobias Boeckers,Gilles Carnac,Julie Perroy,Vincent Ollendorff

    mTOR signaling is an essential nutrient and energetic sensing pathway. Here we describe AIMTOR, a sensitive genetically encoded BRET (Bioluminescent Resonance Energy Transfer) biosensor to study mTOR activity in living cells. As a proof of principle, we show in both cell lines and primary cell cultures that AIMTOR BRET intensities are modified by mTOR activity changes induced by specific inhibitors

  • Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Shuli Liu,Ying Yu,Shengli Zhang,John B Cole,Albert Tenesa,Ting Wang,Tara G McDaneld,Li Ma,George E Liu,Lingzhao Fang

    Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle. We

  • Real-time tracking of stem cell viability, proliferation, and differentiation with autonomous bioluminescence imaging.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Michael Conway,Tingting Xu,Andrew Kirkpatrick,Steven Ripp,Gary Sayler,Dan Close

    Luminescent reporter proteins are vital tools for visualizing cells and cellular activity. Among the current toolbox of bioluminescent systems, only bacterial luciferase has genetically defined luciferase and luciferin synthesis pathways that are functional at the mammalian cell temperature optimum of 37 °C and have the potential for in vivo applications. However, this system is not functional in all

  • Relationship between oxygen consumption and neuronal activity in a defined neural circuit.
    BMC Biol. (IF 6.765) Pub Date : 2020-07-03
    Suzan Özugur,Lars Kunz,Hans Straka

    Neuronal computations related to sensory and motor activity along with the maintenance of spike discharge, synaptic transmission, and associated housekeeping are energetically demanding. The most efficient metabolic process to provide large amounts of energy equivalents is oxidative phosphorylation and thus dependent on O2 consumption. Therefore, O2 levels in the brain are a critical parameter that

  • Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-30
    Pedro Almeida,Estelle Proux-Wera,Allison Churcher,Lucile Soler,Jacques Dainat,Pascal Pucholt,Jessica Nordlund,Tom Martin,Ann-Christin Rönnberg-Wästljung,Björn Nystedt,Sofia Berlin,Judith E Mank

    Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal

  • The evolution of the Puf superfamily of proteins across the tree of eukaryotes.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-30
    Vladimíra Najdrová,Courtney W Stairs,Martina Vinopalová,Luboš Voleman,Pavel Doležal

    Eukaryotic gene expression is controlled by a number of RNA-binding proteins (RBP), such as the proteins from the Puf (Pumilio and FBF) superfamily (PufSF). These proteins bind to RNA via multiple Puf repeat domains, each of which specifically recognizes a single RNA base. Recently, three diversified PufSF proteins have been described in model organisms, each of which is responsible for the maturation

  • Phosphatidic acid-dependent localization and basal de-phosphorylation of RA-GEFs regulate lymphocyte trafficking.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-29
    Sayaka Ishihara,Tsuyoshi Sato,Guangwei Du,Daniele Guardavaccaro,Akihiko Nakajima,Satoshi Sawai,Tohru Kataoka,Koko Katagiri

    Lymphocytes circulate between peripheral lymphoid tissues via blood and lymphatic systems, and chemokine-induced migration is important in trafficking lymphocytes to distant sites. The small GTPase Rap1 is important in mediating lymphocyte motility, and Rap1-GEFs are involved in chemokine-mediated Rap1 activation. Here, we describe the roles and mechanisms of Rap1-GEFs in lymphocyte trafficking. In

  • The evolutionarily conserved ESRE stress response network is activated by ROS and mitochondrial damage.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-29
    Elissa Tjahjono,Aidan P McAnena,Natalia V Kirienko

    Mitochondrial dysfunction causes or contributes to a wide variety of pathologies, including neurodegenerative diseases, cancer, metabolic diseases, and aging. Cells actively surveil a number of mitochondrial readouts to ensure that cellular homeostasis is maintained. In this article, we characterize the role of the ethanol and stress response element (ESRE) pathway in mitochondrial surveillance and

  • A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-26
    Fengli Zhao,Yuexing Wang,Jianshu Zheng,Yanling Wen,Minghao Qu,Shujing Kang,Shigang Wu,Xiaojuan Deng,Kai Hong,Sanfeng Li,Xing Qin,Zhichao Wu,Xiaobo Wang,Cheng Ai,Alun Li,Longjun Zeng,Jiang Hu,Dali Zeng,Lianguang Shang,Quan Wang,Qian Qian,Jue Ruan,Guosheng Xiong

    Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing

  • The merger that made us.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-24
    Buzz Baum,David A Baum

    Darwin was the first to imagine a tree of life with all living organisms at its branch tips, connected back through time to a single common ancestor at the base of the trunk. We now know that all known cellular life descended from a single rootstock, with bacteria and archaea, structurally simple prokaryotic cells that lack internal membrane-bound structures, making up the trees’ two main branches

  • New targeted approaches for epigenetic age predictions.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-24
    Yang Han,Julia Franzen,Thomas Stiehl,Michael Gobs,Chao-Chung Kuo,Miloš Nikolić,Jan Hapala,Barbara Elisabeth Koop,Klaus Strathmann,Stefanie Ritz-Timme,Wolfgang Wagner

    Age-associated DNA methylation changes provide a promising biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis. In this study

  • A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-19
    Timothy P Driscoll,Victoria I Verhoeve,Joseph J Gillespie,J Spencer Johnston,Mark L Guillotte,Kristen E Rennoll-Bankert,M Sayeedur Rahman,Darren Hagen,Christine G Elsik,Kevin R Macaluso,Abdu F Azad

    Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea, Ctenocephalides felis, an

  • The rise of diversity in metabolic platforms across the Candidate Phyla Radiation.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-19
    Alexander L Jaffe,Cindy J Castelle,Paula B Matheus Carnevali,Simonetta Gribaldo,Jillian F Banfield

    A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. Here, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was

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