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  • 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

  • Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-18
    Zhichao Xu,Xiangdong Pu,Ranran Gao,Olivia Costantina Demurtas,Steven J Fleck,Michaela Richter,Chunnian He,Aijia Ji,Wei Sun,Jianqiang Kong,Kaizhi Hu,Fengming Ren,Jiejie Song,Zhe Wang,Ting Gao,Chao Xiong,Haoying Yu,Tianyi Xin,Victor A Albert,Giovanni Giuliano,Shilin Chen,Jingyuan Song

    Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of compounds are found in a handful of distantly related plant genera (Coffea, Camellia, Paullinia, and Ilex for caffeine; Crocus, Buddleja, and Gardenia for crocins) wherein

  • Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-16
    Yanhong Zhong,Carlos Herrera-Úbeda,Jordi Garcia-Fernàndez,Guang Li,Peter W H Holland

    The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and Cdx gene functions, we focus on amphioxus, small marine animals that

  • Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-16
    Joachim Kloehn,Rebecca D Oppenheim,Ghizal Siddiqui,Pieter-Jan De Bock,Sunil Kumar Dogga,Yohann Coute,Mohamed-Ali Hakimi,Darren J Creek,Dominique Soldati-Favre

    Acetyl-CoA is a key molecule in all organisms, implicated in several metabolic pathways as well as in transcriptional regulation and post-translational modification. The human pathogen Toxoplasma gondii possesses at least four enzymes which generate acetyl-CoA in the nucleo-cytosol (acetyl-CoA synthetase (ACS); ATP citrate lyase (ACL)), mitochondrion (branched-chain α-keto acid dehydrogenase-complex

  • Stimulus-specific behavioral responses of zebrafish to a large range of odors exhibit individual variability.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-15
    Florence Kermen,Lea Darnet,Christoph Wiest,Fabrizio Palumbo,Jack Bechert,Ozge Uslu,Emre Yaksi

    Odor-driven behaviors such as feeding, mating, and predator avoidance are crucial for animal survival. The neural pathways processing these behaviors have been well characterized in a number of species, and involve the activity of diverse brain regions following stimulation of the olfactory bulb by specific odors. However, while the zebrafish olfactory circuitry is well understood, a comprehensive

  • DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-15
    Donata Tuminauskaite,Danguole Norkunaite,Marija Fiodorovaite,Sarunas Tumas,Inga Songailiene,Giedre Tamulaitiene,Tomas Sinkunas

    CRISPR-Cas systems, which provide adaptive immunity against foreign nucleic acids in prokaryotes, can serve as useful molecular tools for multiple applications in genome engineering. Diverse CRISPR-Cas systems originating from distinct prokaryotes function through a common mechanism involving the assembly of small crRNA molecules and Cas proteins into a ribonucleoprotein (RNP) effector complex, and

  • A mutation that blocks integrin α4β7 activation prevents adaptive immune-mediated colitis without increasing susceptibility to innate colitis.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-10
    Hailong Zhang,Yajuan Zheng,Youdong Pan,Changdong Lin,Shihui Wang,Zhanjun Yan,Ling Lu,Gaoxiang Ge,Jinsong Li,Yi Arial Zeng,Jianfeng Chen

    β7 integrins are responsible for the efficient recruitment of lymphocytes from the blood and their retention in gut-associated lymphoid tissues. Integrin α4β7 binds MAdCAM-1, mediating rolling adhesion of lymphocytes on blood vessel walls when inactive and firm adhesion when activated, thereby controlling two critical steps of lymphocyte homing to the gut. By contrast, integrin αEβ7 mediates the adhesion

  • Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-09
    Federico Baldini,Johannes Hertel,Estelle Sandt,Cyrille C Thinnes,Lorieza Neuberger-Castillo,Lukas Pavelka,Fay Betsou,Rejko Krüger,Ines Thiele,

    Parkinson’s disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their functional consequences remain unclear. Herein, we addressed this question by an analysis of stool samples from the Luxembourg Parkinson’s Study (n = 147 typical PD cases, n = 162 controls). All

  • The replication machinery of LUCA: common origin of DNA replication and transcription.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-09
    Eugene V Koonin,Mart Krupovic,Sonoko Ishino,Yoshizumi Ishino

    Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative

  • A tissue level atlas of the healthy human virome.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-04
    Ryuichi Kumata,Jumpei Ito,Kenta Takahashi,Tadaki Suzuki,Kei Sato

    Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and humans. Comparing to bacteria, the viral component of the microbiome (i.e., the “virome”) is understudied. Somatic tissues of healthy individuals are usually inaccessible for the virome sampling;

  • Intramembrane proteolysis of an extracellular serine protease, epithin/PRSS14, enables its intracellular nuclear function.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-03
    Youngkyung Cho,Sang Bum Kim,Jiyoon Kim,An Vuong Quynh Pham,Min Ji Yoon,Jeong Hwan Park,Ki-Tae Hwang,Dongeun Park,Yongcheol Cho,Moon Gyo Kim,Chungho Kim

    Epithin/PRSS14, a type II transmembrane serine protease, is an emerging target of cancer therapy because of its critical roles in tumor progression and metastasis. In many circumstances, the protease, through its ectodomain shedding, exists as a soluble form and performs its proteolytic functions in extracellular environments increasing cellular invasiveness. The seemingly functional integrity of the

  • Unraveling the molecular interactions involved in phase separation of glucocorticoid receptor.
    BMC Biol. (IF 6.765) Pub Date : 2020-06-02
    Martin Stortz,Adali Pecci,Diego M Presman,Valeria Levi

    Functional compartmentalization has emerged as an important factor modulating the kinetics and specificity of biochemical reactions in the nucleus, including those involved in transcriptional regulation. The glucocorticoid receptor (GR) is a ligand-activated transcription factor that translocates to the nucleus upon hormone stimulation and distributes between the nucleoplasm and membraneless compartments

  • Deficits in coordinated neuronal activity and network topology are striatal hallmarks in Huntington's disease.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-28
    S Fernández-García,J G Orlandi,G A García-Díaz Barriga,M J Rodríguez,M Masana,J Soriano,J Alberch

    Network alterations underlying neurodegenerative diseases often precede symptoms and functional deficits. Thus, their early identification is central for improved prognosis. In Huntington’s disease (HD), the cortico-striatal networks, involved in motor function processing, are the most compromised neural substrate. However, whether the network alterations are intrinsic of the striatum or the cortex

  • Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-27
    Dick Roelofs,Arthur Zwaenepoel,Tom Sistermans,Joey Nap,Andries A Kampfraath,Yves Van de Peer,Jacintha Ellers,Ken Kraaijeveld

    Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances

  • Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-24
    Timothy G Stephens,Raúl A González-Pech,Yuanyuan Cheng,Amin R Mohamed,David W Burt,Debashish Bhattacharya,Mark A Ragan,Cheong Xin Chan

    BACKGROUND Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms

  • Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-22
    Marco Sazzini,Paolo Abondio,Stefania Sarno,Guido Alberto Gnecchi-Ruscone,Matteo Ragno,Cristina Giuliani,Sara De Fanti,Claudia Ojeda-Granados,Alessio Boattini,Julien Marquis,Armand Valsesia,Jerome Carayol,Frederic Raymond,Chiara Pirazzini,Elena Marasco,Alberto Ferrarini,Luciano Xumerle,Sebastiano Collino,Daniela Mari,Beatrice Arosio,Daniela Monti,Giuseppe Passarino,Patrizia D'Aquila,Davide Pettener

    BACKGROUND The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors

  • Using a chimeric respiratory chain and EPR spectroscopy to determine the origin of semiquinone species previously assigned to mitochondrial complex I.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-20
    John J Wright,Justin G Fedor,Judy Hirst,Maxie M Roessler

    BACKGROUND For decades, semiquinone intermediates have been suggested to play an essential role in catalysis by one of the most enigmatic proton-pumping enzymes, respiratory complex I, and different mechanisms have been proposed on their basis. However, the difficulty in investigating complex I semiquinones, due to the many different enzymes embedded in the inner mitochondrial membrane, has resulted

  • NetConfer: a web application for comparative analysis of multiple biological networks.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-19
    Sunil Nagpal,Krishanu Das Baksi,Bhusan K Kuntal,Sharmila S Mande

    BACKGROUND Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The complexity of biological systems and the interactions of their various components, such as genes, proteins

  • Tropomyosin 1 genetically constrains in vitro hematopoiesis.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-14
    Christopher Stephen Thom,Chintan D Jobaliya,Kimberly Lorenz,Jean Ann Maguire,Alyssa Gagne,Paul Gadue,Deborah L French,Benjamin Franklin Voight

    BACKGROUND Identifying causal variants and genes from human genetic studies of hematopoietic traits is important to enumerate basic regulatory mechanisms underlying these traits, and could ultimately augment translational efforts to generate platelets and/or red blood cells in vitro. To identify putative causal genes from these data, we performed computational modeling using available genome-wide association

  • Modeling confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-12
    Héctor M Sánchez C,Jared B Bennett,Sean L Wu,Gordana Rašić,Omar S Akbari,John M Marshall

    BACKGROUND The discovery of CRISPR-based gene editing and its application to homing-based gene drive systems has been greeted with excitement, for its potential to control mosquito-borne diseases on a wide scale, and concern, for the invasiveness and potential irreversibility of a release. Gene drive systems that display threshold-dependent behavior could potentially be used during the trial phase

  • Discordant evolution of mitochondrial and nuclear yeast genomes at population level.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-11
    Matteo De Chiara,Anne Friedrich,Benjamin Barré,Michael Breitenbach,Joseph Schacherer,Gianni Liti

    BACKGROUND Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome

  • Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-06
    Verónica Mixão,Toni Gabaldón

    BACKGROUND Opportunistic yeast pathogens of the genus Candida are an important medical problem. Candida albicans, the most prevalent Candida species, is a natural commensal of humans that can adopt a pathogenic behavior. This species is highly heterozygous and cannot undergo meiosis, adopting instead a parasexual cycle that increases genetic variability and potentially leads to advantages under stress

  • Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-04
    Helen Ray-Jones,Kate Duffus,Amanda McGovern,Paul Martin,Chenfu Shi,Jenny Hankinson,Oliver Gough,Annie Yarwood,Andrew P Morris,Antony Adamson,Christopher Taylor,James Ding,Vasanthi Priyadarshini Gaddi,Yao Fu,Patrick Gaffney,Gisela Orozco,Richard B Warren,Steve Eyre

    BACKGROUND Genome-wide association studies (GWAS) have uncovered many genetic risk loci for psoriasis, yet many remain uncharacterised in terms of the causal gene and their biological mechanism in disease. This is largely a result of the findings that over 90% of GWAS variants map outside of protein-coding DNA and instead are enriched in cell type- and stimulation-specific gene regulatory regions.

  • An automated aquatic rack system for rearing marine invertebrates.
    BMC Biol. (IF 6.765) Pub Date : 2020-05-04
    Jonathan Q Henry,Maryna P Lesoway,Kimberly J Perry

    BACKGROUND One hundred years ago, marine organisms were the dominant systems for the study of developmental biology. The challenges in rearing these organisms outside of a marine setting ultimately contributed to a shift towards work on a smaller number of so-called model systems. Those animals are typically non-marine organisms with advantages afforded by short life cycles, high fecundity, and relative

  • Direct evidence for transport of RNA from the mouse brain to the germline and offspring.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-30
    Elizabeth A O'Brien,Kathleen S Ensbey,Bryan W Day,Paul A Baldock,Guy Barry

    BACKGROUND The traditional concept that heritability occurs exclusively from the transfer of germline-restricted genetics is being challenged by the increasing accumulation of evidence confirming the existence of experience-dependent transgenerational inheritance. However, questions remain unanswered as to how heritable information can be passed from somatic cells. Previous studies have implicated

  • Microtubule self-organisation during seed germination in Arabidopsis.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-30
    Huifang Yan,Nicole Chaumont,Jean François Gilles,Susanne Bolte,Olivier Hamant,Christophe Bailly

    BACKGROUND Upon water uptake and release of seed dormancy, embryonic plant cells expand, while being mechanically constrained by the seed coat. Cortical microtubules (CMTs) are key players of cell elongation in plants: their anisotropic orientation channels the axis of cell elongation through the guidance of oriented deposition of load-bearing cellulose microfibrils in the cell wall. Interestingly

  • Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-29
    Alfonso Soler-Bistué,Sebastián Aguilar-Pierlé,Marc Garcia-Garcerá,Marie-Eve Val,Odile Sismeiro,Hugo Varet,Rodrigo Sieira,Evelyne Krin,Ole Skovgaard,Diego J Comerci,Eduardo P C Rocha,Didier Mazel

    BACKGROUND In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its

  • Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-22
    Markus Grosch,Sebastian Ittermann,Ejona Rusha,Tobias Greisle,Chaido Ori,Dong-Jiunn Jeffery Truong,Adam C O'Neill,Anna Pertek,Gil Gregor Westmeyer,Micha Drukker

    BACKGROUND Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclear lncRNA condensates in cells, and we sought compounds that can promote the disintegration of lncRNA condensates in vivo. RESULTS As a basis for comparing lncRNAs and cellular properties

  • Integrating evolutionarily novel horns within the deeply conserved insect head.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-20
    David M Linz,Armin P Moczek

    BACKGROUND How novel traits integrate within ancient trait complexes without compromising ancestral functions is a foundational challenge in evo-devo. The insect head represents an ancient body region patterned by a deeply conserved developmental genetic network, yet at the same time constitutes a hot spot for morphological innovation. However, the mechanisms that facilitate the repeated emergence

  • Multiple links between 5-methylcytosine content of mRNA and translation.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-15
    Ulrike Schumann,He-Na Zhang,Tennille Sibbritt,Anyu Pan,Attila Horvath,Simon Gross,Susan J Clark,Li Yang,Thomas Preiss

    BACKGROUND 5-Methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite

  • Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-13
    Tess Cherlin,Rogan Magee,Yi Jing,Venetia Pliatsika,Phillipe Loher,Isidore Rigoutsos

    BACKGROUND The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously showed that the identities and abundances of microRNA isoforms (isomiRs) and transfer

  • Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-09
    Denis V Tikhonenkov,Elisabeth Hehenberger,Anton S Esaulov,Olga I Belyakova,Yuri A Mazei,Alexander P Mylnikov,Patrick J Keeling

    BACKGROUND The origin of animals from their unicellular ancestor was one of the most important events in evolutionary history, but the nature and the order of events leading up to the emergence of multicellular animals are still highly uncertain. The diversity and biology of unicellular relatives of animals have strongly informed our understanding of the transition from single-celled organisms to the

  • Improving the usability and comprehensiveness of microbial databases.
    BMC Biol. (IF 6.765) Pub Date : 2020-04-07
    Caitlin Loeffler,Aaron Karlsberg,Lana S Martin,Eleazar Eskin,David Koslicki,Serghei Mangul

    Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations

  • Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction
    BMC Biol. (IF 6.765) Pub Date : 2020-03-30
    Elena Clementi; Larissa Inglin; Erin Beebe; Corina Gsell; Zuzana Garajova; Enni Markkanen

    Base-excision repair (BER) is a central DNA repair mechanism responsible for the maintenance of genome integrity. Accordingly, BER defects have been implicated in cancer, presumably by precipitating cellular transformation through an increase in the occurrence of mutations. Hence, tight adaptation of BER capacity is essential for DNA stability. However, counterintuitive to this, prolonged exposure

  • Protein assembly systems in natural and synthetic biology
    BMC Biol. (IF 6.765) Pub Date : 2020-03-26
    Giulio Chiesa; Szilvia Kiriakov; Ahmad S. Khalil

    The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles

  • TDP-43 promotes the formation of neuromuscular synapses through the regulation of Disc-large expression in Drosophila skeletal muscles
    BMC Biol. (IF 6.765) Pub Date : 2020-03-26
    Nina Strah; Giulia Romano; Clelia Introna; Raffaella Klima; Marta Marzullo; Laura Ciapponi; Aram Megighian; Monica Nizzardo; Fabian Feiguin

    The ribonuclear protein TDP-43 has been implicated in the pathophysiology of amyotrophic lateral sclerosis (ALS), with genetic mutations being linked to the neurological symptoms of the disease. Though alterations in the intracellular distribution of TDP-43 have been observed in skeletal muscles of patients suffering from ALS, it is not clear whether such modifications play an active role in the disease

  • Identification of berberine as a novel drug for the treatment of multiple myeloma via targeting UHRF1
    BMC Biol. (IF 6.765) Pub Date : 2020-03-25
    Chunming Gu; Zhao Yin; Hong Nie; Yanjun Liu; Juhua Yang; Guiping Huang; Jianping Shen; Liguo Chen; Jia Fei

    Current therapies for multiple myeloma (MM) are associated with toxicity and resistance, highlighting the need for novel effective therapeutics. Berberine (BBR), a botanical alkaloid derived from several Berberis medicinal plants, has exhibited anti-tumor effects, including against multiple myeloma (MM); however, the molecular mechanism underlying the anti-MM effect has not been previously described

  • DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-κB and sensitize to alkylating chemotherapy.
    BMC Biol. (IF 6.765) Pub Date : 2020-03-24
    Szymon J Szymura,Giovanna M Bernal,Longtao Wu,Zhongqin Zhang,Clayton D Crawley,David J Voce,Paige-Ashley Campbell,Diana E Ranoa,Ralph R Weichselbaum,Bakhtiar Yamini

    BACKGROUND Nuclear factor-κB (NF-κB) plays a prominent role in promoting inflammation and resistance to DNA damaging therapy. We searched for proteins that modulate the NF-κB response as a prerequisite to identifying novel factors that affect sensitivity to DNA damaging chemotherapy. RESULTS Using streptavidin-agarose pull-down, we identified the DExD/H-box RNA helicase, DDX39B, as a factor that differentially

  • Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans
    BMC Biol. (IF 6.765) Pub Date : 2020-03-19
    Yu Toyoshima; Stephen Wu; Manami Kanamori; Hirofumi Sato; Moon Sun Jang; Suzu Oe; Yuko Murakami; Takayuki Teramoto; Chanhyun Park; Yuishi Iwasaki; Takeshi Ishihara; Ryo Yoshida; Yuichi Iino

    Annotation of cell identity is an essential process in neuroscience that allows comparison of cells, including that of neural activities across different animals. In Caenorhabditis elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal has been limited due to the lack of quantitative information on the location and identity of neurons

  • A metabolic switch regulates the transition between growth and diapause in C. elegans
    BMC Biol. (IF 6.765) Pub Date : 2020-03-18
    Sider Penkov; Bharath Kumar Raghuraman; Cihan Erkut; Jana Oertel; Roberta Galli; Eduardo Jacobo Miranda Ackerman; Daniela Vorkel; Jean-Marc Verbavatz; Edmund Koch; Karim Fahmy; Andrej Shevchenko; Teymuras V. Kurzchalia

    Metabolic activity alternates between high and low states during different stages of an organism’s life cycle. During the transition from growth to quiescence, a major metabolic shift often occurs from oxidative phosphorylation to glycolysis and gluconeogenesis. We use the entry of Caenorhabditis elegans into the dauer larval stage, a developmentally arrested stage formed in response to harsh environmental

  • The role of T cell trafficking in CTLA-4 blockade-induced gut immunopathology
    BMC Biol. (IF 6.765) Pub Date : 2020-03-17
    Shashuang Zhang; Wenhua Liang; Lingjie Luo; Shan Sun; Feng Wang

    Immune checkpoint inhibitor (ICPI) can augment the anti-tumour response by blocking negative immunoregulators with monoclonal antibodies. The anti-cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) antibody is the first ICPI which has shown remarkable benefits in the clinical treatment of cancers. However, the increased activity of the immune system also causes some side effects called immune-related

  • A heat-sensitive Osh protein controls PI4P polarity
    BMC Biol. (IF 6.765) Pub Date : 2020-03-13
    Deike J. Omnus; Angela Cadou; Ffion B. Thomas; Jakob M. Bader; Nathaniel Soh; Gary H. C. Chung; Andrew N. Vaughan; Christopher J. Stefan

    Phosphoinositide lipids provide spatial landmarks during polarized cell growth and migration. Yet how phosphoinositide gradients are oriented in response to extracellular cues and environmental conditions is not well understood. Here, we elucidate an unexpected mode of phosphatidylinositol 4-phosphate (PI4P) regulation in the control of polarized secretion. We show that PI4P is highly enriched at the

  • Performance analysis of novel toxin-antidote CRISPR gene drive systems
    BMC Biol. (IF 6.765) Pub Date : 2020-03-12
    Jackson Champer; Isabel K. Kim; Samuel E. Champer; Andrew G. Clark; Philipp W. Messer

    CRISPR gene drive systems allow the rapid spread of a genetic construct throughout a population. Such systems promise novel strategies for the management of vector-borne diseases and invasive species by suppressing a target population or modifying it with a desired trait. However, current homing-type drives have two potential shortcomings. First, they can be thwarted by the rapid evolution of resistance

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