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  • Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction
    BMC Biol. (IF 6.723) 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

  • TDP-43 promotes the formation of neuromuscular synapses through the regulation of Disc-large expression in Drosophila skeletal muscles
    BMC Biol. (IF 6.723) 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

  • Protein assembly systems in natural and synthetic biology
    BMC Biol. (IF 6.723) 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

  • DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-κB and sensitize to alkylating chemotherapy
    BMC Biol. (IF 6.723) 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

    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. Using streptavidin-agarose pull-down, we identified the DExD/H-box RNA helicase, DDX39B, as a factor that differentially interacts

  • Identification of berberine as a novel drug for the treatment of multiple myeloma via targeting UHRF1
    BMC Biol. (IF 6.723) 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

  • The role of T cell trafficking in CTLA-4 blockade-induced gut immunopathology
    BMC Biol. (IF 6.723) 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 metabolic switch regulates the transition between growth and diapause in C. elegans
    BMC Biol. (IF 6.723) 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

  • Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans
    BMC Biol. (IF 6.723) 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 heat-sensitive Osh protein controls PI4P polarity
    BMC Biol. (IF 6.723) 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 6.723) 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

  • Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti
    BMC Biol. (IF 6.723) Pub Date : 2020-03-12
    Seth N. Redmond; Atashi Sharma; Igor Sharakhov; Zhijian Tu; Maria Sharakhova; Daniel E. Neafsey

    Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation and speciation in dipteran insects and would be of great utility for studies of Ae. aegypti. However, the large

  • Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells
    BMC Biol. (IF 6.723) Pub Date : 2020-03-04
    Donnchadh S. Dunican; Heidi K. Mjoseng; Leanne Duthie; Ilya M. Flyamer; Wendy A. Bickmore; Richard R. Meehan

    Thousands of mammalian promoters are defined by co-enrichment of the histone tail modifications H3K27me3 (repressive) and H3K4me3 (activating) and are thus termed bivalent. It was previously observed that bivalent genes in human ES cells (hESC) are frequent targets for hypermethylation in human cancers, and depletion of DNA methylation in mouse embryonic stem cells has a marked impact on H3K27me3 distribution

  • Introducing our series: research synthesis and meta-research in biology
    BMC Biol. (IF 6.723) Pub Date : 2020-03-05
    Shinichi Nakagawa; Julia Koricheva; Malcolm Macleod; Wolfgang Viechtbauer

    Research synthesis is the process of bringing together findings and attributes from different publications, for example, to give a more complete description of phenomena than is usually possible in a single work. We bring the Research Synthesis Series to BMC Biology to promote meta-analyses, other research syntheses including meta-research studies, and research synthesis methodologies in biology, facilitating

  • Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids.
    BMC Biol. (IF 6.723) Pub Date : 2020-03-02
    Anzhelika Butenko,Fred R Opperdoes,Olga Flegontova,Aleš Horák,Vladimír Hampl,Patrick Keeling,Ryan M R Gawryluk,Denis Tikhonenkov,Pavel Flegontov,Julius Lukeš

    BACKGROUND The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living

  • Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability.
    BMC Biol. (IF 6.723) Pub Date : 2020-03-02
    Galo A Goig,Silvia Blanco,Alberto L Garcia-Basteiro,Iñaki Comas

    BACKGROUND Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research. RESULTS We used a taxonomic filter to remove

  • The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.
    BMC Biol. (IF 6.723) Pub Date : 2020-03-02
    Michael W Gray,Gertraud Burger,Romain Derelle,Vladimír Klimeš,Michelle M Leger,Matt Sarrasin,Čestmír Vlček,Andrew J Roger,Marek Eliáš,B Franz Lang

    BACKGROUND Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily

  • X-ray computed tomography in life sciences.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-27
    Shelley D Rawson,Jekaterina Maksimcuka,Philip J Withers,Sarah H Cartmell

    Recent developments within micro-computed tomography (μCT) imaging have combined to extend our capacity to image tissue in three (3D) and four (4D) dimensions at micron and sub-micron spatial resolutions, opening the way for virtual histology, live cell imaging, subcellular imaging and correlative microscopy. Pivotal to this has been the development of methods to extend the contrast achievable for

  • Ca2+ mobilization-dependent reduction of the endoplasmic reticulum lumen is due to influx of cytosolic glutathione.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-26
    Beáta Lizák,Julia Birk,Melinda Zana,Gergely Kosztyi,Denise V Kratschmar,Alex Odermatt,Richard Zimmermann,Miklós Geiszt,Christian Appenzeller-Herzog,Gábor Bánhegyi

    BACKGROUND The lumen of the endoplasmic reticulum (ER) acts as a cellular Ca2+ store and a site for oxidative protein folding, which is controlled by the reduced glutathione (GSH) and glutathione-disulfide (GSSG) redox pair. Although depletion of luminal Ca2+ from the ER provokes a rapid and reversible shift towards a more reducing poise in the ER, the underlying molecular basis remains unclear. RESULTS

  • Patterns of African and Asian admixture in the Afrikaner population of South Africa.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-24
    N Hollfelder,J C Erasmus,R Hammaren,M Vicente,M Jakobsson,J M Greeff,C M Schlebusch

    BACKGROUND The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry

  • Unexpected cell type-dependent effects of autophagy on polyglutamine aggregation revealed by natural genetic variation in C. elegans.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-24
    J Alexander-Floyd,S Haroon,M Ying,A A Entezari,C Jaeger,M Vermulst,T Gidalevitz

    BACKGROUND Monogenic protein aggregation diseases, in addition to cell selectivity, exhibit clinical variation in the age of onset and progression, driven in part by inter-individual genetic variation. While natural genetic variants may pinpoint plastic networks amenable to intervention, the mechanisms by which they impact individual susceptibility to proteotoxicity are still largely unknown. RESULTS

  • The tanning hormone, bursicon, does not act directly on the epidermis to tan the Drosophila exoskeleton.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-19
    Justin Flaven-Pouchon,Javier V Alvarez,Candy Rojas,John Ewer

    BACKGROUND In insects, continuous growth requires the periodic replacement of the exoskeleton. Once the remains of the exoskeleton from the previous stage have been shed during ecdysis, the new one is rapidly sclerotized (hardened) and melanized (pigmented), a process collectively known as tanning. The rapid tanning that occurs after ecdysis is critical for insect survival, as it reduces desiccation

  • Membrane and synaptic defects leading to neurodegeneration in Adar mutant Drosophila are rescued by increased autophagy.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-14
    Anzer Khan,Simona Paro,Leeanne McGurk,Nagraj Sambrani,Marion C Hogg,James Brindle,Giuseppa Pennetta,Liam P Keegan,Mary A O'Connell

    BACKGROUND In fly brains, the Drosophila Adar (adenosine deaminase acting on RNA) enzyme edits hundreds of transcripts to generate edited isoforms of encoded proteins. Nearly all editing events are absent or less efficient in larvae but increase at metamorphosis; the larger number and higher levels of editing suggest editing is most required when the brain is most complex. This idea is consistent with

  • The wild species genome ancestry of domestic chickens.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-12
    Raman Akinyanju Lawal,Simon H Martin,Koen Vanmechelen,Addie Vereijken,Pradeepa Silva,Raed Mahmoud Al-Atiyat,Riyadh Salah Aljumaah,Joram M Mwacharo,Dong-Dong Wu,Ya-Ping Zhang,Paul M Hocking,Jacqueline Smith,David Wragg,Olivier Hanotte

    BACKGROUND Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector

  • The quail genome: insights into social behaviour, seasonal biology and infectious disease response.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-12
    Katrina M Morris,Matthew M Hindle,Simon Boitard,David W Burt,Angela F Danner,Lel Eory,Heather L Forrest,David Gourichon,Jerome Gros,LaDeana W Hillier,Thierry Jaffredo,Hanane Khoury,Rusty Lansford,Christine Leterrier,Andrew Loudon,Andrew S Mason,Simone L Meddle,Francis Minvielle,Patrick Minx,Frédérique Pitel,J Patrick Seiler,Tsuyoshi Shimmura,Chad Tomlinson,Alain Vignal,Robert G Webster,Takashi Yoshimura

    BACKGROUND The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. RESULTS We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome

  • A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici.
    BMC Biol. (IF 6.723) Pub Date : 2020-02-11
    Thomas Badet,Ursula Oggenfuss,Leen Abraham,Bruce A McDonald,Daniel Croll

    BACKGROUND The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how

  • The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-27
    Abhinav Joshi,Li Dai,Yanxin Liu,Jungsoon Lee,Nastaran Mohammadi Ghahhari,Gregory Segala,Kristin Beebe,Lisa M Jenkins,Gaelyn C Lyons,Lilia Bernasconi,Francis T F Tsai,David A Agard,Len Neckers,Didier Picard

    BACKGROUND The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. Most studies have found it to be an inhibitor of mitochondrial oxidative phosphorylation (OXPHOS) and an inducer of the Warburg phenotype of cancer cells. However, others have reported the opposite, and there

  • The round goby genome provides insights into mechanisms that may facilitate biological invasions.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-28
    Irene Adrian-Kalchhauser,Anders Blomberg,Tomas Larsson,Zuzana Musilova,Claire R Peart,Martin Pippel,Monica Hongroe Solbakken,Jaanus Suurväli,Jean-Claude Walser,Joanna Yvonne Wilson,Magnus Alm Rosenblad,Demian Burguera,Silvia Gutnik,Nico Michiels,Mats Töpel,Kirill Pankov,Siegfried Schloissnig,Sylke Winkler

    BACKGROUND The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the

  • Control of glutamate release by complexes of adenosine and cannabinoid receptors.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-23
    Attila Köfalvi,Estefanía Moreno,Arnau Cordomí,Ning-Sheng Cai,Victor Fernández-Dueñas,Samira G Ferreira,Ramón Guixà-González,Marta Sánchez-Soto,Hideaki Yano,Verònica Casadó-Anguera,Rodrigo A Cunha,Ana Maria Sebastião,Francisco Ciruela,Leonardo Pardo,Vicent Casadó,Sergi Ferré

    BACKGROUND It has been hypothesized that heteromers of adenosine A2A receptors (A2AR) and cannabinoid CB1 receptors (CB1R) localized in glutamatergic nerve terminals mediate the integration of adenosine and endocannabinoid signaling involved in the modulation of striatal excitatory neurotransmission. Previous studies have demonstrated the existence of A2AR-CB1R heteromers in artificial cell systems

  • A two-pore channel protein required for regulating mTORC1 activity on starvation.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-22
    Fu-Sheng Chang,Yuntao Wang,Phillip Dmitriev,Julian Gross,Antony Galione,Catherine Pears

    BACKGROUND Two-pore channels (TPCs) release Ca2+ from acidic intracellular stores and are implicated in a number of diseases, but their role in development is unclear. The social amoeba Dictyostelium discoideum proliferates as single cells that aggregate to form a multicellular organism on starvation. Starvation is sensed by the mTORC1 complex which, like TPC proteins, is found on acidic vesicles.

  • A straightforward approach for bioorthogonal labeling of proteins and organelles in live mammalian cells, using a short peptide tag.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-14
    Inbar Segal,Dikla Nachmias,Andres Konig,Ariel Alon,Eyal Arbely,Natalie Elia

    BACKGROUND In the high-resolution microscopy era, genetic code expansion (GCE)-based bioorthogonal labeling offers an elegant way for direct labeling of proteins in live cells with fluorescent dyes. This labeling approach is currently not broadly used in live-cell applications, partly because it needs to be adjusted to the specific protein under study. RESULTS We present a generic, 14-residue long

  • Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-14
    Elin Lundin,Chenglin Wu,Albin Widmark,Mikaela Behm,Jens Hjerling-Leffler,Chammiran Daniel,Marie Öhman,Mats Nilsson

    BACKGROUND Adenosine-to-inosine (A-to-I) RNA editing is a process that contributes to the diversification of proteins that has been shown to be essential for neurotransmission and other neuronal functions. However, the spatiotemporal and diversification properties of RNA editing in the brain are largely unknown. Here, we applied in situ sequencing to distinguish between edited and unedited transcripts

  • Optogenetic activation of parvalbumin and somatostatin interneurons selectively restores theta-nested gamma oscillations and oscillation-induced spike timing-dependent long-term potentiation impaired by amyloid β oligomers.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-15
    Kyerl Park,Jaedong Lee,Hyun Jae Jang,Blake A Richards,Michael M Kohl,Jeehyun Kwag

    BACKGROUND Abnormal accumulation of amyloid β1-42 oligomers (AβO1-42), a hallmark of Alzheimer's disease, impairs hippocampal theta-nested gamma oscillations and long-term potentiation (LTP) that are believed to underlie learning and memory. Parvalbumin-positive (PV) and somatostatin-positive (SST) interneurons are critically involved in theta-nested gamma oscillogenesis and LTP induction. However

  • Correction to: Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-09
    Sunjoo Joo,Ming Hsiu Wang,Gary Lui,Jenny Lee,Andrew Barnas,Eunsoo Kim,Sebastian Sudek,Alexandra Z Worden,Jae-Hyeok Lee

    Upon publication of the original article [1], it was noticed that Alexandra Z. Worden's affiliation is not complete. The full affiliation information for Alexandra Z. Worden is can be found below and in the complete affiliation list of this Correction article.

  • Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-08
    Ellie E Armstrong,Ryan W Taylor,Danny E Miller,Christopher B Kaelin,Gregory S Barsh,Elizabeth A Hadly,Dmitri Petrov

    BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here

  • The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-06
    Heike Rampelt,Iva Sucec,Beate Bersch,Patrick Horten,Inge Perschil,Jean-Claude Martinou,Martin van der Laan,Nils Wiedemann,Paul Schanda,Nikolaus Pfanner

    BACKGROUND The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase

  • Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.
    BMC Biol. (IF 6.723) Pub Date : 2020-01-02
    Robert M Waterhouse,Sergey Aganezov,Yoann Anselmetti,Jiyoung Lee,Livio Ruzzante,Maarten J M F Reijnders,Romain Feron,Sèverine Bérard,Phillip George,Matthew W Hahn,Paul I Howell,Maryam Kamali,Sergey Koren,Daniel Lawson,Gareth Maslen,Ashley Peery,Adam M Phillippy,Maria V Sharakhova,Eric Tannier,Maria F Unger,Simo V Zhang,Max A Alekseyev,Nora J Besansky,Cedric Chauve,Scott J Emrich,Igor V Sharakhov

    BACKGROUND New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation

  • Charting the diversity of uncultured viruses of Archaea and Bacteria.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-29
    F H Coutinho,R A Edwards,F Rodríguez-Valera

    BACKGROUND Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However

  • Functional architecture underlying binocular coordination of eye position and velocity in the larval zebrafish hindbrain.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-29
    Christian Brysch,Claire Leyden,Aristides B Arrenberg

    BACKGROUND The oculomotor integrator (OI) in the vertebrate hindbrain transforms eye velocity input into persistent position coding output, which plays a crucial role in retinal image stability. For a mechanistic understanding of the integrator function and eye position control, knowledge about the tuning of the OI and other oculomotor nuclei is needed. Zebrafish are increasingly used to study integrator

  • Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-30
    Sylvain Foissac,Sarah Djebali,Kylie Munyard,Nathalie Vialaneix,Andrea Rau,Kevin Muret,Diane Esquerré,Matthias Zytnicki,Thomas Derrien,Philippe Bardou,Fany Blanc,Cédric Cabau,Elisa Crisci,Sophie Dhorne-Pollet,Françoise Drouet,Thomas Faraut,Ignacio Gonzalez,Adeline Goubil,Sonia Lacroix-Lamandé,Fabrice Laurent,Sylvain Marthey,Maria Marti-Marimon,Raphaelle Momal-Leisenring,Florence Mompart,Pascale Quéré

    BACKGROUND Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps

  • Joint learning improves protein abundance prediction in cancers.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-23
    Hongyang Li,Omer Siddiqui,Hongjiu Zhang,Yuanfang Guan

    BACKGROUND The classic central dogma in biology is the information flow from DNA to mRNA to protein, yet complicated regulatory mechanisms underlying protein translation often lead to weak correlations between mRNA and protein abundances. This is particularly the case in cancer samples and when evaluating the same gene across multiple samples. RESULTS Here, we report a method for predicting proteome

  • Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-18
    Hongbin Liu,Xiangfang Zeng,Guolong Zhang,Chengli Hou,Ning Li,Haitao Yu,Lijun Shang,Xiaoya Zhang,Paolo Trevisi,Feiyun Yang,Zuohua Liu,Shiyan Qiao

    BACKGROUND The early-life microbiota exerts a profound and lifelong impact on host health. Longitudinal studies in humans have been informative but are mostly based on the analysis of fecal samples and cannot shed direct light on the early development of mucosa-associated intestinal microbiota and its impact on GI function. Using piglets as a model for human infants, we assess here the succession of

  • Crossing fitness valleys via double substitutions within codons.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-16
    Frida Belinky,Itamar Sela,Igor B Rogozin,Eugene V Koonin

    BACKGROUND Single nucleotide substitutions in protein-coding genes can be divided into synonymous (S), with little fitness effect, and non-synonymous (N) ones that alter amino acids and thus generally have a greater effect. Most of the N substitutions are affected by purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases potentially could alleviate

  • SATB1 establishes ameloblast cell polarity and regulates directional amelogenin secretion for enamel formation.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-13
    Yan Zhang,Liwei Zheng,Michael Le,Yukiko Nakano,Barry Chan,Yulei Huang,Parisa Moravedje Torbaty,Yoshinori Kohwi,Ralph Marcucio,Stefan Habelitz,Pamela K Den Besten,Terumi Kohwi-Shigematsu

    BACKGROUND Polarity is necessary for epithelial cells to perform distinct functions at their apical and basal surfaces. Oral epithelial cell-derived ameloblasts at secretory stage (SABs) synthesize large amounts of enamel matrix proteins (EMPs), largely amelogenins. EMPs are unidirectionally secreted into the enamel space through their apical cytoplasmic protrusions, or Tomes' processes (TPs), to guide

  • Extracting physiological information in experimental biology via Eulerian video magnification.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-12
    Henrik Lauridsen,Selina Gonzales,Daniela Hedwig,Kathryn L Perrin,Catherine J A Williams,Peter H Wrege,Mads F Bertelsen,Michael Pedersen,Jonathan T Butcher

    BACKGROUND Videographic material of animals can contain inapparent signals, such as color changes or motion that hold information about physiological functions, such as heart and respiration rate, pulse wave velocity, and vocalization. Eulerian video magnification allows the enhancement of such signals to enable their detection. The purpose of this study is to demonstrate how signals relevant to experimental

  • Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-10
    Katharina Jovic,Jacopo Grilli,Mark G Sterken,Basten L Snoek,Joost A G Riksen,Stefano Allesina,Jan E Kammenga

    BACKGROUND The detrimental effects of a short bout of stress can persist and potentially turn lethal, long after the return to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme temperatures, is influenced by the response during stress exposure, as well as the recovery process afterwards. While heat-shock response mechanisms have been studied intensively

  • Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-06
    Shardul D Kulkarni,Fujun Zhou,Neelam Dabas Sen,Hongen Zhang,Alan G Hinnebusch,Jon R Lorsch

    BACKGROUND Translation of an mRNA in eukaryotes starts at an AUG codon in most cases, but near-cognate codons (NCCs) such as UUG, ACG, and AUU can also be used as start sites at low levels in Saccharomyces cerevisiae. Initiation from NCCs or AUGs in the 5'-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main

  • The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-05
    Richard P Meisel,Pablo J Delclos,Judith R Wexler

    BACKGROUND Sex chromosome evolution is a dynamic process that can proceed at varying rates across lineages. For example, different chromosomes can be sex-linked between closely related species, whereas other sex chromosomes have been conserved for > 100 million years. Cases of long-term sex chromosome conservation could be informative of factors that constrain sex chromosome evolution. Cytological

  • Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-03
    Vânia C S Pankievicz,Thomas B Irving,Lucas G S Maia,Jean-Michel Ané

    Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking

  • DPF is a cell-density sensing factor, with cell-autonomous and non-autonomous functions during Dictyostelium growth and development.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-02
    Netra Pal Meena,Pundrik Jaiswal,Fu-Sheng Chang,Joseph Brzostowski,Alan R Kimmel

    BACKGROUND Cellular functions can be regulated by cell-cell interactions that are influenced by extra-cellular, density-dependent signaling factors. Dictyostelium grow as individual cells in nutrient-rich sources, but, as nutrients become depleted, they initiate a multi-cell developmental program that is dependent upon a cell-density threshold. We hypothesized that novel secreted proteins may serve

  • Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.
    BMC Biol. (IF 6.723) Pub Date : 2019-12-02
    Gillian P McHugo,Michael J Dover,David E MacHugh

    Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication

  • Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-29
    Amrita Srivathsan,Emily Hartop,Jayanthi Puniamoorthy,Wan Ting Lee,Sujatha Narayanan Kutty,Olavi Kurina,Rudolf Meier

    BACKGROUND More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately,

  • The intestinal microbiota regulates host cholesterol homeostasis.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-27
    Tiphaine Le Roy,Emelyne Lécuyer,Benoit Chassaing,Moez Rhimi,Marie Lhomme,Samira Boudebbouze,Farid Ichou,Júlia Haro Barceló,Thierry Huby,Maryse Guerin,Philippe Giral,Emmanuelle Maguin,Nathalie Kapel,Philippe Gérard,Karine Clément,Philippe Lesnik

    BACKGROUND Management of blood cholesterol is a major focus of efforts to prevent cardiovascular diseases. The objective of this study was to investigate how the gut microbiota affects host cholesterol homeostasis at the organism scale. RESULTS We depleted the intestinal microbiota of hypercholesterolemic female Apoe-/- mice using broad-spectrum antibiotics. Measurement of plasma cholesterol levels

  • Optimized photo-stimulation of halorhodopsin for long-term neuronal inhibition.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-27
    Chuanqiang Zhang,Shang Yang,Tom Flossmann,Shiqiang Gao,Otto W Witte,Georg Nagel,Knut Holthoff,Knut Kirmse

    BACKGROUND Optogenetic silencing techniques have expanded the causal understanding of the functions of diverse neuronal cell types in both the healthy and diseased brain. A widely used inhibitory optogenetic actuator is eNpHR3.0, an improved version of the light-driven chloride pump halorhodopsin derived from Natronomonas pharaonis. A major drawback of eNpHR3.0 is related to its pronounced inactivation

  • Peripheral cathepsin L inhibition induces fat loss in C. elegans and mice through promoting central serotonin synthesis.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-26
    Yan Lin,Bin Bao,Hao Yin,Xin Wang,Airong Feng,Lin Zhao,Xianqi Nie,Nan Yang,Guo-Ping Shi,Jian Liu

    BACKGROUND Cathepsin L and some other cathepsins have been implicated in the development of obesity in humans and mice. The functional inactivation of the proteases reduces fat accumulation during mammalian adipocyte differentiation. However, beyond degrading extracellular matrix protein fibronectin, the molecular mechanisms by which cathepsins control fat accumulation remain unclear. We now provide

  • Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-22
    Peter J Maughan,Rebekah Lee,Rachel Walstead,Robert J Vickerstaff,Melissa C Fogarty,Cory R Brouwer,Robert R Reid,Jeremy J Jay,Wubishet A Bekele,Eric W Jackson,Nicholas A Tinker,Tim Langdon,Jessica A Schlueter,Eric N Jellen

    BACKGROUND Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As-

  • Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-18
    Jes Alexander,Gregory M Findlay,Martin Kircher,Jay Shendure

    BACKGROUND Recent advances in genome editing have facilitated the direct manipulation of not only the genome, but also the epigenome. Genome editing is typically performed by introducing a single CRISPR/Cas9-mediated double-strand break (DSB), followed by non-homologous end joining (NHEJ)- or homology-directed repair-mediated repair. Epigenome editing, and in particular methylation of CpG dinucleotides

  • Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi.
    BMC Biol. (IF 6.723) Pub Date : 2019-11-18
    Yuanning Li,Michael G Tassia,Damien S Waits,Viktoria E Bogantes,Kyle T David,Kenneth M Halanych

    BACKGROUND Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused

  • Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment
    BMC Biol. (IF 6.723) Pub Date : 2019-11-13
    Hang Ruan; Yingnan Liao; Zongna Ren; Lin Mao; Fang Yao; Peng Yu; Youqiong Ye; Zhao Zhang; Shengli Li; Hanshi Xu; Jiewei Liu; Lixia Diao; Bingying Zhou; Leng Han; Li Wang

    Cardiac differentiation from human pluripotent stem cells provides a unique opportunity to study human heart development in vitro and offers a potential cell source for cardiac regeneration. Compared to the large body of studies investigating cardiac maturation and cardiomyocyte subtype-specific induction, molecular events underlying cardiac lineage commitment from pluripotent stem cells at early stage

  • Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants
    BMC Biol. (IF 6.723) Pub Date : 2019-11-11
    Isidro Álvarez-Escribano; Christoph Sasse; Jin Woo Bok; Hyunsoo Na; Mojgan Amirebrahimi; Anna Lipzen; Wendy Schackwitz; Joel Martin; Kerrie Barry; Gabriel Gutiérrez; Sara Cea-Sánchez; Ana T. Marcos; Igor V. Grigoriev; Nancy P. Keller; Gerhard H. Braus; David Cánovas

    Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of

  • The microbiome of the upper respiratory tract in health and disease
    BMC Biol. (IF 6.723) Pub Date : 2019-11-07
    Christina Kumpitsch; Kaisa Koskinen; Veronika Schöpf; Christine Moissl-Eichinger

    The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the

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