75 found

Year:

  1.  4
    Ubiquitylation Pathways In Insulin Signaling and Organismal Homeostasis.Vishnu Balaji, Wojciech Pokrzywa & Thorsten Hoppe - 2018 - Bioessays 40 (5):1700223.
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  2.  6
    BET‐Ting on Nrf2: How Nrf2 Signaling Can Influence the Therapeutic Activities of BET Protein Inhibitors.Nirmalya Chatterjee & Dirk Bohmann - 2018 - Bioessays 40 (5):1800007.
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  3.  3
    Identifying Human Naïve Pluripotent Stem Cells − Evaluating State‐Specific Reporter Lines and Cell‐Surface Markers.Amanda J. Collier & Peter J. Rugg‐Gunn - 2018 - Bioessays 40 (5):1700239.
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  4.  10
    DNA Repair: The Search for Homology.James E. Haber - 2018 - Bioessays 40 (5):1700229.
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  5.  13
    Let's Talk About Sex − Not Gender.Wolfgang Goymann & Henrik Brumm - 2018 - Bioessays 40 (5):1800030.
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  6.  4
    We're Stressed Out: BET‐Ting on Oxidative Stress?Steven G. Gray - 2018 - Bioessays 40 (5):1800049.
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  7.  8
    Demystifying Eukaryote Lateral Gene Transfer.Michelle M. Leger, Laura Eme, Courtney W. Stairs & Andrew J. Roger - 2018 - Bioessays 40 (5):1700242.
    In a recent BioEssays paper [W. F. Martin, BioEssays 2017, 39, 1700115], William Martin sharply criticizes evolutionary interpretations that involve lateral gene transfer into eukaryotic genomes. Most published examples of LGTs in eukaryotes, he suggests, are in fact contaminants, ancestral genes that have been lost from other extant lineages, or the result of artefactual phylogenetic inferences. Martin argues that, except for transfers that occurred from endosymbiotic organelles, eukaryote LGT is insignificant. Here, in reviewing this field, we seek to correct some (...)
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  8.  3
    Of Contaminated Catalysts − or How a Pleasant Surprise Can Pervert Parsimony.Andrew Moore - 2018 - Bioessays 40 (5):1800066.
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  9.  3
    Hawaiian Drosophila as an Evolutionary Model Clade: Days of Future Past.Patrick O'Grady & Rob DeSalle - 2018 - Bioessays 40 (5):1700246.
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  10.  2
    Multi‐Invasion‐Induced Rearrangements as a Pathway for Physiological and Pathological Recombination.Aurèle Piazza & Wolf‐Dietrich Heyer - 2018 - Bioessays 40 (5):1700249.
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  11.  4
    Getting the Message? Native Reactive Electrophiles Pass Two Out of Three Thresholds to Be Bona Fide Signaling Mediators.Jesse R. Poganik, Marcus J. C. Long & Yimon Aye - 2018 - Bioessays 40 (5):1700240.
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  12.  5
    An Emerging Group of Membrane Property Sensors Controls the Physical State of Organellar Membranes to Maintain Their Identity.Toni Radanović, John Reinhard, Stephanie Ballweg, Kristina Pesek & Robert Ernst - 2018 - Bioessays 40 (5):1700250.
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  13. The Diversification of Early Emerging Metazoans: A Window Into the Evolution of Animal Multicellularity.Roger Revilla-I.-Domingo & Oleg Simakov - 2018 - Bioessays 40 (5):1800029.
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  14.  5
    The Diversification of Early Emerging Metazoans: A Window Into the Evolution of Animal Multicellularity.Roger Revilla‐I.‐Domingo & Oleg Simakov - 2018 - Bioessays 40 (5).
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  15.  3
    New Roles for the Nucleolus in Health and Disease.Lorena Núñez Villacís, Mei S. Wong, Laura L. Ferguson, Nadine Hein, Amee J. George & Katherine M. Hannan - 2018 - Bioessays 40 (5):1700233.
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  16.  2
    A New Way to Treat Brain Tumors: Targeting Proteins Coded by Microcephaly Genes?Patrick Y. Lang & Timothy R. Gershon - 2018 - Bioessays 40 (5):1700243.
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  17. Active Sleep Promotes Functional Connectivity in Developing Sensorimotor Networks.Carlos Del Rio-Bermudez & Mark S. Blumberg - 2018 - Bioessays 40 (4):1700234.
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  18.  5
    Microbiome‐Germline Interactions and Their Transgenerational Implications.Michael Elgart & Yoav Soen - 2018 - Bioessays 40 (4):1700018.
    It is becoming increasingly clear that most, if not all, animals and plants are associated with a diverse array of resident gut microbiota. This symbiosis is regulated by host-microbiome interactions which influence the development, homeostasis, adaptation and evolution of the host. Recent evidence indicated that these interactions can also affect the host germline and have a potential of supporting transgenerational effects, including inheritance of acquired characteristics. Taken together, the influence of gut bacteria on the host soma and germline could potentially (...)
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  19.  7
    Lipoprotein Transport: Greasing the Machines of Outer Membrane Biogenesis.Marcin Grabowicz - 2018 - Bioessays 40 (4):1700187.
    The Gram-negative outer membrane is a potent permeability barrier against antibiotics, limiting clinical options amid mounting rates of resistance. The Lol transport pathway delivers lipoproteins to the OM. All the OM assembly machines require one or more OM lipoprotein to function, making the Lol pathway central for all aspects of OM biogenesis. The Lol pathways of many medically important species clearly deviate from the Escherichia coli paradigm, perhaps with implications for efforts to develop novel antibiotics. Moreover, recent work reveals the (...)
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  20. Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data.Jean-David Grattepanche, Laura M. Walker, Brittany M. Ott, Daniela L. Paim Pinto, Charles F. Delwiche, Christopher E. Lane & Laura A. Katz - 2018 - Bioessays 40 (4):1700198.
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  21.  7
    Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data.Jean‐David Grattepanche, Laura M. Walker, Brittany M. Ott, Daniela L. Paim Pinto, Charles F. Delwiche, Christopher E. Lane & Laura A. Katz - 2018 - Bioessays 40 (4).
    Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular data. The majority (...)
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  22.  2
    PROTACs: An Emerging Targeting Technique for Protein Degradation in Drug Discovery.Shanshan Gu, Danrui Cui, Xiaoyu Chen, Xiufang Xiong & Yongchao Zhao - 2018 - Bioessays 40 (4):1700247.
    Proteolysis-targeting chimeric molecules represent an emerging technique that is receiving much attention for therapeutic intervention. The mechanism is based on the inhibition of protein function by hijacking a ubiquitin E3 ligase for protein degradation. The hetero-bifunctional PROTACs contain a ligand for recruiting an E3 ligase, a linker, and another ligand to bind with the protein targeted for degradation. Thus, PROTACs have profound potential to eliminate “undruggable” protein targets, such as transcription factors and non-enzymatic proteins, which are not limited to physiological (...)
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  23.  11
    The Rise of the Cartwheel: Seeding the Centriole Organelle.Paul Guichard, Virginie Hamel & Pierre Gönczy - 2018 - Bioessays 40 (4):1700241.
    The cartwheel is a striking structure critical for building the centriole, a microtubule-based organelle fundamental for organizing centrosomes, cilia, and flagella. Over the last 50 years, the cartwheel has been described in many systems using electron microscopy, but the molecular nature of its constituent building blocks and their assembly mechanisms have long remained mysterious. Here, we review discoveries that led to the current understanding of cartwheel structure, assembly, and function. We focus on the key role of SAS-6 protein self-organization, both (...)
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  24.  2
    Loss and Rebirth of the Animal Microtubule Organizing Center: How Maternal Expression of Centrosomal Proteins Cooperates with the Sperm Centriole in Zygotic Centrosome Reformation.Daigo Inoue, Joachim Wittbrodt & Oliver J. Gruss - 2018 - Bioessays 40 (4):1700135.
    Centrosomes are the main microtubule organizing centers in animal cells. In particular during embryogenesis, they ensure faithful spindle formation and proper cell divisions. As metazoan centrosomes are eliminated during oogenesis, they have to be reassembled upon fertilization. Most metazoans use the sperm centrioles as templates for new centrosome biogenesis while the egg's cytoplasm re-prepares all components for on-going centrosome duplication in rapidly dividing embryonic cells. We discuss our knowledge and the experimental challenges to analyze zygotic centrosome reformation, which requires genetic (...)
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  25.  2
    Replicating and Cycling Stores of Information Perpetuate Life.Antony M. Jose - 2018 - Bioessays 40 (4):1700161.
    Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information – one replicating with each cell division and the other cycling with a period of one generation – coevolve (...)
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  26.  2
    How Polycomb‐Mediated Cell Memory Deals With a Changing Environment.Federica Marasca, Beatrice Bodega & Valerio Orlando - 2018 - Bioessays 40 (4):1700137.
    Cells and tissues are continuously exposed to a changing microenvironment, hence the necessity of a flexible modulation of gene expression that in complex organism have been achieved through specialized chromatin mechanisms. Chromatin-based cell memory enables cells to maintain their identity by fixing lineage specific transcriptional programs, ensuring their faithful transmission through cell division; in particular PcG-based memory system evolved to maintain the silenced state of developmental and cell cycle genes. In evolution the complexity of this system have increased, particularly in (...)
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  27.  1
    The Value of a Journal Club: Conditioning Around Food, Drink and Socializing!Andrew Moore - 2018 - Bioessays 40 (4):1800040.
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  28.  3
    Advances in Structural Biology and the Application to Biological Filament Systems.David Popp, Fujiet Koh, Clement P. M. Scipion, Umesh Ghoshdastider, Akihiro Narita, Kenneth C. Holmes & Robert C. Robinson - 2018 - Bioessays 40 (4):1700213.
    Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament (...)
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  29.  3
    Active Sleep Promotes Functional Connectivity in Developing Sensorimotor Networks.Carlos Del Rio‐Bermudez & Mark S. Blumberg - 2018 - Bioessays 40 (4).
    A ubiquitous feature of active sleep in mammals and birds is its relative abundance in early development. In rat pups across the first two postnatal weeks, active sleep promotes the expression of synchronized oscillatory activity within and between cortical and subcortical sensorimotor structures. Sensory feedback from self-generated myoclonic twitches – which are produced exclusively during active sleep – also triggers neural oscillations in those structures. We have proposed that one of the functions of active sleep in early infancy is to (...)
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  30.  4
    Active Sleep Promotes Functional Connectivity in Developing Sensorimotor Networks.Carlos Del Rio‐Bermudez & Mark S. Blumberg - 2018 - Bioessays 40 (4).
    A ubiquitous feature of active sleep in mammals and birds is its relative abundance in early development. In rat pups across the first two postnatal weeks, active sleep promotes the expression of synchronized oscillatory activity within and between cortical and subcortical sensorimotor structures. Sensory feedback from self-generated myoclonic twitches – which are produced exclusively during active sleep – also triggers neural oscillations in those structures. We have proposed that one of the functions of active sleep in early infancy is to (...)
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  31.  5
    DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond.Olga Zaytseva & Leonie M. Quinn - 2018 - Bioessays 40 (4):1700235.
    Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. Dissection (...)
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  32.  5
    Integrity of IKK/NF‐κB Shields Thymic Stroma That Suppresses Susceptibility to Autoimmunity, Fungal Infection, and Carcinogenesis.Feng Zhu & Yinling Hu - 2018 - Bioessays 40 (4):1700131.
    A pathogenic connection between autoreactive T cells, fungal infection, and carcinogenesis has been demonstrated in studies of human autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy as well as in a mouse model in which kinase-dead Ikkα knock-in mice develop impaired central tolerance, autoreactive T cell–mediated autoimmunity, chronic fungal infection, and esophageal squamous cell carcinoma, which recapitulates APECED. IκB kinase α is one subunit of the IKK complex required for NF-κB activation. IKK/NF-κB is essential for central tolerance establishment by regulating the development of medullary thymic (...)
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  33.  6
    Are There Really Too Many Eukaryote LGTs? A Reply To William Martin.Luis Boto - 2018 - Bioessays 40 (3):1800001.
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  34.  2
    Surviving Starvation: AMPK Protects Germ Cell Integrity by Targeting Multiple Epigenetic Effectors.Emilie Demoinet & Richard Roy - 2018 - Bioessays 40 (3):1700095.
    Acute starvation can have long-term consequences that are mediated through epigenetic change. Some of these changes are affected by the activity of AMP-activated protein kinase, a master regulator of cellular energy homeostasis. In Caenorhabditis elegans, the absence of AMPK during a period of starvation in an early larval stage results in developmental defects following their recovery on food, while many of them become sterile. Moreover, the loss of AMPK during this quiescent period results in transgenerational phenotypes that can become progressively (...)
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  35.  12
    Mitonuclear Mate Choice: A Missing Component of Sexual Selection Theory?Geoffrey E. Hill - 2018 - Bioessays 40 (3):1700191.
    The fitness of a eukaryote hinges on the coordinated function of the products of its nuclear and mitochondrial genomes in achieving oxidative phosphorylation. I propose that sexual selection plays a key role in the maintenance of mitonuclear coadaptation across generations because it enables pre-zygotic sorting for coadapted mitonuclear genotypes. At each new generation, sexual reproduction creates new combinations of nuclear and mitochondrial genes, and the potential arises for mitonuclear incompatibilities and reduced fitness. In reviewing the literature, I hypothesize that individuals (...)
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  36.  5
    Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA.Jack S. Hardwick, Andrew N. Lane & Tom Brown - 2018 - Bioessays 40 (3):1700199.
    To decode the function and molecular recognition of several recently discovered cytosine derivatives in the human genome – 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine – a detailed understanding of their effects on the structural, chemical, and biophysical properties of DNA is essential. Here, we review recent literature in this area, with particular emphasis on features that have been proposed to enable the specific recognition of modified cytosine bases by DNA-binding proteins. These include electronic factors, modulation of base-pair stability, flexibility, and radical changes (...)
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  37.  4
    Microtubule Inner Proteins: A Meshwork of Luminal Proteins Stabilizing the Doublet Microtubule.Muneyoshi Ichikawa & Khanh Huy Bui - 2018 - Bioessays 40 (3):1700209.
    Motile eukaryotic cilia and flagella are hair-like organelles responsible for cell motility and mucociliary clearance. Using cryo-electron tomography, it has been shown that the doublet microtubule, the cytoskeleton core of the cilia and flagella, has microtubule inner protein structures binding periodically inside its lumen. More recently, single-particle cryo-electron microscopy analyses of isolated doublet microtubules have shown that microtubule inner proteins form a meshwork inside the doublet microtubule. High-resolution structures revealed new types of interactions between the microtubule inner proteins and the (...)
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  38.  5
    Quantum DNA Sequencing: A Peek Into a Dystopic Future?José Luis Lavín & Juan Anguita - 2018 - Bioessays 40 (3):1700248.
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  39.  9
    The Eukaryotic CMG Helicase at the Replication Fork: Emerging Architecture Reveals an Unexpected Mechanism.Huilin Li & Michael E. O'Donnell - 2018 - Bioessays 40 (3):1700208.
    The eukaryotic helicase is an 11-subunit machine containing an Mcm2-7 motor ring that encircles DNA, Cdc45 and the GINS tetramer, referred to as CMG. CMG is “built” on DNA at origins in two steps. First, two Mcm2-7 rings are assembled around duplex DNA at origins in G1 phase, forming the Mcm2-7 “double hexamer.” In a second step, in S phase Cdc45 and GINS are assembled onto each Mcm2-7 ring, hence producing two CMGs that ultimately form two replication forks that travel (...)
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  40.  5
    Oncogenesis as a Selective Force: Adaptive Evolution in the Face of a Transmissible Cancer.Tracey Russell, Thomas Madsen, Frédéric Thomas, Nynke Raven, Rodrigo Hamede & Beata Ujvari - 2018 - Bioessays 40 (3):1700146.
    Similar to parasites, malignant cells exploit the host for energy, resources and protection, thereby impairing host health and fitness. Although cancer is widespread in the animal kingdom, its impact on life history traits and strategies have rarely been documented. Devil facial tumour disease, a transmissible cancer, afflicting Tasmanian devils, provides an ideal model system to monitor the impact of cancer on host life-history, and to elucidate the evolutionary arms-race between malignant cells and their hosts. Here we provide an overview of (...)
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  41.  3
    Bone Marrow Micro‐Environment in Normal and Deranged Hematopoiesis: Opportunities for Regenerative Medicine and Therapies.Shawn M. Sarkaria, Matthew Decker & Lei Ding - 2018 - Bioessays 40 (3):1700190.
    Various cell types cooperate to create a highly organized and dynamic micro-environmental niche in the bone marrow. Over the past several years, the field has increasingly recognized the critical roles of the interplay between bone marrow environment and hematopoietic cells in normal and deranged hematopoiesis. These advances rely on several new technologies that have allowed us to characterize the identity and roles of these niches in great detail. Here, we review the progress of the last several years, list some of (...)
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  42.  1
    Impact Factors, Reads and Real Values.Dave Speijer - 2018 - Bioessays 40 (3):1800014.
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  43.  4
    Reactive Oxygen Species: Radical Factors in the Evolution of Animal Life.Yannick J. Taverne, Daphne Merkus, Ad J. Bogers, Barry Halliwell, Dirk J. Duncker & Timothy W. Lyons - 2018 - Bioessays 40 (3):1700158.
    Introduction of O2 to Earth's early biosphere stimulated remarkable evolutionary adaptations, and a wide range of electron acceptors allowed diverse, energy-yielding metabolic pathways. Enzymatic reduction of O2 yielded a several-fold increase in energy production, enabling evolution of multi-cellular animal life. However, utilization of O2 also presented major challenges as O2 and many of its derived reactive oxygen species are highly toxic, possibly impeding multicellular evolution after the Great Oxidation Event. Remarkably, ROS, and especially hydrogen peroxide, seem to play a major (...)
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  44.  4
    Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics.Lena Voith von Voithenberg & Don C. Lamb - 2018 - Bioessays 40 (3):1700078.
    Conformational changes of proteins and other biomolecules play a fundamental role in their functional mechanism. Single pair Förster resonance energy transfer offers the possibility to detect these conformational changes and dynamics, and to characterize their underlying kinetics. Using spFRET on microscopes with different modes of detection, dynamic timescales ranging from nanoseconds to seconds can be quantified. Confocal microscopy can be used as a means to analyze dynamics in the range of nanoseconds to milliseconds, while total internal reflection fluorescence microscopy offers (...)
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  45.  8
    Cytosolic N‐Glycans: Triggers for Ubiquitination Directing Proteasomal and Autophagic Degradation.Yukiko Yoshida & Keiji Tanaka - 2018 - Bioessays 40 (3):1700215.
    Proteins on the cell surface and secreted proteins are modified with sugar chains that generate and modulate biological complexity and diversity. Sugar chains not only contribute physically to the conformation and solubility of proteins, but also exert various functions via sugar-binding proteins that reside on the cell surface or in organelles of the secretory pathway. However, some glycosidases and lectins are found in the cytosol or nucleus. Recent studies of cytosolic sugar–related molecules have revealed that sugar chains on proteins in (...)
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  46.  2
    Multitasking Ska in Chromosome Segregation: Its Distinct Pools Might Specify Various Functions.Qian Zhang, Yujue Chen, Lu Yang & Hong Liu - 2018 - Bioessays 40 (3):1700176.
    The human spindle and kinetochore associated complex is required for proper mitotic progression. Extensive studies have demonstrated its important functions in both stable kinetochore-microtubule interactions and spindle checkpoint silencing. We suggest a model to explain how various Ska functions might be fulfilled by distinct pools of Ska at kinetochores. The Ndc80-loop pool of Ska is recruited by the Ndc80 loop, or together with some of its flanking sequences, and the recruitment is also dependent on Cdk1-mediated Ska3 phosphorylation. This pool seems (...)
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  47. RNase III Nucleases and the Evolution of Antiviral Systems.Lauren C. Aguado & Benjamin R. tenOever - 2018 - Bioessays 40 (2):1700173.
    Every living entity requires the capacity to defend against viruses in some form. From bacteria to plants to arthropods, cells retain the capacity to capture genetic material, process it in a variety of ways, and subsequently use it to generate pathogen-specific small RNAs. These small RNAs can then be used to provide specificity to an otherwise non-specific nuclease, generating a potent antiviral system. While small RNA-based defenses in chordates are less utilized, the protein-based antiviral invention in this phylum appears to (...)
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  48.  3
    Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity.Simone Ecker, Vera Pancaldi, Alfonso Valencia, Stephan Beck & Dirk S. Paul - 2018 - Bioessays 40 (2):1700148.
    Epigenetic and transcriptional variability contribute to the vast diversity of cellular and organismal phenotypes and are key in human health and disease. In this review, we describe different types, sources, and determinants of epigenetic and transcriptional variability, enabling cells and organisms to adapt and evolve to a changing environment. We highlight the latest research and hypotheses on how chromatin structure and the epigenome influence gene expression variability. Further, we provide an overview of challenges in the analysis of biological variability. An (...)
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  49.  3
    Transmembrane Signal Transduction in Two-Component Systems: Piston, Scissoring, or Helical Rotation?Ivan Gushchin & Valentin Gordeliy - 2018 - Bioessays 40 (2):1700197.
    Allosteric and transmembrane signaling are among the major questions of structural biology. Here, we review and discuss signal transduction in four-helical TM bundles, focusing on histidine kinases and chemoreceptors found in two-component systems. Previously, piston, scissors, and helical rotation have been proposed as the mechanisms of TM signaling. We discuss theoretically possible conformational changes and examine the available experimental data, including the recent crystallographic structures of nitrate/nitrite sensor histidine kinase NarQ and phototaxis system NpSRII:NpHtrII. We show that TM helices can (...)
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  50.  9
    Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms.Katsuhiko Kamada & Daniela Barillà - 2018 - Bioessays 40 (2):1700166.
    Genome maintenance requires various nucleoid-associated factors in prokaryotes. Among them, the SMC protein has been thought to play a static role in the organization and segregation of the chromosome during cell division. However, recent studies have shown that the bacterial SMC is required to align left and right arms of the emerging chromosome and that the protein dynamically travels from origin to Ter region. A rod form of the SMC complex mediates DNA bridging and has been recognized as a machinery (...)
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  51.  6
    Review of “Making Sense of Genes” by Kostas Kampourakis. [REVIEW]Charalambos P. Kyriacou - 2018 - Bioessays 40 (2):1700212.
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  52.  2
    The Many Roles of Type II Phosphatidylinositol 4-Kinases in Membrane Trafficking: New Tricks for Old Dogs.Shane Minogue - 2018 - Bioessays 40 (2):1700145.
    The type II phosphatidylinositol 4-kinases produce the lipid phosphatidylinositol 4-phosphate and participate in a confusing variety of membrane trafficking and signaling roles. This review argues that both historical and contemporary evidence supports the function of the PI4KIIs in numerous trafficking pathways, and that the key to understanding the enzymatic regulation is through membrane interaction and the intrinsic membrane environment. By summarizing new research and examining the trafficking roles of the PI4KIIs in the context of recently solved molecular structures, I highlight (...)
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  53.  2
    Explaining the Origin of Three-Membrane-Bound Plastids in Dinoflagellates and Euglenophytes: Kleptoplastidy Via Myzocytosis?Daniel Moog & Uwe G. Maier - 2018 - Bioessays 40 (2):1700224.
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  54.  3
    Developing a Journal's Influence Without Impact Factor Madness: Quality in Shape.Andrew Moore - 2018 - Bioessays 40 (2):1800002.
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  55.  2
    Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects.Jean Peccoud, Richard Cordaux & Clément Gilbert - 2018 - Bioessays 40 (2):1700177.
    Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer. Between multicellular organisms, the transferred material will likely turn out to be a transposable element. Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large (...)
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  56.  1
    The Wnt Transcriptional Switch: TLE Removal or Inactivation?Aravinda-Bharathi Ramakrishnan, Abhishek Sinha, Vinson B. Fan & Ken M. Cadigan - 2018 - Bioessays 40 (2):1700162.
    Many targets of the Wnt/β-catenin signaling pathway are regulated by TCF transcription factors, which play important roles in animal development, stem cell biology, and oncogenesis. TCFs can regulate Wnt targets through a “transcriptional switch,” repressing gene expression in unstimulated cells and promoting transcription upon Wnt signaling. However, it is not clear whether this switch mechanism is a general feature of Wnt gene regulation or limited to a subset of Wnt targets. Co-repressors of the TLE family are known to contribute to (...)
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  57. Cell Size Control Via an Unstable Accumulating Activator and the Phenomenon of Excess Mitotic Delay.Nicholas Rhind - 2018 - Bioessays 40 (2):1700184.
    Unstable Accumulating Activator models for cellular size control propose an activator that accumulates in a size-dependent manner and triggers cell cycle progression once it has reached a certain threshold. Having a short half life makes such an activator responsive to changes in cell size and makes specific predictions for how cells respond to perturbation. In particular, it explains the curious phenomenon of excess mitotic delay. Excess mitotic delay, first observed in Tetrahymena in the '50s, is a phenomenon in which a (...)
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  58.  2
    Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication.Matthias J. Scherr, Barbara Safaric & Karl E. Duderstadt - 2018 - Bioessays 40 (2):1700159.
    The astonishing efficiency and accuracy of DNA replication has long suggested that refined rules enforce a single highly reproducible sequence of molecular events during the process. This view was solidified by early demonstrations that DNA unwinding and synthesis are coupled within a stable molecular factory, known as the replisome, which consists of conserved components that each play unique and complementary roles. However, recent single-molecule observations of replisome dynamics have begun to challenge this view, revealing that replication may not be defined (...)
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  59.  1
    When MicroRNAs Meet RNA Editing in Cancer: A Nucleotide Change Can Make a Difference.Yumeng Wang & Han Liang - 2018 - Bioessays 40 (2):1700188.
    RNA editing is a major post-transcriptional mechanism that changes specific nucleotides at the RNA level. The most common RNA editing type in humans is adenosine to inosine editing, which is mediated by ADAR enzymes. RNA editing events can not only change amino acids in proteins, but also affect the functions of non-coding RNAs such as miRNAs. Recent studies have characterized thousands of miRNA RNA editing events across different cancer types. Importantly, individual cases of miRNA editing have been reported to play (...)
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  60. It Is Time to Re-Evaluate the Peer Review Process for Preclinical Research.Rajat Bhattacharya & Lee M. Ellis - 2018 - Bioessays 40 (1):1700185.
    Problems in peer review, the backbone of maintaining high standards in scientific publishing, have led to wide spread discontent within the scientific community. Training in the peer review process and a simpler format to assist in decision making are possible courses to improve and expedite the process of peer review and scientific publishing. The authors discuss problems in the peer review process focusing on challenges related to major revisions and reviewer's wish list of experiments; this leads to the loss of (...)
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  61.  5
    Gravity Constraints Drive Biological Systems Toward Specific Organization Patterns.Mariano Bizzarri, Maria Grazia Masiello, Alessandro Giuliani & Alessandra Cucina - 2018 - Bioessays 40 (1):1700138.
    Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...)
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  62.  30
    Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling.Caitlin S. M. Cowan, Alan E. Hoban, Ana Paula Ventura-Silva, Timothy G. Dinan, Gerard Clarke & John F. Cryan - 2018 - Bioessays 40 (1):1700172.
    The amygdala is a key brain area regulating responses to stress and emotional stimuli, so improving our understanding of how it is regulated could offer novel strategies for treating disturbances in emotion regulation. As we review here, a growing body of evidence indicates that the gut microbiota may contribute to a range of amygdala-dependent brain functions from pain sensitivity to social behavior, emotion regulation, and therefore, psychiatric health. In addition, it appears that the microbiota is necessary for normal development of (...)
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  63.  3
    Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling.Caitlin S. M. Cowan, Alan E. Hoban, Ana Paula Ventura-Silva, Timothy G. Dinan, Gerard Clarke & John F. Cryan - 2018 - Bioessays 40 (1):1700172.
    The amygdala is a key brain area regulating responses to stress and emotional stimuli, so improving our understanding of how it is regulated could offer novel strategies for treating disturbances in emotion regulation. As we review here, a growing body of evidence indicates that the gut microbiota may contribute to a range of amygdala-dependent brain functions from pain sensitivity to social behavior, emotion regulation, and therefore, psychiatric health. In addition, it appears that the microbiota is necessary for normal development of (...)
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  64.  3
    The Wisdom of Networks: A General Adaptation and Learning Mechanism of Complex Systems.Peter Csermely - 2018 - Bioessays 40 (1):1700150.
    I hypothesize that re-occurring prior experience of complex systems mobilizes a fast response, whose attractor is encoded by their strongly connected network core. In contrast, responses to novel stimuli are often slow and require the weakly connected network periphery. Upon repeated stimulus, peripheral network nodes remodel the network core that encodes the attractor of the new response. This “core-periphery learning” theory reviews and generalizes the heretofore fragmented knowledge on attractor formation by neural networks, periphery-driven innovation, and a number of recent (...)
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  65.  11
    Unmodern Synthesis: Developmental Hierarchies and the Origin of Phenotypes.Richard Gawne, Kenneth Z. McKenna & H. Frederik Nijhout - 2018 - Bioessays 40 (1):1600265.
    The question of whether the modern evolutionary synthesis requires an extension has recently become a topic of discussion, and a source of controversy. We suggest that this debate is, for the most part, not about the modern synthesis at all. Rather, it is about the extent to which genetic mechanisms can be regarded as the primary determinants of phenotypic characters. The modern synthesis has been associated with the idea that phenotypes are the result of gene products, while supporters of the (...)
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  66.  6
    Evolution Is Linear: Debunking Life's Little Joke.Ronald A. Jenner - 2018 - Bioessays 40 (1):1700196.
    Linear depictions of the evolutionary process are ubiquitous in popular culture, but linear evolutionary imagery is strongly rejected by scientists who argue that evolution branches. This point is frequently illustrated by saying that we didn't evolve from monkeys, but that we are related to them as collateral relatives. Yet, we did evolve from monkeys, but our monkey ancestors are extinct, not extant. Influential voices, such as the late Stephen Jay Gould, have misled audiences for decades by falsely portraying the linear (...)
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  67. RNA Decay Factor UPF1 Promotes Protein Decay: A Hidden Talent.Terra-Dawn M. Plank & Miles F. Wilkinson - 2018 - Bioessays 40 (1):1700170.
    The RNA-binding protein, UPF1, is best known for its central role in the nonsense-mediated RNA decay pathway. Feng et al. now report a new function for UPF1—it is an E3 ubiquitin ligase that specifically promotes the decay of a key pro-muscle transcription factor: MYOD. UPF1 achieves this through its RING-like domain, which confers ubiquitin E3 ligase activity. Feng et al. provide evidence that the ability of UPF1 to destabilize MYOD represses myogenesis. In the future, it will be important to define (...)
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  68.  2
    Supporting Behaviour, Not Sex: The Women in Science Debate Re-Framed….Andrew Moore - 2018 - Bioessays 40 (1):1700230.
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  69.  11
    Soft-Bodied Fossils Are Not Simply Rotten Carcasses - Toward a Holistic Understanding of Exceptional Fossil Preservation.Luke A. Parry, Fiann Smithwick, Klara K. Nordén, Evan T. Saitta, Jesus Lozano-Fernandez, Alastair R. Tanner, Jean-Bernard Caron, Gregory D. Edgecombe, Derek E. G. Briggs & Jakob Vinther - 2018 - Bioessays 40 (1):1700167.
    Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that (...)
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  70.  15
    The PIWI-Interacting RNA Molecular Pathway: Insights From Cultured Silkworm Germline Cells.Kazuhiro Sakakibara & Mikiko C. Siomi - 2018 - Bioessays 40 (1):1700068.
    The PIWI-interacting RNA pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide PIWI protein to target genes through Watson–Crick RNA–RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway. Recent work using cultured silkworm germline cells has also (...)
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  71.  5
    CIN and Aneuploidy: Different Concepts, Different Consequences.Klaske M. Schukken & Floris Foijer - 2018 - Bioessays 40 (1):1700147.
    Chromosomal instability and aneuploidy are similar concepts but not synonymous. CIN is the process that leads to chromosome copy number alterations, and aneuploidy is the result. While CIN and resulting aneuploidy often cause growth defects, they are also selected for in cancer cells. Although such contradicting fates may seem paradoxical at first, they can be better understood when CIN and aneuploidy are assessed separately, taking into account the in vitro or in vivo context, the rate of CIN, and severity of (...)
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  72.  7
    Ca2+ -Dependent Hyperpolarization Pathways in Sleep Homeostasis and Mental Disorders.Shoi Shi & Hiroki R. Ueda - 2018 - Bioessays 40 (1):1700105.
    Although we are beginning to understand the neuronal and biochemical nature of sleep regulation, questions remain about how sleep is homeostatically regulated. Beyond its importance in basic physiology, understanding sleep may also shed light on psychiatric and neurodevelopmental disorders. Recent genetic studies in mammals revealed several non-secretory proteins that determine sleep duration. Interestingly, genes identified in these studies are closely related to psychiatric and neurodevelopmental disorders, suggesting that the sleep-wake cycle shares some common mechanisms with these disorders. Here we review (...)
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  73.  2
    Epigenetics as a Driver of Developmental Origins of Health and Disease: Did We Forget the Fathers?Adelheid Soubry - 2018 - Bioessays 40 (1):1700113.
    What are the effects of our environment on human development and the next generation? Numerous studies have provided ample evidence that a healthy environment and lifestyle of the mother is important for her offspring. Biological mechanisms underlying these environmental influences have been proposed to involve alterations in the epigenome. Is there enough evidence to suggest a similar contribution from the part of the father? Animal models provide proof of a transgenerational epigenetic effect through the paternal germ line, but can this (...)
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  74.  3
    Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the “Gene-Battery” Model.Vasavi Sundaram & Ting Wang - 2018 - Bioessays 40 (1):1700155.
    Transposable elements are no longer considered to be “junk” DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten and EH Davidson hypothesized that TEs can integrate the function of various transcriptional regulators into gene regulatory networks. Uniquely TEs can deposit regulatory sites across the genome when they transpose, and thereby bring multiple genes under control of the same regulatory logic. Several studies together have robustly (...)
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  75.  2
    mRNA Traffic Control Reviewed: N6-Methyladenosine Takes the Driver's Seat.Abhirami Visvanathan & Kumaravel Somasundaram - 2018 - Bioessays 40 (1):1700093.
    Messenger RNA is a flexible tool box that plays a key role in the dynamic regulation of gene expression. RNA modifications variegate the message conveyed by the mRNA. Similar to DNA and histone modifications, mRNA modifications are reversible and play a key role in the regulation of molecular events. Our understanding about the landscape of RNA modifications is still rudimentary in contrast to DNA and histone modifications. The major obstacle has been the lack of sensitive detection methods since they are (...)
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