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    Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling.
    Bioessays 2017 Nov 17. Epub 2017 Nov 17.
    Dr. C. S. M. Cowan, Dr. A. P. Ventura-Silva, Prof. T. G. Dinan, Dr. G. Clarke, Prof. J. F. Cryan, APC Microbiome Institute, University College Cork, Cork, Ireland.
    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 the amygdala at both the structural and functional levels. Read More

    Gravity Constraints Drive Biological Systems Toward Specific Organization Patterns: Commitment of cell specification is constrained by physical cues.
    Bioessays 2017 Nov 14. Epub 2017 Nov 14.
    Department of Surgery "PietroValdoni", Sapienza University of Rome, via A. Scarpa 14, Rome 00161, Italy.
    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. Read More

    Too Much Eukaryote LGT.
    Bioessays 2017 Oct 25. Epub 2017 Oct 25.
    University of Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany.
    The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer (LGT) gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to a quantitatively similar degree. Read More

    Linking Mitochondria and Synaptic Transmission: The CB1 Receptor.
    Bioessays 2017 Oct 23. Epub 2017 Oct 23.
    Department of Biology, Université de Moncton, 18 Av Antonine Maillet, Moncton, New Brunswick, Canada.
    CB1 receptors are functionally present within brain mitochondria (mtCB1), although they are usually considered specifically targeted to plasma membrane. Acute activation of mtCB1 alters mitochondrial ATP generation, synaptic transmission, and memory performance. However, the detailed mechanism linking disrupted mitochondrial metabolism and synaptic transmission is still uncharacterized. Read More

    Broad Chromatin Domains: An Important Facet of Genome Regulation.
    Bioessays 2017 Oct 23. Epub 2017 Oct 23.
    The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom.
    Chromatin composition differs across the genome, with distinct compositions characterizing regions associated with different properties and functions. Whereas many histone modifications show local enrichment over genes or regulatory elements, marking can also span large genomic intervals defining broad chromatin domains. Here we highlight structural and functional features of chromatin domains marked by histone modifications, with a particular emphasis on the potential roles of H3K27 methylation domains in the organization and regulation of genome activity in metazoans. Read More

    Animal Models in Translational Research: Rosetta Stone or Stumbling Block?
    Bioessays 2017 Oct 20. Epub 2017 Oct 20.
    Department of Biological Sciences, University of New Hampshire, Durham, NH, USA.
    Leading animal models are powerful tools for translational research, but they also present obstacles. Poorly conducted preclinical research in animals is a common cause of translational failure, but even when such research is well-designed and carefully executed, challenges remain. In particular, dominant models may bias research directions, elide essential aspects of human disease, omit important context, or subtly shift research targets. Read More

    Crowd-Sourcing of Membrane Fission: How crowding of non-specialized membrane-bound proteins contributes to cellular membrane fission.
    Bioessays 2017 Oct 20. Epub 2017 Oct 20.
    Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France.
    Fission of cellular membranes is ubiquitous and essential for life. Complex protein machineries, such as the dynamin and ESCRT spirals, have evolved to mediate membrane fission during diverse cellular processes, for example, vesicle budding. A new study suggests that non-specialized membrane-bound proteins can induce membrane fission through mass action due to protein crowding. Read More

    Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods: Computational methods to discover and quantify isoforms with alternative untranslated regions.
    Bioessays 2017 Oct 20. Epub 2017 Oct 20.
    Institute of Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
    In this review we highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events in high-throughput transcriptomic data. The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by the position at which transcription starts and ends at a genomic locus. Although the extent of alternative transcription starts and alternative poly-adenylation sites has been revealed by sequencing methods focused on the ends of transcripts, the application of these methods is not yet widely adopted by the community. Read More

    Science: How the Status Quo Harms its Cultural Authority.
    Bioessays 2017 Oct 16. Epub 2017 Oct 16.
    School of Natural and Built Environments, University of South Australia, Mawson Lakes, South Australia, 5095, Australia.
    Three distinct explanatory models are described which underpin the relationship between the cultural authority of science and public trust. This essay describes how current discourses framed around how the enterprise of science is undertaken; damage these models, diminishing knowledge-attitudes, alienating the public while reducing the cultural meaning of science. Read More

    How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications.
    Bioessays 2017 Oct 16. Epub 2017 Oct 16.
    Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
    Nucleosomes "talk" to each other about their modification state to form extended domains of modified histones independently of the underlying DNA sequence. At the same time, DNA elements promote modification of nucleosomes in their vicinity. How do these site-specific and histone-based activities act together to regulate spreading of histone modifications along the genome? How do they enable epigenetic memory to preserve cell identity? Many models for the dynamics of repressive histone modifications emphasize the role of strong positive feedback loops, which reinforce histone modifications by recruiting histone modifiers to preexisting modifications. Read More

    The Function of the Golgi Ribbon Structure - An Enduring Mystery Unfolds!
    Bioessays 2017 Nov 6;39(11). Epub 2017 Oct 6.
    The Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.
    The Golgi apparatus in vertebrate cells consists of individual Golgi stacks fused together in a continuous ribbon structure. The ribbon structure per se is not required to mediate the classical functions of this organelle and the relevance of the "ribbon" structure has been a mystery since first identified ultrastructurally in the 1950s. Recent advances recognize a role for the Golgi apparatus in a range of cellular processes, some mediated by signaling networks which are regulated at the Golgi. Read More

    Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger.
    Bioessays 2017 Oct 6. Epub 2017 Oct 6.
    Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Sheffield, UK.
    Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations. Read More

    How and Why to Build a Unified Tree of Life.
    Bioessays 2017 Nov 5;39(11). Epub 2017 Oct 5.
    Ottawa, ON, Canada.
    Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life? Read More

    Nanog Expression in Embryonic Stem Cells - An Ideal Model System to Dissect Enhancer Function.
    Bioessays 2017 Oct 4. Epub 2017 Oct 4.
    Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
    Embryonic stem cells (ESCs) are derived from the preimplantation embryo and can differentiate into virtually any other cell type (termed pluripotency), which is governed by lineage specific transcriptions factors (TFs) binding to cis regulatory elements (CREs) to mediate changes in gene expression. The reliance on transcriptional regulation to maintain pluripotency makes ESCs a valuable model to study the role of distal CREs such as enhancers in modulating gene expression to affect cell fate decisions. This review will highlight recent advance on transcriptional enhancers, focusing on studies performed in ESCs. Read More

    Phosphoinositide Diversity, Distribution, and Effector Function: Stepping Out of the Box.
    Bioessays 2017 Oct 4. Epub 2017 Oct 4.
    Graduate Program in Molecular Science, Ryerson University, Toronto ON, Canada M5B2K3.
    Phosphoinositides (PtdInsPs) modulate a plethora of functions including signal transduction and membrane trafficking. PtdInsPs are thought to consist of seven interconvertible species that localize to a specific organelle, to which they recruit a set of cognate effector proteins. Here, in reviewing the literature, we argue that this model needs revision. Read More

    RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective.
    Bioessays 2017 Nov 4;39(11). Epub 2017 Oct 4.
    Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland.
    RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO2 fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O2 , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Read More

    The Genes of Life and Death: A Potential Role for Placental-Specific Genes in Cancer: Active retrotransposons in the placenta encode unique functional genes that may also be used by cancer cells to promote malignancy.
    Bioessays 2017 Nov 4;39(11). Epub 2017 Oct 4.
    Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand.
    The placenta invades the adjacent uterus and controls the maternal immune system, like a cancer invades surrounding organs and suppresses the local immune response. Intriguingly, placental and cancer cells are globally hypomethylated and share an epigenetic phenomenon that is not well understood - they fail to silence repetitive DNA sequences (retrotransposons) that are silenced (methylated) in healthy somatic cells. In the placenta, hypomethylation of retrotransposons has facilitated the evolution of new genes essential for placental function. Read More

    Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease.
    Bioessays 2017 Oct 4. Epub 2017 Oct 4.
    Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.
    The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Read More

    A Brake for B Cell Proliferation: Appropriate responses to metabolic stress are crucial to maintain B cell viability and prevent malignant outgrowth.
    Bioessays 2017 Nov 29;39(11). Epub 2017 Sep 29.
    Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
    B cell activation is accompanied by metabolic adaptations to meet the increased energetic demands of proliferation. The metabolic composition of the microenvironment is known to change during a germinal center response, in inflamed tissue and to vary significantly between different organs. To sustain cellular homeostasis B cells need to be able to dynamically adapt to changes in their environment. Read More

    Physical Limits on the Precision of Mitotic Spindle Positioning by Microtubule Pushing forces: Mechanics of mitotic spindle positioning.
    Bioessays 2017 Nov 28;39(11). Epub 2017 Sep 28.
    Shriram Center for Chemical Engineering & Bioengineering, Stanford University, CA 94305, USA.
    Tissues are shaped and patterned by mechanical and chemical processes. A key mechanical process is the positioning of the mitotic spindle, which determines the size and location of the daughter cells within the tissue. Recent force and position-fluctuation measurements indicate that pushing forces, mediated by the polymerization of astral microtubules against- the cell cortex, maintain the mitotic spindle at the cell center in Caenorhabditis elegans embryos. Read More

    The Other Face of an Editor: ADAR1 Functions in Editing-Independent Ways.
    Bioessays 2017 Nov 28;39(11). Epub 2017 Sep 28.
    Department of Cell and Developmental Biology Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.
    The RNA editing enzyme ADAR1 seemingly has more functions besides RNA editing. Mouse models lacking ADAR1 and sensors of foreign RNA show that RNA editing by ADAR1 plays a crucial role in the innate immune response. Still, RNA editing alone cannot explain all observed phenotypes. Read More

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    Bioessays 2017 Oct;39(10)
    The image on this frontispiece shows a schematic of the human brain surrounded by choanoflagellates, filastereans, ichthyosporeans (the closest unicellular relatives of animals), sponges and ctenophores (early branching animals). Recent work highlights how these different, but extremely important organisms provide us with a new understanding on the evolutionary origin of synapses and neurons , as summarized in article 1700024 by Pawel Burkhardt and Simon G. Sprecher. Read More

    DNA Methylation in Embryo Development: Epigenetic Impact of ART (Assisted Reproductive Technologies).
    Bioessays 2017 Nov 21;39(11). Epub 2017 Sep 21.
    Physiology of Reproduction Group, University of Murcia, Murcia, Spain.
    DNA methylation can be considered a component of epigenetic memory with a critical role during embryo development, and which undergoes dramatic reprogramming after fertilization. Though it has been a focus of research for many years, the reprogramming mechanism is still not fully understood. Recent results suggest that absence of maintenance at DNA replication is a major factor, and that there is an unexpected role for TET3-mediated oxidation of 5mC to 5hmC in guarding against de novo methylation. Read More

    ADNP Plays a Key Role in Autophagy: From Autism to Schizophrenia and Alzheimer's Disease.
    Bioessays 2017 Nov 21;39(11). Epub 2017 Sep 21.
    The Lily and Avraham Gildor Chair for the Investigation of Growth Factors The Elton Laboratory for Neuroendocrinology Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv 69978, Israel.
    Activity-dependent neuroprotective protein (ADNP), discovered in our laboratory in 1999, has been characterized as a master gene vital for mammalian brain formation. ADNP de novo mutations in humans result in a syndromic form of autism-like spectrum disorder (ASD), including cognitive and motor deficits, the ADNP syndrome (Helsmoortel-Van Der Aa). One of the most important cellular processes associated with ADNP is the autophagy pathway, recently discovered by us as a key player in the pathophysiology of schizophrenia. Read More

    Cell Polarity and Notch Signaling: Linked by the E3 Ubiquitin Ligase Neuralized?
    Bioessays 2017 Nov 21;39(11). Epub 2017 Sep 21.
    Institut Pasteur,, Dept of Developmental and Stem Cell Biology, F-75015, Paris, France.
    Notch is a mechanosensitive receptor that requires direct cell-cell contact for its activation. Both the strength and the range of notch signaling depend on the size and geometry of the contact sites between cells. These properties of cell-cell contacts in turn depend on cell shape and polarity. Read More

    Intrinsically Disordered Proteins and Desiccation Tolerance: Elucidating Functional and Mechanistic Underpinnings of Anhydrobiosis.
    Bioessays 2017 Nov 13;39(11). Epub 2017 Sep 13.
    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
    Over 300 years ago the father of microscopy, Antonie van Leeuwenhoek, observed dried rotifers (tiny animals) "coming back to life" upon rehydration. Since then, scientists have been fascinated by the enduring mystery of how certain organisms survive losing essentially drying out completely. Historically sugars, such as the disaccharide trehalose, have been viewed as major functional mediators of desiccation tolerance. Read More

    Bacterial Translocation Ratchets: Shared Physical Principles with Different Molecular Implementations: How bacterial secretion systems bias Brownian motion for efficient translocation of macromolecules.
    Bioessays 2017 Oct 12;39(10). Epub 2017 Sep 12.
    Department of Physics Universität zu Köln, Köln, Nordrhein-Westfalen, Germany.
    Secretion systems enable bacteria to import and secrete large macromolecules including DNA and proteins. While most components of these systems have been identified, the molecular mechanisms of macromolecular transport remain poorly understood. Recent findings suggest that various bacterial secretion systems make use of the translocation ratchet mechanism for transporting polymers across the cell envelope. Read More

    Interpreting clinical trial results by deductive reasoning: In search of improved trial design.
    Bioessays 2017 Oct 11;39(10). Epub 2017 Sep 11.
    Clinic for Anesthesiology, Zagreb University Hospital Center, Zagreb, Croatia.
    Clinical trial results are often interpreted by inductive reasoning, in a trial design-limited manner, directed toward modifications of the current clinical practice. Deductive reasoning is an alternative in which results of relevant trials are combined in indisputable premises that lead to a conclusion easily testable in future trials. Read More

    Integrin-FAK-CDC42-PP1A signaling gnaws at YAP/TAZ activity to control incisor stem cells.
    Bioessays 2017 Oct 11;39(10). Epub 2017 Sep 11.
    Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
    How epithelial tissues are able to self-renew to maintain homeostasis and regenerate in response to injury remains a persistent question. The transcriptional effectors YAP and TAZ are increasingly being recognized as central mediators of epithelial stem cell biology, and a wealth of recent studies have been directed at understanding the control and activity of these factors. Recent work by Hu et al. Read More

    PTEN in the maintenance of genome integrity: From DNA replication to chromosome segregation.
    Bioessays 2017 Oct 11;39(10). Epub 2017 Sep 11.
    Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
    Faithful DNA replication and accurate chromosome segregation are the key machineries of genetic transmission. Disruption of these processes represents a hallmark of cancer and often results from loss of tumor suppressors. PTEN is an important tumor suppressor that is frequently mutated or deleted in human cancer. Read More

    Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis.
    Bioessays 2017 Oct 8;39(10). Epub 2017 Sep 8.
    Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Site Jacques Monod, Lyon, France.
    The biogenesis of RNAs and proteins is a threat to the cell. Indeed, the act of transcription and nascent RNAs challenge DNA stability. Both RNAs and nascent proteins can also initiate the formation of toxic aggregates because of their physicochemical properties. Read More

    Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors.
    Bioessays 2017 Oct 8;39(10). Epub 2017 Sep 8.
    School of Systems Biology, George Mason University, Fairfax, VA, USA.
    Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 (CMV) and few other proteins encoded by Herpesviridae, Nef (HIV-1), E1A (human adenovirus 1), NS5A (HCV), PB2 (influenza), HN (human parainfluenza virus 3), L83L (African swine fever), MC155R (molluscum contagiosum virus), other Poxviridae proteins, and some bacteriophages of human associated bacteria. Read More

    The promise and peril of CRISPR gene drives: Genetic variation and inbreeding may impede the propagation of gene drives based on the CRISPR genome editing technology.
    Bioessays 2017 Oct 1;39(10). Epub 2017 Sep 1.
    Department of Biology, Indiana University, Bloomington, IN, USA.
    Gene drives are selfish genetic elements that use a variety of mechanisms to ensure they are transmitted to subsequent generations at greater than expected frequencies. Synthetic gene drives based on the clustered regularly interspersed palindromic repeats (CRISPR) genome editing system have been proposed as a way to alter the genetic characteristics of natural populations of organisms relevant to the goals of public health, conservation, and agriculture. Here, we review the principles and potential applications of CRISPR drives, as well as means proposed to prevent their uncontrolled spread. Read More

    Evolutionary origin of synapses and neurons - Bridging the gap.
    Bioessays 2017 Oct 1;39(10). Epub 2017 Sep 1.
    Institute of Cell and Developmental Biology, Department of Biology, University of Fribourg, Fribourg, Switzerland.
    The evolutionary origin of synapses and neurons is an enigmatic subject that inspires much debate. Non-bilaterian metazoans, both with and without neurons and their closest relatives already contain many components of the molecular toolkits for synapse functions. The origin of these components and their assembly into ancient synaptic signaling machineries are particularly important in light of recent findings on the phylogeny of non-bilaterian metazoans. Read More

    Cancer: Towards a general theory of the target: All successful cancer therapies, actual or potential, are reducible to either (or both) of two fundamental strategies.
    Bioessays 2017 Sep;39(9)
    The University of Western Ontario - Oncology, Ontario, Canada.
    General theories (GT) are reductionist explications of apparently independent facts. Here, in reviewing the literature, I develop a GT to simplify the cluttered landscape of cancer therapy targets by revealing they cluster parsimoniously according to only a few underlying principles. The first principle is that targets can be only exploited by either or both of two fundamentally different approaches: causality-inhibition, and 'acausal' recognition of some marker or signature. Read More

    TssA: The cap protein of the Type VI secretion system tail.
    Bioessays 2017 Oct 17;39(10). Epub 2017 Aug 17.
    Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université - CNRS, Marseille, France.
    The Type VI secretion system (T6SS) is a multiprotein and mosaic apparatus that delivers protein effectors into prokaryotic or eukaryotic cells. Recent data on the enteroaggregative Escherichia coli (EAEC) T6SS have provided evidence that the TssA protein is a key component during T6SS biogenesis. The T6SS comprises a trans-envelope complex that docks the baseplate, a cytoplasmic complex that represents the assembly platform for the tail. Read More

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