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  1. added 2020-05-13
    Philosophy of Immunology.Bartlomiej Swiatczak & Alfred I. Tauber - 2020 - Stanford Encyclopedia of Philosophy 2020.
    Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...)
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  2. added 2020-02-16
    Evidence, Errors, and Ethics.Franklin G. Miller, Steven Joffe & Aaron S. Kesselheim - 2014 - Perspectives in Biology and Medicine 57 (3):299-307.
    Novel therapeutics enter human testing after they show promise in animal and in vitro studies. They then begin a life cycle that extends from early phase trials without control groups, to randomized trials, to approval by regulatory authorities, to coverage by payers, to use in clinical practice. At each stage, scientific evidence is critical to determining whether to progress to the next step in this life cycle. Each of these decisions also implicitly involves issues of value and ethical norms based (...)
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  3. added 2020-02-11
    Philosophy of Experimental Biology.Jacob Stegenga - 2009 - Erkenntnis 71 (3):431-436.
    Philosophers have committed sins while studying science, it is said – philosophy of science focused on physics to the detriment of biology, reconstructed idealizations of scientific episodes rather than attending to historical details, and focused on theories and concepts to the detriment of experiments. Recent generations of philosophers of science have tried to atone for these sins, and by the 1980s the exculpation was in full swing. Marcel Weber’s Philosophy of Experimental Biology is a zenith mea culpa for philosophy of (...)
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  4. added 2020-02-11
    In Mendel's Mirror: Philosophical Reflections on Biology.M. Weisberg - 2005 - Philosophical Review 114 (3):419-423.
  5. added 2020-02-05
    A General Theory of Oxygen Toxicity in Man.D. R. Shanklin - 1969 - Perspectives in Biology and Medicine 13 (1):80-100.
  6. added 2020-02-05
    The Chemical Dynamics of Bone Mineral by William F. Neuman and Margaret W. Neuman.Smith Freeman - 1958 - Perspectives in Biology and Medicine 2 (1):122-123.
  7. added 2020-02-04
    Carotenoid Pigments and Protection Against Photosensitization: How Studies in Bacteria Suggested a Treatment for a Human Disease.Micheline M. Mathews-Roth - 1984 - Perspectives in Biology and Medicine 28 (1):127-139.
  8. added 2019-09-09
    Racial Realism I: Are Biological Races Real?Quayshawn Spencer - 2018 - Philosophy Compass 13 (1).
    In this article, I discuss and critique how metaphysicians of race have conceived of and defended racial realism according to how biologists use “race”. I start by defining “racial realism” in the broadest accepted way in the metaphysics of race. Next, I summarize a representative sample of recent attempts from metaphysicians of race and biologists to defend racial realism and the main criticisms against each attempt. I discuss how metaphysicians of race have defended racial realism according to how ordinary people (...)
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  9. added 2019-08-08
    Ridurre il riduzionismo genetico.Gereon Wolters - 2008 - Humana Mente 2 (6).
    n this article the author develops a critique of reductionism in biological sciences from three different points of view. The first is related to the problem of reduction in the context of scientific theories. More specifically, reduction deals with a special form of intertheoretic relationship between molecular biology and the rest of biology. The second meaning of reductionism has to do with the significance of its genetic outfit for the ontogeny of an organism, i.e. its development from zygote to its (...)
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  10. added 2019-07-08
    Synthetic Versus Analytic Approaches to Protein and DNA Structure Determination.Agnes Bolinska - 2018 - Biology and Philosophy 33 (3-4):26.
    The structures of protein and DNA were discovered primarily by means of synthesizing component-level information about bond types, lengths, and angles, rather than analyzing X-ray diffraction photographs of these molecules. In this paper, I consider the synthetic and analytic approaches to exemplify alternative heuristics for approaching mid-twentieth-century macromolecular structure determination. I argue that the former was, all else being equal, likeliest to generate the correct structure in the shortest period of time. I begin by characterizing problem solving in these cases (...)
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  11. added 2019-06-24
    Indispensability and Effectiveness of Diagrams in Molecular Biology.Javier Anta - 2019 - Quaderns de Filosofia 6 (1):29-46.
    In this paper I aim to defend a twofold thesis. On one hand, I will sup-port, against Perini [7], the indispensability of diagrams when structurally complex biomolecules are concerned, since it is not possible to satisfactorily use linguistic-sentential representations at that domain. On the other hand, even when diagrams are dispensable I will defend than they will generally be more effective than other representations in encoding biomolecular knowledge, relying on Kulvicki-Shimojima’s diagrammatic effectiveness thesis. Finally, I will ground many epistemic virtues (...)
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  12. added 2019-06-12
    Theory Testing in Experimental Biology: The Chemiosmotic Mechanism of ATP Synthesis.Marcel Weber - 2002 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 33 (1):29-52.
    Historians of biology have argued that much of the dynamics of experimental disciplines such as genetics or molecular biology can be understood from studying experimental systems and model organisms alone . Such accounts contrast sharply with more traditional philosophies of science which viewed scientific research essentially as a process of inventing and testing theories. I present a case from the history of biochemistry which can be viewed from both the experimental systems perspective and from the methodology of theory testing. I (...)
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  13. added 2019-06-06
    Jan Sapp, Where the Truth Lies: Franz Moewus and the Origins of Molecular Biology. Cambridge: Cambridge University Press, 1990. Pp. Ix + 340. ISBN 0-521-36550-3, £30, $59.50 ; 0-521-36751-4, £15, $18.95. [REVIEW]David Bloor - 1993 - British Journal for the History of Science 26 (2):260-263.
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  14. added 2019-06-05
    Protein Transport Into Peroxisomes: Knowns and Unknowns.Tânia Francisco, Tony A. Rodrigues, Ana F. Dias, Aurora Barros-Barbosa, Diana Bicho & Jorge E. Azevedo - 2017 - Bioessays 39 (10):1700047.
    Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and rapidly transported into the organelle by a complex machinery. The data gathered in recent years suggest that this machinery operates through a syringe-like mechanism, in which the shuttling receptor PEX5 − the “plunger” − pushes a newly synthesized protein all the way through a peroxisomal transmembrane protein complex − the “barrel” − into the matrix of the organelle. Notably, insertion of cargo-loaded receptor into the “barrel” is an ATP-independent process, whereas extraction (...)
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  15. added 2019-06-05
    A Tale of TALE, PREP1, PBX1, and MEIS1: Interconnections and Competition in Cancer.Francesco Blasi, Chiara Bruckmann, Dmitry Penkov & Leila Dardaei - 2017 - Bioessays 39 (5).
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  16. added 2019-06-05
    Alternating pH Landscapes Shape Epithelial Cancer Initiation and Progression: Focus on Pancreatic Cancer.Stine F. Pedersen, Ivana Novak, Frauke Alves, Albrecht Schwab & Luis A. Pardo - 2017 - Bioessays 39 (6):1600253.
    We present here the hypothesis that the unique microenvironmental pH landscape of acid‐base transporting epithelia is an important factor in development of epithelial cancers, by rendering the epithelial and stromal cells pre‐adapted to the heterogeneous extracellular pH (pHe) in the tumor microenvironment. Cells residing in organs with net acid‐base transporting epithelia such as the pancreatic ductal and gastric epithelia are exposed to very different, temporally highly variable pHe values apically and basolaterally. This translates into spatially and temporally non‐uniform intracellular pH (...)
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  17. added 2019-06-05
    Mutations and Deletions of PRC2 in Prostate Cancer.Payal Jain & Luciano Di Croce - 2016 - Bioessays 38 (5):446-454.
    The Polycomb group of proteins (PcGs) are transcriptional repressor complexes that regulate important biological processes and play critical roles in cancer. Mutating or deleting EZH2 can have both oncogenic and tumor suppressive functions by increasing or decreasing H3K27me3. In contrast, mutations of SUZ12 and EED are reported to have tumor suppressive functions. EZH2 is overexpressed in many cancers, including prostate cancer, which can lead to silencing of tumor suppressors, genes regulating epithelial to mesenchymal transition (EMT), and interferon signaling. In some (...)
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  18. added 2019-05-30
    This is the Synthetic Biology That Is. [REVIEW]Daniel Liu - 2017 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 63:89-93.
    Review of: Sophia Roosth, Synthetic: How Life Got Made (University of Chicago Press, 2017); and Andrew S. Balmer, Katie Bulpin, and Susan Molyneux-Hodgson, Synthetic Biology: A Sociology of Changing Practices (Palgrave Macmillan, 2016).
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  19. added 2019-05-23
    Anthropocene: The philosophy of Biotechnology.Valentin Cheshko, Glazko Valery & Ivanitskaya Lida - 2018 - Moscow, Russia: Kurs INFRA-M.
    The theory of evolution of complex, including the humans system and algorithm for its constructing are a synthesis of evolutionary epistemology, philosophical anthropology and concrete scientific empirical basis in modern science,. In other words, natural philosophy is regaining the status bar element theoretical science in the era of technology-driven evolution. The co-evolutionary concept of 3-modal stable evolutionary strategy of Homo sapiens is developed. The concept based on the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path (...)
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  20. added 2019-04-21
    Human germline editing: a historical perspective.Michel Morange - 2017 - History and Philosophy of the Life Sciences 39 (4):34.
    The development of the genome editing system called CRISPR–Cas9 has opened a huge debate on the possibility of modifying the human germline. But the types of changes that could and/or ought to be made have not been discussed. To cast some light on this debate, I will describe the story of the CRISPR–Cas9 system. Then, I will briefly review the projects for modification of the human species that were discussed by biologists throughout the twentieth century. Lastly, I will show that (...)
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  21. added 2019-04-14
    Prenylation of Viral Proteins by Enzymes of the Host: Virus-Driven Rationale for Therapy with Statins and FT/GGT1 Inhibitors.Ekaterina S. Marakasova, Birgit Eisenhaber, Sebastian Maurer-Stroh, Frank Eisenhaber & Ancha Baranova - 2017 - Bioessays 39 (10):1700014.
    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 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, PB2, HN, L83L, (...)
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  22. added 2019-04-14
    Prenylation of Viral Proteins by Enzymes of the Host: Virus-Driven Rationale for Therapy with Statins and FT/GGT1 Inhibitors.S. Marakasova Ekaterina, Eisenhaber Birgit, Maurer‐Stroh Sebastian, Eisenhaber Frank & Baranova Ancha - 2017 - Bioessays 39 (10):1700014.
    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 and few other proteins encoded by Herpesviridae, Nef, E1A, NS5A, PB2, HN, L83L, (...)
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  23. added 2019-03-30
    Is “Wolf‐Pack” Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even When Working Alongside Kin.Rupert C. Marshall & David E. Whitworth - 2019 - Bioessays 41 (4):1800247.
    For decades, myxobacteria have been spotlighted as exemplars of social “wolf‐pack” predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. In contrast, there is accumulating evidence for predatory mechanisms promoting “selfish” behavior during predation, which together with conflicting definitions of cooperativity, casts doubt on whether microbial “wolf‐pack” predation (...)
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  24. added 2019-03-13
    Mechanisms in Practice: A Methodological Approach.Stavros Ioannidis & Stathis Psillos - 2018 - Journal of Evaluation in Clinical Practice 24 (5):1177-1183.
    In this paper we offer a minimal characterisation of the concept of mechanism in biomedicine, according to which a mechanism is a theoretically described causal pathway. We argue that this conceptionan be drawn from scientific practice, as illustrated by how a central biological and biomedical mechanism, the mechanism of apoptosis, was first identified and characterised. We will use the example of cytological and biochemical theoretical descriptions of the mechanism of apoptosis to draw lessons about the meaning of the concept of (...)
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  25. added 2019-03-07
    Causal Concepts in Biology: How Pathways Differ From Mechanisms and Why It Matters.Lauren N. Ross - forthcoming - British Journal for the Philosophy of Science:axy078.
    In the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term “mechanism” in their explanations of biological phenomena. While scientists appeal to a variety of causal concepts in their explanations, many philosophers argue or assume that all of these concepts are well understood with the single notion of mechanism. This reveals a significant problem with mainstream mechanistic accounts– although philosophers (...)
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  26. added 2019-01-31
    Evolution: A View From the 21st Century James Shapiro Upper Saddle River, NJ: FT Press Science, 2011.Alexander Powell - 2011 - Genomics, Society and Policy 7 (1):1-9.
  27. added 2019-01-27
    Mapping Biological Transmission: An Empirical, Dynamical, and Evolutionary Approach.Livio Riboli-Sasco & Francesca Merlin - 2017 - Acta Biotheoretica 65 (2):97-115.
    The current debate over extending inheritance and its evolutionary impact has focused on adding new categories of non-genetic factors to the classical transmission of DNA, and on trying to redefine inheritance. Transmitted factors have been mainly characterized by their directions of transmission and the way they store variations. In this paper, we leave aside the issue of defining inheritance. We rather try to build an evolutionary conceptual framework that allows for tracing most, if not all forms of transmission and makes (...)
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  28. added 2018-11-25
    Proton Gradients at the Origin of Life.Nick Lane - 2017 - Bioessays 39 (6):1600217.
    Chemiosmotic coupling − the harnessing of electrochemical ion gradients across membranes to drive metabolism − is as universally conserved as the genetic code. As argued previously in these pages, such deep conservation suggests that ion gradients arose early in evolution, and might have played a role in the origin of life. Alkaline hydrothermal vents harbour pH gradients of similar polarity and magnitude to those employed by modern cells, one of many properties that make them attractive models for life's origin. Their (...)
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  29. added 2018-11-25
    Mechanical Systems Biology of C. Elegans Touch Sensation.Michael Krieg, Alexander R. Dunn & Miriam B. Goodman - 2015 - Bioessays 37 (3):335-344.
    The sense of touch informs us of the physical properties of our surroundings and is a critical aspect of communication. Before touches are perceived, mechanical signals are transmitted quickly and reliably from the skin's surface to mechano‐electrical transduction channels embedded within specialized sensory neurons. We are just beginning to understand how soft tissues participate in force transmission and how they are deformed. Here, we review empirical and theoretical studies of single molecules and molecular ensembles thought to be involved in mechanotransmission (...)
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  30. added 2018-11-24
    Innovationstheorie und die Evolution menschlicher Fähigkeiten: Beispiel Empathie.Alfred Gierer - 1998 - Nova Acta Leopoldina 77 (304):85-98.
    A summarizing English version on “Theory of Innovation and the Evolution of General Human Capabilities, such as Cognition-based Empathy” is included in the download. Den biologisch modernen Menschentyp charakterisieren sehr allgemeine Fähigkeiten, wie begriffliche Sprache, strategisches Denken und kognitionsgestützte Empathie. Neurobiologisch kann Empathiefähigkeit als eine Verbindung von Repräsentationen von Mitmenschen mit dem je eigenen Gefühlszentren im Gehirn angesehen werden. In Grundzügen ist sie vor vielleicht 100 000 Jahren als Folge von Mutationen der Erbsubstanz DNA entstanden. Für solche genetische Innovationen spielten (...)
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  31. added 2018-11-18
    Script, Code, Information: How to Differentiate Analogies in the "Prehistory" of Molecular Biology.Werner Kogge - 2012 - History and Philosophy of the Life Sciences 34 (4):603-635.
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  32. added 2018-11-11
    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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  33. added 2018-11-11
    Surveillance of Retroelement Expression and Nucleic‐Acid Immunity by Histone Methyltransferase SETDB1.Yong‐Kook Kang - 2018 - Bioessays 40 (9):1800058.
    In human cancers, histone methyltransferase SETDB1 (SET domain, bifurcated 1) is frequently overexpressed but its significance in carcinogenesis remains elusive. A recent study shows that SETDB1 downregulation induces de‐repression of retroelements and innate immunity in cancer cells. The possibility of SETDB1 functioning as a surveillant of retroelement expression is discussed in this study: the cytoplasmic presence of retroelement‐derived nucleic acids (RdNAs) drives SETDB1 into the nucleus by the RNA‐interference route, rendering the corresponding retroelement transcriptionally inert. These RdNAs could, therefore, be (...)
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  34. added 2018-11-11
    The Light-Driven Sodium Ion Pump: A New Player in Rhodopsin Research.Hideaki E. Kato, Keiichi Inoue, Hideki Kandori & Osamu Nureki - 2016 - Bioessays 38 (12):1274-1282.
    Rhodopsins are one of the most studied photoreceptor protein families, and ion‐translocating rhodopsins, both pumps and channels, have recently attracted broad attention because of the development of optogenetics. Recently, a new functional class of ion‐pumping rhodopsins, an outward Na+ pump, was discovered, and following structural and functional studies enable us to compare three functionally different ion‐pumping rhodopsins: outward proton pump, inward Cl− pump, and outward Na+ pump. Here, we review the current knowledge on structure‐function relationships in these three light‐driven pumps, (...)
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  35. added 2018-11-11
    Golgi Defects Enhance APP Amyloidogenic Processing in Alzheimer's Disease.Gunjan Joshi & Yanzhuang Wang - 2015 - Bioessays 37 (3):240-247.
    Increased amyloid beta (Aβ) production by sequential cleavage of the amyloid precursor protein (APP) by the β‐ and γ‐secretases contributes to the etiological basis of Alzheimer's disease (AD). This process requires APP and the secretases to be in the same subcellular compartments, such as the endosomes. Since all membrane organelles in the endomembrane system are kinetically and functionally linked, any defects in the trafficking and sorting machinery would be expected to change the functional properties of the whole system. The Golgi (...)
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  36. added 2018-11-10
    Oxidative Stress Management in the Hair Follicle: Could Targeting NRF2 Counter Age-Related Hair Disorders and Beyond?Laura Jadkauskaite, Pierre A. Coulombe, Matthias Schäfer, Albena T. Dinkova-Kostova, Ralf Paus & Iain S. Haslam - 2017 - Bioessays 39 (8):1700029.
    Widespread expression of the transcription factor, nuclear factor (erythroid‐derived 2)‐like 2 (NRF2), which maintains redox homeostasis, has recently been identified in the hair follicle (HF). Small molecule activators of NRF2 may therefore be useful in the management of HF pathologies associated with redox imbalance, ranging from HF greying and HF ageing via androgenetic alopecia and alopecia areata to chemotherapy‐induced hair loss. Indeed, NRF2 activation has been shown to prevent peroxide‐induced hair growth inhibition. Multiple parameters can increase the levels of reactive (...)
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  37. added 2018-11-10
    Inflammation and Insulin Resistance: New Targets Encourage New Thinking.Andrew M. F. Johnson, Shaocong Hou & Pingping Li - 2017 - Bioessays 39 (9):1700036.
    Galectin-3 and LTB4 are pro-inflammatory molecules recently shown to directly cause insulin resistance in mouse and human cells. They are highly expressed in the obese state, and can be targeted both genetically and pharmacologically to improve insulin sensitivity in vivo. This expands on previous research showing that targeting inflammatory cytokines can be insulin sensitizing in animal models. However, translating these potential therapies into the human setting remains challenging. Here we review this latest research, and discuss how balancing their pleiotropic functions, (...)
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  38. added 2018-11-10
    A Brake for B Cell Proliferation.Julia Jellusova & Robert C. Rickert - 2017 - Bioessays 39 (11):1700079.
    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. An inability to take up and process available nutrients can result in impaired B cell growth and a diminished humoral immune response. (...)
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  39. added 2018-11-10
    Histone Chaperones FACT and Spt6 Prevent Histone Variants From Turning Into Histone Deviants.Célia Jeronimo & François Robert - 2016 - Bioessays 38 (5):420-426.
    Histone variants are specialized histones which replace their canonical counterparts in specific nucleosomes. Together with histone post‐translational modifications and DNA methylation, they contribute to the epigenome. Histone variants are incorporated at specific locations by the concerted action of histone chaperones and ATP‐dependent chromatin remodelers. Recent studies have shown that the histone chaperone FACT plays key roles in preventing pervasive incorporation of two histone variants: H2A.Z and CenH3/CENP‐A. In addition, Spt6, another histone chaperone, was also shown to be important for appropriate (...)
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  40. added 2018-11-09
    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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  41. added 2018-11-09
    The Microbiota‐Inflammasome Hypothesis of Major Depression.Antonio Inserra, Geraint B. Rogers, Julio Licinio & Ma‐Li Wong - 2018 - Bioessays 40 (9):1800027.
    We propose the “microbiota‐inflammasome” hypothesis of major depressive disorder (MDD, a mental illness affecting the way a person feels and thinks, characterized by long‐lasting feelings of sadness). We hypothesize that pathological shifts in gut microbiota composition (dysbiosis) caused by stress and gut conditions result in the upregulation of pro‐inflammatory pathways mediated by the Nod‐like receptors family pyrin domain containing 3 (NLRP3) inflammasome (an intracellular platform involved in the activation of inflammatory processes). This upregulation exacerbates depressive symptomatology and further compounds gut (...)
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  42. added 2018-11-04
    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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  43. added 2018-11-04
    Primary Cilia Reconsidered in the Context of Ciliopathies: Extraciliary and Ciliary Functions of Cilia Proteins Converge on a Polarity Theme?Kiet Hua & Russell J. Ferland - 2018 - Bioessays 40 (8):1700132.
    Once dismissed as vestigial organelles, primary cilia have garnered the interest of scientists, given their importance in development/signaling, and for their implication in a new disease category known as ciliopathies. However, many, if not all, “cilia” proteins also have locations/functions outside of the primary cilium. These extraciliary functions can complicate the interpretation of a particular ciliopathy phenotype: it may be a result of defects at the cilium and/or at extraciliary locations, and it could be broadly related to a unifying cellular (...)
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  44. added 2018-11-03
    Developmental Roles and Evolutionary Significance of AMPA‐Type Glutamate Receptors.Shinobu Hirai, Kohji Hotta & Haruo Okado - 2018 - Bioessays 40 (9):1800028.
    Organogenesis and metamorphosis require the intricate orchestration of multiple types of cellular interactions and signaling pathways. Glutamate (Glu) is an excitatory extracellular signaling molecule in the nervous system, while Ca2+ is a major intracellular signaling molecule. The first Glu receptors to be cloned are Ca2+‐permeable receptors in mammalian brains. Although recent studies have focused on Glu signaling in synaptic mechanisms of the mammalian central nervous system, it is unclear how this signaling functions in development. Our recent article demonstrated that Ca2+‐permeable (...)
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  45. added 2018-11-03
    The Future of Ancient DNA: Technical Advances and Conceptual Shifts.Michael Hofreiter, Johanna L. A. Paijmans, Helen Goodchild, Camilla F. Speller, Axel Barlow, Gloria G. Fortes, Jessica A. Thomas, Arne Ludwig & Matthew J. Collins - 2015 - Bioessays 37 (3):284-293.
    Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi‐fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and (...)
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  46. added 2018-11-03
    Synchronous tRNA Movements During Translocation on the Ribosome Are Orchestrated by Elongation Factor G and GTP Hydrolysis.Wolf Holtkamp, Wolfgang Wintermeyer & Marina V. Rodnina - 2014 - Bioessays 36 (10):908-918.
    The translocation of tRNAs through the ribosome proceeds through numerous small steps in which tRNAs gradually shift their positions on the small and large ribosomal subunits. The most urgent questions are: (i) whether these intermediates are important; (ii) how the ribosomal translocase, the GTPase elongation factor G (EF‐G), promotes directed movement; and (iii) how the energy of GTP hydrolysis is coupled to movement. In the light of recent advances in biophysical and structural studies, we argue that intermediate states of translocation (...)
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  47. added 2018-11-01
    Temporal and Spatial Regulation of mRNA Export: Single Particle RNA-Imaging Provides New Tools and Insights.Stephanie Heinrich, Carina Patrizia Derrer, Azra Lari, Karsten Weis & Ben Montpetit - 2017 - Bioessays 39 (2):1600124.
    The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA‐labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, (...)
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  48. added 2018-11-01
    Bacterial Translocation Ratchets: Shared Physical Principles with Different Molecular Implementations.Christof Hepp & Berenike Maier - 2017 - Bioessays 39 (10):1700099.
    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. Translocation ratchets are powered by chemical potential differences generated by concentration gradients of ions or molecules that are specific to the respective secretion systems. Bacteria employ these (...)
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  49. added 2018-11-01
    Local Sampling Paints a Global Picture: Local Concentration Measurements Sense Direction in Complex Chemical Gradients.Björn Hegemann & Matthias Peter - 2017 - Bioessays 39 (7):1600134.
    Detecting and interpreting extracellular spatial signals is essential for cellular orientation within complex environments, such as during directed cell migration or growth in multicellular development. Although the molecular understanding of how cells read spatial signals like chemical gradients is still lacking, recent work has revealed that stochastic processes at different temporal and spatial scales are at the core of this gradient sensing process in a wide range of eukaryotes. Fast biochemical reactions like those underlying GTPase activity dynamics form a functional (...)
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  50. added 2018-11-01
    Insider Trading: Extracellular Matrix Proteins and Their Non-Canonical Intracellular Roles.Andrew L. Hellewell & Josephine C. Adams - 2016 - Bioessays 38 (1):77-88.
    In metazoans, the extracellular matrix (ECM) provides a dynamic, heterogeneous microenvironment that has important supportive and instructive roles. Although the primary site of action of ECM proteins is extracellular, evidence is emerging for non‐canonical intracellular roles. Examples include osteopontin, thrombospondins, IGF‐binding protein 3 and biglycan, and relate to roles in transcription, cell‐stress responses, autophagy and cancer. These findings pose conceptual problems on how proteins signalled for secretion can be routed to the cytosol or nucleus, or can function in environments with (...)
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