Bioessays

ISSN: 0265-9247

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  1.  26
    Chewing through challenges: Exploring the evolutionary pathways to wood‐feeding in insects.Cristian F. Beza-Beza, Brian M. Wiegmann, Jessica A. Ware, Matt Petersen, Nicole Gunter, Marissa E. Cole, Melbert Schwarz, Matthew A. Bertone, Daniel Young & Aram Mikaelyan - 2024 - Bioessays 46 (5):2300241.
    Decaying wood, while an abundant and stable resource, presents considerable nutritional challenges due to its structural rigidity, chemical recalcitrance, and low nitrogen content. Despite these challenges, certain insect lineages have successfully evolved saproxylophagy (consuming and deriving sustenance from decaying wood), impacting nutrient recycling in ecosystems and carbon sequestration dynamics. This study explores the uneven phylogenetic distribution of saproxylophagy across insects and delves into the evolutionary origins of this trait in disparate insect orders. Employing a comprehensive analysis of gut microbiome data, (...)
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  2.  9
    Strengths and opportunities in research into extracellular matrix ageing: A consultation with the ECMage research community.Matthew J. Dalby, Vanja Pekovic-Vaughan, Daryl P. Shanley, Joe Swift, Lisa J. White & Elizabeth G. Canty-Laird - 2024 - Bioessays 46 (5):2300223.
    Ageing causes progressive decline in metabolic, behavioural, and physiological functions, leading to a reduced health span. The extracellular matrix (ECM) is the three‐dimensional network of macromolecules that provides our tissues with structure and biomechanical resilience. Imbalance between damage and repair/regeneration causes the ECM to undergo structural deterioration with age, contributing to age‐associated pathology. The ECM ‘Ageing Across the Life Course’ interdisciplinary research network (ECMage) was established to bring together researchers in the United Kingdom, and internationally, working on the emerging field (...)
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  3.  5
    New approaches for low phototoxicity imaging of living cells and tissues.Wiktoria Kasprzycka, Wiktoria Szumigraj, Przemysław Wachulak & Elżbieta Anna Trafny - 2024 - Bioessays 46 (5):2300122.
    Fluorescence microscopy is a powerful tool used in scientific and medical research, but it is inextricably linked to phototoxicity. Neglecting phototoxicity can lead to erroneous or inconclusive results. Recently, several reports have addressed this issue, but it is still underestimated by many researchers, even though it can lead to cell death. Phototoxicity can be reduced by appropriate microscopic techniques and carefully designed experiments. This review focuses on recent strategies to reduce phototoxicity in microscopic imaging of living cells and tissues. We (...)
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  4.  6
    Looking across the gap: Understanding the evolution of eyes and vision among insects.Maike Kittelmann & Alistair P. McGregor - 2024 - Bioessays 46 (5):2300240.
    The compound eyes of insects exhibit stunning variation in size, structure, and function, which has allowed these animals to use their vision to adapt to a huge range of different environments and lifestyles, and evolve complex behaviors. Much of our knowledge of eye development has been learned from Drosophila, while visual adaptations and behaviors are often more striking and better understood from studies of other insects. However, recent studies in Drosophila and other insects, including bees, beetles, and butterflies, have begun (...)
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  5.  6
    The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling.Oné R. Pagán - 2024 - Bioessays 46 (5):2300195.
    Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well‐established lock‐and‐key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor‐mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed (...)
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  6.  9
    Activating the abscission checkpoint: Top2α senses chromatin bridges in cytokinesis.Eleni Petsalaki & George Zachos - 2024 - Bioessays 46 (5):2400011.
    How chromatin bridges are detected by the abscission checkpoint during mammalian cell division is unknown. Here, we discuss recent findings from our lab showing that the DNA topoisomerase IIα (Top2α) enzyme binds to catenated (“knotted”) DNA next to the midbody and forms abortive Top2‐DNA cleavage complexes (Top2ccs) on chromatin bridges. Top2ccs are then processed by the proteasome to promote localization of the DNA damage sensor protein Rad17 to Top2‐generated double‐strand DNA ends on DNA knots. In turn, Rad17 promotes local recruitment (...)
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  7.  12
    How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.Dave Speijer - 2024 - Bioessays 46 (5):2300193.
    Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss (...)
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  8.  21
    The contours of evolution: In defence of Darwin's tree of life paradigm.Peter T. S. van der Gulik, Wouter D. Hoff & Dave Speijer - 2024 - Bioessays 46 (5):2400012.
    Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept (...)
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  9.  8
    Towards an integrated understanding of inflammatory pathway influence on hematopoietic stem and progenitor cell differentiation.Michael Allara & Juliet R. Girard - 2024 - Bioessays 46 (4):2300142.
    Recent research highlights that inflammatory signaling pathways such as pattern recognition receptor (PRR) signaling and inflammatory cytokine signaling play an important role in both on‐demand hematopoiesis as well as steady‐state hematopoiesis. Knockout studies have demonstrated the necessity of several distinct pathways in these processes, but often lack information about the contribution of specific cell types to the phenotypes in question. Transplantation studies have increased the resolution to the level of specific cell types by testing the necessity of inflammatory pathways specifically (...)
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  10.  10
    Epistemic misalignments in microbiome research.Federico Boem & Javier Suárez - 2024 - Bioessays 46 (4):2300220.
    We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call “epistemic misalignment.” An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epistemic misalignments, due (...)
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  11.  7
    Are fetal microchimerism and circulating fetal extracellular vesicles important links between spontaneous preterm delivery and maternal cardiovascular disease risk?Elizabeth A. Bonney, Ryan C. V. Lintao, Carolyn M. Zelop, Ananth Kumar Kammala & Ramkumar Menon - 2024 - Bioessays 46 (4):2300170.
    Trafficking and persistence of fetal microchimeric cells (fMCs) and circulating extracellular vesicles (EVs) have been observed in animals and humans, but their consequences in the maternal body and their mechanistic contributions to maternal physiology and pathophysiology are not yet fully defined. Fetal cells and EVs may help remodel maternal organs after pregnancy‐associated changes, but the cell types and EV cargos reaching the mother in preterm pregnancies after exposure to various risk factors can be distinct from term pregnancies. As preterm delivery‐associated (...)
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  12.  7
    Clathrin controls bidirectional communication between T cells and antigen presenting cells.Audun Kvalvaag & Michael L. Dustin - 2024 - Bioessays 46 (4):2300230.
    In circulation, T cells are spherical with selectin enriched dynamic microvilli protruding from the surface. Following extravasation, these microvilli serve another role, continuously surveying their environment for antigen in the form of peptide‐MHC (pMHC) expressed on the surface of antigen presenting cells (APCs). Upon recognition of their cognate pMHC, the microvilli are initially stabilized and then flatten into F‐actin dependent microclusters as the T cell spreads over the APC. Within 1–5 min, clathrin is recruited by the ESCRT‐0 component Hrs to (...)
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  13.  8
    Aggression modulator: Understanding the multifaceted role of the dorsal raphe nucleus.Koshiro Mitsui & Aki Takahashi - 2024 - Bioessays 46 (4):2300213.
    Aggressive behavior is instinctively driven behavior that helps animals to survive and reproduce and is closely related to multiple behavioral and physiological processes. The dorsal raphe nucleus (DRN) is an evolutionarily conserved midbrain structure that regulates aggressive behavior by integrating diverse brain inputs. The DRN consists predominantly of serotonergic (5‐HT:5‐hydroxytryptamine) neurons and decreased 5‐HT activity was classically thought to increase aggression. However, recent studies challenge this 5‐HT deficiency model, revealing a more complex role for the DRN 5‐HT system in aggression. (...)
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  14.  18
    The evosystem: A centerpiece for evolutionary studies.François Papale, Fabrice Not, Éric Bapteste & Louis-Patrick Haraoui - 2024 - Bioessays 46 (4):2300169.
    In this paper, we redefine the target of evolutionary explanations by proposing the “evosystem” as an alternative to populations, lineages and species. Evosystems account for changes in the distribution of heritable variation within individual Darwinian populations (evolution by natural selection, drift, or constructive neutral evolution), but also for changes in the networks of interactions within or between Darwinian populations and changes in the abiotic environment (whether these changes are caused by the organic entities or not). The evosystem can thereby become (...)
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  15.  10
    MYRF: A unique transmembrane transcription factor‐ from proteolytic self‐processing to its multifaceted roles in animal development.Yingchuan B. Qi, Zhimin Xu, Shiqian Shen, Zhao Wang & Zhizhi Wang - 2024 - Bioessays 46 (4):2300209.
    The Myelin Regulator Factor (MYRF) is a master regulator governing myelin formation and maintenance in the central nervous system. The conservation of MYRF across metazoans and its broad tissue expression suggest it has functions extending beyond the well‐established role in myelination. Loss of MYRF results in developmental lethality in both invertebrates and vertebrates, and MYRF haploinsufficiency in humans causes MYRF‐related Cardiac Urogenital Syndrome, underscoring its importance in animal development; however, these mechanisms are largely unexplored. MYRF, an unconventional transcription factor, begins (...)
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  16.  7
    Symbiont effector‐guided mapping of proteins in plant networks to improve crop climate stress resilience.Laura Rehneke & Patrick Schäfer - 2024 - Bioessays 46 (4):2300172.
    There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe‐derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential of (...)
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  17.  13
    Are non‐protein coding RNAs junk or treasure?Nils G. Walter - 2024 - Bioessays 46 (4):2300201.
    The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non‐protein coding, or non‐coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is “junk”, a term still championed by some geneticists and evolutionary biologists. In contrast, (...)
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  18.  4
    NLRC5/MHC class I transactivator: A key target for immune escape by SARS‐CoV‐2.Baohui Zhu, Ryota Ouda, Yusuke Kasuga, Paul de Figueiredo & Koichi S. Kobayashi - 2024 - Bioessays 46 (4):2300109.
    Antigen presentation to CD8+ T cells by MHC class I molecules is essential for host defense against viral infections. Various mechanisms have evolved in multiple viruses to escape immune surveillance and defense to support viral proliferation in host cells. Through in vitro SARS‐CoV‐2 infection studies and analysis of COVID‐19 patient samples, we found that SARS‐CoV‐2 suppresses the induction of the MHC class I pathway by inhibiting the expression and function of NLRC5, a major transcriptional regulator of MHC class I genes. (...)
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  19.  9
    Design patterns of biological cells.Steven S. Andrews, H. Steven Wiley & Herbert M. Sauro - 2024 - Bioessays 46 (3):2300188.
    Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns (...)
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  20.  14
    Isthmin‐1: A critical regulator of branching morphogenesis and metanephric mesenchyme condensation during early kidney development.Ge Gao & Zhongjun Zhou - 2024 - Bioessays 46 (3):2300189.
    Isthmin‐1 (Ism1) was first described to be syn‐expressed with Fgf8 in Xenopus. However, its biological role has not been elucidated until recent years. Despite of accumulated evidence that Ism1 participates in angiogenesis, tumor invasion, macrophage apoptosis, and glucose metabolism, the cognate receptors for Ism1 remain largely unknown. Ism1 deficiency in mice results in renal agenesis (RA) with a transient loss of Gdnf transcription and impaired mesenchyme condensation at E11.5. Ism1 binds to and activates Integrin α8β1 to positively regulate Gdnf/Ret signaling, (...)
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  21.  14
    Sulfonylurea receptor 2 (SUR2), intricate sensors for intracellular Mg‐nucleotides.Tianyi Hou & Lei Chen - 2024 - Bioessays 46 (3):2300151.
    SUR2, similar to SUR1, is a regulatory subunit of the ATP‐sensitive potassium channel (KATP), which plays a key role in numerous important physiological processes and is implicated in various diseases. Recent structural studies have revealed that, like SUR1, SUR2 can undergo ligand‐dependent dynamic conformational changes, transitioning between an inhibitory inward‐facing conformation and an activating occluded conformation. In addition, SUR2 possesses a unique inhibitory Regulatory helix (R helix) that is absent in SUR1. The binding of the activating Mg‐ADP to NBD2 of (...)
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  22.  10
    Assembling the thymus medulla: Development and function of epithelial cell heterogeneity.Kieran D. James, Emilie J. Cosway, Sonia M. Parnell, Andrea J. White, William E. Jenkinson & Graham Anderson - 2024 - Bioessays 46 (3):2300165.
    The thymus is a unique primary lymphoid organ that supports the production of self‐tolerant T‐cells essential for adaptive immunity. Intrathymic microenvironments are microanatomically compartmentalised, forming defined cortical, and medullary regions each differentially supporting critical aspects of thymus‐dependent T‐cell maturation. Importantly, the specific functional properties of thymic cortical and medullary compartments are defined by highly specialised thymic epithelial cells (TEC). For example, in the medulla heterogenous medullary TEC (mTEC) contribute to the enforcement of central tolerance by supporting deletion of autoreactive T‐cell (...)
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  23.  8
    Contrasting views on the role of AMPK in autophagy.Do-Hyung Kim - 2024 - Bioessays 46 (3):2300211.
    Efficient management of low energy states is vital for cells to maintain basic functions and metabolism and avoid cell death. While autophagy has long been considered a critical mechanism for ensuring survival during energy depletion, recent research has presented conflicting evidence, challenging the long‐standing concept. This recent development suggests that cells prioritize preserving essential cellular components while restraining autophagy induction when cellular energy is limited. This essay explores the conceptual discourse on autophagy regulation during energy stress, navigating through the studies (...)
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  24.  21
    Endosteal stem cells at the bone‐blood interface: A double‐edged sword for rapid bone formation.Yuki Matsushita, Jialin Liu, Angel Ka Yan Chu, Wanida Ono, Joshua D. Welch & Noriaki Ono - 2024 - Bioessays 46 (3):2300173.
    Endosteal stem cells are a subclass of bone marrow skeletal stem cell populations that are particularly important for rapid bone formation occurring in growth and regeneration. These stem cells are strategically located near the bone surface in a specialized microenvironment of the endosteal niche. These stem cells are abundant in young stages but eventually depleted and replaced by other stem cell types residing in a non‐endosteal perisinusoidal niche. Single‐cell molecular profiling and in vivo cell lineage analyses play key roles in (...)
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  25.  7
    Interactions between neural cells and blood vessels in central nervous system development.Keiko Morimoto, Hidenori Tabata, Rikuo Takahashi & Kazunori Nakajima - 2024 - Bioessays 46 (3):2300091.
    The sophisticated function of the central nervous system (CNS) is largely supported by proper interactions between neural cells and blood vessels. Accumulating evidence has demonstrated that neurons and glial cells support the formation of blood vessels, which in turn, act as migratory scaffolds for these cell types. Neural progenitors are also involved in the regulation of blood vessel formation. This mutual interaction between neural cells and blood vessels is elegantly controlled by several chemokines, growth factors, extracellular matrix, and adhesion molecules (...)
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  26.  10
    Significance of the anterior cingulate cortex in neurogenesis plasticity: Connections, functions, and disorders across postnatal and adult stages.Moawiah M. Naffaa - 2024 - Bioessays 46 (3):2300160.
    The anterior cingulate cortex (ACC) is a complex and continually evolving brain region that remains a primary focus of research due to its multifaceted functions. Various studies and analyses have significantly advanced our understanding of how the ACC participates in a wide spectrum of memory and cognitive processes. However, despite its strong connections to brain areas associated with hippocampal and olfactory neurogenesis, the functions of the ACC in regulating postnatal and adult neurogenesis in these regions are still insufficiently explored. Investigating (...)
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  27.  9
    The logic of protein post‐translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments.Marcin J. Suskiewicz - 2024 - Bioessays 46 (3):2300178.
    Protein post‐translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half‐life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino‐acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory (...)
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  28.  8
    More than a bystander: RNAs specify multifaceted behaviors of liquid‐liquid phase‐separated biomolecular condensates.Hui Zheng & Hong Zhang - 2024 - Bioessays 46 (3):2300203.
    Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid‐liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid‐like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of (...)
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  29.  19
    The role of secondary structures in the functioning of 3′ untranslated regions of mRNA.Mariya Zhukova, Paul Schedl & Yulii V. Shidlovskii - 2024 - Bioessays 46 (3):2300099.
    Abstract3′ untranslated regions (3′ UTRs) of mRNAs have many functions, including mRNA processing and transport, translational regulation, and mRNA degradation and stability. These different functions require cis‐elements in 3′ UTRs that can be either sequence motifs or RNA structures. Here we review the role of secondary structures in the functioning of 3′ UTRs and discuss some of the trans‐acting factors that interact with these secondary structures in eukaryotic organisms. We propose potential participation of 3′‐UTR secondary structures in cytoplasmic polyadenylation in (...)
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  30.  12
    Origin and development of primary animal epithelia.Sophia Doerr, Phillip Zhou & Katerina Ragkousi - 2024 - Bioessays 46 (2):2300150.
    Epithelia are the first organized tissues that appear during development. In many animal embryos, early divisions give rise to a polarized monolayer, the primary epithelium, rather than a random aggregate of cells. Here, we review the mechanisms by which cells organize into primary epithelia in various developmental contexts. We discuss how cells acquire polarity while undergoing early divisions. We describe cases where oriented divisions constrain cell arrangement to monolayers including organization on top of yolk surfaces. We finally discuss how epithelia (...)
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  31.  9
    Founding the Wnt gene family: How wingless was found to be a positional signal and oncogene homolog.Nicholas E. Baker - 2024 - Bioessays 46 (2):2300156.
    The Wnt family of developmental regulators were named after the Drosophila segmentation gene wingless and the murine proto‐oncogene int‐1. Homology between these two genes connected oncogenesis to cell‐cell signals in development. I review how wingless was initially characterized, and cloned, as part of the quest to identify developmental cell‐to‐cell signals, based on predictions of the Positional Information Model, and on the properties of homeotic and segmentation gene mutants. The requirements and cell‐nonautonomy of wingless in patterning multiple embryonic and adult structures (...)
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  32.  9
    Diversity and functional specialization of H3K9‐specific histone methyltransferases.Dmitry E. Koryakov - 2024 - Bioessays 46 (2):2300163.
    Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact (...)
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  33.  10
    Towards understanding how bisphosphonate‐dependent alterations to nutrient canal integrity can contribute to risk for atypical femoral fractures: Biomechanical considerations and potential relationship to a real‐world analogy.David A. Hart - 2024 - Bioessays 46 (2):2300117.
    Bisphosphonates are a class of drugs which have shown good efficacy in the treatment of post‐menopausal osteoporosis, as well as a good safety profile. However, side‐effects such as risk for atypical femoral fractures (AFF) have appeared, leading to a decline in use of the drugs by many patients who would benefit from the treatment. While patient characteristics have contributed to improved understanding of risk factors, the mechanisms involved that explain AFF risk have not appeared. Recently, the possibility that the mechanism(s) (...)
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  34.  4
    DREAM a little dREAM of DRM: Model organisms and conservation of DREAM‐like complexes.Marion Hoareau, Aurore Rincheval-Arnold, Sébastien Gaumer & Isabelle Guénal - 2024 - Bioessays 46 (2):2300125.
    DREAM complexes are transcriptional regulators that control the expression of hundreds to thousands of target genes involved in the cell cycle, quiescence, differentiation, and apoptosis. These complexes contain many subunits that can vary according to the considered target genes. Depending on their composition and the nature of the partners they recruit, DREAM complexes control gene expression through diverse mechanisms, including chromatin remodeling, transcription cofactor and factor recruitment at various genomic binding sites. This complexity is particularly high in mammals. Since the (...)
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  35.  9
    D‐galactose might mediate some of the skeletal muscle hypertrophy‐promoting effects of milk—A nutrient to consider for sarcopenia?Jan Homolak, Ana Babic Perhoc, Davor Virag, Ana Knezovic, Jelena Osmanovic Barilar & Melita Salkovic-Petrisic - 2024 - Bioessays 46 (2):2300061.
    Sarcopenia is a process of progressive aging‐associated loss of skeletal muscle mass (SMM) recognized as a serious global health issue contributing to frailty and increased all‐cause mortality. Exercise and nutritional interventions (particularly intake of dairy products and milk) demonstrate good efficacy, safety, and broad applicability. Here, we propose that at least some of the well‐documented favorable effects of milk and milk‐derived protein supplements on SMM might be mediated by D‐galactose, a monosaccharide present in large quantities in milk in the form (...)
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  36.  11
    From pixels to insights: Machine learning and deep learning for bioimage analysis.Mahta Jan, Allie Spangaro, Michelle Lenartowicz & Mojca Mattiazzi Usaj - 2024 - Bioessays 46 (2):2300114.
    Bioimage analysis plays a critical role in extracting information from biological images, enabling deeper insights into cellular structures and processes. The integration of machine learning and deep learning techniques has revolutionized the field, enabling the automated, reproducible, and accurate analysis of biological images. Here, we provide an overview of the history and principles of machine learning and deep learning in the context of bioimage analysis. We discuss the essential steps of the bioimage analysis workflow, emphasizing how machine learning and deep (...)
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  37.  25
    Mutation and evolution: Conceptual possibilities.Adi Livnat & Alan C. Love - 2024 - Bioessays 46 (2):2300025.
    Although random mutation is central to models of evolutionary change, a lack of clarity remains regarding the conceptual possibilities for thinking about the nature and role of mutation in evolution. We distinguish several claims at the intersection of mutation, evolution, and directionality and then characterize a previously unrecognized category: complex conditioned mutation. Empirical evidence in support of this category suggests that the historically famous fluctuation test should be revisited, and new experiments should be undertaken with emerging experimental techniques to facilitate (...)
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  38.  8
    Telomere length is not a useful tool for chronological age estimation in animals.Michael L. Pepke - 2024 - Bioessays 46 (2):2300187.
    Telomeres are short repetitive DNA sequences capping the ends of chromosomes. Telomere shortening occurs during cell division and may be accelerated by oxidative damage or ameliorated by telomere maintenance mechanisms. Consequently, telomere length changes with age, which was recently confirmed in a large meta‐analysis across vertebrates. However, based on the correlation between telomere length and age, it was concluded that telomere length can be used as a tool for chronological age estimation in animals. Correlation should not be confused with predictability, (...)
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  39.  13
    Telomeres cooperate with the nuclear envelope to maintain genome stability.Rekha Rai, Tori Sodeinde, Ava Boston & Sandy Chang - 2024 - Bioessays 46 (2):2300184.
    Mammalian telomeres have evolved safeguards to prevent their recognition as DNA double‐stranded breaks by suppressing the activation of various DNA sensing and repair proteins. We have shown that the telomere‐binding proteins TRF2 and RAP1 cooperate to prevent telomeres from undergoing aberrant homology‐directed recombination by mediating t‐loop protection. Our recent findings also suggest that mammalian telomere‐binding proteins interact with the nuclear envelope to maintain chromosome stability. RAP1 interacts with nuclear lamins through KU70/KU80, and disruption of RAP1 and TRF2 function result in (...)
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  40.  11
    Nuclear envelope budding: Getting large macromolecular complexes out of the nucleus.Kevin C. Sule, Mitsutoshi Nakamura & Susan M. Parkhurst - 2024 - Bioessays 46 (2):2300182.
    Transport of macromolecules from the nucleus to the cytoplasm is essential for nearly all cellular and developmental events, and when mis‐regulated, is associated with diseases, tumor formation/growth, and cancer progression. Nuclear Envelope (NE)‐budding is a newly appreciated nuclear export pathway for large macromolecular machineries, including those assembled to allow co‐regulation of functionally related components, that bypasses canonical nuclear export through nuclear pores. In this pathway, large macromolecular complexes are enveloped by the inner nuclear membrane, transverse the perinuclear space, and then (...)
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  41.  10
    Environmental factor reversibly determines cellular identity through opposing Integrators that unify epigenetic and transcriptional pathways.Hiroki Takahashi, Ryo Ito, Yoshihiro Matsumura & Juro Sakai - 2024 - Bioessays 46 (2):2300084.
    Organisms must adapt to environmental stresses to ensure their survival and prosperity. Different types of stresses, including thermal, mechanical, and hypoxic stresses, can alter the cellular state that accompanies changes in gene expression but not the cellular identity determined by a chromatin state that remains stable throughout life. Some tissues, such as adipose tissue, demonstrate remarkable plasticity and adaptability in response to environmental cues, enabling reversible cellular identity changes; however, the mechanisms underlying these changes are not well understood. We hypothesized (...)
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  42.  9
    The early dorsal signal in vertebrate embryos requires endolysosomal membrane trafficking.Yagmur Azbazdar & Edward M. De Robertis - 2024 - Bioessays 46 (1):2300179.
    Fertilization triggers cytoplasmic movements in the frog egg that lead in mysterious ways to the stabilization of β‐catenin on the dorsal side of the embryo. The novel Huluwa (Hwa) transmembrane protein, identified in China, is translated specifically in the dorsal side, acting as an egg cytoplasmic determinant essential for β‐catenin stabilization. The Wnt signaling pathway requires macropinocytosis and the sequestration inside multivesicular bodies (MVBs, the precursors of endolysosomes) of Axin1 and Glycogen Synthase Kinase 3 (GSK3) that normally destroy β‐catenin. In (...)
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  43.  5
    The eukaryotic translation initiation factor eIF4E unexpectedly acts in splicing thereby coupling mRNA processing with translation.Katherine L. B. Borden - 2024 - Bioessays 46 (1):2300145.
    Recent findings position the eukaryotic translation initiation factor eIF4E as a novel modulator of mRNA splicing, a process that impacts the form and function of resultant proteins. eIF4E physically interacts with the spliceosome and with some intron‐containing transcripts implying a direct role in some splicing events. Moreover, eIF4E drives the production of key components of the splicing machinery underpinning larger scale impacts on splicing. These drive eIF4E‐dependent reprogramming of the splicing signature. This work completes a series of studies demonstrating eIF4E (...)
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  44.  11
    The longevity bottleneck hypothesis: Could dinosaurs have shaped ageing in present‐day mammals?João Pedro de Magalhães - 2024 - Bioessays 46 (1):2300098.
    The evolution and biodiversity of ageing have long fascinated scientists and the public alike. While mammals, including long‐lived species such as humans, show a marked ageing process, some species of reptiles and amphibians exhibit very slow and even the absence of ageing phenotypes. How can reptiles and other vertebrates age slower than mammals? Herein, I propose that evolving during the rule of the dinosaurs left a lasting legacy in mammals. For over 100 million years when dinosaurs were the dominant predators, (...)
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  45.  6
    Isotope effects on radical pair performance in cryptochrome: A new hypothesis for the evolution of animal migration.Ismael Galván, Abbas Hassasfar, Betony Adams & Francesco Petruccione - 2024 - Bioessays 46 (1):2300152.
    Mechanisms occurring at the atomic level are now known to drive processes essential for life, as revealed by quantum effects on biochemical reactions. Some macroscopic characteristics of organisms may thus show an atomic imprint, which may be transferred across organisms and affect their evolution. This possibility is considered here for the first time, with the aim of elucidating the appearance of an animal innovation with an unclear evolutionary origin: migratory behaviour. This trait may be mediated by a radical pair (RP) (...)
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  46.  13
    Emerging small molecule inhibitors of Bach1 as therapeutic agents: Rationale, recent advances, and future perspectives.Dmitry M. Hushpulian, Navneet Ammal Kaidery, Debashis Dutta, Sudarshana M. Sharma, Irina Gazaryan & Bobby Thomas - 2024 - Bioessays 46 (1):2300176.
    The transcription factor Nrf2 is the master regulator of cellular stress response, facilitating the expression of cytoprotective genes, including those responsible for drug detoxification, immunomodulation, and iron metabolism. FDA‐approved Nrf2 activators, Tecfidera and Skyclarys for patients with multiple sclerosis and Friedreich's ataxia, respectively, are non‐specific alkylating agents exerting side effects. Nrf2 is under feedback regulation through its target gene, transcriptional repressor Bach1. Specifically, in Parkinson's disease and other neurodegenerative diseases with Bach1 dysregulation, excessive Bach1 accumulation interferes with Nrf2 activation. Bach1 (...)
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  47.  10
    Re‐examining the evidence that ivermectin induces a melanoma‐like state in Xenopus embryos.Ainsley Hutchison, Chiedza Sibanda, Mackenzie Hulme, Sarah Anwar, Bengisu Gur, Rachael Thomas & Laura Anne Lowery - 2024 - Bioessays 46 (1):2300143.
    Modeling metastasis in animal systems has been an important focus for developing cancer therapeutics. Xenopus laevis is a well‐established model, known for its use in identifying genetic mechanisms underlying diseases and disorders in humans. Prior literature has suggested that the drug, ivermectin, can be used in Xenopus to induce melanocytes to convert into a metastatic melanoma‐like state, and thus could be ideal for testing possible melanoma therapies in vivo. However, there are notable inconsistencies between ivermectin studies in Xenopus and the (...)
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  48.  6
    Loss of DNA methylation disrupts syncytiotrophoblast development: Proposed consequences of aberrant germline gene activation.Georgia Lea & Courtney W. Hanna - 2024 - Bioessays 46 (1):2300140.
    DNA methylation is a repressive epigenetic modification that is essential for development and its disruption is widely implicated in disease. Yet, remarkably, ablation of DNA methylation in transgenic mouse models has limited impact on transcriptional states. Across multiple tissues and developmental contexts, the predominant transcriptional signature upon loss of DNA methylation is the de‐repression of a subset of germline genes, normally expressed in gametogenesis. We recently reported loss of de novo DNA methyltransferase DNMT3B resulted in up‐regulation of germline genes and (...)
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  49.  12
    Dynamic changes in ocular shape during human development and its implications for retina fovea formation.Ashley M. Rasys, Andrew Wegerski, Paul A. Trainor, Robert B. Hufnagel, Douglas B. Menke & James D. Lauderdale - 2024 - Bioessays 46 (1):2300054.
    The human fovea is known for its distinctive pit‐like appearance, which results from the displacement of retinal layers superficial to the photoreceptors cells. The photoreceptors are found at high density within the foveal region but not the surrounding retina. Efforts to elucidate the mechanisms responsible for these unique features have ruled out cell death as an explanation for pit formation and changes in cell proliferation as the cause of increased photoreceptor density. These findings have led to speculation that mechanical forces (...)
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  50.  9
    Lung patterning: Is a distal‐to‐proximal gradient of cell allocation and fate decision a general paradigm?Kuan Zhang, Thin Aung, Erica Yao & Pao-Tien Chuang - 2024 - Bioessays 46 (1):2300083.
    Recent studies support a model in which the progeny of SOX9+ epithelial progenitors at the distal tip of lung branches undergo cell allocation and differentiation sequentially along the distal‐to‐proximal axis. Concomitant with the elongation and ramification of lung branches, the descendants of the distal SOX9+ progenitors are distributed proximally, express SOX2, and differentiate into cell types in the conducting airways. Amid subsequent sacculation, the distal SOX9+ progenitors generate alveolar epithelial cells to form alveoli. Sequential cell allocation and differentiation are integrated (...)
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