Bioessays

ISSN: 0265-9247

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  1.  1
    Vasa, a regulator of localized mRNA translation on the spindle.Paola Alejandra Sundaram Buitrago, Kavya Rao & Mamiko Yajima - 2023 - Bioessays 45 (4):2300004.
    Localized mRNA translation is a biological process that allows mRNA to be translated on-site, which is proposed to provide fine control in protein regulation, both spatially and temporally within a cell. We recently reported that Vasa, an RNA-helicase, is a promising factor that appears to regulate this process on the spindle during the embryonic development of the sea urchin, yet the detailed roles and functional mechanisms of Vasa in this process are still largely unknown. In this review article, to elucidate (...)
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  2. Neddylation‐CRLs regulate the functions of Treg immune cells. Di Wu & Yi Sun - 2023 - Bioessays 45 (4):2200222.
    Neddylation, a ubiquitylation-like post-translational modification, is catalyzed by a cascade composed of three enzymes: E1 activating enzyme, E2 conjugating enzyme, and E3 ligase with cullins as physiological substrates. Specifically, neddylation E2 UBE2M couples with E3 RBX1 to neddylate cullins 1–4, whereas neddylation E2 UBE2F couples with E3 RBX2/SAG to neddylate cullin 5, leading to activation of CRL1-4 (Cullin-RING ligases 1–4) and CRL5, respectively. While over-activation of the neddylation-CRLs axis occurs frequently in many human cancers, how neddylation-CRLs regulate the function of (...)
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  3.  1
    The history and conceptual framework of assays and screens.Christopher J. Giacoletto & Martin R. Schiller - 2023 - Bioessays 45 (4):2200191.
    Since the 16th century, assays and screens have been essential for scientific investigation. However, most methods could be significantly improved, especially in accuracy, scalability, and often lack adequate comparisons to negative controls. There is a lack of consistency in distinguishing assays, in which accuracy is the main goal, from screens, in which scalability is prioritized over accuracy. We dissected and modernized the original definitions of assays and screens based upon recent developments and the conceptual framework of the original definitions. All (...)
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  4.  1
    Are secondary effects of bisphosphonates on the vascular system of bone contributing to increased risk for atypical femoral fractures in osteoporosis?David A. Hart - 2023 - Bioessays 45 (4):2200206.
    Osteoporosis (OP) is a bone disease which affects a number of post-menopausal females and puts many at risk for fractures. A large number of patients are taking bisphosphonates (BPs) to treat their OP and a rare complication is the development of atypical femoral fractures (AFF). No real explanations for the mechanisms underlying the basis for development of where AFF develop while on BPs has emerged. The present hypothesis will discuss the possibility that part of the risk for an AFF is (...)
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  5.  1
    Life of p: A consonant older than speech.Adriano R. Lameira & Steven Moran - 2023 - Bioessays 45 (4):2200246.
    Which sounds composed the first spoken languages? Archetypal sounds are not phylogenetically or archeologically recoverable, but comparative linguistics and primatology provide an alternative approach. Labial articulations are the most common speech sound, being virtually universal across the world's languages. Of all labials, the plosive ‘p’ sound, as in ‘Pablo Picasso’, transcribed /p/, is the most predominant voiceless sound globally and one of the first sounds to emerge in human infant canonical babbling. Global omnipresence and ontogenetic precocity imply that /p/-like sounds (...)
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  6.  3
    ORChestra coordinates the replication and repair music.Dazhen Liu, Jay Sonalkar & Supriya G. Prasanth - 2023 - Bioessays 45 (4):2200229.
    Error-free genome duplication and accurate cell division are critical for cell survival. In all three domains of life, bacteria, archaea, and eukaryotes, initiator proteins bind replication origins in an ATP-dependent manner, play critical roles in replisome assembly, and coordinate cell-cycle regulation. We discuss how the eukaryotic initiator, Origin recognition complex (ORC), coordinates different events during the cell cycle. We propose that ORC is the maestro driving the orchestra to coordinately perform the musical pieces of replication, chromatin organization, and repair.
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  7. Epigenetic rejuvenation by partial reprogramming.Deepika Puri & Wolfgang Wagner - 2023 - Bioessays 45 (4):2200208.
    Rejuvenation of cells by reprogramming toward the pluripotent state raises increasing attention. In fact, generation of induced pluripotent stem cells (iPSCs) completely reverses age-associated molecular features, including elongation of telomeres, resetting of epigenetic clocks and age-associated transcriptomic changes, and even evasion of replicative senescence. However, reprogramming into iPSCs also entails complete de-differentiation with loss of cellular identity, as well as the risk of teratoma formation in anti-ageing treatment paradigms. Recent studies indicate that partial reprogramming by limited exposure to reprogramming factors (...)
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  8.  1
    Emerging role of TAK1 in the regulation of skeletal muscle mass.Anirban Roy, Vihang A. Narkar & Ashok Kumar - 2023 - Bioessays 45 (4):2300003.
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  9. MED26‐containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies.Hidefumi Suzuki, Kazuki Furugori, Ryota Abe, Shintaro Ogawa, Sayaka Ito, Tomohiko Akiyama, Keiko Horiuchi & Hidehisa Takahashi - 2023 - Bioessays 45 (4):2200178.
    Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3′ Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) (...)
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  10.  1
    Deep into the niche: Deciphering local endoderm‐microenvironment interactions in development, homeostasis, and disease of pancreas and intestine.Wojciech J. Szlachcic, Katherine C. Letai, Marissa A. Scavuzzo & Malgorzata Borowiak - 2023 - Bioessays 45 (4):2200186.
    Unraveling molecular and functional heterogeneity of niche cells within the developing endoderm could resolve mechanisms of tissue formation and maturation. Here, we discuss current unknowns in molecular mechanisms underlying key developmental events in pancreatic islet and intestinal epithelial formation. Recent breakthroughs in single-cell and spatial transcriptomics, paralleled with functional studies in vitro, reveal that specialized mesenchymal subtypes drive the formation and maturation of pancreatic endocrine cells and islets via local interactions with epithelium, neurons, and microvessels. Analogous to this, distinct intestinal (...)
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  11.  3
    Distinct TssA proteins converge in coordinating tail biogenesis of the type VI secretion systems.Jemal Ali & Erh-Min Lai - 2023 - Bioessays 45 (2):2200219.
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  12.  1
    Ancient Darwinian replicators nested within eubacterial genomes.Frederic Bertels & Paul B. Rainey - 2023 - Bioessays 45 (2):2200085.
    Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non-autonomous MGEs whose duplication depends on non-jumping RAYT transposases. (...)
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  13.  1
    BTB domains: A structural view of evolution, multimerization, and protein–protein interactions.Artem Bonchuk, Konstantin Balagurov & Pavel Georgiev - 2023 - Bioessays 45 (2):2200179.
    Broad-complex, Tramtrack, and Bric-à-brac/poxvirus and zinc finger (BTB/POZ) is a conserved domain found in many eukaryotic proteins with diverse cellular functions. Recent studies revealed its importance in multiple developmental processes as well as in the onset and progression of oncological diseases. Most BTB domains can form multimers and selectively interact with non-BTB proteins. Structural studies of BTB domains delineated the presence of different interfaces involved in various interactions mediated by BTBs and provided a basis for the specific inhibition of distinct (...)
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  14.  16
    Biological sex is binary, even though there is a rainbow of sex roles.Wolfgang Goymann, Henrik Brumm & Peter M. Kappeler - 2023 - Bioessays 45 (2):2200173.
    Biomedical and social scientists are increasingly calling the biological sex into question, arguing that sex is a graded spectrum rather than a binary trait. Leading science journals have been adopting this relativist view, thereby opposing fundamental biological facts. While we fully endorse efforts to create a more inclusive environment for gender-diverse people, this does not require denying biological sex. On the contrary, the rejection of biological sex seems to be based on a lack of knowledge about evolution and it champions (...)
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  15.  8
    AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution.Khongpon Ponlachantra, Wipa Suginta, Robert C. Robinson & Yoshihito Kitaoku - 2023 - Bioessays 45 (2):2200119.
    The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, (...)
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  16.  1
    What connects splicing of transfer RNA precursor molecules with pontocerebellar hypoplasia?Samoil Sekulovski & Simon Trowitzsch - 2023 - Bioessays 45 (2):2200130.
    Transfer RNAs (tRNAs) represent the most abundant class of RNA molecules in the cell and are key players during protein synthesis and cellular homeostasis. Aberrations in the extensive tRNA biogenesis pathways lead to severe neurological disorders in humans. Mutations in the tRNA splicing endonuclease (TSEN) and its associated RNA kinase cleavage factor polyribonucleotide kinase subunit 1 (CLP1) cause pontocerebellar hypoplasia (PCH), a heterogeneous group of neurodegenerative disorders, that manifest as underdevelopment of specific brain regions typically accompanied by microcephaly, profound motor (...)
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  17. Wild animals as an underused treasure trove for studying the genetics of cancer.Tuul Sepp & Mathieu Giraudeau - 2023 - Bioessays 45 (2):2200188.
    Recent years have seen an emergence of the field of comparative cancer genomics. However, the advancements in this field are held back by the hesitation to use knowledge obtained from human studies to study cancer in other animals, and vice versa. Since cancer is an ancient disease that arose with multicellularity, oncogenes and tumour-suppressor genes are amongst the oldest gene classes, shared by most animal species. Acknowledging that other animals are, in terms of cancer genetics, ecology, and evolution, rather similar (...)
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  18.  3
    MicroRNAs play regulatory roles in genomic balance.Xiaowen Shi, Hua Yang & James A. Birchler - 2023 - Bioessays 45 (2):2200187.
    Classic genetics studies found that genomic imbalance caused by changing the dosage of part of the genome (aneuploidy) has more detrimental effects than altering the dosage of the whole genome (ploidy). Previous analysis revealed global modulation of gene expression triggered by aneuploidy across various species, including maize (Zea mays), Arabidopsis, yeast, mammals, etc. Plant microRNAs (miRNAs) are a class of 20- to 24-nt endogenous small noncoding RNAs that carry out post-transcriptional gene expression regulation. That miRNAs and their putative targets are (...)
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  19. Ancient endosymbiont‐mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes.Gaurav G. Shimpi & Bastian Bentlage - 2023 - Bioessays 45 (2):2200190.
    In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature (...)
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  20. Three dimensions of thermolabile sex determination.Paul D. Waters, Jennifer A. Marshall Graves, Sarah L. Whiteley, Arthur Georges & Aurora Ruiz-Herrera - 2023 - Bioessays 45 (2):2200123.
    The molecular mechanism of temperature-dependent sex determination (TSD) is a long-standing mystery. How is the thermal signal sensed, captured and transduced to regulate key sex genes? Although there is compelling evidence for pathways via which cells capture the temperature signal, there is no known mechanism by which cells transduce those thermal signals to affect gene expression. Here we propose a novel hypothesis we call 3D-TSD (the three dimensions of thermolabile sex determination). We postulate that the genome has capacity to remodel (...)
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  21.  7
    Endosymbiotic ratchet accelerates divergence after organelle origin.Debashish Bhattacharya, Julia Van Etten, L. Felipe Benites & Timothy G. Stephens - 2023 - Bioessays 45 (1):2200165.
    We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne) in accelerating divergence (...)
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  22.  1
    Introducing a new rubric in BioEssays: Reviews.Kerstin Brachhold - 2023 - Bioessays 45 (1):2200216.
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  23.  3
    How germline genes promote malignancy in cancer cells.Jan Willem Bruggeman, Jan Koster, Ans M. M. van Pelt, Dave Speijer & Geert Hamer - 2023 - Bioessays 45 (1):2200112.
    Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a “germline program” promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a (...)
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  24.  1
    Beyond the GTP‐cap: Elucidating the molecular mechanisms of microtubule catastrophe.Veronica J. Farmer & Marija Zanic - 2023 - Bioessays 45 (1):2200081.
    Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The “standard model” of microtubule dynamics implicates a “cap” of GTP-bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP-cap leads to microtubule “catastrophe,” a switch-like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo-EM, and computational modeling approaches, challenge the simple GTP-cap (...)
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  25.  4
    On the origin of plastids.Peter G. Kroth - 2023 - Bioessays 45 (1):2200217.
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  26.  12
    No neonates without adults.Noah B. Lemke, Amy Jean Dickerson & Jeffery K. Tomberlin - 2023 - Bioessays 45 (1):2200162.
    With the potential to process the world's agricultural and food waste, provide sustainable fodder for livestock, aquaculture, and pet animals, as well as act as a source of novel biomolecules, the black soldier fly, Hermetia illucens, has been launched into the leading position within the insects as feed industry. Fulfilment of these goals, however, requires mass-rearing facilities to have a steady supply of neonate larvae, which in-turn requires an efficient mating process to yield fertile eggs; yet, little is known about (...)
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  27.  1
    Acid digestion and symbiont: Proton sharing at the origin of mitochondriogenesis?Mario Mencía - 2023 - Bioessays 45 (1):2200136.
    The initial relationships between organisms leading to endosymbiosis and the first eukaryote are currently a topic of hot debate. Here, I present a theory that offers a gradual scenario in which the origins of phagocytosis and mitochondria are intertwined in such a way that the evolution of one would not be possible without the other. In this scenario, the premitochondrial bacterial symbiont became initially associated with a protophagocytic host on the basis of cooperation to kill prey with symbiont-produced toxins and (...)
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  28.  1
    Somatic cancers: Hijacking germ cell immortality tools.Ewa Rajpert-De Meyts - 2023 - Bioessays 45 (1):2200212.
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  29.  5
    From correlation to causation: The new frontier of transgenerational epigenetic inheritance.Mohd Hafiz Rothi & Eric Lieberman Greer - 2023 - Bioessays 45 (1):2200118.
    While heredity is predominantly controlled by what deoxyribonucleic acid (DNA) sequences are passed from parents to their offspring, a small but growing number of traits have been shown to be regulated in part by the non-genetic inheritance of information. Transgenerational epigenetic inheritance is defined as heritable information passed from parents to their offspring without changing the DNA sequence. Work of the past seven decades has transitioned what was previously viewed as rare phenomenology, into well-established paradigms by which numerous traits can (...)
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  30.  2
    Epigenetics across the evolutionary tree: New paradigms from non‐model animals.Kirsten C. Sadler - 2023 - Bioessays 45 (1):2200036.
    All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude (...)
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  31. Chromosomal breaks at the origin of small tandem DNA duplications.Joost Schimmel, Marloes D. van Wezel, Robin van Schendel & Marcel Tijsterman - 2023 - Bioessays 45 (1):2200168.
    Small tandem DNA duplications in the range of 15 to 300 base-pairs play an important role in the aetiology of human disease and contribute to genome diversity. Here, we discuss different proposed mechanisms for their occurrence and argue that this type of structural variation mainly results from mutagenic repair of chromosomal breaks. This hypothesis is supported by both bioinformatical analysis of insertions occurring in the genome of different species and disease alleles, as well as by CRISPR/Cas9-based experimental data from different (...)
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  32.  2
    Transcription‐independent functions of p53 in DNA repair pathway selection.Yu-Hsiu Wang & Michael P. Sheetz - 2023 - Bioessays 45 (1):2200122.
    Recently discovered transcription-independent features of p53 involve the choice of DNA damage repair pathway after PARylation, and p53's complex formation with phosphoinositide lipids, PI(4,5)P2. PARylation-mediated rapid accumulation of p53 at DNA damage sites is linked to the recruitment of downstream repair factors and tumor suppression. This links p53's capability to sense damaged DNA in vitro and its relevant functions in cells. Further, PI(4,5)P2 rapidly accumulates at damage sites like p53 and complexes with p53, while it is required for ATR recruitment. (...)
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