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Moonlighting on the Fasciola hepatica tegument: enolase, a glycolytic enzyme, interacts with the extracellular matrix and fibrinolytic system of the host bioRxiv. Mol. Biol. Pub Date : 2024-03-18 Eve O'Kelly, Krystyna Cwiklinski, Carolina De Marco Verissimo, Nichola Eliza Davies Calvani, Jesús López Corrales, Heather Jewhurst, Andrew Flaus, Richard Lalor, Judit Serrat, John Pius Dalton, Javier González-Miguel
Enolase is a 47 kDa enzyme that functions within the glycolysis and gluconeogenesis pathways involved in the reversible conversion of D-2-phosphoglycerate (2PGA) to phosphoenolpyruvate (PEP). However, in the context of host-pathogen interactions, enolase from different species of parasites, fungi and bacteria have been shown to contribute to adhesion processes by binding to proteins of the host extracellular
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Insight from Wild Yeast Isolates into the Molecular Mechanisms of Lifespan Variation Mediated by Caloric Restriction bioRxiv. Mol. Biol. Pub Date : 2024-03-17 Samantha McLean, Mitchell Lee, Weiqiang Liu, Rohil Tantray, Vikas Anil Gujjala, Xuming Zhou, Matt Kaeberlein, Alaattin Kaya
Caloric restriction (CR) is known to extend lifespan across different species and holds great promise for preventing human age-onset pathologies. However, two major challenges exist. First, despite extensive research, the mechanisms of lifespan extension in response to CR remain elusive. Second, genetic differences causing variations in response to CR and genetic factors contributing to variability
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Stalling of Transcription by Putative G-quadruplex Sequences and CRISPR-dCas9 bioRxiv. Mol. Biol. Pub Date : 2024-03-17 Mohammed Enamul Hoque, Mohammad Lutful Kabir, Sajad Shiekh, Hamza Balci, Soumitra Basu
Putative G-quadruplex forming sequences (PQS) have been identified in promoter sequences of prominent genes that are implicated among others in cancer and neurological disorders. We explored mechanistic aspects of CRISPR-dCas9-mediated gene expression regulation, which is transient and sequence specific unlike alternative approaches that lack such specificity or create permanent mutations, using the
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End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Brandon Estrem, Richard E Davis, Jianbin Wang
Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little
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GNN codon adjacency regulates protein translation bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Joyce Sun, Pete Hwang, Eric D. Sakkas, Yancheng Zhou, Luis Perez, Ishani Dave, Jack B. Kwon, Audrey E. McMahon, Mia Wichman, Mitsu Raval, Kristen Scopino, Daniel Krizanc, Kelly M. Thayer, Michael P. Weir
The central dogma treats the ribosome as a molecular machine that reads one mRNA codon at a time as it adds each amino acid to its growing peptide chain. However, this and previous studies suggest that ribosomes actually perceive pairs of adjacent codons as they take three-nucleotide steps along the mRNA. We examined GNN codons which we find are surprisingly overrepresented in eukaryote protein-coding
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Alternative silencing states of Transposable Elements in Arabidopsis bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Valentin Hure, Florence Piron-Prunier, Tamara Yehouessi, Clementine Vitte, Aleksandra E. Kornienko, Gabriele Adam, Magnus Nordborg, Angelique Deleris
The DNA methylation/H3K9me2 and Polycomb-group proteins (PcG)-H3K27me3 pathways have long been considered mutually exclusive and specific to TEs and genes, respectively. However, H3K27me3 can be recruited to many TEs in the absence of DNA methylation machinery and sometimes also co-occur with DNA methylation. In this study, we show that TEs can also be solely targeted by H3K27me3 in wild-type Arabidopsis
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Single-animal, single-tube RNA extraction for quantitative analysis of transcripts in the tardigrade Hypsibius exemplaris bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Molly J. Kirk, Chaoming Xu, Joel H. Rothman
The tardigrade Hypsibius exemplaris is an emerging model organism renowned for its ability to survive environmental extremes.1 – 3 To explore the molecular mechanisms and genetic basis of such extremotolerance, many studies rely on transcriptional profiling4, 5 and RNA interference (RNAi)6 to define molecular targets. Such studies require efficient, accurate, and robust RNA extraction methods; however
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Ca2+-independent ZmCPK2 is inhibited by Ca2+-dependent ZmCPK17 during drought response in maize bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Xiaoying Hu, Jinkui Cheng, Minmin Lu, Yujuan Zhu, Tingting Fang, Zhen Li, Xiqing Wang, Yu Wang, Yan Guo, Shuhua Yang, Zhizhong Gong
Calcium oscillations are induced by different stresses. Calcium-dependent protein kinases (CDPKs/CPKs) are one major group of the plant calcium decoders that are involved in various processes including drought response. Some CPKs are calcium-independent. Here, we identified ZmCPK2 as a negative regulator of drought resistance by screening an overexpression transgenic maize pool. We found that ZmCPK2
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Cohesin regulates promoter-proximal pausing of RNA Polymerase II by limiting recruitment of super elongation complex bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Shoin Tei, Toyonori Sakata, Atsunori Yoshimura, Toyoaki Natsume, Masato T Kanemaki, Masashige Bando, Katsuhiko Shirahige
Cohesin is a ring-shaped complex, responsible for establishing sister chromatid cohesion and forming topologically associating domains (TADs) and chromatin loops. Loss-of-function mutations in cohesin subunits and its regulatory factors can cause Cornelia de Lange syndrome (CdLS). Because dysregulated gene expression was observed in CdLS, it has long been thought that cohesin plays a regulatory role
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A Mycobacterium tuberculosis secreted virulence factor disrupts host snRNP biogenesis bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Komal Chauhan, Nishat Passricha, Yogita Kapoor, Dipanwita Datta, Naresh Arora, Mrinmoy Das, Kavya Rao, Lakshyaveer Singh, Ravi Dutt, RamanDeep Sharma, Binayak Sarkar, Basanti Malakkar, Prince Saini, Lalita Mehra, Prasenjit Das, Vineet Ahuja, Amit Singhal, Vinay Nandicoori, Dhiraj Kumar
Mycobacterium tuberculosis (Mtb) infection of human macrophages triggers extensive dysregulation of host alternative splicing (AS). Here, we present an unexpected mechanism exploited by the Mtb to achieve the same. We identify several bacterial secretory proteins that interact with the host splicing factors (SFs) and alter select RNA splicing events in vitro, in cell and during ex vivo infections.
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RNA 3′ end tailing safeguards cells against products of pervasive transcription termination bioRxiv. Mol. Biol. Pub Date : 2024-03-16 Guifen Wu, Jerome O. Rouviere, Manfred Schmid, Torben Heick Jensen
Premature transcription termination yields a wealth of unadenylated (pA-) RNA. Although this can be targeted for degradation by the Nuclear EXosome Targeting (NEXT) complex, possible back-up pathways remain poorly understood. Here, we find RNA 3′ end uridylation and adenylation upon NEXT inactivation. U-tailed RNAs are generally short and modified by the cytoplasmic tailing enzymes, TUT4/7, following
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OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Simone Marini, Alexander Barquero, Anisha Ashok Wadhwani, Jiang Bian, Jamie Ruiz, Christina Boucher, Mattia Prosperi
Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in both clinical and environmental health, e.g., detection of bacterial outbreaks. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be
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Heterochromatin protein 1 (HP1) of Schistosoma mansoni: non-canonical chromatin landscape and fitness effects bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Natalia S da Trindade, Marilia Bergamini Valentini, Anne Rognon, Tiago Manuel Fernandes Mendes, Silmara Marques Allegretti, Christoph Grunau, Fernanda J Cabral
Heterochromatin protein 1 (HP1) is widespread in several organisms playing a role in control of gene expression by heterochromatin formation and maintenance of silent chromatin. Schistosoma mansoni is a human parasite that is responsible for Schistosomiasis, a tropical neglected disease in the tropical and subtropical areas in the world, where the intermediate host Biomphalaria glabrata is present
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BAK knockdown delays bleaching and alleviates oxidative DNA damage in a reef-building coral bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Eva Majerova, Camryn Steinle, Crawford Drury
Climate change is rapidly pushing coral reefs towards extinction. Efforts to restore and protect these ecosystems using resilient corals are increasing, but our understanding of cellular mechanisms of thermal resilience and trade-offs remains limited. Here, we demonstrate downregulation of pa-BAK slows bleaching and stabilizes the symbiosis during acute heat stress in Pocillopora acuta. Counterintuitively
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Non-prime- and Prime-side Profiling of Pro-Pro Endopeptidase Specificity Using Synthetic Combinatorial Peptide Libraries and Mass Spectrometry bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Bart Claushuis, Robert A. Cordfunke, Arnoud H. de Ru, Jordy van Angeren, Ulrich Baumann, Peter A. van Veelen, Manfred Wuhrer, Jeroen Corver, Jan Wouter Drijfhout, Paul Hensbergen
A group of bacterial proteases, the Pro-Pro endopeptidases (PPEPs), possess the unique ability to hydrolyze proline-proline bonds in proteins. Since a protease its function is largely determined by its substrate specificity, methods that can extensively characterize substrate specificity are valuable tools for protease research. Previously, we achieved an in-depth characterization of PPEP prime-side
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Transcription of damage-induced RNA in Arabidopsis was frequently initiated from DSB loci within the genic regions bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Kohei Kawaguchi, Soichirou Satoh, Junichi Obokata
DNA double-strand breaks (DSBs) are the most severe DNA lesions and need to be removed immediately to prevent loss of genomic information. Recently, it has been revealed that DSBs induce de novo transcription from the cleavage sites in various species, resulting in RNAs being referred to as damage-induced RNAs (diRNAs). While diRNA synthesis is an early event in the DNA damage response and plays an
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Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Ana Claudia Raposo, Paulo Caldas, Maria Arez, Joana Jeremias, Pedro Barbosa, Rui Sousa-Luis, Frederico Dias Agua, David Oxley, Annalisa Mupo Mupo, Melanie Eckersley-Maslin, Miguel Casanova, Ana Rita Grosso, Simao Teixeira da Rocha
During culture, female human pluripotent stem cells (hPSCs), including human induced PSCs (hiPSCs) exhibit a propensity for erosion of X-chromosome inactivation (XCI). This phenomenon is characterized by loss of XIST RNA expression and reactivation of a subset of X-linked genes from the inactive X chromosome (Xi). XCI erosion, despite its common occurrence, is often overlooked by the stem cell community
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ADMA-histones define genomic loading of Rhino at the initial step of piRNA cluster formation bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Raku Saito, Hirotsugu Ishizu, Ritsuko Harigai, Kensaku Murano, Mikiko C Siomi
In Drosophila germ cells, piRNAs arise from dual-strand piRNA clusters. These clusters are occupied by H3K9me3, but are transcribed from internal sites in a manner dependent on the binding of HP1 homolog Rhino to H3K9me3 on the clusters. However, how initial loading of Rhino onto the clusters occurs remains unknown. Here, we used cultured ovarian somatic cells (OSCs), which lack endogenous Rhino and
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asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Mara Stadler, Saulius Lukauskas, Till Bartke, Christian L Mueller
Chromatin, the nucleoprotein complex consisting of DNA and histone proteins, plays a crucial role in regulating gene expression by controlling access to DNA. Chromatin modifications are key players in this regulation, as they help to orchestrate DNA transcription, replication, and repair. These modifications recruit epigenetic "reader" proteins, which mediate downstream events. Most modifications occur
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Dynamic conformational changes of acid-sensing ion channels in different desensitizing conditions bioRxiv. Mol. Biol. Pub Date : 2024-03-15 Caroline Marcher Holm, Asli Bahar Topaktas, Johs Dannesboe, Stephan Alexander Pless, Stephanie Andrea Heusser
Acid-sensing ion channels (ASICs) are proton-gated cation channels that contribute to fast synaptic transmission and have roles in fear conditioning and nociception. Apart from activation at low pH, ASIC1a also undergoes several types of desensitization, including ′acute desensitization′ that terminates activation, ′steady-stated desensitization′ that occurs at sub-activating proton concentrations
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The specific AMPK activator A-769662 ameliorates pathological phenotypes following mitochondrial DNA depletion bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Gustavo Carvalho, Bruno Repolês, Tran V. H. Nguyen, Josefin M. E. Forslund, Farahnaz Ranjbarian, Isabela C Mendes, Micol Falabella, Mara Doimo, Sjoerd Wanrooij, Robert DS Pitceathly, Anders Hofer, Paulina H Wanrooij
AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis that also plays a role in preserving mitochondrial function and integrity. Upon a disturbance in the cellular energy state that increases AMP levels, AMPK activity promotes a switch from anabolic to catabolic metabolism to restore energy homeostasis. However, it is currently unclear how severe of a mitochondrial
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Structures of transcription-translation coupling complexes at each stage of the translation cycle bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Jing Zhang, Guoliang Lu, Wei Zhou, Mingxia Yang, Li Li, Huihui Shao, Xiaogen Zhou, Changbin Chen, Yue Gao, Richard H. Ebright, Jinzhong Lin, Chengyuan Wang
Bacterial transcription and translation are frequently linked through a transcribing RNA polymerase following the leading ribosome, a process termed transcription-translation coupling (TTC). Two distinct TTC structures, the collied-TTC (TTC-A) and the coupled-TTC (TTC-B), have been reported, but the biological significance of both complexes is still subject to uncertainty. Furthermore, the ribosomes
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A small molecule inhibitor Mirin prevents TOP3A-dependent mtDNA breakage and segregation bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Koit Aasumets, Anu Hangas, Cyrielle P. J. Bader, Direnis Erdinc, Sjoerd Wanrooij, Paulina H Wanrooij, Steffi Goffart, Jaakko L.O Pohjoismaki
Mirin, the chemical inhibitor of MRE11, has been recently reported to prevent immune response activation caused by mitochondrial DNA (mtDNA) breakage and release upon replication stalling. We show here that Mirin prevents mitochondrial replication fork breakage in mitochondrial 3'-exonuclease MGME1 deficient cells and the resulting innate immune response induction, but that this occurs independently
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FTO-mediated m6A demethylation of ULK1 mRNA promotes autophagy and activation of hepatic stellate cells in liver fibrosis bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Tingjuan Huang, Chunhong Zhang, Junjie Ren, Qizhi Shuai, Xiaonan Li, Xuewei Li, Jun Xie, Jun Xu
The activation of hepatic stellate cells (HSCs) is the central link in the occurrence and development of liver fibrosis. Our previous studies showed that autophagy promotes HSCs activation and ultimately accelerates liver fibrosis. Unc-51-like autophagy activating kinase 1 (ULK1) is an autophagic initiator in mammals and N6-methyladenosine (m6A) modification is closely related to autophagy. In this
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Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Neeraj Kapur, Ashfaqul Alam, Syed Adeel Hassan, Parth H. Patel, Lesley Wempe, Sarayu Bhogoju, Tatiana Goretsky, Jong Hyun Kim, Jeremy Herzog, Yong Ge, Samuel Awuah, Mariana Byndloss, Andreas J Baumler, Mansour Zadeh, R. Balfour Sator, Terrence A. Barrett
Background: Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria) and restricts obligate anaerobes (eg. Firmicutes). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC)
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The peroxiredoxin Tsa1 extends the lifespan of budding yeast by maintaining the stability of the ribosomal RNA gene cluster. bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Junno Ohira, Mariko Sasaki, Takehiko Kobayashi
Tsa1 is a major budding yeast peroxiredoxin that also has nonperoxidase functions. Here we demonstrate that Tsa1 is required for stabilizing the ribosomal RNA gene (rDNA) cluster. Tsa1 deficiency led to lower replication initiation and an elevated recombination frequency in the rDNA. However, the absence of Tsa1 did not affect Fob1-dependent replication fork arrest at the replication fork barrier (RFB)
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Global 5-methylcytosine-RNA disruption reduces the vectorial competence to DENV2 of heatwave-exposed Aedes aegypti mosquitoes bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Fabiola Claudio-Piedras, Benito Recio, Humberto Lanz, Jorge Cime-Castillo
Heatwaves are an increasingly common environmental event linked with climate change. Abnormally high heatwave temperatures can affect several mosquito vector traits that are determinants of pathogen transmission. Understanding how these mosquitoes adapt to high heat is vital for global public health. RNA methylation, a key cellular mechanism in stress response and adaptation, remains understudied in
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Role of non-coding RNA hsa_circ_0001495 in 16HBE cellular inflammation induced by PM2.5 and O3 combined exposure bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Wang Hongjie, Tan Yi, Li Caixia, Jin Wenjia, Yu Ying, Mu Xuan, Peng Xiaowu
Background: PM2.5 and O3 are the main air pollutants in China, and inflammation of the respiratory system is one of their main toxic effects. Cyclic RNAs are involved in many pathophysiological processes, but their relationship to the combined exposure to PM2.5 and O3 has not yet been investigated. Objective: To elucidate the biological function played by hsa_circ_0001495 in the induction of 16HBE
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YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Ning Tsao, Jennifer Olabode, Rebecca Rodell, Hua Sun, Joshua Richard Brickner, Miaw-Sheue Tsai, Elizabeth A. Pollina, Chun-Kan Chen, Nima Mosammaparast
Certain environmental toxins are nucleic acid damaging agents, as are many chemotherapeutics used for cancer therapy. These agents induce various adducts in DNA as well as RNA. Indeed, most of the nucleic acid adducts (>90%) formed due to these chemicals, such as alkylating agents, occur in RNA. However, compared to the well-studied mechanisms for DNA alkylation repair, the biological consequences
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Hsa_circ_0001304 promotes vascular smooth muscle cell autophagy and neointimal hyperplasia through the YTHDF2/mTOR axis bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Shi-Qing Mu, Jia-Jie Lin, Yu Wang, Li-Yun Yang, Sen Wang, Zhao-Yi Wang, An-Qi Zhao, Wen-Jun Luo, Zi-Qi Dong, Yu-Guang Cao, Ze-An Jiang, Si-Fan Wang, Shan-Hu Cao, Li Meng, Yang Li, Shuyan Yang, Shao-Guang Sun
Introduction: Aberrant autophagy in vascular smooth muscle cells (VSMCs) is associated with the progression of cardiovascular diseases. Recently, circular RNAs (circRNAs) have gradually been reported to regulate autophagy in VSMCs. Objectives: This study aims to investigate the role of hsa_circ_0001304 in VSMC autophagy and its underlying mechanism. Methods: The combined use of dual-luciferase reporter
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AQP1 Differentially Orchestrates Endothelial Cell Senescence bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Khatereh Shabanian, Taraneh Shabanian, Gergely Karsai, Sandra Lettlova, Luca Pontiggia, Frank Ruschitzka, Juerg H Beer, Seyed Soheil Saeedi Saravi
Accumulation of senescent endothelial cells (ECs) with age is a pivotal driver of cardiovascular diseases in aging. However, little is known about the mechanisms and signaling pathways that regulate EC senescence. In this report, we delineate a previously unrecognized role of aquaporin 1 (AQP1) in orchestrating extracellular hydrogen peroxide (H2O2)-induced cellular senescence in aortic ECs. Our findings
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Effective Gene Therapy for Metachromatic Leukodystrophy Achieved with Minimal Lentiviral Genomic Integrations bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Lucas Tricoli, Sunetra Sase, Julia Hacker, Vi Pham, Sidney Smith, Maxwell Chappell, Laura Breda, Stephanie Hurwitz, Naoto Tanaka, Carlo Castruccio Castracani, Amaliris Guerra, Zhongqi Hou, Lars Schlotawa, Karthikeyan Radhakrishnan, Peter Kurre, Rebecca Ahrens-Nicklas, Laura Adang, Adeline Vanderver, Stefano Rivella
Metachromatic leukodystrophy (MLD) is a fatal lysosomal storage disease (LSD) characterized by the deficient enzymatic activity of arylsulfatase A (ARSA). Combined autologous hematopoietic stem cell transplant (HSCT) with lentiviral (LV) based gene therapy has great potential to treat MLD. However, if enzyme production is inadequate, this could result in continued loss of motor function, implying a
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Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Qizhang Wang, Guanglin Niu, Zhuang Liu, Maria Alexandra Toma, Jennifer Geara, Xiaowei Bian, Letian Zhang, Minna Piipponen, Dongqing Li, Pehr Sommar, Ning Xu Landen
Both circular RNAs (circRNA) and microRNAs (miRNA) have emerged to play important roles in health and disease. To understand their function in tissue repair, we profiled circRNA, linear RNA, and miRNA expression dynamics in human wound-edge keratinocytes across the wound healing process. Our investigation spotlighted circASH1L(4,5) and its engagement with miR-129-5p, both of which levels were increased
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Emodin: an alveolar macrophage protector in acute pancreatitis induced lung injury bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Zhe Chen, Xuanchi Dong, Yongwei Song, Bowen Lan, Yalan Luo, Haiyun Wen, Hailong Li, Hailong Chen
Emodin (EMO), an anthraquinone derivative from roots and leaves of various plants, has been widely used in many inflammatory diseases. Alveolar macrophages (AMs) play a critical role in maintaining alveolar homeostasis in the lung. To investigate the pathophysiological mechanism of AMs in acute pancreatitis-associated lung injury (AP-ALI) and the potential protective therapeutic of EMO for AP-ALI,
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PURIFICATION METHOD FOR ADENO-ASSOCIATED VIRAL VECTOR SEROTYPE 9 USING CERAMIC HYDROXYAPATITE CHROMATOGRAPHY AND ITS QUALIFICATION bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Yae Kurosawa, Yuji Tsunekawa, Mikako Wada, Yuko Aizen, Yuko Nitahara-Kasahara, Takashi Okada
Adeno-associated virus (AAV) vectors can efficiently transduce exogenous genes into various tissues in vivo. Owing to their convenience, high efficiency, long-term stable gene expression, and minimal side effects, AAV vectors have become one of the gold standards for investigating gene functions in vivo, especially in non-clinical studies. However, challenges persist in efficiently preparing a substantial
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A longevity-specific bank of induced pluripotent stem cells from centenarians and their offspring bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Todd W Dowrey, Samuel F Cranston, Nicholas Skvir, Yvonne Lok, Brian Gould, Bradley Petrowitz, Daniel Villar, Jidong Shan, Marianne James, Mark Dodge, Anna C Belkina, Richard M Giadone, Paola Sebastiani, Thomas T Perls, Stacy L Andersen, George James Murphy
Centenarians provide a unique lens through which to study longevity, healthy aging, and resiliency. Moreover, models of human aging and resilience to disease that allow for the testing of potential interventions are virtually non-existent. We obtained and characterized over 50 centenarian and offspring peripheral blood samples including those connected to functional independence data highlighting resistance
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Intraspecific venom variation in the medically important puff adder (Bitis arietans): comparative venom gland transcriptomics, in vitro venom activity and immunological recognition by antivenom bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Charlotte A Dawson, Keirah E Bartlett, Mark C Wilkinson, Stuart Ainsworth, Laura-Oana Albulescu, Taline Kazandjian, Steven R Hall, Adam Westhorpe, Rachel Hannah Clare, Simon Wagstaff, Cassandra M Modahl, Robert A Harrison, Nicholas R Casewell
Background: Variation in snake venoms is well documented, both between and within species, with intraspecific venom variation often correlated with geographically distinct populations. The puff adder, Bitis arietans, is found widely distributed across sub-Saharan Africa and into the Arabian Peninsula where it is considered a leading cause of the ~310,000 annual snakebites across the region, with its
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Oligonucleotide insecticides (contact unmodified antisense DNA biotechnology) and RNA biocontrols (double-stranded RNA technology): newly born fraternal twins in plant protection bioRxiv. Mol. Biol. Pub Date : 2024-03-14 Volodymyr Oberemok, Nikita Gal'chinsky
The rapid development of molecular genetics, methods of synthesis of nucleic acids, and bioinformatics have created fundamentally new opportunities in plant protection. DNA and RNA have become active ingredients of insecticides, going beyond their usual role as carriers of hereditary information. Now nucleic acids are increasingly acting as active tools for insect pest control using the mechanisms
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EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control bioRxiv. Mol. Biol. Pub Date : 2024-03-13 Olivier Gemin, Victor Armijo, Michael Hons, Caroline Bissardon, Romain Linares, Matthew W Bowler, Georg Wolff, Kirill Kovalev, Anastasiia Babenko, Veijo T Salo, Sarah Schneider, Christopher Rossi, Lea Lecomte, Thibault Deckers, Kevin Lauzier, Robert Janocha, Franck Felisaz, Jeremy Sinoir, Wojciech P. Galej, Julia Mahamid, Christoph W. Muller, Sebastian Eustermann, Simone Mattei, Florent Cipriani, Gergely
Imaging biological macromolecules in their native state with single-particle cryo-electron microscopy (cryo-EM) or in situ cryo-electron tomography (cryo-ET) requires optimized approaches for the preparation and vitrification of biological samples. Here, we describe EasyGrid, a versatile technology enabling systematic, tailored and advanced sample preparation for cellular and structural biology. This
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Eugenol mimics exercise to promote skeletal muscle fiber remodeling and myokine IL-15 expression by activating TRPV1 channel bioRxiv. Mol. Biol. Pub Date : 2024-03-13 Tengteng Huang, Xiaoling Chen, Jun He, Ping Zheng, Yuheng Luo, Aimin Wu, Hui Yan, Bing Yu, Daiwen Chen, Zhiqing Huang
Metabolic disorders are highly prevalent in modern society. Exercise mimetics are defined as pharmacologic compounds that can produce the beneficial effects of fitness. Recently, there has been increased interest in the role of eugenol and transient receptor potential vanilloid 1 (TRPV1) in improving metabolic health. The aim of this study was to investigate whether eugenol acts as an exercise mimetic
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Cell 3D Positioning by Optical encoding (C3PO) and its application to spatial transcriptomics bioRxiv. Mol. Biol. Pub Date : 2024-03-12 James Cotterell, Jim Swoger, Alexandre Robert-Moreno, Heura Cardona Blaya, Marco Musy, James Sharpe
Current state-of-the-art spatial omics approaches suffer from the drawback that they are tissue section-based and thus inherently 2-dimensional. A full understanding of biological processes will only be possible when such data is available in 3-dimensions (3D). Here, we introduce Cell 3D Positioning by Optical encoding (C3PO) - the first technique capable of reconstructing the 3D positions of cells
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Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decay. bioRxiv. Mol. Biol. Pub Date : 2024-03-12 Yujie Zhang, Lilit Nersisyan, Eliska Fuerst, Ioannis Alexopoulos, Susanne Huch, Claudio Bassot, Elena Garre, Per Sunnerhagen, Ilaria Piazza, Vicent Pelechano
Cells need to adapt their transcriptome to quickly match cellular needs in changing environments. mRNA abundance can be controlled by altering both its synthesis and decay. Here we show how, in response to poor nutritional conditions, the bulk of the S. cerevisiae transcriptome undergoes -1 ribosome frameshifts and experiences an accelerated out-of-frame co-translational mRNA decay. Using RNA metabolic
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The histone chaperone CAF-1 maintains the stability of the ribosomal RNA gene cluster by suppressing end resection of replication-associated DNA double-strand breaks. bioRxiv. Mol. Biol. Pub Date : 2024-03-12 Mariko Sasaki, Takehiko Kobayashi, Hajime Futami
In eukaryotes, chromatin assembly is coupled to DNA replication by the histone chaperone chromatin assembly factor-1 (CAF-1). Here, we demonstrate that CAF-1 maintains the stability of the ribosomal RNA gene (rDNA) cluster in budding yeast. Absence of CAF-1 led to homologous recombination (HR)-mediated rDNA copy number changes as well as the production of extrachromosomal rDNA circles in response to
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N-glycosylated molecules act as a co-precipitant in RNA purification bioRxiv. Mol. Biol. Pub Date : 2024-03-12 Sungchul Kim, Yong-geun Choi, Kirsten Janssen, Christian Bull, Bhagyashree S. Joshi, Adam Pomorski, Vered Raz, Marvin E. Tanenbaum, Pascal Miesen, Zeshi Li, Chirlmin Joo
A recent ground-breaking study suggested that small RNA from mammalian cells can undergo N-glycan modifications (termed glycoRNA). The discovery relied upon a metabolic glycan labeling strategy in combination with commonly used phase-separation-based RNA isolation. Following the reported procedure, we likewise identified an N-glycosylated species in the RNA fraction. However, our results suggest that
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The gamma-butyrolactone receptors ScbR and AtrA form a quorum sensing switch between coelimycin and actinorhodin synthesis in Streptomyces coelicolor A3(2) bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Bartosz Bednarz, Magdalena Kotowska, Mateusz Wenecki, Marta Derkacz, Adrianna Jastrzemska, Jarosław Ciekot, Krzysztof Jakub Pawlik
Background: Quorum sensing enables gene expression regulation in response to changes in cell population density and controls diverse processes, such as biofilm formation, virulence and antibiotic production, in bacteria. In one of the largest, soil-dominant phylum Actinobacteria, cell-to-cell communication occurs through the small, membrane-diffusible signalling molecules gamma-butyrolactones (GBLs)
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Mycobacterium tuberculosis FtsB and PerM interact via a C-terminal helix in FtsB to modulate cell division bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Zach Hensel, Ruilan Xu, João Ramalheira Ferreira
Latent infection by Mycobacterium tuberculosis (Mtb) impedes effective tuberculosis therapy and eradication. The protein PerM is essential for chronic Mtb infections in mice and acts via the divisome protein FtsB to modulate cell division. Using transgenic co-expression in Escherichia coli, we studied the Mtb PerM-FtsB interaction in isolation from other Mtb proteins, engineering PerM to enhance expression
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Sacbrood viruses and select Lake Sinai virus variants dominated Apis mellifera colonies symptomatic for European foulbrood bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Poppy J Hesketh-Best, Peter D Fowler, Nkechi M Odogwu, Meghan O Milbrath, Declan C Schroeder
European foulbrood (EFB) is a prevalent disease of the European honey bee (Apis mellifera) in the US, which can lead to colony decline and collapse. The bacterial components of EFB are well studied, but the diversity of viral infections within infected colonies has not been explored. Here we use meta-transcriptomics sequencing of 12 honey bee hives, symptomatic (+) and asymptomatic (-) for EFB to explore
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YmoA functions as a molecular stress sensor in Yersinia bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Tifaine Hechard, Lu Lu, Tomas Edgren, Celestine Chi, Helen Wang
Pathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA in Yersinia adjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms
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WITHDRAWN: Dynamic Regulation of MAVS Protein Function via Reversible Oxidation at Cys79 in Response to Oxidant Stimuli bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Natalia Zamorano Cuervo, Audray Fortin, Alejandro Vallejo Arroyo, Layla Dehbidi, Nathalie Grandvaux
The authors have withdrawn their manuscript owing to changes in the work. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
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RNPS1 in PSAP complex controls periodic pre-mRNA splicing over the cell cycle bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Kazuhiro Fukumura, Akio Masuda, Jun-ichi Takeda, Kinji Ohno, Akila Mayeda
Cell cycle progression requires periodic gene expression through splicing control. However, the splicing factor that directly controls this cell cycle-dependent splicing remain unknown. Cell cycle-dependent expression of the AURKB (aurora kinase B) gene is essential for chromosome segregation and cytokinesis. We previously reported that RNPS1 is essential to maintain precise splicing in AURKB intron
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HIV-1 Nef acts in synergy with APOL1-G1 to induce nephrocyte cell death in a new Drosophila model of HIV-related kidney diseases bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Jun-yi Zhu, Yulong Fu, Joyce van de Leemput, Ying Yu, Jinliang Li, Patricio E Ray, Zhe Han
Background: People carrying two APOL1 risk alleles (RA) G1 or G2 are at greater risk of developing HIV-associated nephropathy (HIVAN). Studies in transgenic mice showed that the expression of HIV-1 genes in podocytes, and nef in particular, led to HIVAN. However, it remains unclear whether APOL1-RA and HIV-1 Nef interact to induce podocyte cell death. Method: We generated transgenic (Tg) flies that
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Dietary restriction reveals sex-specific expression of the mTOR pathway genes in Japanese quails bioRxiv. Mol. Biol. Pub Date : 2024-03-11 Gebrehaweria K. Reda, Sawadi F. Ndunguru, Brigitta Csernus, Renáta Knop, James K. Lugata, Csaba Szabó, Levente Czeglédi, Adam Z. Lendvai
Limited resources affect an organism's physiology through the conserved metabolic pathway, the mechanistic target of rapamycin (mTOR). Males and females often react differently to nutritional limitation, but whether it leads to differential mTOR pathway expression remains unknown. Recently, we found that dietary restriction (DR) induced significant changes in the expression of mTOR pathway genes in
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Improved functions for non-linear sequence comparison using SEEKR bioRxiv. Mol. Biol. Pub Date : 2024-03-10 Shuang Li, Quinn Eberhard, Luke Ni, Mauro Calabrese
SEquence Evaluation through k-mer Representation (SEEKR) is a method of sequence comparison that utilizes sequence substrings called k-mers to quantify non-linear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate p-values that ascribe statistical significance to SEEKR-derived similarities as well as visualize different
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Structure-based probe reveals the presence of large transthyretin aggregates in plasma of ATTR amyloidosis patients bioRxiv. Mol. Biol. Pub Date : 2024-03-10 Rose Pedretti, Lanie Wang, Anna Yakubovska, Qiongfang S Zhang, Binh Nguyen, Justin L Grodin, Ahmad Masri, Lorena Saelices
ATTR amyloidosis is a relentlessly progressive disease caused by the misfolding and systemic accumulation of amyloidogenic transthyretin into amyloid fibrils. These fibrils cause diverse clinical phenotypes, mainly cardiomyopathy and/or polyneuropathy. Little is known about the aggregation of transthyretin during disease development and whether this has implications for diagnosis and treatment. Using
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Interplay between β-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex bioRxiv. Mol. Biol. Pub Date : 2024-03-09 Matthew E.R. Maitland, Gabriel Onea, Dominic D.G Owens, Brianna C Gonga-Cavé, Xu Wang, Cheryl H Arrowsmith, Dalia Barsyte-Lovejoy, Gilles A Lajoie, Caroline Schild-Poulter
The Pro/N-degron recognizing C-terminal to LisH (CTLH) complex is an E3 ligase of emerging interest in the developmental field and for targeted protein degradation (TPD) modalities. The human CTLH complex forms distinct supramolecular ring-shaped structures dependent on the multimerization of WDR26 or muskelin β-propeller proteins. Here, we find that, in human cells, CTLH complex E3 ligase activity
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Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation bioRxiv. Mol. Biol. Pub Date : 2024-03-09 Jared Shaw, Sophie R. Harvey, Chen Du, Zhixin Xu, Eduardo Olmedillas, Erica Ollmann Saphire, Vicki H. Wysocki
Herein, we focus on native mass spectrometry (nMS) combined with a fast, tunable gas-phase charge reduction, electron capture charge reduction (ECCR), and illustrate its utility in the characterization of protein complex topology and glycoprotein heterogeneity. ECCR is illustrated to effectively spread the charge states of tetradecameric GroEL, illustrating Orbitrap m/z measurement out to greater than
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Using RNA-targeting CRISPR-Cas13 and engineered U1 systems to reduce ABCA4 splice variants in Stargardt disease bioRxiv. Mol. Biol. Pub Date : 2024-03-09 Roxanne Hsiang-Chi Liu, Daniel Urrutia-Cabrera, Ida Maria Westin, Irina Golovleva, Guei-Sheung Liu, Satheesh Kumar, Samuel McLenachan, Fred Kuanfu Chen, Fei-Ting Hsu, Tom Edwards, Keith R Martin, Albert Cheng, Raymond CB Wong
Dysregulation of the alternative splicing process results in aberrant mRNA transcripts, leading to dysfunctional proteins or nonsense-mediated decay that cause a wide range of mis-splicing diseases. Development of therapeutic strategies to target the alternative splicing process could potentially shift the mRNA splicing from disease isoforms to a normal isoform and restore functional protein. As a
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Quantitative Real-Time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates bioRxiv. Mol. Biol. Pub Date : 2024-03-09 Annica M. Brink, Anke Kremp, Elena Gorokhova
In the Baltic Sea, the dinoflagellates Apocalathium malmogiense, Biecheleria baltica, and Gymnodinium corollarium are important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to lack of resolution of distinctive morphological features of the three species. Here, we describe a molecular
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Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay bioRxiv. Mol. Biol. Pub Date : 2024-03-09 Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortazar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, Elena Alkalaeva, Sujatha Jagannathan
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that prevents the accumulation of harmful truncated proteins by degrading transcripts with premature termination codons (PTCs). NMD activity varies across many contexts, with the variation having critical consequences during both normal development and disease. However, the factors that influence this variability remain poorly understood
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Estrogen deficiency reduces maximal running capacity and affects serotonin levels differently in the hippocampus and nucleus accumbens in response to acute exercise bioRxiv. Mol. Biol. Pub Date : 2024-03-08 Earric Lee, Tuuli A. Nissinen, Laura Yla-Outinen, Aaro Jalkanen, Jari E. Karppinen, Victoria Vieira-Potter, Arto Lipponen, Sira Karvinen
Objective: Estrogen deficiency is associated with unfavorable changes in body composition and metabolic health. While physical activity ameliorates several of the negative effects, loss of ovarian function is associated with decreased physical activity levels. It has been proposed that the changes in brain neurochemical levels and /or impaired skeletal muscle function may underlie this phenomenon.