Article
Multidisciplinary Sciences
Claire Chung, Bert M. Verheijen, Xinmin Zhang, Biao Huang, Aeowynn Coakley, Eric McGann, Emily Wade, Olivia Dinep-Schneider, Jessica LaGosh, Maria-Eleni Anagnostou, Stephen Simpson, Kelly Thomas, Mimi Ernst, Allison Rattray, Michael Lynch, Mikhail Kashlev, Berenice A. Benayoun, Zhongwei Li, Jeffrey Strathern, Jean-Francois Gout, Marc Vermulst
Summary: To determine the error rate of transcription in human cells, researchers analyzed the transcriptome of H1 human embryonic stem cells using a high-fidelity circle-sequencing approach. They found approximately 100,000 errors in major RNA species, indicating that different RNA species have different error rates. Cross-referencing the errors with genetic and epigenetic features revealed that the error rate changes along the transcript length and is modified by genetic context, repetitive elements, and epigenetic markers. The study also discovered a novel role of BRCA1 in suppressing transcription errors and found that transcription errors preferentially occur in neurons, suggesting their involvement in neurological disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Pawel M. Switonski, Joe R. Delaney, Luke C. Bartelt, Chenchen Niu, Maria Ramos-Zapatero, Nathanael J. Spann, Akshay Alaghatta, Toby Chen, Emily N. Griffin, Jaidev Bapat, Bryce L. Sopher, Albert R. La Spada
Summary: Inherited ataxia commonly involves a vulnerability to DNA damage. SCA7 is characterized by cerebellar and retinal degeneration due to polyglutamine expansion in ataxin-7 protein, which affects transcription by altering histone acetylation. Altered DNA repair function in SCA7 may lead to excessive DNA damage, resulting in neuron demise and highlighting DNA repair as a potential therapy target.
Article
Biochemistry & Molecular Biology
Jisu Im, Tamara Hillenaar, Hui Ying Yeoh, Priyanka Sahasrabudhe, Marjolein Mijnders, Marcel van Willigen, Azib Hagos, Eduardo de Mattos, Peter van der Sluijs, Ineke Braakman
Summary: We have discovered the sequential events involved in the proper folding of the ABC transporter CFTR, a large multi-domain, multi-spanning membrane protein. Our study revealed that CFTR folds in two distinct stages: a co-translational stage involving the folding of certain domains, followed by a post-translational stage involving the assembly of these domains. We also investigated the effects of mutations on CFTR folding and found that a disease-causing mutation disrupted the first stage of folding, but not the second stage, which could be rescued by corrector drugs.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Multidisciplinary Sciences
Dylan M. Plaskon, Kate L. Henderson, Lindsey C. Felth, Cristen M. Molzahn, Claire Evensen, Sarah Dyke, Irina A. Shkel, M. Thomas Record
Summary: Transcription initiation is tightly regulated by promoter sequence, transcription factors, and ligands. Known transcription inhibitors act during initiation. The study found that the productive initiation complex is I3 instead of RPO at all temperatures, and stepwise disruption of RNAP-strand contacts occurs as the hybrid grows and translocates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Nicolaj Inunnguaq Jessen, Joseph A. Izzo, Marek S. Modlinski, Giulio Bertuzzi, Karl Anker Jorgensen
Summary: The development of higher-order cycloadditions has been limited due to the need for highly conjugated and reactive pi-systems. Recent research shows that organocatalysis can be an efficient mediator to overcome these challenges. Computational studies have also found that the impact of benzofusions on higher-order cycloadditions can be explained by changes in energy barriers.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Analytical
Caiyun Liu, Xiwei Li, Xiaodi Rong, Mingzhu Li, Miaohui Yu, Wenlong Sheng, Baocun Zhu
Summary: Nowadays, it is crucial to develop tools for detecting active molecules in specific organelles due to the correlation between abnormal expression of active molecules and diseases. However, most organelle-targeting probes currently developed lack specificity and tend to react with analytes in the cytoplasm, leading to misjudgment of their physiological role. To address this issue, a new strategy is proposed to develop probes with recognition receptors activated by the microenvironment of targeting organelles. The activation of a lysosome-targeting fluorescent probe by the acidic environment in the lysosome allows for high-fidelity imaging of sulfur dioxide with quick response and high sensitivity.
ANALYTICA CHIMICA ACTA
(2023)
Article
Statistics & Probability
Remi Stroh, Julien Bect, Severine Demeyer, Nicolas Fischer, Damien Marquis, Emmanuel Vazquez
Summary: This article discusses the sequential design of experiments for multi-fidelity numerical simulators, proposing a new Bayesian strategy called maximal rate of stepwise uncertainty reduction (MR-SUR) which aims to maximize the ratio between expected reduction of uncertainty and simulation cost. The strategy unifies existing methods and provides a principled approach for developing new ones.
Article
Multidisciplinary Sciences
Tea Lenarcic, Mateusz Jaskolowski, Marc Leibundgut, Alain Scaiola, Tanja Schoenhut, Martin Saurer, Richard G. Lee, Oliver Rackham, Aleksandra Filipovska, Nenad Ban
Summary: The study presents eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. It is discovered that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA. This study sheds light on the structural basis of mammalian mitochondrial ribosome assembly and the role of specific assembly factors.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Yu Chen, Yuanhong Kang, Huiya Yang, Haiming Hua, Jiaxiang Qin, Peng Liu, Yiyong Zhang, Yingjie Zhang, Jinbao Zhao
Summary: The mechanism of multifunctional sulfur-fixing materials is crucial for the design of effective electrocatalysts for lithium-sulfur batteries (LSBs). Metal coordination compounds (M = Co / Fe / CoFe) are chosen as cathode additives to promote reaction kinetics and focus on adsorption-catalysis mechanism. The combination of Co and Fe sites inhibits polysulfides diffusion and induces rapid deposition of lithium sulfide, resulting in excellent cyclability and capacity retention for LSBs.
ENERGY STORAGE MATERIALS
(2023)
Article
Chemistry, Physical
Ye-Guang Fang, Xiaojiao Li, Yurui Gao, Yan-Hong Cui, Joseph S. S. Francisco, Chongqin Zhu, Wei-Hai Fang
Summary: We present an efficient method based on an extension of metadynamics for exploring complex free energy landscapes. The method greatly improves the performance of the metadynamics approach and allows for efficient modeling of chemical systems with complex free energy landscapes.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Yasuhiro Arikawa, Motoki Yamada, Nobuko Takemoto, Takuya Nagaoka, Yusuke Tsujita, Taiji Nakamura, Yusuke Tsuruta, Shinnosuke Horiuchi, Eri Sakuda, Kazunari Yoshizawa, Keisuke Umakoshi
Summary: Sulfite reduction is a crucial process in the global sulfur cycle, and it can be achieved using transition-metal complexes. In our study, we successfully simulated and achieved the stepwise reduction of sulfite from sulfite to sulfur monoxide, then to disulfide, and finally to hydrogen sulfide using a dinuclear ruthenium complex.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Cell & Tissue Engineering
Kitra Cates, Matthew J. McCoy, Ji-Sun Kwon, Yangjian Liu, Daniel G. Abernathy, Bo Zhang, Shaopeng Liu, Paul Gontarz, Woo Kyung Kim, Shawei Chen, Wenjun Kong, Joshua N. Ho, Kyle F. Burbach, Harrison W. Gabel, Samantha A. Morris, Andrew S. Yoo
Summary: This study revealed the activity of miR-9/9* and miR-124 as reprogramming agents in eradicating fibroblast identity and promoting direct conversion into motor neurons. Inhibition of KLF-family transcription factors downstream of miR-9/9*-124 is crucial for erasing fibroblast fate, while the subsequent acquisition of neuronal identity requires upregulation of RN7SK to induce chromatin accessibility and neuronal gene activation. Our research defines deterministic components in the microRNA-mediated reprogramming cascade.
Article
Biochemistry & Molecular Biology
Sebastian R. Najle, Xavier Grau-Bove, Anamaria Elek, Cristina Navarrete, Damiano Cianferoni, Cristina Chiva, Didac Canas-Armenteros, Arrate Mallabiabarrena, Kai Kamm, Eduard Sabido, Harald Gruber-Vodicka, Bernd Schierwater, Luis Serrano, Arnau Sebe-Pedros
Summary: The assembly of neuronal and other major cell programs occurred early in animal evolution. Through studying non-bilaterians like placozoans, we can reconstruct this process and understand the affinities of peptidergic cells. Our findings show that key neuronal developmental and effector gene modules evolved before cnidarian/bilaterian neurons, highlighting the importance of paracrine cell signaling.
Article
Chemistry, Multidisciplinary
Zijing Chen, Xiu-Wen Kang, Yalin Zhou, Zhongneng Zhou, Siwei Tang, Shuhua Zou, Kailin Wang, Jiulong Huang, Bei Ding, Dongping Zhong
Summary: Proton relays through H-bond networks are crucial in protein machines. In this study, we designed a proton rocking blue light and used ultrafast spectroscopy to analyze the individual proton-transfer steps. We found that the proton jumps from E-COOH to FMN- rapidly, followed by a second proton transfer from WH+ to E-COO-, which immediately rocks back to W•. Our findings provide insights into the Grotthuss mechanism on the ultrafast timescale.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Agricultural Engineering
Jie Cui, Lin Mi, Lang Li, Yongjie Liu, Chong Wang, Chao He, Hong Zhang, Yao Chen, Qingyuan Wang
Summary: The tensile behavior of Moso bamboo before and after heat treatment was studied in this paper, including tensile strength, stress-strain curve, and crack propagation process. Microstructure and chemical composition analysis were conducted to reveal the underlying mechanism. The tensile strength decreases with increasing treating temperature, and the decomposition of cellulose and hemicellulose is responsible for the decrease. The unique composite structure of bamboo results in a stepwise failure behavior under uniaxial tensile load, with fiber sheaths breaking dispersively and causing the strain-stress curve to fluctuate like stairs.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Cell Biology
Christina Julius, Yulia Yuzenkova
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2019)
Article
Multidisciplinary Sciences
Mohammad Roghanian, Szabolcs Semsey, Anders Lobner-Olesen, Farshid Jalalvand
SCIENTIFIC REPORTS
(2019)
Article
Microbiology
Stine Vang Nielsen, Kathryn Jane Turnbull, Mohammad Roghanian, Rene Baerentsen, Maja Semanjski, Ditlev E. Brodersen, Boris Macek, Kenn Gerdes
Article
Biochemistry & Molecular Biology
Anurag Kumar Sinha, Kristoffer Skovbo Winther, Mohammad Roghanian, Kenn Gerdes
MOLECULAR MICROBIOLOGY
(2019)
Article
Microbiology
Kathryn Jane Turnbull, Ievgen Dzhygyr, Soren Lindemose, Vasili Hauryliuk, Mohammad Roghanian
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Microbiology
Hiraku Takada, Mohammad Roghanian, Victoriia Murina, Ievgen Dzhygyr, Rikinori Murayama, Genki Akanuma, Gemma C. Atkinson, Abel Garcia-Pino, Vasili Hauryliuk
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Christina Julius, Paula S. Salgado, Yulia Yuzenkova
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
John Harbottle, Nikolay Zenkin
NUCLEIC ACIDS RESEARCH
(2020)
Article
Microbiology
Viralkumar V. Panchal, Caitlin Griffiths, Hamed Mosaei, Bohdan Bilyk, Joshua A. F. Sutton, Oliver T. Carnell, David P. Hornby, Jeffrey Green, Jamie K. Hobbs, William L. Kelley, Nikolay Zenkin, Simon J. Foster
Article
Biochemistry & Molecular Biology
Hiraku Takada, Mohammad Roghanian, Julien Caballero-Montes, Katleen Van Nerom, Steffi Jimmy, Pavel Kudrin, Fabio Trebini, Rikinori Murayama, Genki Akanuma, Abel Garcia-Pino, Vasili Hauryliuk
Summary: This study elucidates the molecular mechanism of the Rel enzyme in B. subtilis, including its conformational changes on the ribosome and the process of synthesizing (p)ppGpp. Rel activates (p)ppGpp synthesis by specifically recognizing and locking onto tRNA on the ribosome, showing high specificity in this process.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Multidisciplinary Sciences
Jana Wiedermannova, Christina Julius, Yulia Yuzenkova
Summary: Recent discoveries have shown the existence of diverse non-canonical 5'-end RNA cap-like modifications in prokaryotes and eukaryotes, including metabolic cofactors and cell wall precursors, installed by specific enzymes. The emerging variety of capping molecules and enzymes reveals an unrecognized level of complexity in RNA metabolism.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Tatsuaki Kurata, Tetiana Brodiazhenko, Sofia Raquel Alves Oliveira, Mohammad Roghanian, Yuriko Sakaguchi, Kathryn Jane Turnbull, Ondrej Bulvas, Hiraku Takada, Hedvig Tamman, Andres Ainelo, Radek Pohl, Dominik Rejman, Tanel Tenson, Tsutomu Suzuki, Abel Garcia-Pino, Gemma Catherine Atkinson, Vasili Hauryliuk
Summary: Multiple families of SAS RSH enzymes have been discovered to inhibit bacterial growth by specifically inhibiting protein synthesis, establishing RSHs as RNA-modifying enzymes.
Article
Biochemistry & Molecular Biology
Mohammad Roghanian, Katleen Van Nerom, Hiraku Takada, Julien Caballero-Montes, Hedvig Tamman, Pavel Kudrin, Ariel Talavera, Ievgen Dzhygyr, Simon Ekstrom, Gemma C. Atkinson, Abel Garcia-Pino, Vasili Hauryliuk
Summary: Amino acid starvation is sensed by RelA and Rel through monitoring the aminoacylation status of ribosomal A-site tRNA, with their synthetic activity controlled by the alarmone nucleotide (p)ppGpp. Stimulation by the alarmone exploits intra-NTD autoinhibition dynamics to activate Rel/RelA. Without pppGpp stimulation, starved ribosomes cannot efficiently activate Rel/RelA, compromising their function in vivo.
Article
Biochemistry & Molecular Biology
Hedvig Tamman, Karin Ernits, Mohammad Roghanian, Andres Ainelo, Christina Julius, Anthony Perrier, Ariel Talavera, Hanna Ainelo, Remy Dugauquier, Safia Zedek, Aurelien Thureau, Javier Perez, Gipsi Lima-Mendez, Regis Hallez, Gemma C. Atkinson, Vasili Hauryliuk, Abel Garcia-Pino
Summary: Stringent factors regulate bacterial cell reprogramming by increasing the level of (p)ppGpp. This study presents the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and reveals the intramolecular regulation mechanism of 'long'-stringent factors. The Core subdomain plays a key role in determining the specialization of long RelA-SpoT homologs towards synthesis or hydrolysis.
NATURE CHEMICAL BIOLOGY
(2023)
Retraction
Multidisciplinary Sciences
Elsa Germain, Mohammad Roghanian, Kenn Gerdes, Etienne Maisonneuve
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)