Article
Biochemistry & Molecular Biology
Katie H. Jameson, Christian J. Rudolph, Michelle Hawkins
Summary: The accurate duplication of genomic information is essential for genome stability. In Escherichia coli, replication termination is confined to the replication fork trap region by Tus protein binding to ter sites. When replication forks fuse at Tus-ter complexes, there is under-replication of DNA template, suggesting the need for further enzymatic processing during fork fusion.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Lance D. Langston, Zuanning Yuan, Roxana Georgescu, Huilin Li, Michael E. O'Donnell
Summary: This article investigates the mechanism of double-strand DNA unwinding during DNA genome replication. The researchers found that two helicases move inward together and unwind the double helix by pulling on opposite strands. They also discovered that in some cases, a single strand helicase can unwind a 150-base pair duplex. These findings contribute to our understanding of the initiation process of DNA replication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Virology
Ugo Moens, Sara Passerini, Mar Falquet, Baldur Sveinbjornsson, Valeria Pietropaolo
Summary: Protein phosphorylation and dephosphorylation are common post-translational modifications that can modulate protein function. Phosphorylation of viral proteins plays an important role in the virus life cycle.
Article
Genetics & Heredity
Weihong Yi, Dazhi Yang, Zhen Xu, Zecai Chen, Guozhi Xiao, Lei Qin
Summary: In cell culture studies, immortalized primary cells are commonly used to investigate the molecular and cellular functions of different types of cells. Astrocytes, the most abundant glial cell type in the central nervous system, have potential therapeutic benefits in neuronal disorders. Immortalized primary astrocytes provide valuable information for astrocyte biology, astrocyte-neuron interactions, glial interactions, and astrocyte-associated neuronal diseases.
Article
Biochemistry & Molecular Biology
Caroline Kellogg, Valentina L. Kouznetsova, Igor F. Tsigelny
Summary: Polyomaviruses, such as SV40 and JCV, can inactivate the tumor suppressor p53 through their viral protein, LT. This study investigates the similarities between different polyomavirus LT proteins and elucidates the mechanism by which SV40 LT inactivates p53. Furthermore, the study suggests that other polyomavirus LT proteins may also have the potential to inactivate p53.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Microbiology
Nichodemus O. Onwubiko, Suraya A. Diaz, Marcela Krecmerova, Heinz Peter Nasheuer
Summary: Cidofovir and its modified derivatives are repurposed as antipolyomavirus agents by inhibiting polyomavirus large tumor antigen (Tag) activities, which leads to the inhibition of viral DNA replication. Further research is needed to fully understand the inhibitory mechanisms of these nucleotide analog-based drugs.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Alexandra M. Pike, Caitlin M. Friend, Stephen P. Bell
Summary: Replication protein A (RPA) plays critical roles in eukaryotic DNA replication, DNA damage response, and DNA repair by binding to single-stranded DNA (ssDNA). We found that Escherichia coli SSB can fully substitute for RPA in promoting origin DNA unwinding, while T4 bacteriophage Gp32 cannot. Our study reveals the requirement for specific modes of ssDNA binding in extensive origin DNA unwinding and identifies different RPA domains that impact replication fork function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Nan Zhou, Ye Zhang, Gongyun Lei, Yifan Chen, Ting Lin, Qin Liu, Yinshuang Zhao, Jiahui Mao, Yongying Jiang, Renfang Mao
Summary: The study found that inhibition of BETs protein family through the use of JQ1 and I-BET-762 can protect cells from heat shock-induced cell death. This effect was observed in SV40 large T antigen transfected cells by upregulating heat shock proteins (HSPs).
Article
Cell Biology
N. Seridi, M. Hamidouche, N. Belmessabih, S. El Kennani, J. Gagnon, G. Martinez, C. Coutton, T. Marchal, Y. Chebloune
Summary: The study successfully established and characterized TISEKC sheep embryo kidney cells through immortalization. TISEKC-5 stood out for its active division and growth, maintaining a similar morphology to the parental primary cells. Immortalized cells displayed heterogeneous polyploidy in early passages but gradually stabilized their karyotype in later passages.
IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL
(2021)
Article
Oncology
Jian Ding, Sarah Guyette, Brett Schrand, Jessica Geirut, Holly Horton, Guangwu Guo, Greg Delgoffe, Ashley Menk, Patrick A. Baeuerle, Robert Hofmeister, Robert Tighe
Summary: TRuC-T cells utilize all signaling subunits of the TCR to activate T cells and effectively kill MSLN+ tumor cells, showing comparable efficacy to MSLN-targeted CAR-T cells. However, TRuC-T cells exhibit faster tumor rejection kinetics, earlier intratumoral accumulation, and signs of activation. Metabolic profiling also indicates that TRuC-T cells have lower glycolytic activity and higher mitochondrial metabolism than CAR-T cells. These findings highlight TRuC-T cells as a promising cell therapy for MSLN-expressing cancers.
Review
Biochemistry & Molecular Biology
Manisha R. Patil, Anand Bihari
Summary: The protein p53 has been extensively studied for the past 43 years since its discovery. It acts as a guardian of the genome by regulating cell division and preventing the growth of cells, thereby inhibiting tumor development. This article traces the history of p53 protein and discusses how its function has evolved over time.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Article
Immunology
Franz Kapplusch, Felix Schulze, Soeren Reinke, Susanne Russ, Mary Linge, Franziska Kulling, Florian Kriechling, Katrin Hoehne, Stefan Winkler, Hella Hartmann, Angela Roesen-Wolff, Konstantinos Anastassiadis, Christian M. Hedrich, Sigrun R. Hofmann
Summary: This study reveals the role of RIP2 in regulating inflammation, cell death processes, and cancer by modulating mitochondrial damage and ULK1 phosphorylation.
CLINICAL IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Hanna P. Roetschke, Guillermo Rodriguez-Hernandez, John A. Cormican, Xiaoping Yang, Steven Lynham, Michele Mishto, Juliane Liepe
Summary: Noncanonical epitopes presented by HLA-I complexes have gained attention in the research of immunotherapies. Proteasomes can catalyze peptide hydrolysis and splicing, and here, we provide a comprehensive database of proteasome-generated spliced and non-spliced peptides. The database contains a variety of peptide products and substrate sequences, which can be valuable for predicting proteasome-catalyzed peptide hydrolysis and splicing.
Article
Immunology
Marika Guercio, Simona Manni, Iolanda Boffa, Simona Caruso, Stefano Di Cecca, Matilde Sinibaldi, Zeinab Abbaszadeh, Antonio Camera, Roselia Ciccone, Vinicia Assunta Polito, Francesca Ferrandino, Sofia Reddel, Maria Luigia Catanoso, Emilia Bocceri, Francesca Del Bufalo, Mattia Algeri, Biagio De Angelis, Concetta Quintarelli, Franco Locatelli
Summary: This study investigates the inclusion of the inducible caspase 9 (iC9) suicide gene in CAR construct design as an effective safety switch to control malignant CAR+ B cells, potentially providing a safe CAR-T cell product even when starting from biological materials contaminated with leukemia blasts.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Phasit Charoenkwan, Nalini Schaduangrat, Watshara Shoombuatong
Summary: This study proposes a new stacking ensemble learning-based framework, StackTTCA, for accurate and large-scale identification of tumor T cell antigens (TTCAs). By constructing 156 different baseline models and creating a new probabilistic feature vector, the StackTTCA model outperforms other machine learning classifiers and existing methods with an accuracy of 0.932 and Matthew's correlation coefficient of 0.866 in independent tests.
BMC BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Humberto Sanchez, Kaley McCluskey, Theo van Laar, Edo van Veen, Filip M. Asscher, Belen Solano, John F. X. Diffley, Nynke H. Dekker
Summary: The study demonstrates the dynamics of the origin recognition complex and subsequent intermediates leading to the loading of an MCM helicase onto DNA using single-molecule optical trapping and confocal microscopy. ORC is shown to be a mobile protein that diffuses rapidly along DNA, with recruitment of MCM molecules in a ORC- and Cdc6-dependent way resulting in slow-moving ORC-MCM intermediates and rapidly scanning MCMs on DNA.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Ariadna Boloix, Natalia Feiner-Gracia, Mariana Kober, Javier Repetto, Rosa Pascarella, Aroa Soriano, Marc Masanas, Nathaly Segovia, Guillem Vargas-Nadal, Josep Merlo-Mas, Dganit Danino, Inbal Abutbul-Ionita, Laia Foradada, Josep Roma, Alba Cordoba, Santi Sala, Josep Sanchez Toledo, Soledad Gallego, Jaume Veciana, Lorenzo Albertazzi, Miguel F. Segura, Nora Ventosa
Summary: The engineering of non-liposomal lipid nanovesicles, known as quatsomes (QS), for delivering miRNAs and other small RNAs into tumor cells' cytosol, triggering a tumor-suppressive response, offers a promising platform for the clinical delivery of miRNA therapeutics.
Article
Cell Biology
Richard Janissen, Behrouz Eslami-Mossallam, Irina Artsimovitch, Martin Depken, Nynke H. Dekker
Summary: This study investigates the transcription dynamics of Escherichia coli RNA polymerase using high-throughput magnetic tweezers, revealing the mechanism of backtracking pauses and recovery, and proposing a unified mechanistic model.
Article
Nanoscience & Nanotechnology
Sara Battista, Mariana Koeber, Pierangelo Bellio, Giuseppe Celenza, Luciano Galantini, Guillem Vargas-Nadal, Lorenza Fagnani, Jaume Veciana, Nora Ventosa, Luisa Giansanti
Summary: The newly developed nanovesicle system of the quatsome family shows noticeable antibacterial activity, demonstrating great potential for the treatment of bacterial infections and can also serve as nanocarriers of pharmaceutical actives.
ACS APPLIED NANO MATERIALS
(2022)
Article
Chemistry, Physical
Judit Morla-Folch, Guillem Vargas-Nadal, Edgar Fuentes, Silvia Illa-Tuset, Mariana Koeber, Cristina Sissa, Silvia Pujals, Anna Painelli, Jaume Veciana, Jordi Faraudo, Kevin D. Belfield, Lorenzo Albertazzi, Nora Ventosa
Summary: The development of bright fluorescent nanoparticles is essential for improving the resolution and signal-to-noise ratio in fluorescence imaging techniques. In this study, we developed FRET-based nanovesicles with different dye loadings and investigated their optical properties at the nanoscopic level. The results show that the dye's molecular diffusion in fluid-like membranes can modulate the optical properties of the nanoparticles, resulting in highly efficient and stable nanoprobes.
CHEMISTRY OF MATERIALS
(2022)
Article
Nanoscience & Nanotechnology
Marc Martinez-Miguel, Miquel Castellote-Borrell, Mariana Kober, Adriana R. Kyvik, Judit Tomsen-Melero, Guillem Vargas-Nadal, Jose Munoz, Daniel Pulido, Edgar Cristobal-Lecina, Solene Passemard, Miriam Royo, Marta Mas-Torrent, Jaume Veciana, Marina Giannotti, Judith Guasch, Nora Ventosa, Imma Ratera
Summary: By utilizing the quatsomes colloidal system, hierarchical nanostructures of RGD peptide can be achieved, leading to significantly enhanced cell adhesion. This novel approach enables the hierarchical immobilization of biomolecules on surfaces, providing a new strategy for tissue engineering.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Mariana Kober, Silvia Illa-Tuset, Lidia Ferrer-Tasies, Evelyn Moreno-Calvo, Witold I. Tatkiewicz, Natascia Grimaldi, David Pina, Alejandro Perez Perez, Vega Lloveras, Jose Vidal-Gancedo, Donatella Bulone, Imma Ratera, Jan Skov Pedersen, Dganit Danino, Jaume Veciana, Jordi Faraudo, Nora Ventosa
Summary: This study investigates the stability and formation mechanism of CHOL/CTAB quatsomes, which are nanovesicles formed through the self-assembly of cholesterol and cetyltrimethylammonium bromide in water. Experimental and simulation results show that CHOL/CTAB quatsomes are thermodynamically stable nanovesicles, but they do not exhibit the classical membrane curvature induced by composition asymmetry.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Review
Pharmacology & Pharmacy
Guillem Vargas-Nadal, Mariana Kober, Audrey Nsamela, Francesca Terenziani, Cristina Sissa, Silvia Pescina, Fabio Sonvico, Amirah Mohd Gazzali, Habibah A. Wahab, Luca Grisanti, Maria Eugenia Olivera, Maria Celeste Palena, Maria Laura Guzman, Laura Carolina Luciani-Giacobbe, Alvaro Jimenez-Kairuz, Nora Ventosa, Imma Ratera, Kevin D. Belfield, Ben M. Maoz
Summary: Fluorescent organic nanoparticles (FONs) are a class of nanostructures made up of organic components, which have high tunability and multifunctionality for diagnostic and therapeutic applications in biology and medicine. This review provides a tutorial overview of the design, preparation, characterization, and applications of FONs, as well as recent biomedical applications.
Article
Biochemistry & Molecular Biology
Clement Rouillon, Bruna Eckhardt, Leonie Kollenstart, Fabian Gruss, Alexander E. E. Verkennis, Inge Rondeel, Peter H. L. Krijger, Giulia Ricci, Alva Biran, Theo van Laar, Charlotte M. Delvaux de Fenffe, Georgiana Luppens, Pascal Albanese, Koichi Sato, Richard A. Scheltema, Wouter de Laat, Puck Knipscheer, Nynke H. Dekker, Anja Groth, Francesca Mattiroli
Summary: During cell cycle, CAF-1 plays a crucial role in chromatin replication, and its interaction with the DNA replication machinery remains unknown. The study reveals that the interaction between CAF-1 and replication forks differs between the leading and lagging strand. Biochemical reconstructions demonstrate that DNA and histones promote CAF-1 recruitment to its binding partner PCNA, and two CAF-1 complexes are required for efficient nucleosome assembly. In the context of the replisome, CAF-1 competes with Pol epsilon for PCNA binding on the leading strand, while it does not affect the activity of Pol delta on the lagging strand.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daniel Ramirez Montero, Humberto Sanchez, Edo van Veen, Theo van Laar, Belen Solano, John F. X. Diffley, Nynke H. Dekker
Summary: In this study, the authors examined the single-molecule motion of fully reconstituted and activated CMG helicases. They found that CMG can move on DNA through both unidirectional translocation and diffusion, with a preference for the former in the presence of ATP and the latter in the absence of ATP. They also demonstrated that nucleotide binding can halt the diffusive motion of CMG. These findings support a mechanism in which nucleotide binding allows newly assembled CMG to engage with the DNA, halting diffusion and facilitating DNA melting for replication initiation.
NATURE COMMUNICATIONS
(2023)
Article
Pharmacology & Pharmacy
Nicolo Bordignon, Mariana Kober, Giorgia Chinigo, Carlotta Pontremoli, Ettore Sansone, Guillem Vargas-Nadal, Maria Jesus Moran Plata, Alessandra Fiorio Pla, Nadia Barbero, Judit Morla-Folch, Nora Ventosa
Summary: Photodynamic therapy is a non-invasive therapeutic strategy that uses external light and a photosensitizer to destroy abnormal cells. The main challenges in this therapy are the photosensitivity, hydrophobicity, and tumor target avidity of the photosensitizer. In this study, brominated squaraine was successfully incorporated into Quatsome nanovesicles to overcome the solubility limitation and maximize the PDT effectiveness. This approach allows for a lower concentration of squaraine compared to traditional PDT, making it a promising photosensitizer for PDT.
Article
Multidisciplinary Sciences
Humberto Sanchez, Zhaowei Liu, Edo van Veen, Theo van Laar, John F. X. Diffley, Nynke H. Dekker
Summary: The study investigates the impact of chromatinizing origins of replication on ORC and MCM at the single-molecule level. The mobility of ORC is reduced, but its binding to the origin remains unchanged. MCM is efficiently recruited and spatially confined to the origin.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Adriana R. Kyvik, Ramon Roca-Pinilla, Karla Mayolo-Deloisa, Xavier Rodriguez Rodriguez, Marc Martinez-Miguel, Marta Martos, Mariana Kober, Nora Ventosa, Jaume Veciana, Judith Guasch, Elena Garcia-Fruitos, Anna Aris, Imma Ratera
Summary: In this study, novel biofunctionalized gold surfaces with the antimicrobial multidomain recombinant protein JAMF1 were developed. The immobilized JAMF1 protein successfully reduced biofilm formation of both Escherichia coli and carbapenem-resistant Klebsiella pneumoniae. This strategy provides new possibilities for biomolecule immobilization in fundamental biological studies and biotechnological applications.
MATERIALS ADVANCES
(2023)
Meeting Abstract
Biophysics
Nynke H. Dekker
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Louis Kuijpers, Theo van Laar, Richard Janissen, Nynke H. Dekker
Summary: This article presents a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases using multiplexed single-molecule magnetic tweezers (MT). The protocol provides a detailed description of the dsRNA construct preparation and the measurement of RdRp RNA synthesis kinetics using MT. This method is suitable for high-throughput screening of RdRp-targeting antiviral compounds for mechanistic function and efficacy.
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.
