Article
Biochemistry & Molecular Biology
Marlena Cichocka, Anna Karlik, Patrycja Plewka, Kishor Gawade, Agata Stepien, Patrycja Swiergiel, Ankur Gadgil, Katarzyna Dorota Raczynska
Summary: hnRNP UL1 plays multiple important roles in the cell nucleus, including involvement in DNA double-strand break repair, stimulation of ribosomal DNA gene transcription, and interaction with various related proteins.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Renke Tan, Wenhao Du, Yiyang Liu, Xiaoji Cong, Meirong Bai, Chenxiao Jiang, Zengxia Li, Minjia Tan, Dengke K. Ma, Qiang Huang, Wei Jiang, Yongjun Dang
Summary: The study shows that the Cas9 protein interacts with nucleolar proteins, and contains a nucleolus detention signal (NoDS). Mutated variants of Cas9 with NoDS have lower stability but minimal effect on gene editing activity. Overexpression of wild-type Cas9 affects transcription and protein translation in the host cell. This finding improves our understanding of Cas9's biological function and suggests the potential to enhance its safety for clinical use by removing the NoDS.
Article
Biochemical Research Methods
Philipp J. Schubert, Sven Dorkenwald, Michal Januszewski, Jonathan Klimesch, Fabian Svara, Andrei Mancu, Hashir Ahmad, Michale S. Fee, Viren Jain, Joergen Kornfeld
Summary: SyConn2 is an open-source toolkit for inferring and analyzing the connectomes in brain tissue using machine learning. It supports large datasets, provides a visualization interface, and allows for complex queries.
Article
Biochemistry & Molecular Biology
Nicolas Thelen, Jean Defourny, Denis L. J. Lafontaine, Marc Thiry
Summary: The study reveals the formation of heterochromatin patches in the nucleoplasm and intranucleolar regions of yeast nucleus under osmotic shock, as well as the presence of osmotic shock-resistant DNA in fibrillar cords and chromatin-associated granules. These findings suggest a less effective compartmentalized organization in yeast nucleus compared to mammals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Courtney M. Gauthier, Josey Legallais, Neda Savic, Sarah Moradi-Fard, Arden Grew, Martin Loe, Baran Kirlikaya, Jennifer Cobb, Christopher J. Nelson
Summary: Nucleoplasmin (NPM) histone chaperones regulate distinct processes in the nucleus and nucleolus. While intrinsically disordered regions (IDRs) are hallmarks of NPMs, it is not clear whether all NPM functions require these unstructured features. We assessed the importance of IDRs in a yeast NPM-like protein and found that regulation of rDNA copy number and genetic interactions with the nucleolar RNA surveillance machinery require the highly conserved FKBP prolyl isomerase domain, but not the NPM domain or IDRs. By contrast, transcriptional repression in the nucleus requires IDRs. Furthermore, multiple lysines in polyacidic serine/lysine motifs of IDRs are required for both lysine polyphosphorylation and NPM-mediated transcriptional repression. These results demonstrate that this NPM-like protein relies on IDRs only for some of its chromatin-related functions.
Article
Cell Biology
Fatemeh Mazloumi Gavgani, Thomas Karlsson, Ingvild L. Tangen, Andrea Papdine Morovicz, Victoria Smith Arnesen, Diana C. Turcu, Sandra Ninzima, Katharina Spang, Camilla Krakstad, Julie Guillermet-Guibert, Aurelia E. Lewis
Summary: In tumors, the PI3K catalytic subunits p110 alpha and p110 beta are differently expressed and targeted. While PIK3CB is less mutated compared to PIK3CA, it may still contribute to tumorigenesis in PTEN-deficient tumors. The high levels of p110 beta in the nucleus and its nucleolar role in endometrial cancer cells suggest its potential involvement in tumorigenesis.
JOURNAL OF CELL SCIENCE
(2021)
Article
Materials Science, Multidisciplinary
Mianzhen Mo, Zhijiang Chen, Siegfried Glenzer
Summary: Intense ultrafast laser excitation leads materials to highly nonequilibrium states with complex solid-liquid phase transitions, resulting in warm dense matter (WDM) conditions. Recent studies using mega-electron-volt ultrafast electron diffraction have provided atomic-level insights into melting behavior of materials under extreme conditions, such as warm dense gold and radiation-damaged tungsten, revealing the sensitivity of melting to factors like electron-ion coupling rates and vacancy defect clusters.
Article
Neurosciences
Szi-Chieh Yu, Jana F. Liewald, Jiajie Shao, Wagner Steuer Costa, Alexander Gottschalk
Summary: The release of neuropeptides is crucial for neuromodulation, and our study demonstrates that synapsin SNN-1 is necessary for cAMP-dependent neuropeptide release in Caenorhabditis elegans. Through capturing dense core vesicles (DCVs) at synapses, synapsin plays a key role in making them available for release. Mutations in synapsin result in altered neuropeptide release and behavior in the nematode, indicating the importance of synapsin in this process.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Nanoscience & Nanotechnology
Hui-Dong Qian, Jung Tae Lim, Jong-Woo Kim, Yang Yang, Kyung Mox Cho, Jihoon Park, Chul-Jin Choi
Summary: This study successfully produced high density sintered Sm(Fe0.8Co0.2)(11)Ti bulk magnets using a newly developed high pressure pressing method. The purity of the hard magnetic ThMn12 phase in the bulk magnet was over 97 wt.%. The phase transformation behavior from amorphous to ThMn12 phase during heat treatment was systematically investigated, achieving high remanent magnetization and maximum energy product. The achieved maximum energy product in the bulk magnet is the highest reported among all SmFe12-based bulk magnets.
SCRIPTA MATERIALIA
(2021)
Article
Biochemistry & Molecular Biology
Tomoko Okada, Toshihiko Ogura
Summary: Autophagy is a crucial intracellular self-devouring system that relies on various autophagy-related proteins. Researchers used a novel scanning electron-assisted dielectric microscope to observe cells containing LC3 and Atg12-containing autophagosomes, revealing differences in the localization and distribution of these proteins during formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Interdisciplinary Applications
Kisuk Lee, Ran Lu, Kyle Luther, H. Sebastian Seung
Summary: This study demonstrates that dense voxel embeddings learned through deep metric learning can accurately segment neurons from 3D electron microscopy images. A metric graph is constructed from the dense voxel embeddings generated by a convolutional network, and partitioning the graph with long-range edges as repulsive constraints results in precise initial segmentation, particularly useful for very thin objects. The convolutional embedding network is reused without modification to aggregate systematic splits caused by complex self-contact motifs, achieving state-of-the-art accuracy in reconstructing 3D neurons from brain images acquired through serial section electron microscopy. The proposed object-centered representation may have broader applications in automated neural circuit reconstruction.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2021)
Article
Biochemistry & Molecular Biology
Noah J. Harris, Meredith L. Jenkins, Udit Dalwadi, Kaelin D. Fleming, Sung-Eun Nam, Matthew A. H. Parson, Calvin K. Yip, John E. Burke
Summary: Transport Protein Particle complexes (TRAPP) are highly conserved regulators of membrane trafficking, with distinct TRAPPII and TRAPPIII complexes showing specificity towards different Rab GTPases. Biochemical assays, HDX-MS, and electron microscopy were used to study the regulation of TRAPPII and TRAPPIII complexes, revealing differences in GEF activity, protein dynamics, and membrane association. The results provide insights into the functions of TRAPP complexes and their mechanisms of achieving Rab specificity.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Neurosciences
Rainer W. Friedrich, Adrian A. Wanner
Summary: Dynamic connectomics in zebrafish can provide insights into the circuit mechanisms underlying higher-order neuronal computations by combining reconstructions of wiring diagrams with measurements of neuronal population activity and behavior.
ANNUAL REVIEW OF NEUROSCIENCE, VOL 44, 2021
(2021)
Article
Environmental Sciences
Sukanya Mehra, Pooja Chadha
Summary: The study demonstrated the genotoxic impact of naphthalene-2-sulfonate (2NS) on fresh water fish Channa punctatus, showing time and dose-dependent DNA damage that peaked after 60 days of exposure but exhibited some recovery after 30 days post-exposure. Spectral evaluation and structural analysis confirmed the toxicity of 2NS on the fish, supporting the findings of comet assay and micronucleus test.
Article
Biochemistry & Molecular Biology
Tomoko Okada, Tomoaki Iwayama, Taku Ogura, Shinya Murakami, Toshihiko Ogura
Summary: The synthesis and transfer of melanins in mammals have been investigated using fixed cells, but this study used scanning electron-assisted dielectric microscopy (SE-ADM) to observe live mammalian cells. Melanosomes were observed as black particles in human melanoma MNT-1 cells, with a toroidal structure in melanoma cells and an ellipsoidal structure in normal melanocytes. A deep neural network (DNN) analysis system was developed to automatically detect and analyze melanosomes in terms of diameter and roundness. SE-ADM and the established DNN analysis system can also be used for the study of other biological particles.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Guus Gijsbertus Hubert van den Akker, Federico Zacchini, Bas Adrianus Catharina Housmans, Laura van der Vloet, Marjolein Maria Johanna Caron, Lorenzo Montanaro, Tim Johannes Maria Welting
Summary: Bicistronic reporter assays are crucial for transgene expression and understanding of internal ribosomal entry site translation. Analysis of literature revealed methodological variability in experiment and data presentation. Adherence to recommended practices can enhance transparency and reproducibility of bicistronic reporter studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Noemi Laprovitera, Mattia Riefolo, Elisa Porcellini, Giorgio Durante, Ingrid Garajova, Francesco Vasuri, Ariane Aigelsreiter, Nadia Dandachi, Giuseppe Benvenuto, Federico Agostinis, Silvia Sabbioni, Ioana Berindan Neagoe, Chiara Romualdi, Andrea Ardizzoni, Davide Trere, Martin Pichler, Antonietta D'Errico, Manuela Ferracin
Summary: In this study, miRNA expression profiling was successfully used to infer the tissue of origin for metastatic cancers of unknown or uncertain origin, providing diagnostic and prognostic value. The molecular test was able to identify the primary site within a week from biopsy, with the most frequently predicted origins being gastrointestinal, pancreas, breast, lung, and bile duct. Additionally, a panel of 13 miRNAs showed prognostic value and relationship with overall survival in CUP patients.
MOLECULAR ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Benno Verbelen, Tiziana Girardi, Sergey O. Sulima, Stijn Vereecke, Paulien Verstraete, Jelle Verbeeck, Jonathan Royaert, Sonia Cinque, Lorenzo Montanaro, Marianna Penzo, Maya Imbrechts, Nick Geukens, Thomas Geuens, Koen Dierckx, Daniele Pepe, Kim Kampen, Kim De Keersmaecker
Summary: This study presents a novel approach to improve protein yields in mammalian cells by directly engineering the cellular translation machinery. The introduction of RPL10-R98S mutation was found to enhance translation levels and fidelity, reduce proteasomal activity, and increase the production of recombinant proteins. However, the extent of production gain depends on culture conditions, cell type, and the nature of the expressed protein.
ENGINEERING IN LIFE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Giulia Venturi, Federico Zacchini, Cinzia Lucia Vaccari, Davide Trere, Lorenzo Montanaro
Summary: Three isoforms of 5.8S rRNA have been identified in human cells, with little known about the specific role of 5.8S long. Traditional techniques have limited studies on the isoforms, but a newly optimized method combining primer extension with fluorescently labeled reverse primers allows for rapid and safe quantification of the isoforms' abundance, even in samples previously considered unsuitable.
Article
Public, Environmental & Occupational Health
Elisa Maietti, Manfredi Greco, Chiara Reno, Flavia Rallo, Davide Trere, Elena Savoia, Maria Pia Fantini, Lawrence M. Scheier, Davide Gori
Summary: During the initial phase of the COVID-19 pandemic, the University of Bologna Medical School surveyed medical students, finding that students had the highest perceived risk of infection in hospital activities. Despite adopting most evidence-based preventive measures, students were only able to use an average of four out of seven types of personal protective equipment.
FRONTIERS IN PUBLIC HEALTH
(2021)
Review
Genetics & Heredity
Chiara Barozzi, Federico Zacchini, Sidra Asghar, Lorenzo Montanaro
Summary: This article provides a summary of the methods currently available for studying rRNA pseudouridylation and discusses the perspectives offered by newly developed approaches.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Laura Gramantieri, Francesca Fornari, Catia Giovannini, Davide Trere
Summary: miRNAs in HCC play a bidirectional role in both immune-related pathways and oncogenic pathways. Understanding their function can help identify patient subgroups and design personalized treatment strategies.
Article
Genetics & Heredity
Lorenza Bacci, Valentina Indio, Guglielmo Rambaldelli, Cristina Bugarin, Franco Magliocchetti, Alberto Del Rio, Daniela Pollutri, Fraia Melchionda, Andrea Pession, Marina Lanciotti, Carlo Dufour, Giuseppe Gaipa, Lorenzo Montanaro, Marianna Penzo
Summary: T-cell acute lymphoblastic leukemia (T-ALL) is a subtype of ALL with various genetic lesions, including mutations in genes encoding for ribosomal proteins (RPs). This study found that mutations in RPs tend to cluster together in different patients with T-ALL, suggesting that their co-occurrence may confer an advantage to leukemia cells. Additionally, a novel mutation in the RPL10 gene associated with a defect in protein synthesis was identified. These findings indicate the importance of considering genetic alterations involving ribosome biogenesis and translational control in precision medicine for T-ALL.
FRONTIERS IN GENETICS
(2022)
Review
Medicine, General & Internal
Carlotta Mazzitelli, Donatella Santini, Angelo Gianluca Corradini, Claudio Zamagni, Davide Trere, Lorenzo Montanaro, Mario Taffurelli
Summary: Liquid biopsy (LB) is an emerging diagnostic tool that analyzes biomarkers in blood to provide information about tumor genetics and response to therapy. In breast cancer patients, LB has shown potential in early detection, monitoring tumor progression and recurrence, and predicting patient response to therapy. However, LB still faces challenges such as lack of standardized assays and further validation. Future applications of LB include identifying minimal residual disease, early detection of recurrence, and monitoring treatment response in various cancer types.
Article
Biotechnology & Applied Microbiology
Federico Zacchini, Giulia Venturi, Veronica De Sanctis, Roberto Bertorelli, Claudio Ceccarelli, Donatella Santini, Mario Taffurelli, Marianna Penzo, Davide Trere, Alberto Inga, Erik Dassi, Lorenzo Montanaro
Summary: The study reveals that dyskerin depletion affects the expression and association with polysomes of specific mRNA isoforms with H/ACA box snoRNA-containing introns, leading to post-transcriptional alterations of gene expression. Dysregulation of dyskerin may impact the dependence on nuclear hormone receptor ligands in breast cancer cells, with implications for the prognosis of primary breast cancer patients.
Meeting Abstract
Oncology
Martina Ghetti, Ivan Vannini, Samantha Bruno, Chiara Liverani, Debora Traversa, Lorenzo Montanaro, Roberta Napolitano, Andrea Ghelli Luserna di Rora, Toni Ibrahim, Clelia Tiziana Storlazzi, Giovanni Martinelli, Giorgia Simonetti
Article
Cell Biology
Igor De Nicola, Ania Naila Guerrieri, Marianna Penzo, Claudio Ceccarelli, Antonio De Leo, Davide Trere, Lorenzo Montanaro
HISTOLOGY AND HISTOPATHOLOGY
(2020)