Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Law
Xiaohong Yu, Zhaoyang Sun
Summary: This study explores how Chinese judges engage in collegial panels and the factors influencing this behavior. Through analyzing 23,564 cases from a local court in Beijing between 2015 and 2017, the study finds that judges tend to form panels with junior judges for mundane cases, but collaborate with more capable judges for complex cases. The research also sheds light on the characteristics of judicial politics in China and has the potential to enhance our understanding of collective judicial decision-making in transitional societies.
JOURNAL OF EMPIRICAL LEGAL STUDIES
(2022)
Review
Plant Sciences
Yanliang Wang, Xinhua He, Fuqiang Yu
Summary: This article summarizes studies on mycorrhizal-mediated host and non-host plant interactions. The research shows that non-host plants can have contact with the hyphae of host plants without forming typical mycorrhizal structures. This non-typical mycorrhizal colonization inhibits the growth but enhances the induced system resistance of non-host plants. Molecular analyses suggest that the colonization of non-hosts by arbuscular mycorrhizal fungi differs from that of pathogenic and endophytic fungi, and the hyphae in non-host roots may have unknown functions. Therefore, non-host plants are also important players in common mycorrhizal networks.
Article
Psychology, Clinical
Tsahi Hayat, Dimitrina Dimitrova, Barry Wellman
Summary: The Covid-19 pandemic has affected organizations' working environment and productivity. The transition to remote work due to lockdown regulations has affected the productivity of researchers in distributed collaborative networks. The diversity of researchers' networks and the presence of structural holes have a positive impact on their productivity. Seniority also moderates the relationship between diversity and productivity.
AMERICAN BEHAVIORAL SCIENTIST
(2023)
Article
Multidisciplinary Sciences
Zachery Mielko, Yuning Zhang, Harshit Sahay, Yiling Liu, Matthew A. Schaich, Brittani Schnable, Abigail M. Morrison, Debbie Burdinski, Sheera Adar, Miles Pufall, Bennett Van Houten, Raluca Gordan, Ariel Afek
Summary: Somatic mutations are highly concentrated at transcription factor binding sites, particularly in melanomas with UV-induced mutations. The inefficient repair of UV lesions within TF-binding sites is proposed as one of the main mechanisms for this hypermutation pattern due to competition between TFs and DNA repair proteins. However, the impact of UV irradiation on TF binding to DNA and whether TFs maintain specificity for their DNA sites after UV exposure remain unclear. Using a high-throughput approach called UV-Bind, researchers found that UV lesions significantly altered the DNA binding preferences of all tested TFs, with a decrease in binding specificity. Despite the overall reduction in DNA-binding specificity, TFs can still compete with repair proteins for lesion recognition, consistent with their specificity for UV-irradiated DNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Hieu T. Van, Peter R. Harkins, Avni Patel, Abhinav K. Jain, Yue Lu, Mark T. Bedford, Margarida A. Santos
Summary: This study provides an in-depth characterization of the PHF20 and PHF20L1 proteins in the context of the NSL complex. It reveals the existence of two distinct NSL complexes, exclusively containing either PHF20 or PHF20L1, and shows that both proteins bind to the same genomic regions. Deletion of PHF20 and PHF20L1 does not affect gene expression or the recruitment of the NSL complex to target gene promoters, suggesting the presence of an alternative mechanism for the transcription of critical cellular functions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Computer Science, Artificial Intelligence
Nadine Braun, Martijn Goudbeek, Emiel Krahmer
Summary: This article explores the impact of linguistic and pragmatic context on individual word valence and emotionality. The study finds that context significantly affects the determination of word and sentence valence. Moreover, context-sensitive lexicons show greater accuracy in determining sentence valence compared to existing affective lexicons.
IEEE TRANSACTIONS ON AFFECTIVE COMPUTING
(2022)
Review
Genetics & Heredity
Martha L. Bulyk, Jacques Drouin, Melissa M. Harrison, Jussi Taipale, Kenneth S. Zaret
Summary: This article discusses the important roles of pioneer factors in gene regulation, including their unique ability to bind to chromatin and promote its remodeling for gene expression. It highlights the unique insights that exploring these proteins can offer in understanding gene regulation and cellular identity.
NATURE REVIEWS GENETICS
(2023)
Article
Medicine, Research & Experimental
Chunshen Long, Hanshuang Li, Pengfei Liang, Lemuge Chao, Yan Hong, Junping Zhang, Qilemuge Xi, Yongchun Zuo
Summary: Single-cell studies have revealed that somatic cell reprogramming is a continuous process of cell fate transition. The activation of pluripotency networks and the mesenchymal-epithelial transition are crucial for successful reprogramming. By reconstructing cellular trajectory, we identified key factors and genes driving cell fate bifurcations, and found several drivers for successful reprogramming and alternative fates.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Biochemistry & Molecular Biology
Kuan-Ting Hsin, Min-Che Hsieh, Yu-Hsuan Lee, Kai-Chun Lin, Yi-Sheng Cheng
Summary: This study reconstructed the phylogeny of WRKY across the plant kingdom and characterized the DNA-binding profile of Arabidopsis thaliana WRKY (WRKY54) based on its W-box recognition sequence. It was found that WRKY TFs could be separated into five clades and the functional zinc-finger motif at the C-terminal of WRKY appeared after several nucleotide substitutions in the zinc-finger region in chlorophytes. The study also showed that W-box flanking regions affect the binding ability of WRKY54.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Yizhao Luan, Zehua Tang, Yao He, Zhi Xie
Summary: In this study, evidence was provided showing that coevolving residues in TF domains contribute to DNA binding specificity. It was demonstrated that the coevolving residues are more likely to coevolve with other TF subclass-determining sites and mutation of these coevolving residues could significantly reduce the stability of the TF-DNA complex. Overall, this study expands our understanding of the interaction among coevolving residues in TFs and their importance in transcriptional regulation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Szymon Turek, Aparna, Agnieszka Skarzynska, Wojciech Plader, Magdalena Pawelkowicz
Summary: Through analysis of the tomato genome, researchers found that transcription factors play an important role in sex determination processes. They identified several transcription factor families, including NAC, bHLH, MYB, and bZIP, that were highly enriched in sex comparisons. By constructing an interaction network, the researchers also identified the most influential transcription factor families, such as AP/ERF, DOF, MYB, and others. These findings contribute to our understanding of the molecular genetics and functional mechanisms underlying sex determination processes in tomatoes.
Article
Plant Sciences
Yi Xu, Juhua Liu, Caihong Jia, Wei Hu, Shun Song, Biyu Xu, Zhiqiang Jin
Summary: The overexpression of MaPIP1;1 in banana was found to enhance the plant's tolerance to multiple stresses by reducing ion leakage and malondialdehyde content, increasing proline, chlorophyll, soluble sugar, and ABA contents. Additionally, the transgenic plants exhibited higher Na+ and K+ content and K+/Na+ ratio under high salt and recovery conditions. The upregulation of ABA biosynthesis and response genes in the transgenic lines under stress conditions indicated a potential mechanism for improved stress resistance.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Immunology
Rebecca Harris, Mobin Karimi
Summary: Transcription factors have a major role in regulating and coordinating immune responses, and the regulatory networks can be altered in different immune contexts. While these networks have been extensively studied in canonical immune contexts, the transcription factor landscape during alloactivation is still unclear. This review focuses on how transcription factors contribute to the functioning of mature alloactivated T cells and explores the regulatory network they form in controlling alloresponses, specifically in graft-versus-host disease (GVHD) and graft-versus-tumor (GVT) responses.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Plant Sciences
Norbert Andrasi, Aladar Pettko-Szandtner, Laszlo Szabados
Summary: Plant heat shock factors (HSFs) are encoded by large gene families and are involved in responses to high temperatures and various abiotic stresses. They are regulated primarily at the transcript level, with alternative splicing and post-translational modifications providing additional variability. Plant HSFs participate in a complex network of protein-protein interactions and play crucial roles in transcriptional control.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Andrea Vandelli, Fernando Cid Samper, Marc Torrent Burgas, Natalia Sanchez De Groot, Gian Gaetano Tartaglia
Summary: Condensation, or liquid-like phase separation, is an important phenomenon for the spatiotemporal regulation of molecules within the cell. Recent studies have shown that components of phase-separated organelles like Stress Granules (SGs) and Processing Bodies (PBs) exhibit high variability and dynamics in their composition and molecular organization. The formation of SGs and PBs is regulated by a dense contact network involving both RNAs and proteins, and the molecular architecture of these organelles is not yet fully understood.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Cell Biology
Alexandra Louka, Sara Bagnoli, Jakob Rupert, Benjamin Esapa, Gian Gaetano Tartaglia, Alessandro Cellerino, Annalisa Pastore, Eva Terzibasi Tozzini
Summary: Research has shown that the killifish Nothobranchius furzeri is a suitable animal model for studying the mechanism of TDP-43 aggregation due to its short lifespan and clear aging phenotype. The study demonstrated that N. furzeri's TDP-43 homologs share high sequence homology with the human protein and spontaneously form insoluble intracellular aggregates with amyloid characteristics during aging, making it a valuable new model for TDP-43-related pathologies.
Article
Biochemical Research Methods
Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia
Summary: In this study, a webserver called Thermometer was developed to assess the thermal stability of proteins using structural information. The server is publicly available and has a user-friendly interface.
Article
Physics, Multidisciplinary
Michele Monti, Jonathan Fiorentino, Edoardo Milanetti, Giorgio Gosti, Gian Gaetano Tartaglia
Summary: In this study, synthetic time series gene expression data was generated and a dual attention RNN model was used to accurately predict gene temporal dynamics. The attention mechanism of the RNN was analyzed using graph theory, allowing for the hierarchical distinction of different GRN architectures.
Article
Multidisciplinary Sciences
Claudia Cava, Alexandros Armaos, Benjamin Lang, Gian G. Tartaglia, Isabella Castiglioni
Summary: Using bioinformatics algorithms, we identified differentially expressed genes, long non-coding RNAs, and RNA binding proteins for different subtypes of breast cancer, and proposed potential signature biomarkers specific to each subtype. We validated these biomarkers using a machine learning approach and found some novel prognostic biomarkers and therapeutic targets.
SCIENTIFIC REPORTS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Andrea Cerase, J. Mauro Calabrese, Gian Gaetano Tartaglia
Summary: This study reveals the molecular mechanisms through which the long non-coding RNA Xist silences genes on the entire X chromosome. By forming dimeric foci, Xist seeds the formation of large protein assemblies that contain various proteins, including SPEN, CIZ1, CELF, PTBP1, and components of Polycomb repressive complexes 1 and 2. These protein assemblies extend spatially beyond each Xist focus, explaining how this long non-coding RNA triggers silencing across the entire chromosome.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andrea Vandelli, Giovanni Vocino, Gian Gaetano Tartaglia
Summary: Identifying human proteins that interact with SARS-CoV-2 genome is important to understand its replication and to identify therapeutic strategies. Recent studies have unveiled protein interactions of SARS-CoV-2 in different cell lines and through a number of high-throughput approaches. This study compared four experimental and one computational studies to characterize the interactions of SARS-CoV-2 genomic RNA. The findings suggest that SARS-CoV-2 genome establishes stable interactions only with a few proteins, while many proteins bind less tightly.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Riccardo Delli Ponti, Laura Broglia, Andrea Vandelli, Alexandros Armaos, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
Summary: RNA molecules undergo chemical modifications that can alter their structure and molecular interactions. This study introduces a predictor of A-to-I effects on RNA structure and finds enrichment of double-stranded regions caused by A-to-I in long intergenic noncoding RNAs. Investigation of specific cases suggests that A-to-I editing is linked to the alteration of interaction sites with proteins involved in phase separation.
Article
Biochemistry & Molecular Biology
Alessio Colantoni, Davide Capauto, Vincenzo Alfano, Eleonora D'Ambra, Sara D'Uva, Gian Gaetano Tartaglia, Mariangela Morlando
Summary: Deregulation of RNA metabolism, specifically mutations on RNA-binding proteins (RBPs) or on proteins involved in RNA metabolism, is a key factor in the degeneration of motor neurons in ALS. The ALS-linked mutation of the RBP FUS greatly affects various RNA-related processes, including splicing regulation and circRNA formation. In this study, the impact of the FUS mutation on circRNA levels and its binding preferences were investigated using in vitro-derived human motor neurons. The findings suggest potential implications of cytoplasmic circRNAs as miRNA sponges in ALS pathogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Nuria Crua Asensio, Stefano Rizzieri, Alessandro Cuomo, Gian Gaetano Tartaglia, Elsa Zacco
Summary: Protein-RNA interactions are crucial for gene expression and cellular functions. To efficiently identify the binding partners of RNA molecules, especially non-canonical ones, an improved method was developed. This method involves pull-down and characterization of interacting proteins using biotinylated RNA loaded on streptavidin-coated beads. The protocol was validated by quantifying the enrichment of a known RNA binder compared to a negative control using mass spectrometry and confirming the selective interactions of computationally predicted protein binders by western blot. This protocol allows for the study of protein-RNA interactions in near-physiological conditions, aiding in the discovery of unique and unpredicted interactions.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Andre P. Gerber, Gian Gaetano Tartaglia
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jakob Rupert, Michele Monti, Elsa Zacco, Gian Gaetano Tartaglia
Summary: This study characterizes the physico-chemical properties of regions involved in amyloid aggregation using a computational approach, and investigates the influence of RNA on protein assembly. Experimental data shows that while the core region is hydrophobic and highly ordered, external regions exhibit a distinct tendency to interact with nucleic acids. RNA is found to accelerate aggregation, especially in a mutant truncated protein with a higher propensity for RNA interaction. The findings suggest that RNA sequestration might be a common phenomenon linked to protein aggregation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Andrea Vandelli, Magdalena Arnal Segura, Michele Monti, Jonathan Fiorentino, Laura Broglia, Alessio Colantoni, Natalia Sanchez de Groot, Marc Torrent Burgas, Alexandros Armaos, Gian Gaetano Tartaglia
Summary: PRALINE is a database that provides information on protein-protein, protein-RNA, and RNA-RNA interactions in stress granules, processing bodies, and other assemblies. It also reports the liquid-liquid and liquid-solid phase separation propensities of proteins and provides predicted secondary structure content of RNAs.
Article
Biochemistry & Molecular Biology
Thomas Schwarzl, Sudeep Sahadevan, Benjamin Lang, Milad Miladi, Rolf Backofen, Wolfgang Huber, Matthias W. Hentze, Gian Gaetano Tartaglia
Summary: Enhanced crosslinking and immunoprecipitation sequencing (eCLIP-seq) is a method for detecting RNA-binding protein binding sites. However, current analysis strategies have low replication and high false positive rates. DEWSeq, a R/Bioconductor package, improves the detection of binding regions by utilizing replicate information and size-matched input controls. It has been shown to significantly increase the number and quality of binding sites.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Clinical Neurology
Magdalena Arnal Segura, Giorgio Bini, Dietmar Fernandez Orth, Eleftherios Samaras, Maya Kassis, Fotis Aisopos, Jordi Rambla De Argila, George Paliouras, Peter Garrard, Claudia Giambartolomei, Gian Gaetano Tartaglia
Summary: In this study, tree-based machine learning algorithms were used to discriminate Alzheimer's disease from unaffected individuals, leading to the identification of specific genomic profiles defined by interactions among single nucleotide variants in gene regions such as PVRL2, TOMM40, APOE, and APOC1.
ALZHEIMER'S & DEMENTIA: DIAGNOSIS, ASSESSMENT & DISEASE MONITORING
(2022)
