bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthologous transcription factor replacement reveals that stable TFIIIC complexes are required for proper mitotic chromosome segregation
Authors: Gupta Akshi , Hsu Po-Chen , Litan Richard Ron R. , Leu Jun-Yi 
Published: February 2025

AbstractTranscription factors are speculated to play crucial roles in adaptive evolution. Using ortholog replacement of essential transcription factors (eTFs) from other yeast species, we investigated how eTFs can change. Several orthologs could not fully complementSaccharomyces cerevisiaemutants, indicating that functions or interactions of these eTFs have changed, rendering them incompatible. We further characterized TFIIIC, a fast-evolving protein complex that assists RNA polymerase III-mediated transcription, which exhibited complete or partial incompatibility in several subunits. In the orthologous Tfc7-replacement line, binding of TFIIIC to tRNA genes was reduced, yet tRNA abundance was not severely affected. However, the chromosomes of Tfc7-replacement cells were often mis-segregated during mitosis and their fitness was further reduced in a spindle checkpoint mutant. Our chromatin-immunoprecipitation experiments uncovered that unstable TFIIIC binding results in defective cohesion loading, leading to chromosome mis-segregation. Swapping the highly divergent C-terminal domain of Tfc7 orthologs rescued its interaction with Tfc1 and cell fitness, supporting that incompatibility is caused by altered interactions between complex subunits. Our results reveal distinct essential functions of a well-studied protein complex.
AnchoRNA: Full virus genome alignments through conserved anchor regions
Authors: Eulenfeld Tom , Triebel Sandra , Marz Manja 
Published: February 2025

AbstractMotivationMultiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), high number of sequences, sequence divergence, and high computational complexity, as e.g., in the context of secondary structure prediction. Standard alignment methods often face these issues, especially when processing highly variable sequences or when specific phylogenetic analysis is required on selected subsequences. We presentAnchoRNA, a Python-based command line tool designed to identify conserved regions, or anchors, within coding sequences. These anchors define split positions, guiding the alignment of complex viral genomes, including those with significant secondary structures.AnchoRNAenhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. The presented approach can be particularly useful when designing primers conserved across a virus family.ResultsAnchoRNAguided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representativePestivirusgenomes,AnchoRNAidentified 56 anchors that are crucial for guiding the alignment process. The incorporation of these anchors led to significant improvements across all tested alignment tools, highlighting the effectiveness ofAnchoRNAin enhancing alignment quality, especially in complex viral genomes.AvailabilityAnchoRNAis available to the scientific community under the MIT license on GitHub athttps://github.com/rnajena/anchorna, with releases archived on Zenodo. The package includes a tutorial featuring aPestivirusdataset and is compatible with all platforms that support Python.
Cellular mechanisms of early brain overgrowth in autistic children: elevated levels of GPX4 and resistance to ferroptosis
Authors: Chen Siwei , Shcherbina Anna , Schafer Simon T. , Mattingly Zoe Alexandra , Ramesh Janani , Narayanan Cyndhavi , Banerjee Sravani , Heath Brianna , Regester Melissa , Chen Ivette , Thakurela Sudhir , Hallmayer Joachim , O’Hara Ruth , Solomon Marjorie , Nordahl Christine Wu , Amaral David G. , Chetty Sundari 
Published: February 2025

AbstractAutistic individuals with disproportionate megalencephaly (ASD-DM), characterized by enlarged brains relative to body height, have higher rates of intellectual disability and face more severe cognitive challenges than autistic children with average brain sizes. The cellular and molecular mechanisms underlying this neurophenotype remain poorly understood. To investigate these mechanisms, we generated human induced pluripotent stem cells from non-autistic typically developing children and autistic children with and without disproportionate megalencephaly. We assessed these children longitudinally from ages two to twelve years using magnetic resonance imaging and comprehensive cognitive and medical evaluations. We show that neural progenitor cells (NPCs) derived from ASD-DM children exhibit increased rates of cell survival and suppressed cell death, accompanied by heightened oxidative stress and ferrous iron accumulation. Despite these stressors, ASD-DM NPCs actively suppress apoptosis and ferroptosis by regulating proteins such as caspase-3 (CASP3), poly(ADP-ribose) polymerase 1 (PARP1), and glutathione peroxidase 4 (GPX4). Cellular ferroptotic signatures are further supported by elevated expression of selenocysteine genes, includingGPX4, in the blood of ASD-DM children and their mothers, suggesting potential hereditary or environmental influences. Furthermore, we show that peripheral expression ofGPX4and other selenocysteine genes correlate with cognitive outcomes (IQ). These findings underscore the role of ferroptosis in autism, pointing to potential diagnostic biomarkers and targets for intervention.
Pathological mutation in SMN impairs modulation of GAR1 phase separation linking condensate dysfunction to Spinal Muscular Atrophy
Authors: Félix Sara S. , O’Toole Philip , Oliveira Nuno A. S. , Pinho Brígida R. , Blacker Thomas S. , Fernandes Fábio , Oliveira Jorge M. A. , Oroz Javier , Laurents Douglas V. , Cabrita Eurico J. 
Published: February 2025

SummaryPathological mutations in liquid-liquid phase separation (LLPS) scaffold proteins have been linked to biomolecular condensate dysfunction in neurodegenerative diseases, while the possible impact of client protein mutations remains unclear. In spinal muscular atrophy (SMA), the disease-associated E134K mutation in the Tudor domain (TD) of the survival motor neuron (SMN) protein disrupts its interaction with GAR1, an RGG-rich protein within the H/ACA small nucleolar ribonucleoprotein complex. The consequences of this impaired interaction have not been elucidated. Here, we identified GAR1 as an LLPS scaffold protein that is phase separated in nuclear compartments and forms gel-like condensates via complex coacervation with RNAin vitro. In cells, we reveal that SMN co-localizes with GAR1 in Cajal bodies and modulates its dynamics. Using confocal microscopy and NMR spectroscopy, we further show that SMN TD is a client protein that regulates the architecture and dynamics of GAR1 condensates through competitive RNA interactions, implicating GAR1 phase separation in RNA accumulation and release processes regulated by SMN. Notably, the SMA-associated E134K variant of SMN exhibits a reduced affinity for GAR1, impairing the modulation of GAR1 condensates and displacement RNA. Our findings suggest a mechanistic link between phase separation dysregulation and SMA, driven by disrupted scaffold-client interactions, that highlights the therapeutic potential of targeting SMN-dependent condensate regulation in SMA.
Parallel hierarchical encoding of linguistic representations in the human auditory cortex and recurrent automatic speech recognition systems
Authors: Keshishian Menoua , Mischler Gavin , Thomas Samuel , Kingsbury Brian , Bickel Stephan , Mehta Ashesh D. , Mesgarani Nima 
Published: February 2025

AbstractThe human brain’s ability to transform acoustic speech signals into rich linguistic representations has inspired advancements in automatic speech recognition (ASR) systems. While ASR systems now achieve human-level performance under controlled conditions, prior research on their parallels with the brain has been limited by the use of biologically implausible models, narrow feature sets, and comparisons that primarily emphasize predictability of brain activity without fully exploring shared underlying representations. Additionally, studies comparing the brain to text-based language models overlook the acoustic stages of speech processing, an essential part in transforming sound to meaning. Leveraging high-resolution intracranial recordings and a recurrent ASR model, this study bridges these gaps by uncovering a striking correspondence in the hierarchical encoding of linguistic features, from low-level acoustic signals to high-level semantic processing. Specifically, we demonstrate that neural activity in distinct regions of the auditory cortex aligns with representations in corresponding layers of the ASR model and, crucially, that both systems encode similar features at each stage of processing—from acoustic to phonetic, lexical, and semantic information. These findings suggest that both systems, despite their distinct architectures, converge on similar strategies for language processing, providing insight in the optimal computational principles underlying linguistic representation and the shared constraints shaping human and artificial speech processing.
An HIV-1 Reference Epitranscriptome
Authors: Bosmeny Michael S. , Pater Adrian A. , Zhang Li , Sha Beverly E. , Lyu Zidi , Larkai Lydia , Damha Masad J. , Mamede Joao I. , Gagnon Keith T. 
Published: February 2025

ABSTRACTPost-transcriptional chemical modifications to RNA, or the epitranscriptome, play important roles in RNA metabolism, gene regulation, and human disease, including viral pathogenesis. Modifications to the RNA viral genome and transcripts of human immunodeficiency virus 1 (HIV-1) have been reported, including methylation of adenosine (m6A) and cytosine (m5C), acetylation of cytosine, pseudouridylation (psi), and conversion of adenosine to inosine, and their effects on virus and host biology have been investigated. However, diverse experimental approaches have been used, making clear correlations across studies difficult to assess. To address this need, we propose the establishment of a reference HIV-1 epitranscriptome. We sequenced the model NL4-3 HIV-1 genome from infected Jurkat CD4+ T cells cells using the latest nanopore chemistry, custom RNA preparation methods, and commercial base-calling algorithms. This resulted in a reproducible sense and preliminary antisense HIV-1 epitranscriptome where m6A, m5C, psi, ands inosine could be identified by multiplexed base-calling. Multiplexed base-calling miscalled modifications due to sequence and neighboring modification contexts, which we demonstrate can be corrected with synthetic HIV-1 RNA fragments. We validate m6A modification sites with a small molecule inhibitor of methyltransferase-like 3 (METTL3), STM2457. We conclude that modifications do not change substantially under combination antiretroviral therapy (cART) treatment or in primary CD4+ T cells. Samples from patients living with HIV reveal conservation of certain modifications, such as m6A. Our approach and reference data offer a straightforward benchmark that can be adopted to help advance rigor, reproducibility, and uniformity across future HIV-1 epitranscriptomics studies.
Ku suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion
Authors: Zhu Yimeng , Li Angelina , Maji Suvrajit , Lee Brian J. , Korn Sophie M. , Gertie Jake A. , Dorrity Tyler J. , Wang Jianhua , Wang Kyle J. , Pelletier Amandine , Moakley Daniel F. , Kelly Rachel D. , Holmes Antony B. , Rabadan Raul , Edgell David R. , Schild Poulter Caroline , Modesti Mauro , Steckelberg Anna-Lena , Hendrickson Eric A. , Chung Hachung , Zhang Chaolin , Zha Shan 
Published: February 2025

SummaryKu70 and Ku80 form Ku, a ring-shaped protein that initiates the non-homologous end-joining (NHEJ) DNA repair pathway.1Specifically, Ku binds to double-stranded DNA (dsDNA) ends and recruits other NHEJ factors (e.g., DNA-PKcs and LIG4). While Ku binds to double-stranded RNA (dsRNA)2and traps mutated-DNA-PKcs on ribosomal RNAin vivo,3,4the physiological significance of Ku-dsRNA interactions in otherwise wild-type cells remains elusive. Intriguingly, while dispensable for murine development,5,6Ku is essential in human cells.7Despite similar genome sizes, human cells express ∼100-fold more Ku than mouse cells, implying functions beyond NHEJ, possibly through a dose-sensitive interaction with dsRNA, which is ∼100 times weaker than with dsDNA.2,8While investigating the essentiality of Ku in human cells, we found that depletion of Ku - unlike LIG4 - induces profound interferon (IFN) and NF-kB responses reliant on the dsRNA-sensor MDA5/RIG-I and adaptor MAVS. Prolonged Ku-degradation also activates other dsRNA-sensors, e.g. PKR that suppresses protein translation, and OAS/RNaseL that cleaves rRNAs and eventually induces growth arrest and cell death. MAVS, RIG-I, or MDA5 knockouts suppressed IFN signaling and, together with PKR knockouts, partially rescued Ku-depleted human cells. Ku-irCLIP analyses revealed that Ku binds to diverse dsRNA, predominantly stem-loops in primate-specific Alu elements9at anti-sense orientation in introns and 3’-UTRs. Ku expression rose sharply in higher primates tightly correlating with Alu-expansion (r = 0.94/0.95). Together, our study identified a vital role of Ku in accommodating Alu-expansion in primates by mitigating a dsRNA-induced innate immune response, explaining the rise of Ku levels and its essentiality in human cells.
Being bigger is better: Size-dependent advantages of plasmodial fusion in a multinucleated slime mould
Authors: Broersma Cathleen M. E. , Rozen Daniel 
Published: February 2025

AbstractLarger body size often enhances survival and reproduction. While most organisms grow to achieve larger sizes, some can rapidly increase size through fusion. Fusion decisions are influenced by genetic relatedness and environmental factors, balancing potential benefits and costs. InPhysarum polycephalum, a multinucleated slime mould, fusion is thought to occur mainly between genetically identical or highly related individuals. However, the frequency of fusion among close relatives, and the drivers and benefits of fusion, remain unclear. This study explored fusion frequency, morphology, and benefits among clonal and closely related individuals ofPhysarum. We also assessed the impact of abiotic stress on fusion and whether genetic relatedness between fusion partners influences survival during exposure to stress. Our results revealed variation in fusion frequency and morphology among different plasmodial lines and pairs of close relatives. Abiotic stress increased fusion rates between both clonal and compatible non-clonal pairs. However, the benefits of fusion did not depend on the whether fusion occurred between clones or non-clones. These findings demonstrate plasmodial fusion provides size-related survival benefits. Furthermore, the promotion of fusion in stressful conditions highlights its adaptive role in responding to environmental challenges. Collectively, these results underscore the evolutionary importance of fusion inPhysarum, shaping its ecological success and resilience.Competing Interests StatementThe authors declare no competing financial interests.
Transcriptional network analysis of PTEN protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication
Authors: Rondon-Lorefice Ivana , Lopez Jose I. , Ugalde-Olano Aitziber , Zufiaurre Maite , Astobiza Ianire , Garcia-Longarte Saioa , Zabala Amaia , Rey Sofia , Santos-Martin Aida , Unda Miguel , Loizaga-Iriarte Ana , Graupera Mariona , Nuciforo Paolo , Carracedo Arkaitz , Mendizabal Isabel 
Published: February 2025

AbstractAmong the extensive genomic alterations in prostate cancer, the genomic deletion ofPTENstands out as one of the most consistently observed and confirmed alteration.PTENloss in prostate tumors is primarily associated with cancer cell proliferation and survival through the activation of the PI3K-AKT-mTOR signalling pathway. However, its use as a robust biomarker in the clinical practice is hampered by the complex epigenetic, transcriptional and post-translational regulation. Here, we undertook an approach that combinedin situassessment of PTEN protein with transcriptional surrogates of its activity to gain insights into the downstream functional effects of PTEN loss in primary tumors. Our extensive bioinformatic analyses, including the integration with single-cell RNA-Seq approaches in a new clinical cohort, highlighted stroma remodeling as the major cancer cell-extrinsic process associated with PTEN loss. By applying similar computational strategy on the transcriptomic data generated from primary prostate tumors of genetically engineeredPten knock-outmouse models, we validated the causal role ofPtenin the stromal reaction observed in clinical specimens. Mechanistically, we provide evidence for the activation of a paracrine program that encompasses enhanced TGF-β signalling and that is compatible with the secretome of PTEN-deficient senescent cancer cells. Our study provides relevant biological context to the cellular and molecular alterations unleashed upon PTEN protein loss.
The core MICOS complex subunit Mic60 has been substituted by two cryptic mitofilin-containing proteins in Euglenozoa
Authors: Sheikh Shaghayegh , Turpin Knotková Barbora , Benz Corinna , Eliáš Marek , Bílý Tomáš , Bondar Alexey , Tesařová Martina , Stríbrná Eva , Heller Jiří , Meinecke Michael , Hashimi Hassan 
Published: February 2025

ABSTRACTCristae enclose respiratory chain protein complexes, making them the bioenergetic subcompartments of mitochondria. The MICOS complex is among the inducers of sharp membrane curvature needed for crista formation. Resembling the respiratory chain complexes, MICOS is organized around a core protein, the mitofilin-domain bearing Mic60, that was inherited from the alphaproteobacterial progenitor of mitochondria. Extant alphaproteobacteria express Mic60 to form their own bioenergetic subcompartments, demonstrating the permeance of Mic60’s form and function during the long span of prokaryotic and eukaryotic evolution. Yet, unlike virtually all aerobic eukaryotes, Mic60 is not encoded in any genome of the multifarious protists that comprise the phylum Euglenozoa, including trypanosomes. Here, we show that Mic60 has been replaced in euglenozoans by two cryptic mitofilin domain-containing MICOS subunits, Mic34 and Mic40. Sharply contrasting Mic60 from two domains of life, these are not integral membrane proteins. Reverse genetics revealed they are intertwined with the oxidative protein folding pathway required for mitochondrial–and crista–biogenesis, veiling a potential membrane remodeling role. Nevertheless, Mic34 binds to phospholipid bilayersin vitro. Mic34 and Mic40 heterologous expression remodels gammaproteobacterial cytoplasmic membranes, like prokaryotic and eukaryotic Mic60. Astoundingly, Mic34 overexpression elaborates the simplified tubular mitochondrion of aTrypanosoma bruceilife cycle stage with repressed oxidative phosphorylation. The structural correspondence of Mic34’s mitofilin domain to Mic60’s predicted mutations to conserved motifs that ablated Mic34’s mitochondria-remodeling activity. Thus, the mitofilin protein family is more diverse than originally supposed, with two of its structurally most divergent members altering the core of euglenozoan MICOS.SIGNIFICANCE STATEMENTCristae are mitochondrial subcompartments that give the organelle its distinctive ruffled appearance. They house multiprotein-complex machinery needed for cellular respiration. These crista-embedded complexes are built around an immutable protein core inherited from the bacterial symbiont that engendered mitochondria. Mic60 represents one such core protein. Because of its fundamental role in crista formation, Mic60 is present in virtually all organisms with cristae, and even in the closest known bacterial relatives of mitochondria, reflecting Mic60’s symbiotic origin. Euglenozoan protists are a strange exception, lacking a recognizable Mic60 despite having cristae. Instead, they have two cryptic Mic60-like proteins that evaded recognition due to their radically altered structures. This demonstrates that even the normally conserved cores of ancient protein complexes can change during evolution.
Structural and Functional Versatility of the Amyloidogenic Antimicrobial Peptide Citropin 1.3
Authors: Strati Fabio , Cali Mariana Pigozzi , Bloch Yehudi , Mostafavi Siavash , Monistrol Jim , Golubev Aleksandr , Rayan Bader , Gustavsson Emil , Landau Meytal 
Published: February 2025

AbstractCitropin 1.3 is an antimicrobial peptide produced by the amphibianLitoria citropa(Southern bell frog), which self-aggregates into distinct fibrillar structures, however, the function of the fibrils remains unclear and largely unexplored. In this study, the structural and functional properties of citropin 1.3 were investigated using cryogenic electron microscopy and fluorescence microscopy in the presence of membrane and cell models, and with X-ray crystallography. Canonical amyloids, multilayered nanotubes, and a novel mixed fibril were observed. Experiments with negatively charged giant unilamellar vesicles revealed that the peptide facilitates membrane fusion while simultaneously undergoing phase separation in the presence of phospholipids. In presence of mammalian cells, citropin 1.3 permeabilizes membranes, leading to cell death, and over time, colocalizes with genetic material. Overall, this work provides new insights into the structural dynamics of the amyloidogenic antimicrobial peptide citropin 1.3 and its interactions with different systems.
Phylodynamic estimation of the within-host mutation rate of extended-spectrum beta-lactamase-producing Enterobacterales
Authors: Windels Etthel M. , Aguilar-Bultet Lisandra , Vock Isabelle , Maurer Perkerman Laura , Tschudin-Sutter Sarah , Stadler Tanja 
Published: February 2025

AbstractDespite their clinical relevance, the within-host evolution of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) is still poorly understood. To estimate the within-host mutation rates of ESBL-producingEscherichia coliandKlebsiella pneumoniaespecies complex, we fitted phylodynamic models to genomic sequence data of longitudinally collected rectal swabs from 64 colonized hospital patients. We estimated an average within-host mutation rate of 7.71e-07 [4.60e-07,1.10e-06] mutations/site/year forE. coliand 4.20e-07 [1.57e-07,7.14e-07] mutations/site/year forK. pneumoniaespecies complex, with limited variation observed across patients and sequence types. These estimates are presumably the most accurate reported so far and are useful for future epidemiological and evolutionary studies.Impact statementUnderstanding the within-patient mutation rates of extended-spectrum beta-lactamase (ESBL)-producingE. coliandK. pneumoniaespecies complex is critical for elucidating their evolutionary dynamics and transmission potential. In this study, we employed Bayesian phylodynamic models to analyze longitudinal isolates collected over a 10-year period from hospitalized patients. Our findings reveal limited variability in mutation rates across patients and sequence types, suggesting evolutionary stability within these pathogens in hospital settings. This work provides new insights into the persistence and evolutionary dynamics of ESBL-PE, offering valuable guidance for antimicrobial resistance surveillance and infection prevention strategies.Data summaryThe data used in this study are publicly available in the NCBI database under the BioProject number PRJNA910977. Supporting metadata are provided in Appendix 1. The code for the phylodynamic analyses, including the BEAST2 XML files, is available athttps://github.com/EtthelWindels/esbl-pe_mutation. All supporting data, code and protocols have been provided within the article, supplementary data files or public repositories.