bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics Analysis of Non-Coding UTR Variants inSTAT1Reveals Disruption of miRNA Binding, mRNA Stability, and Oncogenic Potential
Authors: Kamal Ebtihal , Ahmed Mehad 
Published: January 2025

AbstractSingle nucleotide polymorphisms (SNPs) are associated with a wide range of disorders, including diverse cancer types. In the context of cancer, alterations within non-coding regions, specifically untranslated regions (UTRs), have proven substantially important. SNPs localized in the 3 prime UTRs of theSTAT1gene were assessed for their association with miRNAs using PolymiRTS, miRNASNP, and MicroSNIper. In addition, the 5 UTR SNPs were analyzed by SNP INFO for changes in the transcription factors binding sites. The significant SNPs were further analysed by Cscape to predict their oncogenic probability. The secondary structures of the wild type and the mutant mRNA were analysed by RNAfold.Out of 605 SNPs analyzed, 14 UTR SNPs (six in the 3⍰ UTR region and eight in the 5⍰ UTR region) were identified with functional annotation ≤2a by RegulomeDB. The associations of 8 SNPs with miRNAs common between the 3 databases (PolymiRTS, miRNASNP, and MicroSNIper) were found.Moreover we identified six SNPs (rs1197872838, rs3088307, rs45470392, rs1413522785, rs531009254, and rs190508584) destabilize the mRNA structure resulting in substantial change in free energy (ΔG). The SNP rs45470392 in 5⍰ UTR was predicted to alter the transcription factor binding sites. rs188557905, rs1220766131, rs1413522785, rs1168, and rs999207177 were predicted to be oncogenic SNPs in this study using bioinformatics tools.Our findings highlight the impact of 3⍰ and 5⍰ UTR SNPs on miRNA, transcription, and translation ofSTAT1. These analyses suggest that these SNPs can have substantial functional importance in theSTAT1gene. Future experimental validation could establish their potential role in the diagnosis and therapeutics of various diseases, including cancer.
Zebrafishadamtsl4knockout recapitulates key features of humanADAMTSL4-related diseases: a gene involved in extracellular matrix organization, cell junctions and development
Authors: Tevar Angel , Aroca-Aguilar Jose-Daniel , Atiénzar-Aroca Raquel , Ramírez Ana I. , Fernández-Albarral José A. , Escribano Julio 
Published: January 2025

ABSTRACTLoss-of-function mutations inADAMTSL4,a gene encoding an extracellular matrix-associated protein with incompletely understood biological roles, are linked to autosomal recessive disorders predominantly characterized by lens dislocation. Pupil ectopia, increased intraocular pressure, retinal detachment, cataracts, and skeletal abnormalities are also observed in some patients. To investigateADAMTSL4biology and related diseases we established a zebrafish knockout line using CRISPR/Cas9 genome editing. The generated zebrafish model harboured the c.234-351del mutation inadamstsl4, reducing its mRNA levels by 75% in 6 days post fertilization (dpf) larvae, and predicting to produce an inactive protein (p.(Gln78Hisfs*127)). Forty percent of F3 knockout larvae (6 dpf) displayed lethal phenotypes characterized by multiple ocular and non-ocular developmental defects, including pericardial, perivitelline and periocular edema, absence of swim bladder, craniofacial malformations and microphthalmia. The remaining 60% larvae survived and displayed only reduced pupil area, indicating incomplete penetrance of the lethality. Histology revealed extracellular matrix (ECM) and intercellular junctions abnormalities within the cornea, iris, lens, and retinal pigment epithelium (RPE). Adult knockout zebrafish (6 months) presented phenotypes resembling ectopia lentis et pupillae and craniosynostosis, with optical defects in the lens and impaired visual function. ECM and cell junction disorganization in the cornea, lens and RPE were also present in these animals. Transcriptomic analysis revealed disrupted expression of genes involved in development, ECM and cell junctions among other biological processes. These findings show that adamtsl4recapitulates key features of humanADAMTSL4-related disorders and that this gene is essential for normal ECM structure, cell junctions and embryonic development.HighlightsZebrafishadamtsl4knockout recapitulates humanADAMTSL4-related phenotypes.adamtsl4is involved in embryonic development.adamtsl4participates in ECM organization and cell adhesion.
Ohno-miRNAs: intragenic miRNA pairs derived from whole-genome duplication
Authors: Agasso Leonardo , Molineris Ivan , Caselle Michele 
Published: January 2025

ABSTRACTTwo rounds of whole-genome duplication (WGD) occurred about 500 million years ago and played a major role in the evolution of the vertebrate genomes. Human genes derived from WGD are called “ohnologs”. Ohnologs are involved in fundamental biological processes and significantly contributed to the complexity of the human gene regulatory network. Given the central role of miRNAs in gene regulation, we investigated the contribution of ohnolog miRNAs (Ohno-miRNAs) to the human gene regulatory network. We worked on the identification of miRNA pairs in the human genome derived from the two rounds of whole-genome duplication in early vertebrate lineage and their role in the structure of the human gene regulatory network. By focusing on intragenic miRNAs within ohnolog gene pairs, we identified Ohno-miRNAs as having higher retention rates and sequence similarity compared to miRNAs hosted on paralogue gene pairs from small-scale duplications (SSD). They also show a stronger tendency to regulate common target genes. Analyzing the role of Ohno-miRNAs in the human gene regulatory network, we showed that Ohno-miRNAs are statistically overrepresented in specific network motifs commonly associated with redundancy and complexity, highlighting their central role in this particular layer network.
Spacer Extension Reconciles Specificity and Activity in High-Fidelity Cas9 Genome Editing
Authors: Lu Zhike , Wei Rongwei , Zheng Rong , Shin Young-Cheul , Zhang Qingfeng , Li Jianbo , Wang Xiaoqi , Wei Yi , Liu Botao , Chen Yang , Zhang Heng , Chen Hui , Ma Lijia 
Published: January 2025

AbstractEngineering high-fidelity CRISPR enzymes often leads to reduced cleavage activity, creating a significant hurdle in balancing nuclease specificity and efficiency for clinical applications. Here, we demonstrate that extending the spacer to 21 or 22 nucleotides restores the impaired cleavage activity of SuperFi-Cas9, an engineered high-fidelity Cas9 variant with seven mutations at the PAM-distal region. Structural and mutational analyses reveal that the spacer extension strengthens additional interactions at the PAM-distal end, stabilizing the nuclease– sgRNA–DNA complex, which appears to be disturbed due to the seven mutations. This approach not only provides a high-fidelity Cas9 with uncompromised efficiency but also introduces a novel strategy to enhance CRISPR complex stability. Our findings offer a promising avenue for precise and efficient genome editing, crucial for advancing CRISPR technologies toward clinical translation.
Limit of detection of Raman spectroscopy using polystyrene particles from 25 to 1000 nm in aqueous suspensions
Authors: Mayorga Cindy , Athalye Shreya Milind , Boodaghidizaji Miad , Sarathy Neelesh , Hosseini Mahdi , Ardekani Arezoo , Verma Mohit S. 
Published: January 2025

ABSTRACTRaman spectroscopy is an analytical method capable of detecting various microorganisms and small particles. Here, we used 25-1000 nm polystyrene particles in aqueous suspensions, which are comparable in size to viral particles and viral aggregates, to determine the limit of detection of a confocal Raman microscope. We collected Raman spectra using a 785 nm wavelength laser with a power of 300 mW and a 10 s exposure time, with a 5X objective lens. We detected the most prominent peak of the polystyrene particles at 1001 cm-1, corresponding to the ring breathing mode. We established the minimum and maximum limit of detection (LODminand LODmax) using a partial least squares (PLS) model. The LOD of the smallest size of 50 nm was identified as 7.47 × 1012–7.64 × 1012particle/mL, and for the largest size of 1000 nm, 6.09 × 108–6.24 × 108particle/mL. We demonstrated that Raman spectroscopy was non-destructive under these conditions by comparing the particle size before and after collecting Raman spectra using dynamic light scattering. Due to their size similarity to viral particles and viral aggregates, this systematic characterization of polystyrene particles provides detailed information on their Raman spectral signatures in aqueous suspensions. These findings establish a foundation for using Raman spectroscopy for the detection of small particles in aqueous suspensions and highlight its potential as a tool for real-time monitoring in vaccine manufacturing.
Rescue of hippocampal synaptic plasticity and memory performance by Fingolimod (FTY720) in APP/PS1 model of Alzheimer’s disease is accompanied by correction in metabolism of sphingolipids, polyamines, and phospholipid saturation composition
Authors: Kalecký Karel , Buitrago Luna , Alarcon Juan Marcos , Singh Abanish , Bottiglieri Teodoro , Kaddurah-Daouk Rima , Hernández Alejandro Iván ,   Alzheimer’s Disease Metabolomics Consortium
Published: January 2025

AbstractPreviously, our metabolomic, transcriptomic, and genomic studies characterized the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease, and we demonstrated that FTY720, a sphingosine-1-phospahate receptor modulator approved for treatment of multiple sclerosis, recovers synaptic plasticity and memory in APP/PS1 mice. To further investigate how FTY720 rescues the pathology, we performed metabolomic analysis in brain, plasma, and liver of trained APP/PS1 and wild-type mice. APP/PS1 mice showed area-specific brain disturbances in polyamines, phospholipids, and sphingolipids. Most changes were completely or partially normalized in FTY720-treated subjects, indicating rebalancing the “sphingolipid rheostat”, reactivating phosphatidylethanolamine synthesis via mitochondrial phosphatidylserine decarboxylase pathway, and normalizing polyamine levels that support mitochondrial activity. Synaptic plasticity and memory were rescued, with spermidine synthesis in temporal cortex best corresponding to hippocampal CA3-CA1 plasticity normalization. FTY720 effects, also reflected in other pathways, are consistent with promotion of mitochondrial function, synaptic plasticity, and anti-inflammatory environment, while reducing pro-apoptotic and pro-inflammatory signals.
Deciphering Transcription inCryptosporidium parvum: Polycistronic Gene Expression and Chromatin Accessibility
Authors: Xiao Rui , Baptista Rodrigo P. , Agyabeng-Dadzie Fiifi , Li Yiran , Dong Yinxin , Schmitz Robert J. , Glenn Travis C. , Kissinger Jessica C. 
Published: January 2025

AbstractOnce considered rare in eukaryotes, polycistronic mRNA expression has been identified in kinetoplastids and, more recently, green algae, red algae, and certain fungi. This study provides comprehensive evidence supporting the existence of polycistronic mRNA expression in the apicomplexan parasiteCryptosporidium parvum. Leveraging long-read RNA-seq data from different parasite strains and using multiple long-read technologies, we demonstrate the existence of defined polycistronic transcripts containing 2-4 protein encoding genes, several validated with RT-PCR. Some polycistrons exhibit differential expression profiles, usually involving the generation of internal monocistronic transcripts at different times during development. ATAC-seq in sporozoites reveals that polycistronic transcripts usually have a single open chromatin peak at their 5-prime ends, which contains a single E2F binding site motif. Polycistronic genes do not appear enriched for either male or female exclusive genes. This study elucidates a potentially complex layer of gene regulation with distinct chromatin accessibility akin to monocistronic transcripts. This is the first report of polycistronic transcription in an apicomplexan and expands our understanding of gene expression strategies in this medically important organism.SignificanceCryptosporidium parvumis a parasite that causes human gastrointestinal disease, profoundly impacting infants and immunocompromised individuals worldwide.C. parvumisolation, culturing, cloning, and its compact 9.2 Mb genome pose challenges for research. We have discovered that, unlike most eukaryotes, which express one gene per mRNA,C. parvumexhibits widespread polycistronic transcription, whereby 10% of its protein encoding genes are expressed as multiple genes per single mRNA molecule. Mining the publishedC. parvumsingle-cell atlas with proxy sequences for polycistronic expression, we observed patterns of polycistron expression that vary with developmental stages, suggesting a role in the parasite’s lifecycle. By illuminating this unique aspect ofC. parvumbiology, our findings provide novel insights intoCryptosporidiumgene expression.
Impact of meningioma and glioma on whole-brain dynamics
Authors: Juncá Albert , Escrichs Anira , Martín Ignacio , Deco Gustavo , Patow Gustavo 
Published: January 2025

ABSTRACTBrain tumors, particularly meningiomas and gliomas, can profoundly affect neural function, yet their impact on brain dynamics remains incompletely understood. This study investigates alterations in normal brain function among meningioma and glioma patients by assessing dynamical complexity through the Intrinsic Ignition Framework. We analyzed resting-state fMRI data from 34 participants to quantify brain dynamics using intrinsic ignition and metastability metrics. Our results revealed distinct patterns of disruption: glioma patients showed significant reductions in both metrics compared to controls, indicating widespread network disturbances. In contrast, meningioma patients exhibited significant changes predominantly in regions with substantial tumor involvement. Resting-state network analysis demonstrated strong metastability and metastability/ignition correlations between regions in controls, which were slightly weakened in meningioma patients and severely disrupted in glioma patients. These findings highlight the differential impacts of gliomas and meningiomas on brain function, offering insights into their distinct pathophysiological mechanisms. Furthermore, these results show that brain dynamics metrics can be effective biomarkers for identifying disruptions in brain information transmission caused by tumors.
Language models learn to represent antigenic properties of human influenza A(H3) virus
Authors: Durazzi Francesco , Koopmans Marion P. G. , Fouchier Ron A. M. , Remondini Daniel 
Published: January 2025

AbstractGiven that influenza vaccine effectiveness depends on a good antigenic match between the vaccine and circulating viruses, it is important to assess the antigenic properties of newly emerging variants continuously. With the increasing application of real-time pathogen genomic surveillance, a key question is if antigenic properties can reliably be predicted from influenza virus genomic information. Based on validated linked datasets of influenza virus genomic and wet lab experimental results,in silicomodels may be of use to learn to predict immune escape of variants of interest starting from the protein sequence only. In this study, we compared several machine-learning methods to reconstruct antigenic map coordinates for HA1 protein sequences of influenza A(H3N2) virus, to rank substitutions responsible for major antigenic changes, and to recognize variants with novel antigenic properties that may warrant future vaccine updates. Methods based on deep learning language models (BiLSTM and ProtBERT) were shown to outperform more classical approaches that involved predictions based solely on genetic distances and physicochemical properties of amino acid sequences, particularly for fine-grained features like single amino acid-driven antigenic change andin silicodeep mutational scanning experiments to rank the substitutions with the largest impact on antigenic properties. Given that the best performing model that produces protein embeddings is agnostic to the specific pathogen, the presented approach may be applicable to other pathogens.
VitisC: Visualizing interested target via integrated scaffold of cytoophidium
Authors: Yin Boqi , Hu Huan-Huan , Zhong Jiale , Liu Ji-Long 
Published: January 2025

ABSTRACTCryo-electron microscopy (cryo-EM) single-particle analysis has become a widely used technique for high-resolution structural determination of biological macromolecules and complexes. However, the determination of the structure of small molecule proteins remains a limitation of this technology. To address this issue, here we develop a novel approach termed Visualizing interested target via integrated scaffold of cytoophidium (VitisC). We use a filamentous structure formed byEscherichia coliCTP synthase (CTPS) as the scaffold, termed the scaffold of cytoophidium. Through artificial design and modification, small proteins can be attached to this symmetrical scaffold, which is very suitable for cryo-EM imaging. The formation conditions for stable filament structures of the fusion protein are optimized in vitro, and the three-dimensional structure of the fusion protein is reconstructed using cryo-EM single-particle analysis, achieving an overall resolution of 3.39 Å. Therefore, cryo-EM is successfully applied to visualize small proteins. VitisC not only demonstrates the feasibility of employing cytoophidia as scaffolds, but also provides an approach for high-resolution structural analysis of small proteins using Cryo-EM.
REV7 associates with ATRIP and inhibits ATR kinase activity
Authors: Biller Megan , Kabir Sara , Nipper Sarah , Allen Sydney , Kayali Yara , Kuncik Skyler , Sasanuma Hiroyuki , Zhou Pei , Vaziri Cyrus , Tomida Junya 
Published: January 2025

SUMMARYIntegration of DNA replication with DNA repair, cell cycle progression, and other biological processes is crucial for preserving genome stability and fundamentally important for all life. Ataxia-telangiectasia mutated and RAD3-related (ATR) and its partner ATR-interacting protein (ATRIP) function as a critical proximal sensor and transducer of the DNA Damage Response (DDR). Several ATR substrates, including p53 and CHK1, are crucial for coordination of cell cycle phase transitions, transcription, and DNA repair when cells sustain DNA damage. While much is known about ATR activation mechanisms, it is less clear how ATR signaling is negatively regulated in cells. Here, we identify the DNA repair protein REV7 as a novel direct binding partner of ATRIP. We define a REV7-interaction motif in ATRIP, which when mutated abrogates the REV7-ATRIP interactionin vitroand in intact cells. Usingin vitrokinase assays, we show that REV7 inhibits ATR-mediated phosphorylation of its substrates, including p53. Disruption of the REV7-ATRIP interaction also enhances phosphorylation of CHK1 at Ser317 (a known ATR target site) in intact cells. Taken together our results establish REV7 as a critical negative regulator of ATR signaling. REV7 has pleiotropic roles in multiple DDR pathways including Trans-Lesion Synthesis, DNA Double-Strand Break resection, and p53 stability and may play a central role in the integration of multiple genome maintenance pathways.
Native nucleosome-positioning elements for the investigation of nucleosome repositioning
Authors: Chen Ruo-Wen , Stoeber Shane D. , Nodelman Ilana M. , Chen Hengye , Yang Lloyd , Bowman Gregory D. , Bai Lu , Poirier Michael G. 
Published: January 2025

ABSTRACTNucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, native NPEs are needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) fromSaccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences, and the rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.
Conformational Dynamics and Membrane Insertion Mechanism of B4GALNT1 in Ganglioside Synthesis
Authors: Welland Jack W. J. , Barrow Henry G. , Stansfeld Phillip J. , Deane Janet E. 
Published: January 2025

ABSTRACTGlycosphingolipids (GSLs) are crucial membrane components involved in essential cellular pathways. Complex GSLs, known as gangliosides, are synthesised in the ER/Golgi by a series of glycosyltransferase enzymes. Imbalances in GSL metabolism can lead to severe diseases, often affecting the nervous system. B4GALNT1 is a key enzyme in the ganglioside synthetic pathway, synthesising complex gangliosides including GM2 and GD2 from GM3 and GD3. These products are precursors to the major brain gangliosides. Loss of B4GALNT1 function causes hereditary spastic paraplegia 26 (HSP26), while its overexpression is linked to cancers including childhood neuroblastoma. Here, we present crystal structures of the homodimeric B4GALNT1 enzyme demonstrating conformational changes upon binding of donor substrate ligands and product. These structures support a catalytic mechanism that involves dynamic remodelling of the substrate binding site during catalysis. We also demonstrate that processing of lipid substrates by B4GALNT1 is severely compromised when surface loops flanking the active site are mutated from hydrophobic residues to polar. Molecular dynamics simulations support that these loops can insert into the lipid bilayer explaining how B4GALNT1 accesses and processes lipid substrates. By combining structure prediction and molecular simulations we propose that this mechanism of dynamic membrane insertion is exploited by other, structurally distinct GSL synthesising enzymes.