bluuebunny/crossref_metadata_2025_split huggingface dataset:
ELAVL3 regulates splicing of RNAs encoding synaptic signaling proteins in D1 and D2 striatal medium spiny neurons
Authors: Irmady Krithi , Scheckel Claudia , Singer Ruth A , Carroll Thomas , Darnell Robert B 
Published: November 2024

AbstractThe neuronal RNA-binding protein (RBP) family nELAVL regulates key neuronal processes by binding directly to target RNA transcripts. In this study, we demonstrate that ELAVL3 is the predominant nELAVL paralog expressed in D1 and D2 medium spiny neurons of the striatum. To investigate its function, we developed ELAVL3 cTag-crosslinking and immunoprecipitation (CLIP) to generate RBP-RNA interaction maps from these neurons. By integrating data from ELAVL3-cTag and Elavl3 knockout mice, we identified distinct regulatory effects of ELAVL3 on alternative splicing of its target transcripts. Notably, ELAVL3 modulates splicing of transcripts encoding proteins critical for glutamate and dopamine receptor signaling. These findings underscore the role of ELAVL3 in RNA-mediated regulation of molecular pathways essential for medium spiny neuron function in the striatum.
Nanopore sequencing of intact aminoacylated tRNAs
Authors: White Laura K. , Radakovic Aleksandar , Sajek Marcin P. , Dobson Kezia , Riemondy Kent A. , del Pozo Samantha , Szostak Jack W. , Hesselberth Jay R. 
Published: November 2024

ABSTRACTTransfer RNAs (tRNA) are decorated during biogenesis with a variety of modifications that modulate their stability, aminoacylation, and decoding potential during translation. The complex landscape of tRNA modification presents significant analysis challenges and to date no single approach enables the simultaneous measurement of important but disparate chemical properties of individual, mature tRNA molecules. We developed a new, integrated approach to analyze the sequence, modification, and aminoacylation state of tRNA molecules in a high throughput nanopore sequencing experiment, leveraging a chemical ligation that embeds the charged amino acid in an adapted tRNA molecule. During nanopore sequencing, the embedded amino acid generates unique distortions in ionic current and translocation speed, enabling application of machine learning approaches to classify charging status and amino acid identity. Specific applications of the method indicate it will be broadly useful for examining relationships and dependencies between tRNA sequence, modification, and aminoacylation.
Profiling Human iPSC-Derived Sensory Neurons for Analgesic Drug Screening Using a Multi-Electrode Array
Authors: Kuete Christian Fofie , Granja-Vazquez Rafael , Truong Vincent , Walsh Patrick , Price Theodore , Biswas Swati , Dussor Gregory , Pancrazio Joseph , Kolber Benedict 
Published: November 2024

AbstractChronic pain is a major global health issue, yet effective treatments are limited by poor translation from preclinical studies to humans. To address this, we developed a high-content screening (HCS) platform for analgesic discovery using hiPSC-derived nociceptors. These cells were cultured on multi-well micro-electrode arrays to monitor activity, achieving nearly 100% active electrodes by week two, maintaining stable activity for at least two weeks. After maturation (28 days), we exposed the nociceptors to various drugs, assessing their effects on neuronal activity, with excellent assay performance (Z’ values >0.5). Pharmacological tests showed responses to analgesic targets, including ion channels (Nav, Cav, Kv, TRPV1), neurotransmitter receptors (AMPAR, GABA-R), and kinase inhibitors (tyrosine, JAK1/2). Transcriptomic analysis confirmed the presence of these drug targets, although expression levels varied compared to primary human dorsal root ganglion cells. This HCS platform facilitates the rapid discovery of novel analgesics, reducing the risk of preclinical-to-human translation failure.MotivationChronic pain affects approximately 1.5 billion people worldwide, yet effective treatments remain elusive. A significant barrier to progress in analgesic drug discovery is the limited translation of preclinical findings to human clinical outcomes. Traditional rodent models, although widely used, often fail to accurately predict human responses, while human primary tissues are limited by scarcity, technical difficulties, and ethical concerns. Recent advancements have identified human induced pluripotent stem cell (hiPSC)-derived nociceptors as promising alternatives; however, current differentiation protocols produce cells with inconsistent and physiologically questionable phenotypes.To address these challenges, our study introduces a novel high-content screening (HCS) platform using hiPSC-derived nociceptors cultured on multi-well micro-electrode arrays (MEAs). The “Anatomic” protocol, used to generate these nociceptors, ensures cells with transcriptomic profiles closely matching human primary sensory neurons. Our platform achieves nearly 100% active electrode yield within two weeks and demonstrates sustained, stable activity over time. Additionally, robust Z’ factor analysis (exceeding 0.5) confirms the platform’s reliability, while pharmacological validation establishes the functional expression of critical analgesic targets. This innovative approach improves both the efficiency and clinical relevance of analgesic drug screening, potentially bridging the translational gap between preclinical studies and human clinical trials, and offering new hope for effective pain management.
Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA
Authors: Berger Kyle D. , Puthenpeedikakkal Anees M. K. , Mathews David H. , Fu Dragony 
Published: November 2024

AbstractAll tRNAs undergo a series of chemical modifications to fold and function correctly. In mammals, the C32 nucleotide in the anticodon loop of tRNA-Arg-CCU and UCU is methylated to form 3-methylcytosine (m3C). Deficiency of m3C in arginine tRNAs has been linked to human neurodevelopmental disorders, indicating a critical biological role for m3C modification. However, the structural repercussions of m3C modification are not well understood. Here, we examine the structural effects of m3C32 modification on the anticodon stem loop (ASL) of human tRNA-Arg-UCU-4-1, a unique tRNA with enriched expression in the central nervous system. Optical melting experiments demonstrate that m3C modification can locally disrupt nearby base pairing within the ASL while simultaneously stabilizing the ASL electrostatically, resulting in little net change thermodynamically. The isoenergetic nature of the C32 – A38 pair vs the m3C32 – A38 pair may help discriminate against structures not adopting canonical C32 – A38 pairings, as most other m3C pairings are unfavorable. Furthermore, multidimensional NMR reveals that after m3C modification there are changes in hairpin loop structure and dynamics, the structure of A37, and the neighboring A31 – U39 base pair. However, these structural changes after modification are made while maintaining the shape of the C32 – A38 pairing, which is essential for efficient tRNA function in translation. These findings suggests that m3C32 modification could alter interactions of tRNA-Arg isodecoders with one or more binding partners while simultaneously maintaining the tRNA’s ability to function in translation.
The CDKL5 kinase undergoes liquid-liquid phase separation driven by a serine-rich C-terminal region and impaired by neurodevelopmental disease-related truncations
Authors: Dell’Oca Marco , Bozzo Stefania Boggio , Vaglietti Serena , Gurgone Antonia , Cardinale Vita , Ragazzini Gregorio , Alessandrini Andrea , Colnaghi Luca , Ghirardi Mirella , Giustetto Maurizio , Fiumara Ferdinando 
Published: November 2024

ABSTRACTMutations of thecyclin-dependent kinase-like 5(CDKL5) gene, which encodes a serine/threonine protein kinase, can cause theCDKL5 deficiency disorder(CDD), a severe neurodevelopmental disease characterized by epileptic encephalopathy and neurocognitive impairment. The CDKL5 kinase consists of a catalytic N-terminal domain (NTD) and a less characterized C-terminal domain (CTD). Numerous disease-related mutations truncate CDKL5, leaving the NTD intact while variably shortening the CTD, which highlights the importance of the CTD for CDKL5 function. By systematically analyzing CDKL5 compositional features and evolutionary dynamics, we found that the CTD is a low-complexity region (LCR) highly enriched in serine residues and with a high propensity to undergo liquid-liquid phase separation (LLPS), a biophysical process of condensation controlling protein localization and function. Using a combination of super-resolution imaging, electron microscopy, and molecular and cellular approaches, including optogenetic LLPS induction, we discovered that CDKL5 undergoes LLPS, predominantly driven by its CTD, forming membraneless condensates in neuronal and non-neuronal cells. A CTD internal fragment (CTIF) plays a pivotal LLPS-promoting role, along with the distal portion of the protein. Indeed, two disease-related truncating mutations (S726X and R781X), eliding variable portions of the CTIF, significantly impair LLPS. This impairment is paralleled at the functional level by a reduction in the CDKL5-dependent phosphorylation of EB2, a known CDKL5 target. These findings demonstrate that CDKL5 undergoes LLPS, driven by a CTD region elided by most disease-related truncating mutations. Its loss––through the impairment of CDKL5 LLPS and functional activity––may play a key role in the molecular pathogenesis of CDD.
Eye and hand coarticulation during problem solving reveals hierarchically organized planning
Authors: Eluchans Mattia , Maselli Antonella , Lancia Gian Luca , Pezzulo Giovanni 
Published: November 2024

AbstractDuring everyday activities, such as when preparing a cup of coffee or traveling across cities, we often plan ahead and execute sequences of actions. However, much remains to be understood about how we plan and coordinate sequences of actions (e.g., eye and hand movements) to solve novel problem-solving tasks. This study investigates how participants use gaze and cursor movements to plan and execute problem-solving tasks, for which solutions are not provided in advance but rather have to be found from scratch. We report three key findings. First, we found that participants segment the problem into sequences of gestures; within each gesture, gaze selects a target and remains fixed until the cursor reaches it, then moves to the next target. Second, we observed coarticulation in both cursor-cursor and gaze-cursor movements, occurring within individual gestures and, to a lesser degree, between successive gestures. Third, we demonstrate for the first time that the initial fixation in a sequence is biased toward the direction of the subsequent fixation. This implies that the angular position of the gaze reliably predicts the next fixation’s direction, suggesting a forward-looking coarticulation between successive gaze fixations. Together, these findings suggest that participants employ a hierarchical planning strategy: they divide the problem into gesture sequences and plan multiple eye and cursor movements in advance to efficiently reach both current and upcoming gesture targets. This hierarchical motor plan demonstrates a structure where targets (or subgoals) are defined and achieved through the coordinated actions of the eyes and hand, highlighting the importance of integrated eye-hand planning in complex task performance.
Inhibition of GEF-H1-RhoA signaling in inflammation with a stapled peptide mimicry of the RhoA67-78helix
Authors: Gathmann Clara , Liu Tiansheng , Yang Shuhuai , Wang Weitong Cynthia , Chan Edith , Matter Karl , Balda Maria S. , Selwood A. W. David L. 
Published: November 2024

AbstractGuanine exchange factors (GEFs) are considered hard to drug with conventional small molecules, they lack conventional deep binding pockets and binding ligands are seldom reported. Here we report the design of a stapled peptide stP5 targeting the interaction between cytoskeletal regulator RhoA GTPase and its activator guanine exchange factor H1 (GEF-H1). StP5 is a modified RhoA mimic based on a previously identified bioactive α-helical epitope to GEF-H1. StP5 effectively inhibits GEF-H1-induced morphological and transcriptional changes in cellular models for inflammation and does not affect the related GEF p114RhoGEF (ARHGEF18). StP5 peptide is approximately 100 fold more active in cellular assays than the unstapled P5 peptide. We provide a bioinformatic analysis of the stP5 bindings site in different GEFs, providing a basis for this selectivity. The GEF-H1 inhibitor stP5 represents a step towards fully drugging GEF-H1.Abstract Figure
Compensating for a sensorimotor delay requires a memory buffer, a state observer, and a predictor
Authors: Maris Eric 
Published: November 2024

AbstractEffective motor control requires sensory feedback about our body’s state. However, adjusting motor commands based on sensory feedback is seriously complicated by the time delay between the state of the body at feedback generation and the arrival of the feedback-informed motor commands in the body’s muscles, the so-called sensorimotor delay (SMD). In this paper, I investigate the effect of a SMD on the control performance of a computational system that represents the central nervous system. I specify three SMD compensation mechanisms that operate the level of this computational system: memory-informed state estimation, prediction, and output gain adjustment. I use formal analysis and computer simulations of balance control, both free standing and while riding a bicycle. This study provides strong evidence for the claim that SMD compensation requires a memory buffer of efference copies, a state observer, and a predictor. In addition, for prediction to be an effective SMD compensation mechanism, it needs (1) the output of a state observer as its initial condition and (2) a memory buffer of efference copies that must be convolved with a set of weights that is to be learned. For output gain adjustment to make a substantial contribution to SMD compensation, memory-informed state estimation and prediction must be imperfect.
Microglia States are Susceptible to Senescence and Cholesterol Dysregulation in Alzheimer’s Disease
Authors: Li Boyang , Wang Shaowei , Kerman Bilal , Hugo Cristelle , Shwab E Keats , Shu Chang , Chiba-Falek Ornit , Arvanitakis Zoe , Yassine Hussein 
Published: November 2024

AbstractCellular senescence is a major contributor to aging-related degenerative diseases, including Alzheimer’s disease (AD) but much less is known on the key cell types and pathways driving mechanisms of senescence in the brain. We hypothesized that dysregulated cholesterol metabolism is central to cellular senescence in AD. We analyzed whole transcriptomic data and utilized single-cell RNA seq integration techniques to unveil the convoluted cell-type-specific and sub-cell-type-state-specific senescence pathologies in AD using both ROSMAP and Sea-AD datasets. We identified that microglia are central components to AD associated senescence phenotypes in ROSMAP snRNA-seq data (982,384 nuclei from postmortem prefrontal cortex of 239 AD and 188 non-AD) among non-neuron cell types. We identified that homeostatic, inflammatory, phagocytic, lipid processing and neuronal surveillance microglia states were associated with AD associated senescence in ROSMAP (152,459 microglia nuclei from six regions of brain tissue of 138 early AD, 79 late AD and 226 control subject) and in Sea-AD (82,486 microglia nuclei of 42 dementia, 42 no dementia and 5 reference subjects) via integrative analysis, which preserves the meaningful biological information of microglia cell states across the datasets. We assessed top senescence associated bioprocesses including mitochondrial, apoptosis, oxidative stress, ER stress, endosomes, and lysosomes systems. Specifically, we found that senescent microglia have altered cholesterol related bioprocesses and dysregulated cholesterol. We discovered three gene co-expression modules, which represent the specific cholesterol related senescence transcriptomic signatures in postmortem brains. To validate these findings, the activation of specific cholesterol associated senescence transcriptomic signatures was assessed using integrative analysis of snRNA-seq data from iMGs (microglia induced from iPSCs) exposed to myelin, Abeta, and synaptosomes (56,454 microglia across two replicates of untreated and four treated groups). In vivo cholesterol associated senescence transcriptomic signatures were preserved and altered after treatment with AD pathological substrates in iMGs. This study provides the first evidence that dysregulation of cholesterol metabolism in microglia is a major driver of senescence pathologies in AD. Targeting cholesterol pathways in senescent microglia is an attractive strategy to slow down AD progression.
Combining live cell fluorescence imaging within situcryo electron tomography sheds light on the septation process inDeinococcus radiodurans
Authors: Gaifas L. , Kleman J.P. , Lacroix F. , Schexnaydre E. , Trouve J. , Morlot C. , Sandblad L. , Gutsche I. , Timmins J. 
Published: November 2024

ABSTRACTCell division is a fundamental biological process that allows a single mother cell to produce two daughter cells. In bacteria, different modes of cell division have been reported that are notably associated with distinctive cell shapes, but in all cases, division involves a step of septation, corresponding to the growth of a new dividing cell wall, followed by splitting of the two daughter cells. The radiation-resistantDeinococcus radioduransis a spherical bacterium protected by a thick and unusual cell envelope. It has been reported to divide using a distinctive mode of septation in which two septa originating from opposite sides of the cell progress with a flat leading edge until meeting and fusing at mid-cell. In the present study, we have combined conventional and super-resolution fluorescence microscopy of live bacteria within situcryogenic electron tomography of bacterial lamellae to investigate the septation process inD. radiodurans. This work provides important insight into (i) the complex architecture of the cell envelope of this bacterium, (ii) the ‘sliding doors’ septation process and (iii) the molecular mechanisms underlying septal growth and closure.
Phosphatidylethanolamine is a phagocytic ligand implicated in the binding and removal of microbial extracellular vesicles
Authors: Kavianpour Ava , Meyer Kirsten J. , Le Trieu , Marques Pedro Elias , Nodwell Justin R. , Freeman Spencer A. 
Published: November 2024

AbstractThe efficient recognition and removal of apoptotic cells by phagocytes is critical to prevent secondary necrosis and maintain tissue homeostasis. Such detection involves receptors and bridging molecules that recognize lipids −normally restricted to the inner leaflet of healthy cells− which become exposed on the surface of dead cells and the vesicles they produce. A majority of studies focus on phosphatidylserine (PS) for which there are well-established receptors that either bind to the lipid directly or indirectly via intermediary proteins. Phosphatidylethanolamine (PE) is even more prevalent than PS in the inner leaflet of mammalian cells and also becomes exposed by the action of scramblases during cell death, though little is known about the effects of PE once scrambled. Here, we report that PE can itself serve as a phagocytic ligand for macrophages by engaging CD300 family receptors. CD300a and CD300b specifically modulated PE-mediated uptake, and this process involved integrins and spleen tyrosine kinase (Syk). For bacteria, which contain PE but largely lack PS in their membranes, we report that PE engagement enabled the binding and uptake of spheroplasts and extracellular vesicles (EVs) that were unsheathed by the cell wall. Based on these observations, we posit that the direct recognition of PE facilitates mechanisms of clearance that stand to have a broad impact on the immune response.
A Comprehensive Bibliometric Investigation on Antimicrobials from Fungal Origins with a Biotechnological Perspective
Authors: Lopes Lucas da Silva , Silva Kamila Alves , Correa Thaís da Silva , Campos-da-Paz Mariana , Guilherme Prado Martin José , Gonçalves Ana Alice Maia , Belo Vinícius Silva , Gontijo Tiago Silveira , Galdino Alexsandro Sobreira 
Published: November 2024

ABSTRACTInterest in research related to fungi exploration past few years, given its relevance to bioactive compounds production as these metabolites are a promising source of bacteriostatic or fungistatic compounds. Therefore, their use represents a significant alternative to traditional antibiotics by minimizing the risks related to microbial resistance. In this context, this work aimed to: assess the volume of annual publications on the subject and identify key players, analyze the collaboration network among researchers, and check the patents filed on this topic. For this purpose, the Bibliometrix R-package was used, as well as scientific metadata from the Web of Science and Scopus databases (n=506). In total, 256 sources, authors (n=2,526), keywords (n=1,812), and references (n=19,315) were analyzed from 1989 to 2023. The academic debate on the subject has been promoted by India (29%), United Kingdom (UK) (7%), China (6%) and the United States of America (USA) (6%). The authors identified as the most cited were Liu J (n=142), followed by Jesu Arockiaraj (n=106). There is a knowledge predominance of publications focusing on the life science disciplines. The most prolific institutions were the National Research Center (n=20) and the University of Pittsburgh (n=13). The most cited journals were the World Journal of Microbiology & Biotechnology (n=719) and Applied Microbiology and Biotechnology (n=661). Finally, the United States Patent and Trademark Office represented 85% of the patents filed on the subject (n=28,303). Together, these results can direct researchers and Biotech industries in their search for the most important sources related to antimicrobial biotechnology.
Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering splicing
Authors: Damianov Andrey , Lin Chia-Ho , Zhang Jian , Manley James L. , Black Douglas L. 
Published: November 2024

AbstractMyelodysplastic syndromes and other cancers are often associated with mutations in the U2 snRNP protein SF3B1. Common SF3B1 mutations, including K700E, disrupt SF3B1 interaction with the protein SUGP1 and induce aberrant activation of cryptic 3’ splice sites (ss), presumably resulting from aberrant U2/branch site (BS) recognition by the mutant spliceosome. Here, we apply the new method of U2 IP-seq to profile BS binding across the transcriptome of K562 leukemia cells carrying theSF3B1K700E mutation. For cryptic 3’ ss activated by K700E, we identify their associated BSs and show that they are indeed shifted from the WT sites. Unexpectedly, we also identify thousands of additional changes in BS binding in the mutant cells that do not alter 3’ ss choice. These new BS are usually very close to the natural sites, occur upstream or downstream, and either exhibit stronger base-pairing potential with U2 snRNA or are adjacent to stronger polypyrimidine tracts than the WT sites. The widespread imprecision in BS recognition induced by K700E with limited changes in 3’ ss selection supports a positive role for SUGP1 in early BS choice and expands the physiological consequences of this oncogenic mutation.