bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced systemic autophagy by simultaneous loss of ATG4B, ATG4C and ATG4D leads to accelerated aging in mice
Authors: Martínez-García Gemma G. , Suárez María F. , Rodríguez-Santamaria Mª Del Mar , Roiz-Valle David , Bárcena Clea , Corrochano-Ruiz Andrés , Tamargo-Gómez Isaac , Mayoral Pablo , Astudillo Aurora , Sveen Christina , Engedal Nikolai , López-Otín Carlos , Fernández Álvaro F. , Mariño Guillermo 
Published: January 2025

ABSTRACTAutophagy is a housekeeping catabolic process crucial for maintaining cell, tissue and organism functions. Through the years, the study of animal models with tissue-specific inactivation of autophagy essential genes has allowed us to understand its protective roles in the context of multiple human diseases, including cancer and neurodegeneration. However, due to the essential nature of autophagy, the effects of its systemic inhibition in mammals have not been explored in detail. Here, we report the generation of ATG4A-only mice, simultaneously deficient for three of the four mammalian ATG4 proteases (ATG4B, ATG4C and ATG4D). Through extensive characterization of ATG4A-only cells, which show a severe (albeit not complete) deficiency in autophagic activity, we define the specific roles of ATG4A protease towards ATG8 proteins (its physiological substrates), shedding some light into the evolutionarily-acquired complexity of mammalian ATG4-ATG8 system. Moreover, we show that the profound whole-body autophagy deficiency of ATG4A-only mice not only impacts the function of multiple tissues, but also leads to the development of an accelerated aging phenotype, characterized by the accumulation of genetic damage, systemic senescence, and premature death. Thus, through the analysis of ATG4A-only mice and other murine models deficient for ATG4 proteases, we not only provide new insights on how autophagy maintains cell, tissue, and organismal homeostasis, but also show for the first time that the degree of autophagic competency ultimately emerges as a critical determinant of organismal longevity.
Stable lentiviral-mediated expression of Cytochrome P450 2D6 in HepaRG cells: New means forin vitroassessment of xenobiotic biotransformation and cytotoxicity
Authors: Coppens-Exandier Hugo , Mackanga Franz , Darde Thomas , Bonhomme Corentin , Ribault Catherine , Gicquel Thomas , Pelletier Romain , Roshchina Flyuza , Schaefer Estelle , Chesné Christophe , Jamin Agnès , Corlu Anne , Loyer Pascal 
Published: January 2025

ABSTRACTPrimary cultures of Human Hepatocytes (PHH) are the gold standard to investigate drug-hepatotoxicityin vitro, however, large-scale studies using these primary liver cells are not possible because of the shortage in liver biopsies. HepaRG model is often considered as the closest surrogate to PHH for toxicity studiesin vitro. However, differentiated HepaRG cells express very low levels of the cytochrome P450 2D6 (CYP2D6) protein, which is essential for the biotransformation of nearly 25% of drugs on the market. To overcome this limitation, infection of progenitor HepaRG cells were performed using lentiviral particles containing a transgene encoding a single mRNA translated into a polypeptide undergoing proteolytic cleavage via the T2A peptide to produce both CYP2D6 and GFP. Differentiated HepaRG cells transduced with lentivirus stably expressed GFP and catalytically active human CYP2D6 enzyme at levels close to those found in high PHH metabolizers. As expected, CYP2D6 protein was found mostly located in the endoplasmic reticulum. Using the CYP2D6 transgenic HepaRG cells, we showed that tramadol was metabolized in both, N- and O-desmethyl tramadol as observed in human serum in contrast with the production of N-desmethyl tramadol only in parental HepaRG cells via the CYP3A4 catalytic activity. Similarly, after perhexiline (PHX) treatments, higher IC50were found in CYP2D6 expressing HepaRG cells associated to lower mitochondrial damages compared to those found in parental cells for the same PHX concentrations. Gene profiling between parental and transgenic cells demonstrated that the CYP2D6 expressing HepaRG cells had kept their ability to proliferate and differentiate with low impact on the expression of the hepatocyte specific functions. However, we identified a limited set of genes such as NXF3 and TRIM63, which were up-regulated by the mRNA encoded by the lentiviral transgene. Together, these data confirmed that the CYP2D6 transgenic HepaRG cells represent a suitable optimized transgenic model of HepaRG cells to evaluate biotransformation and toxicity of specific compounds metabolized by CYP2D6.
NCBP2-AS2 is a mitochondrial microprotein, regulates energy metabolism and neurogenesis, and is downregulated in Alzheimer’s disease
Authors: Popova Stanislava , Bhattarai Prabesh , Yilmaz Elanur , Lascu Daniela , Kuo Juo-Han , Erdem Gizem , Coban Basak , Michling Jitka , Cosacak Mehmet Ilyas , Tayran Huseyin , Kurth Thomas , Schambony Alexandra , Buchholz Frank , Gentzel Marc , Kizil Caghan 
Published: January 2025

AbstractMicroproteins, short functional peptides encoded by small genes, are emerging as critical regulators of cellular processes, yet their roles in mitochondrial function and neurodegeneration remain underexplored. In this study, we identify NCBP2-AS2 as an evolutionarily conserved mitochondrial microprotein with significant roles in energy metabolism and neurogenesis. Using a combination of cellular and molecular approaches, including CRISPR/Cas9 knockout models, stoichiometric co- immunoprecipitation, and advanced imaging techniques, we demonstrate that NCBP2-AS2 localizes to the inner mitochondrial space and interacts with translocase of the inner membrane (TIM) chaperones. These interactions suggest a role in ATPase subunit transport, supported by the observed reductions in ATPase subunit levels and impaired glucose metabolism in NCBP2-AS2-deficient cells. In zebrafish, NCBP2-AS2 knockout led to increased astroglial proliferation, microglial abundance, and enhanced neurogenesis, particularly under amyloid pathology. Notably, we show that NCBP2-AS2 expression is consistently downregulated in human Alzheimer’s disease brains and zebrafish amyloidosis models, suggesting a conserved role in neurodegenerative pathology. These findings reveal a novel link between mitochondrial protein transport, energy metabolism, and neural regeneration, positioning NCBP2-AS2 as a potential therapeutic target for mitigating mitochondrial dysfunction and promoting neurogenesis in neurodegenerative diseases such as Alzheimer’s disease.
Optimized vectors for genetic engineering ofAureobasidium pullulans
Authors: Colarusso Analeigha , Williams Audrey , Gladfelter Amy S. , Wirshing Alison C.E. , Lew Daniel J. 
Published: January 2025

ABSTRACTAureobasidium pullulansis a polyextremotolerant black yeast that exhibits impressive morphological plasticity. Consequently, it shows promise as a model system for investigating mechanisms of cell adaptation to different environments and the regulation of cell shape. Here, we build upon the current toolkit for working withA. pullulansand design and test 25 vectors with seven different codon-optimized fluorophores and three selection cassettes. This includes vectors that allow for dual expression of GFP and mCherry tagged proteins at theURA3locus and vectors that enable homology-based deletion or C-terminal tagging of endogenous genes without the need for cloning. This versatile vector series for working withA. pullulanswill enable a broad range of experiments in this emerging model system.SUMMARYAn optimized plasmid toolkit for genetic engineering of the emerging model fungus,A. pullulans.
Basigin Links Altered Skeletal Stem Cell Lineage Dynamics with Glucocorticoid-induced Bone Loss and Impaired Angiogenesis
Authors: Ambrosi Thomas H. , Morales David , Chen Kun , Hunt Ethan , Weldon Kelly , Maifeld Amber N. , Chavez Fatima I.M. , Wang Yuting , Murphy Matthew P. , Cressman Amin , Wheeler Erika E. , Saiz Augustine , Leach J. Kent , Fierro Fernando , Chan Charles K.F. , Lane Nancy E. 
Published: January 2025

AbstractGlucocorticoid (GC) induced osteoporosis (GIOP) and osteonecrosis remain a significant health issue with few approved therapies that can treat the bone loss and dysfunction of skeletal vasculature. Therefore, we aimed to investigate the cellular and molecular processes by which GCs affect osteogenesis and angiogenesis, as well as how treatment with parathyroid hormone (hPTH 1-34) modifies these effects in a mouse model of GIOP. GC treatment reduced bone mass through decreased bone formation by skeletal stem cells (SSCs) while also increasing osteoclast mediated resorption. Concomitantly, endothelial cells were increased in numbers but displayed distorted phenotypical features. However, hPTH treatment reversed GC induced changes in osteogenesis and angiogenesis to control levels. Transplantation studies of SSCs combined with molecular analysis by single cell RNA-sequencing and functional testing of primary human cells tied GC-induced skeletal changes to altered stem and progenitor cell differentiation dynamics. This in turn perpetuated reduced osteogenesis and vascular malformation through direct SSC-endothelial crosstalk mediated at least in part by Basigin. Intriguingly, antibody-mediated blockade of Basigin during GC treatment prevented detrimental bone loss. In addition, when administered to aged mice, anti-Basigin therapy reinstated bone remodeling to significantly improve bone mass independent of sex. These findings, while helping to explain the cellular and molecular basis of how hPTH treatment can mitigate GC induced bone loss, provide new therapeutic vantage points for GIOP and other conditions associated with bone loss.
Psychromonas aestuariisp. nov., a novel bacterial species isolated from estuarine surface sediment
Authors: Nita Iuliana , Kart Yaren , Strube Mikael Lenz , Bentzon-Tilia Mikkel 
Published: January 2025

ABSTRACTUsing an isolation chip (iChip), two bacterial strains, MME1Tand MME2, exhibiting ovoid to curved rod cell morphologies and white-cream colony pigmentation were isolated from the surface of estuarine sediment at Nivå Bugt Strandenge Bird Sanctuary, Denmark (55°55’42.6’N 12°31’23.6’E). Analysis of the 16S rRNA gene sequence of these isolates suggested them to be members of the genusPsychromonas, as both had above 97.5 % 16S rRNA gene similarity withPsychromonas aquimarina strainJAMM 0404T. Further genomic comparisons suggested MME strains to be representatives of a novel species, having an average nucleotide identity (ANI) < 85 % relative to all other genome sequenced species of thePsychromonasgenus. The G+C content was 39.5 mol %. The species was facultative anaerobic, growing optimally at 15 – 20 °C and pH 7.0. The optimal salinity was lower than for other described species of the genus with 1 – 2 % NaCl, reflecting the estuarine source of isolation. GC-MS analyses identified C16:0, C16:1ω7c/C16:1ω7t/and C14:03OHas the predominant cellular fatty acids. Based on molecular, phenotypic, and chemotaxonomic analyses, we propose that MME1 and MME2 represent a novel species of the genusPsychromonaswith the namePsychromonas aestuariisp. nov. with the MME1T(= DSM 118464T=LMG 33722T) as the type strain.
Symmetries and Continuous Attractors in Disordered Neural Circuits
Authors: Clark David G. , Abbott L.F. , Sompolinsky Haim 
Published: January 2025

AbstractA major challenge in neuroscience is reconciling idealized theoretical models with complex, heterogeneous experimental data. We address this challenge through the lens of continuous-attractor networks, which model how neural circuits may represent continuous variables, such as head direction or spatial location, through collective dynamics. In classical continuous-attractor models, a continuous symmetry of the connectivity generates a manifold of stable states, resulting in tuning curves that are identical up to shifts. However, mouse head-direction cells show substantial heterogeneity in their responses that appears incompatible with this classical picture. To understand the mechanistic origin of these data, we use an optimization principle to construct recurrent-network models that match the observed responses while exhibiting quasi-continuous-attractor dynamics. To study how such systems scale with increasing numbers of neuronsN, we develop a statistical generative process that produces artificial tuning curves that match many features of the experimental data quantitatively. Due to a continuous symmetry in the generative process, the connectivity matrix exhibits doublet degeneracy in its spectrum at largeN, reflecting an underlying circular geometry. Unlike classical models, where the ring structure is embedded in the neuronal space through a structured Fourier embedding, our model uses a random, disordered embedding. Analysis of the network dynamics in the large-Nlimit through dynamical mean-field theory reveals that the system becomes equivalent to a classical ring-attractor model. We extend this approach to higher-dimensional symmetries, applying it to grid cells in the medial entorhinal cortex and showing that the mean-field description recovers classical continuous-attractor models. Our work implies that large mammalian neural circuits could represent continuous variables using continuous-attractor dynamics, complete with continuous symmetry, in a way that is fully compatible with their heterogeneity and disorder.
The modification of DNA with indole-linked nucleotides alters its sensitivity to enzymatic cleavage
Authors: Lingala Suresh , Fisiuk Anastasiia , Stephen Michelle , Mohanrao Raja , Klingsberg Judah , Vecchioni Simon , Volvovitz Ealonah S , Rozhkov Sergei , Mallikaratchy Prabodhika 
Published: January 2025

AbstractWe describe the synthesis of C-5 indole-tagged pyrimidine and C-8 indole-tagged purine nucleoside phosphoramidites and their incorporation into double-stranded DNA 15 base pairs in length. Of the 23 sequence modifications tested, two induced the DNA duplex to adopt a Z-like left-handed conformation under physiological salt conditions, bypassing the specific sequences typically required for a left-handed Z-DNA structure. The impact of these modifications varied with the linker type: flexible propyl linkers exhibited distinct effects compared to rigid propargyl linkers. Notably, modifications positioned directly on or near a restriction site emphasized the pivotal role of linker rigidity in controlling DNA conformation. Specifically, the conformational change induced by the flexible linker impacted nuclease and restriction endonuclease cleavage, reducing sequence specificity. In contrast, the rigid linker suppressed this effect. Furthermore, our findings indicate that nucleic acid duplexes modified with indole-linked nucleotides using a flexible propyl linker have a pronounced tendency to form BZ or Z-like regions in longer DNA sequences. A higher density of modifications may even induce a full Z-like conformation throughout the duplex. These modified nucleotides hold potential for the development of novel antisense therapeutics and introducing valuable tools for in vitro screening of small molecules targeting distorted B-DNA, BZ-DNA, and Z-DNA structures.
From Local Interactions to Global Patterns: An Analysis of Silk Density in Spider Webs
Authors: Lin Fangyuan , Nagel Kathryn M. , Lee Seewoo , Jiang Jason , Yang Grant , Chang Patrtick , Li Samuel , Sheu Norman 
Published: January 2025

AbstractThis study explores the structural complexity of spider webs through information-theoretic and harmonicity-based frameworks to quantify spatial patterns in silk density across different web regions and reveal the underlying resource allocation strategies. By analyzing the entropy of silk density distributions across different species, we observed that the entropy values follow a normal distribution with a mean of 1.24 bits and a standard deviation of 0.22 bits when using 10 quantization levels. In the second part of the paper, by measuring the harmonicity of the silk density, we reveal that the silk density at a given point can be inferred from its neighbors, with an average harmonicity value of 0.0039 (fraction of total points in point cloud data). The harmonic behavior is notable for its maximum principle, suggesting that the strongest parts of the web appear at the boundaries, aligning with existing knowledge of spider web construction. These findings provide a new technique for quantifying web-building strategies and offer new insights into spider behavior and evolution.
Neuronal Activity-Dependent Gene Dysregulation inC9orf72i3Neuronal Models of ALS/FTD Pathogenesis
Authors: Ghaffari Layla T. , Welebob Emily , Boehringer Ashley , Cyliax Kelly , Pasinelli Piera , Trotti Davide , Haeusler Aaron R. 
Published: January 2025

AbstractThe GGGGCC nucleotide repeat expansion (NRE) mutation in theC9orf72(C9) gene is the most common cause of ALS and FTD. Neuronal activity plays an essential role in shaping biological processes within both healthy and neurodegenerative disease scenarios. Here, we show that at baseline conditions, C9-NRE iPSC-cortical neurons display aberrations in several pathways, including synaptic signaling and transcriptional machinery, potentially priming diseased neurons for an altered response to neuronal stimulation. Indeed, exposure to two pathophysiologically relevant stimulation modes, prolonged membrane depolarization, or a blockade of K+channels, followed by RNA sequencing, induces a temporally divergent activity-dependent transcriptome of C9-NRE cortical neurons compared to healthy controls. This study provides new insights into how neuronal activity influences the ALS/FTD-associated transcriptome, offering a dataset that enables further exploration of pathways necessary for conferring neuronal resilience or degeneration.
Flickering white light stimulation at 60 Hz induces strong, widespread neural entrainment and synchrony in healthy subjects
Authors: Alamalhoda MohammadAmin , Leesch Friederike , Giovanetti Francesca , Dunne Eoghan , Pilloni Giuseppina , Caffrey Mark , O’Keeffe Jack , Venturino Alessandro , Ferretti Maria Teresa 
Published: January 2025

AbstractBackgroundWhile the effects of 40 Hz externally-induced neural entrainment have been extensively described, little is known about 60 Hz entrainment in humans. Given the role of 60 Hz in cognition, neuroplasticity and neuropsychiatric disorders, this warrants further investigation.ObjectivesThis pilot study characterizes, for the first time, the neural and somatic response to 60 Hz light entrainment in healthy volunteers, over a 3 week-period.MethodsFourteen volunteers were randomized to receive either 60 Hz flickering white light or constant light as sham (30-min sessions, for 3 weeks, 5 days a week). Neural entrainment was assessed with EEG on days 1, 5 and 19. Salivary cortisol and C-reactive protein (CRP) levels, measured with ELISA, assessed the somatic response to stimulation. Side effects and well-being were monitored via questionnaires.Results60 Hz flickering light induced a strong neural entrainment across visual, parietal, temporal and frontal cortex. The signal was highly synchronous but declined significantly by day 19 compared to day 1, indicating neural habituation. Cortisol and CRP salivary levels were unchanged and the stimulation was well tolerated.ConclusionsTo the best of our knowledge this is the first study to characterize both the neural and the somatic response to flickering light over 3 weeks. The observed neural habituation suggests that neuroplasticity could be induced with repeated stimulations over 3 weeks. 60 Hz stimulation for modulating brain activity and induce neuroplasticity has implications for our basic understanding of brain physiology as well as treatment of psychiatric disorders.
Neural sensitivity to radial frequency patterns in the visual cortex of developing macaques
Authors: Rodríguez Deliz C. L. , Lee Gerick M. , Bushnell Brittany N. , Majaj Najib J. , Movshon J. Anthony , Kiorpes Lynne 
Published: January 2025

ABSTRACTVisual resolution, contrast sensitivity and form perception improve gradually with age. In nonhuman primates, the sensitivity and resolution of cells in the retina, lateral geniculate nucleus and primary visual cortex (V1) also improve, but not enough to account for the perceptual changes. So, what aspects of visual system development limit visual sensitivity in infants? Improvements in behavioral sensitivity might arise from maturation of regions downstream of V1 such as V2, V4 and IT, which are thought to support increasingly complex perceptual abilities. We recorded the responses of populations of neurons in areas V1, V2, V4, and IT to radial frequency patterns - a type of global form stimulus. Subjects were three young monkeys between the ages of 19 and 54 weeks, and a single adult animal. We found that neurons and neural populations in V4 reliably encoded global form in radial frequency stimuli at the earliest ages we studied, while V1 neurons do not. V2 and IT populations also showed some degree of selectivity for these patterns at early ages, especially at higher radial frequency values. We did not find significant, systematic changes in neural decoding performance that could account for the improvement in behavioral performance over the same age range in an overlapping group of animals (Rodriguez Deliz et al., 2024). Finally, consistent with our prior behavioral results, neural populations in V4 show highest sensitivity for the higher radial frequency values which contain the highest concentration of curvature and orientation cues.SIGNIFICANCE STATEMENTInfants have remarkably limited ability to discriminate shapes. These limitations cannot be fully explained by postnatal changes in their eyes, visual thalamus, or primary visual cortex. The perception of shape requires integration of local cues across space to create global form information. We therefore examined populations of neurons in extrastriate visual cortex to learn whether information represented in these regions might limit infants’ abilities to process global forms. We found instead that extrastriate areas involved in global form processing function maturely early in life, by the age of 4-6 months, suggesting that infants’ perceptual limits are set by other aspects of brain development.