bluuebunny/crossref_metadata_2025_split huggingface dataset:
Snapshot of 5-HT2Areceptor activation in the mouse brain via IP1detection
Authors: de la Fuente Revenga Mario , González-Maeso Javier 
Published: October 2024

AbstractThe distinct subjective effects that define psychedelics such as LSD, psilocybin or DOI as drug class are causally linked to activation of the serotonin 2A receptor (5-HT2AR). However, some aspects of 5-HT2AR pharmacology remain elusive, such as what molecular drivers differentiate psychedelic from non-psychedelic 5-HT2AR agonists. We developed an ex vivo platform to obtain snapshots of drug-mediated 5-HT2AR engagement of the canonical Gq/11pathway in native tissue. This non-radioactive methodology captures the pharmacokinetic and pharmacodynamic events leading up to changes in inositol monophosphate (IP1) in the mouse brain. The specificity of this method was assessed by comparing IP1levels in homogenates from the frontal cortex in DOI-treated wild-type and 5-HT2AR-KO animals compared to other brain regions, namely striatum and cerebellum. Furthermore, we encountered that head-twitch response (HTR) counts and IP1in the frontal cortex were correlated. We observed that IP1levels in frontal cortex homogenates from mice treated with LSD and lisuride vary in magnitude, consistent with LSD’s 5-HT2AR agonism and psychedelic nature, and lisuride’s lack thereof. MDMA evoked an increase of IP1signal in the frontal cortex that were not matched by the serotonin precursor 5-HTP or the serotonin reuptake inhibitor fluoxetine. We attribute differences in the readout primarily to the indirect stimulation of 5-HT2AR by MDMA via serotonin release from its presynaptic terminals. This methodology enables capturing a snapshot of IP1turnover in the mouse brain that can provide mechanistic insights in the study of psychedelics and other serotonergic agents pharmacodynamics.
Persistent Na+current couples spreading depolarization to seizures inScn8again of function mice
Authors: Aiba Isamu , Ning Yao , Noebels Jeffrey L. 
Published: October 2024

AbstractSpreading depolarization (SD) is a slowly propagating wave of massive cellular depolarization that transiently impairs the function of affected brain regions. While SD typically arises as an isolated hemispheric event, we previously reported that reducing M-type potassium current (IKM) by ablation ofKcnq2in forebrain excitatory neurons results in tightly coupled spontaneous bilateral seizure-SD complexes in the awake mouse cortex. Here we find that enhanced persistent Na+current due to gain-of-function (GOF) mutations inScn8a(N1768D/+, hereafter D/+) produces a similar compound cortical excitability phenotype. Chronic DC-band EEG recording detected spontaneous bilateral seizure-SD complexes accompanied by seizures with a profound tonic motor component, which occur predominantly during the light phase and were detected at ages between P33-100. Laser speckle contrast imaging of cerebral blood flow dynamics resolved SD as a bilateral wave of hypoperfusion and subsequent hour-lasting hypoperfusion inScn8aD/+cortex in awake head-restrained mice evoked by a PTZ injection. Subcortical recordings in freely moving mice revealed that approximately half of the spontaneous cortical seizure-SD complexes arose with a concurrent SD-like depolarization in the thalamus and delayed depolarization in the striatum. In contrast, SD-like DC potential shifts were rarely detected in the hippocampus or upper pons. Consistent with the high spontaneous incidencein vivo, cortical slices fromScn8aD/+mice showed a raised SD susceptibility, and pharmacological inhibition of persistent Na+current (INaP), which is enhanced inScn8aD/+neurons, inhibited SD generation in cortical slicesex vivoas well as in head-fixed micein vivo, indicating that INaPcontributes to SD susceptibility.Ex vivoCa2+imaging studies using acute brain slices expressing genetic Ca2+sensor (Thy1-GCAMP6s) demonstrated that pharmacological activation of IKMsuppressed Ca2+spikes and SD, whereas an IKMinhibitor strongly increased the frequency of hippocampal Ca2+spikes inScn8aD/+, but not WT slices, suggesting that IKMrestrains theScn8aGOF hyperexcitability. Together, our study identifies a cortical SD phenotype inScn8aGOF mice shared with theKcnq2-cKO model of developmental epileptic encephalopathy, and reveals that an imbalance of non-inactivating inward and outward tonic membrane currents bidirectionally modulates spatiotemporal SD susceptibility.
Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage
Authors: Murley Andrew , Popovici Ann Catherine , Hu Xiwen Sophie , Lund Anina , Wickham Kevin , Durieux Jenni , Joe Larry , Koronyo Etai , Dillin Andrew 
Published: October 2024

SummaryTo maintain tissue homeostasis, many cells are kept in a quiescent state until prompted to divide. The re-activation of quiescent cells is perturbed with aging and may underlie declining tissue homeostasis and resiliency. The unfolded protein response regulators IRE-1 and XBP-1 are required for the re-activation of quiescent cells in developmentally L1 arrestedC. elegans.Utilizing a forward genetic screen inC. elegans, we discovered that macroautophagy targets protein aggregates to lysosomes in quiescent cells, leading to lysosome damage that prevents cell cycle re-entry in the absence of IRE-1/XBP-1. Genetic inhibition of macroautophagy and stimulation of lysosomes via the overexpression of HLH-30 (TFEB/TFE3) synergistically reduces lysosome damage. Protein aggregates are also targeted to lysosomes by macroautophagy in quiescent cultured mammalian cells, causing lysosome damage that is associated with reduced re-activation. Thus, lysosome damage is a hallmark of quiescent cells and limiting lysosome damage by restraining macroautophagy can stimulate their re-activation.
Changes in cortical grasp-related activity before and after object contact
Authors: Yan Yuke , Sobinov Anton R. , Goodman James M. , Okorokova Elizaveta V. , Miller Lee E. , Bensmaia Sliman J. 
Published: October 2024

AbstractGrasping, a seemingly simple manual behavior, requires the coordinated control of dozens of joints, guided by sensory signals from muscles, tendons, and skin. As the motor cortex controls finger movement and exerted forces, the somatosensory cortex must process the barrage of proprioceptive and tactile signals that convey details about the object’s shape, its local features (e.g., edges and curvature), and forces applied to it. In the present study, we aimed to understand the transformation in these sensorimotor signals at the time of contact with an object. We analyzed object-specific signals in the primary motor cortex (M1) and Brodmann’s areas 3a, 1, and 2 of the somatosensory cortex of macaque monkeys. We found object information distributed throughout sensorimotor cortex, some of which was independent of contact, while most was dramatically altered by it. While all areas conveyed object information after contact, those carrying postural representations (M1, area 3a) were also informative before contact, during the hand pre-shaping epoch. Although their mappings retained some similarity between epochs, decoders built on the pre-contact epoch did not perform well on the post-contact epoch, suggesting intermixing between postural and force-related signals. After contact, individual neurons in M1 retained some information about the object, but the populational encoding of object identity weakened, reflecting perhaps, the delegation of control to subcortical structures. Unexpectedly, although it was active, area 2 was uninformative about the object before contact, despite its proprioceptive inputs. However, after contact, area 2 emerged as the most informative region of any epoch, likely reflecting its convergent proprioceptive and cutaneous input, and supporting its proposed role in haptic object perception. These results underscore the diverse activity within the sensorimotor cortex during grasping, highlighting the intricate neural processes involved in this fundamental behavior.
DNA methylation either antagonizes or promotes Polycomb recruitment at transposable elements
Authors: Hure Valentin , Piron-Prunier Florence , Déléris Angélique 
Published: October 2024

ABSTRACTTransposable elements (TEs) are primarily silenced by DNA methylation and the associated histone modification H3K9me2 in many multicellular eukaryotes, including plants. However, in the absence of DNA methylation due to mutations in the DNA methylation machinery or in certain developmental contexts, the same TEs can gain Polycomb-associated H3K27me3, another epigenetic silencing mark that is usually linked with the facultative silencing of genes. In this study, we initially aimed to investigate whether DNA methylation and H3K27me3 could compete during the establishment of silencing at TEs in the model plant Arabidopsis. Strikingly, we show that the deposition of the H3K27me3 mark at newly inserted transgenic TE sequences is impaired in plants in which thede novoDNA methyltransferase DRM2 is mutated, contrary to the competition model hypothesized. Further profiling of H3K27me3 indrm2mutants and in the DNA demethylase mutantrddconfirmed this new role of DNA methylation in promoting H3K27me3 deposition at some loci, in addition to the previously described antagonistic role at others; these findings further reveal a new function of DNA demethylation in modulating H3K27me3 levels in vegetative tissues. Finally, by implementing targeted DNA methylation experiments, we demonstrate that DNA methylation has a direct impact on PcG recruitment and can either promote H3K27me3 deposition or antagonize it in a locus-specific manner. Together, our results uncover a novel crosstalk between DNA methylation and Polycomb and reveal that these two pathways, thought to be specialized and antagonistic, can be interdependent and cooperate more than anticipated to maintain genome and epigenome integrity in eukaryotes.
Characteristics of spatial summation in the magnocellular, parvocellular, and koniocellular pathways
Authors: Wu Christopher S. , Coates Daniel R. 
Published: October 2024

ABSTRACTIn this study, we characterize the spatial summation properties of targeted magnocellular, parvocellular, and koniocellular pathways within the central 20° of visual field using chromatic transformations in DKL color space. For the magnocellular and koniocellular conditions, critical areas of complete spatial summation were found for all eccentricities. For the parvocellular conditions, complete spatial summation was absent within the stimulus size ranges tested. We also describe an anatomically and physiologically motivated model of receptive field pooling using probability summation. Model simulations suggest that the critical area of summation can be explained by the dendritic field size of underlying retinal ganglion cells, corroborating our psychophysical data.
LC-MS system for automatically collecting time-resolved metabolomics data of cultured cells
Authors: Chan Carly C.Y. , Groves Ryan A. , Lewis Ian A. 
Published: October 2024

AbstractTemporal metabolic dynamics are a critical, but difficult to study aspect of metabolism. To address this, we developed a liquid chromatography-mass spectrometry (LC-MS) system, temporal uptake and nutritional analysis (TUNA), to automatically collect time-resolved metabolomics data of cultured cells. TUNA enables sub-minute sequential sampling, has broad metabolite coverage, supports robust metabolite identification, can monitor over 72 conditions in parallel, and can be implemented in most LC-MS laboratories. We used TUNA to monitor temporal dynamics of uropathogens (Escherichia coliandProteus mirabilis) and identify novel metabolic phenotypes that cannot be captured from a single time point.
Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions
Authors: Li Rina , Lin Xingcheng 
Published: October 2024

AbstractHistone acetylation is a key regulatory post-translational modification closely as-sociated with gene transcription. In particular, H4K16 acetylation (H4K16ac) is a crucial gene activation marker that induces an open chromatin configuration. While previous studies have explored the effects of H4K16ac on nucleosome interactions, how this local modification affects higher-order chromatin organization remains un-clear. To bridge the chemical modifications of these histone tail lysine residues to global chromatin structure, we utilized a residue-resolution coarse-grained chromatin model and enhanced sampling techniques to simulate charge-neutralization effects of histone acetylation on nucleosome stability, inter-nucleosome interactions, and higher-order chromatin structure. Our simulations reveal that H4K16ac stabilizes a single nucleosome due to the reduced entropic contribution of histone tails during DNA unwrapping. In addition, acetylation modestly weakens inter-nucleosome interactions by diminishing contacts between histone tails, DNA, and nucleosome acidic patches. These weakened interactions are amplified when nucleosomes are connected by linker DNA, whose fluctuation causes significant chromatin destacking and decompaction, exposing nucleosomes for transcriptional activity. Our findings suggest that the geometric constraint imposed by chromatin DNA plays a critical role in driving chromatin structural reorganization upon post-translational modifications.
Regulation of the SOS response and homologous recombination by an integrative and conjugative element
Authors: Heredia Alam García , Grossman Alan D. 
Published: October 2024

AbstractIntegrative and conjugative elements (ICEs) are mobile genetic elements that transfer between bacteria and influence host physiology and promote evolution. ICEBs1ofBacillus subtilismodulates the host DNA damage response by reducing RecA filament formation. We found that the two ICEBs1-encoded proteins, RamT and RamA that modulate the SOS response in donors also function in recipient cells to inhibit both the SOS response and homologous recombination following transfer of the element. Expression of RamT and RamA caused a decrease in binding of the host single strand binding protein SsbA to ssDNA. We found that RamA interacted with PcrA, the host DNA translocase that functions to remove RecA from DNA, likely functioning to modulate the SOS response and recombination by stimulating PcrA activity. These findings reveal how ICEBs1can modulate key host processes, including the SOS response and homologous recombination, highlighting the complex interplay between mobile genetic elements and their bacterial hosts in adaptation and evolution.
The invasion pore induced byToxoplasma gondii
Authors: Kegawa Y. , Male F. , Jiménez-Munguía I. , Blank P. S. , Mekhedov E. , Ward G. , Zimmerberg J. 
Published: October 2024

AbstractObligate intracellular parasites invade host cells to survive. Following host cell contact, the apicomplexanToxoplasma gondiiinjects proteins required for invasion into the host cell. Here, electrophysiological recordings of host cells acquired at sub- 200 ms resolution allowed detection and analysis of a transient increase in host membrane conductance following exposure toToxoplasma gondii. Transients always preceded invasion but parasites depleted of the moving junction protein RON2 generated transients without invading, ruling out a direct structural role for RON2 in generating the conductance pathway or restricting the diffusion of its components. Time-series analysis developed for transients and applied to the entire transient dataset (910,000 data points) revealed multiple quantal conductance changes in the parasite-induced transient, consistent with a rapid insertion, then slower removal, blocking, or inactivation of pore-like conductance steps. Quantal steps for RH had a principal mode with Gaussian mean of 0.26 nS, similar in step size to the apicomplexan protein translocon EXP2. Without RON2 the quantal mean was significantly different (0.19 nS). Because no invasion occurs without poration, the term ‘invasion pore’ is proposed.
Glycyl-tRNA sequestration is a unifying mechanism underlyingGARS1-associated peripheral neuropathy
Authors: Mora Natalia , Slot Erik F.J. , Lewandowski Vanessa , Menafra Maria P. , Mallik Moushami , Lith Pascal van , Sijlmans Céline , van Bakel Nick , Ignatova Zoya , Storkebaum Erik 
Published: October 2024

ABSTRACTDominantly inherited mutations in eight cytosolic aminoacyl-tRNA synthetase genes cause hereditary motor and sensory neuropathy, characterized by degeneration of peripheral motor and sensory axons. We previously identified a pathogenic gain-of-toxic function mechanism underlying peripheral neuropathy (PN) caused by heterozygous mutations in theGARS1gene, encoding glycyl-tRNA synthetase (GlyRS). Specifically, PN-mutant GlyRS variants sequester tRNAGly, which depletes the cellular tRNAGlypool, leading to insufficient glycyl-tRNAGlyavailable to the ribosome and consequently ribosome stalling at glycine codons. Given that GlyRS functions as a homodimer, a subset of PN-GlyRS mutations might alternatively cause peripheral neuropathy through a dominant negative loss-of-function mechanism. To explore this possibility, we here generated three novel PN-GlyRSDrosophilamodels expressing human PN-GlyRS (hGlyRS) variants that do not alter the overall GlyRS protein charge (S211F and H418R) or the single reported PN-GlyRS variant that renders the GlyRS protein charge more negative (K456Q). High-level expression of hGlyRS-K456Q did not induce peripheral neuropathy and the K456Q variant does not affect aminoacylation activity, suggesting that K456Q is not a pathogenic mutation. Expression of hGlyRS-S211F or hGlyRS-H418R inDrosophiladid induce peripheral neuropathy andde novoprotein synthesis defects. Genetic and biochemical evidence indicates that these phenotypes were attributable to tRNAGlysequestration rather than a dominant negative mechanism. Our data identify tRNAGlysequestration as a unifying pathogenic mechanism underlying PN-GlyRS. Thus, elevating tRNAGlylevels may constitute a therapeutic approach for all PN-GlyRS patients, irrespective of their disease-causing mutation.
Unravelling the Enantioselective Mechanism of Benzylsuccinate Synthase: Insights into Anaerobic Hydrocarbon Degradation Through Multiscale Modelling and Kinetics
Authors: Szaleniec Maciej , Oleksy Gabriela , Aleksic Ivana , Krämer Kai , Heider Johann 
Published: October 2024

AbstractFumarate-adding enzymes (FAE) are a subset of the glycyl radical enzyme superfamily involved in anaerobic hydrocarbon degradation. Benzylsuccinate synthase (BSS) catalyzes the enantiospecific formation ofR-benzylsuccinate from toluene and fumarate, initiating anaerobic toluene degradation. In this paper, we present a detailed theoretical study of the reaction mechanism using classical molecular dynamics and multiscale modelling (QM:MM). We describe the potential energy surface of the reaction, confirming the previously postulated mechanism. However, the multiscale character of our model allowed to elucidate the origins of several experimentally observed catalytic phenomena, such as the inversion of the configuration of the benzylic atom upon C-C bond formation,synaddition of the abstracted H atom back to the benzylsuccinyl radical, or kinetic isotope effects in the range of 1.7-2.1. The obtained model is supported by microkinetic analysis and was able to explain and quantitatively predict the strictR-enantioselectivity of BSS, which is not enforced by the binding orientation of the fumarate, but by dynamic kinetic behaviour of toluene in the active site leading to faster production of theR-enantiomer. We were also able to explain the experimentally observed slow H/D exchange in the product during incubation with BSS in D2O, confirming the partial reversibility of the reaction. Our study contributes to the elucidation of the catalytic processes catalyzed by BSS and its role in the bioremediation of hydrocarbon pollutants.
Defining the alpha domain of K1-like killer toxins
Authors: Coss Sarah A. , Ytreberg F. Marty , Rowley Paul A. 
Published: October 2024

AbstractAntifungal killer toxins produced by yeasts undergo post-translational processing to enable the formation of mature and active toxins. The preprocessed, immature K1 killer toxin fromSaccharomyces cerevisiaehas four different domains (delta, alpha, gamma, and beta) that are cleaved to produce a mature toxin consisting of a disulfide-linked alpha and beta heterodimer. K1 homologs from various yeast species of the Saccharomycotina have been previously identified by primary sequence homology. Primary sequence analysis has identified putative cleavage sites across all homologs, with some conservation with cleavage sites identified in K1 and the likely importance of the conserved carboxypeptidases Kex1 and Kex2. The identification of sites of proteolytic processing has enabled an accurate definition of the domain boundaries of delta, alpha, gamma, and beta domains in all K1 homologs. Functional assays revealed that many K1 homologs contain cytotoxic alpha domains. Interestingly, several killer toxins that lacked measurable antifungal activity still exhibited toxic alpha domains when expressed independently. These findings suggest that alpha domain toxicity is conserved across K1 homologs, and that variations in post-translational processing and domain interactions may influence full-length toxin functionality. This work provides insights into the evolutionary conservation and diversity of yeast killer toxins.
Unraveling the Associations Between Voice Pitch and Major Depressive Disorder: A Multisite Genetic Study
Authors: Di Yazheng , Rahmani Elior , Mefford Joel , Wang Jinhan , Ravi Vijay , Gorla Aditya , Alwan Abeer , Kendler Kenneth S. , Zhu Tingshao , Flint Jonathan 
Published: October 2024

AbstractMajor depressive disorder (MDD) often goes undiagnosed due to the absence of clear biomarkers. We sought to identify voice biomarkers for MDD and separate biomarkers indicative of MDD predisposition from biomarkers reflecting current depressive symptoms. Using a two-stage meta-analytic design to remove confounds, we tested the association between features representing vocal pitch and MDD in a multisite case-control cohort study of Chinese women with recurrent depression. Sixteen features were replicated in an independent cohort, with absolute association coefficients (beta values) from the combined analysis ranging from 0.24 to 1.07, indicating moderate to large effects. The statistical significance of these associations remained robust, with P-values ranging from 7.2 × 10−6to 6.8 × 10−58. Eleven features were significantly associated with current depressive symptoms. Using genotype data, we found that this association was driven in part by a genetic correlation with MDD. Significant voice features, reflecting a slower pitch change and a lower pitch, achieved an AUC-ROC of 0.90 (sensitivity of 0.85 and specificity of 0.81) in MDD classification. Our results return vocal features to a more central position in clinical and research work on MDD.