bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-reactive hydrogel nanovials for temporal control of secretion capture from antibody-secreting cells
Authors: Mellody Michael , Nakagawa Yuta , James Richard , Di Carlo Dino 
Published: January 2025

AbstractAntibody discovery can benefit from techniques to screen antibody-secreting cells (ASCs) at scale for the binding and functionality of a diverse set of secreted antibodies. Previously, we demonstrated the use of cavity-containing hydrogel microparticles (nanovials) coated with a single affinity agent, biotin, to capture and identify ASCs secreting antibodies against a recombinant antigen bound to the nanovial through biotin-streptavidin linkages. However, rapidly secreted antibodies from unbound cells or cells in adjacent nanovials can cause crosstalk leading to background signal. Earlier efforts address this by localizing capture sites to the nanovial cavity, emulsifying nanovials, or short secretion times to limit secreted antibodies from binding to neighboring nanovials. Here, we demonstrate a method to functionalize nanovials with moieties that impart orthogonal reactivity, enabling conjugation of cell capture antibodies and antigens at different times. We show that by using a strained alkyne moiety to attach cell-capture antibodies via click chemistry to nanovials, we can capture cells and subsequently quantify secretions via biotin-streptavidin linkages. By delaying the loading of antigens onto the nanovials until after cell capture, we were able to ensure high purity (>95%) isolation of hybridoma secreting an antigen-specific antibody in a background of other hybridoma. This approach allows tight temporal control of the secretion measurement, which is independent of the cell loading time, and requires less convective transfer steps. Click chemistry-based coupling further improved cell loading into nanovials by 58% compared to biotin-streptavidin-biotin coupling and caused no reduction in cell viability. We demonstrate an implementation of this system to improve antigen-specific hybridoma screening, yielding an 8-fold improvement in hybridoma enrichment while maintaining a similar workflow complexity. Hybridomas on nanovials sorted into well plates regrew into colonies following sorting using standard fluorescence-activated cell sorting and maintained secretion of antigen-specific antibodies with high purity (∼90%), as validated via standard enzyme-linked immunosorbent assays. This lab-on-a-particle approach can be applied more generally to decouple cell loading, treatment, or activation, from secretion measurements for single-cell functional assays.
Chronic High Intensity Interval Training (HIIT) exercise in adolescent rat’s result in cocaine place aversion and ΔFosB induction
Authors: Hammond Nikki , Rahman Nabeel , Zhan Sam , Gold Mark S , Blum Kenneth , Quattrin Teresa , Young Yim Yun , Nestler Eric J , Thanos Panayotis K. 
Published: January 2025

AbstractHigh-Intensity Interval Training (HIIT) is a form of exercise that has been greatly popularized over the past few years for its many health benefits. Similar to other forms of exercise, HIIT may be beneficial in the prevention of substance use behaviors; however, the extent to which HIIT can impact the reinforcing effects of drugs of abuse during adolescence has not been fully evaluated. Here, we assess the effects of HIIT during adolescence on subsequent cocaine conditioned place preference (CPP) in male Lewis rats. The HIIT exercise exposed rats ran on a treadmill for 30 minutes daily (ten three-minute cycles) for six weeks with progressive speed-increased up to 0.8 mph (21.5m/min), while the sedentary rats remained in their home cage. Following the six weeks of exercise, rats were tested for cocaine (25 mg/kg) CPP. Following completion of the behavior test ΔFosB levels were measured in the brain. Results showed that the HIIT rats showed significantly attenuated place preference (-19%) in their time spent in the cocaine-paired chamber compared to the sedentary environment rats. In addition, HIIT rats had significantly higher (65%) striatum ΔFosB levels compared to the sedentary rats. Our findings show that HIIT exercise during adolescence could be protective against cocaine abuse which may be mediated by an increase in ΔFosB. This finding has important clinical implications with respect to exercise mediated protection against substance misuse and abuse. Future studies will examine this effect in females as well as the potential underlying mechanisms.
Traveling waves enhance hippocampal-parahippocampal couplings in human episodic and working memory
Authors: Chen Xinyu , Chen Zhe Sage 
Published: January 2025

SummaryMultiple brain regions in the human medial temporal lobe (MTL) are coordinated in memory processing. Traveling waves is a potential mechanism to coordinate information transfer through organizing the timing or spatiotemporal patterns of wave propagation. Based on direct human intracranial EEG recordings, we detected bidirectional hippocampal and parahippocampal traveling waves (4-10 Hz) along the posterior-anterior axis during a verbal memory task. Hippocampal traveling waves enhanced hippocampal-parahippocampal and intra-hippocampal couplings in both amplitude and phase as well as hippocampal theta phase-gamma amplitude coupling, suggesting a facilitatory role of TWs. Granger causality analysis showed asymmetric information flow, with greater predictability in the parahippocampal-to-hippocampal direction and dominant peak at the beta band (20-30 Hz). Hippocampal power and bidirectional hippocampal-parahippocampal information flow at the gamma band (35-50 Hz) showed reductions during successful memory encoding trials. These results support functional significance of frequency-specific parahippocampal-hippocampal and intra-hippocampal communications during memory encoding and retrieval.HighlightsBidirectional hippocampal traveling waves enhance hippocampal-parahippocampal couplings in both amplitude and phase.Hippocampal-parahippocampal gamma coherence is greater in memory retrieval than memory encoding.Intra-hippocampal theta phase-gamma amplitude coupling is greater in memory encoding than recall.Hippocampal power and hippocampal-parahippocampal granger causality in gamma band reduced in successful trials.
4-Phenylbutyric acid modulates Connexin 43 expression restricting murine-β-coronavirus infectivity and virus-induced demyelination
Authors: Kasle Grishma , Sharma Madhav , Kumar Saurav , Das Pranati , Das Sarma Subhajit , Koval Michael , Mahadevan Anita , Kenyon Lawrence C. , Das Sarma Jayasri 
Published: January 2025

AbstractGap junction intercellular communication, particularly involving Connexin 43 and Connexin 47, plays a critical role in maintaining CNS homeostasis and has been implicated in Multiple Sclerosis (MS) pathology. Thus, warranting further studies in experimental animal models to understand how modulation of Cx43 expression can influence MS pathology. Intracranial infection with murine-β-coronavirus Mouse Hepatitis Virus (MHV-A59) in mice results in acute pathology characterized by high viral titers, glial activation in the brain and chronic neuroinflammatory demyelination, effectively mimicking key pathological hallmarks of MS and serving as a robust model to investigate its viral etiology. MHV-A59 infection leads to a pronounced downregulation of Cx43 during the acute phase, emphasizing its critical role in virus-induced CNS pathology. In this study, we investigated the potential ofin vivo4-phenylbutyric acid (4-PBA) administration in modulating Cx43 expression in this MHV-induced model and its consequence on chronic virus-induced demyelination. Our results reveal that 4-PBA treatment reduced acute MHV-A59 infectivity and viral spread in the brain while modulating the glial cell response, mounting host immunity. Treatment with 4-PBA effectively preserved the expression of both Cx43 and Cx47 in infected CNS cells, counteracting their infection-induced downregulation. Furthermore, MHV-A59 infection downregulated the expression of ER-resident thioredoxin family protein (ERp29), a well-known molecular chaperone of Cx43, which was rescued by 4-PBA treatment. We further validated if such downregulation of ERp29 is also evident in MS demyelinating plaques. In human MS patient-derived brain tissue, reduced Cx43 and ERp29 staining was observed in demyelinating plaques. Our studies revealed that 4-PBA treatment not only limits viral replication and spread throughout the brain but also protects the mice against severe chronic neuroinflammatory demyelination. These findings suggest that targeting Cx43 with 4-PBA holds significant therapeutic potential for addressing virus-induced neuroinflammatory demyelination and MS by preserving gap junction intercellular communication.
Resource partitioning in organosulfonate utilization by free-living heterotrophic bacteria during a North Sea microalgal bloom
Authors: Sidhu Chandni , Bartosik Daniel , Kale Vaikhari , Trautwein-Schult Anke , Becher Dörte , Schweder Thomas , Amann Rudolf I. , Teeling Hanno 
Published: January 2025

AbstractBlooming microalgae (phytoplankton) release diverse organic molecules that fuel the marine pools of dissolved and particulate organic matter. A highly specialized community of heterotrophic bacteria rapidly remineralizes substantial parts of this organic matter in the sun-lit upper ocean. In particular, microalgae produce large quantities of various organosulfur compounds that can serve as carbon and sulfur sources for bacteria.Here, we report on the analyses of a time series of previously generated 30 long-read metagenomes, 30 corresponding deeply sequenced short-read metatranscriptomes and 15 metaproteomes from 0.2-3 µm size fractions that we sampled in 2020 during a biphasic phytoplankton bloom in the German Bight (Southern North Sea). We analyzed the assembled contigs as well as 70 bacterial metagenome-assembled genomes that recruited the highest transcript numbers with respect to the utilization of methyl sulfur compounds (dimethylsulfoniopropionate (DMSP), dimethyl sulfide (DMS), dimethyl sulfone (DMSO2)), C3-sulfonates (2,3-dihydroxypropane-1-sulfonate (DHPS), 3-sulfolactate, 3-sulfopyruvate) and 2-aminoethanesulfonic acid (taurine).We observed a pronounced resource partitioning among bacterial clades that utilize distinct organosulfur compounds, which may explain successions of these clades during the studied bloom.Alphaproteobacteriawere the most active and degraded a variety of organosulfonates via various metabolic routes. However, we also found previously underreported roles of members of theBacteroidotaandGammaproteobacteriaas efficient degraders of DMSP, DMS, and DMSO2. One striking observation was a strong preference for DMSP cleavage inBacteroidotaas opposed to DMSP demethylation inAlphaproteobacteriaand indications for a particular proficiency for taurine utilization in Ilumatobacter_A andAcidimicrobiia.ImportanceSulfur-containing low-molecular-weight algal metabolites play an important role in overall marine carbon and sulfur fluxes. This study highlights that such compounds may play a crucial role in governing the succession of distinct bacterioplankton clades in response to phytoplankton blooms in coastal shelf areas of the temperate zone, such as the German Bight of the North Sea. WhileAlphaproteobacteriaare the most versatile and competitive degraders of dissolved organosulfur compounds during such blooms, this study repositions clades previously thought to play only a more limited role in dissolved organosulfur metabolismin situ, such asGammaproteobacteria,Bacteroidota, andAcidimicrobiia, as crucial contributors to the remineralization of organosulfur compounds in the upper ocean. This study also highlights the high level of interconnectedness of bacterial carbon and sulfur cycling during phytoplankton blooms.
cancerSimCraft: A Multi-resolution Cancer Genome Simulator with Comprehensive Ground Truth Tracking
Authors: Jin Haijing , Navin Nicholas , Chen Ken 
Published: January 2025

AbstractCancer evolution follows complex trajectories involving diverse genomic alterations and clonal dynamics, making it challenging to validate computational methods for single-cell DNA sequencing analysis. Here we present cancerSimCraft, a comprehensive framework for simulating cancer genome data at both clonal and single-cell resolution. cancerSimCraft combines deterministic rules with stochastic processes to model various genomic events including CNVs, SNVs, and WGDs. The framework enables integration of real cancer genome patterns with user-defined parameters, supporting customizable simulation designs that reflect both empirical data and theoretical models. Through systematic benchmarking, we demonstrate cancerSimCraft’s utility in evaluating computational methods under various conditions, particularly focusing on the impact of dataset size and parameter sensitivity. We further demonstrated its application in exploring clonal evolution and mutation patterns through controlledin silicoexperiments. These comprehensive simulation capabilities make cancerSimCraft a valuable resource for both computational method development and theoretical studies in cancer genomics.
Modulating Prestimulus Alpha and Beta Power with tRNS Establishes Their Causal Role in Visual Perception
Authors: Wei Jinwen , Zou Huiru , Tang Qianyuan , Yao Ziqing , Huang Gan , Liang Zhen , Zhang Li , Zhou Changsong , Zhang Zhiguo 
Published: January 2025

AbstractVariability in visual perception in response to consistent stimuli is a fundamental phenomenon linked to fluctuations in prestimulus low-frequency neural oscillations—particularly in the alpha (8–13 Hz) and beta (13–30 Hz) bands—typically measured by their power in electroencephalography (EEG) signals. However, the causal role of these prestimulus alpha and beta power fluctuations in visual perception remains unestablished. In this study, we investigated whether prestimulus alpha and beta power causally affect visual perception using transcranial random noise stimulation (tRNS). In a sham-controlled, single-blind, within-subject design, 29 participants performed a visual detection task while receiving occipital tRNS. Online functional near-infrared spectroscopy (fNIRS) was used to measure cortical excitability during stimulation, and offline EEG signals were collected after stimulation. Mental fatigue was incorporated as a state-dependent factor influencing tRNS effects. Our findings demonstrate that, primarily under low fatigue states, tRNS increased cortical excitability during stimulation (indicated by increased fNIRS oxyhemoglobin amplitude), decreased subsequent prestimulus EEG alpha and beta power, and consequently reduced the visual contrast threshold (VCT), indicating enhanced visual perception. Sensitivity analysis revealed that alpha oscillations contributed more significantly to visual perception than beta oscillations under low fatigue. Additionally, the state-dependent effects of tRNS may result from different sensitivities of VCT to neural oscillations across fatigue states. These results provide causal evidence linking prestimulus alpha and beta power to visual perception and underscore the importance of considering brain states in neuromodulation research. Our study advances the understanding of the neural mechanisms underlying visual perception and suggests potential therapeutic applications targeting neural oscillations.Significance statementUnderstanding why we perceive identical visual stimuli differently is a fundamental question in neuroscience. This study provides causal evidence that prestimulus alpha and beta neural oscillations directly influence visual perception, particularly under low mental fatigue state. By using tRNS alongside fNIRS and EEG recordings, we demonstrate that modulating neural excitability can alter perceptual outcomes. Our findings highlight the importance of considering brain state—such as fatigue levels—in neuromodulation research. This work advances our understanding of the neural mechanisms underlying visual perception and opens avenues for developing targeted interventions to enhance sensory processing and cognitive functions, potentially benefiting individuals with perceptual or attentional disorders.
T-type calcium channels participate in intrinsic and synaptic activity of PKCγ neurons of the dorsal horn of the spinal cord during chronic pain
Authors: Cuculière Célia , Bourdon-Alonzeau Rachel , Rulhe Coline , Chemin Jean , François Amaury , Blanchard Marie-Pierre , Fontanaud Pierre , Deval Emmanuel , Mangoni Matteo , Lingueglia Eric , Bourinet Emmanuel , Méry Pierre-François 
Published: January 2025

ABSTRACTThe disinhibition of the excitatory PKCγ interneurons plays a central role during mechanical allodynia in the dorsal horn of the spinal cord, routing harmless information to nociceptive pathways. The T-type calcium channel Cav3.2, necessary for mechanical and cold allodynia, is found in most PKCγ neurons of the spinal cord. In this study, the role of Cav3.2 in PKCγ neurons was studied after its pharmacological inhibition and its conditional deletion (KO) in Cav3.2GFP-FloxKI x PKCγ-CreERT2 x Ai14 mice in normal conditions and in the spared-nerve-injury (SNI) model of neuropathic pain. Conditional deletion of Cav3.2 increased the hind-paw basal mechanical sensitivity before surgery, and decreased mechanical pain 7 days, but not 28 days, after surgery. At the cellular level, Cav3.2 participated in the low-threshold currents of PKCγ neurons and the T-type calcium current of PKCγ neurons was decreased in KO mice as compared to wild-type (WT). This loss did not convert into proportional alterations in subthreshold properties including “rebound” potentials, suggesting the involvement of other T-type channels. Action potential kinetics and firing properties seemed similar in WT and KO mice too, but rebound potentials were diminished in the SNI model in WT but not in KO mice. In addition, the modulations of firing properties induced by T-type channel pharmacological blocker Z944 observed in WT mice were absent in KO mice and after SNI. Furthermore, the pairing of action potentials was modified after SNI in WT mice, and not in KO mice. At the synaptic level, excitatory currents were lowered 7- and 28-days after surgery, while inhibitory currents were lowered only at 28 days. These changes were not found in Cav3.2-ablated neurons. Miniature currents analysis indicated that Cav3.2 was involved in both excitatory and inhibitory synaptic transmissions at the level of PKCγ neurons. Surprisingly, Z944 did not mimic the effects of Cav3.2 ablation in PKCγ neurons, suggesting distinct and eventually opposite roles of other T-type calcium channels. Altogether, our results show that Cav3.2 is not mandatory for firing of PKCγ neurons of the dorsal horn of the spinal cord, but that it participates to the SNI-induced changes in their intrinsic and synaptic activity, including changes in their excitatory and inhibitory controls.Graphical abstract
Macrophage migration-dependent retraction fibers and migrasomes - a structural basis for spatiotemporal cytokine secretion
Authors: Li Xichun , Anbarlou Azadeh , Maste Vrushali , Condon Nicholas D. , Brown Darren , Shen Hongyu , Hsu Hao-Ruei , Ashraf Amina , Tan Jinhui Sylvia , Wang Wanyi , Chernyavskiy Oleksandr , Lucas Richard M. , Luo Lin , Koh Yvette W. H. , Murray Rachael Z. , Lieschke Graham J. , Stow Jennifer L. 
Published: January 2025

ABSTRACTMigrating cells leave behind trails of matrix-bound retraction fibers and migrasomes, but their cell-specific physiological functions are largely unknown. We comprehensively characterize retraction fibers and migrasomes of migrating macrophages in mouse and zebrafishin vitroandin vivomodels. These structures share common and macrophage-centric components of tetraspanin enriched microdomains (TEMs) including tetraspanin 4 (TSPAN4), the integrin CD11b and the pTRAP, SCIMP; like TSPAN4, we show that SCIMP expression modulates retraction fiber and migrasome formation. In immune-activated migrating macrophages, rear-positioned recycling endosomes regulate the secretory trafficking of newly synthesized inflammatory cytokines into retraction fibers and migrasomes. Transmembrane TNF is delivered via SNARE-mediated carriers to the cell surface and to the surfaces of both retraction fibers and migrasomes, from where it can be released. Retraction fibers are thus newly identified here as cytokine secretion sites, and along with migrasomes they allow migrating macrophages to secrete more cytokine compared to stationary cells. Whereas cytokine secretion has been viewed as a process ofad hocdiffusion, instead, we reveal a new mechanism of migration-dependent, localized deposition and spatiotemporal release of bioactive cytokines from RFs and migrasomes. Cytokine deployment is thus organized in a constrained manner facilitating direct influence on local inflammatory responses.
Diverse Intracellular Trafficking of Insulin Analogs by Machine Learning-based Colocalization and Diffusion Analysis
Authors: Bleshøy Sara Vogt , Kæstel-Hansen Jacob , Nielsen Annette Juma , Mishra Narendra Kumar , Jensen Knud J. , Hatzakis Nikos S. 
Published: January 2025

AbstractInsulin signaling is crucial for maintaining cellular function and systemic homeostasis, with its dysregulation leading to metabolic disorders in particular diabetes. While insulin analogs are essential in type 1 diabetes treatment, their intracellular trafficking and sorting compared to endogenous insulin remains largely unresolved at the molecular level. Understanding these are important in improving therapeutics and guiding future drug development. However, current methods rely on static imaging and bulk receptor assays conducted in non-physiological conditions, which often disrupt native insulin signaling and provide only snapshots that fail to capture the temporal dynamics of insulin trafficking and characteristic sorting pathways. Here, we directly observe insulin trafficking and intracellular sorting and compare the characteristics of Atto655 labeled recombinant human insulin (HI655) with insulin aspart (IAsp655), a clinically approved, rapid-acting insulin analog. We developed a combined approach integrating Colocalization Fingerprinting, a machine learning framework for reliable, time-resolved colocalization analysis, together with our recently developed deep learning-assisted single-particle diffusional analysis (DeepSPT). Our analysis revealed subtle, yet significant differences in intracellular behavior between IAsp655and HI655, particularly in diffusional behavior and lysosomal colocalization, highlighting the potential of our approach to decipher subtle differences in intracellular trafficking and sorting characteristics. In addition to contributing to a more detailed understanding of biology of insulin analogs and intracellular sorting, we provide a reliable machine-learning methodology to study intricate cellular processes.