bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathological C-terminal phosphomimetic substitutions alter the mechanism of liquid-liquid phase separation of TDP-43 low complexity domain
Authors: Haider Raza , Shipley Brandon , Surewicz Krystyna , Hinczewski Michael , Surewicz Witold K 
Published: March 2024

AbstractC-terminally phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) marks the proteinaceous inclusions that characterize a number of age-related neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal lobar degeneration and Alzheimer’s disease. TDP-43 phosphorylation at S403/S404, and especially at S409/S410, is in fact accepted as a biomarker of proteinopathy. These residues are located within the low complexity domain (LCD), which also drives the protein’s liquid-liquid phase separation (LLPS). The impact of phosphorylation at these LCD sites on phase separation of the protein is a topic of great interest, as these post-translational modifications and LLPS are both implicated in proteinopathies. Here, we employed a combination of experimental and simulation-based approaches to explore this question on a phosphomimetic model of the TDP-43 LCD. Our turbidity and fluorescence microscopy data show that Ser-to-Asp substitutions at residues S403, S404, S409 and S410 alter the LLPS behavior of TDP-43 LCD. In particular, in contrast to the unmodified protein, the phosphomimetic variants display a biphasic dependence on salt concentration. Through coarse-grained modeling, we find that this biphasic salt dependence is derived from an altered mechanism of phase separation, in which LLPS-driving short-range intermolecular hydrophobic interactions are modulated by long-range attractive electrostatic interactions. Overall, thisin vitroandin silicostudy provides a physiochemical foundation for understanding the impact of pathologically-relevant C-terminal phosphorylation on the LLPS of the TDP-43 in a more complex cellular environment.Statement of SignificanceProteinaceous inclusions composed of phosphorylated, C-terminal TDP-43 fragments have long been recognized as hallmarks of several neurodegenerative diseases, in particular amyotrophic lateral sclerosis and frontotemporal dementia. A rapidly growing number of studies indicate that these proteinopathies may be closely related to liquid-liquid phased separation (LLPS) of TDP-43, but the impact of phosphorylation on TDP-43 LLPS remains largely unexplored. In this study we used a combination of experimental methods and coarse-grained simulations to ascertain, in mechanistic terms, how phosphorylation at pathologically-critical C-terminal sites impacts liquid-liquid phase separation of the low complexity domain of TDP-43. Our results broaden our understanding of the mechanisms driving pathogenic process in these neurodegenerative diseases.
One signal activated TIL enables potent anti-tumor activity across solid tumor types
Authors: Wu Yongqiang , Ye Xueshuai , Zhu Yufeng , Liu Shengchao , Yuan Qichen , Kong Dejing , Zhao Lianmei 
Published: March 2024

AbstractAdoptive T cell therapy (ACT) with autologous tumor-infiltrating lymphocytes (TIL) has shown compelling anti-tumor activity across various solid tumors. The function and status of TIL significantly influence its anti-tumor potential. In this study, we present the development of One-Signal-Activated TIL (OSAT), highlighting its robust anti-tumor activity in various syngeneic tumor models. We designed 10 unique signals by integrating CD3Zwith a secondary signaling molecule. From these, we identified a specific signal, denoted as OSAT, which efficiently induces T cell activation when paired with a sole CD3 antibody. Subsequently, we benchmarked delivery approaches for OSAT, through genome editing, lentivirus integration, and plasmid electroporation. We found that electroporation yielded the most potent expression effect among these methods. Further, we demonstrated that OSAT exhibited robust antitumor activity bothin vitroandin vivoacross diverse solid tumors. Finally, we synergized OSAT with PD-1 blockade therapy to achieve a highly effective and enduring anti-tumor impact in cancer immunotherapy, facilitating sustained enhancement of anti-tumor activity.
Enhancing tonic arousal improves voluntary but not involuntary attention in humans
Authors: Grandjean Aurélie , Mathieu Anne , Chen Sophie , Widmann Andreas , Wetzel Nicole , Bidet-Caulet Aurélie 
Published: March 2024

AbstractArousal and attention are pivotal brain functions for optimizing performance. Kahneman’s attention model (1973) theorizes a key interplay between attention and arousal, yet this relationship remains poorly understood. We investigated this interaction in 16 healthy young adults performing an auditory attention task that simultaneously assessed phasic arousal, voluntary attention and involuntary attention. Tonic arousal was modulated by low or high arousing music, as measured using skin conductance, pupil size, and heart rate. Pupil dilation responses to distracting sounds highlight an intricate interplay between tonic and phasic arousal. Importantly, increasing tonic arousal does not influence involuntary attention, whereas it does improve voluntary attention, as shown by shorter and less variable reaction times and larger electroencephalographic brain responses to task-relevant targets. This study provides experimental evidence in humans that tonic arousal can influence the attentional balance by improving voluntary attention in a transient and sustained manner, rather than by impacting involuntary attention.
Feedback and Feedforward Regulation of Interneuronal Communication
Authors: Gambrell Oliver , Vahdat Zahra , Singh Abhyudai 
Published: March 2024

AbstractWe formulate a mechanistic model capturing the dynamics of neurotransmitter release in a chemical synapse. The proposed modeling framework captures key aspects such as the random arrival of action potentials (AP) in the presynaptic (input) neuron, probabilistic docking and release of neurotransmitter-filled vesicles, and clearance of the released neurotransmitter from the synaptic cleft. Feedback regulation is implemented by having the released neurotransmitter impact the vesicle docking rate that occurs biologically through “autoreceptors” on the presynaptic membrane. Our analytical results show that these feedbacks can amplify or buffer fluctuations in neurotransmitter levels depending on the relative interplay of neurotransmitter clearance rate with the AP arrival rate and the vesicle replenishment rate, with faster clearance rates leading to noise amplification. We next consider a postsynaptic (output) neuron that fires an AP based on integrating upstream neurotransmitter activity. Investigating the postsynaptic AP firing times, we identify scenarios that lead to band-pass filtering, i.e., the output neuron frequency is maximized at intermediate input neuron frequencies. We extend these results to consider feedforward regulation where in addition to a direct excitatory synapse, the input neuron also impacts the output indirectly via an inhibitory interneuron, and we identify parameter regimes where feedforward neuronal networks result in band-pass filtering.
Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents
Authors: Abel Tamar R. , Kosarek Noelle N. , Parvizi Rezvan , Jarnagin Helen , Torres Gretel M. , Bhandari Rajan , Huang Mengqi , Toledo Diana M. , Smith Avi , Popovich Dillon , Mariani Michael P. , Yang Heetaek , Wood Tammara , Garlick Jonathan , Pioli Patricia A. , Whitfield Michael L. 
Published: March 2024

AbstractSystemic sclerosis (SSc) is an autoimmune disease characterized by skin fibrosis, internal organ involvement and vascular dropout. We previously developed and phenotypically characterized anin vitro3D skin-like tissue model of SSc, and now analyze the transcriptomic (scRNA-seq) and epigenetic (scATAC-seq) characteristics of this model at single-cell resolution. SSc 3D skin-like tissues were fabricated using autologous fibroblasts, macrophages, and plasma from SSc patients or healthy control (HC) donors. SSc tissues displayed increased dermal thickness and contractility, as well as increased α-SMA staining. Single-cell transcriptomic and epigenomic analyses identified keratinocytes, macrophages, and five populations of fibroblasts (labeled FB1 – 5). Notably, FB1 APOE-expressing fibroblasts were 12-fold enriched in SSc tissues and were characterized by high EGR1 motif accessibility. Pseudotime analysis suggests that FB1 fibroblasts differentiate from a TGF-β1-responsive fibroblast population and ligand-receptor analysis indicates that the FB1 fibroblasts are active in macrophage crosstalk via soluble ligands including FGF2 and APP. These findings provide characterization of the 3D skin-like model at single cell resolution and establish that it recapitulates subsets of fibroblasts and macrophage phenotypes observed in skin biopsies.
Thermal tolerance of mosquito eggs is associated with urban adaptation and human interactions
Authors: Chakraborty Souvik , Zigmond Emily , Shah Sher , Sylla Massamba , Akorli Jewelna , Otoo Sampson , Rose Noah H. , McBride Carolyn S. , Armbruster Peter A. , Benoit Joshua B. 
Published: March 2024

AbstractClimate change is expected to profoundly affect mosquito distributions and their ability to serve as vectors for disease, specifically with the anticipated increase in heat waves. The rising temperature and frequent heat waves can accelerate mosquito life cycles, facilitating higher disease transmission. Conversely, higher temperatures could increase mosquito mortality as a negative consequence. Warmer temperatures are associated with increased human density, suggesting a need for anthropophilic mosquitoes to adapt to be more hardy to heat stress. Mosquito eggs provide an opportunity to study the biological impact of climate warming as this stage is stationary and must tolerate temperatures at the site of female oviposition. As such, egg thermotolerance is critical for survival in a specific habitat. In nature,Aedesmosquitoes exhibit different behavioral phenotypes, where specific populations prefer depositing eggs in tree holes and prefer feeding non-human vertebrates. In contrast, others, particularly human-biting specialists, favor laying eggs in artificial containers near human dwellings. This study examined the thermotolerance of eggs, along with adult stages, forAedes aegyptiandAe. albopictuslineages associated with known ancestry and shifts in their relationship with humans. Mosquitoes collected from areas with higher human population density, displaying increased human preference, and having a human-associated ancestry profile have increased egg viability following high-temperature stress. Unlike eggs, thermal tolerance among adults showed no significant correlation based on the area of collection or human-associated ancestry. This study highlights that the egg stage is likely critical to mosquito survival when associated with humans and needs to be accounted when predicting future mosquito distribution.
3D live imaging and phenotyping of the subcellular cytotoxicity in cancer immunotherapy using event-triggered Bessel oblique plane microscopy
Authors: Wang Zhaofei , Wang Jie , Zhao Yuxuan , Jin Jin , Si Wentian , Chen Longbiao , Zhang Man , Zhou Yao , Mao Shiqi , Zhang Yicheng , Zheng Chunhong , Chen Liting , Fei Peng 
Published: March 2024

AbstractClarification of the cytotoxic function of T cells is crucial for understanding human immune responses and immunotherapy procedures. Here, we report an event-triggered Bessel oblique plane microscopy (EBOPM) platform capable of smart 3D live imaging and phenotyping of chimeric antigen receptor (CAR)-modified T-cell cytotoxicity in cancer immunotherapy; the EBOPM platform has the following characteristics: an isotropic subcellular resolution of 320 nm, large-scale scouting over 400 interacting cell pairs, long-term observation across 5 hours, and quantitative analysis of the Terabyte-scale 3D, multichannel, time-lapse image datasets. Using this advanced microscopy platform, several key subcellular events in CAR-T cells were captured and comprehensively analyzed; these events included the instantaneous formation of immune synapses and the sustained changes in the microtubing morphology. Furthermore, we identified the actin retrograde flow speed, the actin depletion coefficient, the microtubule polarization and the contact area of the CAR-T/target cell conjugates as essential parameters strongly correlated with CAR-T-cell cytotoxic function. Our approach will be useful for establishing criteria for quantifying T-cell function in individual patients for all T-cell-based immunotherapies.
Cause and effect in the natural selection of the population ecological life histories of mammals
Authors: Witting Lars 
Published: March 2024

AbstractThe inter-specific life history and ecological variation of mammals is often explained as allometric consequences of physiological adaptations to unexplained body mass variation. But these hypotheses are unnecessary because the allometric scaling is explained already by the natural selection that explains the variation in mass. I decompose the population ecological life histories of 4,936 species of mammals to show how the selection of mass accounts for the life history and population ecological variation in mammals. This shows that 55% of the within order variance, and 91% of the between order differences, in the body mass, demography, and population ecological traits are reconciled by the response of population dynamic feedback selection to variation in net energy, mortality, and intra-specific interactive competition.
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca
Authors: Weine Eric , Carbonetto Peter , Stephens Matthew 
Published: March 2024

AbstractSummaryMotivated by theoretical and practical issues that arise when applying Principal Components Analysis (PCA) to count data, Townes et al introduced “Poisson GLM-PCA”, a variation of PCA adapted to count data, as a tool for dimensionality reduction of single-cell RNA sequencing (RNA-seq) data. However, fitting GLM-PCA is computationally challenging. Here we study this problem, and show that a simple algorithm, which we call “Alternating Poisson Regression” (APR), produces better quality fits, and in less time, than existing algorithms. APR is also memory-efficient, and lends itself to parallel implementation on multi-core processors, both of which are helpful for handling large single-cell RNA-seq data sets. We illustrate the benefits of this approach in two published single-cell RNA-seq data sets. The new algorithms are implemented in an R package, fastglmpca.Availability and implementationThe fastglmpca R package is released on CRAN for Windows, macOS and Linux, and the source code is available at github.com/stephenslab/fastglmpca under the open source GPL-3 license. Scripts to reproduce the results in this paper are also available in the GitHub repository.Contactmstephens@uchicago.eduSupplementary informationSupplementary data are available onBioRxivonline.
An Innovative Mitochondrial-targeted Gene Therapy for Cancer Treatment
Authors: Chen Kai , Ernst Patrick , Kim Seulhee , Si Yingnan , Varadkar Tanvi , Ringel Matthew D. , Liu Xiaoguang “Margaret” , Zhou Lufang 
Published: March 2024

AbstractTargeting cancer cell mitochondria holds great therapeutic promise, yet current strategies to specifically and effectively destroy cancer mitochondriain vivoare limited. Here, we introduce mLumiOpto, an innovative mitochondrial-targeted luminoptogenetics gene therapy designed to directly disrupt the inner mitochondrial membrane (IMM) potential and induce cancer cell death. We synthesize a blue light-gated channelrhodopsin (CoChR) in the IMM and co-express a blue bioluminescence-emitting Nanoluciferase (NLuc) in the cytosol of the same cells. The mLumiOpto genes are selectively delivered to cancer cellsin vivoby using adeno-associated virus (AAV) carrying a cancer-specific promoter or cancer-targeted monoclonal antibody-tagged exosome-associated AAV. Induction with NLuc luciferin elicits robust endogenous bioluminescence, which activates mitochondrial CoChR, triggering cancer cell IMM permeability disruption, mitochondrial damage, and subsequent cell death. Importantly, mLumiOpto demonstrates remarkable efficacy in reducing tumor burden and killing tumor cells in glioblastoma or triple-negative breast cancer xenografted mouse models. These findings establish mLumiOpto as a novel and promising therapeutic strategy by targeting cancer cell mitochondriain vivo.
Self-quenched fluorophore-DNA labels for super-resolution fluorescence microscopy
Authors: Kessler Laurell , Balakrishnan Ashwin , Menche Tanja , Wang Dongni , Li Yunqing , Mantel Maximilian , Glogger Marius , Dietz Marina S. , Heilemann Mike 
Published: March 2024

AbstractProtein labeling through transient and repetitive hybridization of short, fluorophore-labeled DNA oligonucleotides has become widely applied in various optical super-resolution microscopy methods. The main advantages are multi-target imaging and molecular quantification. A challenge is the high background signal originating from the presence of unbound fluorophore-DNA labels in solution. Here, we report self-quenching of fluorophore dimers conjugated to DNA oligonucleotides as a general concept to reduce the fluorescence background. Upon hybridization, the fluorescence signal of both fluorophores is fully restored. Here, we expand the toolbox of fluorophores suitable for self-quenching and report their spectra and hybridization equilibria. We apply self-quenched fluorophore-DNA labels to stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM) and report improved imaging performances.
Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
Authors: Tarbier Marcel , Mackowiak Sebastian D. , Sekar Vaishnovi , Bonath Franziska , Yapar Etka , Fromm Bastian , Faridani Omid R. , Biryukova Inna , Friedländer Marc R. 
Published: March 2024

AbstractMicroRNAs are small RNA molecules that can repress the expression of protein coding genes post-transcriptionally. Previous studies have shown that microRNAs can also have alternative functions including target noise buffering and co-expression, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells, by genetically deletingDrosha- leading to global loss of microRNAs. We apply complementary single-cell RNA-seq methods to study the variation of the targets and the microRNAs themselves, and transcriptional inhibition to measure target half-lives. We find that microRNAs form four distinct co-expression groups across single cells. In particular the mir-290 and the mir-182 clusters are abundantly, variably and inversely expressed. Intriguingly, some cells have global biases towards specific miRNAs originating from either end of the hairpin precursor, suggesting the presence of unknown regulatory cofactors. We find that miRNAs generally increase variation and covariation of their targets at the RNA level, but we also find miRNAs such as miR-182 that appear to have opposite functions. In particular, miRNAs that are themselves variable in expression, such as miR-291a, are more likely to induce covariations. In summary, we apply genetic perturbation and multi-omics to give the first global picture of microRNA dynamics at the single cell level.
Multi-omics characterization of highly enriched human plasma extracellular vesicles
Authors: Su Huaqi , Fowler Christopher , Masters Colin L , Barnham Kevin J. , Reid Gavin E. , Vella Laura J. 
Published: March 2024

AbstractExtracellular vesicles (EVs) in blood plasma offer a valuable reservoir of intracellular cellular cargo, making them a promising source of liquid based biomarkers. The molecular cargo of small EVs (sEVs) is of particular interest because some EV subtypes encapsulate cargo from organelles including mitochondria, endosomes, and the autophagy pathways, which are implicated in multiple diseases. However, the complexity of plasma, with its abundance of non-EV particles and plasma proteins, presents challenges for their molecular characterization using mass spectrometry based ‘omics technologies.Here, we optimised a rigorous method to isolate sEVs from human plasma based on both density and size. Following this, we analysed the protein and lipid content of sEVs from multiple individuals. We demonstrate the advantage of obtaining highly enriched sEVs from plasma for enhancing the detection of protein networks associated with mitochondria and the endosomal network, and also tissue types including the central nervous system. Some of the EV associated proteins reported here have not been detected in plasma, nor plasma sEVs, previously. We show that sphingomyelin lipids are the most abundant lipids in plasma sEVs (33.7 mol% total lipids) and provide the first report on cholesterol ester content. We demonstrate a 16-fold decrease in cholesterol ester lipids in sEVs compared to platelet free plasma and suggest that cholesterol ester content could serve as a valuable measure for assessing the effectiveness of plasma separation protocols or kits in enriching for sEVs.Our study highlights the benefit of reducing co-isolates from plasma sEV preparations to enable the detection of proteins and lipids with potential biomarker utility, and underscores the need for ongoing development of improved high throughput sEV isolation technologies.