bluuebunny/crossref_metadata_2025_split huggingface dataset:
An enzyme activation network provides evidence for extensive regulatory crosstalk between metabolic pathways
Authors: Al Zubaidi Sultana Mohammed , Nasar Muhammad Ibtisam , Ralser Markus , Notebaart Richard A. , Alam Mohammad Tauqeer 
Published: November 2023

AbstractEnzyme activation by cellular metabolites plays a pivotal role in regulating metabolic processes. Nevertheless, our comprehension of such activation events on a global network scale remains incomplete. In this study, we conducted a comprehensive investigation into the optimization of cell-intrinsic activation interactions withinSaccharomyces cerevisiae. To achieve this, we integrated a genome-scale metabolic model with enzyme kinetic data sourced from the BRENDA database. Our objective was to map the distribution of enzyme activators throughout the cellular network. Our findings indicate that virtually all biochemical pathways encompass enzyme activators, frequently originating from disparate pathways, thus revealing extensive regulatory crosstalk between metabolic pathways. Indeed, activators have short pathway lengths, indicating they are activated quickly upon nutrient shifts, and in most instances, these activators target key enzymatic reactions to facilitate downstream metabolic processes. Interestingly, non-essential enzymes exhibit a significantly higher degree of activation compared to their essential counterparts. This observation suggests that cells employ enzyme activators to finely regulate secondary metabolic pathways that are only required under specific conditions. Conversely, the activator metabolites themselves are more likely to be essential components, and their activation levels surpass those of non-essential activators. In summary, our study unveils the widespread importance of enzymatic activators, and suggests that feed-forward activation of conditional metabolic pathways through essential metabolites mediates metabolic plasticity.
Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling
Authors: Saunders Nell , Monel Blandine , Cayet Nadège , Archetti Lorenzo , Moreno Hugo , Jeanne Alexandre , Marguier Agathe , Wai Timothy , Schwartz Olivier , Fréchin Mathieu 
Published: November 2023

SummaryAssessing the impact of SARS-CoV-2 on organelle dynamics allows a better understanding of the mechanisms of viral replication. We combine label-free holo-tomographic microscopy (HTM) with Artificial Intelligence (AI) to visualize and quantify the subcellular changes triggered by SARS-CoV-2 infection. We study the dynamics of shape, position and dry mass of nucleoli, nuclei, lipid droplets (LD) and mitochondria within hundreds of single cells from early infection to syncytia formation and death. SARS-CoV-2 infection enlarges nucleoli, perturbs LD, changes mitochondrial shape and dry mass, and separates LD from mitochondria. We then used Bayesian statistics on organelle dry mass states to define organelle cross-regulation (OCR) networks and report modifications of OCR that are triggered by infection and syncytia formation. Our work highlights the subcellular remodeling induced by SARS-CoV-2 infection and provides a new AI-enhanced, label-free methodology to study in real-time the dynamics of cell populations and their content.
Human microbiota is a reservoir of SARS-CoV-2 advantageous mutations
Authors: Cao Birong , Wang Xiaoxi , Yin Wanchao , Gao Zhaobing , Xia Bingqing 
Published: November 2023

AbstractSARS-CoV-2 mutations are rapidly emerging, in particular advantageous mutations in the spike (S) protein, which either increase transmissibility or lead to immune escape, are posing a major challenge to pandemic prevention and treatment. However, how the virus acquires a high number of advantageous mutations in a short time remains a mystery. Here, we show that the human microbiota may contribute to mutations in variants of concern (VOCs). We identified a mutation and adjacent 6 amino acids (aa) in a viral mutation fragment (VMF) and searched for homologous fragments (HFs) in the National Center for Biotechnology Information (NCBI) database. Among the approximate 8000 HFs obtained, 61 mutations in S and other outer membrane proteins were found in bacteria, accounting for 62% of all mutation sources, which is a 12-fold higher than the natural variable proportion. Approximately 70% of these bacterial species belong to the human microbiota, are primarily distributed in the gut or lung and exhibit a composition pattern similar to that of COVID-19 patients. Importantly, SARS- CoV-2 RNA-dependent RNA polymerase (RdRp) replicates corresponding bacterial mRNAs harboring mutations, producing chimeric RNAs. Collectively, SARS-CoV-2 may acquire mutations from the human microbiota, resulting in alterations in the binding sites or antigenic determinants of the original virus. Our study sheds light on the evolving mutational mechanisms of SARS-CoV-2.
Insulin at the Intersection of Thermoregulation and Glucose Homeostasis
Authors: Winn Nathan C. , Schleh Michael W. , Garcia Jamie N. , Lantier Louise , McGuinness Owen P. , Blair Joslin A. , Hasty Alyssa H. , Wasserman David H. 
Published: November 2023

ABSTRACTMammals are protected from changes in environmental temperature by altering energetic processes that modify heat production. Insulin is the dominant stimulus of glucose uptake and metabolism, which are fundamental for thermogenic processes. The purpose of this work was to determine the interaction of ambient temperature induced changes in energy expenditure (EE) on the insulin sensitivity of glucose fluxes. Short-term and adaptive responses to thermoneutral temperature (TN, ∼28°C) and room (laboratory) temperature (RT, ∼22°C) were studied in mice. This range of temperature does not cause detectable changes in circulating catecholamines or shivering and postabsorptive glucose homeostasis is maintained. We tested the hypothesis that a decrease in EE that occurs with TN causes insulin resistance and that this reduction in insulin action and EE is reversed upon short term (<12h) transition to RT. Insulin-stimulated glucose disposal (Rd) and tissue specific glucose uptake were assessed combining isotopic tracers with hyperinsulinemic-euglycemic clamps. EE and insulin-stimulated Rd are both decreased (∼50%) in TN-adapted vs RT-adapted mice. When RT-adapted mice are switched to TN, EE rapidly decreases and Rd is reduced by ∼50%. TN-adapted mice switched to RT exhibit a rapid increase in EE, but whole body insulin-stimulated Rd remains at the low rates of TN-adapted mice. In contrast, whole body glycolytic flux rose with EE. This higher EE occurs without increasing glucose uptake from the blood, but rather by diverting glucose from glucose storage to glycolysis. In addition to adaptations in insulin action, ‘insulin-independent’ glucose uptake in brown fat is exquisitely sensitive to thermoregulation. These results show that insulin action adjusts to non-stressful changes in ambient temperature to contribute to the support of body temperature homeostasis without compromising glucose homeostasis.HighlightsEnergy expenditure and insulin-mediated glucose fluxes are reduced in thermoneutral (TN)-adapted mice versus room ‘laboratory’ temperature (RT)-adapted mice.Reduced insulin sensitivity manifests in TN mice regardless of whether they are TN-adapted or short-term transitioned from RT-adapted to TN.TN-adapted mice are resistant to the RT-induced increase in whole-body insulin sensitivity even though metabolic rate is increased.TN-adapted mice switched to RT meets increased thermogenic needs, not by increasing glucose uptake, but by partitioning a greater fraction of glucose from glycogen storage to glycolysis.Brown fat glucose uptake sensitively increases with RT and decreases with TN by an insulin-independent mechanism.
Flowtigs: safety in flow decompositions for assembly graphs
Authors: Sena Francisco , Ingervo Eliel , Khan Shahbaz , Prjibelski Andrey , Schmidt Sebastian , Tomescu Alexandru I. 
Published: November 2023

AbstractAdecompositionof a network flow is a set of weighted paths whose superposition equals the flow. The problem of characterising and computing safe walks for flow decompositions has so far seen only a partial solution by restricting the flow decomposition to consist of paths, and the graph to be directed and acyclic (DAG). However, the problem of decomposing into closed walks in a general graph (allowing cycles) is still open.In this paper, we give a simple and linear-time-verifiable complete characterisation (flowtigs) of walks that aresafein such general flow decompositions, i.e. that are subwalks of any possible flow decomposition. Our characterisation generalises over the previous one for DAGs, using a more involved proof of correctness that works around various issues introduced by cycles. We additionally provide an optimalO(mn)-time algorithm that identifies all maximal flowtigs and represents them inside a compact structure. We also implement this algorithm and show that it is very fast in practice.On the practical side, we study flowtigs in the use-case of metagenomic assembly. By using the species abundances as flow values of the metagenomic assembly graph, we can model the possible assembly solutions as flow decompositions into weighted closed walks.Compared to reporting unitigs or maximal safe walks based only on the graph structure (structural contigs), reporting flowtigs results in a notably more contiguous assembly. Specifically, on shorter contigs (75-percentile), we get an improvement in assembly contiguity of up to 99% over unitigs, and on the 50-percentile of contiguity we get an improvement of up to 17% over unitigs. These improvements that flowtigs bring over unitigs are 4–14× larger that what structural contigs bring over unitigs.
Sexually dimorphic role of diet and stress on behavior, energy metabolism, and the ventromedial hypothalamus
Authors: Shetty Sanutha , Duesman Samuel J. , Patel Sanil , Huyhn Pacific , Shroff Sanjana , Das Anika , Chowhan Disha , Sebra Robert , Beaumont Kristin , McAlpine Cameron S. , Rajbhandari Prashant , Rajbhandari Abha K. 
Published: November 2023

AbstractScientific evidence underscores the influence of biological sex on the interplay between stress and metabolic dysfunctions. However, there is limited understanding of how diet and stress jointly contribute to metabolic dysregulation in both males and females. To address this gap, our study aimed to investigate the combined effects of a high-fat diet (HFD) and repeated footshock stress on fear-related behaviors and metabolic outcomes in male and female mice. Using a robust rodent model that recapitulates key aspects of post-traumatic stress disorder (PTSD), we subjected mice to footshock stressor followed by weekly reminder footshock stressor or no stressor for 14 weeks while on either an HFD or chow diet. Our findings revealed that HFD impaired fear memory extinction in male mice that received initial stressor but not in female mice. Blood glucose levels were influenced by both diet and sex, with HFD-fed female mice displaying elevated levels that returned to baseline in the absence of stress, a pattern not observed in male mice. Male mice on HFD exhibited higher energy expenditure, while HFD-fed female mice showed a decreased respiratory exchange ratio (RER). Sex-specific alterations in pro-inflammatory markers and abundance of hematopoietic stem cells were observed in chronically stressed mice on an HFD in different peripheral tissues, indicating the manifestation of distinct comorbid disorders. Single-nuclei RNA sequencing of the ventromedial hypothalamus from stressed mice on an HFD provided insights into sex-specific glial cell activation and cell-type-specific transcriptomic changes. In conclusion, our study offers a comprehensive understanding of the intricate interactions between stress, diet, sex, and various physiological and behavioral outcomes, shedding light on a potential brain region coordinating these interactions.
Mapping responses to focal injections of bicuculline in the lateral parafacial region identifies core regions for maximal generation of active expiration
Authors: Pisanski Annette , Prostebby Mitchell , Dickson Clayton T. , Pagliardini Silvia 
Published: November 2023

AbstractThe lateral parafacial area (pFL) is a crucial region involved in respiratory control, particularly in generating active expiration through an expiratory oscillatory network. Active expiration involves rhythmic abdominal (ABD) muscle contractions during late-expiration, increasing ventilation during elevated respiratory demands. The precise anatomical location of the expiratory oscillator within the ventral medulla’s rostro-caudal axis is debated. While some studies point to the caudal tip of the facial nucleus (VIIc) as the oscillator’s core, others suggest more rostral areas. Our study employed bicuculline (a GABA-A receptor antagonist) injections at various pFL sites (-0.2 to +0.8mm from VIIc) to investigate the impact of GABAergic disinhibition on respiration. These injections consistently elicited ABD recruitment, but the response strength varied along the rostro-caudal zone. Remarkably, the most robust and enduring changes in tidal volume, minute ventilation and combined respiratory responses occurred at more rostral pFL locations (+0.6/+0.8 mm from VIIc). Multivariate analysis of the respiratory cycle further differentiated between locations, revealing the core site for active expiration generation. Our study advances our understanding of neural mechanisms governing active expiration and emphasizes the significance of investigating the rostral pFL region.
Lipidome profiling of human and equine neutrophil-derived extracellular vesicles and their potential contribution to the ensemble of synovial fluid-derived extracellular vesicles during joint inflammation
Authors: Varela Laura , Mol Sanne , Taanman-Kueter Esther W. , Ryan Sarah E. , Taams Leonie S. , de Jong Esther , van Weeren P. René , van de Lest Chris H.A. , Wauben Marca H.M. 
Published: November 2023

ABSTRACTThe molecular signature of cell-derived extracellular vesicles (EVs) from synovial fluid (SF) offers valuable insights into the cells and molecular processes associated with joint disorders and can be exploited to define biomarkers. The signature of EVs is determined by cargo molecules and the lesser-studied lipid bilayer. We here investigated the lipidome of SF-EVs in inflamed joints derived from Rheumatoid Arthritis (RA) and Spondyloarthritis (SpA) patients, two autoimmune-driven joint diseases, and compared these signatures to the lipid profile of equine SF-EVs obtained during induced acute synovitis. Since neutrophils are primary SF-infiltrating cells during these inflammatory joint diseases, we also analyzed how inflammatory stimuli alter the lipidomic profile of human and equine neutrophil-derived EVs (nEVs)in vitroand how these signatures relate to the lipidome signatures of SF-EVs from inflamed joints. We identified neutrophil stimulation-intensity dependent changes in the lipidomic profile of nEVs with elevated presence of dihexosylceramide (lactosylceramide), phosphatidylserine, and phosphatidylethanolamine ether-linked lipid classes in human nEVs upon full neutrophil activation. In horses, levels of monohexosylceramide (glucosylceramide) increased instead of dihexosylceramide, indicating species-specific differences. The lipid profiles of RA and SpA SF-EVs were relatively similar and showed a relative resemblance with stimulated human nEVs. Similarly, the lipidome of equine synovitis-derived SF-EVs closer resembled the one of stimulated equine nEVs. Hence, lipidome profiling can provide insights into the contribution of nEVs to the heterogeneous pool of SF-EVs, deepening our understanding of inflammatory joint diseases and revealing molecular changes in joint homeostasis, which can lead to the development of more precise disease diagnosis and treatment strategies.
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics
Authors: Martinek Vlastimil , Martin Jessica , Belair Cedric , Payea Matthew J , Malla Sulochan , Alexiou Panagiotis , Maragkakis Manolis 
Published: November 2023

AbstractQuantification of the dynamics of RNA metabolism is essential for understanding gene regulation in health and disease. Existing methods rely on metabolic labeling of nascent RNAs and physical separation or inference of labeling through PCR-generated mutations, followed by short-read sequencing. However, these methods are limited in their ability to identify transient decay intermediates or co-analyze RNA decay with cis-regulatory elements of RNA stability such as poly(A) tail length and modification status, at single molecule resolution. Here we use 5-ethynyl uridine (5EU) to label nascent RNA followed by direct RNA sequencing with nanopores. We developed RNAkinet, a deep convolutional and recurrent neural network that processes the electrical signal produced by nanopore sequencing to identify 5EU-labeled nascent RNA molecules. RNAkinet demonstrates generalizability to distinct cell types and organisms and reproducibly quantifies RNA kinetic parameters allowing the combined interrogation of RNA metabolism and cis-acting RNA regulatory elements.
Single-cell transcriptomic and neuropathologic analysis reveals dysregulation of the integrated stress response in progressive supranuclear palsy
Authors: Whitney Kristen , Song Won-Min , Sharma Abhijeet , Dangoor Diana K. , Farrell Kurt , Krassner Margaret M. , Ressler Hadley W. , Christie Thomas D. , Walker Ruth H. , Nirenberg Melissa J. , Zhang Bin , Frucht Steven J. , Riboldi Giulietta M , Crary John F. , Pereira Ana C. 
Published: November 2023

ABSTRACTProgressive supranuclear palsy (PSP) is a sporadic neurodegenerative tauopathy variably affecting brainstem and cortical structures and characterized by tau inclusions in neurons and glia. The precise mechanism whereby these protein aggregates lead to cell death remains unclear. To investigate the contribution of these different cellular abnormalities to PSP pathogenesis, we performed single-nucleus RNA sequencing and analyzed 45,559 high quality nuclei targeting the subthalamic nucleus and adjacent structures from human post-mortem PSP brains with varying degrees of pathology compared to controls. Cell-type specific differential expression and pathway analysis identified both common and discrete changes in numerous pathways previously implicated in PSP and other neurodegenerative disorders. This included EIF2 signaling, an adaptive pathway activated in response to diverse stressors, which was the top activated pathway in vulnerable cell types. Using immunohistochemistry, we found that activated eIF2α was positively correlated with tau pathology burden in vulnerable brain regions. Multiplex immunofluorescence localized activated eIF2α positivity to hyperphosphorylated tau (p-tau) positive neurons and ALDH1L1-positive astrocytes, supporting the increased transcriptomic EIF2 activation observed in these vulnerable cell types. In conclusion, these data provide insights into cell-type-specific pathological changes in PSP and support the hypothesis that failure of adaptive stress pathways play a mechanistic role in the pathogenesis and progression of PSP.
Early life pain alters the response to an immune challenge in adult male and female rats
Authors: Gomez Morgan G. , Macik Melani , Harder Hannah J. , Pandit Malika H. , Murphy Anne Z. 
Published: November 2023

AbstractInfants born prematurely are more likely to be admitted to the Neonatal Intensive Care Unit (NICU) where they experience upwards of 10-18 painful procedures each day, often with no anesthesia or analgesia. Pre-clinical studies have shown that early exposure to pain disrupts CNS development in multiple ways that persist into adulthood, with similar findings observed clinically. The present study explores the effects of neonatal injury on the response to an immune challenge in adulthood. Male and female rats were exposed to a short-term inflammatory insult induced by intraplantar administration of 1% carrageenan (CGN) on the day of birth (P0). In adulthood (P60-P90), rats were implanted with Thermicron iButtons to monitor core body temperature; 14 days later, lipopolysaccharide (LPS) was administered to elicit an immune response. Rats were sacrificed after 24 hours or at their peak fever point and brain tissue collected for immunohistochemical analysis. LPS administration resulted in a significantly greater febrile response in males and females exposed to early life pain compared to controls. Immunohistological analysis revealed sex and treatment differences in Fos labeling in several brain regions, including the PVN. No sex or treatment differences were observed for VGat, VGlut2, or EP3R expression in the MnPO; however, all three increased significantly following LPS administration. Together, these studies are consistent with clinical studies reporting children experiencing unresolved pain during the perinatal period show an increased severity of sickness behavior and altered immune signaling following exposure to a pathogen and will provide a foundation for future studies examining the biological underpinnings.
Monocyte subpopulations exhibit distinct TNF-dependent aging signatures
Authors: Bentz Anna Woo , Gutierrez Monica , Loukov Dessi , Eckman Blair , Gadhvi Gaurav , Cuda Carla , Bowdish Dawn M. E. , Winter Deborah R. 
Published: November 2023

AbstractMonocytes are a key cell type contributing to age-associated inflammation or inflammaging. Since monocytes have the potential to enter circulation and differentiate into macrophages in tissues, they are capable of having a systemic effect on health. Here, we characterize the effect of aging on the transcriptional regulation of monocyte subpopulations in the bone marrow. We find that aging classical (Ly6c high) and non-classical (Ly6c low) monocytes exhibit distinct transcriptional profiles. These were associated with changes to the epigenomic landscape driven by the activity of specific TFs that often had opposing effects in monocyte subpopulations. Next, we determined that the aging signature was diminished in TNF-KO mice indicating that monocytes are altered in a TNF-dependent manner. Finally, we found that a subset of the aging signature was triggered by TNF over-expression. Together, our results implicate key factors driving age-associated changes to the transcriptional regulation of monocyte subpopulations. This study provides a better understanding of the impact of aging on monocytes and identifies targets for future investigation aiming to improve health in aging.
Retinal neurons establish mosaic patterning by excluding homotypic somata from their dendritic territory
Authors: Kozlowski Christopher , Hadyniak Sarah E. , Kay Jeremy N. 
Published: November 2023

ABSTRACTIn vertebrate retina, individual neurons of the same type are distributed regularly across the tissue in a pattern known as a mosaic. Establishment of mosaics during development requires cell-cell repulsion among homotypic neurons, but the mechanisms underlying this repulsion remain unknown. Here we show that two mouse retinal cell types, OFF and ON starburst amacrine cells, establish mosaic spacing by using their dendritic arbors to repel neighboring homotypic somata. Using newly-generated transgenic tools and single cell labeling, we identify a transient developmental period when starburst somata receive extensive contacts from neighboring starburst dendrites; these serve to exclude somata from settling within the neighbor’s dendritic territory. Dendrite-soma exclusion is mediated by MEGF10, a cell-surface molecule required for starburst mosaic patterning. Our results implicate dendrite-soma exclusion as a key mechanism underlying starburst mosaic spacing, and suggest that this could be a general mechanism for mosaic patterning across many cell types and species.