bluuebunny/crossref_metadata_2025_split huggingface dataset:
The endosymbiontSpiroplasma poulsoniiincreasesDrosophila melanogasterresistance to pathogens by enhancing iron-sequestration and melanization
Authors: Serra Canales Marina , Hrdina Alexandra , Arias-Rojas Aranzazu , Frahm Dagmar , Iatsenko Igor 
Published: December 2023

AbstractFacultative endosymbiotic bacteria, such asWolbachiaandSpiroplasmaspecies, are commonly found in association with insects and can dramatically alter their host physiology. Many endosymbionts are defensive and protect their hosts against parasites or pathogens. Despite the widespread nature of defensive insect symbioses and their importance for the ecology and evolution of insects, the mechanisms of symbiont-mediated host protection remain poorly characterized. Here, we utilized the fruit flyDrosophila melanogasterand its facultative endosymbiontSpiroplasma poulsoniito characterize the mechanisms underlying symbiont-mediated host protection against bacterial and fungal pathogens. Our results indicate a variable effect ofS. poulsoniion infection outcome, with endosymbiont-harbouring flies being more resistant toRhyzopus oryzae,Staphylococcus aureus,andProvidencia alcalifaciens, but more sensitive or as sensitive as endosymbiont-free flies to the infections withPseudomonasspecies. Further focusing on the protective effect, we identified Transferrin-mediated iron sequestration induced bySpiroplasmaas being crucial for the defense againstR. oryzaeandP. alcalifaciens. In case ofS. aureus, enhanced melanization inSpiroplasma-harbouring flies plays a major role in the protection. Both iron sequestration and melanization induced bySpiroplasmarequire the host immune sensor protease Persephone, suggesting a role of proteases secreted by the symbiont in the activation of host defense reactions. Hence, our work reveals a broader defensive range ofSpiroplasmathan previously appreciated and adds nutritional immunity and melanization to the defensive arsenal of symbionts.ImportanceDefensive endosymbiotic bacteria conferring protection to their hosts against parasites and pathogens are widespread in insect populations. However, the mechanisms by which most symbionts confer protection are not fully understood. Here, we studied the mechanisms of protection against bacterial and fungal pathogens mediated by theDrosophila melanogasterendosymbiontSpiroplasma poulsonii. We demonstrate that besides previously described protection against wasps and nematodes,Spiroplasmaalso confers increased resistance to pathogenic bacteria and fungi. We identifiedSpiroplasma-induced iron sequestration and melanisation as key defense mechanisms. Our work broadens the known defense spectrum ofSpiroplasmaand reveals a previously unappreciated role of melanization and iron sequestration in endosymbiont-mediated host protection. We propose that the mechanisms we have identified here may be of broader significance and could apply to other endosymbionts, particularly toWolbachia, and potentially explain their protective properties.
High-throughput discovery of inhibitory protein fragments with AlphaFold
Authors: Savinov Andrew , Swanson Sebastian , Keating Amy E. , Li Gene-Wei 
Published: December 2023

AbstractPeptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predictde novowhich of the many possible protein fragments bind to protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length proteins in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. Comparisons with experimental measurements establish that our approach is a sensitive predictor of fragment function: Evaluating inhibitory fragments from known protein-protein interaction interfaces, we find 87% are predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. Deep mutational scanning experiments support the predicted binding modes and uncover superior inhibitory peptides in high throughput. Further, FragFold is able to predict previously unknown protein binding modes, explaining prior genetic and biochemical data. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.Significance StatementPeptides can regulate protein interactions by binding to specific interfaces, and fragments of larger proteins have high potential to function in this manner. Recently developed experimental methods allow massively parallel measurement of protein fragment-based inhibitionin vivo. However, we have lacked comparable computational methods to predict which protein fragments act as inhibitors and how they bind. Here we report a new approach, FragFold, which leverages high-throughput AlphaFold predictions of protein – fragment binding to tackle these problems at scale. FragFold is successful at predicting inhibitory protein fragments and their binding modes across diverse protein structures and functions. This new approach stands to enable proteome-wide discovery of inhibitory protein fragments and aid the interpretation of high-throughput experimental measurements of inhibitory activity.ClassificationBiological Sciences / Biophysics and Computational Biology
Identification of arginine-vasopressin receptor 1a (Avpr1a/AVPR1A) as a novel candidate gene for chronic visceral pain
Authors: Kader Leena , Willits Adam , Meriano Sebastian , Christianson Julie A. , La Jun-Ho , Feng Bin , Knight Brittany , Kosova Gulum , Deberry Jennifer , Coates Matthew , Hyams Jeffrey , Baumbauer Kyle , Young Erin E. 
Published: December 2023

AbstractChronic abdominal pain in the absence of ongoing disease is the hallmark of disorders of gut-brain interaction (DGBIs), including irritable bowel syndrome (IBS). While the etiology of DGBIs remains poorly understood, there is evidence that both genetic and environmental factors play a role. In this study, we report the identification and validation ofAvpr1aas a novel candidate gene for visceral hypersensitivity (VH), a primary peripheral mechanism underlying abdominal pain in DGBI/IBS. Comparing two C57BL/6 (BL/6) substrains (C57BL/6NTac and C57BL/6J) revealed differential susceptibility to the development of chronic VH following intrarectal zymosan (ZYM) instillation, a validated preclinical model for post-inflammatory IBS. Using whole genome sequencing, we identified a SNP differentiating the two strains in the 5’ intergenic region upstream ofAvpr1a, encoding the protein arginine-vasopressin receptor 1A (AVPR1A). We used behavioral, histological, and molecular approaches to identify distal colon- specific gene expression differences and neuronal hyperresponsiveness covarying withAvpr1agenotype and VH susceptibility. While the two BL/6 substrains did not differ across other gastrointestinal (GI) phenotypes (e.g., GI motility), VH-susceptible BL/6NTac mice had higher colonicAvpr1amRNA and protein expression. Moreover, neurons of the enteric nervous system were hyperresponsive to the AVPR1A agonist AVP, suggesting a role for enteric neurons in the pathology underlying VH. These results parallel our findings that patients’ colonicAvpr1amRNA expression was higher in patients with higher pain ratings. Taken together, these findings implicate differential regulation ofAvpr1aas a novel mechanism of VH-susceptibility as well as a potential therapeutic target specific to VH.SummaryA combination of approaches, from genomic analysis to functional analyses, confirmAvpr1aas a high priority candidate gene for visceral pain.
Phosphatidylinositol 3-phosphate mediates Arc capsids secretion through the multivesicular body pathway
Authors: Mehta Kritika , Yentsch Henry , Lee Jungbin , Gao Tianyu Terry , Zhang Kai 
Published: December 2023

AbstractActivity-regulated cytoskeleton-associated protein (Arc/Arg3.1) is an immediate early gene that plays a vital role in learning and memory. The recent discovery that Arc mediates the inter-neuronal RNA transfer implies its role in regulating neuronal functions across long distances. Arc protein has structural and functional properties similar to viral Group-specific antigen (Gag). By assembling into high-order, virus-like capsids, Arc mediates the intercellular RNA transfer. However, the exact secretion pathway through which Arc capsids maneuver cargos is unclear. Here, we identified that Arc capsids assemble and secrete through the endosomal-multivesicular body (MVB) pathway. Arc’s endosomal entry is likely mediated by phosphatidylinositol-3-phosphate (PI3P). Indeed, reconstituted Arc protein preferably binds to PI3P. In mammalian cells, Arc forms puncta that colocalizes with FYVE, an endosomal PI3P marker, and competitive binding to PI3P via prolonged FYVE expression reduces the average number of Arc puncta per cell. Overexpression of MTMR1, a PI3P phosphatase, significantly reduces Arc capsid secretion. Arc capsids secrete through the endosomal-MVB axis as extracellular vesicles. Live-cell imaging shows that fluorescently labeled Arc primarily colocalizes Rab5 and CD63, early endosomal and MVB markers, respectively. Superresolution imaging resolves Arc accumulates within the intraluminal vesicles of MVB. CRISPR double knockout of RalA and RalB, crucial GTPases for MVB biogenesis and exocytosis, severely reduces Arc-mediated RNA transfer efficiency. These results suggest that, unlike the Human Immunodeficiency Virus Gag, which assembles on and bud off from the plasma membrane, Arc capsids assemble at the endocytic membranes of the endosomal-MVB pathway mediated by PI3P. Understanding Arc’s secretion pathway helps gain insights into its role in intercellular cargo transfer and highlights the commonality and distinction of trafficking mechanisms between structurally resembled capsid proteins.
Senolytics enhance longevity inCaenorhabditis elegansby altering betaine metabolism
Authors: Lan Wenning , Xiao Xiaolian , Zhang Xiaojing , Nian Jingjing , Wang Ziran , Wu Yajiao , Zhang Dongcheng , Chen Junkun , Bao Wenqiang , Li Chutao , Zhu An , Zhang Yun , Zhang Fangrong 
Published: December 2023

ABSTRACTAging triggers physiological changes in organisms, which are tightly interlinked to metabolic changes. Senolytics are being developed. However, metabolic responses to natural senescence and the molecular intricacies of how senolytics confer antiaging benefits remain enigmatic. We performed a metabolomics study on natural senescence based on theC.elegansmodel. The results suggest that age-dependent metabolic changes of natural aging occur inC. elegans. Betaine was identified as a crucial metabolite in the natural aging process. To explore the common pathway coregulated by different senolytics prolonging nematodes’ lifespan, we fed nematodes three antiaging drugs metformin, quercetin, and minocycline. Our data show that the coregulated metabolic pathways associated with aging include the forkhead box transcription factor (FoxO), p38-mitogen-activated protein kinase (MAPK) and the target of rapamycin (mTOR) signaling pathway, etc. Three antiaging drugs raised betaine levels, consistent with high betaine levels in the younger nematode. Supplement of betaine prolonged the lifespan of nematodes via stimulating autophagy and improving antioxidant capacity. Altogether, our data support proof-of-concept evidence that betaine at appropriate concentrations can extend the lifespan of nematodes.
A programmable dual-targeting di-valent siRNA scaffold supports potent multi-gene modulation in the central nervous system
Authors: Belgrad Jillian , Tang Qi , Hildebrand Sam , Summers Ashley , Sapp Ellen , Echeverria Dimas , O’Reilly Dan , Luu Eric , Bramato Brianna , Allen Sarah , Cooper David , Alterman Julia , Yamada Ken , Aronin Neil , DiFiglia Marian , Khvorova Anastasia 
Published: December 2023

ABSTRACTDi-valent short interfering RNA (siRNA) is a promising therapeutic modality that enables sequence-specific modulation of a single target gene in the central nervous system (CNS). To treat complex neurodegenerative disorders, where pathogenesis is driven by multiple genes or pathways, di-valent siRNA must be able to silence multiple target genes simultaneously. Here we present a framework for designing unimolecular “dual-targeting” di-valent siRNAs capable of co-silencing two genes in the CNS. We reconfigured di-valent siRNA – in which two identical, linked siRNAs are made concurrently – to create linear di-valent siRNA – where two siRNAs are made sequentially attached by a covalent linker. This linear configuration, synthesized using commercially available reagents, enables incorporation of two different siRNAs to silence two different targets. We demonstrate that this dual-targeting di-valent siRNA is fully functional in the CNS of mice, supporting at least two months of maximal target silencing. Dual-targeting di-valent siRNA is highly programmable, enabling simultaneous modulation of two different disease-relevant gene pairs (e.g., Huntington’s disease:MSH3andHTT; Alzheimer’s disease:APOEandJAK1) with similar potency to a mixture of single-targeting di-valent siRNAs against each gene. This work potentiates CNS modulation of virtually any pair of disease-related targets using a simple unimolecular siRNA.
Cellular distribution and motion of essential magnetosome proteins expressed in mammalian cells
Authors: Sun Qin , Fradin Cécile , Thompson R. Terry , Prato Frank S. , Goldhawk Donna E. 
Published: December 2023

AbstractMagnetosomes are organelle-like structures within magnetotactic bacteria that store iron biominerals in membrane-bound vesicles. In the bacteria, formation of these structures is highly regulated by approximately 30 genes which are conserved throughout different species. To compartmentalize iron in mammalian cells for magnetic resonance imaging using gene-based contrast, we are introducing key magnetosome proteins. We have previously expressed essential magnetosome genesmamIandmamLas fluorescent fusion proteins in the human melanoma cell line MDA-MB-435 and confirmed their co-localization and interaction. Here we investigate the expression of magnetosome genesmamBandmamEin MDA-MB-435 cells, using confocal fluorescence microscopy to observe expression patterns and to analyze particle mobility. Custom software was developed to characterize fluorescent particle trajectories. In mammalian cells, essential magnetosome proteins displayed different diffusive behaviours. However, all magnetosome proteins travelled at similar velocities when undergoing directed motion, suggesting that MamL, MamL+MamI, MamB, and MamE interact with similar mammalian mobile elements. These results confirm that localization and interaction of essential magnetosome proteins is tenable in the mammalian intracellular compartment.
Role of Ethanolamine Utilization and Bacterial Microcompartment Formation inListeria monocytogenesIntracellular Infection
Authors: Chatterjee Ayan , Kaval Karan Gautam , Garsin Danielle A. 
Published: December 2023

ABSTRACTEthanolamine (EA) affects the colonization and pathogenicity of certain human bacterial pathogens in the gastrointestinal tract. However, EA can also affect the intracellular survival and replication of host-cell invasive bacteria such asListeria monocytogenes(LMO) andSalmonella entericaserovar Typhimurium (S.Typhimurium). The EA utilization (eut)genes can be categorized as regulatory, enzymatic, or structural, and previous work in LMO showed that loss of genes encoding functions for the enzymatic breakdown of EA inhibited LMO intracellular replication. In this work, we sought to further characterize the role of EA utilization during LMO infection of host cells. Unlike what was previously observed forS.Typhimurium, in LMO, an EA regulator mutant (ΔeutV)was equally deficient in intracellular replication compared to an EA metabolism mutant (ΔeutB), and this was consistent across Caco-2, RAW 264.7 and THP-1 cell lines. The structural genes encode proteins that self-assemble into bacterial microcompartments (BMCs) that encase the enzymes necessary for EA metabolism. For the first time, native EUT BMCs were fluorescently tagged, and EUT BMC formation was observed in vitro, and in vivo. Interestingly, BMC formation was observed in bacteria infecting Caco-2 cells, but not the macrophage cell lines. Finally, the cellular immune response of Caco-2 cells to infection witheutmutants was examined, and it was discovered thatΔeutBandΔeutVmutants similarly elevated the expression of inflammatory cytokines. In conclusion, EA sensing and utilization during LMO intracellular infection are important for optimal LMO replication and immune evasion but are not always concomitant with BMC formation.
YAP1 status defines two intrinsic subtypes of LCNEC with distinct molecular features and therapeutic vulnerabilities
Authors: Stewart C. Allison , Diao Lixia , Xi Yuanxin , Wang Runsheng , Ramkumar Kavya , Serrano Alejandra G. , Rodriguez B. Leticia , Morris Benjamin B. , Shen Li , Zhang Bingnan , Yang Yan , Hamad Samera H. , Cardnell Robert J. , Duarte Alberto , Sahu Moushumi , Novegil Veronica Y. , Weissman Bernard E. , Frumovitz Michael , Kalhor Neda , Soto Luisa Solis , da Rocha Pedro , Vokes Natalie , Gibbons Don L. , Wang Jing , Heymach John V. , Glisson Bonnie , Byers Lauren Averett , Gay Carl M. 
Published: December 2023

AbstractLarge cell neuroendocrine carcinoma (LCNEC) is a high-grade neuroendocrine malignancy that, like the more common small cell lung cancer (SCLC), is associated with an absence of druggable oncogenic driver mutations, a clinically aggressive disease course, and dismal prognosis. In contrast to SCLC, however, there is little evidence to guide optimal treatment strategies which are, instead, often adapted from SCLC and non-small cell lung cancer (NSCLC) approaches. While there have been some efforts to describe the molecular landscape of LCNEC, to date there are few links between distinct biologic phenotypes of LCNEC and therapeutic vulnerabilities. Here, we demonstrate that the presence or absence of the transcription factor YAP1 distinguishes two roughly equal subsets of LCNEC. The YAP1-high subset is mesenchymal and inflamed and characterized, alongsideTP53mutations, by co-occurring alterations inCDKN2A/BandSMARCA4. Therapeutically, the YAP1-high subset demonstrates vulnerability to MEK and AXL targeting strategies, including a novel preclinical AXL CAR-T cell, as well as predicted vulnerability to SMARCA2 degraders and CDK4/6 inhibitors. Meanwhile, the YAP1-low subset is epithelial and immune-cold and more commonly featuresTP53andRB1co-mutations, similar to those observed in pure SCLC. Notably, the YAP1-low subset is also characterized by expression of SCLC subtype-defining transcription factors -especially ASCL1 and NEUROD1 - and, as expected given its transcriptional similarities to SCLC, exhibits putative vulnerabilities reminiscent of SCLC, including Delta-like ligand 3 (DLL3) and CD56 targeting, as with novel preclinical DLL3 and CD56 CAR T-cells, and DNA damage repair (DDR) inhibition. These findings highlight the potential for YAP1 to guide the first personalized treatment strategies for LCNEC.
Sex-specific Effects of the Endocannabinoid Agonist 2-Arachidonoylglycerol on Sleep and Circadian Disruptions during Fentanyl Withdrawal
Authors: Gamble Mackenzie C. , Miracle Sophia , Williams Benjamin R. , Logan Ryan W. 
Published: December 2023

AbstractFentanyl has become the leading driver of opioid overdoses. Cessation of opioid use represents a challenge as the experience of withdrawal drives subsequent relapse. One of the most prominent withdrawal symptoms that can contribute to opioid craving and vulnerability to relapse is sleep disruption. The endocannabinoid agonist, 2-Arachidonoylglycerol (2-AG), may promote sleep and reduce withdrawal severity; however, the effects of 2-AG on sleep disruption during opioid withdrawal have yet to be assessed. Here, we investigate the effects of 2-AG administration on sleep-wake behavior and diurnal activity in mice during withdrawal from fentanyl. Sleep-wake activity was continuously recorded before and after chronic fentanyl administration in both male and female C57BL/6J mice. Immediately following cessation of fentanyl administration, 2-AG was administered intraperitoneally to investigate the impact of endocannabinoid agonism on opioid-induced sleep disruption. Female mice maintained higher activity levels in response to chronic fentanyl than male mice. Furthermore, fentanyl increased wake and decreased sleep during the light period and inversely increased sleep and decreased wake in the dark period in both sexes. 2-AG treatment increased arousal and decreased sleep in both sexes during first 24 hrs of withdrawal. On withdrawal day 2, only female showed increased wakefulness with no changes in males, but by withdrawal day 3 male mice displayed decreased rapid-eye movement sleep during the dark period with no changes in female mice. Overall, repeated administration of fentanyl altered sleep and diurnal activity and administration of the endocannabinoid agonist, 2-AG, had sex-specific effects on fentanyl-induced sleep and diurnal changes.
Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing
Authors: Leary Jack R. , Bacher Rhonda 
Published: December 2023

AbstractThe rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to determine which genes exhibit changes in expression that are significantly associated with progression through the biological trajectory. While a few techniques for performing trajectory differential expression exist, most rely on the flexibility of generalized additive models in order to account for the inherent nonlinearity of changes in gene expression. As such, the results can be difficult to interpret, and biological conclusions often rest on subjective visual inspections of the most dynamic genes. To address this challenge, we propose scLANE testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several different simulation scenarios, we apply it to a set of diverse biological datasets and display its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods.