bluuebunny/crossref_metadata_2025 huggingface dataset:
PARP-1, EpCAM, and FRα as potential targets for intraoperative detection and delineation of endometriosis: a quantitative tissue expression analysis
Authors: Belmonte Beatrice , Di Lorenzo Giovanni , Mangogna Alessandro , Bortot Barbara , Bertolazzi Giorgio , Sammataro Selene , Merighi Simona , Martorana Anna , Zito Gabriella , Romano Federico , Giorgiutti Anna , Bottin Cristina , Zanconati Fabrizio , Romano Andrea , Ricci Giuseppe , Biffi Stefania
Published: December 2023

Endometriosis is a gynecological disease characterized by the presence of endometrial tissue in abnormal locations, leading to severe symptoms, inflammation, pain, organ dysfunction, and infertility. Surgical removal of endometriosis lesions is crucial for improving pain and fertility outcomes, with the goal of complete lesion removal. Incomplete surgery often results in recurring symptoms and the need for additional interventions. This study aims to explore the biological significance of PARP-1, EpCAM, and FRα as potential targets for molecular imaging in endometriosis, assessing their suitability for targeted intraoperative imaging.

Gene expression analysis was performed using the EndometDB. By immunohistochemistry, we investigated the presence and distribution of PARP-1, EpCAM, and FRα in endometriosis foci and adjacent tissue. We also applied an ad hoc platform for the analysis image to perform a quantitative immunolocalization analysis. Additionally, double immunofluorescence analysis was carried out for PARP-1 and EpCAM, as well as PARP-1 and FRα, to explore the expression of these combined markers within endometriosis foci and their potential simultaneous utilization in surgical treatment.

The analysis of gene expression revealed that PARP-1, EpCAM, and FRα exhibit higher levels of expression in endometriotic lesions compared to the peritoneum, used for control tissue. Immunohistochemical analysis also highlighted a significant increase in expression of all three biomarkers in endometriosis foci compared to surrounding tissues, as well as the quantitative analysis of immunolocalization of the signal. Furthermore, the double immunofluorescence analysis consistently revealed nuclear expression of PARP-1 and membrane and cytoplasmatic expression of EpCAM and FRα, although relatively weaker.

Overall, the three markers demonstrate significant potential for effective imaging of endometriosis. Particularly, the results emphasize the importance of PARP-1 expression as a possible indicator for distinguishing endometriotic lesions from adjacent tissue. PARP-1, as a potential biomarker for endometriosis, offers promising avenues for further investigation in terms of both pathophysiology and diagnostic-therapeutic approaches.
Distribution and Triazole Susceptibility of Aspergilli from Clinical, Soils and Veterinary Samples in Ogun State, Nigeria
Authors: Olugbenga O.M. , Easter T. , Shittu O.B. , Obuotor T.M. , Sam-Wobo S.O. , Ejilude O. , van Rhijn N.
Published: December 2023

Resistance of Aspergilli to azole compounds have been on the rise globally with the majority of data coming from Europe and the Americas. However, little data from Africa is available comparing antifungal susceptibility of isolates from the environment and the clinic directly. Differences between fungal species present in the environment and their susceptibility will have a direct impact on human health and policies regarding fungal infections. Hence a One Health approach of the susceptibility of Aspergilli isolated from human, environment and veterinary samples from South western of Nigeria was carried out. Sputum, soil and animal litters/feeds samples were collected and processed using Potato Dextrose Agar (PDA) and Malt Extract Agar (MEA) supplemented with chloramphenicol to isolateAspergillusspecies. The majority of isolates recovered wereA. nigerandA. flavus, with littleA. fumigatusrecovered. Susceptibility testing to voriconazole was carried out using the microdilution method results interpreted according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. All isolates were found to be susceptible to itraconazole and voriconazole. These results show differences between species present in the environment and from patient samples compared to Europe and the Americas, highlighting a need for more fungal research focused on Africa.
Air monitoring by nanopore sequencing
Authors: Reska Tim , Pozdniakova Sofya , Borràs Sílvia , Schloter Michael , Cañas Lídia , Puente Albert Perlas , Rodó Xavier , Wang Yuanyuan , Winkler Barbro , Schnitzler Jörg-Peter , Urban Lara
Published: December 2023

While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome’s composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions throughde novometagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city’s boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.
Climate change impacts dryland multifunctionality: A cascade of precipitation variability to species replacement in multitrophic microbiota
Authors: Guo Xiaoyu , Li Hua , Wang Zuowen , Yang Haijian , Hu Chunxiang , Song Lirong , Wang Weibo
Published: December 2023

In the Anthropocene, the pervasive impacts of climate change on arid ecosystems are increasingly evident, resulting in significant alterations in both biodiversity and functionality. Although soil microbes are anticipated to be sensitive to changes in precipitation regimes, the mechanisms through which multifaceted precipitation changes impair the delivery of multiple functions by multitrophic microbiota in soils remain largely unexplored. In the drylands of Northwestern China, we examined the direct effects of historical precipitation regimes on the soil multifunctionality of biocrusts, a model system, and their indirect impacts mediated by microbial communities. Among abiotic predictors, precipitation variability, rather than mean annual precipitation, emerged as the primary driver of multifunctionality, leading to a convergence of less functionally beneficial species. By utilizing a biodiversity-ecosystem function relationship framework, our results underscore the crucial roles ofα- andβ-diversity of heterotrophic bacteria, fungi, and phototrophic cyanobacteria in maintaining soil functionality. However, the underlying mechanisms are distinct. We found that the local richness of heterotrophs and phylogenetic dissimilarity of photoautotrophs exert positive influences on multifunctionality, while species replacement, a component ofβ-diversity, primarily enhances the variance in soil multifunctionality. Importantly, the findings illuminate the cascading effect of precipitation variability on dryland ecosystems, amplified by microbial diversity, potentially triggering a silent collapse of vulnerable arid habitats. Our study highlights the importance of considering indirect climate impacts via soil microbiota, contributing to a deeper understanding of the real-world consequences of climate change on drylands, and offering valuable insights for the management of biodiversity theory-inspired ecosystem restoration.
Direct comparison of SARS-CoV-2 variant specific neutralizing antibodies in human and hamster sera
Authors: Rössler Annika , Netzl Antonia , Knabl Ludwig , Wilks Samuel H. , Mühlemann Barbara , Türeli Sina , Mykytyn Anna , von Laer Dorothee , Haagmans Bart L. , Smith Derek J. , Kimpel Janine
Published: December 2023

Antigenic characterization of newly emerging SARS-CoV-2 variants is important to assess their immune escape and judge the need for future vaccine updates. As exposure histories for human sera become more and more complex, animal sera may provide an alternative for antigenic characterization of new variants. To bridge data obtained from animal sera with human sera, we here analyzed neutralizing antibody titers in human and hamster first infection sera in a highly controlled setting using the same live-virus neutralization assay performed in one laboratory. Using a Bayesian framework, we found that titer fold changes in hamster sera corresponded well to human sera and that hamster sera generally exhibited higher reactivity. Our results indicate that sera from infected hamsters are a good surrogate for the antigenic characterization of new variants.
Conformational Dynamics and metal-ion interactions in human small Ubiquitin-like modifier (SUMO2)
Authors: Kaur Anupreet , Singh Harpreet , Kumar Dinesh , Gahlay Gagandeep Kaur , Mithu Venus Singh
Published: December 2023

SUMO (Small Ubiquitin-like Modifiers) proteins are involved in a crucial post-translational modification commonly termed as SUMOylation. Currently little is known about localisation and accumulation of SUMO2 conjugates in response to proteasome inhibitors. In this work, we have investigated a strong binding of Cu2+ions in the C-terminal region of SUMO2 resulting in its aggregation and seems to interefere in it’s non-covalent interaction with a V/I-X-V/I-V/I based SIM. In Ubiquitin-proteasome system, SUMO2 controls many targets in regulation of all aspects of metabolism. The conformational flexibility of SUMO2 could play a crucial role, therefore we have also characterized native-state flexibility of human SUMO2. We show that compared to SUMO1, several amino acids in SUMO2 around α1-helix region access energetically similar near-native conformations. This could play a fundamental role in its non-covalent interactions with SUMO interaction motifs (SIMs).
Temporal Dynamics of Faster Neo-Z Evolution in Butterflies
Authors: Höök Lars , Vila Roger , Wiklund Christer , Backström Niclas
Published: December 2023

The faster-Z/X hypothesis predicts that sex-linked genes should diverge faster than autosomal genes. However, studies across different lineages have shown mixed support for this effect. So far, most analyses have focused on old and well differentiated sex chromosomes, but less is known about divergence of more recently acquired neo-sex chromosomes. In Lepidoptera (moths and butterflies), Z-autosome fusions are frequent, but the evolutionary dynamics of neo-Z chromosomes have not been explored in detail. Here, we analysed the faster-Z effect inLeptidea sinapis, a butterfly with three Z chromosomes. We show that the neo-Z chromosomes have been acquired stepwise, resulting in strata of differentiation and masculinization. While all Z chromosomes showed evidence of the faster-Z effect, selection for genes on the youngest neo-Z chromosome (Z3) appears to have been hampered by a largely intact, homologous neo-W chromosome. However, the intermediately aged neo-Z chromosome (Z2), which lacks W gametologs, showed less evolutionary constraints, resulting in particularly fast evolution. Our results therefore support that neo-sex chromosomes can constitute temporary hot-spots of adaptation and divergence. The underlying dynamics are likely causally linked to shifts in selective constraints, evolution of gene expression, and degeneration of W-linked gametologs which gradually expose Z-linked genes to selection.
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

Facultative 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.

Importance

Defensive 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

Peptides 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 Statement

Peptides 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.

Classification

Biological 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

Chronic 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.

A 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

Activity-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

Aging 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

Di-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

Magnetosomes 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

Ethanolamine (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

Large 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

Fentanyl 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

The 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.
Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion
Authors: Lapuente-Santana Óscar , Sturm Gregor , Kant Joan , Ausserhofer Markus , Zackl Constantin , Zopoglou Maria , McGranahan Nicholas , Rieder Dietmar , Trajanoski Zlatko , de Miranda Noel Filipe da Cunha Carvalho , Eduati Federica , Finotello Francesca
Published: December 2023

The cellular and molecular heterogeneity of tumors is a major obstacle to cancer immunotherapy. Here, we use a systems biology approach to derive a signature of the main sources of heterogeneity in the tumor microenvironment (TME) from lung cancer transcriptomic data. We demonstrate that this signature, which we callediHet, is conserved in different cancers and associated with antitumor immunity. Through the analysis of single-cell and spatial transcriptomics data, we trace back the cellular origin of the variability that explains the iHet signature. Finally, we demonstrate that iHet has predictive value for cancer immunotherapy, which can be further improved by disentangling three major determinants of anticancer immune responses: activity of immune cells, immune infiltration or exclusion, and cancer-cell foreignness. This work shows how transcriptomics data can be integrated to derive a holistic representation of the phenotypic heterogeneity of the TME, and ultimately to determine its unfolding and fate during immunotherapy with immune checkpoint blockers.
High CD44 expression identifies rare chemoresistant leukemic cells endowed with enhanced E-Selectin binding in T-ALL
Authors: Calvo Julien , Naguibneva Irina , Kypraios Anthony , Uzan Benjamin , Gaillard Baptiste , Bellenger L Lea , Renou Laurent , Antoniewski Christophe , Lapillone Helene , Petit Arnaud , Ballerini Paola , Mancini Stéphane JC. , Marchand Tony , Peyron Jean-François , Pflumio Françoise
Published: December 2023

T-cell acute lymphoblastic leukemia (T-ALL) is a hematopoietic malignancy characterized by an increased proliferation and incomplete maturation of T-cell progenitors. Despite therapeutic improvements, relapses are often of bad prognosis. Therapeutic vulnerabilities and chemoresistance mechanisms arising from cell plasticity induced by the bone marrow (BM) microenvironment remain an important field of investigation. Employing single cell RNA sequencing (scRNAseq) of human T-ALL cells recovered from adipocyte-rich and -poor BM, a distinct leukemic stem cell (LSC) population defined by quiescence and elevated CD44 level (Ki67neg/lowCD44high) expression is identified in both territories.In vivochemotherapy demonstrated that the LSC population evades drug treatment. Patient sample analyses confirmed the presence of Ki67neg/lowCD44highLSC both at diagnosis and relapse that displayed a specific transcriptomic signature. Interestingly, the intense expression of CD44 in T-ALL Ki67neg/lowLSC was associated with E-selectin binding. Importantly, when 39 human T-ALL samples were analyzed, the E-selectin binding ability was found significantly higher in Relapse/Refractory compared to drug-sensitive patients. These findings characterize a T-ALL LSC population with chemoresistant properties and shade light on new strategies for prognostic stratification while opening avenues for novel therapeutic options.
Development of a quantitative colorimetric LAMP assay for fast and targeted molecular detection of the invasive lionfishPterois milesfrom environmental DNA
Authors: Hartle-Mougiou Katherine , Gubili Chrysoula , Xanthopoulou Panagiota , Kasapidis Panagiotis , Valiadi Martha , Gizeli Electra
Published: December 2023

The Mediterranean basin has seen an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species,Pterois miles, has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantifyP. milesenvironmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete whereP. mileshad been sighted.P. mileswas indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggest that populations are still at a low density. We also demonstrate the feasibility ofP. mileseDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together with the quantitative real-time colorimetric detection approach open new possibilities for monitoring invasiveP. milesin the field.
Cell Types or Cell States? An Investigation of Adrenergic and Mesenchymal Cell Phenotypes in Neuroblastoma
Authors: Bukkuri Anuraag , Andersson Stina , Brown Joel S. , Hammarlund Emma U. , Mohlin Sofie
Published: December 2023

Neuroblastoma is a pediatric cancer that exhibits two cellular phenotypes: adrenergic (ADRN) and mesenchymal (MES). ADRN is differentiated and therapy-sensitive, while MES is less differentiated with elevated therapy resistance. To understand neuroblastoma and its treatment response, it is important to elucidate how these phenotypes impact the eco-evolutionary dynamics of cancer cell populations and whether they represent distinct cell types or dynamic cell states. Here, we show that neuroblastoma cells undergo an ADRN to a MES phenotypic switch under chemotherapy treatment. We use a strong inference approach to generate four hypotheses on how this switch may occur: cell types without resistance, cell types with resistance, cell states without resistance, and cell states with resistance. For each of these hypotheses, we create theoretical models to make qualitative predictions about their resulting eco-evolutionary dynamics. Our results provide a framework to further experimentally determine whether ADRN and MES phenotypes are distinct cell types or dynamic cell states.
The crucible of the unfinished master plans for Cairo and a plan for the new administrative capital city
Authors: Soliman Ahmed , Soliman Yahya A. , Hassan Ghada Farouk , Afifi Samy
Published: December 2023

Purpose

The purpose of this article is to examine Cairo's master plans during the past 70 years, including the establishment of the New Administrative Capital City—which is based on two fundamental courses on the phenomenon of urbanisation—and other initiatives to address Cairo's Plans based on the thoughts of three planning schools—Chicago, Los Angeles and Liverpool. The aim is to determine if the right time to relocate Egypt's capital to a different place makes sense.

Design/methodology/approach

Cairo has experienced significant urban challenges throughout its millennial history due to the continually shifting socioeconomic and political changes. This research uses prospective and retrospective methods to examine how planning theories have historically influenced building Cairo’s urban fabric and provides insight into the city’s master plans from the July Revolution of 1952.

Findings

It is assumed that Cairo's socio-spatial transitions over time were caused by scattered expansion, leading to contemporary Cairo's socio-spatial evolution. The paper ends with some questions about the future of the city. Should planning policies change to cope with socioeconomic, spatial and political transitions?

Originality/value

The article's significance stems from the necessity of adaptable and considerate ideas that move Cairo's communities towards a better setting and provide a crucial route for enhancing their environments. Using digital technologies to implement new capital while creating platform urbanism may be accomplished even with constrained budgets and short course lengths.
Beyond purchase intention in sports sponsorship: an alternative approach to measuring brand equity using best-worst scaling
Authors: Almaiman Khaled Hamad , Ang Lawrence , Winzar Hume
Published: December 2023

Purpose

The purpose of this paper is to study the effects of sports sponsorship on brand equity using two managerially related outcomes: price premium and market share.

Design/methodology/approach

This study uses a best–worst discrete choice experiment (BWDCE) and compares the outcome with that of the purchase intention scale, an established probabilistic measure of purchase intention. The total sample consists of 409 fans of three soccer teams sponsored by three different competing brands: Nike, Adidas and Puma.

Findings

With sports sponsorship, fans were willing to pay more for the sponsor’s product, with the sponsoring brand obtaining the highest market share. Prominent brands generally performed better than less prominent brands. The best–worst scaling method was also 35% more accurate in predicting brand choice than a purchase intention scale.

Research limitations/implications

Future research could use the same method to study other types of sponsors, such as title sponsors or other product categories.

Practical implications

Sponsorship managers can use this methodology to assess the return on investment in sponsorship engagement.

Originality/value

Prior sponsorship studies on brand equity tend to ignore market share or fans’ willingness to pay a price premium for a sponsor’s goods and services. However, these two measures are crucial in assessing the effectiveness of sponsorship. This study demonstrates how to conduct such an assessment using the BWDCE method. It provides a clearer picture of sponsorship in terms of its economic value, which is more managerially useful.
Unraveling unemployment hysteresis in Nordic countries: a multifaceted analysis of age, gender and frequency differentials
Authors: Yılancı Veli , Kırca Mustafa , Canbay Şeri̇f , Sağlam Muhlis Selman
Published: December 2023

Purpose

This study aims to test the unemployment hysteresis hypothesis for Nordic countries by considering age and gender differentials at various frequencies.

Design/methodology/approach

First, the authors test the linearity of the unemployment series and apply appropriate unit root tests based on the linearity test results. The authors use these tests for both original and wavelet-decomposed unemployment rates.

Findings

The authors' findings indicate that the results obtained from the original and decomposed series differ. While the authors find evidence of unemployment hysteresis in the six unemployment rates in the short run, they observe supportive results for hysteresis in the three unemployment rates in the long run.

Originality/value

The authors take into account different age and gender groups. Furthermore, the authors propose a testing strategy for unemployment hysteresis that considers the nonlinearity and structural breaks in unemployment rates. Finally, the authors determine whether the unemployment hysteresis is valid at various frequencies.