bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating and correcting index hopping misassignments in single-cell RNA-seq data
Authors: Miao Lingling , Collado Loren , Barkdull Savannah , Saito Yoshine , Jo Jay-Hyun , Han Jungmin , Dell’Orso Stefania , Kelly Michael C. , Kong Heidi H. , Brownell Isaac 
Published: October 2024

ABSTRACTBackgroundIndex hopping causes read assignment errors in data from multiplexed sequencing libraries. This issue has become more prevalent with the widespread use of high-capacity sequencers and highly multiplexed single-cell RNA sequencing (scRNA- seq).ResultsWe conducted deep, plate-based scRNA-seq on a mixed population of mouse skin cells. Analysis of transcriptomes from 1152 cells identified four distinct cell types. To estimate the error rate in sample assignment due to index hopping, we employed differential expression analysis to identify signature genes that were highly and specifically expressed in each cell type. We quantified the proportion of misassigned reads by examining the detection rates of signature genes in other cell types. Remarkably, regardless of gene expression levels, we estimated that 0.65% of reads per gene were assigned to incorrect cell across our data. To computationally compensate for index hopping, we developed a simple correction method wherein, for each gene, 0.65% of the library’s average expression level was subtracted from the expression in each cell. This correction had notable effects on transcriptome analyses, including increased cell-cell clustering distance and alterations in intermediate state assignments of cell differentiation.ConclusionsIndex hopping misassignments are measurable and can impact the experimental interpretation of sequencing results. We devised a straightforward method to estimate and correct for the index hopping rate by quantifying misassigned genes in distinct cell types within an scRNA-seq library. This approach can be applied to any barcoded, multiplexed scRNA-seq library containing cells with distinct expression profiles, allowing for correction of the expression matrix before conducting biological analysis.
Multigenerational Proteolytic Inactivation of Restriction Upon Subtle Genomic Hypomethylation
Authors: Shmidov Esther , Villani Alexis , Mendoza Senén D. , Avihu Ellay , Lebenthal-Loinger Ilana , Karako-Lampert Sarit , Shoshani Sivan , Ye Chang , Wang Yiding , Yan Hao , Tang Weixin , Bondy-Denomy Joseph , Banin Ehud 
Published: October 2024

AbstractRestriction-modification (R-M) systems, present in most bacterial genomes, protect against phage infection by detecting and degrading invading foreign DNA. However, like many prokaryotic anti-phage systems, R-M systems pose a significant risk of auto-immunity, exacerbated by the presence of hundreds to thousands of potential cleavage sites in the bacterial genome. InPseudomonas aeruginosa, restriction inactivation upon growth at high temperatures was previously described, however, which system is being inactivated, the underlying mechanism, as well as the timing of recovery, remain unknown. Here, we report thatP. aeruginosaType I methyltransferase (HsdMS) and restriction endonuclease (HsdR) components are degraded by two Lon-like proteases when replicating above 41 °C, which induces partial genome hypomethylation and simultaneously prevents self-targeting, respectively. Interestingly, upon return to 37 °C, methyltransferase activity returns gradually, with restriction activity not fully recovering for over 60 bacterial generations, representing the longest bacterial memory to our knowledge. Forced expression of HsdR over the first 45 generations is toxic, demonstrating the fitness benefit of HsdR inactivation. Our findings demonstrate that type I R-M is tightly regulated post-translationally with a remarkable memory effect to ensure genomic stability and emphasize the importance of mitigating auto-toxicity for bacterial defense systems.
Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection
Authors: Neugent Michael L. , Hulyalkar Neha V. , Ghosh Debasish , Zimmern Philippe E. , Shulaev Vladimir , De Nisco Nicole J. 
Published: October 2024

AbstractRecurrent urinary tract infections (rUTIs) are a major clinical challenge in postmenopausal women and their increasing prevalence underscores the need to define interactions between the host and the urinary microbiome that may underlie rUTI susceptibility. A body of work has identified the taxonomic profile of the female urinary microbiome associate with aging, menopause, and urinay disease. However, how this microbial community engages with the host niche, including the local biochemical environment of the urogenital tract, in health and disease is yet to be fully defined. This study directly assesses differences in the biochemical environment of the urine, or biochemical ecology, associated with recurrent urinary tract infection (UTI) and defines a microbe-metabolite association network of the female urinary microbiome. By integrating metagenomic and metabolomic data collected from a controlled cohort of women with rUTI, we find that distinct metabolites, such as methionine sulfoxide (Met-SO) and trimethylamine oxide (TMAO), are associated with differences in urinary microbiome diversity. We observe associations between microbial and biochemical beta diversity and unique metabolic networks of uropathogenicEscherichia coliand uroprotectiveLactobacillusspecies, highlighting potential metabolite-driven ecological shifts that may influence UTI susceptibility. We identify a urinary lipid signature of active rUTI that can accurately distinguish (AUC = 0.987) cases controls. Finally, using time-to-relapse data we identify deoxycholic acid (DCA) as a new prognostic indicator for rUTI recurrence. Together these findings suggest that systemic metabolic processes may influence susceptibility, opening new avenues for therapeutic intervention and the development of more accurate diagnostic and prognostic to improve patient outcomes.
What is true for plants may not be true forPhaeodactylum tricornutum: The case ofVanilla planifoliavanillin synthase (VpVAN) targeted to four subcellular compartments of the diatom
Authors: Diaz-Garza Aracely Maribel , Lavoie-Marchand Félix , Merindol Natacha , Diamond Andrew , Desgagné-Penix Isabel 
Published: October 2024

ABSTRACTVanillin is the major organoleptic compound of the vanilla flavor. Since the extraction process from its natural source (Vanilla planifolia) is limited by a low yield, the market demand for vanillin is met by producing it through chemical synthesis or biotechnologically using microorganisms to convert ferulic acid, lignin, and guaiacol into vanillin. Our aim was to use the diatomPhaeodactylum tricornutum, a photosynthetic model organism already used to produce eukaryotic proteins and high-value compounds, to characterizeV. planifoliavanillin synthase (VpVAN). This enzyme is the subject of conflicting results and was reported to be localized in the plastid ofV. planifoliacells, which may play a role in its activity. For this purpose, we targetedVpVAN linked by anin vitrocleavable sequence (Xa) to the enhanced green fluorescent protein (eGFP) to the cytoplasm, peroxisomes, plastid, and Golgi apparatus. We used an episomal expression system transformingP. tricornutumwithVpVAN:Xa:eGFPby bacterial conjugation. Positive cell lines were selected by fluorescence and characterized by sequencing the episomes, confirming stable replication in the diatom, as well as assessing the subcellular localization in the targeted cell compartments. Strategies such as enriching GFP-positive cells by cell sorting, protein purification, and organelle isolation did not yield detectable levels of the fusion protein. A better understanding of the diatom expression system is needed to complete the characterization of this enzyme and reveal whether the subcellular localization could be a missing aspect ofVpVAN expression in microorganisms.
SETD2 promotes PAF1C interactions with the elongating RNA Pol II and is required for neuronal differentiation
Authors: Ambrosi Christina , Pfaendler Ramon , Butz Stefan , Recchia Davide , Bao Xue , Schmolka Nina , Baubec Tuncay 
Published: October 2024

AbstractChromatin modifications are relevant for mammalian development and their aberrant deposition is associated with human disease. While the mechanisms that deposit and remove these modifications have been largely elucidated, their role in regulating gene activity during cellular differentiation have yet to be completely understood. By differentiating a panel of mouse embryonic stem cells lacking major chromatin regulators towards neuronal cells, we identified their requirement at different stages of cellular differentiation. We show that the H3K36me3 methyltransferase SETD2 is important for the establishment of neuronal gene expression during late stages of differentiation, but is dispensable once the cells have fully differentiated. This function is largely independent of the histone methyltransferase activity. By measuring the protein interaction network of elongating RNA Pol II, we identify a novel role for SETD2 in mediating interactions between the PAF1 complex and the elongating RNA Pol II, which is required to ensure optimal transcriptional processivity of neuronal genes.
Imaging of live bacterial whole-cell biosensors illuminates spatial sialic acid availability within the inflamed mammalian gut
Authors: Carreño David , Robinson Clare M , Jackson Raphaella , Li Peirong , Nunes Vanessa , Palma-Duran Susana A. , Nye Emma , MacRae James I. , Riglar David T. 
Published: October 2024

AbstractHost mucin-derived sialic acids are key drivers of microbial colonisation, growth and pathogenicity within the mammalian gut. However, their study is hindered by complex spatiotemporal dynamics, with availability driven by the interplay of microbial sialidase enzyme activity and microbial utilisation. Here, we demonstrate regional increases in the bioavailability of sialic acid in the inflamed mouse gut. We monitor metabolite availabilityin situusing an engineered bacterial whole-cell biosensor colonised within the gut. Through organ-scale imaging of cleared tissues at single bacterial resolution we observe strong correlations between global inflammation status and biosensor response. Profiling along the length of the gut uncovers regional variations between the peak sialic acid sensing and the peak inflammatory response within host tissues. These data illuminate the complex spatial dynamics involved in shared host-microbiome metabolism and demonstrate the broader power of using engineered bacterial biosensors to monitor bioavailabilityin situwithin the gut.
Enhanced Fear Extinction Through Infralimbic Perineuronal Net Digestion: The Modulatory Role of Adolescent Alcohol Exposure
Authors: Obray J. Daniel , Denton Adam R. , Carroll-Deaton Jayda , Marquardt Kristin , Chandler L. Judson , Scofield Michael D. 
Published: October 2024

AbstractPerineuronal nets (PNNs) are specialized components of the extracellular matrix that play a critical role in learning and memory. In a Pavlovian fear conditioning paradigm, degradation of PNNs affects the formation and storage of fear memories. This study examined the impact of adolescent intermittent ethanol (AIE) exposure by vapor inhalation on the expression of PNNs in the adult rat prelimbic (PrL) and infralimbic (IfL) subregions of the medial prefrontal cortex. Results indicated that following AIE, the total number of PNN positive cells in the PrL cortex increased in layer II/III but did not change in layer V. Conversely, in the IfL cortex, the number of PNN positive cells decreased in layer V, with no change in layer II/III. In addition, the intensity of PNN staining was significantly altered by AIE exposure, which narrowed the distribution of signal intensity, reducing the number of high and low intensity PNNs. Given these changes in PNNs, the next experiment assessed the effects of AIE and PNN digestion on extinction of a conditioned fear memory. In Air control rats, digestion of PNNs by bilateral infusion of Chondroitinase ABC (ChABC) into the IfL cortex enhanced fear extinction and reduced contextual fear renewal. In contrast, both fear extinction learning and contextual fear renewal remained unchanged following PNN digestion in AIE exposed rats. These results highlight the sensitivity of prefrontal PNNs to adolescent alcohol exposure and suggest that ChABC-induced plasticity is reduced in the IfL cortex following AIE exposure.
Omega-3 fatty acid normalizes postsynaptic density proteins via miRNAs regulation in hippocampus and prevents DEHP-induced impairment of learning and memory in mice
Authors: Ding Muyao , Ma Hongyu , Du Hui , Yang Yinglong , Yu Min , Zhang Cong 
Published: October 2024

AbstractsDEHP is the most widely used plasticizer in many products. However, growing evidence has indicated that DEHP may induce neurotoxicity. DEHP exposure affects mircoRNAs (miRNAs) expression in brain. A growing body of evidence suggests that nutrients and other bioactive food components prevent neurotoxicity through regulation of miRNA expression. Due to the increasing concern about the risks of DEHP to human health, we explored the neuroprotective effect of Omega-3 fatty acid (Omega-3FA) on subchronic DEHP-induced neurotoxicity in mice, and the potential involved miRNAs and their targets in the protective action of Omega-3FA against DEHP-induced neurotoxicity. Omega-3FA protected against the DEHP-induced impairment of learning and memory and alleviated the thinning of postsynaptic density (PSD) thickness in hippocampal synapses. We observed that there are fourteen up or down regulated miRNAs associated PSD in DEHP exposure which were normalized by Omega-3FA treatment. Protein targets in PSD of these differentially expressed miRNAs were predicted. Furthermore, the expression levels of protein mGluR5, Homer1, and NMDAR2B were carried out via Western blot, for further verifying PSD associated miRNAs’ targets are involved in neuroprotection of Omega-3FA against DEHP. These findings suggested that Omega-3FA protected DEHP-induced impairment of learning and memory as well as synaptic structure alteration in the hippocampus by regulating the expression of PSD associated miRNAs and their targets. Thus, Omega-3FA should be included in diet to prevent or suppress neurotoxicity caused by continuous exposure to DEHP.
Simulated larvae dispersion of the invasive sun-coral (Tubastreaspp.) along Rio de Janeiro’s coast: the role of submesoscale filaments on offshore transport and connectivity
Authors: Calado Leandro , Cosenza Bernardo , Moraes Francisco , Luko Caique Dias , Mizrahi Damián , Xavier Fabio C. , Batista Daniela , Domingos Roberto , Calazans Sávio , Araújo Fernanda , Coutinho Ricardo 
Published: October 2024

AbstractThe spread of invasive species in marine ecosystems is a growing global concern, particularly in regions with high economic and ecological importance. sun corals (Tubastraeaspp.) are scleractinians native to the Pacific Ocean that have spread along most of the Brazilian coast. This exotic species initially established populations in Rio de Janeiro, reaching high levels of abundance. Although the ecological aspects and impacts caused by this organism have been studied in detail, the natural mechanisms that drive its dispersal have attracted little attention. In this research, we focus on the offshore transport of sun coral larvae between Cabo de São Tomé and Ilha Grande Bay, RJ, investigating how submesoscale oceanographic features such as filaments, eddies and upwelling influence connectivity among different population. High-resolution numerical simulations were used to model the coastal dynamics, incorporating the influence of the Brazil Current, wind-driven circulation, and submesoscale structures. Larval dispersal was examined under different wind scenarios, including northeasterly winds that drive southward currents which enhance offshore transport via submesoscale filaments. Results show that submesoscale features, particularly filaments emerged from upwelling regions, play a significant role on sun coral larvae dispersion. These features act as pathways that connect larvae from coastal to offshore oil exploration areas, highlighting the importance of both natural and anthropogenic processes for the dissemination of this invasive species. This research provides critical insights into the ecological mechanisms governing the spread of invasive marine species, emphasizing the need for integrated coastal management strategies. Understanding how physical processes drive larval transport is essential for developing targeted control measures to mitigate the impact of invasive species like sun coral on native ecosystems and local economies. Furthermore, the study underscores the importance of monitoring both natural and anthropogenic influences on marine bioinvasions, particularly in regions with significant offshore industrial activities.
Larval surveys reveal breeding site preferences of malaria vectorAnophelesspp. in Zanzibar City
Authors: Hill Kaeden K. , Kobe Dickson , Kreppel Katharina 
Published: October 2024

ABSTRACTMalaria is a serious illness that causes over 500,000 deaths annually worldwide, mainly affecting children under five years of age. Tanzania, in Africa, contributes to approximately 4% of those deaths. Malaria is caused byPlasmodiumspp. parasites, and it is vectored by mosquitoes in theAnophelesgenus. In Zanzibar City, the capital of the Zanzibar archipelago in Tanzania, the incidence of malaria has decreased over the past few decades due to standardized treatment protocols in hospitals and dispensaries and public health interventions targeting adult mosquitoes. However, the incidence remains between 1-2%, with an increasing trend observed over the past few years likely stemming from continued exchange ofPlasmodiumspp. from other malaria-endemic areas (including mainland Tanzania). While larvicides are a powerful tool to reduce vector populations, this control strategy relies on information on breeding sites and their productivity. In Zanzibar City, no larval surveys have been done in the last few years. Our aim was to characterizeAnophelesspp. breeding sites in Zanzibar City during the rainy season. We first conducted systematic larval surveys across 16 semipermanent/permanent water bodies and 30 temporary water bodies. Then, we used Principal Component Analysis and logistic regression to model the effect of physical and chemical parameters, and rainfall onAnophelespresence. We found thatAnophelesspp. utilize mostly concrete, semipermanent breeding sites with high levels of dissolved oxygen concentrations but can utilize natural sites after heavy rains. The logistic regression model incorporating rainfall was able to predict the presence of Anopheles larvae with a positive predictive power of 65.7% and a negative predictive power of 88.8%. The data from our study suggest thatAnophelesspp. have not yet expanded to using more polluted breeding sites in Zanzibar City (as they have in some mainland locations). These results can inform targeted larvicidal strategies in Zanzibar City.
The impact of tropodithietic acid on microbial physiology under varying culture complexities
Authors: Shlakhter Olesia , Segev Einat 
Published: October 2024

AbstractResearch has increasingly focused on understanding marine bacterial physiology under environmentally relevant conditions. Biotic interactions have a key influence on microbial physiology and are often modeled in the lab by manipulating the complexity of microbial cultures. Notably, findings from low-complexity cultures that have been re-evaluated in more complex systems, occasionally lead to different outcomes. Here, we assess how the genomic capability of bacteria to produce secondary metabolites, specifically the antibiotic tropodithietic acid (TDA), influences microbial physiology and interactions, under varying microbial complexity.We investigate the impact of TDA production on microbial physiology across systems with increasing complexity: from bacterial mono-cultures, to bacterial co-cultures ofPhaeobacter inhibenswithDinoroseobacter shibae, and a more complex tri-culture that includes both bacteria and their algal hostEmiliania huxleyi. In these systems, we examine both wild-type (WT)P. inhibensbacteria and mutant bacteria with atdaBdeletion (ΔtdaB) that are not capable of producing TDA. This systematic approach allowed us to explore the relationship between thetdaBgene, microbial physiology, and system complexity.Our findings show that deleting thetdaBgene affected bacteria-bacteria interactions in co-cultures but not in tri-cultures with the algal host. Additionally, our data revealed that algal death was delayed in cultures containingP. inhibensΔtdaBmutants compared to those with WT bacteria.Results of our study highlight the importance of microbial complexity in the study of bacterial physiology and point to the understudied role of TDA in algal-bacterial interactions.ImportanceThis study advances our understanding of marine bacterial physiology under varying levels of microbial complexity. We uncover how the production of secondary metabolites, specifically the antibiotic tropodithietic acid (TDA), influences microbial interactions. Our systematic approach, which includes bacterial mono-cultures, co-cultures, and tri-cultures involving algal hosts, allows us to evaluate the impact of thetdaBgene on microbial interactions. Notably, our findings reveal that the deletion of this gene affects bacteria-bacteria interactions in co-culture but does not have the same effect in more complex systems that include algae. Additionally, the observation that algal death is delayed in cultures with TDA-deficient bacteria underscores the significance of TDA in these interactions. Overall, our research highlights the influence of the microbial culture complexity on bacterial physiology and emphasizes the overlooked role of TDA in algal-bacterial dynamics.
Repulsion of CA3 / dentate gyrus representations is driven by distinct internal beliefs in the face of ambiguous sensory input
Authors: Wanjia Guo , Han Subin , Kuhl Brice A. 
Published: October 2024

ABSTRACTRecent human neuroimaging studies of episodic memory have revealed a counterintuitive phenomenon in the hippocampus: when events are highly similar, corresponding hippocampal activity patterns are sometimes less correlated than activity patterns associated with unrelated events. This phenomenon—repulsion—is not accounted for by most theories of the hippocampus, and the conditions that trigger repulsion remain poorly understood. Here, we used a spatial route-learning task and high-resolution fMRI in humans to test whether hippocampal repulsion is fundamentally driven by internal beliefs about the environment. By precisely measuring participants’ internal beliefs and actively manipulating them, we show that repulsion selectively occurred in hippocampal subfields CA3 and dentate gyrus when visual input was ambiguous—or evenidentical—but internal beliefs were distinct. These findings firmly establish conditions that elicit repulsion and have broad relevance to theories of hippocampal function and to the fields of human episodic memory and rodent spatial navigation.