bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial sodium/calcium exchanger NCLX regulates glycolysis in astrocytes, impacting on cognitive performance
Authors: Cabral-Costa João Victor , Vicente-Gutiérrez Carlos , Agulla Jesús , Lapresa Rebeca , Elrod John W. , Almeida Ángeles , Bolaños Juan P. , Kowaltowski Alicia J. 
Published: September 2022

AbstractIntracellular Ca2+ concentrations are strictly controlled by plasma membrane transporters, the endoplasmic reticulum, and mitochondria, in which Ca2+ uptake is mediated by the mitochondrial calcium uniporter complex (MCUc), while efflux occurs mainly through the mitochondrial Na+/Ca2+ exchanger (NCLX). RNAseq database repository searches led us to identify the Nclx transcript as highly enriched in astrocytes when compared to neurons. To assess the role of NCLX in mouse primary culture astrocytes, we inhibited its function both pharmacologically or genetically. This resulted in re-shaping of cytosolic Ca2+ signaling and a metabolic shift that increased glycolytic flux and lactate secretion in a Ca2+-dependent manner. Interestingly, in vivo genetic deletion of NCLX in hippocampal astrocytes improved cognitive performance in behavioral tasks, whereas hippocampal neuron-specific deletion of NCLX impaired cognitive performance. These results unveil a role for NCLX as a novel modulator of astrocytic glucose metabolism, impacting on cognition.
Transcriptome-wide analysis of pseudouridylation inDrosophila melanogaster
Authors: Song Wan , Podicheti Ram , Rusch Douglas B. , Tracey W. Daniel 
Published: September 2022

AbstractPseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptomewide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organismDrosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The three mRNAs most enriched for Psi encode highly-expressed yolk proteins (Yp1, Yp2, Yp3). By comparing the pseudouridine profiles in theRluA-2mutant and thew1118control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.
In vitro evaluation of immune responses to bacterial hydrogels for the development of living therapeutic materials
Authors: Yanamandra Archana , Bhusari Shardul , del Campo Aránzazu , Sankaran Shrikrishnan , Qu Bin 
Published: September 2022

AbstractIn living therapeutic materials, organisms genetically programmed to produce and deliver drugs are encapsulated in porous matrices or hydrogels acting as physical barriers between the therapeutic organisms and the host cells. The therapeutic potential of such constructs has been highlighted in in vitro studies, but the translation to in vivo scenarios requires evaluation of the immune response to the presence of the encapsulated, living organisms. In this study, we investigate the responses of human peripheral blood mononuclear cells (PBMCs) exposed to a living therapeutic material consisting of engineered E. coli encapsulated in Pluronic F127-based hydrogels. The release of inflammation-related cytokines (IL-2, IL-4, IL-6, IL-10, IL-17A, TNFα and IFNγ) and cytotoxic proteins (granzyme A, granzyme B, perforin, granulysin, sFas, and sFasL) in response to the bacterial hydrogels, as well as the subsets of natural killer cells and T cells after exposure to the bacterial hydrogel for up to three days were examined. In direct contact with PBMCs, both E. coli and its endotoxin-free variant, ClearColi, induce apoptosis of the immune cells and trigger IL-6 release from the surviving cells. However, we found that encapsulation of the bacteria in Pluronic F127 diacrylate hydrogels considerably lowers their immunogenicity and practically abolishes apoptosis triggered by ClearColi. In comparison with E. coli, free and hydrogel-encapsulated ClearColi induced significantly lower levels of NK cell differentiation into the more cytolytic CD16dim subset. Our results demonstrate that ClearColi-encapsulated hydrogels generate low immunogenic response and are suitable candidates for the development of living therapeutic materials for in vivo testing to assess a potential clinical use. Nevertheless, we also observed a stronger immune response in pro-inflammatory PBMCs, possibly from donors with underlying infections. This suggests that including anti-inflammatory measures in living therapeutic material designs could be beneficial for such recipients.
Molecular Acclimation of Halobacterium salinarum to Halite Brine Inclusions
Authors: Favreau C. , Tribondeau A. , Marugan M. , Guyot F. , Alpha-Bazin B. , Marie A. , Puppo R. , Dufour T. , Huguet A. , Zirah S. , Kish A. 
Published: September 2022

1AbstractHalophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by the change in color for salt crystals containing pigmented halophiles. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, “-omics” based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusion microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
Detection of neuronal OFF periods as low amplitude neural activity segments
Authors: Harding Christian D. , Guillaumin Mathilde C.C. , Krone Lukas B. , Kahn Martin C. , Blanco-Duque Cristina , Mikutta Christian , Vyazovskiy Vladyslav V. 
Published: September 2022

AbstractDuring non-rapid eye movement sleep (NREM), synchronised neuronal activity is reflected in a specific neural oscillation observed in neocortical electrophysiological signals: a low frequency component characterised by depth-positive/surface-negative potentials known as slow waves, corresponding to alternating periods of high (ON period) and low (OFF period) spiking activity. Often overlooked in favour of slow waves, there is an interest in understanding how neuronal silencing during OFF periods leads to the generation of slow waves and whether this relationship changes between cortical layers. The foremost issue in detecting population OFF periods is the absence of a formal, widely adopted definition. Here, we grouped segments of high frequency neural activity containing spikes, recorded from the neocortex, on the basis of amplitude and asked whether the population of low amplitude (LA) segments displayed the expected characteristics of OFF periods. We corroborate previous studies showing that LA segments in neural activity signals are a uniquely identifiable structure with distinct characteristics from the surrounding signal that identify them as OFF periods including NREM sleep predominance and association with a local field potential (LFP) slow wave. In addition, we attribute new characteristics to these segments not previously associated with OFF periods: vigilance-state-dependent duration and duration-dependent homeostatic response. This could suggest that ON/OFF periods are currently underdefined, and their appearance is less binary than previously considered, instead representing a continuum.
Enrichment and application of bacterial sialic acids containing polymers from the extracellular polymeric substances of “Candidatus Accumulibacter”
Authors: Tomás-Martínez Sergio , Chen Le Min , Pabst Martin , Weissbrodt David G. , van Loosdrecht Mark C.M. , Lin Yuemei 
Published: September 2022

AbstractPseudaminic and legionaminic acids are a subgroup of nonulosonic acids (NulOs) unique to bacterial species. There is a lack of advances in the study of these NulOs due to their complex synthesis and production. Recently, it was seen that “Candidatus Accumulibacter” can produce Pse or Leg analogues as part of its extracellular polymeric substances (EPS). In order to employ a “Ca. Accumulibacter” enrichment as production platform for bacterial sialic acids, it is necessary to determine which fractions of the EPS of “Ca. Accumulibacter” contain NulOs and how to enrich and/or isolate them. We extracted the EPS from granules enriched with “Ca. Accumulibcater” and used size-exclusion chromatography to separate them into different molecular weight fractions. This separation resulted in two high molecular weight (> 5,500 kDa) fractions dominated by polysaccharides, with a NulO content up to 4 times higher than the extracted EPS. This suggests that NulOs in “Ca. Accumulibacter” are likely located in high molecular weight polysaccharides. Additionally, it was seen that the extracted EPS and the NulO-rich fractions can bind and neutralize histones. This suggest that they can serve as source for sepsis treatment drugs, although further purification needs to be evaluated.Graphical abstractHighlightsNulOs in “Ca. Accumulibacter” are likely located in high molecular weight polysaccharides.Size exclusion chromatography allows to obtain high molecular weight polysaccharide-rich fractions enriched with NulOs.EPS and the NulOs-rich fractions can serve as source for sepsis treatment drugs.
Notch directs telencephalic development and controls neocortical neuron fate determination by regulating microRNA levels
Authors: Han Jisoo S. , Fishman-Williams Elizabeth , Decker Steven C. , Hino Keiko , Reyes Raenier V. , Brown Nadean L. , Simó Sergi , Torre Anna La 
Published: September 2022

ABSTRACTThe central nervous system (CNS) contains myriads of different types of cells produced from multipotent neural progenitors. Neural progenitors acquire distinct cell identities depending on their spatial position, but they are also influenced by temporal cues to give rise to different cell populations over time. For instance, the progenitors of the cerebral neocortex generate different populations of excitatory projection neurons following a well-known sequence. The Notch signaling pathway plays crucial roles this process but the molecular mechanisms by which Notch impacts progenitor fate decisions have not been fully resolved. Here, we show that Notch signaling is essential for neocortical and hippocampal morphogenesis, and for the development of the corpus callosum and choroid plexus. Our data also indicate that, in the neocortex, Notch controls projection neuron fate determination through the regulation of two microRNA (miRNA) clusters that include let-7, miR-99a/100, and miR-125b. Our findings collectively suggest that balanced Notch signaling is crucial for telencephalic development and that the interplay between Notch and miRNAs is critical to control neocortical progenitor behaviors and neuron cell fate decisions.
GPCR signaling promotes severe stress-induced organismic death inC. elegans
Authors: Wang Changnan , Long Yong , Wang Bingying , Zhang Chao , Ma Dengke K. 
Published: September 2022

AbstractHow an organism dies is a fundamental yet poorly understood question in biology. An organism can die of many causes, including stress-induced phenoptosis, also defined as organismic death that is regulated by its genome-encoded programs. The mechanism of stress-induced phenoptosis is still largely unknown. Here we show that transient but severe freezing-thaw stress (FTS) inC. elegansinduces rapid and robust phenoptosis that is regulated by G-protein coupled receptor (GPCR) signaling. RNAi screens identify the GPCR-encodingfshr-1in mediating transcriptional responses to FTS. FSHR-1 increases ligand interaction upon FTS and activates a cyclic AMP-PKA cascade leading to a genetic program to promote organismic death under severe stress. FSHR-1/GPCR signaling up-regulates the bZIP-type transcription factor ZIP-10, linking FTS to expression of genes involved in lipid remodeling, proteostasis and aging. A mathematical model suggests that genes may promote organismic death under severe stress conditions, potentially benefiting growth of the clonal population with individuals less stressed and more reproductively privileged. Our studies reveal roles of FSHR-1/GPCR-mediated signaling in stress-induced gene expression and phenoptosis inC. elegans, providing empirical new insights into mechanisms of stress-induced phenoptosis with evolutionary implications.
Day-to-day spontaneous social behaviours is quantitatively and qualitatively affected in a 16p11.2 deletion mouse model
Authors: Rusu Anna , Chevalier Claire , de Chaumont Fabrice , Nalesso Valérie , Brault Véronique , Hérault Yann , Ey Elodie 
Published: September 2022

AbstractBackgroundAutism spectrum disorders affect more than one percent of the population, impairing social communication and increasing stereotyped behaviours. A micro-deletion of the 16p11.2 BP4-BP5 chromosomic region has been identified in one percent of patients also displaying intellectual disabilities. In mouse models generated to understand the mechanisms of this deletion, learning and memory deficits were pervasive in most genetic backgrounds, while social communication deficits were only detected in some models.MethodsBased on previous study (Arbogast et al. 2016 PLoS genetics), we itemized the social deficits in the mouse model of 16p11.2 deletion on a hybrid C57BL/6NxC3H.Pde6b+genetic background. We examined whether behavioural deficits were visible over long-term observation periods, to parallel everyday-life assessment of patients. We recorded the individual and social behaviours of 16p11.2 Del/+ mice and their wild-type littermates from both sexes in long-term (over two and three consecutive nights) social interactions of familiar mixed-genotype quartets of males and of females, and of same-genotype unfamiliar female pairs.ResultsWe observed that Del/+ mice of both sexes increased significantly their locomotor activity compared to wild-type littermates over long-term monitoring. In the social domain, Del/+ mice of both sexes displayed widespread deficits over long-term monitoring, even more so in males than in females in quartets of familiar individuals. In pairs, significant perturbations of the organisation of the social communication and behaviours appeared in Del/+ females.DiscussionAltogether, this suggests that, over long recording periods, the phenotype of the 16p11.2 Del/+ mice was differently affected in the locomotor activity and the social domains and between the two sexes. These findings confirm the importance of testing models in long-term conditions to provide a comprehensive view of their phenotype that will refine the study of cellular and molecular mechanisms and complement pre-clinical targeted therapeutic trials.
Characterizing the Resolution and Throughput of the Apollo Direct Electron Detector
Authors: Peng Ruizhi , Fu Xiaofeng , Mendez Joshua H. , Randolph Peter S. , Bammes Benjamin E. , Stagg Scott M. 
Published: September 2022

AbstractAdvances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.
Morphological and temporal variation in early embryogenesis contributes to species divergence in Malawi cichlid fishes
Authors: Marconi Aleksandra , Yang Cassandra , McKay Samuel , Santos M. Emília 
Published: September 2022

AbstractThe cichlid fishes comprise the largest extant vertebrate family and are the quintessential example of rapid “explosive” adaptive radiations and phenotypic diversification. Despite low genetic divergence, East African cichlids harbour a spectacular intra- and interspecific morphological diversity, including the hyper-variable, neural crest (NC)-derived traits such as colouration and craniofacial skeleton. Although the genetic and developmental basis of these phenotypes has been investigated, understanding of when, and specifically how early, in ontogeny species-specific differences emerge, remains limited. Since adult traits often originate during embryonic development, the processes of embryogenesis could serve as a potential source of species-specific variation. Consequently, we compared the features of embryogenesis between three Malawi cichlid species – Astatotilapia calliptera, Tropheops sp. ‘mauve’ and Rhamphochromis sp. ‘chilingali’ – representing a wide spectrum of variation in pigmentation and craniofacial morphologies. Our results showed fundamental differences in multiple aspects of embryogenesis that could underlie interspecific divergence in adult adaptive traits. Firstly, we identified variation in the somite number and signatures of temporal variation, or heterochrony, in the rates of somite formation. The heterochrony was also evident within and between species throughout ontogeny, up to the juvenile stages. Finally, the identified interspecific differences in the development of pigmentation and craniofacial cartilages, present at the earliest stages of their overt formation, provide compelling evidence that the species-specific trajectories begin divergence during early embryogenesis, potentially during somitogenesis and NC development. Altogether, our results expand our understanding of fundamental cichlid biology and provide new insights into the developmental origins of vertebrate morphological diversity.Research highlightsThis work details the early development of three divergent Lake Malawi cichlids. A comparative analysis reveals anatomical and timing differences during embryogenesis and indicates divergence of species’ morphologies prior to their overt formation.
Catch me if you can: Capturing extracellular DNA transformation in mixed cultures via Hi-C sequencing
Authors: Calderón-Franco David , van Loosdrecht Mark C.M. , Abeel Thomas , Weissbrodt David G. 
Published: September 2022

AbstractEnvironmental microorganisms evolve constantly under various stressors using different adaptive mechanisms, including horizontal gene transfer. Microorganisms benefit from transferring genetic information that code for antibiotic resistance via mobile genetic elements (plasmids). Due to the complexity of natural microbial ecosystems, quantitative data on the transfer of genetic information in microbial communities remain unclear. Two 1-L chemostats (one control and one test) were inoculated with activated sludge, fed with synthetic wastewater, and operated for 45 days at a hydraulic retention time of 1 day to study the transformation capacity of a rolling-circle plasmid encoding GFP and kanamycin resistance genes, at increasing concentrations of kanamycin (0.01-2.5-50-100 mg L−1) representing environmental, wastewater, lab-selection, and gut or untreated pharmaceutical wastewater discharge environments. The plasmid DNA was spiked daily at 5 µg L−1 in the test chemostat. The evolution of the microbial community composition was analyzed by 16S rRNA gene amplicon sequencing and metagenomics, and the presence of the plasmid by quantitative PCR. We used Hi-C sequencing to identify natural transformant microorganisms under steady-state conditions with low (2.5 mg L−1) and high (50 mg L−1) concentrations of kanamycin. Both chemostats selected for the same 6 predominant families of Spirosomaceae, Comamonadaceae, Rhodocyclaceae, Rhizobiaceae, Microbacteriaceae, and Chitinophagaceae, while biomass formation in the presence of kanamycin was higher with the plasmid. Hence, the antibiotic exerted the main pressure on microbial selection, while the plasmid helped these populations better resist the antibiotic treatment and grow. The kanamycin resistance gene increased in both reactors (log 7 gene copies g VSS−1). When higher antibiotic concentrations were applied, the GFP/16S ratio was increased, highlighting plasmids accumulation in the test reactor over time. The plasmid transformed mainly inside populations of Bosea sp., Runella spp., and Microbacterium sp.. This study made one significant step forward by demonstrating that microorganisms in enrichments from activated sludge biomasses can acquire exogenous synthetic plasmids by transformation.Graphical abstract