bluuebunny/crossref_metadata_2025_split huggingface dataset:
An optimized method for the isolation of urinary extracellular vesicles for molecular phenotyping: detection of biomarkers for radiation exposure
Authors: Hinzman Charles P. , Jayatilake Meth , Bansal Sunil , Fish Brian L. , Li Yaoxiang , Zhang Yubo , Bansal Shivani , Girgis Michael , Iliuk Anton , Xu Xiao , Fernandez Jose A. , Griffin John H. , Ballew Elizabeth A , Unger Keith , Boerma Marjan , Medhora Meetha , Cheema Amrita K. 
Published: January 2022

ABSTRACTBackgroundUrinary extracellular vesicles (EVs) are a source of biomarkers with broad potential applications across clinical research, including monitoring radiation exposure. A key limitation to their implementation is minimal standardization in EV isolation and analytical analysis methods. Further, most urinary EV isolation protocols necessitate large volumes of sample. This study aimed to compare and optimize isolation and analytical methods for EVs from small volumes of urine.Methods3 EV isolation methods were compared: ultracentrifugation, magnetic bead-based, and size-exclusion chromatography from 0.5 mL or 1 mL of rat and human urine. EV yield and mass spectrometry signals (Q-ToF and Triple Quad) were evaluated from each method. Metabolomic profiling was performed on EVs isolated from the urine of rats exposed to ionizing radiation 1-, 14-, 30- or 90-days post-exposure, and human urine from patients receiving thoracic radiotherapy for the treatment of lung cancer pre- and post-treatment.ResultsSize-exclusion chromatography is the preferred method for EV isolation from 0.5 mL of urine. Mass spectrometry-based metabolomic analyses of EV cargo identified biochemical changes induced by radiation, including altered nucleotide, folate, and lipid metabolism. We have provided standard operating procedures for implementation of these methods in other laboratories.ConclusionsWe demonstrate that EVs can be isolated from small volumes of urine and analytically investigated for their biochemical contents to detect radiation induced metabolomic changes. These findings lay a groundwork to develop future methods to monitor response to radiotherapy and can be extended to an array of molecular phenotyping studies aimed at characterizing EV cargo.
Mapping SARS-CoV-2 antigenic relationships and serological responses
Authors: Wilks Samuel H. , Mühlemann Barbara , Shen Xiaoying , Türeli Sina , LeGresley Eric B. , Netzl Antonia , Caniza Miguela A. , Chacaltana-Huarcaya Jesus N. , Corman Victor M. , Daniell Xiaoju , Datto Michael B. , Dawood Fatimah S. , Denny Thomas N. , Drosten Christian , Fouchier Ron A. M. , Garcia Patricia J. , Halfmann Peter J. , Jassem Agatha , Jeworowski Lara M. , Jones Terry C. , Kawaoka Yoshihiro , Krammer Florian , McDanal Charlene , Pajon Rolando , Simon Viviana , Stockwell Melissa S. , Tang Haili , van Bakel Harm , Veguilla Vic , Webby Richard , Montefiori David C. , Smith Derek J. 
Published: January 2022

AbstractDuring the SARS-CoV-2 pandemic, multiple variants escaping pre-existing immunity emerged, causing concerns about continued protection. Here, we use antigenic cartography to analyze patterns of cross-reactivity among a panel of 21 variants and 15 groups of human sera obtained following primary infection with 10 different variants or after mRNA-1273 or mRNA-1273.351 vaccination. We find antigenic differences among pre-Omicron variants caused by substitutions at spike protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months post-2nd dose. We find changes in immunodominance of different spike regions depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine strain selection.One sentence summary:Antigenic Cartography of SARS-CoV-2 variants reveals amino acid substitutions governing immune escape and immunodominance patterns.
From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape
Authors: Ionescu D. , Bizic M. , Karnatak R. , Musseau C. L. , Onandia G. , Kasada M. , Berger S.A. , Nejstgaard J.C. , Ryo M. , Lischeid G. , Gessner M. O. , Wollrab S. , Grossart H.-P. 
Published: January 2022

AbstractLocal biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices and other anthropogenic influences. In contrast, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity and metacommunity structure in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse, differ in the degree of coupling with their surroundings. We assessed biodiversity patterns of eukaryotes, Bacteria and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of eDNA. First, we asked whether deep sequencing of eDNA provides a representative picture of KH biodiversity across the three domains of life. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land-use. Our data shows that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but, has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. The latter, coupled with landscape wide nutrient enrichment (including by atmospheric deposition), groundwater connectivity between KH and organismal movement in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, levelling off today’s detectable differences in KH biodiversity between land-use types.
mGluR5 PAMs rescue cortical and behavioural defects in a mouse model of CDKL5 deficiency disorder
Authors: Gurgone Antonia , Pizzo Riccardo , Raspanti Alessandra , Chiantia Giuseppe , Devi Sunaina , Morello Noemi , Pilotto Federica , Gnavi Sara , Lupori Leonardo , Mazziotti Raffaele , Sagona Giulia , Putignano Elena , Nocentini Alessio , Supuran Claudiu T. , Marcantoni Andrea , Pizzorusso Tommaso , Giustetto Maurizio 
Published: January 2022

AbstractCyclin-dependent kinase-like 5 (CDKL5) deficiency disorder (CDD) is a devastating rare neurodevelopmental disease without a cure, caused by mutations of the serine/threonine kinase CDKL5 highly expressed in the forebrain. CDD is characterized by early-onset seizures, severe intellectual disabilities, autistic-like traits, sensorimotor and cortical visual impairments (CVI). The lack of an effective therapeutic strategy for CDD urgently demands the identification of novel druggable targets potentially relevant for CDD pathophysiology.To this aim, we studied metabotropic glutamate receptors 5 (mGluR5) for their important role in critical mechanisms involved in CDD, i.e.: synaptogenesis, dendritic spines formation/maturation and synaptic plasticity, and because mGluR5 function depends on the postsynaptic protein Homer1bc that is downregulated in the cerebral cortex of CDKL5−/y mice. In this study, we reveal that CDKL5 loss tampers with (i) the strength of Homer1bc-mGluR5 binding, (ii) the synaptic localization of mGluR5 and (iii) the mGluR5-mediated enhancement of NMDA-induced neuronal responses. Importantly, we showed that the stimulation of mGluR5 activity by administering in mice specific positive-allosteric-modulators, i.e.: 3-Cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (CDPPB) or RO6807794, corrected the synaptic, functional and behavioural defects shown by CDKL5−/y mice. Notably, the cerebral cortex of 2 CDD patients show similar changes in the synaptic organization to mutant CDKL5 mice, including a reduced mGluR5 expression, suggesting that mGluR5 represent a promising therapeutic target for CDD patients.
Sex-specific regulation of binge drinking, social, and arousal behaviors by subcortical serotonin 5HT2creceptor-containing neurons
Authors: Flanigan M.E. , Hon O.J. , D’Ambrosio S. , Boyt K.M. , Hassanein L. , Castle M. , Haun H.L. , Pina M.M. , Kash T.L. 
Published: January 2022

SummarySerotonin 5HT2creceptors have been implicated in the pathophysiology of both mood disorders and alcohol use disorder, but the circuits mediating the effects of systemic pharmacological manipulations of this receptor on behavior have not been identified. Binge alcohol consumption induces discrete social and arousal disturbances in human populations, which are thought to promote increased drinking. However, whether models of binge drinking in rodents can induce these same long-term negative behavioral symptoms is unknown. In this study, we employed multiple anatomical, physiological, and behavioral approaches to identify two populations of neurons expressing serotonin 5HT2creceptors, one in the lateral habenula (LHb5HT2c) and one in the bed nucleus of the stria terminalis (BNST5HT2c), that display coordinatedin-vivoresponses to social, arousal, and alcohol-related stimuli and are physiologically modulated by binge alcohol consumption in a sex-specific manner. Critically, these physiological changes were associated with sex-specific behavioral disturbances that closely mirror social and arousal symptoms observed in humans during abstinence from binge drinking. Specifically, we observed that one week of abstinence from three weeks of binge alcohol drinking induced social recognition deficits in females and potentiated acoustic startle responses in males. While both populations of neurons (BNST and LHb) and the 5HT2creceptor itself contribute to the sex-specific effects of alcohol on social and arousal behaviors to some degree, the primary causal mechanism underlying these phenomena appears to be excessive activation of LHb5HT2cneurons. These findings may have implications for the development of sex-specific treatments for mood and alcohol use disorders targeting the brain’s serotonin system.
Curiosity and mesolimbic functional connectivity drive information seeking in real life
Authors: Eschmann Kathrin C. J. , Pereira Duarte F. M. M. , Valji Ashvanti , Dehmelt Vera , Gruber Matthias J. 
Published: January 2022

ABSTRACTCuriosity reflects the intrinsic motivation of an individual to seek information in order to close information gaps. Laboratory-based experiments have shown that both curiosity and information seeking are associated with enhanced neural dynamics in the mesolimbic dopaminergic circuit. However, it is unclear whether curiosity and its associated neural dynamics in the dopaminergic circuit drive information seeking in real life. The present study investigated (i) whether curiosity traits predict different characteristics of real-life information seeking and (ii) whether functional connectivity within the mesolimbic dopaminergic circuit is associated with information seeking outside of the laboratory. Up to 15 month before the COVID-19 pandemic, we conducted curiosity and anxiety questionnaires as well as a 10-minute resting-state fMRI session. In a follow-up survey early during the COVID-19 pandemic, participants repeated the questionnaires and filled out an additional questionnaire about their COVID-19-related information seeking. Curiosity but not anxiety remained stable over time. Individual differences in curiosity were positively associated with the frequency of information-seeking behaviour. Anxiety during the pandemic was not linked to any characteristics of real-life information seeking. Interestingly, the frequency of information seeking was also independently predicted by individual differences in resting-state functional connectivity between the ventral tegmental area and the nucleus accumbens. The present translational study paves the way for future studies on the role of curiosity in real-life information seeking by showing that curiosity drives information seeking in real-life situations and that the curiosity-promoting mesolimbic dopaminergic functional network supports the frequency of real-life information-seeking behaviour.SIGNIFICANCE STATEMENTCuriosity is a key driver of learning and information seeking in everyday life. However, the temporal stability of curiosity traits, their relationship to real-life information seeking, and the associated dopaminergic brain activity are poorly understood. The present study provides evidence that curiosity traits are stable over time – even through a major event, such as the COVID-19 pandemic – and that both curiosity and intrinsic functional connectivity within the mesolimbic dopaminergic circuit are associated with the frequency of real-life information seeking. These findings contribute to a better understanding of cognitive and neural differences that shape how individuals seek out information and may offer the opportunity to help individuals with suboptimal information-seeking behaviour that negatively affects their well-being or mental health.
A Chemical Mutagenesis Approach to Insert Post-Translational Modifications in Aggregation-Prone Proteins
Authors: Ge Ying , Masoura Athina , Yang Jingzhou , Aprile Francesco A. 
Published: January 2022

ABSTRACTNeurodegenerative diseases are a class of disorders linked to the formation in the nervous system of fibrillar protein aggregates called amyloids. This aggregation process is affected by a variety of post-translational modifications, whose specific mechanisms are not fully understood yet. Emerging chemical mutagenesis technology is currently striving to address the challenge of introducing protein post-translational modifications, while maintaining proteins stable and soluble during the modification reaction. Several amyloidogenic proteins are highly aggregation-prone, and current modification procedures lead to unexpected precipitation of these proteins, affecting their yield and downstream characterization. Here, we present a method for maintaining amyloidogenic proteins soluble during chemical mutagenesis. As proof-of-principle, we applied our method to mimic the phosphorylation of the serine 26 and the acetylation of the lysine 28 of the 40-residue long variant of amyloid-β peptide, whose aggregation is linked to Alzheimer’s disease.
A study of thermally-induced sex reversal in casque-headed lizards
Authors: Suárez-Varón Gabriel , Mendoza-Cruz Eva , Acosta Armando , Cruz Maricela Villagrán-Santa , Cortez Diego , Hernández-Gallegos Oswaldo 
Published: January 2022

ABSTRACTNon-avian reptiles, unlike mammals and birds, have undergone numerous sex determination turnovers. For example, casque-headed lizards replaced the ancestral XY system shared across pleurodonts with a new pair of XY chromosomes. However, the evolutionary forces that triggered this transition have remained unclear. An interesting evolutionary hypothesis suggests that species with intermediate states, with sex chromosomes but also thermal-induced sex reversal at specific incubation temperatures, could be more susceptible to sex determination turnovers. We contrasted genotypic data (presence/absence of the Y chromosome) against the histology of gonads of embryos from stages 35-37 incubated at various temperatures, including typical male-producing (26°C) and female-producing (32°C) temperatures. We observed perfect concordance between genotype and phenotype at all temperatures. However, analysis of transcriptomic data from embryos incubated at 26°C and 32°C identified transcript variants of the chromatin modifiers JARID2 and KDM6B that have been linked to temperature-dependent sex determination in other reptiles. Besides, our work reports for the first time to our knowledge the histology of gonads, including morphological changes, from stages 35-37 of development in the Corytophanidae family. We also observed that all embryos developed hemipenes, suggesting sex-linked developmental heterochrony.Our work tested the validity of a mixed sex determination system in the Corytophanidae family. We showed that XY chromosomes are dominant, however, our work supports the hypothesis of a conserved transcriptional response to incubation temperatures across non-avian reptiles that could be the reminiscence of an ancestral sex determination system.
Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics
Authors: Pantazopoulou Chrysoula K. , Buti Sara , Nguyen Chi Tam , Oskam Lisa , Farmer Edward E. , Kajala Kaisa , Pierik Ronald 
Published: January 2022

AbstractPlants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit in upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca2+]cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes inhibit touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.
Vagus nerve stimulation recruits the central cholinergic system to enhance perceptual learning
Authors: Martin Kathleen A. , Papadoyannis Eleni S. , Schiavo Jennifer K. , Fadaei Saba Shokat , Valencia Sofia Orrey , Temiz Nesibe Z. , McGinley Matthew J. , McCormick David A. , Froemke Robert C. 
Published: January 2022

AbstractPerception can be refined by experience up to certain limits. It is unclear if perceptual limitations are absolute or could be partially overcome via enhanced neuromodulation and/or plasticity. Recent studies suggest the utility of peripheral nerve stimulation - specifically vagus nerve stimulation (VNS) - for altering neural activity and augmenting experience-dependent plasticity, although little is known about central mechanisms recruited by VNS. Here we developed an auditory discrimination task for mice implanted with a VNS electrode. VNS occurring during behavior gradually improved discrimination abilities beyond the level achieved by training alone. Using two-photon imaging, we identified changes to auditory cortical responses and activation of cortically-projecting cholinergic axons with VNS. Anatomical and optogenetic experiments indicated that VNS could enhance task performance via activation of the central cholinergic system. These results highlight the importance of cholinergic modulation for the efficacy of VNS, perhaps enabling further refinement of VNS methodology for clinical conditions.
A methodology for co-simulation-based optimization of biofabrication protocols
Authors: Giannantoni Leonardo , Bardini Roberta , Di Carlo Stefano 
Published: January 2022

AbstractBiofabrication processes are complex and often unsatisfactory. Trial-and-error methods are costly and yield only incremental innovation, starting from sub-optimal and poorly represented existing processes. Although computational techniques might support efficient process design to find optimal process configurations, intelligent computational approaches must comprise biological complexity to provide meaningful insights. This paper proposes a novel co-simulation-based optimization methodology for the systematic design of protocols for cell culture and biofabrication. The proposed strategy integrates evolutionary computation and simulation for efficient design space exploration and assessment of candidate protocols. A generic library supports the modular and flexible composition of multiscale and multidomain co-simulation scenarios. The feasibility of the presented approach was demonstrated in the automatic generation of protocols for the biofabrication of an epithelial cell monolayer. The results are twofold. First, the prototype co-simulation library helps build flexible, loosely coupled simulation scenarios. Second, the in-silico experimentation on the use case shows that the proposed approach is a viable first step towards standard and automated design in biofabrication.
Multimodal single cell sequencing of human diabetic kidney disease implicates chromatin accessibility and genetic background in disease progression
Authors: Wilson Parker C. , Muto Yoshiharu , Wu Haojia , Karihaloo Anil , Waikar Sushrut S. , Humphreys Benjamin D. 
Published: January 2022

AbstractMultimodal single cell sequencing is a powerful tool for interrogating cell-specific changes in transcription and chromatin accessibility. We performed single nucleus RNA (snRNA-seq) and assay for transposase accessible chromatin sequencing (snATAC-seq) on human kidney cortex from donors with and without diabetic kidney disease (DKD) to identify altered signaling pathways and transcription factors associated with DKD. Both snRNA-seq and snATAC-seq had an increased proportion ofVCAM1+injured proximal tubule cells (PT_VCAM1) in DKD samples. PT_VCAM1 has a pro-inflammatory expression signature and transcription factor motif enrichment implicated NFkB signaling. We used stratified linkage disequilibrium score regression to partition heritability of kidney-function-related traits using publicly-available GWAS summary statistics. Cell-specific PT_VCAM1 peaks were enriched for heritability of chronic kidney disease (CKD), suggesting that genetic background may regulate chromatin accessibility and DKD progression. snATAC-seq found cell-specific differentially accessible regions (DAR) throughout the nephron that change accessibility in DKD and these regions were enriched for glucocorticoid receptor (GR) motifs. Changes in chromatin accessibility were associated with decreased expression of insulin receptor, increased gluconeogenesis, and decreased expression of the GR cytosolic chaperone,FKBP5, in the diabetic proximal tubule. Cleavage under targets and release using nuclease (CUT&RUN) profiling of GR binding in bulk kidney cortex and anin vitromodel of the proximal tubule (RPTEC) showed that DAR co-localize with GR binding sites. CRISPRi silencing of GR response elements (GRE) in theFKBP5gene body reducedFKBP5expression in RPTEC, suggesting that reducedFKBP5chromatin accessibility in DKD may alter cellular response to GR. We developed an open-source tool for single cell allele specific analysis (SALSA) to model the effect of genetic background on gene expression. Heterozygous germline single nucleotide variants (SNV) in proximal tubule ATAC peaks were associated with allele-specific chromatin accessibility and differential expression of target genes within cis-coaccessibility networks. Partitioned heritability of proximal tubule ATAC peaks with a predicted allele-specific effect was enriched for eGFR, suggesting that genetic background may modify DKD progression in a cell-specific manner.