bluuebunny/crossref_metadata_2025_split huggingface dataset:
Butyrate Protects against SARS-CoV-2-induced Tissue Damage in Golden Hamsters
Authors: Yu Huan , Yuan Lunzhi , Yan Zhigang , Zhou Ming , Ye Jianghui , Wu Kun , Chen Wenjia , Chen Rirong , Xia Ningshao , Guan Yi , Zhu Huachen 
Published: July 2023

ABSTRACTButyrate, produced by gut microbe during dietary fiber fermentation, plays anti-inflammatory and antioxidant effects in chronic inflammation diseases, yet it remains to be explored whether butyrate has protective effects against viral infections. Here, we demonstrated that butyrate alleviated tissue injury in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected golden hamsters with supplementation of butyrate before and during the infection. Butyrate-treated hamsters showed augmentation of type I interferon (IFN) response and activation of endothelial cells without exaggerated inflammation. In addition, butyrate regulated redox homeostasis by enhancing the activity of superoxide dismutase (SOD) to inhibit excessive apoptotic cell death. Therefore, butyrate exhibited an effective prevention against SARS-CoV-2 by upregulating antiviral immune responses and promoting cell survival.IMPORTANCESince SARS-CoV-2 has caused severe disease characterized by acute respiratory distress syndrome (ARDS) in humans, it is essential to develop therapeutics based on relieving such severe clinical symptoms. Current therapy strategies mainly focus on individuals who have COVID-19, however, there is still a strong need for prevention and treatment of SARS-CoV-2 infection. This study showed that butyrate, a bacterial metabolite, improved the response of SARS-CoV-2-infected hamsters by reducing immunopathology caused by impaired antiviral defenses and inhibiting excessive apoptosis through reduction in oxidative stress.
To unscramble an egg: admixed captive breeding populations can be rescued using local ancestry information
Authors: Lawson Daniel J. , Howard-McCombe Jo , Beaumont Mark , Senn Helen 
Published: July 2023

AbstractThis paper asks the question: can genomic information recover a species that is already on the pathway to extinction due to genetic swamping from a related and more numerous population? We show that whole genome sequencing can be used to identify and remove hybrid segments of DNA, when used as part of the breeding policy in a captive breeding program. The proposed policy uses a generalised measure of kinship or heterozygosity accounting for local ancestry, that is, whether a specific genetic location was inherited from from the target of conservation. We then show that optimising these measures would minimise undesired ancestry whilst also controlling undesired kinship or heterozygosity respectively, in a simulated breeding population. The process is applied to real data representing the hybridized Scottish wildcat breeding population, with the result that it should be possible to breed out the domestic cat ancestry. The ability to reverse introgression is a powerful new tool brought about from both sequencing and computational advances in ancestry estimation. Since it works best when applied early in the process, important decisions need to be made about which genetically distinct populations should benefit from it and which should be left to reform into a single population.
Prolonged exposure to lung-derived cytokines is associated with inflammatory activation of microglia in patients with COVID-19
Authors: Grant Rogan A. , Poor Taylor A. , Sichizya Lango , Diaz Estefani , Bailey Joseph I. , Soni Sahil , Senkow Karolina J. , Pérez-Leonor Xochítl G. , Abdala-Valencia Hiam , Lu Ziyan , Donnelly Helen K. , Tighe Robert M. , Lomasney Jon W. , Wunderink Richard G. , Singer Benjamin D. , Misharin Alexander V. , Budinger GR Scott ,   The NU SCRIPT Investigators
Published: July 2023

AbstractNeurological impairment is the most common finding in patients with post-acute sequelae of COVID-19. Furthermore, survivors of pneumonia from any cause have an elevated risk of dementia1–4. Dysfunction in microglia, the primary immune cell in the brain, has been linked to cognitive impairment in murine models of dementia and in humans5. Here, we report a transcriptional response in human microglia collected from patients who died following COVID-19 suggestive of their activation by TNF-ɑ and other circulating pro-inflammatory cytokines. Consistent with these findings, the levels of 55 alveolar and plasma cytokines were elevated in a cohort of 341 patients with respiratory failure, including 93 unvaccinated patients with COVID-19 and 203 patients with other causes of pneumonia. While peak levels of pro-inflammatory cytokines were similar in patients with pneumonia irrespective of etiology, cumulative cytokine exposure was higher in patients with COVID-19. Corticosteroid treatment, which has been shown to be beneficial in patients with COVID-196, was associated with lower levels of CXCL10, CCL8, and CCL2—molecules that sustain inflammatory circuits between alveolar macrophages harboring SARS-CoV-2 and activated T cells7. These findings suggest that corticosteroids may break this cycle and decrease systemic exposure to lung-derived cytokines and inflammatory activation of microglia in patients with COVID-19.
Development of a PNGase Rc column for online deglycosylation of complex glycoproteins during HDX-MS
Authors: Lambert Thomas , Gramlich Marius , Stutzke Luisa , Smith Luke , Deng Dingyu , Kaiser Philipp D. , Rothbauer Ulrich , Benesch Justin L.P. , Wagner Cornelia , Koenig Maximiliane , Pompach Petr , Novak Petr , Zeck Anne , Rand Kasper 
Published: July 2023

ABSTRACTProtein glycosylation is one of the most common PTMs and many cell surface receptors, extracellular proteins and biopharmaceuticals are glycosylated. However, HDX-MS analysis of such important glycoproteins has so far been limited by difficulties in determining the HDX of the protein segments that contain glycans. We have developed a column containing immobilized PNGase Rc (fromRudaea cellulosilytica) that can readily be implemented into a conventional HDX-MS setup to allow improved analysis of glycoproteins. We show that HDX-MS with the PNGase Rc column enables efficient online removal of N-linked glycans and the determination of the HDX of glycosylated regions in several complex glycoproteins. Additionally, we use the PNGase Rc column to perform a comprehensive HDX-MS mapping of the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Importantly, the column retains high activity in the presence of common quench-buffer additives like TCEP and urea and performed consistent across 114 days of extensive use. Overall, our work shows that HDX-MS with the integrated PNGase Rc column can enable fast and efficient online deglycosylation at harsh quench conditions to provide comprehensive analysis of complex glycoproteins.
Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture
Authors: Glass Madison R , Waxman Elisa A. , Yamashita Satoshi , Lafferty Michael , Beltran Alvaro , Farah Tala , Patel Niyanta K , Matoba Nana , Ahmed Sara , Srivastava Mary , Drake Emma , Davis Liam T. , Yeturi Meghana , Sun Kexin , Love Michael I. , Hashimoto-Torii Kazue , French Deborah L. , Stein Jason L. 
Published: July 2023

ABSTRACTBackground:Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes.Methods:Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites.Results:In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to thein vivobrain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs.Conclusions:We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
The Neuron-specific IIS/FOXO Transcriptome in Aged Animals Reveals Regulatory Mechanisms of Cognitive Aging
Authors: Weng Yifei , Zhou Shiyi , Morillo Katherine , Kaletsky Rachel , Lin Sarah , Murphy Coleen T. 
Published: July 2023

AbstractCognitive decline is a significant health concern in our aging society. Here, we used the model organismC. elegansto investigate the impact of the IIS/FOXO pathway on age-related cognitive decline. Thedaf-2Insulin/IGF-1 receptor mutant exhibits a significant extension of learning and memory span with age compared to wild-type worms, an effect that is dependent on the DAF-16 transcription factor. To identify possible mechanisms by which agingdaf-2mutants maintain learning and memory with age while wild-type worms lose neuronal function, we carried out neuron-specific transcriptomic analysis in aged animals. We observed downregulation of neuronal genes and upregulation of transcriptional regulation genes in aging wild-type neurons. By contrast, IIS/FOXO pathway mutants exhibit distinct neuronal transcriptomic alterations in response to cognitive aging, including upregulation of stress response genes and downregulation of specific insulin signaling genes. We tested the roles of significantly transcriptionally-changed genes in regulating cognitive functions, identifying novel regulators of learning and memory. In addition to other mechanistic insights, comparison of the aged vs youngdaf-2neuronal transcriptome revealed that a new set of potentially neuroprotective genes is upregulated; instead of simply mimicking a young state,daf-2may enhance neuronal resilience to accumulation of harm and take a more active approach to combat aging. These findings suggest a potential mechanism for regulating cognitive function with age and offer insights into novel therapeutic targets for age-related cognitive decline.
Application of monolayer graphene to cryo-electron microscopy grids for high-resolution structure determination
Authors: Grassetti Andrew V. , May Mira B. , Davis Joseph H. 
Published: July 2023

ABSTRACTIn cryogenic electron microscopy (cryo-EM), purified macromolecules are typically applied to a grid bearing a holey carbon foil, blotted to remove excess liquid and rapidly frozen in a roughly 20-100 nm thick layer of vitreous ice that is suspended across roughly 1 μm-wide foil holes. The resulting sample is then imaged using cryogenic transmission electron microscopy and, after substantial image processing, near-atomic resolution structures can be determined. Despite cryo-EM’s widespread adoption, sample preparation remains a severe bottleneck in cryo-EM workflows, with users often encountering challenges related to samples behaving poorly in the suspended vitreous ice. Recently, methods have been developed to modify cryo-EM grids with a single continuous layer of graphene, which acts as a support surface that often increases particle density in the imaged area and can reduce interactions between particles and the air-water interface. Here, we provide detailed protocols for the application of graphene to cryo-EM grids, and for rapidly assessing the relative hydrophilicity of the resulting grids. Additionally, we describe an EM-based method to confirm the presence of graphene by visualizing its characteristic diffraction pattern. Finally, we demonstrate the utility of these graphene supports by rapidly reconstructing a 2.7 Å resolution density map of an exemplar Cas9 complex using a highly pure sample at a relatively low concentration.SUMMARYThe application of support layers, such as graphene, to cryo-electron microscopy grids can increase the density of particles imaged, limit particle interactions with the air-water interface, reduce the extent of beam-induced motion, and, in some instances, improve the distribution of particle orientations. This paper describes a robust protocol for coating cryo-EM grids with a monolayer of graphene for improved cryo-sample preparation.
Emergence and spread of the barley net blotch pathogen coincided with crop domestication and cultivation history
Authors: Taliadoros Demetris , Feurtey Alice , Wyatt Nathan , Gladieux Pierre , Friesen Timothy , Stukenbrock Eva 
Published: July 2023

AbstractFungal pathogens cause devastating disease in crops. Understanding the evolutionary origin of pathogens is essential to the prediction of future disease emergence and the potential of pathogens to disperse. The fungusPyrenophora teresf.terescauses net form net blotch (NFNB), an economically significant disease of barley. In this study, we have used 104P. teresf.teresgenomes from four continents to explore the population structure and demographic history of the fungal pathogen. We showed thatP. teresf.teresis structured into populations that tend to be geographically restricted to different regions. Using Multiple Sequentially Markovian Coalescent and machine learning approaches we demonstrated that the demographic history of the pathogen correlates with the history of barley, highlighting the importance of human migration and trade in spreading the pathogen. Exploring signatures of natural selection, we identified several population-specific selective sweeps that colocalized with genomic regions enriched in putative virulence genes, and loci previously identified as determinants of virulence specificities by quantitative trait locus analyses. This reflects rapid adaptation to local hosts and environmental conditions ofP. teresf.teresas it spread with barley. Our research highlights how human activities can contribute to the spread of pathogens that significantly impact the productivity of field crops.
Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines
Authors: Prithiviraj Sujeethkumar , Garcia Alejandro Garcia , Linderfalk Karin , Yiguang Bai , Ferveur Sonia , Falck Ludvig Nilsén , Subramaniam Agatheeswaran , Mohlin Sofie , Hidalgo David , Dupard Steven J , Zacharaki Dimitra , Raina Deepak Bushan , Bourgine Paul E 
Published: July 2023

AbstractTissue engineering strategies predominantly rely on the production of living substitutes, whereby implanted cells actively participate in the regenerative process. Beyond cost and delayed graft availability, the patient-specific performance of engineered tissues poses serious concerns on their clinical translation ability. A more exciting paradigm consists in exploiting cell-laid, engineered extracellular matrices (eECM), which can be used as off-the-shelf materials. Here, the regenerative capacity solely relies on the preservation of the eECM structure and embedded signals to instruct an endogenous repair. We recently described the possibility to exploit custom human stem cell lines for eECM manufacturing. In addition to the conferred standardization, the availability of such cell lines opened avenues for the design of tailored eECMs by applying dedicated genetic tools. In this study, we demonstrated the exploitation of CRISPR/Cas9 as a high precision system for editing the composition and function of eECMs. Human mesenchymal stromal/stem cell (hMSC) lines were modified to knockout VEGF and RUNX2 and assessed for their capacity to generate osteoinductive cartilage matrices. We report the successful editing of hMSCs, subsequently leading to targeted VEGF and RUNX2-knockout cartilage eECMs. Despite the absence of VEGF, eECMs retained full capacity to instruct ectopic endochondral ossification. Conversely, RUNX2-edited eECMs exhibited impaired hypertrophy, reduced ectopic ossification and superior cartilage repair in a rat osteochondral defect. In summary, our approach can be harnessed to identify the necessary eECM factors driving endogenous repair. Our work paves the road towards the compositional eECMs editing and their exploitation in broad regenerative contexts.
Neuroprotective role of lactate in a humanin vitromodel of the ischemic penumbra
Authors: Cerina Marta , Levers Marloes , Keller Jason M. , Frega Monica 
Published: July 2023

SummaryIn patients suffering from cerebral ischemic stroke, there is an urgent need for treatments to protect brain cells. Recently, treatment strategies that induce neuronal activity have been shown to be neuroprotective. However, the biological mechanisms underlying the benefit from neuronal activation are unknown. We hypothesized that neuronal activation might trigger the astrocyte-to-neuron lactate shuttle, whereby lactate is released from astrocytes to support the energy requirements of hypoxic neurons, and this leads to the observed neuroprotection. We tested this by establishing a human cell basedin vitromodel of the ischemic penumbra. We found that lactate transporters are involved in the neuroprotective effect mediated by neuronal activation, that lactate exogenously administered before hypoxia correlated with neuroprotection, and that stimulation of astrocyte with consequent endogenous production of lactate resulted in neuroprotection. We presented evidence that lactate contributes to neuroprotection during hypoxia providing a potential basis for therapeutic approaches in ischemic stroke.
A molecularly-defined non-redundant subpopulation of OPCs controls the generation of myelinating oligodendrocytes during postnatal development
Authors: Moghimyfiroozabad Shayan , Paul Maela A. , Bellenger Lea , Selimi Fekrije 
Published: July 2023

AbstractOligodendrocyte precursor cells (OPCs) are a class of glial cells that uniformly tiles the whole central nervous system. They play several key functions across the brain including the generation of oligodendrocytes and the control of myelination. Whether the functional diversity of OPCs is the result of genetically defined subpopulations or of their regulation by external factors has not been definitely established. We discovered that a subpopulation of OPCs found across the brain is defined by the expression ofC1ql1, a gene previously described for its synaptic function in neurons. This subpopulation starts to appear during the first postnatal week in the mouse brain. Ablation ofC1ql1-expressing OPCs in the mouse is not compensated by the remaining OPCs, and results in a massive lack of oligodendrocytes and myelination in many brain regions. Therefore,C1ql1is a molecular marker of a functionally non-redundant subpopulation of OPCs, which controls the generation of myelinating oligodendrocytes.
Neural correlates of spatiotemporal properties of lightness induction
Authors: Malik Amna , Boyaci Huseyin 
Published: July 2023

AbstractThe lightness of a surface depends not only on the amount of light reflected off it but also on the context it is embedded in. Despite a long history of research, neural correlates of context-dependent lightness perception remain a question of ongoing debate. The current study seeks to expand upon the existing literature by measuring fMRI responses to a dynamic version of a classical effect called simultaneous lightness induction (SLI), where a central disk appears lighter when embedded in a darker surround compared to when embedded in a lighter surround. During the fMRI experiment, we presented ten participants with a dynamic SLI stimulus by modulating the luminance of either the achromatic surround (surround-modulation condition) or the achromatic disk (disk-modulation condition) at four different frequencies ranging from 1 to 8 Hz. Behaviorally, when the surround luminance is modulated at low frequencies, participants perceive an illusory change in the lightness of the disk (lightness induction). In contrast, they perceive little or no induction at higher frequencies. Utilizing this temporal dependence and controlling for long-range responses to border contrast and luminance changes, we found that activity in the primary visual cortex (V1) correlates with lightness induction. However, such a correlation was not evident in extrastriate areas, V2, V3, and V4. These findings provide evidence for the involvement of V1 in the processing of context-dependent lightness.
Systematic characterization of site-specific proline hydroxylation using hydrophilic interaction chromatography and mass spectrometry
Authors: Jiang Hao , Druker Jimena , Wilson James W. , Bensaddek Dalila , Swedlow Jason R. , Rocha Sonia , Lamond Angus I. 
Published: July 2023

AbstractTo improve understanding of the role of site-specific proline hydroxylation in controlling protein function, we have developed a robust workflow for the identification of proline hydroxylation sites in proteins using a combination of hydrophilic interaction chromatography (HILIC) enrichment and high-resolution nano-Liquid Chromatography-Mass Spectrometry (LC-MS). Using this approach, together with refining and filtering parameters during data analysis, by combining the results from cell lines being treated with either the prolyl hydroxylase inhibitor Roxadustat (FG-4592, FG) or the proteasome inhibitor MG-132 (MG), or DMSO, a total of 4,993 and 3,247 proline hydroxylation sites were identified in HEK293 and RCC4 samples, respectively. A subset of 1,954 and 1,253 high confident proline hydroxylation sites (non-collagen) from HEK293 and RCC4 samples were inhibited by FG-4592 treatment. A set of features characteristic of proline hydroxylated peptides were identified in both datasets, which differ from either unmodified peptides, or oxidised peptides. Peptides containing hydroxyproline were enriched in the more hydrophilic HILIC fractions and showed characteristic differences in charge and mass distribution, as compared with unmodified or oxidised peptides. Furthermore, we discovered that the intensity of the diagnostic hydroxyproline immonium ion was greatly influenced by parameters including the MS collision energy setting, parent peptide concentration and the sequence of adjacent amino acids neighbouring the modified proline. We show using synthetic peptides that a combination of retention time in LC and optimised MS parameter settings allows reliable identification of proline hydroxylation sites in peptides, even when multiple prolines residues are present. By matching all the proline hydroxylated, non-collagen proteins to the Pfam database, the most common protein family domains identified in both HEK293 and RCC4 datasets were RNA recognition motif (RRM_1), WD40 repeat (WD40), and protein kinase domain (Pkinase). Sequence analysis of the hydroxylated peptides showed enrichment for the motif GxPGxx, including the Gxx repeats found in collagen proteins, as well as the protein kinase domain GTP motif. Glycine (G), serine (S) and glutamic acid (E) residues were found frequently in the sequence window from the hydroxylated peptides. Reactome pathway analysis for the proteins of these newly identified proline hydroxylation sites (FG inhibited), showed enrichment for proteins involved in metabolism of RNA, mRNA splicing and cell cycle regulation, potentially mediated by prolyl hydroxylase enzymes (PHDs).