bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient in vivo genome editing mediated by stem cells-derived extracellular vesicles carrying designer nucleases
Authors: Bobis-Wozowicz Sylwia , Kania Karolina , Nit Kinga , Blazowska Natalia , Kmiotek-Wasylewska Katarzyna , Paw Milena , Karnas Elzbieta , Szyposzynska Agnieszka , Tyszka-Czochara Malgorzata , Woznicka Olga , Boruczkowski Dariusz , Mussolino Claudio , Łabaj Paweł P. , Schambach Axel , Madeja Zbigniew , Cathomen Toni , Zuba-Surma Ewa K. 
Published: February 2021

AbstractPrecise genome editing using designer nucleases (DNs), such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) system, has become a method of choice in a variety of biological and biomedical applications in recent years. Notably, efficacy of these systems is currently under scrutiny in about 50 clinical trials. Although high DNs activity in various cell typesin vitrohas already been achieved, efficientin vivogenome editing remains a challenge. To solve this problem, we employed stem cells-derived extracellular vesicles (EVs) as carriers of DNs. We used umbilical cord-derived mesenchymal stem cells (UC-MSCs) and induced pluripotent stem cells (iPSCs) as EV-producer cells, since they are both applied in regenerative medicine. In our proof-of-concept studies, we achieved up to 50% of EGFP marker gene knockoutin vivousing EVs carrying either ZFN, TALEN or the CRISPR/Cas9 system, particularly in the liver. Importantly, we obtained almost 50% of modified alleles in the liver of the experimental animals, when targeting thePcsk9gene, whose overexpression is implicated in hypercholesterolemia. Taken together, our data provide strong evidence that stem cells-derived EVs constitute a robust tool in delivering DNsin vivo, which may be harnessed to clinical practice in the future.
The CCL2 Chemokine Promotes Early Seeding of the Latent HIV Reservoir
Authors: Packard Thomas A. , Schwarzer Roland , Herzig Eytan , Rao Deepashri , Luo Xiaoyu , Egedal Johanne H. , Hsiao Feng , Widera Marek , Hultquist Judd F. , Grimmett Zachary W. , Messer Ronald J. , Krogan Nevan J. , Deeks Steven G. , Roan Nadia R. , Dittmer Ulf , Hasenkrug Kim J. , Greene Warner C. 
Published: February 2021

ABSTRACTHIV infects long-lived CD4 memory T cells establishing a latent viral reservoir that necessitates lifelong anti-retroviral therapy (ART). How this reservoir is formed so swiftly remains unknown. We now show the innate inflammatory response to HIV infection results in CCL2 chemokine release, which can drive recruitment of cells expressing the CCR2 receptor including a subset of central memory CD4 T cells. Supporting a role for the CCL2/CCR2 axis in rapid reservoir formation, we find 1) treatment of humanized mice with anti-CCL2 antibodies during HIV infection decreases reservoir seeding and 2) CCR2/5+ cells from the blood of HIV-infected individuals on long term ART contain significantly more provirus than CCR2/5-negative memory or naïve cells. Together, these studies support a model where the host’s innate inflammatory CCL2 response to HIV infection recruits CCR2/5+ central memory CD4 T cells to zones of virus-associated inflammation likely contributing to rapid formation of the latent HIV reservoir.GRAPHICAL ABSTRACTWhy is the latent HIV reservoir established so early following infection? An innate immune response occurs during acute infection that establishes a “zone of inflammation” (step 1). The CCL2 chemokine is produced in part through IFI16 sensing of HIV DNA in abortively infected cells. CCL2 promotes rapid recruitment of CCR2/5+ memory CD4 T cells (step 2). Many of these cells become productively infected (step 3) and a fraction become latently infected (step 4). Thus, HIV hijacks the host inflammatory response to rapidly establish the latent reservoir. In support of this model, we find HIV reservoir reduction in humanized mice treated with anti-CCL2 antibodies during early infection. Further, we find that CCR2/5+ CD4 T cells harbor a substantial fraction of detectable proviruses in the blood of HIV-infected individuals on long-term suppressive ART.Abstract Figure
Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation
Authors: Velasco Cassandra , Dunn Christopher , Sturdy Cassandra , Izda Vladislav , Martin Jake , Rivas Alexander , McNaughton Jeffrey , Jeffries Matlock A. 
Published: February 2021

AbstractObjectiveAdult cartilage has limited repair capacity. MRL/MpJ mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and nonhealer mice and to evaluate microbiome transplantation as a novel regenerative therapy.MethodsWe transplanted C57BL/6J mice with MRL/MpJ cecal contents in mice at weaning and as adults (n=57) and measured earhole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n=25) and B6-transplanted MRL (n=20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n=58), cecal microbiomes were profiled by 16S sequencing and compared to earhole closure rates. Microbial metagenomes were imputed using PICRUSt.ResultsTransplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved earhole closure rates. Transplantation prior to ear punch was associated with the greatest earhole closure. Offspring of transplanted mice healed better than controls. Several microbiome clades were correlated with healing, including Firmicutes, Lactobacillales, and Verrucomicrobia. Gram-negative organisms were reduced. Females of all groups tended to heal better than males, female microbiota resembled MRL mice.ConclusionIn this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to nonhealer mice via microbiome transplantation. We identified several microbiome clades associated with healing. Future studies should evaluate the mechanisms underlying these findings and confirm our results in murine OA.
Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen
Authors: Bitar Ahmad Naoras , Zawiah Mohammed , Al-Ashwal Fahmi Y. , Kubas Mohammed , Saeed Ramzi Mukred , Abduljabbar Rami , Jaber Ammar Ali Saleh , Sulaiman Syed Azhar Syed , Khan Amer Hayat 
Published: February 2021

BackgroundSince the beginning of the COVID-19 outbreak, many pharmaceutical companies were racing to develop a safe and effective COVID-19 vaccine. Simultaneously, rumors and misinformation about COVID-19 were and still widely spreading. Therefore, this study aimed to investigate the prevalence of COVID-19 misinformation among the Yemeni population and its association with vaccine acceptance and perceptions.MethodsA cross-sectional online survey was conducted in four major cities in Yemen. The constructed questionnaire consisted of four main sections (sociodemographic data, misinformation, perceptions (perceived susceptibility, severity and worry), and vaccination acceptance evaluation). Subject recruitment and data collection were conducted online utilizing social websites and using the snowball sampling technique. Descriptive and inferential analyses were performed using SPSS version 27.ResultsThe total number of respondents was 484. Over 60% of them were male and had a university education, more than half had less than 100$ monthly income and were Khat chewers, while only 18% were smokers. Misinformation prevalence ranged from 8.9% to 38.9%, depending on the statement being asked. Men, university education, higher income, employment, and living in urban areas were associated with a lower misinformation level (p<0.05). Statistically significant association (p<0.05) between university education, living in urban areas, and being employed with perceived susceptibility were observed. The acceptance rate was 61.2% for free vaccines, but it decreased to 43% if they had to purchase it. Females, respondents with lower monthly income, and those who believed that pharmaceutical companies made the virus for financial gains were more likely to reject the vaccination (p<0.05).ConclusionThe study revealed that the acceptance rate to take a vaccine was suboptimal and significantly affected by gender, misinformation, cost, and income. Furthermore, being female, Nonuniversity educated, low-income, and living in rural areas were associated with higher susceptibility to misinformation about COVID-19. These findings show a clear link between misinformation susceptibility and willingness to vaccinate. Focused awareness campaigns to decrease misinformation and emphasize the vaccination’s safety and efficacy might be fundamental before initiating any mass vaccination in Yemen.
A systematic analysis of metabolic pathways in the human gut microbiota
Authors: Andreu Victòria Pascal , Augustijn Hannah E. , Chen Lianmin , Zhernakova Alexandra , Fu Jingyuan , Fischbach Michael A. , Dodd Dylan , Medema Marnix H. 
Published: February 2021

AbstractThe gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here, we systematically profile primary metabolic genes from the gut microbiome, identifying 19,885 gene clusters in 4,240 high-quality microbial genomes. We find marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 subjects from a Dutch population-based cohort shows that the level of 14 microbiome-derived metabolites in plasma is almost completely uncorrelated with the metagenomic abundance of the corresponding biosynthetic genes, revealing a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
Decoupling the bridge helix of Cas12a results in a reduced trimming activity and impaired conformational transitions
Authors: Wörle Elisabeth , Jakob Leonhard , Schmidbauer Andreas , Zinner Gabriel , Grohmann Dina 
Published: February 2021

AbstractThe widespread and versatile prokaryotic CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR-Cas system was added to the Cas enzymes repertoire employed for gene editing purposes. Cas12a is a bilobal enzyme composed of the REC and Nuc lobe connected by a central structural element, the so-called bridge helix (BH). We generated BH mutants and integrated biochemical and single-molecule FRET (smFRET) studies to elucidate the role of the BH for the enzymatic activity and conformational flexibility ofFrancisella novicidaCas12a. We demonstrate that the BH impacts the trimming activity of Cas12a resulting in Cas12a variants with improved cleavage accuracy. Single-molecule FRET measurements reveal the hitherto unknown open and closed state of apo Cas12a. BH mutants preferentially adopt the open state. Transition to the closed state of the Cas12a-crRNA complex is inefficient in BH mutants but the semi-closed state of the ternary complex can be adopted even if the BH is deleted in its entirety. Taken together, these insights reveal that the BH is a structural element that influences the catalytic activity and impacts conformational transitions of FnCas12a.
Screening of different cytotoxicity methods for the assessment of ENDS toxicity relative tobacco cigarettes
Authors: Caruso Massimo , Emma Rosalia , Rust Sonja , Distefano Alfio , Carota Giuseppe , Pulvirenti Roberta , Polosa Riccardo , Volti Giovanni Li 
Published: February 2021

AbstractElectronic Nicotine Delivery Systems (ENDS), i.e., electronic cigarettes (e-cigs) and Tobacco Heating Products (THPs), are rapidly growing in popularity. The marketing of these products is regulated by specific rules in the European Union and in the US, which permit their legal sales. Nonetheless, comprehensive quality and safety requirements for regulatory purposes are still under development. Cytotoxicity studies are an important initial step in appraising the potential toxicity of ENDS. The aim of the present study was to screen a battery of different in vitro cytotoxicity methods for the assessment of toxicity induced by ENDS. We evaluated different cytotoxicity assays, including neutral red uptake (NRU), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), Annexin V apoptosis, High Content Screening (HCS) assays and Real Time Cell Analysis (RTCA), to compare two e-cigs (Vype ePen 3 and Vype eStick Maxx) and two THPs (IQOS and GLO™) with the 1R6F reference tobacco cigarette. Human bronchial epithelial cells (H292) were exposed to 1R6F smoke (5 puffs by HCI regime), ePen vapor (10 puffs by modified HCI regime), eStick vapor (25 puffs by CRM81 regime), IQOS vapor (7 puffs by HCI regime) and GLO vapor (8 puffs by HCI regime) at air-liquid interface. All tests showed reduced cell viability following 1R6F smoke exposure and slight or no reduction with ENDS at 24 hours compared to controls. In addition, Annexin V and RTCA exhibited a further significant reduction in cell viability following 1R6F exposure compared with other assays. Furthermore, Annexin V allowed to discriminate viable cells from those in early/late apoptosis. Finally, RTCA and HCS being time-resolved analyses allowed also to determine the kinetic dependency parameter for toxicity of smoke/vapor chemicals on cell viability. In conclusion, NRU assay may be considered a suitable test, especially when combined with a time-resolved test, for assessing the kinetic of cytotoxicity induced by these products.
Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells
Authors: Ma Huabin , Zhu Zhoujie , Lin Huaipeng , Wang Shanshan , Zhang Peipei , Li Yanguo , Li Long , Wang Jinling , Zhao Yufen , Han Jiahuai 
Published: February 2021

AbstractSARS-Cov-2 infected cells fused with the ACE2-positive neighboring cells forming syncytia. However, the effect of syncytia in disease development is largely unknown. We established anin vitrocell-cell fusion system and used it to mimic the fusion of SARS-CoV-2 infected cells with ACE2-expressing cells to form syncytia. We found that Caspase-9 was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9, but it triggered GSDME-dependent pyroptosis rather than apoptosis. What is more, single cell RNA-sequencing data showed that both ACE2 and GSDME were expression in alveolar type 2 cells in human lung. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host cells and ACE2-positive cells, which indicated that lytic death of syncytia may contribute to the excessive inflammatory responses in severe COVID-19 patients.
Systems biology analysis identifies TCF7L1 as a key regulator of metastasis in Ewing sarcoma
Authors: Cidre-Aranaz Florencia , Li Jing , Hölting Tilman L. B. , Orth Martin F. , Imle Roland , Kutschmann Stefanie , Ammirati Giulia , Ceranski Katharina , Carreño-Gonzalez Martha Julia , Kasan Merve , Marchetto Aruna , Funk Cornelius M. , Bestvater Felix , Bersini Simone , Arrigoni Chiara , Moretti Matteo , Romero-Pérez Laura , Banito Ana , Ohmura Shunya , Musa Julian , Kirchner Thomas , Knott Maximilian M. L. , Grünewald Thomas G. P. 
Published: February 2021

ABSTRACTIdentification of cancer stemness genes is crucial to understanding the underlying biology of therapy resistance, relapse, and metastasis. Ewing sarcoma (EwS) is the second most common bone tumor in children and adolescents. It is a highly aggressive cancer associated with a dismal survival rate (<30%) for patients with metastatic disease at diagnosis (∼25% of cases). Hence, deciphering the underlying mechanisms of metastasis is imperative. EwS tumors are characterized by a remarkably ‘silent’ genome with a single driver mutation generating an oncogenic fusion transcription factor (EWSR1-ETS). Thus, EwS constitutes an ideal model to study how perturbation of a transcriptional network by a dominant oncogene can mediate metastasis, even though canonical metastasis-associated genes are not mutated.Here, through the implementation of an integrative systems biology approach, we identified transcription factor 7 like 1 (TCF7L1, aliasTCF3) as a prognostically-relevant andEWSR1-ETSsuppressed determinant of metastasis in EwS. We demonstrated that conditionalTCF7L1re-expression significantly reduces EwS single-cell migration, invasion and anchorage-independent growth in 3D assaysin vitro, and tumorigenesisin vivomediated by its DNA binding domain. In primary EwS tumors as well as in functional orthotopicin vivomodels, lowTCF7L1expression was associated with pro-metastatic gene signatures and a much higher migratory and metastatic capacity of EwS cells, which correlated with poor outcome of EwS patients.Collectively, our findings establish TCF7L1 as a major regulator of metastasis in EwS, which may be utilized as a prognostic biomarker and open inroads to future therapeutic intervention.
Mechanically Sensitive HSF1 is a Key Regulator of Left-Right Symmetry Breaking in Zebrafish Embryos
Authors: Du Jing , Li Shu-Kai , Guan Liu-Yuan , Guo Zheng , Yin Jiang-Fan , Gao Li , Kawanishi Toru , Shimada Atsuko , Zhang Qiu-Ping , Zheng Li-Sha , Liu Yi-Yao , Feng Xi-Qiao , Chen Dong-Yan , Takeda Hiroyuki , Fan Yu-Bo 
Published: February 2021

AbstractThe left-right symmetry breaking of vertebrate embryos requires fluid flow (called nodal flow in zebrafish). However, the molecular mechanisms that mediate the asymmetric gene expression regulation under nodal flow remain elusive. In this paper, we report that heat shock factor 1 (HSF1) is asymmetrically activated in the Kuppfer’s vesicle at the early stage of zebrafish embryos in the presence of nodal flow. Deficiency in HSF1 expression caused a significantsitus inversusand disrupted gene expression asymmetry of nodal signaling proteins in zebrafish embryos. Further studies demonstrated that HSF1 could be immediately activated by fluid shear stress. The mechanical sensation ability of HSF1 is conserved in a variety of mechanical stimuli in different cell types. Moreover, cilia and the Ca2+-Akt signaling axis are essential for the activation of HSF1 under mechanical stressin vitroandin vivo. Considering the conserved expression of HSF1 in organisms, these findings unveil a fundamental mechanism of gene expression regulation triggered by mechanical clues during embryonic development and other physiological and pathological transformations.
Dissociable oscillatory networks support gain and loss processing in human orbitofrontal cortex
Authors: Saez Ignacio , Lin Jack , Chang Edward , Parvizi Josef , Knight Robert T. , Hsu Ming 
Published: February 2021

AbstractHuman neuroimaging and animal studies have linked neural activity in orbitofrontal cortex (OFC) to valuation of positive and negative outcomes. Additional evidence shows that neural oscillations, representing the coordinated activity of neuronal ensembles, support information processing in both animal and human prefrontal regions. However, the role of OFC neural oscillations in reward-processing in humans remains unknown, partly due to the difficulty of recording oscillatory neural activity from deep brain regions. Here, we examined the role of OFC neural oscillations (<30Hz) in reward processing by combining intracranial OFC recordings with a gambling task in which patients made economic decisions under uncertainty. Our results show that power in different oscillatory bands are associated with distinct components of reward evaluation. Specifically, we observed a double dissociation, with a selective theta band oscillation increase in response to monetary gains and a beta band increase in response to losses. These effects were interleaved across OFC in overlapping networks and were accompanied by increases in oscillatory coherence between OFC electrode sites in theta and beta band during gain and loss processing, respectively. These results provide evidence that gain and loss processing in human OFC are supported by distinct low-frequency oscillations in networks, and provide evidence that participating neuronal ensembles are organized functionally through oscillatory coherence, rather than local anatomical segregation.
Can we fish on stocks that need rebuilding? Illustrating the trade-offs between stock conservation and fisheries considerations
Authors: Trijoulet Vanessa , Berg Casper W. , Sparrevohn Claus R. , Nielsen Anders , Pastoors Martin A. , Mosegaard Henrik 
Published: February 2021

AbstractIn the Northeast Atlantic, advice for many fish stocks follows the ICES MSY approach, where a zero catch will be recommended if the stock is below its limit reference point,Blim, and cannot rebuild in the short-term. How-ever, zero catch advice are rarely implemented by managers. This study used medium-term stochastic forecasts with harvest control rules (HCRs) to investigate the consequences of allowing reduced fishing belowBlim. We applied the method to western Baltic herring and North Sea cod, two contrasting species currently estimated belowBlim. We show that the minimum rebuilding probability of 95% required by the MSY approach could be impossible to reach in the short-to medium-term. When this is the case, a lower probability may need to be considered instead in the short-term. Recruitment is the largest source of uncertainty in stock response to management, and can exceed differences between HCRs. Reference points should be estimated in accordance with current recruitment levels if they are to be used for short-term advice or as realistic rebuilding targets. For both stocks, it is possible to keep fishing at reduced levels for similar cumulative catch, SSB and risk on the stock in the medium-term compared to no catch belowBlim. Medium-term trade-offs between stock conservation and fisheries considerations may be needed when fishery closure cannot be implemented in practice.
Metabolomics of aging in primary fibroblasts from small and large breed dogs
Authors: Brookes Paul S. , Jimenez Ana G. 
Published: February 2021

AbstractAmong several animal groups (eutherian mammals, birds, reptiles) lifespan positively correlates with body mass over several orders of magnitude. Contradicting this pattern are domesticated dogs, with small dog breeds exhibiting significantly longer lifespans than large dog breeds. The underlying mechanisms of differing aging rates across body masses are unclear, but it is generally agreed that metabolism is a significant regulator of the aging process. Herein, we performed a targeted metabolomics analysis on primary fibroblasts isolated from small and large breed young and old dogs. Regardless of size, older dogs exhibited lower glutathione and ATP, consistent with a role for oxidative stress and bioenergetic decline in aging. Furthermore, several size-specific metabolic patterns were observed with aging, including: (i) An apparent defect in the lower half of glycolysis in large old dogs at the level of pyruvate kinase. (ii) Increased glutamine anaplerosis into the TCA cycle in large old dogs. (iii) A potential defect in co-enzyme A biosynthesis in large old dogs. (iv) Low nucleotide levels in small young dogs that corrected with age. (v) An age dependent increase in carnitine in small dogs that was absent in large dogs. Overall, these data support the hypothesis that alterations in metabolism may underlie the different lifespans of small versus large breed dogs, and further work in this area may afford potential therapeutic strategies to improve the lifespan of large dogs.