bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico analysis and molecular investigation of the nuclear shuttle protein-interacting kinase 1 (NIK1) in six Solanaceous species
Authors: Safaeizadeh Mehdi , Malpica Nachelli 
Published: July 2021

AbstractThe first layer of innate immunity in plants is initiated through the perception of microbe-associated molecular patterns (MAMPs) or damage-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs). MAMP/DAMP perception initiates downstream defense responses, a process which ultimately leads to pattern triggered immunity (PTI). In Arabidopsis, the nuclear shuttle protein-interacting kinase 1 (NIK1), among other PRRs, is one of the most important central components of PTI signaling and kinase signaling cascade, since it is involved in the plant antiviral response against geminiviruses. Despite the characterization of the structure and function of the NIK1 receptors made by some groups, studies related to NIK1 importance in the current gene-editing era are missing. By simple in silico analysis, in this study we investigated the NIK1 homologues from six Solanaceous plant species including: tomato (Solanum lycopersicum), potato (Solanum tuberosum), Solanum pennellii, eggplant (Solanum melongena), pepper (Capsicum annum), and Nicotiana benthamiana. The phylogenetic analyses of different NIK1 proteins from Arabidopsis and six Solanaceous plants revealed nine different clades. As expected, we found that these NIK1 orthologs have similar genomic structures suggesting a similar function. We could identify that SotubNIK1, SolyNIK1, SopenNIK1, CANIK1, NibenNIK1, SmeNIK1 have the highest sequence homology with AtNIK1. Additionally, the conserved protein kinase domain (PKD) that is present in NIK1 from Arabidopsis thaliana was bioinformatically analyzed and found in other species. As this highly conserved NIK1 region is present in several crops of economic importance, its potential is highlighted as a possible target site for gene editing, to develop crops tolerant to geminiviral infections.
Optimization of the TeraTox assay for preclinical teratogenicity assessment
Authors: Manuela Jaklin , David Zhang Jitao , Nicole Schäfer , Nicole Clemann , Paul Barrow , Erich Küng , Lisa Sach-Peltason , Claudia McGinnis , Marcel Leist , Stefan Kustermann 
Published: July 2021

AbstractCurrent animal-free methods to assess teratogenicity of drugs under development still deliver high numbers of false negatives, and more sensitive approaches of toxicity prediction are required. To address this issue, we characterized the TeraTox test, a newly developed multi-lineage differentiation assay for human teratogenicity prediction using 3D human induced pluripotent stem cells. TeraTox produces as primary output concentration-dependent data sets for each test compound on cytotoxicity and altered gene expression. These data are then fed into a prediction model based on an interpretable machine-learning approach. The final information obtained relates to the concentration-dependent human teratogenicity potential of drug candidates. We applied TeraTox to profile 33 approved pharmaceuticals and 12 proprietary drug candidates with known in vivo data. This way, it was possible to relate the test predictions to known human or animal toxicity. The TeraTox had an accuracy of 69% (specificity: 53%, sensitivity: 79%). It clearly performed better than two quantitative structure-activity relationship (QSAR) models and it had a higher sensitivity than the murine embryonic stem cell test (mEST) run in the same laboratory. By combining TeraTox and mEST data, the overall prediction accuracy was further improved. The knowledge on the pattern of altered gene expression may provide additional value in grouping toxicologically similar compounds and possibly deducing common modes of action. The assay will thus be a helpful additional tool in drug discovery, and the dataset provided here will be a valuable resource for the field of stem cell-based drug profiling.
A single-cell transcriptomic atlas characterizes liver non-parenchymal cells in healthy and diseased mice
Authors: Wang Zheng , Qian Jingyang , Lu Xiaoyan , Zhang Ping , Guo Rongfang , Lou He , Zhang Shuying , Yang Jihong , Fan Xiaohui 
Published: July 2021

ABSTRACTThe heterogeneity of liver non-parenchymal cells (NPCs) is essential for liver structure and function. However, the current understanding of liver NPCs, especially in different liver diseases, remains incompletely elucidated. Here, a single-cell transcriptome atlas of 171,814 NPCs from healthy and 5 typical liver disease mouse models, including alcoholic liver disease, nonalcoholic steatohepatitis (NASH), drug-induced liver injury, cholestatic, and ischemia-reperfusion liver injury is constructed. The inter- and intra-group heterogeneity of 12 types (and numerous subtypes) of NPCs involving endothelial cells, hepatic stellate cells (HSCs), neutrophils, T cells, and mononuclear phagocytes (MPs) are summarized. A protective subtype of neutrophils characterized by Chil3high is validated and found significantly increasing only in drug-induced and cholestatic liver injury models. Transcriptional regulatory network analysis reveals disease-specific transcriptional reprogramming. Metabolic activity analysis indicates that fibrosis is accompanied by increases in glycolysis and retinol metabolism in activated HSCs and MPs. Moreover, we found that cell-cell interactions between cholangiocytes and immune cells contribute more to cholestatic liver fibrosis compared with NASH, while HSCs are more important for NASH fibrosis. Our atlas, together with an interactive website provides a systematic view of highly heterogeneous NPCs and a valuable resource to better understand pathological mechanisms underlying liver diseases.
Defining the Immune Responses for SARS-CoV-2-Human Macrophage Interactions
Authors: Abdelmoaty Mai M. , Yeapuri Pravin , Machhi Jatin , Olson Katherine E. , Shahjin Farah , Zhou You , Jingjing Liang , Pandey Kabita , Acharya Arpan , Byrareddy Siddappa N. , Lee Mosley R. , Gendelman Howard E. 
Published: July 2021

AbstractHost innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end organ malfunctions. All follow an abortive viral infection. To elucidate SARS-CoV-2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the SARS-CoV-2 receptor, the angiotensin-converting enzyme 2, paralleled monocyte-macrophage differentiation it failed to affect productive viral infection. In contrast, simple macrophage viral exposure led to robust pro-inflammatory cytokine and chemokine expression but attenuated type I interferon (IFN) activity. Both paralleled dysregulation of innate immune signaling pathways specifically those linked to IFN. We conclude that the SARS-CoV-2-infected host mounts a robust innate immune response characterized by a pro-inflammatory storm heralding consequent end-organ tissue damage.
High-throughput functional analysis of CFTR and other apically localized channels in iPSC derived intestinal organoids
Authors: Xia Sunny , Bozóky Zoltán , Laselva Onofrio , Di Paola Michelle , Ahmadi Saumel , Jiang Jia Xin , Pitstick Amy , Jiang Chong , Rotin Daniela , Mayhew Christopher N. , Jones Nicola L. , Bear Christine E. 
Published: July 2021

AbstractInduced Pluripotent Stem Cells (iPSCs) can be differentiated into epithelial organoids that recapitulate the relevant context for CFTR and enable testing of therapies targeting Cystic Fibrosis (CF)-causing mutant proteins. However, to date, CF-iPSC-derived organoids have only been used to study pharmacological modulation of mutant CFTR channel activity and not the activity of other disease relevant membrane protein constituents. In the current work, we describe a high-throughput, fluorescence-based assay of CFTR channel activity in iPSC-derived intestinal organoids and describe how this method can be adapted to study other apical membrane proteins. In these proof-of-concept studies, we show how this fluorescence-based assay of apical membrane potential can be employed to study CFTR and ENaC channels and an electrogenic acid transporter in the same iPSC-derived intestinal tissue. This multiparameter phenotypic platform promises to expand CF therapy discovery to include strategies to target multiple determinants of epithelial fluid transport.
CAT, AGTR2, L-SIGN and DC-SIGN are potential receptors for the entry of SARS-CoV-2 into human cells
Authors: Guo Dongjie , Guo Ruifang , Li Zhaoyang , Zhang Yuyang , Zheng Wei , Huang Xiaoqiang , Aziz Tursunjan , Zhang Yang , Liu Lijun 
Published: July 2021

AbstractSince December 2019, the COVID-19 caused by SARS-CoV-2 has been widely spread all over the world. It is reported that SARS-CoV-2 infection affects a series of human tissues, including lung, gastrointestinal tract, kidney, etc. ACE2 has been identified as the primary receptor of the SARS-CoV-2 Spike (S) protein. The relatively low expression level of this known receptor in the lungs, which is the predominantly infected organ in COVID-19, indicates that there may be some other co-receptors or alternative receptors of SARS-CoV-2 to work in coordination with ACE2. Here, we identified twenty-one candidate receptors of SARS-CoV-2, including ACE2-interactor proteins and SARS-CoV receptors. Then we investigated the protein expression levels of these twenty-one candidate receptors in different human tissues and found that five of which CAT, MME, L-SIGN, DC-SIGN, and AGTR2 were specifically expressed in SARS-CoV-2 affected tissues. Next, we performed molecular simulations of the above five candidate receptors with SARS-CoV-2 S protein, and found that the binding affinities of CAT, AGTR2, L-SIGN and DC-SIGN to S protein were even higher than ACE2. Interestingly, we also observed that CAT and AGTR2 bound to S protein in different regions with ACE2 conformationally, suggesting that these two proteins are likely capable of the co-receptors of ACE2. Conclusively, we considered that CAT, AGTR2, L-SIGN and DC-SIGN were the potential receptors of SARS-CoV-2. Moreover, AGTR2 and DC-SIGN tend to be highly expressed in the lungs of smokers, which is consistent with clinical phenomena of COVID-19, and further confirmed our conclusion. Besides, we also predicted the binding hot spots for these putative protein-protein interactions, which would help develop drugs against SARS-CoV-2.
UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
Authors: Wallmeroth Damaris , Boehm Volker , Lackmann Jan-Wilm , Altmüller Janine , Dieterich Christoph , Gehring Niels H. 
Published: July 2021

AbstractThe paralogous human proteins UPF3A and UPF3B are involved in recognizing mRNAs targeted by nonsense-mediated mRNA decay (NMD). While UPF3B has been demonstrated to support NMD, contradicting reports describe UPF3A either as an NMD activator or inhibitor. Here, we present a comprehensive functional analysis of UPF3A and UPF3B in human cells using combinatory experimental approaches. Overexpression or knockout of UPF3A as well as knockout of UPF3B did not detectably change global NMD activity. In contrast, the co-depletion of UPF3A and UPF3B resulted in a marked NMD inhibition and a transcriptome-wide upregulation of NMD substrates, demonstrating a functional redundancy between both NMD factors. Although current models assume that UPF3 bridges NMD-activating exon-junction complexes (EJC) to the NMD factor UPF2, UPF3B exhibited only slightly impaired NMD activity in rescue experiments when UPF2 or EJC binding was impaired. Further rescue experiments revealed partially redundant functions of UPF3B domains in supporting NMD, involving both UPF2 and EJC interaction sites and the central region of UPF3. Collectively, UPF3A and UPF3B serve as fault-tolerant NMD activators in human cells.
Oncogenic RABL6A promotes NF1-associated MPNST progression in vivo
Authors: Kohlmeyer Jordan L , Kaemmer Courtney A , Lingo Joshua J , Leidinger Mariah R , Meyerholz David K , Tanas Munir R , Dodd Rebecca D , Quelle Dawn E 
Published: July 2021

AbstractBackgroundMalignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that display complex molecular and genetic alterations. Powerful tumor suppressors CDKN2A and TP53 are commonly disrupted in these lesions along with NF1, a gene that encodes a negative regulator of Ras. Many additional factors have been implicated in MPNST pathogenesis. A greater understanding of critical drivers of the disease is needed to guide more informed targeted therapies for patients. RABL6A is a newly identified driver of MPNST cell survival and proliferation whose in vivo role in the disease is unknown.MethodsUsing CRISPR-Cas9 targeting of Nf1+Cdkn2a or Nf1+Tp53 in the sciatic nerve to form de novo MPNSTs, we investigated the biological significance of RABL6A in MPNST development. Molecular evaluation of terminal tumors (western blot, qRT-PCR, immunohistochemistry) yielded several insights.ResultsMice lacking Rabl6 displayed slower tumor growth and extended survival relative to wildtype animals in both genetic contexts. YAP oncogenic activity was selectively downregulated in RABL6A-null, Nf1+Cdkn2a lesions but not in RABL6A-null, Nf1+Tp53 tumors. Regardless of genetic context, loss of RABL6A caused upregulation of the CDK inhibitor, p27 in tumors. Paradoxically, both models displayed elevated Myc protein expression and Ki67 staining in terminal tumors lacking RABL6A.ConclusionsThese findings demonstrate RABL6A is required for optimal tumor progression of NF1 mutant MPNSTs in vivo in both Cdkn2a and p53 inactivated settings. However, sustained RABL6A loss may provide selective pressure for molecular alterations, such as Myc upregulation, that ultimately promote an unwanted, hyper-proliferative tumor phenotype akin to drug resistant lesions.Importance of the StudyMPNSTs are aggressive, deadly, and challenging to treat tumors due to location around nerves and high mutational burden. Many factors implicated in MPNST genesis have yet to be fully tested for biological significance in disease formation. We establish a critical physiological role for a new oncoprotein, RABL6A, in promoting NF1-associated MPNST progression. We identify novel RABL6A-regulated pathways that likely contribute to tumor growth, specifically YAP and Myc signaling, and found that sustained RABL6A loss eventually yields more proliferative tumors. We liken RABL6A deficient tumors to those being treated with therapies targeting RABL6A effectors, such as CDKs. Therefore, those lesions should provide a powerful platform to uncover key mediators of drug resistance. Our data suggest oncogenic YAP and Myc could be such mediators of resistance. This study provides a novel system to examine one of the most pressing clinical challenges, drug resistant tumor growth and relapse, in cancer therapy.
Immunogenicity of low dose prime-boost vaccination of mRNA vaccine CV07050101 in non-human primates
Authors: van Doremalen Neeltje , Fischer Robert J. , Schulz Jonathan E. , Holbrook Myndi G. , Smith Brian J. , Lovaglio Jamie , Petsch Benjamin , Munster Vincent J. 
Published: July 2021

AbstractMany different vaccine candidates against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of COVID-19, are currently approved and under development. Vaccine platforms vary from mRNA vaccines to viral-vectored vaccines, and several candidates have been shown to produce humoral and cellular responses in small animal models, non-human primates and human volunteers. In this study, six non-human primates received a prime-boost intramuscular vaccination with 4 µg of mRNA vaccine candidate CV07050101, which encodes a pre-fusion stabilized spike (S) protein of SARS-CoV-2. Boost vaccination was performed 28 days post prime vaccination. As a control, six animals were similarly injected with PBS. Humoral and cellular immune responses were investigated at time of vaccination, and two weeks afterwards. No antibodies could be detected two and four weeks after prime vaccination. Two weeks after boost vaccination, binding but no neutralizing antibodies were detected in 4 out of 6 non-human primates. SARS-CoV-2 S protein specific T cell responses were detected in these 4 animals. In conclusion, prime-boost vaccination with 4 µg of vaccine candidate CV07050101 resulted in limited immune responses in 4 out of 6 non-human primates.
The E. coli helicase does not use ATP during replication
Authors: Spenkelink Lisanne M. , Spinks Richard R. , Jergic Slobodan , Lewis Jacob S. , Dixon Nicholas E. , van Oijen Antoine M. 
Published: July 2021

AbstractThe replisome is responsible for replication of DNA in all domains of life, with several of its individual enzyme components relying on hydrolysis of nucleoside triphosphates to provide energy for replisome function. Half a century of biochemical studies have demonstrated a dependence on ATP as an energy source for helicases to unwind duplex DNA during replication. Through single-molecule visualization of DNA replication by the Escherichia coli replisome, we demonstrate that the DnaB helicase does not rely on hydrolysis of ATP (or any ribo-NTPs) in the context of the elongating replisome. We establish that nucleotide incorporation by the leading-strand polymerase is the main motor driving the replication process.One Sentence SummaryPolymerases provide the energy for helicase-mediated DNA unwinding during E. coli DNA replication.
Performance and characterization of the FinEstBeAMS beamline at the MAX IV Laboratory
Authors: Chernenko Kirill , Kivimäki Antti , Pärna Rainer , Wang Weimin , Sankari Rami , Leandersson Mats , Tarawneh Hamed , Pankratov Vladimir , Kook Mati , Kukk Edwin , Reisberg Liis , Urpelainen Samuli , Käämbre Tanel , Siewert Frank , Gwalt Grzegorz , Sokolov Andrey , Lemke Stephanie , Alimov Svyatoslav , Knedel Jeniffa , Kutz Oliver , Seliger Tino , Valden Mika , Hirsimäki Mika , Kirm Marco , Huttula Marko 
Published: July 2021

FinEstBeAMS (Finnish–Estonian Beamline for Atmospheric and Materials Sciences) is a multidisciplinary beamline constructed at the 1.5 GeV storage ring of the MAX IV synchrotron facility in Lund, Sweden. The beamline covers an extremely wide photon energy range, 4.5–1300 eV, by utilizing a single elliptically polarizing undulator as a radiation source and a single grazing-incidence plane grating monochromator to disperse the radiation. At photon energies below 70 eV the beamline operation relies on the use of optical and thin-film filters to remove higher-order components from the monochromated radiation. This paper discusses the performance of the beamline, examining such characteristics as the quality of the gratings, photon energy calibration, photon energy resolution, available photon flux, polarization quality and focal spot size.
Perception of street vendors and their effect on urban settings in Portobello Road, London
Authors: Torky Esraa , Heath Tim 
Published: July 2021

PurposeStreet vendors create a vital urban street and a significant and important part of our urban areas are streets, they cater to our leisure, social and functional needs. There are many debates concerning street vendors; on one hand, there are those who argue against them because they believe they create problems and should be abolished, and on the other hand, there are arguments that defend them and believe that they are vital to the street life.Design/methodology/approachThis paper aims to identify people's perception and acceptance of street vending and its effect on experience of the street. Observations and user interviews were undertaken in Portobello and Golborne Road to explore the influence of street vendors on urban settings and analyze their vending patterns and their relationship with urban users.FindingsFindings state that street vending takes up a large part in the liveliness and attractiveness of the market in London. People tend to accept street vendors because they have many benefits for vitality and liveliness of the urban environment; however, they sometimes cause problems with ease of mobility in the area for pedestrians and the public in general.Originality/valueStreet vendors create a vital urban street and provide affordable goods. There are many debates concerning street vendors; on the one hand, there are those who argue against them because they believe they create problems and should be abolished, and on the other hand, there are arguments that defend them and believe that they are vital to the street life. It was important to study street vending in detail in order to explore this unique and important activity that takes place in almost all cities of the world. The case study chosen was quite unique and street vending taking place in Portobello Road and London in general is mostly formal street vending, which wasn't studied in detail previously.
When leaders forgive: encouraging radical innovation in more altruistic organizations
Authors: Mallén-Broch Francisco Fermín , Domínguez-Escrig Emilio 
Published: July 2021

PurposeThere is general agreement on the importance of innovation to improve business performance and competitiveness. In recent years, many studies have sought to unravel what conditions are conducive to innovation. Following this trend, the present study seeks to broaden the understanding of the antecedents of radical innovation. To this end, and drawing on positive organizational psychology, the study focuses on the role of leaders and the importance of improving working conditions within companies, favoring innovation in more respectful and prosocial organizations.Design/methodology/approachThe study provides, through structural equations, empirical evidence of the relationship between leader's forgiveness and radical innovation, using altruism as an explanatory variable. The study was conducted in a population of 11,594 Spanish companies. A sample frame of 554 questionnaires from 277 different firms was obtained.FindingsResults confirm the hypotheses proposed in the model. Forgiveness, analyzed as a leader behavior, promotes altruism within companies and, in turn, radical innovation.Originality/valueThis is one of the few empirical studies that analyzes the consequences of leader's forgiveness in the organizational context.