bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts
Authors: Moustaqil Mehdi , Ollivier Emma , Chiu Hsin-Ping , Van Tol Sarah , Rudolffi-Soto Paulina , Stevens Christian , Bhumkar Akshay , Hunter Dominic J.B. , Freiberg Alex , Jacques David , Lee Benhur , Sierecki Emma , Gambin Yann 
Published: June 2020

AbstractThe genome of SARS-CoV-2 (SARS2) encodes for two viral proteases (NSP3/ papain-like protease and NSP5/ 3C-like protease or major protease) that are responsible for cleaving viral polyproteins for successful replication. NSP3 and NSP5 of SARS-CoV (SARS1) are known interferon antagonists. Here, we examined whether the protease function of SARS2 NSP3 and NSP5 target proteins involved in the host innate immune response. We designed a fluorescent based cleavage assay to rapidly screen the protease activity of NSP3 and NSP5 on a library of 71 human innate immune proteins (HIIPs), covering most pathways involved in human innate immunity. By expressing each of these HIIPs with a genetically encoded fluorophore in a cell-free system and titrating in the recombinant protease domain of NSP3 or NSP5, we could readily detect cleavage of cognate HIIPs on SDS-page gels. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type- I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. Surprisingly, both NLRP12 and TAB1 have each two distinct cleavage sites. We demonstrate that in mice, the second cleavage site of NLRP12 is absent. We pushed this comparative alignment of IRF-3 and NLRP12 homologs and show that the lack or presence of cognate cleavage motifs in IRF-3 and NLRP12 could contribute to the presentation of disease in cats and tigers, for example. Our findings provide an explanatory framework for in-depth studies into the pathophysiology of COVID-19 and should facilitate the search or development of more effective animal models for severe COVID-19. Finally, we discovered that one particular species of bats, David’s Myotis, possesses the five cleavage sites found in humans for NLRP12, TAB1 and IRF3. These bats are endemic from the Hubei province in China and we discuss its potential role as reservoir for the evolution of SARS1 and SASR2.
Pharmacological CDK4/6 inhibition unravels a p53-induced secretory phenotype in senescent cells
Authors: Wang Boshi , Brandenburg Simone , Hernandez-Segura Alejandra , van Vliet Thijmen , Jongbloed Elisabeth M. , Wilting Saskia M , Ohtani Naoko , Jager Agnes , Demaria Marco 
Published: June 2020

AbstractCellular senescence is a state of stable growth arrest that acts as a tumor suppressive mechanism. Several anti-cancer interventions function partly by inducing malignant cells into senescence. However, because of systemic administration and lack of specificity, anti-cancer treatments are associated with premature senescence of various non-malignant cells. Therapy-induced non-malignant senescent cells can have profound detrimental pro-tumorigenic and pro-disease functions via activation of a pro-inflammatory and NF-κB-mediated secretory phenotype (SASP). Inhibitors of the cyclin-dependent kinases 4/6 (CDK4/6i) has recently shown to have potent cytostatic effects with reduced toxicities. Here, we show that CDK4/6i lead non-malignant cells to a senescent state that lacks the pro-inflammatory and NF-κB-associated SASP. Interestingly, CDK4/6i-induced senescence overexpressed a number of genes encoding for secreted proteins, which we show being dependent on p53 transcriptional activity. CDK4/6i-induced p16+senescent cells with a p53-associated (PASP), but not NF-κB-associated (NASP), secretory phenotype do not exert detrimental and pro-tumorigenic functions, but still retain the capacity to induce paracrine senescence and undergo clearancein vivo.Our data suggest that that senescent cells with a PASP but without a NASP may be well-tolerated and may represent a less toxic outcome for cancer interventions.
Anesthetics fragment hippocampal network activity, alter spine dynamics and affect memory consolidation
Authors: Yang Wei , Chini Mattia , Pöpplau Jastyn A. , Formozov Andrey , Dieter Alexander , Piechocinski Patrick , Rais Cynthia , Morellini Fabio , Sporns Olaf , Hanganu-Opatz Ileana L. , Wiegert J. Simon 
Published: June 2020

ABSTRACTGeneral anesthesia is characterized by reversible loss of consciousness accompanied by transient amnesia. Yet, long-term memory impairment is an undesirable side-effect. How different types of general anesthetics (GAs) affect the hippocampus, a brain region central to memory formation and consolidation, is poorly understood. Using extracellular recordings, chronic 2-photon imaging and behavioral analysis, we monitor the effects of isoflurane (Iso), medetomidine/midazolam/fentanyl (MMF), and ketamine/xylazine (Keta/Xyl) on network activity and structural spine dynamics in the hippocampal CA1 area of adult mice. GAs robustly reduced spiking activity, decorrelated cellular ensembles, albeit with distinct activity signatures, and altered spine dynamics. CA1 network activity under all three anesthetics was different to natural sleep. Iso anesthesia most closely resembled unperturbed activity during wakefulness and sleep, and network alterations recovered more readily than with Keta/Xyl and MMF. Correspondingly, memory consolidation was impaired after exposure to Keta/Xyl and MMF, but not Iso. Thus, different anesthetics distinctly alter hippocampal network dynamics, synaptic connectivity, and memory consolidation, with implications for GA strategy appraisal in animal research and clinical settings.
Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos
Authors: Alanis-Lobato Gregorio , Zohren Jasmin , McCarthy Afshan , Fogarty Norah M.E. , Kubikova Nada , Hardman Emily , Greco Maria , Wells Dagan , Turner James M.A. , Niakan Kathy K. 
Published: June 2020

AbstractCRISPR-Cas9 genome editing is a promising technique for clinical applications, such as the correction of disease-associated alleles in somatic cells. The use of this approach has also been discussed in the context of heritable editing of the human germline. However, studies assessing gene correction in early human embryos report low efficiency of mutation repair, high rates of mosaicism and the possibility of unintended editing outcomes that may have pathologic consequences. We developed computational pipelines to assess single-cell genomics and transcriptomics datasets from OCT4 (POU5F1) CRISPR-Cas9-targeted and control human preimplantation embryos. This allowed us to evaluate on-target mutations that would be missed by more conventional genotyping techniques. We observed loss-of-heterozygosity in edited cells that spanned regions beyond thePOU5F1on-target locus, as well as segmental loss and gain of chromosome 6, on which thePOU5F1gene is located. Unintended genome editing outcomes were present in approximately 16% of the human embryo cells analysed and spanned 4 to 20kb. Our observations are consistent with recent findings indicating complexity at on-target sites following CRISPR-Cas9 genome editing. Our work underscores the importance of further basic research to assess the safety of genome editing techniques in human embryos, which will inform debates about the potential clinical use of this technology.
SARS-CoV-2 neutralizing human recombinant antibodies selected from pre-pandemic healthy donors binding at RBD-ACE2 interface
Authors: Bertoglio Federico , Meier Doris , Langreder Nora , Steinke Stephan , Rand Ulfert , Simonelli Luca , Heine Philip Alexander , Ballmann Rico , Schneider Kai-Thomas , Roth Kristian Daniel Ralph , Ruschig Maximilian , Riese Peggy , Eschke Kathrin , Kim Yeonsu , Schäckermann Dorina , Pedotti Mattia , Kuhn Philipp , Zock-Emmenthal Susanne , Wöhrle Johannes , Kilb Normann , Herz Tobias , Becker Marlies , Grasshoff Martina , Wenzel Esther Veronika , Russo Giulio , Kröger Andrea , Brunotte Linda , Ludwig Stephan , Fühner Viola , Krämer Stefan Daniel , Dübel Stefan , Varani Luca , Roth Günter , Čičin-Šain Luka , Schubert Maren , Hust Michael 
Published: June 2020

AbstractCOVID-19 is a severe acute respiratory disease caused by SARS-CoV-2, a novel betacoronavirus discovered in December 2019 and closely related to the SARS coronavirus (CoV). Both viruses use the human ACE2 receptor for cell entry, recognizing it with the Receptor Binding Domain (RBD) of the S1 subunit of the viral spike (S) protein. The S2 domain mediates viral fusion with the host cell membrane. Experience with SARS and MERS coronaviruses has shown that potent monoclonal neutralizing antibodies against the RBD can inhibit the interaction with the virus cellular receptor (ACE2 for SARS) and block the virus cell entry. Assuming that a similar strategy would be successful against SARS-CoV-2, we used phage display to select from the human naïve universal antibody gene libraries HAL9/10 anti-SARS-CoV-2 spike antibodies capable of inhibiting interaction with ACE2. 309 unique fully human antibodies against S1 were identified. 17 showed more than 75% inhibition of spike binding to cells expressing ACE2 in the scFv-Fc format, assessed by flow cytometry and several antibodies showed even an 50% inhibition at a molar ratio of the antibody to spike protein or RBD of 1:1. All 17 scFv-Fc were able to bind the isolated RBD, four of them with sub-nanomolar EC50. Furthermore, these scFv-Fc neutralized active SARS-CoV-2 virus infection of VeroE6 cells. In a final step, the antibodies neutralizing best as scFv-Fc were converted into the IgG format. The antibody STE73-2E9 showed neutralization of active SARS-CoV-2 with an IC50 0.43 nM and is binding to the ACE2-RBD interface. Universal libraries from healthy human donors offer the advantage that antibodies can be generated quickly and independent from the availability of material from recovered patients in a pandemic situation.
Dopaminergic Modulation of Working Memory and Cognitive Flexibility in a Zebrafish Model of Aging-Related Cognitive Decline
Authors: Cleal Madeleine , Fontana Barbara D. , Double Molly , Mezabrovschi Roxana , Parcell Leah , Redhead Edward , Parker Matthew O. 
Published: June 2020

AbstractHealthy aging is associated with a decline in memory and executive function, which have both been linked with aberrant dopaminergic signalling. We examined the relationship between cognitive performance and dopamine function of young and aging zebrafish (Danio rerio). We revealed age-related decreases in working memory and cognitive flexibility in the Free-Movement Pattern (FMP) Y-maze. An increase indrd5gene expression in aging adults coincided with a decrease in cognitive performance. Treatment with a D1/D5 receptor agonist (SKF-38393, 35 μM) 30 minutes prior to behavioural assessment resulted in improved working memory in aging zebrafish, but no effect in younger adults. However, an ‘overdosing’ effect caused by agonist treatment resulted in downregulation ofdatexpression in 6-month old, treated zebrafish. The translational relevance of these findings was tested in humans by analysing exploratory behaviour in young-adult, 18-35-year olds, and aged adults, 70+ year olds, in a virtual FMP Y-maze. Our findings revealed similar age-related decline in working memory. Thus, strongly supporting zebrafish as a translational model of aging and cognitive decline.
HYPERTRIGLICERIDEMIC WAIST, PHYSICAL ACTIVITY AND CARDIOVASCULAR RISK FACTORS IN SCHOOLCHILDREN
Authors: Guilherme Flávio Ricardo , dos Santos Stevan Ricardo , Fiorillo Rodrigo Garcia , Rinaldi Wilson 
Published: June 2020

AbstractThe present study aimed to analyze the prevalence of the Hypertriglyceridemic Waist (HTW) and its rates with levels of physical activity, nutritional status and lipid profile of students from public schools. A sample consisted of 448 schoolchildren between 10 and 18 years old, who are assessed by body mass, height, BMI (waist circumference), triglycerides, total cholesterol, HDL-C, LDL-C, non-HDL cholesterol, fasting blood glucose and weekly physical activity time. The survey results showed a high prevalence of the HTW phenotype in schoolchildren (n = 125; 27.9%). The group diagnosed with phenotype has higher body mass, BMI, total cholesterol, LDL-C and non-HDL cholesterol and a lower level of HDL-C about the group without a diagnosis of the phenotype. However, for fasting blood glucose measurements and time of physical activity, the groups are no different. An association analysis using logistic regression showed the HTW phenotype associated with sex, nutritional status, and total cholesterol, where boys presented 2.0 (95% CI 1.3 - 3.2); obese 6.2 (95% CI 2.7 - 17.2) and cholesterol levels above 150 mg / dL 3.5 (95% CI 2.1 - 5.7) times more likely to have the phenotype. In this way, the present research showed a high prevalence of HTW in schoolchildren from public schools, with boys, obese and schoolchildren with total cholesterol levels, the individuals most likely to have the phenotype. However, it is worth emphasizing the importance of monitoring these variables throughout the year in all courses, given the period of strong, biological, behavioral and psychological changes, as they can quickly change the values of the analyzed variables.
Sublethal concentrations of clothianidin affect honey bee colony behavior and interact with landscapes to affect colony growth
Authors: Meikle William G. , Adamczyk John J. , Weiss Milagra , Ross Janie , Werle Chris , Beren Eli 
Published: June 2020

AbstractHoney bee colonies were exposed to sublethal concentrations (5 and 20 ppb) of clothianidin in sugar syrup, while control colonies were fed syrup with no pesticide. In addition to standard colony assessments of adult bees and brood, hive weight and internal temperature were monitored on a continuous basis at all sites. Experiments were conducted twice in Arizona, in successive years at the same site, and once in Mississippi, to examine the concomitant effects of weather and landscape. Adult bee masses at the Arizona site were significantly affected by clothianidin concentration. Newly-emerged bee dry weights, measured only at the Arizona site, were significantly lower for colonies fed 5 ppb clothianidin compared to the other groups. CO2concentration, also only measured at the Arizona site, was higher in colonies fed 20 ppb clothianidin. Neither daily hive weight change nor colony thermoregulation were affected by clothianidin exposure. The Mississippi site had higher rainfall, more diverse land use, and a different temperature regime, and bee colonies there did not show any effects of clothianidin. These results suggest that bee colonies in more stressful environments, such as the Sonoran desert of southern Arizona, are affected more by clothianidin exposure than colonies at sites with higher rainfall and more forage. Clothianidin was also found to be, like imidacloprid, highly stable in honey in the hive environment at least over several months. These results also showed that CO2concentration within the hive is potentially valuable in measuring the effects of stressors on bee health.
No evidence for insecticide resistance in a homogenous population ofAedes albopictusin Mecklenburg County, North Carolina
Authors: Mundis Stephanie J. , Hamerlinck Gabriela , Stone Emily K. , Whiteman Ari , Delmelle Eric , Rapp Tyler , Dulin Michael , Ryan Sadie J. 
Published: June 2020

AbstractAedes albopictusis a cosmopolitan mosquito species capable of transmitting arboviral diseases such as dengue, chikungunya, and Zika. To control this and similar species, public and private entities often rely on pyrethroid insecticides. Insecticide resistance status and physiological traits, such as body size, may contribute to local patterns of abundance, which is important for planning vector control. In this study, we genetically screenedAe. albopictuscollected from June to August, 2017, in Mecklenburg County, North Carolina, for mutations conferring pyrethroid resistance, and examined spatiotemporal patterns of specimen size, as measured by wing length. We hypothesized that size variation would be associated with factors found to influence abundance in similar populations ofAe. albopictus, and could therefore serve as a proxy measure. The genetic screening results indicated that known pyrethroid resistance alleles in twokdrregions are not present in this population. We detected no significant associations between wing length and socioeconomic and landscape factors, but mosquitoes collected in June had significantly longer wing length than in July or August. The lack of resistance indicators suggest that this population has not developed insecticide resistance via voltage-gated sodium channel mutations. The greater wing lengths in June are likely driven by meteorological patterns, suggesting that short-term weather cues may modulate morphological characteristics that, in turn, affect local fecundity and virus transmission potential.
Biochemical and structural insights into the activation of PBP1b by the essential domain of FtsN
Authors: Boes Adrien , Kerff Frederic , Herman Raphael , Touze Thierry , Breukink Eefjan , Terrak Mohammed 
Published: June 2020

AbstractPeptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division PG synthesis localizes at mid-cell under the control of a multiprotein complex, the divisome. InEscherichia coli, septal PG synthesis and cell constriction rely on the accumulation of FtsN at the division site. The region L75 to Q93 of FtsN (EFtsN) was shown to be essential and sufficient for its functioningin vivobut the specific target and the molecular mechanism remained unknown. Here, we show thatEFtsN binds specifically to the major PG synthase PBP1b and is sufficient to stimulate its GTase activity. We also report the crystal structure of PBP1b in complex withEFtsN which provides structural insights into the mode of binding ofEFtsN at the junction between the GTase and UB2H domains of PBP1b. Interestingly, the mutations R141A/R397A of PBP1b, within theEFtsN binding pocket, reduce the activation of PBP1b by FtsN. This mutant was unable to rescue ΔponB-ponAtsstrain at nonpermissive temperature and induced a mild cell chaining phenotype and cell lysis. Altogether, the results show that PBP1b is a target ofEFtsN and suggest that binding of FtsN to PBP1b contributes to trigger septal PG synthesis and cell constriction.
Mis-annotated multi nucleotide variants in public cancer genomics datasets can lead to inaccurate mutation calls with significant implications
Authors: Srinivasan Sujaya , Kalinava Natallia , Aldana Rafael , Li Zhipan , van Hagen Sjoerd , Rodenburg Sander Y.A. , Wind-Rotolo Megan , Sasson Ariella S. , Tang Hao , Qian Xiaozhong , Kirov Stefan 
Published: June 2020

AbstractBackgroundNext generation sequencing is widely used in cancer to profile tumors and detect variants. Most somatic variant callers used in these pipelines identify variants at the lowest possible granularity – single nucleotide variants (SNVs). As a result, multiple adjacent SNVs are called individually instead of as a multi-nucleotide variant (MNV). The problem with this level of granularity is that the amino acid change from the individual SNVs within a codon could be different from the amino acid change based on the MNV that results from combining the SNVs. Most variant annotation tools do not account for this, leading to incorrect conclusions about the downstream effects of the variants.MethodHere, we used Variant Call Files (VCFs) from the TCGA Mutect2 caller, and developed a solution to merge SNVs to MNVs. Our custom script takes the phasing information from the SNV VCFs and based on a gene model, determines if SNVs are at the same codon and need to be merged into a MNV prior to variant annotation.ResultsWe analyzed 10,383 VCFs from TCGA and found 12,141 MNVs that were incorrectly annotated. Strikingly, the analysis of seven commonly mutated genes from 178 studies from cBioPortal revealed that MNVs were consistently missed in 20 of these studies, while they were correctly annotated in 15 more recent studies. The best and most common example of MNVs was found at the BRAF V600 locus, where several public datasets reported separate BRAF V600E and BRAF V600M variants, instead of a single merged V600K variant.ConclusionWhile some datasets merged MNVs correctly, many public datasets have not been corrected for this problem. As a best practice for variant calling, we recommend that MNVs be accounted for in NGS processing pipelines, thus improving analyses on the impact of somatic variants in cancer genomics.
JNK signalling regulates antioxidant responses in neurons
Authors: Ugbode Chris , Garnham Nathan , Fort-Aznar Laura , Evans Gareth , Chawla Sangeeta , Sweeney Sean T. 
Published: June 2020

AbstractReactive oxygen species (ROS) are generated during physiological bouts of synaptic activity and as a consequence of pathological conditions in the central nervous system. How neurons respond to and distinguish between ROS in these different contexts is currently unknown. In Drosophila mutants with enhanced JNK activity, lower levels of ROS are observed and these animals are resistant to both changes in ROS and changes in synapse morphology induced by oxidative stress. In wild type flies, disrupting JNK-AP-1 signalling perturbs redox homeostasis suggesting JNK activity positively regulates neuronal antioxidant defense. We validated this hypothesis in mammalian neurons, finding that JNK activity regulates the expression of the antioxidant geneSrxn-1, in a c-Jun dependent manner. We describe a conserved ‘adaptive’ role for neuronal JNK in the maintenance of redox homeostasis that is relevant to several neurodegenerative diseases.
Acute knockdown of extracellular matrix protein Tinagl1 disrupts heart laterality and pronephric cilia in zebrafish embryonic development
Authors: Neiswender Hannah , LeMosy Ellen K. 
Published: June 2020

AbstractA highly-conserved extracellular matrix protein, Tinagl1, modulates Wnt, integrin, TGF-β, and EGF-R signalingin vitro,but its significancein vivohas remained in doubt. To bypass possible genetic compensation by an ortholog encoded exclusively in mammalian genomes, we examine Tinagl1 function in zebrafish embryos. In this model,tinagl1mRNA is detected in the developing spinal cord and pronephros. Acute knockdown using either CRISPR/Cas9 somatic mutagenesis or splice-blocking morpholinos reveals left-right (LR) heart looping defects, pronephros dilatations, and ventral body curvature. This constellation of defects characteristically results from the loss of motile cilia function, and we confirm the presence of shortened and fewer cilia in the pronephric duct and in the Kupffer’s vesicle where LR asymmetry is established. A link to known Wnt3a/β-catenin signaling that activates the motile cilia transcriptional program is supported by manipulation of Wnt3a and β-catenin levels intinagl1knockdown embryos. In addition to ciliopathy-like defects, thetinagl1knockdown shows disorganization of longitudinal axon tracts in the spinal cord and defects in motor neuron outgrowth. Together, these results provide evidence that Tinagl1 is important in development, and that zebrafish is an ideal model in which to explore its relationships to cilia and secreted signaling molecules.