bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxidative switch drives mitophagy defects in dopaminergicparkinmutant patient neurons
Authors: Schwartzentruber Aurelie , Boschian Camilla , Lopes Fernanda Martins , Myszczynska Monika A , New Elizabeth J , Beyrath Julien , Smeitink Jan , Ferraiuolo Laura , Mortiboys Heather 
Published: May 2020

AbstractBackground Mutations in parkin are the most common cause of early onset Parkinson’s disease. Parkin is an E3 ubiquitin ligase, functioning in mitophagy. Mitochondrial abnormalities are present in parkin mutant models. Patient derived neurons are a promising model in which to study pathogenic mechanisms and therapeutic targets. Here we generate induced neuronal progenitor cells from parkin mutant patient fibroblasts with a high dopaminergic neuron yield. We reveal changing mitochondrial phenotypes as neurons undergo a metabolic switch during differentiation. Methods Fibroblasts from 4 controls and 4 parkin mutant patients were transformed into induced neuronal progenitor cells and subsequently differentiated into dopaminergic neurons. Mitochondrial morphology, function and mitophagy were evaluated using live cell fluorescent imaging, cellular ATP and reactive oxygen species production quantification. Results Direct conversion of control and parkin mutant patient fibroblasts results in induced neuronal progenitor and their differentiation yields high percentage of dopaminergic neurons. We were able to observe changing mitochondrial phenotypes as neurons undergo a metabolic switch during differentiation. Our results show that when pre-neurons are glycolytic early in differentiation mitophagy is unimpaired by PRKN deficiency. However as neurons become oxidative phosphorylation dependent, mitophagy is severely impaired in the PRKN mutant patient neurons. These changes correlate with changes in mitochondrial function and morphology; resulting in lower neuron yield and altered neuronal morphology. Conclusions Induced neuronal progenitor cell conversion can produce a high yield of dopaminergic neurons. The mitochondrial phenotype, including mitophagy status, is highly dependent on the metabolic status of the cell. Only when neurons are oxidative phosphorylation reliant the extent of mitochondrial abnormalities are identified. These data provide insight into cell specific effects of PRKN mutations, in particular in relation to mitophagy dependent disease phenotypes and provide avenues for alternative therapeutic approaches.
Decision-making in a synthetic cell: the limits of biological computation
Authors: Greiss Ferdinand , Daube Shirley S. , Noireaux Vincent , Bar-Ziv Roy 
Published: May 2020

AbstractWe measured the dynamics of decision-making by a minimal bistable gene network integrated in a synthetic cell model, free of external perturbations. Reducing the number of gene copies from 105to about 10 per cell revealed a transition from deterministic and slow computation to a fuzzy and rapid regime dominated by singleprotein fluctuations. Fuzzy computation appeared at DNA and protein concentrations 100-fold lower than necessary in equilibrium, suggesting rate enhancement by co-expressional localization. Whereas the high-copy regime was characterized by a sharp transition, hysteresis and robust memory, the low-copy limit showed incipient strong fluctuations, switching between states, and a signature of cellular individuality across the decision-making point. Our work establishes synthetic cells operating rapidly at the single molecule level to integrate gene regulatory networks with metabolic pathways for sustained survival with low energetic cost.One Sentence SummaryDecision-making in a synthetic cell can be slow and precise or rapid and probabilistic by reducing the number of computing molecules by five decades down to single-molecule fluctuations.
Understanding the diversity of DNA methylation in Mycobacterium tuberculosis
Authors: Ndhlovu Victor , Kiran Anmol , Sloan Derek , Mandala Wilson , Nliwasa Marriot , Everett Dean B , Mwapasa Mphatso , Kontogianni Konstantina , Kamdolozi Mercy , Corbett Elizabeth L , Caws Maxine , Davies Gerry 
Published: May 2020

AbstractAlthoughMycobacterium tuberculosis (Mtb)strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity inMtbare not well understood but epigenetic variation is thought to contribute. At present the methylome ofMtbhas not been completely characterized. We completed methylomes of 18Mycobacterium tuberculosis(Mtb) clinical isolates from Malawi representing the largest number ofMtbgenomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date. We replicate and confirm four methylation disrupting mutations in lineages ofMtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in theMamBgene of Indo-oceanic lineage ofMtb. We also conducted a genomic and methylome comparison of the Malawian samples against a global sample. We confirm that methylation inMtbis lineage specific although some unresolved issues still remain.
The MNK1/2-eIF4E axis drives melanoma plasticity, progression, and resistance to immunotherapy
Authors: Huang Fan , Gonçalves Christophe , Bartish Margarita , Rémy-Sarrazin Joelle , Guo Qianyu , Emond Audrey , Yang William , Plourde Dany , Su Jie , Gimeno Marina Godoy , Zhan Yao , Attias Mikhael , Galán Alba , Rzymski Tomasz , Mazan Milena , Masiejczyk Magdalena , Faber Jacek , Khoury Elie , Benoit Alexandre , Gagnon Natascha , Dankort David , Piccirillo Ciriaco A. , Journe Fabrice , Ghanem Ghanem , Saragovi H. Uri , Sonenberg Nahum , Topisirovic Ivan , Miller Wilson H. , del Rincón Sonia V. 
Published: May 2020

AbstractMelanomas commonly undergo a phenotype switch, from a proliferative to an invasive state. Melanoma plasticity exhibited as phenotype switching contributes to immunotherapy resistance, however the mechanisms are not completely understood and thus therapeutically unexploited. Here, using a transgenic melanoma mouse model, we demonstrated a critical role of the MNK1/2-eIF4E axis in melanoma plasticity and resistance to immunotherapy. We showed that phospho-eIF4E deficient murine melanomas express high levels of melanocytic antigens, with similar results verified in patient melanomas. Mechanistically, we identified that phospho-eIF4E controls the translation of NGFR, a critical effector of phenotype switching. In patients with melanoma, the expression of MKNK1, the kinase for eIF4E, positively correlated with markers of immune exhaustion. Genetic ablation of phospho-eIF4E reprogrammed the immunosuppressive microenvironment, exemplified by lowered production of inflammatory factors and increased CD8+ T cell infiltrates. Blocking phospho-eIF4E, using MNK1/2 inhibitors, offers a new strategy to inhibit melanoma plasticity and improve the survival response to anti-PD-1 immunotherapy.
Epigenetic heterogeneity afterde novoassembly of native full-length Hepatitis B Virus genomes
Authors: Goldsmith Chloe , Cohen Damien , Dubois Anaëlle , Martinez Maria-Guadalupe , Petitjean Kilian , Corlu Anne , Testoni Barbara , Hernandez-Vargas Hector , Chemin Isabelle 
Published: May 2020

AbstractHepatitis B Virus (HBV) is a 3.2KB DNA virus that causes acute and chronic hepatitis. HBV infection is a world health problem, with 350 million chronically infected people at increased risk of developing liver disease and hepatocellular carcinoma (HCC). Methylation of HBV DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. With cas9 guided RNPs to specifically target the HBV genome, we enriched in HBV DNA from Primary Human Hepatocytes (PHH) infected with different HBV genotypes, as well as enriching in HBV from infected patient liver tissue; followed by sequencing with Oxford Nanopore Technologies MinION. Detection of 5mCpG by Nanopore sequencing was benchmarked with Bisulfite-quantitative Methyl Specific PCR (BS-qMSP). 5mCpG levels in HBV determined by BS-qMSP and Nanopore sequencing were highly correlated. Our Nanopore sequencing approach achieved a coverage of ∼2000x of HBV depending on infection efficacy, sufficient coverage to perform ade novoassembly and detect small fluctuations in HBV methylation, providing the firstde novoassembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences. Moreover, by capturing entire HBV genomes, we explored the epigenetic heterogeneity of HBV in infected patients and identified 4 epigenetically distinct clusters based on methylation profiles. This method is a novel approach that enables the enrichment of viral DNA in a mixture of nucleic acid material from different species and will serve as a valuable tool for infectious disease monitoring.
Comparison of Different Kits for SARS-CoV-2 RNA Extraction Marketed in Brazil
Authors: Eisen Ana Karolina Antunes , Demoliner Meriane , Gularte Juliana Schons , Hansen Alana Witt , Schallenberger Karoline , Mallmann Larissa , Hermann Bruna Saraiva , Heldt Fágner Henrique , de Almeida Paula Rodrigues , Fleck Juliane Deise , Spilki Fernando Rosado 
Published: May 2020

ABSTRACTDecember 2019 marked the begining of the greatest pandemic since Spanish Flu, the disease named Covid-19 that cause severe pneumonia. Until May 19, 2020 more than 4 million and 700 thousand cases were oficially notified with about 316 thousand deaths. Etiological agent of the disease was identified as being a new coronavirus,Severe acute respiratory syndrome-related coronavirus(SARS-CoV-2). In this study we compared four different manual methods for RNA isolation and purification for detection of SARS-CoV-2 through qRT-PCR, as well as the extraction quality itself through detection of RNAse P. Magnetic beads-based (MagMax™) and silica column-based (Biopur®) methods presented the better performances. Concerning to the mean delay in CT values when compared to MagMax™, TRIzol™, Biopur®and EasyExtract presented 0,39, 0,95 and 5,23 respectively. Agreement between positive and negative results of different methods when compared with the one with better performance MagMax™ was 94,44% for silica column-based method (Biopur®), 88,89% for phenol-chroloform-based method (TRIzol™) and 77,78% for EasyExtract. We aimed to evaluate how reliable each method is for diagnostic purposes and to propose alternatives when usual methods are not available. In this regard, magnectic beads and silica column-based methods are convenient and reliable choices and phenol-chloroform-based method could also be chosen as an alternative.
Spatiotemporal chloride dynamics in hypothalamic CRHPVNneurons
Authors: Lanz Aaron , Gordon Grant , Bains Jaideep 
Published: May 2020

AbstractChloride (Cl-) dynamics shape inhibitory neurotransmission in the brain. In the hypothalamus, GABA signalling onto corticotropin-releasing hormone (CRHPVN) neurons can switch from inhibitory to excitatory during stress. Although Cl-fluctuations mediate this stress-dependent shift in GABA signalling, the underlying Cl-dynamics are poorly understood. Here, using a novel optogenetic strategy to load intracellular Cl-using halorhodopsin, we demonstrate that KCC2 rapidly restores Cl-setpoints in CRHPVNneurons from naïve animals, but that this process is slowed following stress. Further, we report that somatic Cl-homeostasis remains intact after stress. Our results strongly support the idea that KCC2 functions primarily to maintain Cl-setpoints and that inhibitory synapses onto dendritic and somatic compartments of CRHPVNneurons are differentially regulated during stress.
A minimally disruptive method for measuring water potential in-planta using hydrogel nanoreporters
Authors: Jain Piyush , Liu Weizhen , Zhu Siyu , Melkonian Jeff , Pauli Duke , Riha Susan Jean , Gore Michael A. , Stroock Abraham D. 
Published: May 2020

AbstractLeaf water potential is a critical indicator of plant water status, integrating soil moisture status, plant physiology, and environmental conditions. There are few tools for measuring plant water status (water potential) in situ, presenting a critical barrier for the development of appropriate phenotyping (measurement) methods for crop development and modeling efforts aimed at understanding water transport in plants. Here, we present the development of an in situ, minimally-disruptive hydrogel nanoreporter (AquaDust) for measuring leaf water potential. The gel matrix responds to changes in water potential in its local environment by swelling; the distance between covalently linked dyes changes with the reconfiguration of the polymer, leading to changes in the emission spectrum via Fluorescence Resonance Energy Transfer (FRET). Upon infiltration into leaves, the nanoparticles localize within the apoplastic space in the mesophyll; they do not enter the cytoplast or the xylem. We characterize the physical basis for AquaDust’s response and demonstrate its function in intact maize (Zea maysL.) leaves as a reporter of leaf water potential. We use AquaDust to measure gradients of water potential along intact, actively transpiring leaves as a function of water status; the localized nature of the reporters allows us to define a hydraulic model that distinguishes resistances inside and outside the xylem. We also present field measurements with AquaDust through a full diurnal cycle to confirm the robustness of the technique and of our model. We conclude that AquaDust offers potential opportunities for high-throughput, field measurements and spatially resolved studies of water relations within plant tissues.
GermlineERBB3mutation in familial non-small cell lung carcinoma: expanding ErbB’s role in oncogenesis
Authors: McInerney-Leo Aideen M. , Chew Hui Yi , Inglis Po-Ling , Leo Paul J. , Joseph Shannon R. , Cooper Caroline L. , Okano Satomi , Hassall Tim , Anderson Lisa , Bowman Rayleen V. , Gattas Michael , Harris Jessica E. , Marshall Mhairi S. , Shaw Janet G. , Wheeler Lawrie , Yang Ian A. , Brown Matthew A. , Fong Kwun M. , Simpson Fiona , Duncan Emma L. 
Published: May 2020

ABSTRACTBackgroundLung cancer is the commonest cause of cancer deaths worldwide. Although strongly associated with smoking, predisposition to lung cancer is also heritable with multiple common risk variants identified. Rarely, dominantly inherited non-small-cell lung cancer (NSCLC) has been reported due to somatic mutations inEGFR/ErbB1andERBB2.MethodsGermline exome sequencing was performed in a multi-generation family with autosomal dominant NSCLC, including an affected child. Tumour samples were also sequenced. Full-length wild-type (wtErbB3) and mutant ERBB3 (mutErbB3) constructs were transfected into HeLa cells. Protein expression, stability, and sub-cellular localisation were assessed; and cellular proliferation, pAkt/Akt, and pERK levels were determined.ResultsA novel germline variant inERBB3(c.1946T>G: p.Iso649Arg), coding for receptor tyrosineprotein kinase erbB-3 (ErbB3), was identified, with appropriate segregation. There was no loss-of-heterozygosity in tumour samples. Both wtErbB3 and mutErbB3 were stably expressed. MutErbB3-transfected cells demonstrated an increased ratio of the 80kD form (which enhances proliferation) compared to the full-length (180kD) form. MutErbB3 and wtErbB3 had similar punctate cytoplasmic localisation pre- and post-EGF stimulation; however, EGFR levels decreased faster post-stimulation in mutErbB3-transfected cells, suggesting more rapid processing of the mutErbB3/EGFR heterodimer. Cellular proliferation was increased in mutErbB3-transfected cells compared to wtErbB3 transfection. MutErbB3-transfected cells also showed decreased pAkt/tAkt ratios and increased pERK/tERK 30 minutes post-stimulation compared to wtErbB3 transfection, demonstrating altered signalling pathway activation by mutErbB3. Cumulatively, these results support this mutation as tumorogenic.ConclusionsThis is the first reported family with a germlineERBB3mutation causing heritable NSCLC, furthering understanding of the ErbB family pathway in oncogenesis.
Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding
Authors: Yperman Klaas , Papageorgiou Anna C. , Merceron Romain , De Munck Steven , Bloch Yehudi , Eeckhout Dominique , Tack Pieter , Evangelidis Thomas , Van Leene Jelle , Vincze Laszlo , Vandenabeele Peter , Potocký Martin , De Jaeger Geert , Savvides Savvas N. , Tripsianes Konstantinos , Pleskot Roman , Van Damme Daniel 
Published: May 2020

AbstractClathrin-mediated endocytosis (CME) is the gatekeeper of the plasma membrane. In contrast to animals and yeasts, CME in plants depends on the TPLATE complex (TPC), an evolutionary ancient adaptor complex. The mechanistic contribution of the individual TPC subunits to plant CME remains however elusive. In this study, we used a multidisciplinary approach to elucidate the structural and functional roles of the evolutionary conserved N-terminal Eps15 homology (EH) domains of the TPC subunit AtEH1/Pan1. By integrating high-resolution structural information obtained by X-ray crystallography and NMR spectroscopy with all-atom molecular dynamics simulations, we provide structural insight into the function of both EH domains. Whereas one EH domain binds negatively charged PI(4,5)P2lipids, unbiased peptidome profiling by mass-spectrometry revealed that the other EH domain interacts with the double N-terminal NPF motif of a novel TPC interactor, the integral membrane protein Secretory Carrier Membrane Protein 5 (SCAMP5). Furthermore, we show that AtEH/Pan1 proteins control the internalization of SCAMP5 via this double NPF peptide interaction motif. Collectively, our structural and functional studies reveal distinct but complementary roles of the EH domains of AtEH/Pan1 have in plant CME and connect the internalization of SCAMP5 to the TPLATE complex.
Phenological, Physiological and yield markers as efficient tools to identify drought tolerant rice genotypes in Eastern India
Authors: Sahoo Soumya Kumar , Dash Goutam Kumar , Guhey Arti , Baig Mirza Jaynul , Barik Madhusmita , Parida Selukash , Swain Padmini 
Published: May 2020

ABSTRACTRice production is severely threatened by drought stress in Eastern India. To develop drought tolerant varieties, selection of donors for breeding programme is crucial. Twenty one selected rice genotypes including both tolerant and sensitive to drought were grown under well-watered and drought stress conditions in dry seasons of two successive years of 2017 and 2018. Leaf water potential, relative water content displayed significant difference among the genotypes during vegetative screening. At reproductive stage drought screening, days to 50% flowering was delayed in all genotypes except N22 and Anjali (showed early flowering) however grain yield and other yield related traits decreased significantly compared to well watered condition. Correlation analysis of phenological and yield related traits with grain yield revealed that tiller numbers and panicle numbers are highly correlated with grain yield both under well-watered and water stress conditions and contributes maximum towards grain yield. The dendrogram grouped Mahamaya, Sahabhagidhan, Poornima, IBD 1, Hazaridhan, Samleshwari and Danteshwari into one cluster which performed better under water stress conditions and had grain yield more than 1.69 tha−1. Sahabhagidhan, Poornima, Vandana, and N22 displayed tolerance to drought both under vegetative and reproductive conditions which could be a good selection for the breeders to develop drought tolerant rice cultivars for eastern region of India.
drICE restrains DIAP2-mediated inflammatory signalling and intestinal inflammation
Authors: Kietz Christa , Pollari Vilma , Tuominen Ida-Emma , Ribeiro Paulo S , Meier Pascal , Meinander Annika 
Published: May 2020

AbstractTheDrosophilaIAP protein, DIAP2, is a key mediator of NF-κB signalling and is required for immune activation, both locally in the intestinal epithelia and during systemic, fat body-induced responses. We have found that transgenic expression of DIAP2 induces inflammation in the intestine, but not in the fat body, indicating a need for regulating DIAP2 in microbiotic environments. We describe theDrosophilacaspase drICE, a known interaction partner of DIAP2, as a regulator of DIAP2 and NF-κB signalling in the intestinal epithelium. drICE acts by cleaving, and interfering with DIAP2’s ability to ubiquitinate and, thereby, activate mediators of the NF-κB pathway. The drICE-cleaved form of DIAP2 is, moreover, unable to induce inflammation during basal conditions in the intestine. Interestingly, cleavage of DIAP2 does not interfere with pathogen-induced signalling, suggesting that drICE protects from immune responses induced by resident microbes. Accordingly, the negative regulatory effect of drICE is lost when rearing flies axenic. Hence, we show that drICE halts unwanted inflammatory signalling in the intestine by forming an inhibitory complex with DIAP2, interfering with the ability of DIAP2 to induce downstream signalling and NF-κB target gene activation.
Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain
Authors: Iftimie Simona , López-Azcona Ana F. , Vicente-Miralles Manuel , Descarrega-Reina Ramon , Hernández-Aguilera Anna , Riu Francesc , Simó Josep M. , Garrido Pedro , Joven Jorge , Camps Jordi , Castro Antoni 
Published: May 2020

ABSTRACTSpain is one of the countries that has suffered the most from the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the strain that causes coronavirus disease 2019 (COVID-19). However, there is a lack of information on the characteristics of this disease in the Spanish population. The objective of this study has been to characterize our patients from an epidemiological point of view and to identify the risk factors associated with mortality in our geographical area. We performed a prospective, longitudinal study on 188 hospitalized cases of SARS-Cov-2 infection inHospital Universitari de Sant Joan, in Reus, Spain, admitted between 15thMarch 2020 and 30thApril 2020. We recorded demographic data, signs and symptoms and comorbidities. We also calculated the Charlson and McCabe indices. A total of 43 deaths occurred during the study period. Deceased patients were older than the survivors (77.7 ± 13.1vs. 62.8 ± 18.4 years;p< 0.001). Logistic regression analyses showed that fever, pneumonia, acute respiratory distress syndrome, diabetes mellitus and cancer were the variables that showed independent and statistically significant associations with mortality. The Charlson index was more efficient than the McCabe index in discriminating between deceased and survivors. This is one of the first studies to describe the factors associated with mortality in patients infected with SARS-CoV-2 in Spain, and one of the few in the Mediterranean area. We identified the main factors independently associated with mortality in our population. Further studies in are needed to complete and confirm our findings.