bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2
Authors: Limonta Daniel , Dyna-Dagman Lovely , Branton William , Makio Tadashi , Wozniak Richard W. , Power Christopher , Hobman Tom C. 
Published: November 2020

ABSTRACTIn the present report, we describe two small molecules with broad-spectrum antiviral activity. These drugs block formation of the nodosome. The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. A drug that targets NOD2 was shown to have potent broad-spectrum antiviral activity against other flaviviruses, alphaviruses and SARS-CoV-2, the causative agent of COVID-19. Another drug that inhibits the receptor-interacting serine/threonine-protein kinase 2 (RIPK2) which functions downstream of NOD2, also decreased replication of these pathogenic RNA viruses. The broad-spectrum action of nodosome targeting drugs is mediated, at least in part, by enhancement of the interferon response. Together, these results suggest that further preclinical investigation of nodosome inhibitors as potential broad-spectrum antivirals is warranted.
Finger Sweat Analysis Enables Short Interval Metabolic Biomonitoring in Humans
Authors: Brunmair Julia , Niederstaetter Laura , Neuditschko Benjamin , Bileck Andrea , Slany Astrid , Janker Lukas , Feuerstein Max Lennart , Langbauer Clemens , Gotsmy Mathias , Zanghellini Jürgen , Meier-Menches Samuel M. , Gerner Christopher 
Published: November 2020

AbstractMetabolic biomonitoring in humans is typically based on the sampling of blood, plasma or urine. Although established in the clinical routine, these sampling procedures are often associated with a variety of compliance issues and are impractical for performing time-course studies. The analysis of the minute amounts of sweat sampled from the fingertip enables a solution to this challenge. Sweat sampling from the fingertip is non-invasive and robust and can be accomplished repeatedly by untrained personnel. This matrix represents a rich source for metabolomic phenotyping, which is exemplified by the detection of roughly 50’000 features per sample. Moreover, the determined limits of detection demonstrate that the ingestion of 200 μg of a xenobiotic may be sufficient for its detection in sweat from the fingertip. The feasibility of short interval sampling of sweat from the fingertips was confirmed in three time-course studies after coffee consumption or ingestion of a caffeine capsule, successfully monitoring all known caffeine metabolites. Fluctuations in the rate of sweat production were accounted for by mathematical modelling to reveal individual rates of caffeine uptake, metabolism and clearance. Biomonitoring using sweat from the fingertip has far reaching implications for personalised medical diagnostics and biomarker discovery.
Allosteric Hotspots in the Main Protease of SARS-CoV-2
Authors: Strömich Léonie , Wu Nan , Barahona Mauricio , Yaliraki Sophia N. 
Published: November 2020

AbstractInhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites withouta prioriknowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.
Visualising Cholesterol in Brain by On-Tissue Derivatisation and Quantitative Mass Spectrometry Imaging
Authors: Angelini Roberto , Yutuc Eylan , Wyatt Mark F , Newton Jillian , Yusuf Fowzi Adam , Griffiths Lauren , Cooze Benjamin Jordan , El Assad Dana , Frache Gilles , Rao Wei , Allen Luke B. , Korade Zeljka , Nguyen Thu TA , Rathnayake Rathnayake AC , Cologna Stephanie M , Howell Owain W , Clench Malcolm R , Wang Yuqin , Griffiths William J 
Published: November 2020

SummaryDespite being a critical molecule for neurobiology and brain health, mass spectrometry imaging (MSI) of cholesterol has been under reported compared to other lipids, due to the difficulty in ionising the sterol molecule. In the present work we have employed an on-tissue enzyme-assisted derivatisation strategy to improve detection of cholesterol in brain tissue sections. We report distribution and levels of cholesterol across specific brain structures of the mouse brain, in a model of Niemann-Pick type C1 (NPC1) disease, and during brain development. MSI revealed how cholesterol changes during development and that in the adult is highest in pons and medulla of the brain stem. Cholesterol was significantly reduced in the corpus callosum and other brain regions in theNpc1null mouse, confirming hypomyelination at the molecular level. Our study demonstrates the potential of MSI to the study of sterols in neuroscience.
An antibiotic-resistance conferring mutation in a neisserial porin: Structure, ion flux, and ampicillin binding
Authors: Bartsch A. , Ives C.M. , Kattner C. , Pein F. , Diehn M. , Tanabe M. , Munk A. , Zachariae U. , Steinem C. , Llabrés S. 
Published: November 2020

ABSTRACTGram-negative bacteria cause the majority of highly drug-resistant bacterial infections. To cross the outer membrane of the complex Gram-negative cell envelope, antibiotics permeate through porins, trimeric channel proteins that enable the exchange of small polar molecules. Mutations in porins contribute to the development of drug-resistant phenotypes. In this work, we show that a single point mutation in the porin PorB fromNeisseria meningitidis, the causative agent of bacterial meningitis, can strongly affect the binding and permeation of beta-lactam antibiotics. Using X-ray crystallography, high-resolution electrophysiology, atomistic biomolecular simulation, and liposome swelling experiments, we demonstrate differences in drug binding affinity, ion selectivity and drug permeability of PorB. Our work further reveals distinct interactions between the transversal electric field in the porin eyelet and the zwitterionic drugs, which manifest themselves under applied electric fields in electrophysiology and are altered by the mutation. These observations may apply more broadly to drug-porin interactions in other channels. Our results improve the molecular understanding of porin-based drug-resistance in Gram-negative bacteria.
The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasitePlasmodium falciparum
Authors: Carrington Eilidh , Cooijmans Roel H. M. , Keller Dominique , Toenhake Christa G. , Bártfai Richárd , Voss Till S. 
Published: November 2020

AbstractMalaria parasites undergo a highly complex life cycle in the human host and the mosquito vector. The ApiAP2 family of sequence-specific DNA-binding proteins plays a dominant role in parasite development and life cycle progression. Of the ApiAP2 factors studied to date, most act as transcription factors regulating stage-specific gene expression. Here, we characterised a new ApiAP2 factor inPlasmodium falciparum(PF3D7_1456000) that we termed PfAP2-HC. Via detailed investigation of several single or double genetically engineered parasite lines, we demonstrate that PfAP2-HC specifically binds to heterochromatin throughout the genome. Intriguingly, PfAP2-HC does not bind DNAin vivoand recruitment of PfAP2-HC to heterochromatin is independent of its DNA-binding domain but strictly dependent on heterochromatin protein 1. Furthermore, our results suggest that PfAP2-HC functions neither in the regulation of gene expression nor in heterochromatin formation or maintenance. In summary, our findings reveal that PfAP2-HC constitutes a core component of heterochromatin in malaria parasites. They furthermore identify unexpected properties of ApiAP2 factors and suggest substantial functional divergence among the members of this important family of regulatory proteins.
A novel Mn-dependent peroxidase contributes to tardigrade anhydrobiosis
Authors: Yoshida Yuki , Satoh Tadashi , Ota Chise , Tanaka Sae , Horikawa Daiki D. , Tomita Masaru , Kato Koichi , Arakawa Kazuharu 
Published: November 2020

AbstractTardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated ametabolic state known as anhydrobiosis. While antioxidative stress genes, antiapoptotic pathways and tardigrade-specific intrinsically disordered proteins have been implicated in the anhydrobiotic machinery, conservation of these mechanisms is not universal within the phylum Tardigrada, suggesting the existence of overlooked components. Here, we show that a novel Mn-dependent peroxidase is an important factor in tardigrade anhydrobiosis. Through comparative time-series transcriptome analysis ofRamazzottius varieornatusspecimens exposed to desiccation or ultraviolet light, we first identified several novel gene families without similarity to existing sequences that are induced rapidly after stress exposure. Among these, a single gene family with multiple orthologs that is highly conserved within the phylum Tardigrada and enhances oxidative stress tolerance when expressed in human cells was identified. Crystallographic study of this protein suggested Zn or Mn binding at the active site, and we further confirmed that this protein has Mn-dependent peroxidase activityin vitro. Our results demonstrated novel mechanisms for coping with oxidative stress that may be a fundamental mechanism of anhydrobiosis in tardigrades. Furthermore, localization of these sets of proteins in the Golgi apparatus suggests an indispensable role of the Golgi stress response in desiccation tolerance.
Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago
Authors: Qiang Min , Ma Peixiang , Li Yu , Liu Hejun , Harding Adam , Min Chenyu , Liu Lili , Yuan Meng , Ji Qun , Tao Pingdong , Shi Xiaojie , Li Zhean , Wang Fulian , Zhang Yu , Wu Nicholas C. , Lee Chang-Chun D. , Zhu Xueyong , Gilbert-Jaramillo Javier , Saxena Abhishek , Huang Xingxu , Wang Hou , James William , Dwek Raymond A. , Wilson Ian A. , Yang Guang , Lerner Richard A. 
Published: November 2020

ABSTRACTCombinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The SARS-CoV-2 pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, we used a combinatorial human antibody library constructed 20 years before the COVID-19 pandemic to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in crystal structures with SARS-CoV-2 spike RBD. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of human immune responses to SARS-CoV-2.
Acrylamide Fragment Inhibitors that Induce Unprecedented Conformational Distortions in Enterovirus 71 3C and SARS-CoV-2 Main Protease
Authors: Qin Bo , Craven Gregory B. , Hou Pengjiao , Lu Xinran , Child Emma S. , Morgan Rhodri M. L. , Armstrong Alan , Mann David J. , Cui Sheng 
Published: November 2020

ABSTRACTRNA viruses are critically dependent upon virally encoded proteases that cleave the viral polyproteins into functional mature proteins. Many of these proteases are structurally conserved with an essential catalytic cysteine and this offers the opportunity to irreversibly inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that selectively target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we effectively re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold as well as similar catalytic-triad. We demonstrate that the hit fragments covalently link to the catalytic cysteine of Mproto inhibit its activity. In addition, we provide the first demonstration that targeting the active site cysteine of Mprocan also have profound allosteric effects, distorting secondary structures required for formation of the active dimeric unit of Mpro. These new data provide novel mechanistic insights into the design of EV71 3Cproand SARS-CoV-2 Mproinhibitors and identify acrylamide-tagged pharmacophores for elaboration into more selective agents of therapeutic potential.
The worldwide invasion ofDrosophila suzukiiis accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions
Authors: Mérel Vincent , Gibert Patricia , Buch Inessa , Rada Valentina Rodriguez , Estoup Arnaud , Gautier Mathieu , Fablet Marie , Boulesteix Matthieu , Vieira Cristina 
Published: November 2020

AbstractTransposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we portrayed the TE content of the spotted wing flyDrosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequencesde novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations (ofD. suzukii). We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversitya proxy of effective population size. We did not find any correlation between TE contents and bio-climatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed thatca. 5,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.
Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa and related species
Authors: Mehraj Hasan , Shea Daniel J. , Takahashi Satoshi , Miyaji Naomi , Akter Ayasha , Seki Motoaki , Dennis Elizabeth S. , Ryo Fujimoto , Osabe Kenji 
Published: November 2020

AbstractLong noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression were analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels and when both were present, there were further increase in DNA methylation levels. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. Brassica rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events, but the detailed mechanism is not known. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of the B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and offers insights into the function of lncRNA in the Brassica genus.
Badger territoriality maintained despite disturbance of major road construction
Authors: Gaughran Aoibheann , Mullen Enda , MacWhite Teresa , Maher Peter , Kelly David J. , Kelly Ruth , Good Margaret , Marples Nicola M. 
Published: November 2020

ABSTRACTRoad ecology has traditionally focused on the impact of in-situ and functional roads on wildlife. However, road construction also poses a major, yet understudied, threat and any implications for key aspects of animal behaviour are unknown. There are also concerns that environmental disturbances, including major roadworks, can disrupt badger territoriality, promoting the spread of tuberculosis to cattle. To address these knowledge gaps, the ranging behaviour of a medium-density Irish badger population was monitored, using GPS-tracking collars, before, during and after a major road realignment project that bisected the study area. We estimated badgers’ home range sizes, nightly distances travelled and the distance and frequency of extra-territorial excursions during each phase of the study and quantified any changes to these parameters. We show that roadworks had a very limited effect on ranging behaviour. A small increase in nightly distance during the roadworks did not translate into an increase in home range size, nor an increase in the distance or frequency of extra-territorial excursions during the roadworks. In addition, suitable mitigation measures to prevent badger deaths appeared to ensure that normal patterns of ranging behaviour continued once the new road was in place. Our analysis supports the view that road construction did not cause badgers to change their ranging behaviour in ways likely to increase the spread of tuberculosis.
Doxycycline inhibits α-synuclein-associated pathologiesin vitroandin vivo
Authors: Dominguez-Meijide Antonio , Parrales Valeria , Vasili Eftychia , González-Lizárraga Florencia , König Annekatrin , Lázaro Diana F. , Lannuzel Annie , Haik Stéphane , Del Bel Elaine , Chehín Rosana , Raisman-Vozari Rita , Michel Patrick P , Bizat Nicolas , Outeiro Tiago Fleming 
Published: November 2020

AbstractParkinson’s disease (PD) and dementia with Lewy bodies (DLB) are neurodegenerative disorders characterized by the misfolding and aggregation of alpha-synuclein (aSyn). Doxycycline, a tetracyclic antibiotic shows neuroprotective effects, initially proposed to be due to its anti-inflammatory properties. More recently, an additional mechanism by which doxycycline may exert its neuroprotective effects has been proposed as it has been shown that it inhibits amyloid aggregation. Here, we studied the effects of doxycycline on aSyn aggregationin vivo, in vitroand in a cell free system using real-time quaking induced conversion (RT-QuiC). Our results show that doxycycline decreases the number and size of aSyn aggregates in cells. In addition, doxycycline inhibits the aggregation and seeding of recombinant aSyn, and attenuates the production of mitochondrial-derived reactive oxygen species. Finally, we found doxycycline induces a cellular redistribution of the aggregates in an animal model of PD that is associated with a recovery of dopaminergic function. In summary, we provide strong evidence that doxycycline treatment may be an effective strategy against synucleinopathies.
Mitochondrial pathway polygenic risk scores are associated with Alzheimer’s Disease
Authors: Paliwal Devashi , McInerney Tim W. , Pa Judy , Swerdlow Russell H. , Easteal Simon , Andrews Shea J. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: November 2020

ABSTRACTINTRODUCTIONGenetic, animal and epidemiological studies involving biomolecular and clinical endophenotypes implicate mitochondrial dysfunction in Alzheimer’s disease (AD) pathogenesis. Polygenic risk scores (PRS) provide a novel approach to assess biological pathway-associated disease risk by combining the effects of variation at multiple, functionally related genes.METHODSWe investigated associations of PRS for genes involved in 12 mitochondrial pathways (pathway-PRS) related to AD in 854 participants from Alzheimer’s Disease Neuroimaging Initiative.RESULTSPathway-PRS for four mitochondrial pathways are significantly associated with increased AD risk: (i) response to oxidative stress (OR: 2.01 [95% Cl: 1.71, 2.37]); (ii) mitochondrial transport (OR: 1.81 [95% Cl: 1.55, 2.13]); (iii) hallmark oxidative phosphorylation (OR: 1.23 [95% Cl: 1.07, 1.41]); and (iv) mitochondrial membrane potential regulation (OR: 1.18 [95% Cl: 1.03, 1.36]).DISCUSSIONTherapeutic approaches targeting these pathways may have potential for modifying AD pathogenesis. Further investigation is required to establish a causal role for these pathways in AD pathology.
DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions
Authors: Ghosh Anirban , Largy Eric , Gabelica Valérie 
Published: November 2020

ABSTRACTG-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually 100 mM) K+, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM TMAA. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in theg4dbrpackage (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).