bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic analysis deciphers the molecular toolbox in the endophytic/pathogenic behavior inF. oxysporumf. sp.vanillae-V. planifoliaJacks interaction
Authors: Solano De la Cruz MT , Escobar Hernández EE , Arciniega González JA , Rueda Zozaya RP , Adame García J , Luna – Rodríguez M 
Published: March 2021

AbstractBackgroundF. oxysporumas a species complex (FOSC) possesses the capacity to specialize into host-specific pathogens known asformae speciales. This with the help of horizontal gene transfer (HGT) between pathogenic and endophytic individuals of FOSC. From these pathogenicforma specialis, F. oxysporumf. sp.vanillae(Fov) is the causal agent of fusarium wilt producing root and stem rot (RSR) and is positioned as the main phytosanitary problem in vanilla plantations worldwide. Nonetheless, the origin of this forma speciales and the behavioral genetics dictating the endophytic/pathogenicFusariumlifestyles still unknown. To elucidate the underlying molecular mechanisms that establish these behaviors we analyzed the RNA-seq libraries of two-times frames of vanilla-Fov interactions.ResultsOur analyses identified the sets of transcripts corresponding toFovpathogenic strain JAGH3 during the two-times frames of the infection as the sets of the transcripts belonging to endophyticFoxin vanilla. Functional predictions ofde novoannotated transcripts as the enriched GO terms with the overrepresented metabolic pathways, allowed us to identify the processes that establish the pathogenic lifestyle inFovbeing virulence, hypervirulence, sporulation, conidiation, necrosis and fusaric acid related genes with the carbohydrates, amino acids, proteins, glycerophospholipids and autophagy metabolic pathways that are key regulators of spores germination and pathogenicity establishment as the underlying mechanisms behind this behavior. As the absence of these were found in the vanilla endophyticFox.ConclusionsThis work reveals the main players of the behavioral genetics in pathogenicFov/endophyticFoxinV. planifoliaJacks. Its pathogenic strategy allowsFovto infect in a SIX genes-independent manner. As the other pathogenic elements found in this study could be explained by the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes inFov. These play a central role as carriers of genes involved with pathogenic activity and could be obtained through HGT.
Comparative Multiomic Analysis Reveals Low T Cell Infiltration as the Primary Feature of Tobacco Use in HPV(+) Oropharyngeal Cancer
Authors: Wahle Benjamin M. , Zolkind Paul , Ramirez Ricardo , Skidmore Zachary L. , Mazul Angela , Hayes D. Neil , Sandulache Vlad C. , Thorstad Wade L. , Adkins Douglas , Griffith Obi L. , Griffith Malachi , Zevallos Jose P. 
Published: March 2021

ABSTRACTPurposeTobacco use is an independent adverse prognostic feature in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Despite this, the biologic features associated with tobacco use have not been systematically investigated in this population. We sought to characterize the genomic and immunologic features of HPV(+) OPSCC associated with tobacco use and adverse oncologic outcomes.Experimental DesignWhole exome sequencing of 47 primary HPV(+) OPSCC tumors was performed to investigate mutational differences associated with tobacco exposure. To characterize the tumor immune microenvironment (TIME), targeted mRNA hybridization was performed and immunohistochemical (IHC) staining was used to validate these findings.ResultsLow expression of transcripts in a T cell-inflamed gene expression profile (TGEP) was associated with tobacco use at the time of diagnosis and lower overall and disease-free survival. Tobacco use was associated with an increased proportion of T>C substitutions and a lower proportion of mutational signatures typically observed in HPV(+) OPSCC tumors, but was not associated with increases in mutational burden or the rate of recurrent oncogenic mutations.ConclusionsIn HPV(+) OPSCC, low T cell infiltration of primary tumors is associated with current tobacco use and worse oncologic outcomes. Rather than an increased mutational burden, tobacco’s primary and clinically relevant association is immunosuppression of the primary TIME. An objective clinical assay like the TGEP, which quantifies immune infiltration of the primary TIME, may have value for HPV(+) OPSCC risk stratification in future clinical trials.
Generation of functional ciliated cholangiocytes from human pluripotent stem cells
Authors: Ogawa Mina , Jiang Jia-Xin , Xia Sunny , Yang Donghe , Ding Avrilynn , Laselva Onofrio , Chin Stephanie , Hernandez Marcela , Cui Changyi , Higuchi Yuichiro , Suemizu Hiroshi , Dorrell Craig , Grompe Markus , Bear Christine E , Keller Gordon , Ogawa Shinichiro 
Published: March 2021

AbstractThe derivation of mature functional cholangiocytes from human pluripotent stem cells (hPSCs) would provide a model for studying the pathogenesis of cholangiopathies and for developing novel therapies to treat them. Current differentiation protocols are not efficient and give rise to cholangiocytes that are not fully mature, limiting their therapeutic applications. Here, we describe a new strategy to generate functional hPSC-derived cholangiocytes that display many characteristics of mature bile duct cells including high levels of CFTR and the presence of primary cilia capable of sensing flow. With this level of maturation, these cholangiocytes are amenable for testing the efficacy of new cystic fibrosis drugs and for studying the role of cilia in cholangiocyte development and function. Transplantation studies showed that the mature cholangiocytes generate ductal structures in the liver of immunocompromised mice providing the first indication that it may be possible to develop cell-based therapies to restore bile duct function in patients with biliary disease.
Additive manufactured scaffolds for bone tissue engineering: physical characterization of thermoplastic composites with functional fillers
Authors: Sinha Ravi , Sanchez Alberto , Camara-Torres Maria , Uriszar-Aldaca Iñigo Calderon , Calore Andrea Roberto , Harings Jules , Gambardella Ambra , Ciccarelli Lucia , Vanzanella Veronica , Sisani Michele , Scatto Marco , Wendelbo Rune , Perez Sergio , Villanueva Sara , Matanza Amaia , Patelli Alessandro , Grizzuti Nino , Mota Carlos , Moroni Lorenzo 
Published: March 2021

AbstractThermoplastic polymer – filler composites are excellent materials for bone tissue engineering (TE) scaffolds, combining the functionality of fillers with suitable load bearing ability, biodegradability, and additive manufacturing (AM) compatibility of the polymer. Two key determinants of their utility are their rheological behavior in the molten state, determining AM processability, and their mechanical load-bearing properties. We report here the characterization of both these physical properties for four bone TE relevant composite formulations with poly(ethylene oxide terephthalate) / poly(butylene terephthalate (PEOT/PBT) as a base polymer, which is often used to fabricate TE scaffolds. The fillers used were reduced graphene oxide (rGO), hydroxyapatite (HA), gentamycin intercalated in zirconium phosphate (ZrP-GTM) and ciprofloxacin intercalated in MgAl layered double hydroxide (MgAl-CFX). The rheological assessment showed that generally the viscous behavior dominated the elastic behavior (G’’ > G’) for the studied composites, at empirically determined extrusion temperatures. Coupled rheological-thermal characterization of ZrP-GTM and HA composites showed that the fillers increased the solidification temperatures of the polymer melts during cooling. Both these findings have implications for the required extrusion temperatures and bonding between layers. Mechanical tests showed that the fillers generally made the polymer stiffer but more brittle in proportion to the filler fractions. Furthermore, the elastic moduli of scaffolds did not directly correlate with the corresponding bulk material properties, implying composite-specific AM processing effects on the mechanical properties. Lastly, we show computational models to predict multi-material scaffold elastic moduli using measured single material scaffold and bulk moduli. The reported characterizations are essential for assessing the AM processability and ultimately the suitability of the manufactured scaffolds for the envisioned bone regeneration application.
Perturbation of ribosomal subunits dynamics by inhibitors of tRNA translocation
Authors: Belardinelli Riccardo , Sharma Heena , Peske Frank , Rodnina Marina V. 
Published: March 2021

AbstractMany antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA translocation), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, EF-G-induced transition to the rotated/swiveled state of the SSU is hardly affected. The major effect of the antibiotics is observed at the stage when the SSU body and the head domain move backward. Vio, Spc and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.
DNA replication during acute MEK inhibition drives acquisition of resistance through amplification of theBRAFoncogene
Authors: Channathodiyil Prasanna , Segonds-Pichon Anne , Smith Paul D. , Cook Simon J. , Houseley Jonathan 
Published: March 2021

AbstractMutations and gene amplifications that confer drug resistance emerge frequently during chemotherapy, but their mechanism and timing is poorly understood. Here, we investigateBRAFV600Eamplification events that underlie resistance to the MEK inhibitor selumetinib (AZD6244/ARRY-142886) in COLO205 cells, a well-characterised model for reproducible emergence of drug resistance, and show thatde novoamplification ofBRAFis the primary path to resistance irrespective of pre-existing amplifications. Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. Most DNA replication and repair genes are re-expressed as cells enter S and G2, however, mRNAs encoding a subset of factors important for error-free replication and chromosome segregation including TIPIN, PLK2 and PLK3 remain at low abundance. This suggests that DNA replication in drug is more error prone and provides an explanation for the DNA damage observed under long-term RAF-MEK-ERK1/2 pathway inhibition. To test the hypothesis that DNA replication in drug promotesde novo BRAFamplification, we exploited the combination of palbociclib and selumetinib. Combined treatment with selumetinib and a dose of palbociclib sufficient to reinforce G1 arrest in selumetinib-sensitive cells, but not to impair proliferation of resistant cells, delays the emergence of resistant colonies, meaning that escape from G1 arrest is critical in the formation of resistant clones. Our findings demonstrate that acquisition of MEK inhibitor resistance often occurs throughde novogene amplification and can be suppressed by impeding cell cycle entry in drug.
Identification, crystallization and epitope determination of public TCR shared and expanded in COVID-19 patients
Authors: Lu Xiuyuan , Hosono Yuki , Ishizuka Shigenari , Nagae Masamichi , Ishikawa Eri , Motooka Daisuke , Ozaki Yuki , Sax Nicolas , Shinnakasu Ryo , Inoue Takeshi , Onodera Taishi , Matsumura Takayuki , Shinkai Masaharu , Sato Takashi , Nakamura Shota , Mori Shunsuke , Kanda Teru , Nakayama Emi E. , Shioda Tatsuo , Kurosaki Tomohiro , Arase Hisashi , Yamashita Kazuo , Takahashi Yoshimasa , Yamasaki Sho 
Published: March 2021

SummaryT cells play pivotal roles in protective immunity against SARS-CoV-2 infection. Follicular helper T (Tfh) cells mediate the production of antigen-specific antibodies; however, T cell receptor (TCR) clonotypes used by SARS-CoV-2-specific Tfh cells have not been well characterized. Here, we first identified and crystallized public TCR of Tfh clonotypes that are shared and expanded in unhospitalized COVID-19-recovered patients. These clonotypes preferentially recognized SARS-CoV-2 spike (S) protein epitopes which are conserved among emerging SARS-CoV-2 variants. These clonotypes did not react with S proteins derived from common cold human coronaviruses, but cross-reacted with symbiotic bacteria, which might confer the publicity. Among SARS-CoV-2 S epitopes, S864-882, presented by frequent HLA-DR alleles, could activate multiple public Tfh clonotypes in COVID-19-recovered patients. Furthermore, S864-882-loaded HLA tetramer preferentially bound to CD4+T cells expressing CXCR5. In this study, we identified and crystallized public TCR for SARS-CoV-2 that may contribute to the prevention of COVID-19 aggravation.
Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site
Authors: Lacham-Hartman Shiran , Shmidov Yulia , Radisky Evette S. , Bitton Ronit , Lukatsky David B. , Papo Niv 
Published: March 2021

AbstractAlthough myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.Impact statementLacham-Hartmanet al. demonstrate enhancement of binding affinity through avidity in a complex between a bivalent ligand and a soluble monomeric target with a single binding site. Avidity effects have previously been demonstrated only for clustered receptor molecules presenting multiple binding sites. Our model may explain how polyvalent ligands can agonize or antagonize biological interactions involving nonclustered target molecules that are crucial for intra- and extracellular structural, metabolic, signaling, and regulatory pathways.
Immune StimulationviaWounding Alters Chemical Profiles of AdultTribolium castaneum
Authors: Lo Lai Ka , Reshma R , Tewes Lisa Johanna , Milutinović Barbara , Müller Caroline , Kurtz Joachim 
Published: March 2021

AbstractGroup-living individuals experience immerse risk of disease transmission and parasite infection. Especially in social, but also in some non-social insects, disease control with immunomodulation takes place not onlyviaindividual immune defenses, but alsoviainfochemicals such as contact cues and (defensive) volatiles to mount a group level immunity. However, little is known about whether an activation of the immune system leads to changes in chemical phenotypes, which may mediate these responses. We here asked whether individual immune experience resulting from wounding or injection of heat-killedBacillus thuringiensisleads to changes in the chemical profiles of female and male adult red flour beetles (Tribolium castaneum), which are non-social but gregarious. We analyzed insect extracts using GC-FID to study the chemical composition of (1) cuticular hydrocarbons (CHCs) as candidates for the transfer of immunity-related information between individualsviacontact, and (2) stink gland secretions, with target analysis of benzoquinones as main active compounds regulating ‘external immunity’. Despite a pronounced sexual dimorphism in CHC profiles, wounding stimulation led to similar profile changes in males and females with increases in the proportion of methyl-branched alkanes compared to naïve beetles. While changes in the overall secretion profiles were less pronounced, absolute amounts of benzoquinones were transiently elevated in wounded compared to naïve females. We suggest that the changes in different infochemicals may mediate immune status signaling in the context of both internal and external immune responses in groups of this non-social insect, thus showing parallels to social immunity.
Phospholipidosis is a shared mechanism underlying thein vitroantiviral activity of many repurposed drugs against SARS-CoV-2
Authors: Tummino Tia A. , Rezelj Veronica V. , Fischer Benoit , Fischer Audrey , O’Meara Matthew J. , Monel Blandine , Vallet Thomas , Zhang Ziyang , Alon Assaf , O’Donnell Henry R. , Lyu Jiankun , Schadt Heiko , White Kris M , Krogan Nevan J. , Urban Laszlo , Shokat Kevan M. , Kruse Andrew C. , García-Sastre Adolfo , Schwartz Olivier , Moretti Francesca , Vignuzzi Marco , Pognan Francois , Shoichet Brian K. 
Published: March 2021

AbstractRepurposing drugs as treatments for COVID-19 has drawn much attention. A common strategy has been to screen for established drugs, typically developed for other indications, that are antiviral in cells or organisms. Intriguingly, most of the drugs that have emerged from these campaigns, though diverse in structure, share a common physical property: cationic amphiphilicity. Provoked by the similarity of these repurposed drugs to those inducing phospholipidosis, a well-known drug side effect, we investigated phospholipidosis as a mechanism for antiviral activity. We tested 23 cationic amphiphilic drugs—including those from phenotypic screens and others that we ourselves had found—for induction of phospholipidosis in cell culture. We found that most of the repurposed drugs, which included hydroxychloroquine, azithromycin, amiodarone, and four others that have already progressed to clinical trials, induced phospholipidosis in the same concentration range as their antiviral activity; indeed, there was a strong monotonic correlation between antiviral efficacy and the magnitude of the phospholipidosis. Conversely, drugs active against the same targets that did not induce phospholipidosis were not antiviral. Phospholipidosis depends on the gross physical properties of drugs, and does not reflect specific target-based activities, rather it may be considered a confound in early drug discovery. Understanding its role in infection, and detecting its effects rapidly, will allow the community to better distinguish between drugs and lead compounds that more directly impact COVID-19 from the large proportion of molecules that manifest this confounding effect, saving much time, effort and cost.One Sentence SummaryDrug-induced phospholipidosis is a single mechanism that may explain thein vitroefficacy of a wide-variety of therapeutics repurposed for COVID-19.
A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA
Authors: Yang Weiwei , Lin Yu-Cheng , Johnson William , Dai Nan , Vaisvila Romualdas , Weigele Peter R. , Lee Yan-Jiun , Corrêa Ivan R. , Schildkraut Ira , Ettwiller Laurence 
Published: March 2021

AbstractShotgun metagenomic sequencing is a powerful approach to study microbiomes in an unbiased manner and of increasing relevance for identifying novel enzymatic functions. However, the potential of metagenomics to relate from microbiome composition to function has thus far been underutilized. Here, we introduce the Metagenomics Genome-Phenome Association (MetaGPA) study framework, which allows to link genetic information in metagenomes with a dedicated functional phenotype. We applied MetaGPA to identify enzymes associated with cytosine modifications in environmental samples. From the 2365 genes that met our significance criteria, we confirm known pathways for cytosine modifications and proposed novel cytosine-modifying mechanisms. Specifically, we characterized and identified a novel nucleic acid modifying enzyme, 5-hydroxymethylcytosine carbamoyltransferase, that catalyzes the formation of a previously unknown cytosine modification, 5-carbamoyloxymethylcytosine, in DNA and RNA. Our work introduces MetaGPA as a novel and versatile tool for advancing functional metagenomics.
Species richness determinesC. difficileinvasion outcome in synthetic human gut communities
Authors: Hromada Susan , Clark Ryan L. , Qian Yili , Watson Lauren , Safdar Nasia , Venturelli Ophelia S. 
Published: March 2021

AbstractUnderstanding the principles of colonization resistance of the gut microbiome to the pathogenClostridioides difficilewill enable the design of next generation defined bacterial therapeutics. We investigate the ecological principles of community resistance toC. difficileinvasion using a diverse synthetic human gut microbiome. Our results show that species richness is a key determinant ofC. difficilegrowth across a wide range of ecological contexts. Using a dynamic computational model, we demonstrate thatC. difficilereceives the largest number and magnitude of incoming negative interactions. We identify molecular mechanisms of inhibition including acidification of the environment and competition over glucose. We demonstrate thatC. difficile’s close relativeClostridium hiranonisstrongly inhibitsC. difficilevia a pH-independent mechanism. While increasing the initial density ofC. difficilecan increase its abundance in the assembled community, the community context determines the maximum achievableC. difficileabundance. Our work suggests that theC. difficileinhibitory potential of defined bacterial therapeutics can be optimized by designing communities that feature a combination of mechanisms including species richness, environment acidification, and resource competition.