bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective interferon responses of intestinal epithelial cells minimize TNFα cytotoxicity
Authors: Van Winkle Jacob A. , Constant David A. , Li Lena , Nice Timothy J. 
Published: March 2020

ABSTRACTInterferon (IFN) family cytokines stimulate genes (ISGs) that are integral to antiviral host defense. Type I IFNs act systemically whereas type III IFNs act preferentially at epithelial barriers. Among barrier cells, intestinal epithelial cells (IECs) are particularly dependent on type III IFN for control and clearance of virus infection, but the physiological basis of this selective IFN response is not well understood. Here, we confirm that type III IFN treatment elicits robust and uniform ISG expression in neonatal mouse IECs and inhibits replication of IEC-tropic rotavirus. In contrast, type I IFN elicits a marginal ISG response in neonatal mouse IECs and does not inhibit rotavirus replication.In vitrotreatment of IEC organoids with type III IFN results in ISG expression that mirrors thein vivotype III IFN response. However, the response of IEC organoids to type I IFN is strikingly increased relative to type III IFN in magnitude and scope. The expanded type I IFN-specific response includes pro-apoptotic genes and potentiates toxicity triggered by tumor necrosis factor alpha (TNFα). The ISGs stimulated in common by types I and III IFN have strong interferon-stimulated response element (ISRE) promoter motifs, whereas the expanded set of type I IFN-specific ISGs, including pro-apoptotic genes, have weak ISRE motifs. Thus, preferential responsiveness of IECs to type III IFNin vivoenables selective ISG expression during infection that confers antiviral protection but minimizes disruption of intestinal homeostasis.
COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes
Authors: Prachar Marek , Justesen Sune , Steen-Jensen Daniel Bisgaard , Thorgrimsen Stephan , Jurgons Erik , Winther Ole , Bagger Frederik Otzen 
Published: March 2020

AbstractThe recent outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cells via the HLA complex. SARS-CoV-2 is a large RNA virus and testing of all overlapping peptidesin vitroto deconvolute an immune response is not feasible. Therefore HLA-binding prediction tools are often used to narrow down the number of peptides to test. We tested 19 epitope-HLA-binding prediction tools, and using anin vitropeptide MHC stability assay, we assessed 777 peptides that were predicted to be good binders across 11 MHC allotypes. In this investigation of potential SARS-CoV-2 epitopes we found that current prediction tools vary in performance when assessing binding stability, and they are highly dependent on the MHC allotype in question. Designing a COVID-19 vaccine where only a few epitope targets are included is therefore a very challenging task. Here, we present 174 SARS-CoV-2 epitopes with high prediction binding scores, validated to bind stably to 11 HLA allotypes. Our findings may contribute to the design of an efficacious vaccine against COVID-19.
Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity
Authors: Mathur Jairaj , Shenoy Vivek B. , Pathak Amit 
Published: March 2020

ABSTRACTEmerging evidence shows that cells are able to sense and store a memory of their past mechanical environment. Since existing mechanotransduction models are based on adhesion and cytoskeletal dynamics that occurs over seconds and minutes, they do not capture memory observed over days or weeks. We postulate that transcriptional activity and epigenetic plasticity, upstream of adhesion-based signaling, need to be invoked to explain long-term mechanical memory. Here, we present a theory for mechanical memory in cells governed by three key components. First, cells on a stiff matrix are primed by a transcriptional reinforcement of cytoskeletal signaling. Second, longer stiff-priming progressively produces more memory-regulating factors and reduces epigenetic plasticity. Third, when stiff-primed cells move to soft matrix, the reduced epigenetic plasticity blocks new transcription required for cellular adaptation to the new matrix. This stalled transcriptional state gives rise to memory. We validate this model against previous experimental findings of memory storage and decay in epithelial cell migration and stem cell differentiation. We also predict wide-ranging memory responses for different cell types of varying protein kinetics and priming conditions. This theoretical framework for mechanical memory expands the timescales of mechanotransduction captured by conventional models by integrating cytoskeletal signaling with transcriptional activity and epigenetic plasticity. Our model predictions explain mechanical memory and propose new experiments to test spatiotemporal regulation of cellular memory in diverse contexts ranging from cell differentiation to migration and growth.
Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
Authors: Li Xiaojun , Giorgi Elena E. , Marichann Manukumar Honnayakanahalli , Foley Brian , Xiao Chuan , Kong Xiang-Peng , Chen Yue , Korber Bette , Gao Feng 
Published: March 2020

AbstractCOVID-19 has become a global pandemic caused by a novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis and for drug discovery and vaccine development. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike gene and in other genes among bat, pangolin and human coronaviruses, indicating similar strong evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species and frequent recombination among coronaviruses suggest a common evolutionary mechanism that could lead to new emerging human coronaviruses.One Sentence SummaryExtensive Recombination and Strong Purifying Selection among coronaviruses from different hosts facilitate the emergence of SARS-CoV-2
Ciliation of muscle stem cells is critical to maintain regenerative capacity and is lost during aging
Authors: Palla A.R. , Hilgendorf K.I. , Yang A.V. , Kerr J.P. , Hinken A.C. , Demeter J. , Kraft P. , Mooney N.A. , Yucel N. , Jackson P.K. , Blau H.M. 
Published: March 2020

AbstractDuring aging, the regenerative capacity of muscle stem cells (MuSCs) decreases, diminishing the ability of muscle to repair following injury. We performed a small molecule library screen and discovered that the proliferation and expansion of aged MuSCs is regulated by signal transduction pathways organized by the primary cilium, a cellular protrusion that serves as a sensitive sensory organelle. Abolishing MuSC ciliain vivoseverely impaired injury-induced muscle regeneration. In aged muscle, a cell intrinsic defect in MuSC ciliation leading to impaired Hedgehog signaling was associated with the decrease in regenerative capacity. This deficit could be overcome by exogenous activation of Hedgehog signaling which promoted MuSC expansion, bothin vitroandin vivo. Delivery of the small molecule Smoothened agonist (SAG) to muscles of aged mice restored regenerative capacity leading to increased strength post-injury. These findings provide fresh insights into the signaling dysfunction in aging and identify the ciliary Hedgehog signaling pathway as a potential therapeutic target to counter the loss of muscle regenerative capacity which accompanies aging.
DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP
Authors: Bruce Emily A. , Huang Meei-Li , Perchetti Garrett A. , Tighe Scott , Laaguiby Pheobe , Hoffman Jessica J. , Gerrard Diana L. , Nalla Arun K. , Wei Yulun , Greninger Alexander L. , Diehl Sean A. , Shirley David J. , Leonard Debra G. B. , Huston Christopher D. , Kirkpatrick Beth D. , Dragon Julie A. , Crothers Jessica W. , Jerome Keith R. , Botten Jason W. 
Published: March 2020

ABSTRACTThe ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.
Conductance mechanisms of rapidly desensitizing cation channelrhodopsins from cryptophyte algae
Authors: Sineshchekov Oleg A. , Govorunova Elena G. , Li Hai , Wang Yumei , Melkonian Michael , Wong Gane K.-S. , Brown Leonid S. , Spudich John L. 
Published: March 2020

ABSTRACTChannelrhodopsins guide algal phototaxis and are widely used as optogenetic probes for control of membrane potential with light. “Bacteriorhodopsin-like” cation channelrhodopsins (BCCRs) from cryptophytes differ in primary structure from other CCRs, lacking usual residues important for their cation conductance. Instead, BCCR sequences match more closely those of rhodopsin proton pumps, containing residues responsible for critical proton transfer reactions. We report 19 new BCCRs, which, together with the earlier 6 known members of this family, form three branches (subfamilies) of a phylogenetic tree. Here we show that the conductance mechanisms in two subfamilies differ with respect to involvement of the homolog of the proton donor in rhodopsin pumps. Two BCCRs from the genusRhodomonasgenerate photocurrents that rapidly desensitize under continuous illumination. Using a combination of patch clamp electrophysiology, absorption and Raman spectroscopy, and flash photolysis, we found that the desensitization is due to rapid accumulation of a long-lived nonconducting intermediate of the photocycle with unusually blue-shifted absorption with a maximum at 330 nm. These observations reveal diversity within the BCCR family and contribute to deeper understanding of their independently evolved cation channel function.IMPORTANCECation channelrhodopsins, light-gated channels from flagellate green algae, are extensively used as optogenetic photoactivators of neurons in research and recently have progressed to clinical trials for vision restoration. However, the molecular mechanisms of their photoactivation remain poorly understood. We recently identified cryptophyte cation channelrhodopsins, structurally different from those of green algae, which have separately evolved to converge on light-gated cation conductance. This study reveals diversity within this new protein family and describes a subclade with unusually rapid desensitization that results in short transient photocurrents in continuous light. Such transient currents have not been observed in the green algae channelrhodopsins and are potentially useful in optogenetic protocols. Kinetic UV-vis spectroscopy and photoelectrophysiology reveal the desensitization is caused by rapid accumulation of a non-conductive photointermediate in the photochemical reaction cycle. The absorption maximum of the intermediate is 330 nm, the shortest wavelength reported in any rhodopsin, indicating a novel chromophore structure.
The pathognomonic FOXL2 C134W mutation alters DNA binding specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Rachelle , Grace Cheng S.-W. , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin 
Published: March 2020

AbstractThe somatic missense point mutation c.402C>G (p.C134W) in the FOXL2 transcription factor is pathognomonic for adult-type granulosa cell tumours (AGCT) and a diagnostic marker for this tumour type. However, the molecular consequences of this mutation and its contribution to the mechanisms of AGCT pathogenesis remain unclear. To explore the mechanisms driving FOXL2C134W pathogenicity we engineered V5-FOXL2WT and V5-FOXL2C134W inducible isogenic cell lines and performed ChIP-seq and transcriptome profiling. We found that FOXL2C134W associates with the majority of the FOXL2 WT DNA elements as well as a large collection of unique elements genome-wide. We confirmed an altered DNA binding specificity for FOXL2C134Win vitro and identified unique targets of FOXL2C134W including SLC35F2 whose expression increased sensitivity to YM155 in our model.Statement of SignificanceMechanistic understanding of FOXL2C134W induced regulatory state alterations drives discovery of a rationally designed therapeutic strategy.
Combining mass spectrometric platforms for lipidome investigation - Application to the characterisation of disruptions in the lipid profile of pig serum upon β-agonist treatment
Authors: Marchand Jérémy , Guitton Yann , Martineau Estelle , Royer Anne-Lise , Balgoma David , Le Bizec Bruno , Giraudeau Patrick , Dervilly Gaud 
Published: March 2020

AbstractIn the last decade, many mass spectrometric fingerprinting methods dedicated to lipidomics have been proposed: either non-targeted approaches, coupled with annotation methods, or targeted strategies, aiming at specifically monitoring a limited number of substances.In a general public health perspective and through a strategy combining non-targeted and targeted lipidomics MS-based approaches, this study aims at identifying disrupted patterns in serum lipidome upon growth promoter treatment in pig and evaluating the relative contributions of the three platforms involved.Pig serum samples collected during an animal experiment involving control and treated animals, whose food had been supplemented with ractopamine, were extracted and characterised using three MS strategies: Non-targeted RP LC-HRMS; the targeted Lipidyzer™ platform (differential ion mobility associated with shotgun lipidomics) and a homemade LC-HRMS triglyceride platform.The three different platforms showed complementarity insight into lipid characterisation, which, applied to a selected set of samples, enabled highlighting specific lipid profile patterns involving various lipid classes, mainly in relation with cholesterol esters, sphingomyelins, lactosylceramide, phosphatidylcholines and triglycerides.Thanks to the combination of both non-targeted and targeted MS approaches, the exploration of various compartments of the pig serum lipidome could be performed, including commonly characterised lipids (Lipidyzer™), triglyceride isomers (Triglyceride platform) -whose accurate analysis was considered an analytical challenge, and unique lipid features (non-targeted LC-HRMS). Thanks to their respective characteristics, the complementarity of the three tools could be demonstrated for public health purposes, with enhanced lipidome coverage, level of characterisation and applicability.
Analysis ofPlasmodium vivaxschizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions
Authors: Siegel Sasha V. , Chappell Lia , Hostetler Jessica B. , Amaratunga Chanaki , Suon Seila , Böhme Ulrike , Berriman Matthew , Fairhurst Rick M. , Rayner Julian C. 
Published: March 2020

AbstractPlasmodium vivaxgene regulation remains difficult to study due to the lack of a robustin vitroculture method, low parasite densities in peripheral circulation and asynchronous parasite development. We adapted an RNA-seq protocol “DAFT-seq” to sequence the transcriptome of fourP. vivaxfield isolates that were cultured for a short periodex vivobefore using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5’ and 3’ untranslated regions (UTRs), some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity betweenP. vivaxschizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lackPlasmodium falciparumhomologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity withinP. vivaxtranscriptomes will be essential for the prioritisation of novel vaccine targets.
Sulfopin, a selective covalent inhibitor of Pin1, blocks Myc-driven tumor initiation and growthin vivo
Authors: Dubiella Christian , Pinch Benika J. , Zaidman Daniel , Manz Theresa D. , Poon Evon , He Shuning , Resnick Efrat , Langer Ellen M. , Daniel Colin J. , Seo Hyuk-Soo , Chen Ying , Ficarro Scott B. , Jamin Yann , Lian Xiaolan , Kibe Shin , Kozono Shingo , Koikawa Kazuhiro , Doctor Zainab M. , Nabet Behnam , Browne Christopher M. , Yang Annan , Stoler-Barak Liat , Shah Richa B. , Vangos Nick E. , Geffken Ezekiel A. , Oren Roni , Sidi Samuel , Shulman Ziv , Wang Chu , Marto Jarrod A. , Dhe-Paganon Sirano , Look Thomas , Zhou Xiao Zhen , Lu Kun Ping , Sears Rosalie C. , Chesler Louis , Gray Nathanael S. , London Nir 
Published: March 2020

AbstractThe peptidyl-prolyl cis-trans isomerase, Pin1, acts as a unified signaling hub that is exploited in cancer to activate oncogenes and inactivate tumor suppressors, in particular through up-regulation of c-Myc target genes. However, despite considerable efforts, Pin1 has remained an elusive drug target. Here, we screened an electrophilic fragment library to discover covalent inhibitors targeting Pin1’s active site nucleophile - Cys113, leading to the development of Sulfopin, a double-digit nanomolar Pin1 inhibitor. Sulfopin is highly selective for Pin1, as validated by two independent chemoproteomics methods, achieves potent cellular andin vivotarget engagement, and phenocopies genetic knockout of Pin1. Although Pin1 inhibition had a modest effect on viability in cancer cell cultures, Sulfopin induced downregulation of c-Myc target genes and reduced tumor initiation and tumor progression in murine and zebrafish models of MYCN-driven neuroblastoma. Our results suggest that Sulfopin is a suitable chemical probe for assessing Pin1-dependent pharmacology in cells andin vivo. Moreover, these studies indicate that Pin1 should be further investigated as a potential cancer target.
Development of Nanobodies as first-in-class inhibitors for the NEDP1 deNEDDylating enzyme
Authors: Abidi Naima , Trauchessec Helene , Hassanzadeh-Ghassabeh Gholamreza , Pugniere Martine , Muyldermans Serge , Xirodimas Dimitris P. 
Published: March 2020

AbstractProtein NEDDylation emerges as an important post-translational modification and an attractive target for therapeutic intervention. Modification of NEDD8 onto substrates is finely balanced by the co-ordinated activity of conjugating and deconjugating enzymes. The NEDP1/DEN1/SENP8 protease is a NEDD8 specific processing and deconjugating enzyme that regulates the NEDDylation mainly of non-cullin substrates. Here, we report the development and characterisation of nanobodies as first-in-class inhibitors for NEDP1. The nanobodies display high-affinity (low nM) against NEDP1 and specifically inhibit NEDP1 processing activityin vitroand NEDP1 deconjugating activity in tissue-culture cells and in cell extracts. We also isolated nanobodies that bind to NEDP1 with high-affinity but do not affect NEDP1 activity. The developed nanobodies provide new tools to study the function of NEDP1 and to prevent deNEDDylation in cell extracts used in biochemical assays.
True S-cones are concentrated in the ventral mouse retina for color detection in the upper visual field
Authors: Nadal-Nicolás Francisco M. , Kunze Vincent P. , Ball John M. , Peng Brian , Krisnan Akshay , Zhou Gaohui , Dong Lijin , Li Wei 
Published: March 2020

ABSTRACTColor, an important visual cue for survival, is encoded by comparing signals from photoreceptors with different spectral sensitivities. The mouse retina expresses a short wavelength-sensitive and a middle/long wavelength-sensitive opsin (S- and M-opsin), forming opposing, overlapping gradients along the dorsal-ventral axis. Here, we analyzed the distribution of all cone types across the entire retina for two commonly used mouse strains. We found, unexpectedly, that ‘true’ S-cones (S-opsin only) are highly concentrated (up to 30% of cones) in ventral retina. Moreover, S-cone bipolar cells (SCBCs) are also skewed towards ventral retina, with wiring patterns matching the distribution of true S-cones. In addition, true S-cones in the ventral retina form clusters, which may augment synaptic input to SCBCs. Such a unique true S-cone pattern forms a basis for mouse color vision, likely reflecting evolutionary adaption to enhance color coding for the upper visual field suitable for mice’s habitat and behavior.
Iodine staining as a useful probe for distinguishing amyloid fibril polymorphs
Authors: Hiramatsu Takato , Yamamoto Naoki , Ha Seongmin , Masuda Yuki , Yasuda Mitsuru , Ishigaki Mika , Yuzu Keisuke , Ozaki Yukihiro , Chatani Eri 
Published: March 2020

ABSTRACTIt is recently suggested that amyloid polymorphism, i.e., structural diversity of amyloid fibrils, has a deep relationship with pathology. However, its prompt recognition is almost halted due to insufficiency of analytical methods for detecting polymorphism of amyloid fibrils sensitively and quickly. Here, we propose that iodine staining, a historically known reaction that was firstly found by Virchow, can be used as a method for distinguishing amyloid polymorphs. When insulin fibrils were prepared and iodine-stained, they exhibited different colors depending on polymorphs. Each of the colors was inherited to daughter fibrils by seeding reactions. The colors were fundamentally represented as a sum of three absorption bands in visible region between 400-750 nm, and the bands showed different titration curves against iodine, suggesting that there are three specific iodine binding sites. The analysis of resonance Raman spectra and polarization microscope suggested that several polyiodide ions composed of I3−and/or I5−were formed on the grooves or the edges of β-sheets. It was concluded that the polyiodide species and conformations formed are sensitive to surface structure of amyloid fibrils, and the resultant differences in color will be useful for detecting polymorphism in a wide range of diagnostic samples.