bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal control of phenylpropanoid biosynthesis by inducible complementation of a cinnamate 4-hydroxylase mutant
Authors: Kim Jeong Im , Hidalgo-Shrestha Christopher , Bonawitz Nicholas D. , Franke Rochus B. , Chapple Clint 
Published: July 2020

ABSTRACTCinnamate 4-hydroxylase (C4H) is a cytochrome P450-dependent monooxygenase that catalyzes the second step of the general phenylpropanoid pathway. Arabidopsisreduced epidermal fluorescence 3(ref3) mutants, which carry hypomorphic mutations inC4H, exhibit global alterations in phenylpropanoid biosynthesis and have developmental abnormalities including dwarfing. Here we report the characterization of a conditional Arabidopsis C4H line (ref3-2pOpC4H), in which wild-typeC4His expressed in theref3-2background. Expression ofC4Hin plants with well-developed primary inflorescence stems resulted in restoration of fertility and the production of substantial amounts of lignin, revealing that the developmental window for lignification is remarkably plastic. Following induction ofC4Hexpression inref3-2pOpC4H, we observed rapid and significant reductions in the levels of numerous metabolites, including several benzoyl and cinnamoyl esters and amino acid conjugates. These atypical conjugates were quickly replaced with their sinapoylated equivalents, suggesting that phenolic esters are subjected to substantial amounts of turnover in wild-type plants. Furthermore, using localized application of dexamethasone toref3-2pOpC4H, we show that phenylpropanoids are not transported appreciably from their site of synthesis. Finally, we identified a defective Casparian strip diffusion barrier in theref3-2mutant root endodermis, which is restored by induction ofC4Hexpression.HighlightThe work presented this paper provides evidence of metabolite turnover, plasticity of the developmental window for lignification, and the impact of reduced and restored cinnamate-4-hydroxylase (C4H)expression on the Casparian strip.
Prophylactic and Therapeutic Inhibition of In Vitro SARS-CoV-2 Replication by Oleandrin
Authors: Plante Kenneth S. , Plante Jessica A. , Fernandez Diana , Mirchandani Divya , Bopp Nathen , Aguilar Patricia V. , Sastry K. Jagannadha , Newman Robert A. , Weaver Scott C. 
Published: July 2020

ABSTRACTWith continued expansion of the COVID-19 pandemic, antiviral drugs are desperately needed to treat patients at high risk of life-threatening disease and even to limit spread if administered early during infection. Typically, the fastest route to identifying and licensing a safe and effective antiviral drug is to test those already shown safe in early clinical trials for other infections or diseases. Here, we testedin vitrooleandrin, derived from theNerium oleanderplant and shown previously to have inhibitory activity against several viruses. Using Vero cells, we found that prophylactic oleandrin administration at concentrations down to 0.05 μg/ml exhibited potent antiviral activity against SARS-CoV-2, with an 800-fold reduction in virus production, and a 0.1 μg/ml dose resulted in a greater than 3,000-fold reduction in infectious virus production. The EC50values were 11.98ng/ml when virus output was measured at 24 hours post-infection, and 7.07ng/ml measured at 48 hours post-infection. Therapeutic (post-infection) treatment up to 24 hours after infection of Vero cells also reduced viral titers, with the 0.1 μg/ml dose causing greater than 100-fold reductions as measured at 48 hours, and the 0.05 μg/ml dose resulting in a 78-fold reduction. The potent prophylactic and therapeutic antiviral activities demonstrated here strongly support the further development of oleandrin to reduce the severity of COVID-19 and potentially also to reduce spread by persons diagnosed early after infection.IMPORTANCECOVID-19, a pandemic disease caused by infection with SARS-CoV-2, has swept around the world to cause millions of infections and hundreds-of-thousands of deaths due to the lack of vaccines and effective therapeutics. We tested oleandrin, derived from theNerium oleanderplant and shown previously to reduce the replication of several viruses, against SARS-CoV-2 infection of Vero cells. When administered both before and after virus infection, nanogram doses of oleandrin significantly inhibited replication by up to 3,000-fold, indicating the potential to prevent disease and virus spread in persons recently exposed to SARS-CoV-2, as well as to prevent severe disease in persons at high risk. These results indicate that oleandrin should be tested in animal models and in humans exposed to infection to determine its medical usefulness in controlling the pandemic.
Intraperitoneal oil application causes local inflammation with depletion of resident peritoneal macrophages
Authors: Alsina-Sanchis Elisenda , Mülfarth Ronja , Moll Iris , Mogler Carolin , Rodriguez-Vita Juan , Fischer Andreas 
Published: July 2020

AbstractOil is frequently used as a solvent to inject lipophilic substances into the peritoneum of laboratory animals. Although mineral oil causes chronic peritoneal inflammation, little is known whether other oils are better suited. Here we show that olive, peanut, corn or mineral oil causes xanthogranulomatous inflammation with depletion of resident peritoneal macrophages. However, there were striking differences in the severity of the inflammatory response. Peanut and mineral oil caused severe chronic inflammation with persistent neutrophil and monocyte recruitment, expansion of the vasculature and fibrosis. Corn and olive oil provoked no or only mild signs of chronic inflammation. Mechanistically, the vegetal oils were taken up by macrophages leading to foam cell formation and induction of cell death. Olive oil triggered caspase-3 cleavage and apoptosis, which facilitates the resolution of inflammation. Peanut oil and, to a lesser degree, corn oil triggered caspase-1 activation and macrophage pyroptosis, which impairs the resolution of inflammation. As such, intraperitoneal oil administration can interfere with the outcome of subsequent experiments. As a proof-of-principle, intraperitoneal peanut oil injection was compared to its oral delivery in a thioglycolate-induced peritonitis model. The chronic peritoneal inflammation due to peanut oil injection impeded the proper recruitment of macrophages and the resolution of inflammation in this peritonitis model. In summary, the data indicate that it is advisable to deliver lipophilic substances like tamoxifen by oral gavage instead of intraperitoneal injection.
Transcriptome analysis of sevoflurane exposure effects at the different brain regions
Authors: Yamamoto Hiroto , Uchida Yutaro , Chiba Tomoki , Kurimoto Ryota , Matsushima Takahide , Ishikawa Chihiro , Li Haiyan , Shiga Takashi , Muratani Masafumi , Uchida Tokujiro , Asahara Hiroshi 
Published: July 2020

AbstractBackgroundsSevoflurane is a most frequently used volatile anaesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in whole brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis.MethodsEight-week old mice were exposed to sevoflurane. RNA from four medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted. Their gene ontology terms and the transcriptome array data of the cerebral cortex of sleeping mice were analysed using Metascape, and the gene expression patterns were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes.ResultsThe gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in the whole brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anaesthetized mice. Sevoflurane inducedKlf4upregulation in the whole brain. The transcriptional analysis result suggests that KLF4 is a potential transcriptional regulator of angiogenesis and neural development.ConclusionsKlf4was upregulated by sevoflurane inhalation in whole brain. KLF4 might promote angiogenesis and cause the appearance of undifferentiated neural cells by transcriptional regulation. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.
The ITS region provides a reliable DNA barcode for identifying reishi/lingzhi (Ganoderma) from herbal supplements
Authors: Gunnels Tess , Creswell Matthew , McFerrin Janis , Whittall Justen B. 
Published: July 2020

AbstractThe dietary supplement industry is a growing enterprise, valued at over $100 billion by 2025 yet, a recent study revealed that up to 60% of herbal supplements may have substituted ingredients not listed on their labels, some with harmful contaminants. Substituted ingredients make rigorous quality control testing a necessary aspect in the production of supplements. Traditionally, species have been verified morphologically or biochemically, but this is not possible for all species if the identifying characteristics are lost in the processing of the material. One approach to validating plant and fungal ingredients in herbal supplements is through DNA barcoding complemented with a molecular phylogenetic analysis. This method provides an efficient, objective, rigorous and repeatable method for species identification. We employed a molecular phylogenetic analysis for species authentication of the commonly used fungal supplement, reishi (Ganoderma lingzhi), by amplifying and sequencing the nuclear ribosomal internal transcribed spacer regions (ITS) with genus-specific primers. PCR of six powdered samples and one dried sample sold asG. lucidumrepresenting independent suppliers produced single, strong amplification products in the expected size-range forGanoderma. Both best-hit BLAST and molecular phylogenetic analyses using a reference panel assembled from Genbank clearly identified the predominant fungal DNA wasG. lingzhiin all seven herbal supplements. We detected variation in ITS among our samples, but all samples still fall within a large clade ofG. lingzhi. ITS is a successful and cost-effective method for DNA-based species authentication that could be used in the herbal supplement industry for this and other fungal and plant species that are otherwise difficult to identify.
TheMycobacterium tuberculosissRNA F6 modifies expression of essential chaperonins, GroEL2 and GroES
Authors: Houghton Joanna , Rodgers Angela , Rose Graham , D’Halluin Alexandre , Kipkorir Terry , Barker Declan , Waddell Simon J , Arnvig Kristine B. 
Published: July 2020

ABSTRACTAlmost 140 years after the identification ofMycobacterium tuberculosisas the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of theM. tuberculosissRNA, F6, and shown it to be dependent on SigF for expression, and significantly induced in starvation conditionsin vitroand in a mouse model of infection. Further exploration of F6 using anin vitrostarvation model of infection indicates that F6 affects the expression of the essential chaperonins, GroEL2 and GroES. Our results point towards a role for F6 during periods of low metabolic activity typically associated with long-term survival ofM. tuberculosisin human granulomas.
Evaluation of Micronuclei Frequency in Both Shelter and Family Cats and Dogs
Authors: Santovito Alfredo , Buglisi Martina , Scarfo’ Manuel 
Published: July 2020

AbstractEach year a lot of animals are cared for in shelters in Italy. Many of these animals have received minimal or no prior healthcare. Thus, the beneficial role animal shelters play is undeniable. Nonetheless, even well-run shelters lack the necessary resources to provide adequate conditions. It is common knowledge that group-housing can increase stress levels in family cats (Felis silvestris lybica) and dogs (Canis lupus familiaris) contributing to the development of infectious diseases and/or behavioural problems.The aim of this study is to evaluate, through the buccal micronucleus assay, the level of genomic damage in shelter cats and dogs and compare it with that of family cats and dogs. The hypothesis is that environmental conditions such as those potentially present in shelters can affect the level of genomic damage.The study population included thirty healthy mixed breed cats and dogs, randomly sampled, with at a minimum two-year presence in a shelter. The control group consisted of thirty healthy cats and dogs living in a home environment, using age/sex matching. The micronucleus assay was performed on one thousand exfoliated buccal mucosa cells per subject and standardized protocols were used for stress score tests.Significant differences were found between shelter and family cats and dogs in terms of micronuclei, indicating that a condition of stress found in sheltered cats may increase the levels of genomic damage. Conversely, no significant differences in the frequency of micronuclei were found between the sexes, as well as no correlation was found between age and the frequencies of the used genomic markers.
Modeling gene regulation in response to wounding: temporal variations, hormonal variations, and specialized metabolism pathways induced by wounding
Authors: Moore Bethany M. , Lee Yun Sun , Grotewold Erich , Shiu Shin-Han 
Published: July 2020

AbstractPlants respond to wounding stress by changing gene expression patterns and inducing jasmonic acid (JA), as well as other plant hormones. This includes activating some specialized metabolism pathways, including the glucosinolate pathways, in the case ofArabidopsis thaliana. We model how these responses are regulated by using machine learning to incorporate putative cis-regulatory elements (pCREs), known transcription factor binding sites from literature,in-vitroDNA affinity purification sequencing (DAP-seq) and DNase I hypersensitive sites to predict gene expression for genes clustered by their wound response using machine learning. We found temporal patterns where regulatory sites and regions of open chromatin differed between clusters of genes up-regulated at early and late wounding time points as well as clusters where JA response was induced relative to clusters where JA response was not induced. Overall, we identified pCREs that improved model predictions of expression clusters over known binding sites. We discovered 4,255 pCREs related to wound response at different time points and 2,569 pCREs related to differences between JA-induced and non-JA induced wound response. In addition, pCREs found to be important at different wounding time points were mapped to the promoters of genes in a glucosinolate biosynthesis pathway indicating regulation of this pathway under wounding stress. Finally, we experimentally validated a predicted cis-regulatory element, CCGCGT, showing that knock-out via CRISPR-Cas9 reduces gene expression in response to wounding.
In situgeneration of RNA complexes for synthetic molecular strand displacement circuits in autonomous systems
Authors: Bae Wooli , Stan Guy-Bart V. , Ouldridge Thomas E. 
Published: July 2020

AbstractSynthetic molecular circuits implementing DNA or RNA strand-displacement reactions can be used to build complex systems such as molecular computers and feedback control systems. Despite recent advances, application of nucleic acid-based circuitsin vivoremains challenging due to a lack of efficient methods to produce their essential components – multi-stranded complexes known as “gates” –in situ, i.e. in living cells or other autonomous systems. Here, we propose the use of naturally occurring self-cleaving ribozymes to cut a single-stranded RNA transcript into a gate complex of shorter strands, thereby opening new possibilities for the autonomous and continuous production of RNA strands in a stoichiometrically and structurally controlled way.
Transcripts of vaccinia virus postreplicative genes do not contain a 5’ methylguanosine cap
Authors: Vopálenský Václav , Sýkora Michal , Mělková Zora , Mašek Tomáš , Pospíšek Martin 
Published: July 2020

AbstractVaccinia virus (VACV) is a prototypical poxvirus originally used for eradication of smallpox. Investigation into VACV mRNAs carried out almost half a century ago substantially contributed to the fundamental discovery of the 5’ mRNA cap, a hallmark of all eukaryotic and many viral mRNAs. VACV research also facilitated the identification and understanding of the general mechanism of 5’ mRNA cap synthesis. We characterized the VACV transcripts at the individual mRNA molecule level and found that vaccinia postreplicative mRNAs, containing nontemplated 5’ poly(A) leaders, surprisingly lack the 5’ cap structurein vivo. We also show that the lengths of the nontemplated leaders and the presence or absence of cap structures at the 5’ mRNA ends are controlled by the initiator sequence of the VACV postreplicative promoters.One Sentence SummaryThe promoter sequence determines the synthesis of the 5’ cap and poly(A) leaders in vaccinia virus postreplicative mRNAs.
Neural tube closure requires the endocytic receptor Lrp2 and its functional interaction with intracellular scaffolds
Authors: Kowalczyk Izabela , Lee Chanjae , Schuster Elisabeth , Hoeren Josefine , Trivigno Valentina , Riedel Levin , Görne Jessica , Wallingford John B. , Hammes Annette , Feistel Kerstin 
Published: July 2020

AbstractRecent studies have revealed that pathogenic mutations in the endocytic receptor LRP2 in humans are associated with severe neural tube closure defects (NTDs) such as anencephaly and spina bifida. Here, we combined analysis of neural tube closure in mouse and in the African Clawed FrogXenopus laevisto elucidate the etiology of Lrp2-related NTDs.Lrp2loss-of-function (LOF) impaired neuroepithelial morphogenesis, culminating in NTDs that impeded anterior neural plate folding and neural tube closure in both model organisms. Loss of Lrp2 severely affected apical constriction as well as proper localization of the core planar cell polarity (PCP) protein Vangl2, demonstrating a highly conserved role of the receptor in these processes essential for neural tube formation. In addition, we identified a novel functional interaction of Lrp2 with the intracellular adaptor proteins Shroom3 and Gipc1 in the developing forebrain. Our data suggest that during neurulation, motifs within the intracellular domain of Lrp2 function as a hub that orchestrates endocytic membrane removal for efficient apical constriction as well as PCP component trafficking in a temporospatial manner.Summary statementAnalysis of neurulation in mouse andXenopusreveals novel roles for Lrp2-mediated endocytosis in orchestrating apical constriction and planar cell polarity essential for neural tube closure.
Exposure to a mixture of BMAA and MCLR synergistically modulates behavior in larval zebrafish while exacerbating molecular changes related to neurodegeneration
Authors: Martin Rubia M. , Bereman Michael S. , Marsden Kurt C. 
Published: July 2020

AbstractExposure to toxins produced by cyanobacteria (i.e., cyanotoxins) is an emerging health concern due to their increased occurrence and previous associations with neurodegenerative disease including amyotrophic lateral sclerosis (ALS). The objective of this study was to evaluate the neurotoxic effects of a mixture of two co-occurring cyanotoxins, β-methylamino-L-alanine (BMAA) and microcystin leucine and arginine (MCLR), using the larval zebrafish model. We combined high-throughput behavior based toxicity assays with discovery proteomic techniques to identify behavioral and molecular changes following 6 days of exposure. While neither toxin caused mortality, morphological defects, or altered general locomotor behavior in zebrafish larvae, both toxins increased acoustic startle sensitivity in a dose-dependent manner by at least 40% (p<0.0001). Furthermore, startle sensitivity was enhanced by an additional 40% in larvae exposed to the BMAA/MCLR mixture relative to those exposed to the individual toxins. Supporting these behavioral results, our proteomic analysis revealed a 4-fold increase in the number of differentially expressed proteins (DEPs) in the mixture exposed group. Additionally, prediction analysis reveals activation and/or inhibition of 8 enriched canonical pathways (enrichment p-value<0.01; z-score≥|2|), including ILK, Rho Family GTPase, RhoGDI, and calcium signaling pathways, which have been implicated in neurodegeneration. We also found that expression of TDP-43, of which cytoplasmic aggregates are a hallmark of ALS pathology, was significantly upregulated by 5.7-fold following BMAA/MCLR mixture exposure. Together, our results emphasize the importance of including mixtures of cyanotoxins when investigating the link between environmental cyanotoxins and neurodegeneration as we reveal that BMAA and MCLR interactin vivoto enhance neurotoxicity.
Re-exposure to a sensorimotor perturbation produces opposite effects on explicit and implicit learning processes
Authors: Avraham Guy , Morehead J Ryan , Kim Hyosub E , Ivry Richard B 
Published: July 2020

AbstractThe motor system demonstrates an exquisite ability to adapt to changes in the environment, and to quickly reset when these changes prove transient. If similar environmental changes are encountered in the future, learning may be faster, a phenomenon known as savings. In studies of sensorimotor learning, a central component of savings is attributed to the explicit recall of the task structure and appropriate compensatory strategies. Whether implicit adaptation also contributes to savings remains subject to debate (Leow et al., 2020; Yin and Wei, 2020). We tackled this question by measuring, in parallel, explicit and implicit adaptive responses in a visuomotor rotation task, employing a protocol that typically elicits savings. While the initial rate of learning was faster in the second exposure to the perturbation, an analysis decomposing the two processes showed the benefit to be solely associated with explicit re-aiming. Surprisingly, we found a significant decrease after relearning in aftereffect magnitudes during no-feedback trials, a direct measure of implicit adaptation. In a second experiment, we isolated implicit adaptation using clamped visual feedback, a method known to eliminate the contribution of explicit learning processes. Consistent with the results of the first experiment, participants exhibited a marked reduction in the adaptation function, as well as an attenuated aftereffect when re-learning from the clamped feedback. Motivated by these results, we re-analyzed data from prior studies and observed a consistent, yet unappreciated pattern of attenuation of implicit adaptation during relearning. These results indicate that explicit and implicit sensorimotor processes exhibit opposite effects upon relearning: Explicit learning shows savings, while implicit adaptation becomes attenuated.