Miracle-dz/UniFAR-FTUs huggingface dataset:
Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses

The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared “core” genes detected in certain virus groups (e.g., the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique or multiple origin(s). These arguments also underline the risk of establishing premature high level viral taxonomic classifications. Those limitations are direct consequences of the random mechanisms governing the reductive/retrogressive evolution of all obligate intracellular parasites.
Charge Redistribution Mechanisms in SnSe2 Surfaces Exposed to Oxidative and Humid Environments and Their Related Influence on Chemical Sensing

Tin diselenide (SnSe2) is a van der Waals semiconductor, which spontaneously forms a subnanometric SnO2 skin once exposed to air. Here, by means of surface-science spectroscopies and density functional theory, we have investigated the charge redistribution at the SnO2–SnSe2 heterojunction in both oxidative and humid environments. Explicitly, we find that the work function of the pristine SnSe2 surface increases by 0.23 and 0.40 eV upon exposure to O2 and air, respectively, with a charge transfer reaching 0.56 e–/SnO2 between the underlying SnSe2 and the SnO2 skin. Remarkably, both pristine SnSe2 and defective SnSe2 display chemical inertness toward water, in contrast to other metal chalcogenides. Conversely, the SnO2–SnSe2 interface formed upon surface oxidation is highly reactive toward water, with subsequent implications for SnSe2-based devices working in ambient humidity, including chemical sensors. Our findings also imply that recent reports on humidity sensing with SnSe2 should be reinterpreted, considering the pivotal role of the oxide skin in the interaction with water molecules.
Terpenes and Terpenoids in Plants: Interactions with Environment and Insects

The interactions of plants with environment and insects are bi-directional and dynamic. Consequently, a myriad of mechanisms has evolved to engage organisms in different types of interactions. These interactions can be mediated by allelochemicals known as volatile organic compounds (VOCs) which include volatile terpenes (VTs). The emission of VTs provides a way for plants to communicate with the environment, including neighboring plants, beneficiaries (e.g., pollinators, seed dispersers), predators, parasitoids, and herbivores, by sending enticing or deterring signals. Understanding terpenoid distribution, biogenesis, and function provides an opportunity for the design and implementation of effective and efficient environmental calamity and pest management strategies. This review provides an overview of plant–environment and plant–insect interactions in the context of terpenes and terpenoids as important chemical mediators of these abiotic and biotic interactions.
Restudy on Effect of Various Physical and Chemical Factors on Infectivity of A Rabies Virus Isolate

Objective To analyze the effect of various physical and chemical factors on infectivity of a rabies street virus isolate.Methods A cell-adapted rabies street virus strain isolated in 2006,BD06 of passage 18,was exposed to various physical and chemical factors,and observed for infectivity by inoculation into BHK-21 cells and determination of titer(TCID50). Results BD06 strain was completely inactivated after being heated at 100℃ for 10 s or at 56℃ for 2 min,while survived for 6 d at 37℃,for 2 weeks at 4℃,and for more than 6 months at-20℃ below.The strain was completely inactivated within 2 min under ultraviolet lamp in a distance of 30 cm and within 10 min at pH values of less than 5 or more than 10,while survived at pH 6 ～ 10.The strain was stable to trypsin,while was completely inactivated within 20 min with acetone at a concentration of more than 30%,within 5 min with twice volumes of chloroform,within 2 min with 75% ethanol,within 6 h with 0.05% formaldehyde,and within 11 min with 10% formaldehyde.Conclusion The effect of various physical and chemical factors on infectivity of strain BD06 was analyzed,which provided a reference for rabies virus inactivation or disinfection during production.
Geographic ranges of genera and their constituent species: structure, evolutionary dynamics, and extinction resistance

Abstract. We explore the relationships among the geographic ranges of genera, the ranges and positions of their constituent species, and the number of species they contain, considering variation among coeval genera and changes within genera over time. Measuring range size as the maximal distance, or extent, between occurrences within a taxon, we find that the range of the most widespread species is a good predictor of the range of the genus, and that the number of species is a better predictor still. This analysis is complicated by a forced correlation: the range of a genus must be at least as large as that of each of its constituent species. We therefore focus on a second measure of range, the mean squared distance, or dispersion, of occurrences from the geographic centroid, which, by analogy to the analysis of variance, allows the total dispersion of a genus to be compared to the mean within-species dispersion and the dispersion among species centroids. We find that among-species dispersion is the principal determinant of genus dispersion. Within-species dispersion also plays a major role. The role of species richness is relatively small. Our results are not artifacts of temporal variation in the geographic breadth of sampled data. The relationship between changes in genus dispersion and changes in within- and among-species dispersion shows a symmetry, being similar in cases when the genus range is expanding and when it is contracting. We also show that genera with greater dispersion have greater extinction resistance, but that within- and among-species dispersion are not demonstrable predictors of survival once the dispersion of the genus is accounted for. Thus it is the range of the genus, rather than how it is attained, that is most relevant to its fate. Species richness is also a clear predictor of survival, beyond its effects on geographic range.
Therapeutic Potential of Endothelial Colony-Forming Cells in Ischemic Disease: Strategies to Improve their Regenerative Efficacy

Cardiovascular disease (CVD) comprises a range of major clinical cardiac and circulatory diseases, which produce immense health and economic burdens worldwide. Currently, vascular regenerative surgery represents the most employed therapeutic option to treat ischemic disorders, even though not all the patients are amenable to surgical revascularization. Therefore, more efficient therapeutic approaches are urgently required to promote neovascularization. Therapeutic angiogenesis represents an emerging strategy that aims at reconstructing the damaged vascular network by stimulating local angiogenesis and/or promoting de novo blood vessel formation according to a process known as vasculogenesis. In turn, circulating endothelial colony-forming cells (ECFCs) represent truly endothelial precursors, which display high clonogenic potential and have the documented ability to originate de novo blood vessels in vivo. Therefore, ECFCs are regarded as the most promising cellular candidate to promote therapeutic angiogenesis in patients suffering from CVD. The current briefly summarizes the available information about the origin and characterization of ECFCs and then widely illustrates the preclinical studies that assessed their regenerative efficacy in a variety of ischemic disorders, including acute myocardial infarction, peripheral artery disease, ischemic brain disease, and retinopathy. Then, we describe the most common pharmacological, genetic, and epigenetic strategies employed to enhance the vasoreparative potential of autologous ECFCs by manipulating crucial pro-angiogenic signaling pathways, e.g., extracellular-signal regulated kinase/Akt, phosphoinositide 3-kinase, and Ca2+ signaling. We conclude by discussing the possibility of targeting circulating ECFCs to rescue their dysfunctional phenotype and promote neovascularization in the presence of CVD.
Comparison of the Pathogenicity of Classical Swine Fever Virus Subgenotype 2.1c and 2.1d Strains from China

Classical swine fever (CSF) caused by classical swine fever virus (CSFV) is a highly contagious and devastating disease. The traditional live attenuated C-strain vaccine is widely used to control disease outbreaks in China. Since 2000, subgenotype 2.1 has become dominant in China. Here, we isolated subgenotype 2.1c and 2.1d strains from CSF-suspected pigs. The genetic variations and pathogenesis of subgenotype 2.1c and 2.1d strains were investigated experimentally. We aimed to evaluate and compare the replication characteristics and clinical signs of subgenotype 2.1c and 2.1d strains with those of the typical highly virulent CSFV SM strain. In PK-15 cells, the three CSFV isolates exhibited similar replication levels but significantly lower replication levels compared with the CSFV SM strain. The experimental animal infection model showed that the pathogenicity of subgenotype 2.1c and 2.1d strains was less than that of the CSFV SM strain. According to the clinical scoring system, subgenotype 2.1c (GDGZ-2019) and 2.1d (HBXY-2019 and GXGG-2019) strains were moderately virulent. This study showed that the pathogenicity of CSFV field strains will aid in the understanding of CSFV biological characteristics and the related epidemiology.
A Simplified Procedure for Titrating Hemagglutinating Capacity of Influenza-Virus and the Corresponding Antibody

A simplified procedure, based upon Hirst's test for titrating hemagglutinating capacity of influenza-virus and the corresponding antibody, has been described. The chief modifications involve reduction in the quantity of cells employed, determination of the endpoint of agglutination and inhibition by the pattern of the sedimented cells, and less rigid adherence to a specific time-interval. The influences of temperature, time, concentration of erythrocytes and order of addition of reagents have been investigated. The method has been standardized for optimal sensitivity and simple criteria have been adopted for measuring agglutination. The test for antibody-content of a serum has been simplified so as to reduce the amount of material required and by preparation of dilutions of serum directly in the suspension of red cells, thus involving the addition of one rather than two reagents to the serially diluted serum. The desirability of adopting some uniform scale for expressing the titer of antihemagglutinins in a serum has been discussed.
Role of Two-Component Regulatory Systems in Mechanisms of Antibiotic Resistance in Pesudomona aeruginosas

The Gram-negative opportunistic human pathogen Pseudomonas aeruginosa exists wide and also causes serious infections in hospitals.Two-component regulatory systems are designated to sense diverse stimuli and enact an appropriate and rapid adaptive physiological response,which are also involved in the mechanisms of antibiotic resistance.The major two-component regulatory systems include PhoP-PhoQ,PmrA-PmrB,CzcR-CzcS,CopR-CopS,GacA-GacS,RetS,LadS.Here we summarize the papers about these systems and provide insight into the mechanisms of antibiotic resistance in P.aeruginosa and novel therapeutic targets to conquer antibiotic resistance.
A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway

Simple Summary Temporal signaling dynamics are important for controlling the fate decisions of mammalian cells. In this study, we developed BioMASS, a computational platform for prediction and analysis of signaling dynamics using RNA-sequencing gene expression data. We first constructed a detailed mechanistic model of early transcriptional regulation mediated by ErbB receptor signaling pathway. After training the model parameters against phosphoprotein time-course datasets obtained from breast cancer cell lines, the model successfully predicted signaling activities of another untrained cell line. The result indicates that the parameters of molecular interactions in these different cell types are not particularly unique to the cell type, and the expression levels of the components of the signaling network are sufficient to explain the complex dynamics of the networks. Our method can be further expanded to predict signaling activity from clinical gene expression data for in silico drug screening for personalized medicine. Abstract A current challenge in systems biology is to predict dynamic properties of cell behaviors from public information such as gene expression data. The temporal dynamics of signaling molecules is critical for mammalian cell commitment. We hypothesized that gene expression levels are tightly linked with and quantitatively control the dynamics of signaling networks regardless of the cell type. Based on this idea, we developed a computational method to predict the signaling dynamics from RNA sequencing (RNA-seq) gene expression data. We first constructed an ordinary differential equation model of ErbB receptor → c-Fos induction using a newly developed modeling platform BioMASS. The model was trained with kinetic parameters against multiple breast cancer cell lines using autologous RNA-seq data obtained from the Cancer Cell Line Encyclopedia (CCLE) as the initial values of the model components. After parameter optimization, the model proceeded to prediction in another untrained breast cancer cell line. As a result, the model learned the parameters from other cells and was able to accurately predict the dynamics of the untrained cells using only the gene expression data. Our study suggests that gene expression levels of components within the ErbB network, rather than rate constants, can explain the cell-specific signaling dynamics, therefore playing an important role in regulating cell fate.
The Contractile Phenotype of Skeletal Muscle in TRPV1 Knockout Mice Is Gender-Specific and Exercise-Dependent

The transient receptor potential vanilloid 1 (TRPV1) belongs to the transient receptor potential superfamily of sensory receptors. TRPV1 is a non-selective cation channel permeable to Ca2+ that is capable of detecting noxious heat temperature and acidosis. In skeletal muscles, TRPV1 operates as a reticular Ca2+-leak channel and several TRPV1 mutations have been associated with two muscle disorders: malignant hyperthermia (MH) and exertional heat stroke (EHS). Although TRPV1−/− mice have been available since the 2000s, TRPV1’s role in muscle physiology has not been thoroughly studied. Therefore, the focus of this work was to characterize the contractile phenotype of skeletal muscles of TRPV1-deficient mice at rest and after four weeks of exercise. As MS and EHS have a higher incidence in men than in women, we also investigated sex-related phenotype differences. Our results indicated that, without exercise, TRPV1−/− mice improved in vivo muscle strength with an impairment of skeletal muscle in vitro twitch features, i.e., delayed contraction and relaxation. Additionally, exercise appeared detrimental to TRPV1−/− slow-twitch muscles, especially in female animals.
Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments

Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10−7 substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.
N-Butylidenephthalide Inhibits the Phenotypic Switch of VSMCs through Activation of AMPK and Prevents Stenosis in an Arteriovenous Fistula Rat Model

The phenotypic switch of vascular smooth muscle cells (VSMCs) plays a pivotal role in the development of vascular disorders, such as atherosclerosis, stenosis and restenosis, after vascular intervention. In our previous study, n-butylidenephthalide (BP) was reported to have anti-proliferating and apoptotic effects on VSMCs. The purpose of the current study is to further investigate its role in platelet-derived growth factor (PDGF)-induced VSMC phenotypic modulation in an arteriovenous fistula model. In vitro, we observed that BP inhibited the PDGF-induced cytoskeleton reorganization of the VSMCs. The enhanced expression of vimentin and collagen, as well as the migration ability induced by PDGF, were also inhibited by BP. By cell cycle analysis, we found that BP inhibited the PDGF-induced VSMCs proliferation and arrested the VSMCs in the G0/G1 phase. In an arteriovenous fistula rat model, the formation of stenosis, which was coupled with a thrombus, and the expression of vimentin and collagen in VSMCs, were also inhibited by administration of BP, indicating that BP inhibited the PDGF-induced phenotypic switch and the migration of VSMCs. Besides, the inhibitory effects of BP on the phenotypic switch were found to accompany the activated 5’ AMP-activated protein kinase (AMPK) as well as the inhibited phosphorylation of mTOR. Knockdown of AMPK by gene silencing conflicted the effects of BP and further exacerbated the PDGF-induced VSMCs phenotypic switch, confirming the modulating effect that BP exerted on the VSMCs by this pathway. These findings suggest that BP may contribute to the vasculoprotective potential in vasculature.
Interleukin-33 rescues perivascular adipose tissue anti-contractile function in obesity.

Perivascular adipose tissue (PVAT) depots are metabolically active and play a major vasodilator role in healthy lean individuals. In obesity they become inflamed and eosinophil-depleted and the anti-contractile function is lost with the development of diabetes and hypertension. Moreover, eosinophil-deficient ΔdblGATA-1 mice lack PVAT anti-contractile function, and exhibit hypertension. Here we have investigated the effects of inducing eosinophilia on PVAT function in health and obesity. Control, obese and ΔdblGATA-1 mice were administered intraperitoneal injections of interleukin-33 (IL-33) for five days. Conscious restrained blood pressure was measured, and blood was collected for glucose and plasma measurements. Wire myography was used to assess the contractility of mesenteric resistance arteries. IL-33 injections induced a hypereosinophilic phenotype. Obese animals had significant elevations in blood pressure, blood glucose and plasma insulin, which were normalised with IL-33. Blood glucose and insulin levels were also lowered in lean treated mice. In arteries from control mice, PVAT exerted an anti-contractile effect on the vessels, which was enhanced with IL-33 treatment. In obese mice, loss of PVAT anti-contractile function was rescued by IL-33. Exogenous application of IL-33 to isolated arteries induced a rapidly decaying endothelium-dependent vasodilation. The therapeutic effects were not seen in IL-33 treated ΔdblGATA-1 mice thereby confirming that the eosinophil is crucial. In conclusion, IL-33 treatment restored PVAT anti-contractile function in obesity, and reversed development of hypertension, hyperglycaemia, and hyperinsulinemia. These data suggest that targeting eosinophil numbers in PVAT offers a novel approach to the treatment of hypertension and type-2 diabetes in obesity.
Protein O-GlcNAcylation Promotes Trophoblast Differentiation at Implantation

Embryo implantation begins with blastocyst trophectoderm (TE) attachment to the endometrial epithelium, followed by the breaching of this barrier by TE-derived trophoblast. Dynamic protein modification with O-linked β-N-acetylglucosamine (O-GlcNAcylation) is mediated by O-GlcNAc transferase and O-GlcNAcase (OGA), and couples cellular metabolism to stress adaptation. O-GlcNAcylation is essential for blastocyst formation, but whether there is a role for this system at implantation remains unexplored. Here, we used OGA inhibitor thiamet g (TMG) to induce raised levels of O-GlcNAcylation in mouse blastocysts and human trophoblast cells. In an in vitro embryo implantation model, TMG promoted mouse blastocyst breaching of the endometrial epithelium. TMG reduced expression of TE transcription factors Cdx2, Gata2 and Gata3, suggesting that O-GlcNAcylation stimulated TE differentiation to invasive trophoblast. TMG upregulated transcription factors OVOL1 and GCM1, and cell fusion gene ERVFRD1, in a cell line model of syncytiotrophoblast differentiation from human TE at implantation. Therefore O-GlcNAcylation is a conserved pathway capable of driving trophoblast differentiation. TE and trophoblast are sensitive to physical, chemical and nutritive stress, which can occur as a consequence of maternal pathophysiology or during assisted reproduction, and may lead to adverse neonatal outcomes and associated adult health risks. Further investigation of how O-GlcNAcylation regulates trophoblast populations arising at implantation is required to understand how peri-implantation stress affects reproductive outcomes.
Study on Endophytic Fungi of Pteris multifida II:A Preliminary Study on a Strain of Rutin-Producing Endophytic Fungi

This article reports a sort of endophytic fungi(JJF006)which was separated from the rhizome of Pteris multifida.We conducted a preliminary study on its morphological characteristics,and used TLC to analyze the culture of the fungal strain,JJF006.The preliminary result indicates that the liquid culture media of the fungi contain rutin.