NutriFD: Proving the medicinal value of food nutrition based on food-disease association and treatment networks

There is rising evidence of the health benefit associated with specific dietary interventions. Current food-disease databases focus on associations and treatment relationships but haven't provided a reasonable assessment of the strength of the relationship, and lack of attention on food nutrition. There is an unmet need for a large database that can guide dietary therapy. We fill the gap with NutriFD, a scoring network based on associations and therapeutic relationships between foods and diseases. NutriFD integrates 9 databases including foods, nutrients, diseases, genes, miRNAs, compounds, disease ontology and their relationships. To our best knowledge, this database is the only one that can score the associations and therapeutic relationships of everyday foods and diseases by weighting inference scores of food compounds to diseases. In addition, NutriFD demonstrates the predictive nature of nutrients on the therapeutic relationships between foods and diseases through machine learning models, laying the foundation for a mechanistic understanding of food therapy

Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus

Influenza C virus (ICV) was first identified in humans and swine, but recently also in cattle, indicating a wider host range and potential threat to both the livestock industry and public health than was originally anticipated. The ICV hemagglutinin-esterase (HE) glycoprotein has multiple functions in the viral replication cycle and is the major determinant of antigenicity. Here, we developed a comparative approach integrating genetics, molecular selection analysis, and structural biology to identify the codon usage and adaptive evolution of ICV. We show that ICV can be classified into six lineages, consistent with previous studies. The HE gene has a low codon usage bias, which may facilitate ICV replication by reducing competition during evolution. Natural selection, dinucleotide composition, and mutation pressure shape the codon usage patterns of the ICV HE gene, with natural selection being the most important factor. Codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of ICV was to humans, followed by cattle and swine. Additionally, similarity index (SiD) analysis revealed that swine exerted a stronger evolutionary pressure on ICV than humans, which is considered the primary reservoir. Furthermore, a similar tendency was also observed in the M gene. Of note, we found HE residues 176, 194, and 198 to be under positive selection, which may be the result of escape from antibody responses. Our study provides useful information on the genetic evolution of ICV from a new perspective that can help devise prevention and control strategies

A shift in Porcine circovirus 3 (PCV‐3) history paradigm: Phylodynamic analyses reveal an ancient origin and prolonged undetected circulation in the worldwide swine population

The identification of a new circovirus (Porcine circovirus 3, PCV-3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV-2). Preliminary results suggest an extremely recent PCV-3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV-3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV-3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV-3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10 −5 –10 −6 substitution/site/ year) than the PCV-2 one. Accordingly, the action of selective pressures on PCV-3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV-2, suggesting either a reduced PCV-3 plasticity or a less efficient host-induced natural selection. A complex and not-directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium.info:eu-repo/semantics/publishedVersio

Host-range shift of H3N8 canine influenza virus: a phylodynamic analysis of its origin and adaptation from equine to canine host

International audiencePrior to the emergence of H3N8 canine influenza virus (CIV) and the latest avian-origin H3N2 CIV, there was no evidence of a circulating canine-specific influenza virus. Molecular and epidemiological evidence suggest that H3N8 CIV emerged from H3N8 equine influenza virus (EIV). This host-range shift of EIV from equine to canine hosts and its subsequent establishment as an enzootic CIV is unique because this host-range shift was from one mammalian host to another. To further understand this host-range shift, we conducted a comprehensive phylodynamic analysis using all the available whole-genome sequences of H3N8 CIV. We found that (1) the emergence of H3N8 CIV from H3N8 EIV occurred in approximately 2002; (2) this interspecies transmission was by a reassortant virus of the circulating Florida-1 clade H3N8 EIV; (3) once in the canine species, H3N8 CIV spread efficiently and remained an enzootic virus; (4) H3N8 CIV evolved and diverged into multiple clades or sublineages, with intra and inter-lineage reassortment. Our results provide a framework to understand the molecular basis of host-range shifts of influenza viruses and that dogs are potential “mixing vessels” for the establishment of novel influenza viruses

Promoting neuro-supportive properties of astrocytes with epidermal growth factor hydrogels

Biomaterials provide novel platforms to deliver stem cell and growth factor therapies for central nervous system (CNS) repair. The majority of these approaches have focused on the promotion of neural progenitor cells and neurogenesis. However, it is now increasingly recognized that glial responses are critical for recovery in the entire neurovascular unit. In this study, we investigated the cellular effects of epidermal growth factor (EGF) containing hydrogels on primary astrocyte cultures. Both EGF alone and EGF‐hydrogel equally promoted astrocyte proliferation, but EGF‐hydrogels further enhanced astrocyte activation, as evidenced by a significantly elevated Glial fibrillary acidic protein (GFAP) gene expression. Thereafter, conditioned media from astrocytes activated by EGF‐hydrogel protected neurons against injury and promoted synaptic plasticity after oxygen–glucose deprivation. Taken together, these findings suggest that EGF‐hydrogels can shift astrocytes into neuro‐supportive phenotypes. Consistent with this idea, quantitative‐polymerase chain reaction (qPCR) demonstrated that EGF‐hydrogels shifted astrocytes in part by downregulating potentially negative A1‐like genes (Fbln5 and Rt1‐S3) and upregulating potentially beneficial A2‐like genes (Clcf1, Tgm1, and Ptgs2). Further studies are warranted to explore the idea of using biomaterials to modify astrocyte behavior and thus indirectly augment neuroprotection and neuroplasticity in the context of stem cell and growth factor therapies for the CNS. Stem Cells Translational Medicine 2019 Biomaterials provide novel platforms to deliver stem cell and growth factor therapies for central nervous system repair. Our data suggest that epidermal growth factor‐containing hydrogels can shift astrocytes into potentially beneficial A2‐like phenotypes that may augment neuroprotection and neuroplasticity during the recovery phase after brain injury

Magnetoelectric interaction and transport behaviours in magnetic nanocomposite thermoelectric materials

How to suppress the performance deterioration of thermoelectric materials in the intrinsic excitation region remains a key challenge. The magnetic transition of permanent magnet nanoparticles from ferromagnetism to paramagnetism provides an effective approach to finding the solution to this challenge. Here, we have designed and prepared magnetic nanocomposite thermoelectric materials consisting of BaFe12O19 nanoparticles and Ba0.3In0.3Co4Sb12 matrix. It was found that the electrical transport behaviours of the nanocomposites are controlled by the magnetic transition of BaFe12O19 nanoparticles from ferromagnetism to paramagnetism. BaFe12O19 nanoparticles trap electrons below the Curie temperature (TC) and release the trapped electrons above the TC, playing an ‘electron repository’ role in maintaining high figure of merit ZT. BaFe12O19 nanoparticles produce two types of magnetoelectric effect—electron spiral motion and magnon-drag thermopower—as well as enhancing phonon scattering. Our work demonstrates that the performance deterioration of thermoelectric materials in the intrinsic excitation region can be suppressed through the magnetic transition of permanent magnet nanoparticles

Common variants in SOX-2 and congenital cataract genes contribute to age-related nuclear cataract

Nuclear cataract is the most common type of age-related cataract and a leading cause of blindness worldwide. Age-related nuclear cataract is heritable (h2 = 0.48), but little is known about specific genetic factors underlying this condition. Here we report findings from the largest to date multi-ethnic meta-analysis of genome-wide association studies (discovery cohort N = 14,151 and replication N = 5299) of the International Cataract Genetics Consortium. We confirmed the known genetic association of CRYAA (rs7278468, P = 2.8 × 10−16) with nuclear cataract and identified five new loci associated with this disease: SOX2-OT (rs9842371, P = 1.7 × 1

Study on the Mechanism of Solid-Phase Oxidant Action in Tribochemical Mechanical Polishing of SiC Single Crystal Substrate

Na2CO3—1.5 H2O2, KClO3, KMnO4, KIO3, and NaOH were selected for dry polishing tests with a 6H-SiC single crystal substrate on a polyurethane polishing pad. The research results showed that all the solid-phase oxidants, except NaOH, could decompose to produce oxygen under the frictional action. After polishing with the five solid-phase oxidants, oxygen was found on the surface of SiC, indicating that all five solid-phase oxidants can have complex tribochemical reactions with SiC. Their reaction products are mainly SiO2 and (SiO2)x. Under the action of friction, due to the high flash point temperature of the polishing interface, the oxygen generated by the decomposition of the solid-phase oxidant could oxidize the surface of SiC and generate a SiO2 oxide layer on the surface of SiC. On the other hand, SiC reacted with H2O and generated a SiO2 oxide layer on the surface of SiC. After polishing with NaOH, the SiO2 oxide layer and soluble Na2SiO3 could be generated on the SiC surface; therefore, the surface material removal rate (MRR) was the highest, and the surface roughness was the largest, after polishing. The lowest MRR was achieved after the dry polishing of SiC with KClO3

Adsorption Studies on the Removal of Anionic and Cationic Dyes from Aqueous Solutions Using Discarded Masks and Lignin

The carbon materials derived from discarded masks and lignin are used as adsorbent to remove two types of reactive dyes present in textile wastewater: anionic and cationic. This paper introduces the results of batch experiments where Congo red (CR) and Malachite green (MG) are removed from wastewater onto the carbon material. The relationship between adsorption time, initial concentration, temperature and pH value of reactive dyes was investigated by batch experiments. It is discovered that pH 5.0–7.0 leads to the maximum effectiveness of CR and MG removal. The equilibrium adsorption capacities of CR and MG are found to be 232.02 and 352.11 mg/g, respectively. The adsorption processes of CR and MG are consistent with the Freundlich and Langmuir adsorption models, respectively. The thermodynamic processing of the adsorption data reveals the exothermic properties of the adsorption of both dyes. The results show that the dye uptake processes follow secondary kinetics. The primary adsorption mechanisms of MG and CR dyes on sulfonated discarded masks and alkaline lignin (DMAL) include pore filling, electrostatic attraction, π-π interactions and the synergistic interactions between the sulphate and the dyes. The synthesized DMAL with high adsorption efficiency is promising as an effective recyclable adsorbent for adsorbing dyes, especially MG dyes, from wastewater

Generation of Monoclonal Antibodies against Variable Epitopes of the M Protein of Rabies Virus

Rabies virus (RABV), the causative agent of rabies, is highly neurovirulent for warm-blooded animals with a mortality rate of up to 100%. The RABV matrix protein (M) is required for virus particle assembly and budding. However, little is known about antigenic differences in the M protein. In this study, five monoclonal antibodies (mAbs), designated 3B9, 4A1, 2B11, 2C1, and 4B11, against the RABV M protein were generated using a recombinant M protein. All five mAbs reacted with the CVS-11 strain but showed no reactivity against the HEP-Flury strain in indirect immunofluorescence and western blotting. The epitope targeted by these mAbs was further identified by peptide scanning using GST-fused peptides. The 25PPYDDD30 peptide was defined as the minimal linear epitope. Alignment of amino acid sequences and phylogenetic analysis of different RABV strains indicated that the variable epitope 25PPDGDD30 is only present in the HEP-Flury and variant Flury strains of clade III, while the other strains resembling ERA and SRVA9 within the clade had another variable epitope, 25PLDDDD30. A Y27D mutation within the epitope was found among the rest of the RABV strains distributed in different clades. However, a single D28G mutation eliminated the reactivity of these five mAbs. In addition, the mAbs were able to recognize wildtype RABV strain in indirect immunofluorescence and western blotting and detect RABV-infected brain tissue using immunohistochemistry. The newly established mAbs and identified epitope may facilitate future investigations in the structure and function of the M protein and the development of diagnostic methods for the detection of different RABV strains worldwide. Most importantly, the epitope recognized by the mAbs against M protein might serve as a novel target for the development of a vaccine targeting RABV virulent strains