Comparative transcriptomics analysis on Senecavirus A-infected and non-infected cells.

Senecavirus A (SVA) is an emerging virus that causes the vesicular disease in pigs, clinically indistinguishable from other high consequence vesicular diseases. This virus belongs to the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded RNA, approximately 7,300 nt in length, with a 3' poly(A) tail but without 5'-end capped structure. SVA can efficiently propagate in different cells, including some non-pig-derived cell lines. A wild-type SVA was previously rescued from its cDNA clone using reverse genetics in our laboratory. In the present study, the BSR-T7/5 cell line was inoculated with the passage-5 SVA. At 12 h post-inoculation, SVA-infected and non-infected cells were independently collected for the analysis on comparative transcriptomics. The results totally showed 628 differentially expressed genes, including 565 upregulated and 63 downregulated ones, suggesting that SVA infection significantly stimulated the transcription initiation in cells. GO and KEGG enrichment analyses demonstrated that SVA exerted multiple effects on immunity-related pathways in cells. Furthermore, the RNA sequencing data were subjected to other in-depth analyses, such as the single-nucleotide polymorphism, transcription factors, and protein-protein interactions. The present study, along with our previous proteomics and metabolomics researches, provides a multi-omics insight into the interaction between SVA and its hosts.

Genomic profile of eGFP-tagged senecavirus A subjected to serial plaque-to-plaque transfers.

Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. This virus possesses a positive-sense, single-stranded RNA genome, approximately 7200 nt in length, composed of a single 5' untranslated region, encoding region and 3' untranslated region. In this study, a recombinant SVA tagged with enhanced green fluorescent protein (eGFP) sequence, rSVA-eGFP, was rescued from its cDNA clone using reverse genetics. The passage-5 (P5) rSVA-eGFP was totally subjected to 55 rounds of consecutive fluorescent plaque-to-fluorescent plaque (FP-FP) transfers, and one extra common passaging in vitro. The P61 viral stock was analyzed by next-generation sequencing. The result showed ten single-nucleotide mutations (SNMs) in the rSVA-eGFP genome, including nine transitions and only one transversion. The P61 progeny still showed a complete eGFP sequence, indicating no occurrence of copy-choice recombination within the eGFP region during serial FP-FP transfers. In other words, this progeny was genetically deficient in the recombination of eGFP sequence (RES), namely, an RES-deficient strain. Out of ten SNMs, three were missense mutations, leading to single-amino acid mutations (SAAMs): F15V in L protein, A74T in VP2, and E53R in 3D protein. The E53R was predicted to be spatially adjacent to the RNA channel of 3D protein, perhaps involved in the emergence of RES-deficient strain. In conclusion, this study uncovered a global landscape of rSVA-eGFP genome after serial FP-FP transfers, and moreover shed light on a putative SAAM possibly related to the RES-deficient mechanism.

Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets.

BACKGROUND: In modern animal husbandry, breeders pay increasing attention to improving sow nutrition during pregnancy and lactation to favor the health of neonates. Sow milk is a main food source for piglets during their first three weeks of life, which is not only a rich repository of essential nutrients and a broad range of bioactive compounds, but also an indispensable source of commensal bacteria. Maternal milk microorganisms are important sources of commensal bacteria for the neonatal gut. Bacteria from maternal milk may confer a health benefit on the host. METHODS: Sow milk bacteria were isolated using culturomics followed by identification using 16S rRNA gene sequencing. To screen isolates for potential probiotic activity, the functional evaluation was conducted to assess their antagonistic activity against pathogens in vitro and evaluate their resistance against oxidative stress in damaged Drosophila induced by paraquat. In a piglet feeding trial, a total of 54 newborn suckling piglets were chosen from nine sows and randomly assigned to three treatments with different concentrations of a candidate strain. Multiple approaches were carried out to verify its antioxidant function including western blotting, enzyme activity analysis, metabolomics and 16S rRNA gene amplicon sequencing. RESULTS: The 1240 isolates were screened out from the sow milk microbiota and grouped into 271 bacterial taxa based on a nonredundant set of 16S rRNA gene sequencing. Among 80 Pediococcus isolates, a new Pediococcus pentosaceus strain (SMM914) showed the best performance in inhibition ability against swine pathogens and in a Drosophila model challenged by paraquat. Pretreatment of piglets with SMM914 induced the Nrf2-Keap1 antioxidant signaling pathway and greatly affected the pathways of amino acid metabolism and lipid metabolism in plasma. In the colon, the relative abundance of Lactobacillus was significantly increased in the high dose SMM914 group compared with the control group. CONCLUSION: P. pentosaceus SMM914 is a promising probiotic conferring antioxidant capacity by activating the Nrf2-Keap1 antioxidant signaling pathway in piglets. Our study provided useful resources for better understanding the relationships between the maternal microbiota and offspring. Video Abstract.

Detailed 3D micro-modeling of rat aqueous drainage channels based on two-photon imaging: simulating aqueous humor through trabecular meshwork and Schlemm's canal by two-way fluid structure interaction approach.

Elevated intraocular pressure (IOP) appears to have a broader impact on increased resistance to aqueous humor (AH) outflow through the conventional aqueous outflow system (AOS). However, it is still unknown how AH drainage resistance is produced or why it becomes increased in glaucoma. It is hard to accurately obtain hydrodynamic parameters of AH within the trabecular meshwork (TM) outflow pathway tissues based on current technology. In this study, we reconstructed the rat AOS model with high-resolution two-photon imaging, and simulated the AH outflow process. The resolution of the two-photon imaging system can be up to 0.5 µm for imaging the AOS tissues. Quite a few morphological parameters of rat TM in conditions of normal and elevated IOP were determined using the experiment integrated with the simulation method. We determined that the TM thickness is 49.51 ± 6.07 µm with an IOP of 5.32 kPa, which significantly differed from the TM thickness of 66.4 ± 5.14 µm in the normal IOP group. Furthermore, 3D reconstruction of local aqueous drainage channels from two-photon microscopy images revealed detailed structures of the AOS and permitted the identification of 3D relationships of Schlemm's canal, collector channel, and trabecular drainage channels. An algorithm of finite element micro-modeling of the rat TM outflow pathways reveals the importance of TM for mechanical performance, with the potential to assist clinical therapies for glaucoma that seek to steer clear of an abnormal TM.

Genome-Wide Association Study of Muscle Glycogen in Jingxing Yellow Chicken.

Glucose metabolism plays an important role in many normal and pathological physiological processes in the body. The breakdown and synthesis of muscle glycogen provides ATP for muscle activities. A genome-wide association study for muscle glycogen was performed in 473 Jingxing yellow chickens to identify significant single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) involved in muscle glycogen metabolism. A total of nine SNPs (p < 1/699341) and three INDELs (p < 1/755733) reached a significant level of potential association. The following results were obtained through a series of analyses, including additive effects and gene function annotation. Two significant SNPs were found in introns 12 and 13 of copine 4 (CPNE4) on chromosome 2. The wild-type and mutant individuals had significant differences in glycogen metabolism at two loci (p < 0.01 for both). Individuals carrying two mutations had increased muscle glycogen content. According to the gene annotation of chromosome 11, there is a significant INDEL in intron 6 of naked cuticle homolog 1 (NKD1). After the INDEL mutation, the glycogen content increased significantly. There was a significant difference between wild-type and mutant individuals (p < 0.01). These mutations likely affecting two genes (CPNE4 and NKD1) may affect glycogen storage in a pleiotropic manner. Gene annotation indicates that CPNE4 and NKD1 may affect the process of glucose metabolism. Our findings contribute to understanding the genetic regulation of muscle glycogen metabolism and provide theoretical support.

Carboxymethyl konjac glucomannan mechanically reinforcing gellan gum microspheres for uranium removal.

Biosorbents have been a promising adsorbent to remove uranium while their poor mechanical properties prevent them from being widely used in practice. In this study, carboxymethyl konjac glucomannan (CMKGM) was incorporated to gellan gum to form a double-network gel micro spheres (CMKGM/GG-Al) for uranium removal with its mechanical strength fairly being reinforced. The compressive strength of the CMKGM/GG-Al microspheres was about 6 times than that of GG-Ca microspheres we prepared before while the adsorption capacity still be at a better value with the fitting maximum adsorption capacity being of 97.94 mg/g. Its uranium adsorption properties were investigated by considering the influence of pH, the adsorbent dosage, temperature, initial uranium concentration, time and coexisting ions. The adsorption mechanism was also investigated according to the SEM, EDX, FT-IR and XPS data analysis. The isotherm equilibrium data which were best fitted with Langmuir model and the kinetics data which were best fitted with pseudo-second-order model. It was inferred that the adsorption process was mainly the ion-exchange and the coordination with hydroxyl groups on the adsorbent surface and the adsorption process was endothermic and spontaneous. The CMKGM/GG-Al microspheres prepared in this study would be more conducive to practical application for uranium removal.