Genomic Characteristics of Feline Anelloviruses Isolated from Domestic Cats in Shanghai, China.

Viral metagenomics techniques allow the high-throughput discovery of possible pathogens carried by companion animals from their feces and other excreta. In this study, the viral metagenomics of 22 groups of fecal samples from domestic cats revealed a high prevalence of feline anelloviruses (FcTTV) infection in domestic cats in Shanghai, China. Serum samples from 30 cat individuals were further detected by polymerase chain reaction, and an average positive rate of 36.67% (11/30) of FcTTV infection was found. Next, the full-length sequences of five Shanghai FcTTV variants were obtained and submitted to GenBank with access numbers OP186140 to OP186144. Phylogenetic analysis indicates that the Shanghai FcTTV variants have relatively consistent genomic characteristics, with two variants from Zhejiang 2019 and one variant from the Czech Republic 2010. The recombination event analysis of the variants showed that one variant (OP186141_SH-02) had a primary parental sequence derived from a variant (KM229764) from the Czech Republic in 2010, while the secondary parental sequence was derived from OP186140_SH-01. The results revealed that FcTTV infection is prevalent in domestic cats and that the use of viral metagenomics to rapidly identify some infecting viruses whose hosts lack clinical features would be an effective approach.

Identification and Genome Characterization of Novel Feline Parvovirus Strains Isolated in Shanghai, China.

Feline panleukopenia virus (FPV) is the causative agent of hemorrhagic gastroenteritis in feline animals. FPV has been evolving over time, and there have been several different strains of the virus identified. Some of these strains may be more virulent or more resistant to current vaccines than others, which highlights the importance of ongoing research and monitoring of FPV evolution. For FPV genetic evolution analysis, many studies focus on the main capsid protein (VP2), but limited information is available on the nonstructural gene NS1 and structural gene VP1. In the present study, we firstly isolated two novel FPV strains circulating in Shanghai, China, and performed full-length genome sequencing for the desired strains. Subsequently, we focused on analyzing the NS1, VP1 gene, and the encoding protein, and conducted a comparative analysis among the worldwide circulating FPV and Canine parvovirus Type 2 (CPV-2) strains, which included the strains isolated in this study. We found that the 2 structural viral proteins, VP1 and VP2, are splice variants, and VP1 has a 143 amino-acid-long N-terminal compared to VP2. Furthermore, phylogenetic analysis showed that divergent evolution between FPV and CPV-2 virus strains were clustered mostly by country and year of detection. In addition, much more continuous antigenic type changes happened in the process of CPV-2 circulating and evolution compared to FPV. These results stress the importance of the continuous study of viral evolution and provide a comprehensive perspective of the association between viral epidemiology and genetic evolution.

Phylogenetic Characteristics of Canine Parvovirus Type 2c Variant Endemic in Shanghai, China.

Canine parvovirus type 2 (CPV-2) has spread and mutated globally over the past 40 years. In the present study, 206 samples from dogs suspected of CPV-2 infection were collected from five veterinary clinics in Shanghai city, China. The average positive rate for CPV-2 was detected to be 40.78% using the PCR method. Using an F81 cell (feline kidney cell) culture, the isolates of three CPV-2c strains were obtained. The near full-length genome sequences of the isolates were determined and submitted to GenBank: CPV-SH2001 (MW650830), CPV-SH2002 (MW811188), and CPV-SH2003 (MW811189). By comparing the amino acid sequences of 12 CPV strains with those of 48 related strains retrieved from GenBank, all of the CPV strains from Shanghai were typed as belonging to a relatively new CPV-2c variant spreading in Asia, with typical amino acid residues (5Gly, 267Tyr, 324Ile, and 370Arg) in the VP2 protein. The divergence time of this new CPV-2c clade was estimated by the phylogenetic tree using the maximum likelihood and RelTime with Dated Tips (RTDT) approaches. Our results indicate that the 426 and 324 VP2 amino acid residues are under strong selection pressure with a posterior probability of 0.966 and 0.943, respectively. Therefore, this study provides insight into the phylogenetic characteristics of the current CPV-2c variant in Shanghai city, China.

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus).

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14-20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion-deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide F ST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

Correction: Polygalacturonase gene pgxB in Aspergillus niger is a virulence factor in apple fruit.

[This corrects the article DOI: 10.1371/journal.pone.0173277.].

Polygalacturonase gene pgxB in Aspergillus niger is a virulence factor in apple fruit.

Aspergillus niger, a saprophytic fungus, is widely distributed in soil, air and cereals, and can cause postharvest diseases in fruit. Polygalacturonase (PG) is one of the main enzymes in fungal pathogens to degrade plant cell wall. To evaluate whether the deletion of an exo-polygalacturonase gene pgxB would influence fungal pathogenicity to fruit, pgxB gene was deleted in Aspergillus niger MA 70.15 (wild type) via homologous recombination. The ΔpgxB mutant showed similar growth behavior compared with the wild type. Pectin medium induced significant higher expression of all pectinase genes in both wild type and ΔpgxB in comparison to potato dextrose agar medium. However, the ΔpgxB mutant was less virulent on apple fruits as the necrosis diameter caused by ΔpgxB mutant was significantly smaller than that of wild type. Results of quantitive-PCR showed that, in the process of infection in apple fruit, gene expressions of polygalacturonase genes pgaI, pgaII, pgaA, pgaC, pgaD and pgaE were enhanced in ΔpgxB mutant in comparison to wild type. These results prove that, despite the increased gene expression of other polygalacturonase genes in ΔpgxB mutant, the lack of pgxB gene significantly reduced the virulence of A. niger on apple fruit, suggesting that pgxB plays an important role in the infection process on the apple fruit.

Human adenosine deaminases ADA1 and ADA2 bind to different subsets of immune cells.

At sites of inflammation and tumor growth, the local concentration of extracellular adenosine rapidly increases and plays a role in controlling the immune responses of nearby cells. Adenosine deaminases ADA1 and ADA2 (ADAs) decrease the level of adenosine by converting it to inosine, which serves as a negative feedback mechanism. Mutations in the genes encoding ADAs lead to impaired immune function, which suggests a crucial role for ADAs in immune system regulation. It is not clear why humans and other mammals possess two enzymes with adenosine deaminase activity. Here, we found that ADA2 binds to neutrophils, monocytes, NK cells and B cells that do not express CD26, a receptor for ADA1. Moreover, the analysis of CD4+ T-cell subset revealed that ADA2 specifically binds to regulatory T cells expressing CD39 and lacking the receptor for ADA1. Also, it was found that ADA1 binds to CD16- monocytes, while CD16+ monocytes preferably bind ADA2. A study of the blood samples from ADA2-deficient patients showed a dramatic reduction in the number of lymphocyte subsets and an increased concentration of TNF-α in plasma. Our results suggest the existence of a new mechanism, where the activation and survival of immune cells is regulated through the activities of ADA2 or ADA1 anchored to the cell surface.

Application of ADA1 as a new marker enzyme in sandwich ELISA to study the effect of adenosine on activated monocytes.

Enzyme-linked immunosorbent assay (ELISA) is a valuable technique to detect antigens in biological fluids. Horse radish peroxidase (HRP) is one of the most common enzymes used for signal amplification in ELISA. Despite new advances in technology, such as a large-scale production of recombinant enzymes and availability of new detection systems, limited research is devoted to finding alternative enzymes and their substrates to amplify the ELISA signals. Here, HRP-avidin was substituted with the human adenosine deaminase (hADA1)-streptavidin complex and adenosine as a detection system in commercial ELISA kits. The hADA1 ELISA was successfully used to demonstrate that adenosine, bound to A1 and A3 adenosine receptors, increases cytokine secretion by LPS activated monocytes. We show that hADA1-based ELISA has the same sensitivity, and also provides identical results, as HRP ELISA. In addition, the sensitivity of hADA1-based ELISA could be easily adjusted by changing the adenosine concentration and the incubation time. Therefore, hADA1 could be used as a detection enzyme with any commercial ELISA kit with a wide range of concentration of antigens.

Function of CD163 fragments in porcine reproductive and respiratory syndrome virus infection.

Monocyte/macrophage scavenger receptor CD163 plays an important role in porcine reproductive and respiratory syndrome virus (PRRSV) infection. To identify the domains of CD163 involved in PRRSV infection, CD163 fragments P1 (1-798 bp), P2 (790-2046 bp), P3 (2023-3345 bp), Y-P1 (160-798 bp), Y-P2 (790-2046 bp) and Y-P3 (2143-3084 bp) were expressed by eukaryotic and prokaryotic expression systems, respectively. Infection experiments revealed that non-permissive BHK-21 cells transfected with pCD163 could be infected by PRRSV. However, cells with truncated CD163 (P1, P2, or P3) were not susceptible to PRRSV. Meanwhile, Y-P1, Y-P2, and Y-P3 were expressed in E. coli and antisera to these peptides were prepared in mice. A virus blocking test showed that Y-P2 protein and anti-Y-P2 mouse serum could block PRRSV infection in a dose-dependent manner, while Y-P3 protein could improve virus infection.

Molecular characterization of a virulent genotype VIId strain of Newcastle disease virus from farmed chickens in Shanghai.

A virulent Newcastle disease virus strain was isolated from diseased chickens in Shanghai, China. The isolated strain was initially characterized as highly virulent because of a short mean death time in embryonated chicken eggs and specific-pathogen-free chickens and was typed as neurotropic by intracloacal inoculation of chickens. The isolated strain had a dibasic amino acid motif in the fusion protein cleavage site sequence required for systemic replication in the host cell. The strain fell into subgenotype VIId by phylogenetic analysis of the fusion protein gene. Although these results demonstrated some sequence similarity between the isolated strain and strains responsible for outbreaks of Newcastle disease in China and Taiwan, the unusually high mortality (86.4%) set this strain aside from other VII strains. Finally, a cross-protection assay demonstrated that La Sota and clone 30 live vaccines could not protect chickens from infection with the isolated strain, with a zero survival rate being observed when chickens were challenged with a high dose of virulent VIId virus.

Detecting Newcastle disease virus in combination of RT-PCR with red blood cell absorption.

Reverse transcription-polymerase chain reaction (RT-PCR) has limited sensitivity when treating complicated samples, such as feces, waste-water in farms, and nucleic acids, protein rich tissue samples, all the factors may interfere with the sensitivity of PCR test or generate false results. In this study, we developed a sensitive RT-PCR, combination of red blood cell adsorption, for detecting Newcastle disease virus (NDV). One pair of primers which was highly homologous to three NDV pathotypes was designed according to the consensus nucleocapsid protein (NP) gene sequence. To eliminate the interfere of microbes and toxic substances, we concentrated and purified NDV from varied samples utilizing the ability of NDV binding red blood cells (RBCs). The RT-PCR coupled with red blood cell adsorption was much more sensitive in comparison with regular RT-PCR. The approach could also be used to detect other viruses with the property of hemagglutination, such as influenza viruses.

Efficient silencing of gene expression by an ASON-bulge-DNAzyme complex.

BACKGROUND: DNAzymes are DNA molecules that can directly cleave cognate mRNA, and have been developed to silence gene expression for research and clinical purposes. The advantage of DNAzymes over ribozymes is that they are inexpensive to produce and exhibit good stability. The "10-23 DNA enzyme" is composed of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of approximately eight nucleotides in each direction, which provides the complementary sequence required for specific binding to RNA substrates. However, these eight nucleotides might not afford sufficient binding energy to hold the RNA substrate along with the DNAzyme, which would interfere with the efficiency of the DNAzyme or cause side effects, such as the cleavage of non-cognate mRNAs. METHODOLOGY: In this study, we inserted a nonpairing bulge at the 5' end of the "10-23 DNA enzyme" to enhance its efficiency and specificity. Different sizes of bulges were inserted at different positions in the 5' end of the DNAzyme. The non-matching bulge will avoid strong binding between the DNAzyme and target mRNA, which may interfere with the efficiency of the DNAzyme. CONCLUSIONS: Our novel DNAzyme constructs could efficiently silence the expression of target genes, proving a powerful tool for gene silencing. The results showed that the six oligo bulge was the most effective when the six oligo bulge was 12-15 bp away from the core catalytic domain.

Coordinated regulation of gene expression for carotenoid metabolism in Chlamydomonas reinhardtii.

Carotenoids are important plant pigments for both light harvesting and photooxidation protection. Using the model system of the unicellular green alga Chlamydomonas reinhardtii, we characterized the regulation of gene expression for carotenoid metabolism by quantifying changes in the transcript abundance of dxs, dxr and ipi in the plastidic methylerythritol phosphate pathway and of ggps, psy, pds, lcyb and bchy, directly involved in carotenoid metabolism, under different photoperiod, light and metabolite treatments. The expression of these genes fluctuated with light/dark shifting. Light treatment also promoted the accumulation of transcripts of all these genes. Of the genes studied, dxs, ggps and lcyb displayed the typical circadian pattern by retaining a rhythmic fluctuation of transcript abundance under both constant light and constant dark entrainments. The expression of these genes could also be regulated by metabolic intermediates. For example, ggps was significantly suppressed by a geranylgeranyl pyrophosphate supplement and ipi was upregulated by isopentenyl pyrophosphate. Furthermore, CrOr, a C. reinhardtii homolog of the recently characterized Or gene that accounts for carotenoid accumulation, also showed co-expression with carotenoid biosynthetic genes such as pds and lcyb. Our data suggest a coordinated regulation on carotenoid metabolism in C. reinhardtii at the transcriptional level.

Molecular characterization of porcine circovirus 2 isolated from diseased pigs co-infected with porcine reproductive and respiratory syndrome virus.

In this study, we isolated a porcine circovirus 2 (PCV2) strain from piglets co-infected with porcine reproductive and respiratory syndrome virus (PRRSV). The complete genome of this strain was sequenced, phylogenetic and polymorphic analyses were carried out. BLAST searches revealed the highest sequence identity (99.5% nt and 99.3% aa) to Guangxi strain EF675230. The phylogenetic tree showed that clustering of the isolates didn't strongly correlate to geographical distribution. Polymorphic analyses demonstrated that the amino acids at most of the polymorphic sites in Open Reading Frame 1(ORF1) and 2 (ORF2)belong to the same amino acid group according to chemical or structural properties, and revealed that highly polymorphic regions overlapped with the known immunoreactive epitopes of ORF2.

[Expression in Escherichia coli, purification and enzymatic properties of porcine urate oxidase].

The aims of this research were to construct prokaryotic expression vector containing the gene of porcine urate oxidase (pUOX), optimize the conditions of the expression of pUOX in recombinant Escherichia coli BL21(DE3), and analyze the in vitro activity and the enzymological properties of pUOX. The pUOX gene was amplified by RT-PCR from the extracted total RNA of porcine liver, and was inserted into the prokaryotic expression vector pET30a(+) to construct a recombinant expression vector pET30a(+)/pUOX. We identified the recombinant vector by endonuclease digestion and sequence analysis. The pUOX gene was amplified and cloned into the vector pET30a(+) successfully. And then the recombinant vector was transformed into E. coli BL21(DE3). The expression of pUOX with a molecular of approximately 41 kD was induced by IPTG. We also optimized the expression conditions of the recombinant protein. The recombinant protein was mostly located in the cytoplasm and it was insoluble. After the inclusion body was solved in 8 mol/L urea and refolding in 2 mol/L urea, the recombinant protein was collected and purified by Ni2+-NTA column. This recombinant protein had a specific activity of 50.61 IU/mg and showed similar properties of optimum temperature and thermal stability, base on the enzymatic assay and analysis of enzymological properties. These results would help to analyze the in vivo activity by testing animal.