[Research advances in trait-based approaches in soil animal community ecology]. / åŸºäºŽåŠŸèƒ½æ€§çŠ¶çš„åœŸå£¤åŠ¨ç‰©ç¾¤è½ç”Ÿæ€å­¦ç ”ç©¶è¿›å±•.

Functional traits are indicators of the responses and adaptation of organisms to environmental changes and cascade to a series of ecosystem functions. The functional traits of soil animals are sensitive to environmental factors and may characterize and predict the changes of ecosystem functions. Multiple dimensions of biodiversity that combing species, phylogenetic, and functional diversity improves the understanding of distribution patterns, community assembly mechanisms and ecosystem functions of soil animals. In this review, we listed the categories of soil animal functional traits and their ecological significance, and summarized current researches on the responses of soil animal communities to environmental changes and the community assembly processes based on trait-based approaches. We proposed to strengthen the study on the impacts of eco-evolution processes of biotic interactions to soil animal functional traits, establish the database of soil animal functional traits, and apply trait-based approaches in the ecological restoration in the future, which would benefit soil biodiversity conservation and sustainability of soil ecosystems.

IGF2BP1 Significantly Enhances Translation Efficiency of Duck Hepatitis A Virus Type 1 without Affecting Viral Replication.

As a disease characterized by severe liver necrosis and hemorrhage, duck viral hepatitis (DVH) is mainly caused by duck hepatitis A virus (DHAV). The positive-strand RNA genome of DHAV type 1 (DHAV-1) contains an internal ribosome entry site (IRES) element within the 5' untranslated region (UTR), structured sequence elements within the 3' UTR, and a poly(A) tail at the 3' terminus. In this study, we first examined that insulin-like growth factor-2 mRNA-binding protein-1 (IGF2BP1) specifically interacted with the DHAV-1 3' UTR by RNA pull-down assay. The interaction between IGF2BP1 and DHAV-1 3' UTR strongly enhanced IRES-mediated translation efficiency but failed to regulate DHAV-1 replication in a duck embryo epithelial (DEE) cell line. The viral propagation of DHAV-1 strongly enhanced IGF2BP1 expression level, and viral protein accumulation was identified as the key point to this increment. Collectively, our data demonstrated the positive role of IGF2BP1 in DHAV-1 viral proteins translation and provided data support for the replication mechanism of DHAV-1.

Identification of a functional nuclear localization signal in 3Dpol/3CD of duck hepatitis A virus 1.

The nuclear localization signals (NLS) were usually composed of basic residues (K and R) and played an important role in delivery of genomes and structural protein into nucleus. In this research, we identified that 3Dpol/3CD entered into nucleus during viral propagation of duck hepatitis A virus type 1 (DHAV-1). To investigate the reason that 3Dpol/3CD entered into nucleus, the amino acid sequence of 3CD was analyzed through NLS Mapper program. The basic region 17PRKTAYMRS25 was subsequently proved to be a functional NLS to guide 3Dpol/3CD into nucleus. 18R, 19K and 24R were found essential for maintaining the nuclear targeting activity, and exchange between 24R and 24K had no impact on cellular localization of 3Dpol. Since the entry of 3Dpol/3CD into nucleus was essential for shutoff of host cell transcription and maintaining the viral propagation of picornavirus numbers, our study provided new insights into the mechanism of DHAV-1 propagation.

The Functional Role of the 3' Untranslated Region and Poly(A) Tail of Duck Hepatitis A Virus Type 1 in Viral Replication and Regulation of IRES-Mediated Translation.

The duck hepatitis A virus type 1 (DHAV-1) is a member of Picornaviridae family, the genome of the virus contains a 5' untranslated region (5' UTR), a large open reading frame that encodes a polyprotein precursor and a 3' UTR followed by a poly(A) tail. The translation initiation of virus proteins depends on the internal ribosome-entry site (IRES) element within the 5' UTR. So far, little information is known about the role of the 3' UTR and poly(A) tail during the virus proliferation. In this study, the function of the 3' UTR and poly(A) tail of DHAV-1 in viral replication and IRES-mediated translation was investigated. The results showed that both 3' UTR and poly(A) tail are important for maintaining viral genome RNA stability and viral genome replication. During DHAV-1 proliferation, at least 20 adenines were required for the optimal genome replication and the virus replication could be severely impaired when the poly (A) tail was curtailed to 10 adenines. In addition to facilitating viral genome replication, the presence of 3' UTR and poly(A) tail significantly enhance IRES-mediated translation efficiency. Furthermore, 3' UTR or poly(A) tail could function as an individual element to enhance the DHAV-1 IRES-mediated translation, during which process, the 3' UTR exerts a greater initiation efficiency than the poly(A)25 tail.

Circulation and in vivo distribution of duck hepatitis A virus types 1 and 3 in infected ducklings.

The circulation of duck hepatitis A virus types 1 (DHAV-1) and 3 (DHAV-3) in Southeast Asia has resulted in a continuously changing epidemiological scenario. In this study, a duplex real-time PCR assay for simultaneous quantitative detection of DHAV-1 and DHAV-3 was established, and 200 liver samples from dead ducklings collected from 31 different flocks in Shandong province, China, were tested. Fifty-eight (29.0 %) samples from 13 flocks were positive for DHAV-1 single infection, 113 (56.5 %) samples from 13 other flocks were positive for DHAV-3 single infection, and 24 samples (12.0 %) from four flocks were positive for both viruses. DHAV-1 and DHAV-3 were detected with high viral loads in all of the organs tested (liver, spleen, pancreas, kidney, heart, thymus, bursa of Fabricius and brain). No significant difference in DHAV-1 and DHAV-3 viral loads was found between singly infected and coinfected samples, and there was no correlation between the viral loads of the two viruses and the age of dead ducklings. To the best of our knowledge, this is the first report about the in vivo distribution of DHAV-1 and DHAV-3 in clinically infected ducklings.

Improved duplex RT-PCR assay for differential diagnosis of mixed infection of duck hepatitis A virus type 1 and type 3 in ducklings.

Infection with duck hepatitis A virus (DHAV) causes an acute, rapidly spreading, and fatal disease of young ducklings. DHAV type 1 (DHAV-1) and type 3 (DHAV-3) have been identified in China. In this study, a duplex RT-PCR assay was developed to identify DHAV-1 and DHAV-3 with mixed infection. The method was shown to be high specificity and sensitivity. The minimum detection limit of the method has been determined to be 10pg total RNA templates extracted from duck liver samples or 10² copies viral RNA of DHAV-1 and DHAV-3 respectively. Using the method, from 60 clinical liver samples of 26 duckling flocks in Shandong, Guangdong, Sichuan and Henan provinces of China, 15 (57.7%) flocks were identified as mixed infection of DHAV-1 and DHAV-3, and 9 (34.6%) flocks were DHAV-1 or DHAV-3 single infection. Among them, 38.3% (23/60) of duckling samples were detected as mixed infection of DHAV-1 and DHAV-3, and 48.3% (29/60) of samples were DHAV-1 or DHAV-3 single infection. These results indicated that the improved duplex RT-PCR method provides a rapid and cost-effective laboratory differential diagnosis for mixed infection of DHAV-1 and DHAV-3 in ducklings.

Dog to dog transmission of a novel influenza virus (H5N2) isolated from a canine.

In 2009, an influenza virus (IV), A/canine/Shandong/JT01/2009 (CA/SD/JT01/09), was isolated from the dog exhibiting respiratory signs in China, and was a novel H5N2. Intraspecies transmission of the virus in dog population had thus far remained unclear. To determine whether the novel H5N2 was transmitted among dogs, we conducted contact exposure and inoculation experiments. Susceptible dogs were housed in the room which the novel H5N2 infected dogs were housed in. As a result, the direct contact resulted in intraspecies transmission. Most of the infected dogs and the sentinel animals developed mild respiratory syndrome, including transient increased body temperatures, conjunctivitis, sneezing, nasal discharge and mild coughing, virus shedding and seroconversion, but no fatal disease. These data suggest that dogs may play a role in transmission and spread of influenza virus.

Identification of two functional nuclear localization signals in the capsid protein of duck circovirus.

The capsid protein (CP) of duck circovirus (DuCV) is the major immunogenic protein and has a high proportion of arginine residues concentrated at the N terminus of the protein, which inhibits efficient mRNA translation in prokaryotic expression systems. In this study, we investigated the subcellular distribution of DuCV CP expressed via recombinant baculoviruses in Sf9 cells and the DNA binding activities of the truncated recombinant DuCV CPs. The results showed that two independent bipartite nuclear localization signals (NLSs) situated at N-terminal 1-17 and 18-36 amino acid residue of the CP. Moreover, two expression level regulatory signals (ELRSs) and two DNA binding signals (DBSs) were also mapped to the N terminus of the protein and overlapped with the two NLSs. The ability of CP to bind DNA, coupled with the karyophilic nature of this protein, strongly suggests that it may be responsible for nuclear targeting of the viral genome.

[Sequence analysis of VP1 gene of the duck hepatitis A virus type 3 strains isolated from Shandong Province of China in 2012].

To reveal the genetic variation of the viral protein 1 (VP1) gene of the duck hepatitis A virus type 3 (DHAV-3), the VP1 gene of 13 virulent DHAV-3 strains isolated from Shandong province of China in 2012 were amplified by RT-PCR, sequenced and analyzed. The results showed that all the VP1 genes of the 13 isolates contained 720 nucleotides encoding 240 amino acids, and shared with nucleotide identities of 94. 6%-99.9% and amino acid identities of 95.0%-100%. The nucleotide and amino acid sequence homologies between the 13 DHAV-3 isolates and other 31 DHAV-3 reference strains were 92.5%-100% and 90. 8%-100%, respectively. Phylogenetic analysis showed that the VP1 gene of DHAV-3 had distinct geographical characteristics. Distribution of genotypes of the 44 DHAV-3 strains was as follows: except the vaccine strain B63, all the other Chinese isolates belonged to genotype I (GI), Vietnamese wild isolates mainly belonged to subtype 1 (S1) of genotype II (GII), and all Korean isolates belonged to subtype 2 (S2) of GII.

Complete genome sequence of a novel porcine parvovirus in China.

The porcine parvovirus JT strain (PPV-JT) was isolated from a piglet showing nonsuppurative myocarditis in Shandong, China, in 2010. The complete genomic sequence of PPV-JT, 4,941 bp long, was determined from clones made from replicative form (RF) DNA. The genomic analysis demonstrated that the PPV-JT might be involved in a recombination event, which will help us understand the molecular characteristics and evolutionary of PPV in China.

Complete genome sequence analysis of duck circovirus strains from Cherry Valley duck.

To investigate molecular epidemiology of DuCV in Cherry Valley ducks in China, the complete genomes of six DuCV strains, which were detected from Cherry Valley ducks in China between 2007 and 2008, were sequenced. Sequence and phylogenetic analysis were carried out to compare these six strains with another 27 DuCV strains from Mulard duck, Muscovy duck, Pekin ducks and Mule duck. The analysis showed that the six DuCV strains exhibited typical genetic features of the family of DuCV, such as a stem-loop structure, three major open reading frames (Rep, Cap and ORF3), four intergenic repeats and the conserved motifs for rolling circle replication and for the dNTP binding domain located in the Rep protein. Phylogenetic analysis of the nucleotide sequences of the complete genome and Cap gene of these strains together with those that have been previously published demonstrated two distinct DuCV genotypes. The DuCV strains with complete genomes containing 1988 and 1989 nucleotides clustered in genotype A, whereas the strains with complete genomes containing 1991, 1992, 1995 and 1996 nucleotides lay in genotype B. The six DuCV strains from Cherry Valley ducks were divided into the two groups. The results of the study provides some insight into the variation of DuCVs in Cherry Valley ducks.

ORF3 of duck circovirus: a novel protein with apoptotic activity.

Duck circovirus (DuCV) is classified in the genus Circovirus of the Circoviridae family. Two major open reading frames (ORFs), encoding the replicase (ORF1/rep) and the capsid protein (ORF2/cap), have been recognized for DuCV. Sequence analysis show that another major conserved ORF (named ORF3) is located in the complementary strand of ORF1/rep of DuCV, and its function remains to be investigated. In this study, the ORF3 of DuCV was expressed in recombinant baculovirus-infected Sf9 cells. By IFA and Western blot analysis, the ORF3 protein was positive for the sera from ducks infected with DuCV. The percentages of apoptotic cells of the Sf9 cells infected with the recombinant baculovirus encoding ORF3 of DuCV were significantly higher than (P<0.05) that of the Sf9 cells infected with wild-type baculovirus at 24, 48 and 72 h postinfection. Based on our knowledge, we deduced that the ORF3 protein of DuCV might play an important role in viral pathogenesis via its apoptotic activity.

Genetic characterization of a novel influenza A virus H5N2 isolated from a dog in China.

An influenza virus, A/canine/Shandong/JT01/2009, has been isolated from a dog exhibiting classical flu signs in China. HAI and NAI assays subtyped A/canine/Shandong/JT01/2009 as a H5N2 like virus. Phylogenetic reconstructions indicated strong relationships with viruses from various hosts and dispersed geographic locations. These analyses indicate A/canine/Shandong/JT01/2009 is a novel virus generated by complex reassortment of the viral segments.

Genetic diversity of parvovirus isolates from dogs and wild animals in China.

We isolated three new parvovirus variants in China. The isolate from a blue fox was related to feline parvovirus, but possessed a mutation of VP2 residue A300P. Isolates from a raccoon dog and a masked civet were antigenically similar to canine parvovirus-2a but had a substitution of VP2 residue G300S.

Development of an indirect ELISA for the detection of duck circovirus infection in duck flocks.

Infection with duck circovirus (DuCV) is associated with growth retardation and developmental problems in farmed ducks. To detect DuCV-specific antibody in duck serum, an indirect enzyme-linked immunosorbent assay (iELISA) method was developed using the recombinant capsid protein antigen prepared by cloning the cap (Cap) gene of DuCV FJ0601 strain into pET-32a (+) vector and expressed in Escherichia coli. Using the optimized iELISA method, DuCV-specific antibodies were detected in 157 (12.96%) of 1211 samples obtained from 17 (89.47%) of 19 meat duck flocks aged from 25 to 40 days and in 89 (22.08%) of 403 samples obtained from 9 (75%) of 12 breeder flocks aged from 14 to 61 weeks. These results indicated that the iELISA method is useful for serological diagnosis of DuCV infection and epidemiological investigation.

Evaluation of two experimental infection models for Avibacterium paragallinarum.

The clinical symptoms of infectious coryza are multiple and include nasal discharge, facial swelling, lacrimation, and anorexia. In general, the disease is not fatal to chicken; so, in experiments where animals are infected with Avibacterium paragallinarum, there have been debates about conducting the challenge model and evaluating the clinical signs. In this experiment, 150 chickens, aged 30 days, were randomly divided into different groups. Some groups were infected with the 'in-contact' challenge model and others with the artificial intrasinus-injection-route model. The bacterial isolates used were three field isolates of different serogroups of A. paragallinarum, including Hpg-8 (Page serovar A), CCM6075 (Page serovar B) and Hpg-668 (Page serovar C). During this study, a scoring system was used to record the clinical signs of the infected birds and evaluate the pathogenic diversity of the two models. The final results indicated that the 'in-contact' challenge model of the three isolates showed a more reliable representation of the natural infection under field conditions than the artificial intrasinus-injection-route model. Thus, on carrying out animal experiments, the effect of 'in-contact' challenge model is more accurate than the artificial intrasinus-injection-route model.

[Construction and identification of recombinant canine adenovirus type 2 expressing exogenous rabies glycoprotein (Rgp)].

Safe and effective vaccination is important for rabies prevention. Here, genetically engineered rabies vaccine CAV2-deltaE3-Rgp was developed and characterized. The recombinant genome pPoly2-CAV2-deltaE3-Rgp carrying the rabies glycoprotein (Rgp) cDNA was generated by a series of strictly gene cloning steps and infectious recombinant virus CAV2-deltaE3-Rgp was obtained by transfecting the recombinant genome into a canine kidney cell line, MDCK. To efficiently construct cloned recombinant canine adenovirus type 2 genome pPoly2-CAV2-deltaE3-Rgp bearing exogenous Rgp gene, The Rgp gene was first subcloned from the clone vector pMD18-T into the eukaryon expression vector pVAX1. The Rgp expression cassette was then subcloned into the shuttle vector pVAXdeltaE3 and subsequently into the canine adenovirus type 2 backbone vector pPoly2-CAV2. To indirectly confirm pPoly2-CAV2-deltaE3-Rgp, conventional restriction endonuclease digestion was performed. CAV2-deltaE3-Rgp can generate typical CPE of CAV-2. CAV2-deltaE3-Rgp was tested by restriction endonuclease digestion, PCR, DNA sequencing. As a result, The Rgp expression cassette was successfully integrated into the target region of the CAV2 genome. It is confirmed by RT-PCR, Western blot that CAV2-deltaE3-Rgp can express Rgp antigen in MDCK cell. This recombinant virus, CAV2-deltaE3-Rgp, was intramuscularly injected into dogs. All vaccinated dogs produced effective antibodies against CAV and RV after three inoculations. This recombinant virus would be prospective in immunizing dogs against CAV and RV.

[Construction of recombinant canine adenovirus type 2 expressing Canine coronavirus spike glycoprotein and its immunogenicity].

In order to construct a recombinant Canine adenovirus type 2 (CAV-2) expressing the spike glycoprotein of Canine coronavirus (CCV), the S1 gene fragment of CCV strain DXMV, encoding major antigenic region A, B, C and D of S protein, was amplified by RT-PCR and cloned into pVAX1 vector. The complete S1 expression cassette was subcloned into the shuttle vector pVAXE3, then further cloned into the backbone vector pPoly2-CAV2 containing complete genome of CAV-2. To gain the recombinant Canine adenovirus, the recombinant plasmid pCAV-2-CCV-S1 was linearized by Cla I/Asc I to release recombinant genome, and then transfected into MDCK cell. The recombinant virus CAV-2-S1 was gained through 4 passages in MDCK, which showed classical CPE of CAV-2. The expressed S1 protein of CCV, which was identified by RT-PCR and Western blot, can be specifically recognized by polyclonal antibody against CCV. The immunization in dogs indicated that the recombinant CAV-2 could effectively induce the specific antibodies against CCV and CAV.