NanoSTR: A method for detection of target short tandem repeats based on nanopore sequencing data.

Short tandem repeats (STRs) are widely present in the human genome. Studies have confirmed that STRs are associated with more than 30 diseases, and they have also been used in forensic identification and paternity testing. However, there are few methods for STR detection based on nanopore sequencing due to the challenges posed by the sequencing principles and the data characteristics of nanopore sequencing.

Nano2NGS-Muta: a framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection.

Nanopore sequencing, also known as single-molecule real-time sequencing, is a third/fourth generation sequencing technology that enables deciphering single DNA/RNA molecules without the polymerase chain reaction. Although nanopore sequencing has made significant progress in scientific research and clinical practice, its application has been limited compared with next-generation sequencing (NGS) due to specific design principle and data characteristics, especially in hotspot mutation detection. Therefore, we developed Nano2NGS-Muta as a data analysis framework for hotspot mutation detection based on long reads from nanopore sequencing.

Pathogenicity and molecular characterization of a fowl adenovirus 4 isolated from chicken associated with IBH and HPS in China.

Background: Since July in 2015, an emerging infectious disease, Fowl adenovirus (FAdV) species C infection with Hepatitis-Hydropericardium syndrome was prevalent in chicken flocks in China. In our study, one FAdV strain was isolated from commercial broiler chickens and was designated as SDSX1.The phylogenetic information, genetic mutations and pathogenicity of SDSX1 were evaluated.

A real-time loop-mediated isothermal amplification method for rapid detection of Lawsonia intracellularis in porcine fecal samples.

Porcine proliferative enteritis is a common diarrheal disease characterized by thickening of the intestinal mucosa in swine due to enterocyte proliferation, which is caused by Lawsonia intracellularis. In this study, a real-time loop-mediated isothermal amplification (LAMP) assay was developed to detect L. intracellularis based on the conserved region of the 16S ribosomal RNA gene.

Development and application of an indirect ELISA for the detection of antibodies against encephalomyocarditis virus.

Encephalomyocarditis virus (EMCV) can cause acute myocarditis in young pigs or reproductive failure in sows. It has been recognized worldwide as a pathogen infecting many species and causes substantial economic losses. In the present study, an indirect ELISA was developed for the detection of antibodies to EMCV.

Complete Genomic Characterization of Porcine Reproductive and Respiratory Syndrome Virus Strain HB-XL.

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causal agent of a serious disease of swine. Here, we report the genome sequence of PRRSV strain HB-XL isolated from a pig farm with a clinical outbreak of porcine reproductive and respiratory syndrome. The genome is 15,323 bp long and has nine open reading frames (GenBank: KP162169).

Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus.

Porcine epidemic diarrhea virus (PEDV) is an important pig pathogen that can cause vomiting, diarrhea, and dehydration, leading to serious damage to the swine industry worldwide. In this study, a nanoparticle-assisted polymerase chain reaction (nanoPCR) assay targeting the N gene of PEDV was developed and the sensitivity and specificity were investigated. Under the optimized conditions for detection of PEDV RNA, the nanoPCR assay was 100-fold more sensitive than a conventional RT-PCR assay.

Complete Genome Sequence of Porcine Circovirus Type 2 Strain HB-MC1.

Porcine circovirus type 2 (PCV2) is the primary causative agent of porcine circovirus-associated disease (PCVAD). Here, we report the complete genome sequence of PCV2 strain HB-MC1, which belongs to PCV2d.

Development of a TaqMan-based real-time reverse transcription polymerase chain reaction assay for the detection of encephalomyocarditis virus.

Encephalomyocarditis virus (EMCV) is one of the major zoonosis pathogens and can cause acute myocarditis in young pigs or reproductive failure in sows. In this study, a TaqMan-based real-time reverse transcription polymerase chain reaction (RT-PCR) assay targeting 3D gene of EMCV was developed and their sensitivities and specificities were investigated. The results indicated that the standard curve had a wide dynamic range (10(1)-10(6) copies/μL) with a linear correlation (R(2)) of 0.

Distinct promoters affect pyrroloquinoline quinone production in recombinant Escherichia coli and Klebsiella pneumoniae.

Pyrroloquinoline quinone (PQQ) is a versatile quinone cofactor participating in numerous biological processes. Klebsiella pneumoniae can naturally synthesize PQQ for harboring intact PQQ synthesis genes. Previous metabolic engineering of K.

Rapid detection of encephalomyocarditis virus by one-step reverse transcription loop-mediated isothermal amplification method.

The encephalomyocarditis virus (EMCV) can cause acute myocarditis in young pigs or reproductive failure in sows. In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect EMCV RNA. The RT-LAMP assay was highly sensitive and able to detect 2.

Complete Genome Sequence of Porcine Encephalomyocarditis Virus Strain BD2.

Encephalomyocarditis virus (EMCV) causes acute myocarditis in young pigs or reproductive failure in sows, and it is divided into two main groups. Here, we report the complete genome sequence of EMCV strain BD2, which belongs to group I.

[Construction and characterization of EGFP reporter gene labeled Sindbis virus].

Objective: To construct and characterize EGFP reporter gene labeled Sindbis virus (SINV).

Methods: The reporter gene EGFP was inserted into the genome of infectious clone pBR-XJ160 by using multi-fusion long fragment PCR method. Then apply reverse genetic manipulation technique to rescue and obtain EGFP labeled SINV.

Isolation and molecular analysis of porcine encephalomyocarditis virus strain BD2 from northern China.

Encephalomyocarditis virus (EMCV) can cause acute myocarditis in young pigs or reproductive failure in sows. In this study, an EMCV strain (BD2) was isolated from the suspected piglets with EMCV in China. It was identified by an indirect immunofluorescence assay and reverse-transcription polymerase chain reaction.