A duplex fluorescent quantitative PCR assay to distinguish the genotype I, II and I/II recombinant strains of African swine fever virus in China.

African swine fever (ASF) is a severe, hemorrhagic, and highly contagious disease caused by the African swine fever virus (ASFV) in both domestic pigs and wild boars. In China, ASFV has been present for over six years, with three genotypes of strains prevalent in field conditions: genotype I, genotype II, and genotype I/II recombinant strains. In order to differentiate among these three ASFV genotypes, a duplex fluorescent quantitative PCR method was established using specific probes and primers designed based on viral genes MGF_110-1L and O61R from ASFV strains reported in the GenBank database. Following optimization of reaction conditions, a duplex fluorescent quantitative PCR method was successfully developed. This method demonstrated no cross-reactivity with porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine reproductive and respiratory syndrome virus (PRRSV), classic swine fever virus (CSFV), porcine pseudorabies virus (PRV), porcine circovirus 2 (PCV2), porcine circovirus 3 (PCV3), highlighting its specificity. Sensitivity analysis revealed that the limits of detection (LODs) of this method were 2.95 × 10-1 copies/µL for the MGF_110-1L gene and 2.95 × 100 copies/µL for the O61R gene. The inter- and intra-group coefficients of variation were both <1%, indicating high reproducibility. In summary, the establishment of this duplex fluorescent quantitative PCR method not only addresses the identification of the ASFV recombinant strains but also allows for simultaneous identification of the three epidemic genotype strains.

A novel photoelectrochemical array platform for ultrasensitive multiplex detection and subtype identification of HPV genes.

The rapid, low-cost and user-friendly methods for nucleic acid detection is urgently needed. Here we developed a miniaturized and convenient photoelectrochemical biosensor array (PEBA) platform for multiplexing and simultaneous detection of nucleic acid. The array system containing nine sensing units was integrated on one piece of conductive glass by laser etching and screen printing. Moreover, human papillomavirus (HPV), the main cause of cervical cancer, was selected as the model marker to evaluate the applicability of the fabricated PEBA. The proposed PEBA for HPV genotyping involved the TiO2@Au nanoparticles (NPs) as the photoelectrochemical (PEC) material and CdS quantum dots (CdS QDs)-labeled DNA hairpin probe anchored on the TiO2@Au NPs as the recognition element. With the addition of HPV target, the probe undergoes a significant conformational change and forces CdS QDs away from TiO2@Au, resulting in decreased PEC signals. The established array platform coupled with nucleic acid amplification exhibited high sensitivity as low as 0.1 copies/µL and a linear range of 0.6-600 copies/µL for nine HPV genotyping. Method evaluation with 40 clinical samples including 20 HPV-positive and 20 negative samples, gave a 97.5% concordance result in comparison with commercial kits. The genotyping results obtained by the PEBA reveal that HPV52, HPV18, and HPV11 are the most prevalent genotypes in positive samples, which is in good concordance with the official report concerning the trend of HPV prevalence among women with cervical lesions in Shenzhen. The designed PEBA platform has potential applications in extensive fields like biomedicine analysis and clinical healthcare diagnosis.

Construction of Fzd6Q152E mice through CRISPR/Cas9 technology and their reproduction and identification.

BACKGROUND: The CRISPR/Cas9 system is widely used for genome editing in human, rat and mouse cells. In this study, we established Fzd6 mutant mice using CRISPR/Cas9 technology, and obtained Fzd6 homozygous mutant (Fzd6Q152E) mice through breeding. Fzd6 plays a role in depression, but there are few related reports. We used this model to investigate the mechanism of Fzd6 involved in depression, and build a solid foundation for subsequent in-depth studies. METHODS AND RESULTS: The target of Fzd6 mutation was obtained by CRISPR/Cas9 technology and hippocampal tissue was collected for Nissl staining and histological analysis. Blood was collected for enzyme linked immunosorbent assay (ELISA); The gene expression of Fzd6 and the related genes expression in wnt pathway was quantified by quantitative real-time PCR (qRT-PCR), and then expression of Fzd6 and proteins in the Wnt pathway were identified by western blotting. ELISA results showed that the expression levels of brain derived neurotrophic factor (BDNF), 5-hydroxytryptamine (5-HT), and Noradrenaline (NE) in serum were significantly decreased in Fzd6Q152E mice, whereas the mRNA expression of Lrp5, Lrp6, and Dkk2 is increased. The western blotting revealed that the expression of Fzd6 and Lrp6 is decreased, although the expression of Dkk2 and Gsk-3ß increased. CONCLUSION: Our study successfully established homozygous Fzd6 mutant mice model. The relationship between Fzd6-Wnt and depression was preliminarily clarified, which provides an ideal animal model for subsequent research on diseases induced by the Fzd6 mutation.

Application of Allele Specific PCR in Identifying Offspring Genotypes of Bi-Allelic SbeIIb Mutant Lines in Rice.

Bi-allelic mutant lines induced by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems are important genetic materials. It is very important to establish a rapid and cheap method in identifying homozygous mutant plants from offspring segregation populations of bi-allelic mutant lines. In this study, the offspring genotypes of rice bi-allelic starch branching enzyme IIb mutant lines were identified using the allele specific PCR (AS-PCR) method. The target sequences of two alleles were aligned from their 5' to 3' ends, and the first different bases were used as the 3' ends of mismatch primers. Another mismatched base was introduced at the third nucleotide from the 3' end of mismatch primer. The PCR reaction mixture and amplification program were optimized according to the differences of mutation target sequence and mismatch primers. The offspring plant genotypes of bi-allelic mutant lines could be accurately identified using the amplified DNA fragments by agarose gel electrophoresis. This study could provide a method reference for the rapid screening of homozygous mutant plants from offspring segregation population of heterozygous and bi-allelic mutant lines.

Construction of aquaporin 9 gene knockout mice using CRISPR/Cas9 gene editing system / 解剖学报

Objective To construct homozygous aquaporin 9(AQP-9)

Genetic Characterization of Echinococcus granulosus Sensu Lato in Livestock and Human Isolates from North of Iran Indicates the Presence of E. ortleppi in Cattle.

PURPOSE: Identification of different genotypes of echinococcal cyst in various domestic herbivores and humans within the target area was the principal aim of the present study, performed using sequence data of cox1 and nad1 mitochondrial genes. METHODS: A total of 57 cystic echinococcosis (CE) cysts were isolated from indigenous livestock including 45 cattle, 9 sheep and 3 goats from several slaughterhouses in Guilan Province. Moreover, 12 formalin-fixed paraffin-embedded (FFPE) CE cyst tissues from humans were also included, obtained from the archives of several hospitals in Rasht, the capital of Guilan. Genetic sequencing was conducted using mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes. RESULTS: Our results found that E. granulosus sensu stricto (s.s.) and E. ortleppi were present in 92.7% and 7.2% isolates, respectively. E. granulosus s.s. (genotypes G1 and G3) and E. ortleppi were isolated from various livestock whereas all CE cysts isolated from humans were E. granulosus s.s. G1 genotype. CONCLUSION: We found that E. granulosus s.s. G1 was the predominant genotype within the study region. This is the first study to report E. ortleppi in cattle in Iran.

Identification and survival analysis of TTA/TETO-CCKR-2 double transgenic mice / 中国组织工程研究

BACKGROUND: The inducible forebrain-specific cholecystokinin receptor-2 (CCKR-2) double transgenic (tTA/tetO-CCKR-2 tg, abbreviated as dtg) mice are an ideal model of anxiety-related diseases. However, there is still a lack of model identification and life related data OBJECTIVE: To identify the genomic DNA of the offspring and the specific expression of CCKR-2 transgene in the forebrain, and to analyze the survival probability of dtg mice. METHODS: α-CaMKII/tTA single transgenic mice and tetO-CCKR-2 single transgenic mice were cross-fertilized to construct a dtg mouse model. The genomic DNA was extracted from the tail of the offspring, and the genotypes were detected by PCR and agarose gel electrophoresis. Wild-type (WT) mice were used as controls. In situ hybridization was used to detect the expression of CCKR-2. Survival of dtg mice and WT mice (30 females and 30 males) was observed and recorded within 2 years. The study protocol was approved by the Experimental Animal Ethics Committee of Southwest Medical University, with an approval No. 20150068. RESULTS AND CONCLUSION: Agarose gel electrophoresis results showed the molecular weight of the PCR products of dtg mice was consistent with the expected target gene fragment. In situ hybridization results showed a strong signal of CCKR-2 was detected in the forebrain of dtg mice, but hardly present in the WT mice. The median survival time of dtg mice was 76 weeks in females and 77 weeks in males. The survival probability was decreased with age in dtg mice. The survival probability of WT mice was significantly better than that of dtg mice (P < 0.001). There was no significant sex difference between males and females of dtg mice (P=0.577). Therefore, the specific expression of CCKR-2 transgene in the forebrain can be identified using PCR amplification, genomic DNA extraction, agarose gel electrophoresis, and in situ hybridization. tTA/tetO-CCKR-2 double transgenic induction may shorten the survival time of mice, but no significant difference is observed between the females and males of dtg mice.

Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato.

The larval stages of tapeworms in the species complex Echinococcus granulosus sensu lato cause a zoonotic disease known as cystic echinococcosis (CE). Within this species complex, genotypes G6 and G7 are among the most common genotypes associated with human CE cases worldwide. However, our understanding of ecology, biology and epidemiology of G6 and G7 is still limited. An essential first step towards this goal is correct genotype identification, but distinguishing genotypes G6 and G7 has been challenging. A recent analysis based on complete mitogenome data revealed that the conventional sequencing of the cox1 (366 bp) gene fragment mistakenly classified a subset of G7 samples as G6. On the other hand, sequencing complete mitogenomes is not practical if only genotype or haplogroup identification is needed. Therefore, a simpler and less costly method is required to distinguish genotypes G6 and G7. We compared 93 complete mitogenomes of G6 and G7 from a wide geographical range and demonstrate that a combination of nad2 (714 bp) and nad5 (680 bp) gene fragments would be the best option to distinguish G6 and G7. Moreover, this method allows assignment of G7 samples into haplogroups G7a and G7b. However, due to very high genetic variability of G6 and G7, we suggest to construct a phylogenetic network based on the nad2 and nad5 sequences in order to be absolutely sure in genotype assignment. For this we provide a reference dataset of 93 concatenated nad2 and nad5 sequences (1394 bp in total) containing representatives of G6 and G7 (and haplogroups G7a and G7b), which can be used for the reconstruction of phylogenetic networks.

Measles in Italy: Viral strains and crossing borders.

In 2017, Italy experienced one of the largest outbreaks of measles in recent years, with 5404 notified cases and 4347 confirmed cases. A further 2029 cases were notified during the first 6 months of 2018, and 1516 of them were laboratory-confirmed. The B3 and D8 genotypes were identified as those responsible for the outbreak. Possible transmission routes can be established by monitoring the circulating measles virus strains in support of the national health authorities to warn people and travellers.

Distinguishing Echinococcus granulosus sensu stricto genotypes G1 and G3 with confidence: A practical guide.

Cystic echinococcosis (CE), a zoonotic disease caused by tapeworms of the species complex Echinococcus granulosus sensu lato, represents a substantial global health and economic burden. Within this complex, E. granulosus sensu stricto (genotypes G1 and G3) is the most frequent causative agent of human CE. Currently, there is no fully reliable method for assigning samples to genotypes G1 and G3, as the commonly used mitochondrial cox1 and nad1 genes are not sufficiently consistent for the identification and differentiation of these genotypes. Thus, a new genetic assay is required for the accurate assignment of G1 and G3. Here we use a large dataset of near-complete mtDNA sequences (n = 303) to reveal the extent of genetic variation of G1 and G3 on a broad geographical scale and to identify reliable informative positions for G1 and G3. Based on extensive sampling and sequencing data, we developed a new method, that is simple and cost-effective, to designate samples to genotypes G1 and G3. We found that the nad5 is the best gene in mtDNA to differentiate between G1 and G3, and developed new primers for the analysis. Our results also highlight problems related to the commonly used cox1 and nad1. To guarantee consistent identification of G1 and G3, we suggest using the sequencing of the nad5 gene region (680 bp). This region contains six informative positions within a relatively short fragment of the mtDNA, allowing the differentiation of G1 and G3 with confidence. Our method offers clear advantages over the previous ones, providing a significantly more consistent means to distinguish G1 and G3 than the commonly used cox1 and nad1.

Molecular Reconstruction of an Old Pedigree of Diploid and Triploid Hydrangea macrophylla Genotypes.

The ornamental crop species Hydrangea macrophylla exhibits diploid and triploid levels of ploidy and develops lacecap (wild type) or mophead inflorescences. In order to characterize a H. macrophylla germplasm collection, we determined the inflorescence type and the 2C DNA content of 120 plants representing 43 cultivars. We identified 78 putative diploid and 39 putative triploid plants by flow cytometry. In our collection 69 out of 98 flowering plants produced lacecap inflorescences, whereas 29 plants developed mophead inflorescences. Surprisingly, 12 cultivars included diploid as well as triploid plants, while 5 cultivars contained plants with different inflorescence types. We genotyped this germplasm collection using 12 SSR markers that detected 2-7 alleles per marker, and identified 51 different alleles in this collection. We detected 62 distinct fingerprints, revealing a higher genetic variation than the number of cultivars suggested. Only one genotype per cultivar is expected due to the vegetative propagation of Hydrangea cultivars; however we identified 25 cultivars containing 2-4 different genotypes. These different genotypes explained the variation in DNA content and inflorescence type. Diploid and triploid plants with the same cultivar name were exclusively mix-ups. We therefor assume, that 36% of the tested plants were mislabeled. Based on the "Wädenswil" pedigree, which includes 31 of the tested cultivars, we predicted cultivar-specific fingerprints and identified at least 21 out of 31 cultivars by SSR marker-based reconstruction of the "Wädenswil" pedigree. Furthermore, we detected 4 putative interploid crosses between diploid and triploid plants in this pedigree. These interploid crosses resulted in diploid or/and triploid offspring, suggesting that crosses with triploids were successfully applied in breeding of H. macrophylla.

Breeding and genotype identification of Arrb2 gene knockout mice / 中国药理学通报

Aim To explore the optimal way of breeding and genotype identification of Arrb2 knockout mice, and to find a simple and quick polymerase chain reaction ( PCR) method for the genotyping of Arrb2 knockout mice. Methods Breeding homozygote genotype of Arrb2 gene knockout mice were copula-ted with wild-type C57BL/6J mice, and then the heterozygous mating were used for mating. The growth and development of off-spring were observed. The genomic DNA was extracted from the tail of two-week-old mice. PCR was employed to amplify the Arrb2 gene fragment, and electrophoresis was used to present the gene type. Results The breeding and reproducing were successful and three genotype offspring, including wild-type,heterozygous and homozygous knockout mice were obtained. Agarose gel electrophoresis results showed the size of PCR prod-ucts was about 186 bp and 224 bp, which was consistent with the expected target gene fragment, and identified Arrb2 gene knockout mice of different genotypes successfully. Western blot analysis demonstrated the lack ofβ-arrestin2 protein in the major organs from Arrb2 -/ - mice compared with Arrb2 +/ + and Arrb2 +/ - mice. Conclusions It is feasible to obtain the homo-zygous Arrb2 knockout mice by inbreeding heterozygotes. It is simple, rapid and reliable to identify mouse genetype by PCR.

Detection of HCV genotypes 1b and 2a by a reverse transcription loop-mediated isothermal amplification assay.

Hepatitis C virus (HCV) genotypes 1b and 2a are the major cause of liver disease in northern China; however, conventional detection tools are labor-consuming, technically demanding, and costly. Here, we assessed the specificity, sensitivity, and clinical utility of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of HCV genotypes 1b and 2a. Firstly, clinical samples were collected from HCV genotype 1b and 2a infected patients and the RNA were extracted. Secondly, specificity of RT-LAMP assay for detection HCV genotypes 1b and 2a were tested against viral genomes of other hepatitis viruses. Sensitivity of RT-LAMP assay was determined using serial dilutions of standard HCV genotypes 1b and 2a. The amplified products were detected by both electrophoresis and calcein/Mn2+ -dependent visual methods. Finally, we compared the clinical detection rate of RT-LAMP to that of real-time PCR. RT-LAMP assay showed high specificity to detect HCV genotypes 1b and 2b since there was no cross-reactivity with other hepatitis viruses. Sensitivity of RT-LAMP was 100 IU/mL for both genotypes detected by either electrophoresis or calcein/Mn2+ -dependent visual methods. The detection rate of RT-LAMP assay in clinical samples was also comparable to that of real-time PCR without significant difference between the both assays. This study proposes a newly developed RT-LAMP assay for detection of HCV genotypes 1b and 2a. RT-LAMP is highly specific, sensitive, and simple diagnostic tool which would be useful for screening and early diagnosis of HCV especially in resource-limited environments.

Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing.

The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by transferring non-1a/1b samples to a center where HRCS is available, if further characterization is needed.

A method for rapid detection and genotype identification of hepatitis C virus 1-6 by one-step reverse transcription loop-mediated isothermal amplification.

OBJECTIVE: Hepatitis C virus (HCV) is probably the leading cause of liver cirrhosis and hepatocellular carcinoma globally. Diagnostic tools conventionally used for the detection and identification of HCV infection are technically demanding, time-consuming, and costly for resource-limited environments. This study reports the development of the first rapid loop-mediated reverse transcription isothermal amplification assay that rapidly detects and identifies HCV genotypes in blood components. METHODS: RNA extracted from donor plasma and serum specimens was applied to a one-step reverse transcription loop-mediated isothermal amplification reaction performed with HCV-specific oligonucleotides. Reactions were conducted at 63.5 °C for 30-60 min. The diagnostic characteristics of the assay were investigated and validated with clinical specimens. RESULTS: Electrophoretic analysis of amplification revealed detection and identification of HCV genotypes 1-6. Positive amplification revealed unique ladder-like banding patterns that identified each HCV genotype. The assay demonstrated a sensitivity of 91.5% and specificity of 100%. Rapid naked-eye detection of HCV infection was facilitated by observation of an intense fluorescent glow of amplified targets under UV illumination. CONCLUSION: These diagnostic characteristics highlight the potential utility of this assay for the rapid detection and genotype identification of HCV infection in field and point-of-care settings in endemic regions and resource-limited environments.

Comparison of three methods for total DNA extraction from mouse models / 中国比较医学杂志

Objective To establish a simple , fast and economic total DNA extraction method to serve the rapid identification of model mouse genotype in large number of mice .Methods Three methods, i.e.phenol extraction, isopropyl alcohol precipitation and mouse ear boiling methods were used to extract the total DNA from ten C 57-rasmodel mice.The purity and yield of DNA obtained by the three methods were compared , and polymerase chain reaction ( PCR) assay was used to compare the efficacy of the three extraction methods .Results Among the three methods , phenol extraction was the best and isopropyl alcohol precipitation was the poorest in DNA yield .In terms of DNA purity , the phenol extraction was the best and the mouse ear boiling method was the poorest .All the three methods could be used to extract the total DNA from mice serving as template of PCR reaction for the mouse genotype identification .The time consumption of three methods are 12.5 hr ,13 hr and 0.18 hr.Mouse ear boiling method was significantly lower than that of the other two methods ( P <0.01 ) ,.The obtained total DNA can be stored at conventional -20℃for 7 days and 30 days later still can be used as a template for PCR reaction .Conclusions Among the three methods studied , the mouse ear boiling method is simple and with the lowest cost , so it is feasible for total DNA extraction in scaled genotyping experiments .

Identification of the method of establishment of a DKO mouse model of Duchenne muscular dystrophy and regeneration of dystrophin expression in vivo after stem cell transplantation / 中国实验动物学报

Objective To establish a method of identification of DKO mouse model of Duchenne muscular dystro-phy, and to assess the dystrophin regeneration after stem cell transplantation.Methods Heterozygous mice were mated and the resulting offspring were used to identify their genotype by SSP-PCR.The plasma creatine kinase level was measured by biochemical analyzer and histological changes in the DKO mice were analyzed using HE staining.Human umbilical cord mesenchymal stem cells were prepared and injected into the DKO mice hindlimb muscle, and dystrophin expression was de-tected by immunofluorescence staining at 2 months after injection.Results Mating of heterozygous mice generated three kinds of genotype offsprings, and 21.2%of the offsprings were identified as DKO genotype (285 bp) .DKO mice showed dystrophic symptoms, their plasma creatine kinase level was as high as 16988.52 ±617.48 IU/L, and significant histologi-cal changes including diverse myocyte sizes, numerous centrally nucleated cells and connective tissue proliferation or in-flammatory cells infiltration.Human dystrophin expression was detected in the DKO mouse hindlimb muscle at two months after injection of human umbilical cord mesenchymal stem cells.Conclusion DKO mouse genotype can be identified by SSP-PCR, and DKO mouse is an ideal animal model for studies of stem cell therapy for Duchenne muscular dystrophy.