Completely Free from PAM Limitations: Asymmetric RPA with CRISPR/Cas12a for Nucleic Acid Assays

Experimentally, Cas12a can recognize multiple protospacer adjacent motif (PAM) sequences and is not restricted to the "TTTN". However, the application of the CRISPR/Cas12a system is still limited by the PAM for double-stranded DNA (dsDNA). Here, we developed asymmetric RPA (Asy-RPA) to completely break the limitations of PAM. Asy-RPA not only achieved efficient amplification but also converted dsDNA to single-stranded DNA (ssDNA) without complicated steps. The ssDNA products activated the trans-cleavage activity of Cas12a, outputting signals. The application of Asy-RPA completely freed Cas12a from the PAM, which can be more widely used in nucleic acid detection, such as lumpy skin disease virus, with an actual detection limit as low as 1.21 × 101 copies·μL-1. More importantly, Cas12a was intolerant to mutations on ssDNA. This provided technical support for the detection and identification of wild-type Mycobacterium tuberculosis (WT-TB) and rifampin-resistant mutant-type M. tuberculosis (MT-TB). The detection limit was as low as 1 fM for 1% mixed samples. The detection and availability of different treatment options for treatment-resistant and WT-TB were significant for the elimination of TB. In summary, the platform consisting of Asy-RPA and CRISPR/Cas12a was suitable for the detection of various viruses and bacteria and was a boon for the detection of dsDNA without recognizable PAM.

Field-friendly and ultra-fast detection platform without nucleic acid extraction for virus detection

The polymeric chain reaction (PCR) has come under fire for being time-consuming, requiring expensive equipments, and requiring the extraction and purification of nucleic acids. Here, an ultra-fast and sensitive detection platform without nucleic acid extraction solved the above problems. Firstly, the RoomTemp Sample Lysis Kit released the nucleic acid in 3 min and removed the inhibition to facilitate the amplification reaction. What's more, ultra-fast PCR (UF-PCR) can complete 40 cycles in just 15 min and 50 s. To improve the sensitivity and provide more convenient reading modes, CRISPR/Cas12a was mediated to detect Lumpy skin disease virus (LSDV). The platform output fluorescence and Lateral flow dipstick (LFD) signals. The actual detection limit was 2 × 101 copies·μL-1. The portable platform realized visualization, excellent sensitivity and quick speed. In summary, the field-friendly testing platform had great potential in practical testing.

Development of the isothermal recombinase polymerase amplification assays for rapid detection of the genus Capripoxvirus

Sheeppox virus (SPPV), goatpox virus (GTPV) and lumpy skin disease virus (LSDV) belong to the genus Capripoxvirus (CaPV), and are important pathogens of sheep, goat and cattle, respectively. Rapid and reliable detection of CaPV is critical to prevent its spread and promote its eradication. This study aimed to develop the recombinase polymerase amplification (RPA) assays combined with real-time fluorescence (real-time RPA) and naked-eye visible lateral flow strip (LFS RPA) for rapid detection of CaPV. Both developed RPA assays worked well at 39 °C within 20 min. They were highly specific for the detection of GTPV, SPPV and LSDV, while no cross-reactivity was observed for other non-targeted pathogens and genomic DNA of goat, sheep and cattle. The limit of detection for real-time RPA and LFS RPA were 1.0 × 102 and 1.0 × 101 copies per reaction, respectively. In the artificially contaminated samples with GTPV, the detection results of RPA assays were consistent with those of real-time PCR. For 15 clinical samples, LSDV was detected by real-time RPA, LFS RPA and real-time PCR in 13, 15 and 15 samples, respectively. The developed RPA assays were specific, sensitive, and user-friendly for the rapid detection of CaPV, and could be a better alternative method applied in low-resources settings.

Enzyme-free and sensitive method for single-stranded nucleic acid detection based on CHA and HCR

Simple, rapid, and highly sensitive methods for single-stranded nucleic acid detection are of great significance in clinical testing. Meanwhile, common methods are inseparable from the participation of enzymes, which greatly increases their complexity. Herein, an enzyme-free and sensitive method combining HCR and CHA is established to detect single-stranded nucleic acid. A target induces the auxiliary hairpin strands to open their secondary structure, exposing partial sequences that can trigger catalytic hairpin assembly (CHA) and hybridization chain reactions (HCR), respectively. To avoid additional signaling substances, 2-aminopurines (which fluoresces differently in double-stranded DNA and G-quadruplex) are modified in the substrate chains of CHA and HCR. Compared with methods that adopt CHA or HCR alone, the sensitivity of this method is increased by nearly 10 times. Moreover, this method can effectively improve the specific recognition of the target. To "turn on" the method, two regions that can pair with H5 and H6 are required. Taking foot-and-mouth disease virus (FMDV) as the object, this method can specifically detect FMDV to 2.78 × 101 TCID50. Although the sensitivity is not as good as RT-qPCR, it owns the advantages of simplicity and speed. We think this method can be used for the primary screening of FMDV, and has application potential in some grassroots.

Multiple accurate and sensitive arrays for Capripoxvirus (CaPV) differentiation

Capripoxvirus (CaPV) contains three viruses that have caused massive losses in the livestock and dairy industries. Accurate CaPV differentiation has far-reaching implications for effectively controlling outbreaks. However, it has a great challenge to distinguishing three viruses due to high homology of 97%. Here, we established a sensitive CRISPR/Cas12a array based on Multiple-recombinase polymerase amplification (M-RPA) for CaPV differentiation, which provided a more comprehensive and accurate differentiation mode targeting VARV B22R and RPO30 genes. By sensitive CRISPR/Cas12a and M-RPA, the actual detection limits of three viruses were as low as 50, 40 and 60 copies, respectively. Moreover, Lateral flow dipstick (LFD) array based on CRISPR/Cas12a achieved portable and intuitive detection, making it suitable for point-of-care testing. Therefore, CRISPR/Cas12a array and LFD array paved the way for CaPV differentiation in practice. Additionally, we constructed a real-time quantitative PCR (qPCR) array to fill the qPCR technical gap in differentiation and to facilitate the quarantine departments.

The End of the Gray Zone: One-Tube Nested Recombinase Polymerase Amplification with Ultrahigh Signal-to-Noise Ratio for Precisely Detecting and Surveilling Viruses

The samples were difficult to accurately determine positive or negative between 35 and 40 cycles by real-time quantitative PCR (qPCR) as the standard method. Here, we developed one-tube nested recombinase polymerase amplification (ONRPA) technology with CRISPR/Cas12a to overcome this difficulty. ONRPA broke the amplification plateau to substantially enhance the signals, which considerably improved the sensitivity and eliminated the problem of gray area. Using two pairs of primers one after another, it improved precision by lowering the probability of magnifying several target zones, which was completely free of contamination by nonspecific amplification. This was important in nucleic acid testing. Finally, by the CRISPR/Cas12a system as a terminal output, the approach achieved a high signal output as few as 2.169 copies·μL^-1 in 32 min. ONRPA was 100-fold more sensitive than conventional RPA and 1000-fold compared to qPCR. ONRPA coupled with CRISPR/Cas12a will be an important and new promoter of RPA in clinical applications.

Current Knowledge on Epizootic Haemorrhagic Disease in China

Epizootic haemorrhagic disease (EHD) is an infectious, non-contagious viral disease of ruminants caused by epizootic haemorrhagic disease virus (EHDV) and is transmitted by insects of the genus Culicoides. In 2008, EHD was listed on the World Organization for Animal Health (WOAH) list of notifiable terrestrial and aquatic animal diseases. This article reviews the distribution of EHD in China and relevant studies and proposes several suggestions for the prevention and control of EHD. There have been reports of positivity for serum antibodies against EHDV-1, EHDV-2, EHDV-5, EHDV-6, EHDV-7, EHDV-8 and EHDV-10 in China. Strains of EHDV-1, -5, -6, -7, -8 and -10 have been isolated, among which the Seg-2, Seg-3 and Seg-6 sequences of serotypes -5, -6, -7 and -10 belong to the eastern topotype. The emergence of western topotype Seg-2 in EHDV-1 strains indicates that EHDV-1 strains in China are reassortant strains of the western and eastern topotypes. A novel serotype strain of EHDV named YNDH/V079/2018 was isolated in 2018. Chinese scholars have successfully expressed the EHDV VP7 protein and developed a variety of ELISA detection methods, including antigen capture ELISA and competitive ELISA. A variety of EHDV nucleic acid detection methods, including RT-PCR and qRT-PCR, have also been developed. LAMP and the liquid chip detection technique are also available. To prevent and control EHD, several suggestions for controlling EHD transmission have been proposed based on the actual situation in China, including controlling the number of Culicoides, reducing contact between Culicoides and hosts, continued monitoring of EHDV and Culicoides in different areas of China and further development and application of basic and pioneering research related to EHD prevention and control.

[Advances on optic disc morphological features and peripapillary structure changes in high myopia]

High myopia is an important cause of low vision and blindness in the world, most of which are characterized by the prolongation of the axial length, accompanied by various degenerative changes of fundus posterior pole, especially in the optic disc area and peripapillary structures, such as optic disc tilt, optic cup and rim changes, chorioretinal atrophy, posterior staphyloma and intrachoroidal cavitation, and so on. This article reviews the optic disc morphological features and peripapillary structure changes of high myopia, in order to reveal the pathogenesis of high myopia and provide new ideas for finding more effective prevention and treatment methods.

Carbon nanodots combined with loop-mediated isothermal amplification (LAMP) for detection of African swine fever virus (ASFV)

The spread of African swine fever virus (ASFV) caused huge economic costs, so early detection is particularly important. Here, we established a fluorescence biosensor based on carbon nanodots (CNDs) and loop-mediated isothermal amplification (LAMP) to ultra-sensitively detect ASFV. LAMP with high efficiency produced a large amount of pyro phosphoric acid and caused pH change in a short time. CNDs with strong light stability had a large fluorescence response at the emission wavelength of 585.5 nm to small pH change by the excitation wavelength of 550 nm. The biosensor realized “turn-off–on” mode for ASFV detection with the detection limit as low as 15.21 copies μL⁻¹. In addition, the biosensor had high accuracy in the actual sample assay. Therefore, the biosensor achieved rapid, sensitive, low-cost, and simple detection for ASFV. Moreover, the biosensor broadened the detection pathway of LAMP as a tool with great development prospect.

Analysis of vaccine-like lumpy skin disease virus from flies near the western border of China

Lumpy skin disease (LSD) is a devastating viral disease that occurs in cattle. In China, it was first detected in the Xin-Jiang autonomous region, near the border with Kazakhstan, in August 2019. As there were no new occurrences of LSD in either country following the first detection, the initial introduction of the virus remains unknown. Arthropod vectors were considered as potential vectors. Consequently, to identify the arthropod vectors involved in transmitting LSD virus (LSDV), an insect surveillance campaign was launched at four different sites scattered along the border, and samples from 22 flying insect species were collected and subjected to PCR assays. Following the Agianniotaki LSDV vaccine and Sprygin's general LSDV assays, two kinds of non-biting flies, namely, Musca domestica L and Muscina stabulans, were positive for LSDV. However, all the other insects tested negative. Viral DNA was only detected in wash fluid, implying body surface contamination of the virus. The negative test results suggest that non-biting flies are the dominant insects involved in the observed local epidemic. Three genomic regions encoding RPO30, GPCR, and LW126 were successfully sequenced and subjected to phylogenetic analysis. The sequences shared high homology with LSDV/Russia/Saratov/2017, a recombinant vaccine-like strain formerly identified in Russia, and clustered with LSDV vaccine strains in phylogenetic trees of RPO30 and LW126. However, the GPCR gene was seen to be solely clustered with LSDV field strains, implying differences in host affinity between these closely related vaccine-like strains. Despite this, there is no direct evidence to support cross-border transmission of the vaccine-like LSDV. To our knowledge, this is the first report of vaccine-like LSDV DNA detection in non-biting flies in China.

Non-nucleic acid extraction and ultra-sensitive detection of African swine fever virus via CRISPR/Cas12a

Early diagnosis of the African swine fever virus (ASFV) is the main preventive measure for ASFV. Here, we developed a fluorescent biosensor and lateral flow assay (LFA) strip based on direct PCR combined with CRISPR/Cas12a system for ASF. Direct PCR can simultaneously split samples and efficiently amplify without sacrificing sensitivity, which eliminated the steps of nucleic acid extraction. Furthermore, by the CRISPR/Cas12a, the biosensor addressed false positives caused by non-specific amplification and had high sensitivity with the actual limit of detection (LOD) of 7.6×10^-4 ng·μL^-1 (4 copies·μL^-1). In addition, the strategy was built on the lateral flow assay (LFA) strip to achieve visual and portable detection for point-of-care testing. Moreover, the biosensor by a fluorometer and LFA strip showed a high accuracy to rival qPCR in actual sample detection. Therefore, the biosensor is an ultra-sensitive and specific tool that can replace traditional methods. KEY POINTS: • No nucleic acid extraction, direct PCR-simplified steps, and reduced time and cost • CRISPR/Cas12a solved the false positives caused by nonspecific amplification • The combination of the LFA strip and biosensor is more convenient for POC detection.

Lipid accumulation product is a reliable indicator for identifying metabolic syndrome: the China Multi-Ethnic Cohort (CMEC) Study

BACKGROUND

Previous studies have shown that lipid accumulation product (LAP) was associated with the risk of cardiometabolic disease. It is not clear whether LAP could be used as a marker to identify metabolic syndrome (MetS) among Chinese ethnic groups.

AIM

To assess the reliability of LAP as a maker to identify MetS among Dong adults.

DESIGN

Population-based cross-sectional study.

METHOD

We included 6494 Dong individuals (1403 patients) aged 30-79 years from southwest China. MetS was established by Chinese Diabetes Society. Logistic regression model was utilized to calculate odds ratios (ORs) and 95% confidence intervals (CIs). Receiver operating characteristic (ROC) curve was utilized to calculate area under the ROC curve (AUC) and 95% CIs to obtain the identification ability for MetS.

RESULTS

The risk of MetS was increased with per 5 units increase of LAP (OR 1.37 [95% CI, 1.34-1.39]). Similar results were found in subgroup analyses and sensitivity analyses. Clustered metabolic risk associated with per 5 units increase of LAP was observed for people with 1 (OR 1.59 [95% CI, 1.53-1.65]), 2 (2.15 [2.06-2.24]), 3 (2.59 [2.48-2.71]), 4 (2.81 [2.69-2.95]) and 5 (3.03 [2.87-3.21]) MetS components. LAP presented higher AUC (0.915 [95% CI, 0.907-0.923]) than other included obesity indices (P < 0.05).

CONCLUSION

These data support evidence that LAP was related to the risk of MetS, had a high AUC and could be a reliable index for identifying MetS patients among Dong adults in Chinese.

Ultra-sensitive and point-of-care detection of Capripoxvirus (CaPV) based on loop-mediated amplification (LAMP) and trans-cleavage activity of CRISPR/Cpf1

Capripoxvirus (CaPV) is one of the common skin diseases infecting cattle and sheep which can cause serious economic losses. Establishing ultra-sensitive, rapid, and point-of-care detection of CaPV is particularly important for hindering its spread. Here, we use the principle that CRISPR/Cpf1 can specifically recognize the target DNA and activate its trans-cleavage activity to identify the CaPV product amplified by loop-mediated amplification (LAMP). Under the designed specific primers, a set of LAMP which can amplify CaPV specifically was established and optimized firstly. Then, the CRISPR/Cpf1 was introduced to identify LAMP products. LAMP can be completed at a constant temperature, thus avoiding the use of temperature-variable instruments, making it possible to detect viruses outside the laboratory. To further satisfy the point-of-care detection of CaPV, we introduced a portable fluorometer and CRISPR-based lateral flow test. Due to the introduction of CRISPR/Cpf1, the sensitivity of the method is greatly increased, which is of great significance for the early detection of viruses. Through CRISPR/Cpf1-mediated fluorescence detection, we can detect CaPV as low as 1.47 × 10^-3 TCID₅₀ in 50 min, 1000 times more sensitive than quantitative real-time PCR. Through CRISPR-based lateral flow test, we can visually detect CaPV as low as 1.47 × 10^-2 TCID₅₀. Besides, this strategy can be used for the primary samples obtained from the cell culture of CaPV after simple ultrasonic disruption, which eliminates the complicated nucleic acid extraction steps required by traditional methods.

One-pot platform for rapid detecting virus utilizing recombinase polymerase amplification and CRISPR/Cas12a

The livestock industry has been deeply affected by African swine fever virus (ASFV) and Capripoxvirus (CaPV), which caused an enormous economic damage. It is emergent to develop a reliable detection method. Here, we developed a rapid, ultra-sensitive, and one-pot DNA detection method combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a for ASFV and CaPV, named one-pot-RPA-Cas12a (OpRCas) platform. It had the virtue of both RPA and CRISPR/Cas12a, such as high amplification efficiency, constant temperature reaction, and strict target selectivity, which made diagnosis simplified, accurate and easy to be operated without expensive equipment. Meanwhile, the reagents of RPA and CRISPR/Cas12a were added to the lid and bottom of tube in one go, which overcame the incompatibility of two reactions and aerosol contamination. To save cost, we only need a quarter of the amount of regular RPA per reaction which is enough to achieve clinical diagnosis. The OpRCas platform was 10 to 100 times more sensitive than qPCR; the limit of detection (LOD) was as low as 1.2 × 10^-6 ng/µL (3.07 copies/µL by ddPCR) of ASFV and 7.7 × 10^-5 ng/µL (1.02 copies/µL by ddPCR) of CaPV with the portable fluorometer in 40 min. In addition, the OpRCas platform combined with the lateral flow assay (LFA) strip to suit for point-of-care (POC) testing. It showed 93.3% consistency with qPCR for clinical sample analysis. Results prove that OpRCas platform is an easy-handling, ultra-sensitive, and rapid to achieve ASFV and CaPV POC testing. KEY POINTS: • The platform realizes one-pot reaction of RPA and Cas12a. • Sensitivity is 100 times more than qPCR. • Three output modes are suitable to be used to quantitative test or POC testing.

Single-nucleotide variant of PIK3CA H1047R gene assay by CRISPR/Cas12a combined with rolling circle amplification

PIK3CA ^H1047R gene plays an important role in the PI3K/Akt/mTOR signaling pathway, and its mutation is closely related to the occurrence and development of breast cancer and Lipoblastoma. Therefore, it is of great value to detect the PIK3CA ^H1047R mutant gene. Here, an analytical method coupled CRISPR/Cas12a with rolling circle amplification (RCA) technology was constructed for ultra-sensitive and specific detection of the single-nucleotide variant (SNV) of the PIK3CA ^H1047R gene. With efficient amplification of RCA and CRISPR/Cas12a, the detection limit of the mutant target and mixture of the mutant with wild-type target were as low as 10 aM and 0.036%, respectively. The detection limit of the RCA-CRISPR/Cas12a method was lower than that of allelic specific PCR (AS-PCR) for detecting SNV of the PIK3CA ^H1047R gene. Hence, this RCA-CRISPR/Cas12a method is sensitive and specific for the detection of SNV. What's more, this strategy provides a new idea for medical diagnosis and lays a technical foundation for the research of PI3K/Akt/mTOR signaling pathways.

[Application of dual-channel contrast-enhanced ultrasound in classification of hilar cholangiocarcinoma and diagnosis of etiology of low biliary obstruction]

Objective: To investigate the clinical value of dual-channel contrast-enhanced ultrasound (DCUS) in the classification of hilar cholangiocarcinoma and the diagnosis of the etiology of low obstructive jaundice. Methods: The data of 114 patients with obstructive jaundice examined by the Department of Ultrasound of Lanzhou University Second Hospital from October 2018 to February 2020 were retrospectively collected. There were 60 males and 54 females, aged 37~84 (63±10) years. All patients underwent preoperative transvenous contrast-enhanced ultrasound (CEUS), intraoperative puncture needles, postoperative ultrasound-guided percutaneous transhepatic cholangiocarcinography (UG-PTC) and three-dimensional ultrasound cholangiography (3D-USC) through an external drainage tube, known as DCUS. The classification of hilar cholangiocarcinoma and the nature of low biliary tract obstruction were determined according to the characteristics of DCUS images. All patients who have received DCUS underwent magnetic resonance cholangiopancreatography (MRCP) and X-ray cholangiography. X-ray cholangiography was used as the gold standard for classification of hilar cholangiocarcinoma, and the accuracy of US, CEUS and DCUs was analyzed. Low obstructive jaundice was characterized by surgical pathology as the gold standard, and the diagnostic efficacy of conventional ultrasound (US), CEUS and DCUs was analyzed. At the same time, the receiver operating characteristic (ROC) curve was used to compare the efficacy of MRI+MRCP and DCUS in determination of the nature of low biliary obstruction. Results: The coincidence rates of US, CEUS, and DCUS in the classification of hilar cholangiocarcinoma and X-ray cholangiography were: 75.6% (34/45), 82.2% (37/45), and 93.3% (42/45), respectively. The coincidence rates of US, CEUS, and DCUS in the determination of the nature of low biliary obstruction and surgical pathology were 56.5% (39/69), 82.6% (57/69), and 85.5% (59/69), respectively. Compared with conventional ultrasound, CEUS had no statistically significant difference in the diagnosis of hilar cholangiocarcinoma (P=0.438), and DCUS had statistically significant difference in the diagnosis of hilar cholangiocarcinoma (P=0.039).ROC curve analysis suggested that the cut-off value of MRI+MRCP grade and DCUS grade for diagnosing benign and malignant low biliary obstruction were both 2.5; the area under the curve (AUC) were 0.897 and 0.906, respectively (both P<0.01); sensitivity were 77.5% and 93.1%, respectively; and the specificity were 87.5% and 82.8%, respectively. Conclusion: The value of DCUS in the classification of hilar cholangiocarcinoma and the qualitative diagnosis of low biliary tract obstruction was comparable to that of X-ray cholangiography and MRCP. DCUS had important clinical application value in the classification of hilar cholangiocarcinoma and the etiological diagnosis of low obstructive jaundice.

Development of multiplex oligonucleotide microarray for simultaneous detection of six swine pathogens

In order to establish a high-throughput identification technique that simultaneously detects six major pathogens including APP, HPS, PRRSV, Mhp, PCV-2 and CSFV, six pairs of primers and probes were designed based on the specific conservative sequences of the pathogens, a multiplex PCR system was developed, hybrid parameters were optimized, and evaluation of the technology was performed. The results showed that the present detection method had a sensitivity of 5.8 × 10²copies/μL for APP, 7.8 × 10³ copies/μL for HPS, 6.8 × 10³ copies/μL for Mhp, 6.3 × 10² copies/μL for PCV-2, 4.8 × 10³ copies/μL for PRRSV, and 5.5 × 10² copies/μL for CSFV, respectively; and it produced no cross reaction against the other nine pathogens like swine-origin pseudorabies virus, porcine parvovirus, Japanese B encephalitis virus, swine vesicular disease virus, vesicular stomatitis virus, foot-and-mouth disease virus, bluetongue virus, peste des petits ruminants virus and salmonella. Application of the multiplex oligonucleotide microarray established here to testing 285 clinical blood samples indicated a single infection rate of 18.2 % (52/285) and a mixed infection rate of 6.3 % (18/285) which were consistent with the results of the sequencing verification. This technique might serve as a rapid and high-throughput method of detection for epidemic investigation and clinical diagnosis of multiple pathogens.

Establishment of a Multiplex Real-Time TaqMan-MGB Polymerase Chain Reaction (PCR) Method for the Simultaneous Detection of Three Animal Chlamydia Species

BACKGROUND Chlamydiae are spread globally and cause infectious diseases in both humans and animals. The existing detection methods for this disease have numerous shortcomings, including low sensitivity, time consuming procedures, and high contamination vulnerability. MATERIAL AND METHODS To overcome shortcomings for detecting animal chlamydiosis, a multiplex quantitative polymerase chain reaction (PCR) assay was established for simultaneously detecting and differentiating 3 Chlamydia species (C. pecorum, C. abortus, and C. psittaci) by real time PCR based on TaqMan-MGB technology. RESULTS The limit of detection was 20.2 copies/µL for Chlamydophila (Cp.) abortus, 30.8 copies/µL for Cp. pecorum, and 16 copies/µL for Cp. psittaci. This method has good repeatability and stability as coefficients of variation range from 0.04% to 1.38%. Furthermore, compared with OIE (World Organization for Animal Health) recommended PCR assay and previously reported animal chlamydia shell PCR, this multiplex PCR assay demonstrated 99% concordance in detecting clinical samples of porcine nasal swabs and vaginal swabs. CONCLUSIONS The novel established method in this study was able to detect 3 types of Chlamydia species simultaneously, and had high sensitivity, strong specificity, and good stability. It provided a rapid, reliable, and convenient method for epidemiological and clinical diagnosis of chlamydiosis in animals.

Simultaneous typing of seven porcine pathogens by multiplex PCR with a GeXP analyser

A novel high-throughput method was developed for simultaneous detection and differentiation of seven porcine pathogens by multiplex PCR based on a GenomeLab Gene Expression Profiler (GeXP) analyser. The pathogens included in this study were pseudorabies virus (PRV), classical swine fever virus (CSFV), African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine parvovirus (PPV), porcine circovirus type 2 (PCV-2) and Japanese encephalitis virus (JEV). Seven pairs of chimeric primers, consisting of a pathogen-specific sequence fused to a universal sequence at the 5' end, were used to initiate the PCR, after which a set of universal primers was used for the subsequent cycles of the PCR. Amplification products were separated by capillary electrophoresis and identified using fluorescence spectrophotometry. The specificity of the GeXP assay was examined with single and mixed pathogen cDNA/DNA templates. The specific DNA product amplification peaks of seven pathogens were observed on the GeXP analyser. Negative controls did not produce DNA products. The sensitivity was evaluated by performing the assay on serial 10-fold dilutions of the plasmids containing the target sequence. Under optimised conditions this assay achieved a sensitivity of 100-1000 copies/μL for a single virus and 1000 copies/μL when all of the seven pre-mixed viral targets were present. Furthermore, the GeXP-PCR assay was 100% specific when 58 clinical samples were tested in comparison with the conventional PCR method. In conclusion, the GeXP assay is a rapid, cost-effective, sensitive, specific and high throughput method for simultaneously detecting seven pathogens that infect swine.

MicroRNA expression profiling identifies miR-328 regulates cancer stem cell-like SP cells in colorectal cancer

Background:

Side population (SP) cells and their relationship to stem cell-like properties have been insufficiently studied in colorectal cancer (CRC). MicroRNAs (miRNAs) have attracted much attention but their roles in the maintenance of SP phenotype remain unclear.

Methods:

The SPs from CRC cell lines and primary cell cultures were analysed for stem cell-like properties. MiRNA microarray analysis identified miR-328 as a potential stemness miRNA of SP phenotype. The level of miR-328 expression in clinical samples and its correlation with SP fraction were determined. Gain-of-function and loss-of-function studies were performed to examine its roles in cancer stem-like SP cells. Furthermore, bioinformatics prediction and experimental validation were used to identify miR-328 target genes.

Results:

The SP cells sorted from CRC possess cancer stem cell (CSC)-like properties, including self-renewal, differentiation, resistance to chemotherapy, invasive and strong tumour formation ability. MiR-328 expression was significantly reduced in SP cells compared with Non-SP cells (P<0.05). Moreover, miR-328 expression was downregulated in CRC (n=33, P<0.05) and low miR-328 expression tend to correlate with high SP fraction (n=15, r=0.6559, P<0.05, Pearson's correlation). Functional studies indicated that miR-328 expression affects the number of SP cells. In addition, miR-328 overexpression reversed drug resistance and inhibited cell invasion of SP cells. Furthermore, luciferase reporter assay demonstrated that miR-328 directly targets ABCG2 and MMP16 and affects the levels of mRNA and protein expression in SP cells.

Conclusion:

These findings indicate that CRC contain cancer stem-like SP cells. MiR-328 has an important role in maintaining cancer stem-like SP phenotype that may be a potential target for effective CRC therapy.

A nested multiplex polymerase chain reaction assay for the differential identification of three zooanthroponotic chlamydial strains in porcine swab samples

Porcine chlamydial infection is an enzootic infectious disease caused by multiple members of the family Chlamydiaceae (e.g. Chlamydophila abortus, Chlamydia suis, and Chlamydophila pneumoniae). Rapid and accurate differentiation of these pathogens is critical in the control and prevention of disease. The aim of the current study was to develop a nested multiplex polymerase chain reaction (nmPCR) assay to simultaneously detect the 3 chlamydial pathogens in clinical samples. In the first round of the nmPCR, 1 pair of family-specific primers were used to amplify the 1,100 base pair (bp) fragment of chlamydial ompA gene. In the second round of the nmPCR, 4 inner primers were designed for Ch. abortus, C. suis, and Ch. pneumoniae. Each pathogen produced a specific amplicon with a size of 340 bp, 526 bp, and 267 bp respectively. The assay was sensitive and specific for detecting target pathogens in both cell cultures and clinical specimens. The results, incorporated with the improved rapid DNA extraction protocol, suggest that the nmPCR could be a promising assay for differential identification of different chlamydial strains in pigs.

Effects of Rapamycin on Breast Cancer Cell Migration through the Cross-Talk of MAPK Pathway

Phase I/II clinical studies with rapamycin analogs in breast and other cancers have demonstrated favorable responses. However, little is known on the effects of the mTOR inhibitor on breast cancer cell metastasis, which is a major cause of morbidity and death. We developed a highly sensitive 3-dimensional (3D) proliferation/invasion assay using quantitative bioluminescence (BL) imaging and applied this assay to evaluate the effects of rapamycin on the triple negative breast cancer cell line MDA-MB231. Without cytotoxicity of rapamycin on this cell line, rapamycin at 10nM inhibited the cell migration/invasion, but not at 1nM and 100nM, which was confirmed by the time-lapse single cell tracking analysis. The quantification of cytoskeleton changes showed most potent effects of 10nM rapamycin on the MDA-MB231 cells, with the formation and rearrangement of specialized cell membrane structures and actin fiber implicated in cell motility. Then, the Panorama Cell Signaling Antibody Microarray, enabling the global comparative analysis of cell signal proteins simultaneously, was exploited to analyze the effects of rapamycin on the cellular signaling network of the MDA-MB231 breast cancer cell line. 100nM rapamycin activated the MAPK pathway obviously, through the attenuated negative feedback of activated S6K1 to PI3K-Raf, which increased the expressions of activated Jun N-terminus kinase (JNK), Erk1/2, MEK-1, Raf-pS621, and MAPK-activated protein kinase 2 (MAPKAPK2) in the cells exposed to 100nM rapamycin. MEK inhibitor U0126 or PD98059 could restore the anti-migration effects of 100nM rapamycin on the MDA-MB231 cells. Furthermore, the combination of MEK inhibitors and rapamycin performed synergism on inhibiting the cell proliferation and migration/invasion. Accordingly, rapamycin at a certain dose suppresses MDA-MB231 cell migration/invasion, and the co-targeting of mTOR and MAPK pathways enhances the inhibition on cell proliferation and migration/invasion, underscoring the potential therapeutic utility of rapamycin, and rapamycin combining with MAPK inhibitors in triple negative breast cancer progression, and the results highlight the cross-talk homeostasis of mTOR and MAPK pathways in cancer treatment.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5080.

[Morphological and microscopic identification of herba artemisiae scopariae and its adulterants]

Pharmacognostical studies of Herba Artemisiae Scopariae and its adulterants were compared on morphological and microscopic characteristics. The detailed characteristics of powder microscopic identification were described.

Human nuclear respiratory factor 2 alpha subunit cDNA: isolation, subcloning, sequencing, and in situ hybridization of transcripts in normal and monocularly deprived macaque visual system

Nuclear respiratory factor 2 (NRF-2) has been shown to contribute to the transcriptional regulation of a number of subunits of respiratory chain enzymes, including cytochrome c oxidase (CO). Our recent study demonstrated a parallel distribution of the alpha subunit proteins of NRF-2 (NRF-2 alpha) with CO in the monkey striate cortex, and that it can be regulated by neuronal activity. To determine whether this regulation is at the transcriptional level, the present study examined the expression of NRF-2 alpha mRNA in normal and monocularly deprived adult monkeys. A partial NRF-2 alpha cDNA was isolated from a human brain cDNA library. Sequence analysis revealed that it shared 99% identity with the published sequence from human HeLa cells. Riboprobes of NRF-2 alpha was generated and labeled with digoxigenin-11-UTP for in situ hybridization. The expression pattern of NRF-2 alpha mRNA in the normal striate cortex paralleled that of CO activity. It was highly expressed in layers IVC and VI, which contained high levels of CO, and more densely expressed in puffs of layers II and III than in interpuffs. In monkeys monocularly treated with tetrodotoxin for 1 day to 2 weeks, both NRF-2 alpha expression and CO activity were reduced in deprived ocular dominance columns of the visual cortex and in deprived layers of the lateral geniculate nucleus. These data indicate that, in the normal and visually deprived adult monkeys, NRF-2 alpha is regulated by neuronal activity at the transcriptional level.

Nuclear respiratory factor-2 subunit protein: correlation with cytochrome oxydase and regulation by functional activity in the monkey primary visual cortex

Previous studies have shown that a transcription factor of the Ets family, nuclear respiratory factor 2 (NRF-2), can activate in vitro the gene expression of cytochrome oxidase (CO), a mitochondrial enzyme of oxidative metabolism. The goals of our present study were to determine whether the distribution of NRF-2 alpha subunit proteins correlated with that of CO activity in the macaque monkey visual cortex and whether the level could be perturbed by visual deprivation. We generated polyclonal antibodies specifically against human NRF-2 alpha subunit. In normal monkeys, patterns of NRF-2 alpha distribution resembled closely that of CO activity: 1) NRF-2 alpha immunoreactivity was localized in both nuclei and cytoplasm of neurons, but the levels differed among various laminae; 2) layers IVA, IVC, and VI, which had high CO activity, were labeled more densely by NRF-2 alpha than layers I, IVB, and V, which contained lower levels of both NRF-2 alpha and CO activity; and 3) CO-rich puffs in layers II and III contained a higher level of NRF-2 alpha than CO-poor interpuffs. From 1 day to 7 days after monocular impulse blockade with tetrodotoxin, there was a progressive reduction of NRF-2 alpha in deprived ocular dominance columns, in parallel with decreases in CO activity. These results suggest that local levels of NRF-2 in the monkey visual cortex closely reflect neuronal physiological and metabolic levels revealed by CO activity and that the expression of NRF-2 alpha, like that of CO, is regulated tightly by neural functional activity.

Neurochemical organization of the macaque retina: effect of TTX on levels and gene expression of cytochrome oxidase and nitric oxide synthase and on the immunoreactivity of Na+ K+ ATPase and NMDA receptor subunit I

The present study examined the relationship between an important energy-generating enzyme (cytochrome oxidase; CO), a key energy-consuming enzyme (Na+ K+ ATPase) and neurochemicals associated with excitatory glutamatergic synapses (NMDAR1 and neuronal nitric oxide synthase, nNOS) in the adult macaque retina. Polyclonal antibodies against neuronal nitric oxide synthase and N-methyl-D-aspartate receptor subunit I were generated for immunohistochemical examination and labeled sites not previously reported were found. We have also isolated cDNAs for cytochrome oxidase subunits III (mitochondrial-encoded) and IV (nuclear-encoded), as well as for a fragment of neuronal nitric oxide synthase, from a human cDNA library. The distributions of mRNAs of these genes were analyzed by in situ hybridization. We found that three or more of the markers examined coexisted in a number of sites: (a) In the inner segments of photoreceptors, high energy demand for maintaining the dark current was placed by Na+ K+ ATPase. This was partially met by ATP-generating enzymes such as CO. Neuronal NOS was also present there for the synthesis of NO and the cascading event leading to the generation of cGMP and the gating of channels for visual transduction. (b) Both the outer and inner plexiform layers had detectable amounts of all four markers, although the levels varied among them. This was most likely due to the presence of depolarizing glutamatergic synapses arising from photoreceptors and bipolar cells and such synaptic events were energy-demanding. The involvement of NMDA receptors and nNOS in these synaptic layers is strongly implicated in the present study. (c) All four markers were present in the majority of retinal ganglion cells, with some inherent heterogeneity related to intensity and size. Retinal ganglion cells are known to receive excitatory synapses from glutamatergic bipolar cells and are themselves highly active. The presence of both NMDAR1 and nNOS in these cells were verified in the present study and the energy demands related to these synaptic activities were necessarily high. Thus, active ion transporting functions related to synaptic or non-synaptically induced repolarization from the basis for an interrelationship between the neurochemicals/enzymes studied. Finally, (d) all four markers and the gene expression of CO and nNOS in the macaque retina were regulated by neuronal activity.

Mitochondrial- and nuclear-encoded subunits of cytochrome oxidase in neurons: differences in compartmental distribution, correlation with enzyme activity, and regulation by neuronal activity

Cytochrome oxidase (CO), a mitochondrial energy-generating enzyme, contains both mitochondrial- and nuclear-encoded subunits. In neurons, local levels of CO activity vary among different neuronal compartments, reflecting local demands for energy. The goals of the present study were to determine if compartmental distribution of CO subunit proteins from the two genomes was correlated with local CO activity, and if their expression was regulated proportionately in neurons. The subcellular distributions of mitochondrial-encoded CO III and nuclear-encoded CO Vb proteins were quantitatively analyzed in mouse cerebellar sections subjected to postembedding immunocytochemistry. Local levels of subunit proteins were also compared to local CO activity, as revealed by CO cytochemistry. In order to study the regulation of subunit protein expression, we assessed changes in immunoreactivity of the two CO subunits as well as changes in CO activity in mouse superior colliculus after 1 to 7 days of monocular enucleation. We found that immunoreaction product for both CO III and CO Vb existed almost exclusively in mitochondria, but their compartmental distributions were different. CO III was nonhomogeneously distributed among different neuronal compartments, where its local level was positively correlated with that of CO activity. In contrast, the subcellular distribution of CO Vb was relatively uniform and did not bear a direct relationship with that of CO activity. Moreover, the two subunit proteins were disproportionately regulated by neuronal activity. CO III and CO activity exhibited parallel decreases after the deprivation of afferent input, and their changes were earlier and to a greater degree than that of CO Vb proteins. Thus, the present findings indicate that the local expression and/or distribution of CO subunit proteins from the two genomes may involve different regulatory mechanisms in neurons. Our data also suggest that the activity-dependent regulation of mitochondrial-encoded CO subunits is likely to play a major role in controlling the local levels of CO content and its activity.

Metabolic and neurochemical plasticity of gamma-aminobutyric acid-immunoreactive neurons in the adult macaque striate cortex following monocular impulse blockade: quantitative electron microscopic analysis

The purpose of the present study was to examine the effects of retinal impulse blockade on gamma-aminobutyric acid (GABA)-immunoreactive (GABA-IR) neurons in cytochrome oxidase (CO)-rich puffs of the adult monkey striate cortex. Specifically, we wished to know if changes occurred in their CO activity, GABA immunoreactivity, and synaptic organization. A double-labeling technique, which combined CO histochemistry and postembedding GABA immunocytochemistry on the same ultrathin sections, was used to reveal simultaneously the distribution of the two markers. We quantitatively compared changes in GABA-IR neurons of deprived puffs (DPs) with respect to non-deprived puffs (NPs) 2 weeks after monocular tetrodotoxin treatment. We found that the proportion of darkly CO reactive mitochondria in GABA-IR neurons of DPs drastically decreased to about half of those in NPs. There was a greater reduction of CO levels in GABA-IR axon terminals than in their cell bodies and dendrites. In contrast, most non-GABA-IR neurons displayed no significant change in their CO levels. Morphologically, GABA-IR neurons and axon terminals in DPs showed a significant shrinkage in their mean size. GABA immunoreactivity, as indicated by the density of immunogold particles in GABA-IR neurons, declined in DPs, and a greater decrease was also found in axon terminals than in cell bodies or dendrites. Moreover, the numerical density of GABA-IR axon terminals and synapses in DPs was significantly reduced without changes in that of asymmetric and symmetric synapses. Thus, the present results support the following conclusions: 1) Oxidative metabolism and neurotransmitter expression in GABA-IR neurons are tightly regulated by neuronal activity in adult monkey striate cortex; 2) GABA-IR neurons are much more vulnerable to functional deprivation than non-GABA-IR ones, suggesting that these inhibitory neurons have stringent requirement for sustained excitatory input to maintain their heightened oxidative capacity; and 3) intracortical inhibition mediated by GABA transmission following afferent deprivation may be decreased in deprived puffs, because the oxidative capacity and transmitter level in GABAergic neurons, especially in their axon terminals, are dramatically reduced.

Differential glutamatergic innervation in cytochrome oxidase-rich and -poor regions of the macaque striate cortex: quantitative EM analysis of neurons and neuropil

One of the hallmarks of the primate striate cortex is the presence of cytochrome oxidase (CO)-rich puffs and CO-poor interpuffs in its supragranular layers. However, the neurochemical basis for their differences in metabolic activity and physiological properties is not well understood. The goals of the present study were to determine whether CO levels in postsynaptic neuronal compartments were correlated with the proportion of excitatory glutamate-immunoreactive (Glu-IR) synapses they received and if Glu-IR terminals and synapses in puffs differed from those in interpuffs. By combining CO histochemistry and postembedding Glu immunocytochemistry on the same ultrathin sections, the simultaneous distribution of the two markers in individual neuronal profiles was quantitatively analyzed. As a comparison, adjacent sections were identically processed for the double labeling of CO and GABA, an inhibitory neurotransmitter. In both puffs and interpuffs, most axon terminals forming asymmetric synapses (84%)--but not symmetric ones, which were GABA-IR--were intensely immunoreactive for Glu. GABA-IR neurons received mainly Glu-IR synapses on their cell bodies, and they had three times as many mitochondria darkly reactive for CO than Glu-rich neurons, which received only GABA-IR axosomatic synapses. In puffs, GABA-IR neurons received a significantly higher ratio of Glu-IR to GABA-IR axosomatic synapses and contained about twice as many darkly CO-reactive mitochondria than those in interpuffs. There were significantly more Glu-IR synapses and a higher ratio of Glu- to GABA-IR synapses in the neuropil of puffs than of interpuffs. Moreover, Glu-IR axon terminals in puffs contained approximately three times more darkly CO-reactive mitochondria than those in interpuffs, suggesting that the former may be synaptically more active. Thus, the present results are consistent with our hypothesis that the levels of oxidative metabolism in postsynaptic neurons and neuropil are positively correlated with the proportion of excitatory synapses they receive. Our findings also suggest that excitatory synaptic activity may be more prominent in puffs than in interpuffs, and that the neurochemical and synaptic differences may constitute one of the bases for physiological and functional diversities between the two regions.

Double labeling of GABA and cytochrome oxidase in the macaque visual cortex: quantitative EM analysis

In the primate striate cortex, cytochrome oxidase (CO)-rich puffs differ from CO-poor interpuffs in their metabolic levels and physiological properties. The neurochemical basis for their metabolic and physiological differences is not well understood. The goal of the present study was to examine the relationship between the distribution of gamma aminobutyric acid (GABA)/non-GABA synapses and CO levels in postsynaptic neuronal profiles and to determine whether or not a difference existed between puffs and interpuffs. By combining CO histochemistry and postembedding GABA immunocytochemistry on the same ultrathin sections, the simultaneous distribution of the two markers in individual neuronal profiles was quantitatively analyzed. In both puffs and interpuffs, GABA-immunoreactive (GABA-IR) neurons were the only cell type that received both non-GABA-IR (presumed excitatory) and GABA-IR (presumed inhibitory) axosomatic synapses, and they had three times as many mitochondria darkly reactive for CO than non-GABA-IR neurons, which received only GABA-IR axosomatic synapses. GABA-IR neurons and terminals in puffs had a larger mean size, about twice as many darkly reactive mitochondria, and a higher ratio of non-GABA-IR to GABA-IR axosomatic synapses than those in interpuffs (2.3:1 vs. 1.6:1; P < 0.01). There were significantly more synapses of both non-GABA-IR and GABA-IR types in the neuropil of puffs than of interpuffs; however, the ratio of non-GABA-IR to GABA-IR synapses was significantly higher in puffs (2.86:1) than in interpuffs (2.08:1; P < 0.01). Our results are consistent with the hypothesis that the level of oxidative metabolism in postsynaptic neurons and neuronal processes is tightly governed by the strength and proportion of excitatory over inhibitory synapses. Thus, the present results suggest that (1) GABA-IR neurons in the macaque striate cortex have a higher level of oxidative metabolism than non-GABA ones because their somata receive direct excitatory synapses and their terminals are more tonically active; (2) the higher proportion of presumed excitatory synapses in puffs imposes a greater energy demand there than in interpuffs; and (3) excitatory synaptic activity may be more prominent in puffs than in interpuffs because puffs receive a greater proportion of excitatory synapses from multiple sources including the lateral geniculate nucleus, which is not known to project to the interpuffs.