基于定量PCR方法初步分析西藏开菲尔粒中细菌与酵母菌数量变化

运用实时荧光定量PCR方法分析西藏开菲尔粒中细菌与酵母菌的数量变化规律,需要有效提取其微生物总基因组DNA。本文通过同时添加溶菌酶与溶壁酶优化实验方案,成功获得西藏开菲尔粒中微生物的总基因组DNA。荧光定量PCR分析提取自培养1、4、8和12周的西藏开菲尔粒的微生物总基因组DNA,结果显示:4个时间点细菌16S rRNA与酵母菌26S rRNA基因拷贝数均分别约为每微升107拷贝与105拷贝,表明细菌与酵母菌的数量相对稳定。该结果为进一步研究西藏开菲尔粒中细菌与酵母菌间的共生关系奠定了一定的基础。     

基于TaqMan qPCR检测凡纳滨对虾样品中虾肝肠胞虫并样检测方法的评价

对山东海阳和潍坊的2个养殖凡纳滨对虾群体取样,采用TaqMan qPCR逐尾检测肝胰腺中的虾肝肠胞虫(Enterocytozoon hepatopenaei, EHP)载量,再将提取的DNA样品按5并1(5∶1)、25并1(25∶1)、50并1(50∶1)、100并1(100∶1)和150并1(150∶1)进行并样,检测并样的EHP载量。设定不同临界循环数为假定灵敏度,定性判断各单尾检测阳性及并样组阳性,比较不同并样模式与检测阳性率、诊断灵敏度、诊断特异性等之间的关系以及定量的准确性。结果表明,检测灵敏度过低,会降低高并样率检测的准确性;阳性率在30%以上时,高并样率的检测结果与单样品检测相符性很好;高载量感染的阳性率不低于6.7%时,50∶1以内的并样能准确得出检测结果;低载量感染的阳性率不低于16%时,25∶1以内的并样能得出较好结果;高载量感染的1.3%阳性率和低载量感染的8%阳性率可能导致所有并样出现假阴性结果;各种并样模式均有很好的诊断特异性,50∶1并样的诊断灵敏度与OIE标准推荐的5∶1并样的接近;各并样检测的EHP载量与单样品检测平均值之比在0.27~2.83范围,二者存在极显著相关性,各种并样模式的定量检测结果在数量级水平能大致反映样品的平均EHP载量。本研究为水生动物疫病诊断和流行病学调查的样品检测提供了参考依据。     

Design and validation of a RT‐qPCR procedure for diagnosis and quantification of most types of infectious pancreatic necrosis virus using a single pair of degenerated primers

Infectious pancreatic necrosis virus (IPNV) is an important virus which affects the salmonid aquaculture industry worldwide; therefore, it is important to develop rapid and reliable methods of diagnosis to detect the disease at early stages. Nowadays, RT‐qPCR is replacing other methods because it provides additional information on the viral load, which is important to have a better understanding of the virus replication level and of the stage of the infection and its risk level. The main problem stems from the high diversity of this virus, which can compromise the reliability of the diagnosis. In this study, we have designed an RT‐qPCR procedure for diagnosis and quantification of IPNV based on a single pair of primers targeted to segment B. The procedure has been validated, in vitro and in vivo, testing two different types of standards against seven reference strains and 23 field isolates from different types. The procedure is reliable for the detection of any type, with a detection limit of 31 TCID₅₀ mL^?1, 50 pfu mL^?1 or 66 RNA copies mL^?1, depending on the standard. All the standard curves showed high reliability (R² > 0.95). The results support the high reliability of this new procedure for the diagnosis and quantification of IPNV.     

Alterations in activated T‐cell cytokine expression in healthy dogs over the initial 7 days of twice daily dosing with oral cyclosporine

Cyclosporine is a powerful T‐cell inhibitor used in the treatment of immune‐mediated and inflammatory diseases in the dog. There is limited information on how to best monitor patients on cyclosporine therapy. Currently, pharmacokinetic and pharmacodynamic assays are available. Pharmacokinetic assays that measure the concentration of cyclosporine in the blood are used to assess if an appropriate drug concentration has been achieved; however, target blood drug concentrations have not been shown to reliably correlate with suppression of T‐cell function in the dog. In human transplant recipients, therapeutic drug monitoring has shifted to include pharmacodynamic‐based monitoring. Our laboratory has validated a RT‐qPCR assay to measure the pharmacodynamic effects of cyclosporine in the dog. In this study, activated T‐cell expression of IL‐2 and IFN‐γ was measured using RT‐qPCR daily for 7 consecutive days in 8 healthy Walker hounds receiving oral cyclosporine at a dosage of 10 mg/kg every 12 hr. Cytokine production was found to be markedly decreased within 24 hr after the initiation of cyclosporine and remained significantly decreased for the duration of the project. Based on these results, cyclosporine causes a rapid drop in T‐cell cytokine production that is sustained with continued dosing in healthy dogs. Although performed in healthy dogs, this study demonstrated a marked decrease in cytokine suppression within 24 hr of drug administration, suggesting that pharmacodynamic monitoring of cyclosporine's effects on T cells could be considered within several days of commencing therapy in dogs suffering from life‐threatening immune‐mediated disorders.     

Detection of HEV in naturally infected swine from central Argentina by an optimized HEV/MS2 duplex RT‐qPCR

Hepatitis E virus (HEV) is currently considered as a global health concern due to the recognition of its zoonotic transmission to humans, mainly from swine, and its association with the development of severe cases of hepatitis in human risk populations. The lack of updated data on HEV state of infection in swineherds of Argentina, and the necessity of robust technologies for its detection in complex biological samples, positions HEV as an emerging issue in public health. Here, we have optimized a RT‐qPCR with internal control for a more precise and accurate HEV RNA detection in swine stool samples. We implemented this optimized molecular tool to analyse the current epidemiological scenario of HEV infection in swine from the core region of commercial activity of Argentina. A total of 135 stool samples were collected from 16 different farms and tested for HEV presence, resulting in 11 positive cases (8.1%). Phylogenetic analysis demonstrated that all of them correspond to HEV genotype 3 and that different subtypes circulate in the region. Moreover, two of the detected strains presented a high nucleotide similarity with a previously identified isolate from human sewage discharges, suggesting the zoonotic transmission of HEV to humans. Collectively, this work provides a better understanding of HEV epidemiology in Argentina while contributes to the improvement of HEV detection technologies.     

Development of a qPCR for the detection of infectious laryngotracheitis virus (ILTV) based on the gE gene

1. Infectious laryngotracheitis is a respiratory disease that affects the poultry industry worldwide. It is common in flocks with high-bird density, causing major economic losses.

2. In this study, a SYBR® FAST polymerase chain reaction (PCR) double-strand DNA intercalating agent assay was performed for the detection of infectious laryngotracheitis virus (ILTV) in clinical samples in comparison with a conventional nested-PCR, both based on the glycoprotein E encoding gene. This assay amplified 56 bp and was capable of detecting 1⁹ to 1 copies of virus.

3. In total, 164 clinical samples were obtained from birds with respiratory problems from the period of 2009–2016. In the nested-PCR, there were 45.12% positive samples and 54.88% negative samples, while in the real-time PCR (qPCR), there were 81.1% positive samples and 18.9% negative samples.

4. In conclusion, qPCR from the DNA double-strand intercalating agent SYBR® GREEN FAST was useful for the diagnosis of ILTV because it detected samples that were negative in nested-PCR. This assay has advantages, such as a shortened processing-time, and no need for post-amplification processing (electrophoresis) with additional reagents, such as MgCl₂ and agarose. Hence, qPCR proved to be useful, rapid and low cost for use with clinical samples.     

Parent material and vegetation influence bacterial community structure and nitrogen functional genes along deep tropical soil profiles at the Luquillo Critical Zone Observatory

Microbial communities mediate every step of the soil nitrogen cycle, yet the structure and associated nitrogen cycle functions of soil microbial communities remain poorly studied in tropical forests. Moreover, tropical forest soils are often many meters deep, but most studies of microbial nitrogen cycling have focused exclusively on surface soils. The objective of our study was to evaluate changes in bacterial community structure and nitrogen functional genes with depth in soils developed on two contrasting geological parent materials and two forest types that occur at different elevations at the Luquillo Critical Zone Observatory in northeast Puerto Rico. We excavated three soil pits to 140 cm at four different sites representing the four soil × forest combinations (n = 12), and collected samples at ten-centimeter increments from the surface to 140 cm. We used bacterial 16S rRNA gene-DGGE (denaturant gradient gel electrophoresis) to fingerprint microbial community structures, and quantitative PCR to measure the abundance of five functional genes involved in various soil nitrogen transformations: nifH (nitrogen fixation), chiA (organic nitrogen decomposition), amoA (ammonia oxidation), nirS (nitrite reduction) and nosZ (nitrous oxide reduction). Multivariate analyses of DGGE fingerprinting patterns revealed differences in bacterial community structure across the four soil × forest types that were strongly correlated with soil pH (r = 0.69, P < 0.01) and nutrient stoichiometry (r² ≥ 0.36, P < 0.05). Across all soil and forest types, nitrogen functional genes declined significantly with soil depth (P < 0.001). Denitrification genes (nirS and nosZ) accounted for the largest proportion of measured nitrogen functional genes. Measured nitrogen functional genes were positively correlated with soil carbon, nitrogen and phosphorus concentrations (P < 0.001) and all genes except amoA were significantly more abundant in the Inceptisol soil type compared with the Oxisol soil type (P < 0.03). Greater abundances and a stronger vertical zonation of nitrogen functional genes in Inceptisols suggest more dynamic nitrogen transformation processes in this soil type. As the first study to examine bacterial nitrogen functional gene abundances below the surface 20 cm in tropical forest soils, our work provides insight into how pedogenically-driven vertical gradients control the nitrogen-cycling capacity of soil microbial communities. While previous studies have shown evidence for redox-driven hotspots in tropical nitrogen cycling on a watershed scale, our study corroborates this finding on a molecular scale.     

Improvement of Leptospira spp. diagnosis in aborted bovine fetuses by qPCR

Leptospirosis is a disease with major economic impact on livestock industry. The objective of this work was to determine the presence of Leptospira spp. DNA by qPCR in bovine fetuses with presumptive diagnosis of leptospirosis as the cause of abortion. Leptospira spp. DNA was detected by qPCR in 11 out of 34 fetuses. These specimens (10/11) had histopathological findings in hepatic and/or renal tissues compatible with leptospirosis. qPCR detection rate (32.4 %) was higher compared with direct immuno-fluorescence antibody test (DFAT) (11.8 %). The concordance coefficient between both techniques was 0.44. qPCR is a rapid and sensitive technique for the diagnosis of leptospirosis and improved the detection rate in fetal tissues compared with DFAT. Implementation of molecular techniques may increase the accurate detection of leptospirosis as a cause of bovine abortion allowing the application of rapid therapeutic and prophylactics measures in order to reduce the impact of this zoonotic disease.