Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding

Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.

Effect of sludge redistribution strategy on stability of partial nitrification-anammox process: Further exploration of the potential value of sludge

The stability of the two-stage partial nitrification-anammox (PN/A) system was compromised by the inappropriate conversion of insoluble organic matter. In response, a sludge redistribution strategy was implemented. Through the redistribution of PN sludge and anammox sludge in the two-stage PN/A system, a transition was made to the Anammox-single stage PN/A (A-PN/A) system. This specific functional reorganization, facilitated by the rapid reorganization of microbial communities, has the potential to significantly decrease the current risk of suppression. The results of the study showed that implementing the sludge redistribution strategy led to a substantial enhancement in the total nitrogen removal rate (TNRR) by 87.51%, accompanied by a significant improvement of 34.78% in the chemical oxygen demand removal rate (CRR). Additionally, this approach resulted in a remarkable two-thirds reduction in the aeration requirements. High-throughput sequencing revealed that the strategy enriched anammox and ammonia-oxidizing bacteria while limiting denitrifying bacteria, as confirmed by quantitative polymerase chain reaction analysis. Furthermore, the principal component analysis revealed that the location and duration of aeration had direct and indirect effects on functional gene expression and the evolution of microbial communities. This study emphasizes the potential benefits of restructuring microbial communities through a sludge redistribution strategy, especially in integrated systems that encounter challenges with suppression.

Microbial nitrogen mineralization is slightly affected by conversion from farmland to apple orchards in thick loess deposits

Organic nitrogen mineralization, indispensable to soil carbon and nitrogen cycles, is the largest contributor to nitrate reservoirs in deep vadose zones. The microbial nitrogen mineralization (MNM) within deep soils, particularly in regions with intensive agricultural activities and thick soil horizons, has been largely disregarded. As such, this study aims to address this knowledge gap by investigating the chiA-harboring microbial structure and network within nine 10-m profiles beneath cultivated farmland and two apple orchards. The results showed that apple orchards, compared to farmland, had considerable water deficit and nitrogen accumulation within deeper soil layers due to well-developed root systems and the overuse of chemical fertilizers. However, the chiA-harboring microbial diversity, composition, and abundance all exhibited significant variations with soil depths rather than being influenced by different land use types. Moreover, the diversity indices and gene abundances decreased with soil depths, and the related soil microbes included 19 phyla, 29 classes, 72 orders, 114 families, and 197 genera, with Actinobacteria and Proteobacteria being the two major bacterial phyla. The microbial co-occurrence network was simper beneath apple orchards. The chiA-harboring microorganisms within deep unsaturated zones were greatly influenced by the depth-dependent soil nutrients, such as total nitrogen, organic carbon, and available potassium. The limited plant root biomass and the inhibitory effects of dried soil layers both restricted the availability of carbon sources, which further interfered with the MNM processes within deep soils insignificantly. Therefore, despite the considerable plant-induced ecohydrological consequences, the depth-dependent MNM processes were slightly affected after the transformation from farmland to apple orchards within thick loess deposits. This study offers crucial insights into microbial dynamics of the deep biosphere, thereby contributing to our understanding of depth-dependent biogeochemical cycles within global deep unsaturated zones.

Quantification of arbuscular mycorrhizal fungi root colonization in wheat, tomato, and leek using absolute qPCR

Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and are known to have a positive effect on plant growth and health. Different methodologies have been developed to assess the AMF-plant symbiosis. The most applied method, which involves staining of roots and microscopic observation of the AMF structures, is tedious and time-consuming and the results are highly dependent on the observer. Using quantitative polymerase chain reaction (qPCR) to quantify AMF root colonization represents a reliable, high-throughput technique that allows the assessment of numerous samples. Quantification with qPCR can be performed through two methods: relative quantification and absolute quantification. In relative quantification, the target gene is normalized with a reference gene. On the other hand, absolute quantification involves the use of a standard curve, for which template DNA is serially diluted. In a previous paper, we validated the primer pair AMG1F and AM1 for a relative quantification approach to assess AMF root colonization in Petunia. Here, we tested the same primers with an absolute quantification approach and compared the results with the traditional microscopy method. We evaluated the qPCR method with three different crops, namely, wheat (cv. Colmetta and Wiwa), tomato, and leek. We observed a strong correlation between microscopy and qPCR for Colmetta (r = 0.90, p < 0.001), Wiwa (r = 0.94, p < 0.001), and tomato (r = 0.93, p < 0.001), but no correlation for leek (r = 0.27, p = 0.268). This highlights the importance of testing the primer pair for each specific crop.

qPCR Genotyping of Polyploid Species

A simple and cost-effective method for genotyping polyploid plants using quantitative PCR (qPCR) is described in this chapter. There is no additional operation, only simultaneous amplification of alleles and reference sequences with constant copy number in the genome. The qPCR genotyping can detect the genotypes of important traits in polyploid plants without whole genome sequencing data.

Quantitative Analysis of Periodontal Pathogens Using Real-Time Polymerase Chain Reaction (PCR)

The quantitative polymerase chain reaction (qPCR) is a variant of PCR aimed to detect and quantify a targeted DNA molecule. This is made through the addition of probes labeled with fluorescent molecules that emit fluorescence within each amplification cycle, resulting in fluorescence values proportional to the amount of accumulated PCR product. This chapter presents the detailed procedures for quantification of different periodontal pathogens (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Campylobacter rectus, Streptococcus oralis, and Fusobacterium spp.) using qPCR. It also includes the description of the most frequent problems encountered, how to solve them, and recommendations to minimize the risks for laboratory staff handling oral samples. In addition, a detailed protocol for multiplex qPCR to detect and quantify Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Tannerella forsythia is also included.

Gene Expression Analysis by Quantitative Real-Time PCR for Floral Tissues

Real-time, or quantitative, reverse transcription polymerase chain reaction (qRT-PCR) is a powerful method for rapid and reliable quantification of mRNA abundance. Although it has not featured prominently in flower development research in the past, the availability of novel techniques for the synchronized induction of flower development, or for the isolation of cell-specific mRNA populations, suggests that detailed quantitative analyses of gene expression over time and in specific tissues and cell types by qRT-PCR will become more widely used. In this chapter, we discuss specific considerations for studying gene expression by using qRT-PCR, such as the identification of suitable reference genes for the experimental set-up used. In addition, we provide protocols for performing qRT-PCR experiments in a multiwell plate format (with the LightCycler® 480 system, Roche) and with nanofluidic arrays (BioMark™ system, Fluidigm), which allow the automatic combination of sets of samples with sets of assays, and significantly reduce reaction volume and the number of liquid-handling steps performed during the experiment.

Identifying stable reference genes in polyethene glycol precipitated urinary extracellular vesicles for RT-qPCR-based gene expression studies in renal graft dysfunction patients

BACKGROUND

Urinary extracellular vesicles (UEVs) hold RNA in their cargo and are potential sources of biomarkers for gene expression studies. The most used technique for gene-expression studies is quantitative polymerase chain reaction (qPCR). It is critical to use stable reference genes (RGs) as internal controls for normalising gene expression data, which aren't currently available for UEVs.

METHODS

UEVs were precipitated from urine of graft dysfunction patients and healthy controls by Polyethylene glycol, Mn6000 (PEG6K). Vesicular characterisation confirmed the presence of UEVs. Gene expression levels of five commonly used RGs, i.e., Beta-2-Microglobulin (B2M), ribosomal-protein-L13a (RPL13A), Peptidylprolyl-Isomerase-A (PPIA), hydroxymethylbilane synthase (HMBS), and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) were quantified, and their stability was established through the RefFinder. The stability of identified RGs was validated by quantification of Perforin and granzyme B, signature molecules of renal graft dysfunction.

RESULTS

Urine precipitated with 12% 6 K PEG yielded round and double-membraned UEVs of size ranging from 30 to 100 nm, as confirmed through transmission electron microscopy. Nanoparticle tracking analysis (59 ± 22 nm) and Dynamic-light-scattering (78 ± 56.5 nm) confirmed their size profile. Semi-quantitative Exocheck antibody array demonstrated the presence of EV protein markers in UEV. Using the comparative ΔCт method and RefFinder analysis, B2M (1.6) and RPL13A (1.8) genes emerged as the most stable reference genes. Validation of target gene expression in renal graft dysfunction patients confirmed the efficiency of B2M and RPL13A through significant upregulation compared to other RGs.

CONCLUSIONS

Our study identified and validated B2M and RPL13A as optimal RGs for mRNA quantification studies in the UEVs of patients with renal graft dysfunction.

Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi

Arbuscular mycorrhiza fungi (AMF) are beneficial soil fungi that can promote the growth of their host plants. Accurate quantification of AMF in plant roots is important because the level of colonization is often indicative of the activity of these fungi. Root colonization is traditionally measured with microscopy methods which visualize fungal structures inside roots. Microscopy methods are labor-intensive, and results depend on the observer. In this study, we present a relative qPCR method to quantify AMF in which we normalized the AMF qPCR signal relative to a plant gene. First, we validated the primer pair AMG1F and AM1 in silico, and we show that these primers cover most AMF species present in plant roots without amplifying host DNA. Next, we compared the relative qPCR method with traditional microscopy based on a greenhouse experiment with Petunia plants that ranged from very high to very low levels of AMF root colonization. Finally, by sequencing the qPCR amplicons with MiSeq, we experimentally confirmed that the primer pair excludes plant DNA while amplifying mostly AMF. Most importantly, our relative qPCR approach was capable of discriminating quantitative differences in AMF root colonization and it strongly correlated (Spearman Rho = 0.875) with quantifications by traditional microscopy. Finally, we provide a balanced discussion about the strengths and weaknesses of microscopy and qPCR methods. In conclusion, the tested approach of relative qPCR presents a reliable alternative method to quantify AMF root colonization that is less operator-dependent than traditional microscopy and offers scalability to high-throughput analyses.

Development of cost-effective quantitative PCR method for parallel detection of porcine circovirus2 and porcine parvovirus in perspective of North-eastern India

Pig farming performs as an intricate part in the socio-economic situation in the north-eastern region of India. This region contributes 38% (3.95 million) of total pigs in India. In spite of this, the region unables to flourish as an enterprise as per the expectation due to a low productivity rate. Porcine infectious pathogens like porcine cirovirus2 (PCV2) and porcine parvovirus (PPV) have a direct economic impact on pig farming through slow growth rate, abortion, and mortality and ultimately maximize the production cost by increasing the usage of antibiotic or antiviral drugs. The veterinary diagnostic infrastructure is a fundamental aspect of the development of livestock status by rapid and effective detection of pathogens. Quantitative PCR (qPCR) is a precise and fast-track technique used for the routine diagnostic method. Hence, we developed a highly precise and comparatively cost-effective SYBR Green reporter dye-based qPCR assay for parallel identification of PCV2 and PPV. In the present assay, the correlation coefficient (R²) value was 0.99, and 10 copies of the gene/μl were the least limit of detection (LOD) concerning both viruses. Melt curve analysis of this study represented PCV2-specific melt curve (Tm) at 81.2 °C and PPV-specific melt curve (Tm) at 73.5 °C. Therefore, the assay easily differentiates the true positive amplicons of PCV2 and PPV through specific Tm values. Among the 50 field samples, 26 (52%) samples were PCV2 positive, 18 (36%) samples PPV positive, and 11 (22%) samples were co-infected of both the viruses. This method is cost-effective, precise, and sensitive to diagnose the concurrent or individual infection of the PCV2 and PPV in the pig. Hence, considering the impact of pig farming in the north-eastern part of the country, the present assay gives an unprecedented achievement in disease diagnosis.

Towards understanding the liver fluke transmission dynamics on farms: Detection of liver fluke transmitting snail and liver fluke-specific environmental DNA in water samples from an irrigated dairy farm in Southeast Australia

Livestock production around the world is impacted by liver fluke (Fasciola spp.) infection resulting in serious economic losses to the beef, dairy and sheep industries with significant losses of about $90 million per annum in Australia. Triclabendazole (TCBZ) is the most effective anthelmintic treatment available to control liver fluke infections; however, the widespread emergence of TCBZ resistance in livestock threatens liver fluke control. Alternative control measures to lower exposure of livestock to liver fluke infection would help to preserve the usefulness of current anthelmintic treatments. Environmental DNA (eDNA) based identification of liver fluke and the intermediate snail host in the water bodies is a robust method to assess the risk of liver fluke infection on farms. In this study, we used a multiplex quantitative PCR assay of water samples to detect and quantify eDNA of Fasciola hepatica (F. hepatica) and Austropeplea tomentosa (A. tomentosa), a crucial intermediate snail host for liver fluke transmission in South-east Australia. Water samples were collected from an irrigation channel for a period of 7 months in 2016 (February, March, May, September, October, November and December) at a dairy farm located at Maffra, Victoria, South-east Australia. Using an effective eDNA extraction method, the multiplex qPCR assay allows for the independent but simultaneous detection of eDNA released from liver fluke life stages and snails using specific primers and a probe targeting the ITS-2 region of the liver fluke and snail, respectively, with minimal inhibition from contaminants in field collected water samples. The sensitivity of this assay to detect eDNA of liver fluke and snails was observed to be 14 fg and 50 fg, respectively, in the presence of field collected water samples. Differential levels of liver fluke and snail specific eDNA in water were observed at the time points analysed in this study. The successful detection of eDNA specific to liver fluke and snails from the field collected water samples provides a precedent for the use of this method as a monitoring tool to determine the prevalence of liver fluke and liver fluke-transmitting snails in irrigation regions. Further, this method has the enormous potential to allow an assessment of the liver fluke transmission zones on farms and to inform the application of effective control strategies.

JUUL e-liquid exposure elicits cytoplasmic Ca2+ responses and leads to cytotoxicity in cultured airway epithelial cells

RATIONALE

The popularity of new and emerging tobacco products such as E-cigarettes (E-cigs) is rapidly expanding worldwide. However, uncertainties surrounding the potential health consequences due to the use of such products exist and warrant further study.

METHODS

Cultured A549 and Calu-3 airway epithelia were exposed to three out of the eight types of JUUL brand e-liquids ("Mint", "Virginia Tobacco" and "Menthol", all containing 3% nicotine at 1% and 3% (vol/vol) dilutions) and assessed for viability using a resazurin-based assay. Intracellular Ca2+ levels were measured using fluorescent indicators and pro-inflammatory cytokine levels were monitored by quantitative PCR (qPCR). Cultures were also analyzed by flow cytometry to evaluate apoptotic markers and cell viability.

RESULTS

Exposing the airway epithelial cells to the flavored JUUL e-liquids led to significant cytotoxicity, with the "Mint" flavor being the overall most cytotoxic. The "Mint" flavored e-liquid also led to significant elevations in intracellular Ca2+ and upregulation of the pro-inflammatory cytokine IL-6 and early apoptotic marker Annexin V.

CONCLUSIONS

JUUL e-liquid challenge resulted in a loss of airway epithelial cell viability, induced pro-inflammatory responses and eventually caused apoptosis.

Highly specific, quantitative polymerase chain reaction probe for the quantification of human cells in cynomolgus monkeys

Quantification of human cells may be performed using quantitative polymerase chain reaction (qPCR). In preclinical studies, the human Alu sequence is widely used as biomarker for human DNA. However, because the Alu gene is shared by primates, its use is limited to non-primate studies. The biodistribution of human cells in primates is also necessary for translational studies. Therefore, we aimed to design a novel, human-specific primer/probe that enables the quantification of human cells in primates and other animal models. A novel primer/probe set was successfully designed based on highly repetitive LINE1 sequences. qPCR efficiency (94.95-99.21%) and linearity of calibration curves (r² = 0.996-0.999) were confirmed in tissue homogenates of cynomolgus monkey. The lower limit of detection was 10 cells per 15-mg tissue sample, a sensitivity that is equivalent to existing Alu primers/probes. The set was also effective in other animal models such as mice, rabbits, pigs, and common marmosets. To our knowledge, this is the first study describing the successful design of a human-specific qPCR primer/probe for human cell quantification in various animals, including non-human primates, using LINE1 sequence. The excellent selectivity, sensitivity, and versatility of the LINE1 primers/probes make it a promising quantification tool in preclinical biodistribution studies.

Template copy number and the sensitivity of quantitative PCR for Plasmodium falciparum in asymptomatic individuals

BACKGROUND

The identification of asymptomatic individuals with Plasmodium falciparum infection is difficult because they do not seek medical treatment and often have too few asexual parasites detectable using microscopy or rapid diagnostic tests (≤ 200 parasites per μl). Quantitative PCR (qPCR) may provide greater sensitivity and permits estimation of the initial template DNA concentration. This study examined the hypothesis that qPCR assays using templates with higher copy numbers may be more sensitive for P. falciparum than assays based on templates with lower copy numbers.

METHODS

To test this hypothesis, ten qPCR assays for DNA sequences with template copy numbers from 1 to 160 were compared using parasite DNA standards (n = 2) and smear-positive filter paper blots from asymptomatic smear-positive subjects (n = 96).

RESULTS

Based on the testing of P. falciparum parasite DNA standards and filter paper blots, cycle threshold values decreased as the concentrations of template DNA and template copy numbers increased (p < 0.001). Likewise, the analytical and clinical sensitivities of qPCR assays for P. falciparum DNA (based on DNA standards and filter paper blots, respectively) increased with template copy number. Despite the gains in clinical sensitivity from increased template copy numbers, qPCR assays failed to detect more than half of the filter paper blots with low parasite densities (≤ 200 asexual parasites per μl).

CONCLUSIONS

These results confirm the hypothesis that the sensitivity of qPCR for P. falciparum in the blood of individuals with asymptomatic infection increases with template copy number. However, because even the most sensitive qPCR assays (with template copy numbers from 32 to 160) detected fewer than 50% of infections with ≤ 200 asexual parasites per μl, the sensitivity of qPCR must be increased further to identify all smear-positive, asymptomatic individuals in order to interrupt transmission.

One-year survey of opportunistic premise plumbing pathogens and free-living amoebae in the tap-water of one northern city of China

In this study, qPCR was used to quantify opportunistic premise plumbing pathogens (OPPPs) and free-living amoebae in 11 tap water samples collected over four seasons from a city in northern China. Results demonstrated that the average numbers of gene copies of Legionella spp. and Mycobacterium spp. were significantly higher than those of Aeromonas spp. (p < 0.05). Legionella spp. and Mycobacterium spp. were 100% (44/44) positively detected while P. aeruginosa and Aeromonas spp. were 79.54% (35/44) and 77.27% (34/44) positively detected. Legionella pneumophila was only detected in 4 samples (4/44), demonstrating its occasional occurrence. No Mycobacterium avium or Naegleria fowleri was detected in any of the samples. The average gene copy numbers of target OPPPs were the highest in summer, suggesting seasonal prevalence of OPPPs. Average gene copy numbers of OPPPs in the taps of low-use-frequency were higher than in taps of high-use-frequency, but the difference was not significant for some OPPPs (p > 0.05). Moderate negative correlations between the chlorine concentration and the gene copy numbers of OPPPs were observed by Spearman analysis (r_s ranged from -0.311 to -0.710, p < 0.05). However, no significant correlations existed between OPPPs and AOC, BDOC, or turbidity. Moderate positive correlations were observed between the target microorganisms, especially for Acanthamoeba spp., through Spearman analysis (p < 0.05). Based on our studies, it is proposed that disinfectant concentration, season, taps with different-use frequency, OPPP species, and potential microbial correlations should be considered for control of OPPPs in tap water.

Quantitative PCR-Based Assessment of Vaccinia Virus RNA and DNA in Infected Cells

Quantitative PCR-based methods have proven to be easy-to-use, cost-effective procedures for the quantification of viral gene expression and viral genome numbers. Quantitative PCR (qPCR) and quantitative reverse transcriptase-PCR (qRT-PCR) are rapid and sensitive approaches that can be used to pinpoint defects in viral DNA replication and transcriptional activity, respectively. Due to the significant nucleotide overlap between Poxviridae these methods can be employed across a wide range of viruses from this family. Here we provide methods for the quantification of vaccinia DNA replication by qPCR and quantification of the three classes of vaccinia gene transcription by qRT-PCR.

The clinical significance of FAM19A4 methylation in high-risk HPV-positive cervical samples for the detection of cervical (pre)cancer in Chinese women

Background

To explore the diagnostic value of FAM19A4 methylation in high-risk human papilloma virus (hrHPV)-positive cervical samples from Chinese women for estimating cervical cancer or its precancerous lesions.

Methods

Cervical samples from 215 women infected with high-risk HPV were collected by smear testing. We purposely chose 61 patients with cervical cancer, 57 with high-grade squamous intraepithelial lesions (HSIL), 31 with low-grade squamous intraepithelial lesions (LSIL), and 66 without cervical intraepithelial neoplasia (CIN) after histological confirmation. Taqman probe-based quantitative PCR (qPCR) was utilized to detect the methylation status of FAM19A4 in the cervical samples and further evaluate the use of this gene in the diagnosis of cervical cancer.

Results

(1) An increasing level of FAM19A4 methylation was detected with increasing progression of cervical lesions, with methylation rates of 10.61%(7/66), 35.48%(11/31), 56.14%(32/57) and 93.44%(57/61) in no CIN, LSIL, HSIL and cervical carcinoma samples respectively. (2) In all hrHPV-positive samples, the levels of FAM19A4 methylation in HPV16/18 groups were higher than that in 12 other hrHPV groups (P < 0.05), but there was no significant difference between two groups after grouping cervical lesions into cervical cancer, HSIL, LSIL and no CIN groups (P>0.05). (3)There were no significant differences of FAM19A4 methylation in different clinicopathological parameters of cervical cancer. (4) Though the sensitivity of FAM19A4 methylation test was inferior to that of cytology and FAM19A4 combining with HPV16/18 genotyping, but showed the best specificity with 81.44% both for detection HSIL alone and ≥ HSIL, with favorable youden index (YI) and area under curve (AUC).

Conclusion

FAM19A4 is a specific biomarker of cancerous lesions of the cervix. FAM19A4 methylation analysis may serve as an auxiliary screening method for diagnosis of cervical (pre)cancer. However, in consideration of the limitations of this retrospective study, prospective population-based studies are necessary for further confirmation of the diagnostic value of FAM19A4 methylation for detection of cervical (pre)cancer in Chinese women.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4877-5) contains supplementary material, which is available to authorized users.

Prevalence of antibiotic resistance genes from effluent of coastal aquaculture, South Korea

The wide use of antibiotics in aquaculture for prophylactic and therapeutic purposes can potentially lead to the prevalence of antibiotic resistance genes (ARGs). This study reports for the first time the profile of ARGs from effluents of coastal aquaculture located in South Jeolla province and Jeju Island, South Korea. Using quantitative PCR (qPCR), twenty-two ARGs encoding tetracycline resistance (tetA, tetB, tetD, tetE, tetG, tetH, tetM, tetQ, tetX, tetZ, tetBP), sulfonamide resistance (sul1, sul2), quinolone resistance (qnrD, qnrS, aac(6')-Ib-cr), β-lactams resistance (bla_TEM, bla_CTX, bla_SHV), macrolide resistance (ermC), florfenicol resistance (floR) and multidrug resistance (oqxA) and a class 1 integrons-integrase gene (intI1) were quantified. In addition, Illumina Miseq sequencing was applied to investigate microbial community differences across fish farm effluents. Results from qPCR showed that the total number of detected ARGs ranged from 4.24 × 10^-3 to 1.46 × 10^-2 copies/16S rRNA gene. Among them, tetB and tetD were predominant, accounting for 74.8%-98.0% of the total ARGs. Furthermore, intI1 gene showed positive correlation with tetB, tetD, tetE, tetH, tetX, tetZ tetQ and sul1. Microbial community analysis revealed potential host bacteria for ARGs and intI1. Two genera, Vibrio and Marinomonas belonging to Gammaproteobacteria, showed significant correlation with tetB and tetD, the most dominant ARGs in all samples. Also, operational taxonomic units (OTUs)-based network analysis revealed that ten OTUs, classified into the phyla Proteobacteria, Cyanobacteria/Chloroplast, Bacteroidetes, Verrucomicrobia and an unclassified phylum, were potential hosts of tetracycline resistance genes (i.e., tetA, tetG, tetH, tetM, tetQ and tetZ). Further systematic monitoring of ARGs is warranted for risk assessment and management of antibacterial resistance from fish farm effluents.

Quantitative Analysis of Periodontal Pathogens Using Real-Time Polymerase Chain Reaction (PCR)

The quantitative polymerase chain reaction (qPCR) is a variant of PCR aimed to detect and quantify a targeted DNA molecule through the addition of probes labeled with fluorescent molecules that emit fluorescence within each amplification cycle, what results in fluorescence values proportional to the amount of accumulated PCR product. This chapter presents the detailed procedures for quantification of different periodontal pathogens (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Campylobacter rectus, and Fusobacterium spp.) using qPCR. It also includes the description of the most frequent problems encountered and how to solve them. In addition, a detailed protocol for multiplex qPCR to detect and quantify P. gingivalis and A. actinomycetemcomitans is included.

Culture-dependent and independent techniques to monitor yeast species during cold soak carried out at different temperatures in winemaking

Transformation of grape must into wine is a process that may vary according to the consumers' requirements. Application of cold soak prior to alcoholic fermentation is a common practice in cellars in order to enhance flavor complexity and extraction of phenolic compounds. However, the effect of this step on wine yeast microbiota is not well-known. The current study simultaneously analyzed the effect of different cold soak temperatures on the microbiological population throughout the process and the use of culture-dependent and independent techniques to study this yeast ecology. The temperatures assayed were those normally applied in wineries: 2.5, 8 and 12°C. PCR-DGGE allowed detection of the most representative species such as Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae. As could be expected, highest diversity indices were obtained at the beginning of each process, and survival of H. uvarum or S. bacillaris depended on the temperature. Our results are in agreement with those obtained with culture independent methods, but qPCR showed higher precision and a different behavior was observed for each yeast species and at each temperature assayed. Comparison of both culture-independent techniques can provide a general overview of the whole process, although DGGE does not reveal the diversity expected due to the reported problems with the sensitivity of this technique.

Gene expression profiling and DNA methylation analyses of CTCs

A variety of molecular assays have been developed for CTCs detection and molecular characterization. Molecular assays are based on the nucleic acid analysis in CTCs and are based on total RNA isolation and subsequent mRNA quantification of specific genes, or isolation of genomic DNA that can be for DNA methylation studies and mutation analysis. This review is mainly focused on gene expression and methylation studies in CTCs in various types of cancer.

Comparison between a chimeric lysin ClyH and other enzymes for extracting DNA to detect methicillin resistant Staphylococcus aureus by quantitative PCR

Extracting DNA from Staphylococcus aureus cells is important for detecting MRSA by PCR. However, S. aureus cells are known to be difficult to disrupt due to their compact cell walls. Here, we systematically studied the efficiency of a highly active lysin ClyH for extracting DNA of S. aureus in comparison with commonly used enzymes, such as lysostaphin and achromopeptidase (ACP), and its compatibility in quantitative PCR (qPCR) detection of MRSA. qPCR analysis of S. aureus specific gene femB showed that ClyH was much faster than lysostaphin, ACP and lysozyme for releasing DNA. Five minutes disruption with ClyH at room temperature was enough to release all the DNA from S. aureus. Analysis of the spiked nasal swabs by a dual qPCR assay of the β-lactam resistance mecA gene and the staphylococcal cassette chromosome (SCCmec)-open reading frame X (orfX) junction (SCCmec-orfX) after ClyH lysis showed 100% sensitivity and specificity to the commercial BD GeneOhm™ MRSA test with ACP lysis, but the lysis time was reduced from 20 min by ACP to 5 min by ClyH. Our research shows that ClyH could be a better option than the currently used enzymes for DNA extraction from S. aureus, which can provide simpler and faster PCR detection of MRSA.

Viable and culturable populations of Saccharomyces cerevisiae, Hanseniaspora uvarum and Starmerella bacillaris (synonym Candida zemplinina) during Barbera must fermentation

The present study analyzed the viable and/or culturable populations of Saccharomyces cerevisiae, Hanseniaspora uvarum and Starmerella bacillaris (synonym Candida zemplinina) during laboratory grape must fermentation, in order to investigate the interaction between the three species considered. Firstly, population dynamics during wine fermentation were followed by culture-dependent techniques, and non-Saccharomyces yeast became non-culturable at late stages of fermentation when S. cerevisiae dominated. Four different culture-independent techniques were further applied to detect viable yeast cells at the late stage of fermentation. Both quantitative PCR techniques applied, namely ethidium monoazide bromide (EMA)-qPCR and Reverse Transcription (RT)-qPCR, detected H. uvarum and Starm. bacillaris at a concentration of 10⁵ to 10⁶cells/mL. These non-culturable cells had membranes impermeable to EMA and stable rRNA. The background signals from dead cells did not interfere with the quantification of viable cells in wine samples by EMA-qPCR technique. As a qualitative culture-independent technique, DGGE technique was coupled with EMA treatment (EMA-PCR-DGGE) or with RT (RT-PCR-DGGE). With EMA-PCR-DGGE non-Saccharomyces species during fermentation were detected although it was limited by the predominance of S. cerevisiae.

Differentially circulating miRNAs after recent osteoporotic fractures can influence osteogenic differentiation

Osteoporosis is the consequence of altered bone metabolism resulting in the systemic reduction of bone strength and increased risk of fragility fractures. MicroRNAs (miRNAs) regulate gene expression on a post-transcriptional level and are known to take part in the control of bone formation and bone resorption. In addition, it is known that miRNAs are secreted by many cell types and can transfer "messages" to recipient cells. Thus, circulating miRNAs might not only be useful as surrogate biomarkers for the diagnosis or prognosis of pathological conditions, but could be actively modulating tissue physiology. Therefore, the aim of this study was to test whether circulating miRNAs that exhibit changes in recent osteoporotic fracture patients could be causally related to bone metabolism. In the first step we performed an explorative analysis of 175 miRNAs in serum samples obtained from 7 female patients with recent osteoporotic fractures at the femoral neck, and 7 age-matched female controls. Unsupervised cluster analysis revealed a high discriminatory power of the top 10 circulating miRNAs for patients with recent osteoporotic fractures. In total 6 miRNAs, miR-10a-5p, miR-10b-5p, miR-133b, miR-22-3p, miR-328-3p, and let-7g-5p exhibited significantly different serum levels in response to fracture (adjusted p-value<0.05). These miRNAs were subsequently analyzed in a validation cohort of 23 patients (11 control, 12 fracture), which confirmed significant regulation for miR-22-3p, miR-328-3p, and let-7g-5p. A set of these and of other miRNAs known to change in the context of osteoporotic fractures were subsequently tested for their effects on osteogenic differentiation of human mesenchymal stem cells (MSCs) in vitro. The results show that 5 out of 7 tested miRNAs can modulate osteogenic differentiation of MSCs in vitro. Overall, these data suggest that levels of specific circulating miRNAs change in the context of recent osteoporotic fractures and that such perturbations of "normal" levels might affect bone metabolism or bone healing processes.

Distribution of Alexandrium fundyense and A. pacificum (Dinophyceae) in the Yellow Sea and Bohai Sea

This study characterizes the distribution of two closely related, causative species of paralytic shellfish poisoning – Alexandrium fundyense and A. pacificum – within the Yellow Sea (YS) and Bohai Sea (BS). These two Alexandrium species are distinguished for the first time in a regional field study using species-specific, quantitative PCR (qPCR) based assays. Both qPCR assays target the large subunit ribosomal DNA gene and were used to analyze net-concentrated phytoplankton samples collected in May 2012. A. fundyense was mainly distributed in YS, while A. pacificum was confined to an area adjacent to the Changjiang River estuary. The different distribution of the two species is interpreted as evidence of their distinct bloom ecology. Expanded efforts implementing these assays offer the ability to discriminate the dynamics of A. fundyense and A. pacificum blooms and provide a more sound basis for monitoring toxic Alexandrium species in this region.

Comparison of next-generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples

Clinical microbiology laboratories rely on quantitative PCR for its speed, sensitivity, specificity and ease-of-use. However, quantitative PCR quantitation requires the use of a standard curve or normalisation to reference genes. Droplet digital PCR provides absolute quantitation without the need for calibration curves. A comparison between droplet digital PCR and quantitative PCR-based analyses was conducted for the enteric parasite Cryptosporidium, which is an important cause of gastritis in both humans and animals. Two loci were analysed (18S rRNA and actin) using a range of Cryptosporidium DNA templates, including recombinant plasmids, purified haemocytometer-counted oocysts, commercial flow cytometry-counted oocysts and faecal DNA samples from sheep, cattle and humans. Each method was evaluated for linearity, precision, limit of detection and cost. Across the same range of detection, both methods showed a high degree of linearity and positive correlation for standards (R(2)⩾0.999) and faecal samples (R(2)⩾0.9750). The precision of droplet digital PCR, as measured by mean Relative Standard Deviation (RSD;%), was consistently better compared with quantitative PCR, particularly for the 18S rRNA locus, but was poorer as DNA concentration decreased. The quantitative detection of quantitative PCR was unaffected by DNA concentration, but droplet digital PCR quantitative PCR was less affected by the presence of inhibitors, compared with quantitative PCR. For most templates analysed including Cryptosporidium-positive faecal DNA, the template copy numbers, as determined by droplet digital PCR, were consistently lower than by quantitative PCR. However, the quantitations obtained by quantitative PCR are dependent on the accuracy of the standard curve and when the quantitative PCR data were corrected for pipetting and DNA losses (as determined by droplet digital PCR), then the sensitivity of both methods was comparable. A cost analysis based on 96 samples revealed that the overall cost (consumables and labour) of droplet digital PCR was two times higher than quantitative PCR. Using droplet digital PCR to precisely quantify standard dilutions used for high-throughput and cost-effective amplifications by quantitative PCR would be one way to combine the advantages of the two technologies.

Measuring RNAi knockdown using qPCR

We describe a scalable method for measuring changes in gene expression following RNAi in mammalian cells. This protocol outlines methods to transfect cells, isolate total RNA, perform cDNA synthesis, run qPCR reactions with multiplexed TaqMan dual hydrolysis probes, and analyze the results from qPCR using relative quantification (Fleige et al., 2006). These methods can be used to assess the relative knockdown of a set of siRNAs against a target in order to identify the most effective molecule and they can be used to assess the potency of a siRNA or group of siRNAs when performed over a range of doses. When screening panels of siRNAs targeting a given gene, knockdown can be assessed in two phases. In the first phase, the most active molecules are identified in a single dose screen. In the second phase a dose response screen is used to identify the subset of efficacious molecules that are the most potent.

Measuring RNAi knockdown using qPCR

We describe a scalable method for measuring changes in gene expression following RNAi in mammalian cells. This protocol outlines methods to transfect cells, isolate total RNA, perform cDNA synthesis, run qPCR reactions with multiplexed TaqMan dual hydrolysis probes, and analyze the results from qPCR using relative quantification (Fleige et al., 2006). These methods can be used to assess the relative knockdown of a set of siRNAs against a target in order to identify the most effective molecule and they can be used to assess the potency of a siRNA or group of siRNAs when performed over a range of doses. When screening panels of siRNAs targeting a given gene, knockdown can be assessed in two phases. In the first phase, the most active molecules are identified in a single dose screen. In the second phase a dose response screen is used to identify the subset of efficacious molecules that are the most potent.