Single cells are basic physiological and biological units that can function individually as well as in groups in tissues and organs. It is central to identify, characterize and profile single cells at molecular level to be able to distinguish different kinds, to understand their functions and determine how they interact with each other. During the last decade several technologies for single-cell profiling have been developed and used in various applications, revealing many novel findings. Quantitative PCR (qPCR) is one of the most developed methods for single-cell profiling that can be used to interrogate several analytes, including DNA, RNA and protein. Single-cell qPCR has the potential to become routine methodology but the technique is still challenging, as it involves several experimental steps and few molecules are handled. Here, we discuss technical aspects and provide recommendation for single-cell qPCR analysis. The workflow includes experimental design, sample preparation, single-cell collection, direct lysis, reverse transcription, preamplification, qPCR and data analysis. Detailed reporting and sharing of experimental details and data will promote further development and make validation studies possible. Efforts aiming to standardize single-cell qPCR open up means to move single-cell analysis from specialized research settings to standard research laboratories.

• Klíčová slova
• MIQE guidelines, Single-cell analysis, Single-cell qPCR, Single-cell workflow, qPCR,
• MeSH
• analýza jednotlivých buněk metody   MeSH
• kvantitativní polymerázová řetězová reakce metody   MeSH
• lidé MeSH
• polymerázová řetězová reakce MeSH
• stanovení celkové genové exprese metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Reverse transcription quantitative PCR (RT-qPCR) has delivered significant insights in understanding the gene expression landscape. Thanks to its precision, sensitivity, flexibility, and cost effectiveness, RT-qPCR has also found utility in advanced single-cell analysis. Single-cell RT-qPCR now represents a well-established method, suitable for an efficient screening prior to single-cell RNA sequencing (scRNA-Seq) experiments, or, oppositely, for validation of hypotheses formulated from high-throughput approaches. Here, we aim to provide a comprehensive summary of the scRT-qPCR method by discussing the limitations of single-cell collection methods, describing the importance of reverse transcription, providing recommendations for the preamplification and primer design, and summarizing essential data processing steps. With the detailed protocol attached in the appendix, this tutorial provides a set of guidelines that allow any researcher to perform scRT-qPCR measurements of the highest standard.

• Klíčová slova
• RT-qPCR, gene expression, preamplification, quantitative PCR, reverse transcription, sample collection, single cell,
• MeSH
• analýza jednotlivých buněk metody   normy   MeSH
• kvantitativní polymerázová řetězová reakce metody   normy   MeSH
• lidé MeSH
• reverzní transkripce genetika   MeSH
• senzitivita a specificita MeSH
• stanovení celkové genové exprese metody   normy   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

The aim of this study was to test the detection performance of the cpsA, lytA and ply genes through qPCR in the identification of Streptococcus pneumoniae in respiratory tract samples. Specificity was tested on a panel of 128 streptococci and other bacteria DNA samples. The qPCR assay was tested on a total of 51 respiratory tract samples from patients with community-acquired pneumonia (CAP). The specificity of the cpsA, lytA and ply genes was 100%, 100%, and 86%, respectively. The quantitative assessment, based on lytA, determined a cutoff value of ~2x104, 4x102 and 4x102 DNA copies per 1 mL of valid sputum, tracheal aspirate and bronchial aspirate samples, respectively. The results from the present study suggest that qPCR detection of all three genes would be optimal in the accurate detection of Streptococcus pneumoniae.

• Klíčová slova
• Streptococcus pneumoniae, community-acquired pneumonia, qPCR, quantification, specificity,
• MeSH
• DNA bakterií genetika   MeSH
• dýchací soustava mikrobiologie   MeSH
• infekce získané v komunitě * diagnóza   mikrobiologie   MeSH
• kvantitativní polymerázová řetězová reakce * MeSH
• lidé MeSH
• pneumonie pneumokoková * diagnóza   mikrobiologie   MeSH
• senzitivita a specificita MeSH
• Streptococcus pneumoniae genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA bakterií MeSH

We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1-16 qPCR replicates per concentration and we tested 2-10 μl volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3-4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range.

• Klíčová slova
• ANCOVA, analysis of covariance, Amplification efficiency, CLSI, Clinical and Laboratory Standards Institute, Cq, cycle of quantification, Dilution series, E, PCR efficiency, EPA, Environmental protection agency, FDA, food and Drug Administration, GMO, genetically modified organism, IEC, International Electrotechnical Commission, ISO, International Organization for Standardization, MIQE, minimum information for publication of quantitative real-time PCR experiments, NTC, no template control, RIN, RNA Integrity Number, RT-qPCR, reverse transcription-quantitative polymerase chain reaction, Real-time quantitative PCR, Standard curve, qPCR, qPCR assay validation,
• Publikační typ
• časopisecké články MeSH

Quantitative Real-Time Polymerase Chain Reaction, better known as qPCR, is the most sensitive and specific technique we have for the detection of nucleic acids. Even though it has been around for more than 30 years and is preferred in research applications, it has yet to win broad acceptance in routine practice. This requires a means to unambiguously assess the performance of specific qPCR analyses. Here we present methods to determine the limit of detection (LoD) and the limit of quantification (LoQ) as applicable to qPCR. These are based on standard statistical methods as recommended by regulatory bodies adapted to qPCR and complemented with a novel approach to estimate the precision of LoD.

• Klíčová slova
• Data analysis, GenEx software, Limit of detection, Limit of quantification, LoD, LoQ, MIQE, Quality control, Real-time PCR, Replicates, Standardization, qPCR,
• Publikační typ
• časopisecké články MeSH

The emerging use of qPCR and dPCR in regulated bioanalysis and absence of regulatory guidance on assay validations for these platforms has resulted in discussions on lack of harmonization on assay design and appropriate acceptance criteria for these assays. Both qPCR and dPCR are extensively used to answer bioanalytical questions for novel modalities such as cell and gene therapies. Following cross-industry conversations on the lack of information and guidelines for these assays, an American Association of Pharmaceutical Scientists working group was formed to address these gaps by bringing together 37 industry experts from 24 organizations to discuss best practices to gain a better understanding in the industry and facilitate filings to health authorities. Herein, this team provides considerations on assay design, development, and validation testing for PCR assays that are used in cell and gene therapies including (1) biodistribution; (2) transgene expression; (3) viral shedding; (4) and persistence or cellular kinetics of cell therapies.

• Klíčová slova
• AAV, RT-qPCR, biodistribution, cell therapy, cellular kinetics, dPCR, gene therapy, qPCR, shedding, transgene expression,
• MeSH
• genetická terapie * MeSH
• polymerázová řetězová reakce MeSH
• tkáňová distribuce MeSH
• vyvíjení léků * MeSH
• Publikační typ
• časopisecké články MeSH

PREMISE: Despite the high functional importance of endophytes, we still have limited understanding of the biotic and abiotic factors that influence colonization of plant hosts along major ecological gradients and lack quantitative estimates of their colonization extent. In this study, we hypothesized that the developmental stage of the ecosystem will affect the levels of bacterial and fungal endophytic assemblages in the foliar endosphere. METHODS: We quantified levels of bacterial and fungal endophytes in leaves of four plant hosts at four stages of vegetation succession using an optimized qPCR protocol with bacteria-specific 16S and fungi-targeting primers. RESULTS: (1) The ecosystem developmental stage did not have a significant effect on the colonization levels of bacterial or fungal endophytes. (2) Colonization levels by bacterial and fungal endophytes were governed by different mechanisms. (3) Endophytic colonization levels and their relationship to foliar tissue stoichiometry were highly host specific. CONCLUSIONS: Quantifying colonization levels is important in the study of endophytic ecology, and the fast, relatively low-cost qPCR-based method can supply useful ecological information, which can significantly enhance the interpretation potential of descriptive data generated, for example, by next-generation sequencing.

• Klíčová slova
• cell counts, ecological succession, foliar endophyte, fungi‐bacteria ratios, qPCR, soil chronosequence,
• MeSH
• Bacteria genetika   klasifikace   izolace a purifikace   MeSH
• endofyty * fyziologie   MeSH
• hostitelská specificita MeSH
• houby * fyziologie   genetika   MeSH
• kvantitativní polymerázová řetězová reakce * MeSH
• listy rostlin * mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH

Degradation of undesirable biogenic amines (BAs) in foodstuffs by microorganisms is considered one of the most effective ways of eliminating their toxicity. In this study, we designed two sets of primers for the detection and quantification of the multicopper oxidase gene (MCO), which encodes an enzyme involved in BAs degradation, and endogenous (glyceraldehyde-3-phosphate dehydrogenase) gene (GAPDH) in Lactobacillus casei group by real-time PCR (qPCR). We tested 15 Lactobacillus strains in the screening assays (thus, MCO gene possessing assay (PCR) and monitoring of BAs degradation by HPLC-UV), in which Lactobacillus casei CCDM 198 exhibited the best degradation abilities. For this strain, we monitored the expression of the target gene (MCO) in time (qPCR), the effect of redox treatments (cysteine, ascorbic acid) on the expression of the gene, and the ability to degrade BAs not only in a modified MRS medium (MRS/2) but also in a real food sample (milk). Moreover, decarboxylase activity (ability to form BAs) of this strain was excluded. According to the results, CCDM 198 significantly (P < 0.05) reduced BAs (putrescine, histamine, tyramine, cadaverine), up to 25% decline in 48 h. The highest level of relative expression of MCO (5.21 ± 0.14) was achieved in MRS/2 media with cysteine.

• Klíčová slova
• Biogenic amines degradation, Histamine, Lactobacillus casei, Primers, qPCR,
• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• biogenní aminy analýza   metabolismus   MeSH
• cystein analýza   metabolismus   MeSH
• glyceraldehyd-3-fosfátdehydrogenasy genetika   MeSH
• kultivační média chemie   MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• kyselina askorbová analýza   metabolismus   MeSH
• Lactobacillus casei enzymologie   genetika   růst a vývoj   metabolismus   MeSH
• Lactobacillus enzymologie   genetika   růst a vývoj   metabolismus   MeSH
• mléko chemie   MeSH
• oxidoreduktasy genetika   metabolismus   MeSH
• regulace genové exprese u bakterií MeSH
• vysokoúčinná kapalinová chromatografie MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny MeSH
• biogenní aminy MeSH
• cystein MeSH
• glyceraldehyd-3-fosfátdehydrogenasy MeSH
• kultivační média MeSH
• kyselina askorbová MeSH
• oxidoreduktasy MeSH

Embryos, juveniles, and even adults of many bird species lack pronounced external sexually dimorphic characteristics. Accurate identification of sex is crucial for research (e.g., developmental, population, and evolutionary studies), management of wildlife species, and captive breeding programmes for both conservation and poultry. An accurate molecular sexing method applicable across the entire bird radiation is theoretically possible thanks to the long-term stability of their ZZ/ZW sex chromosomes, but current methods are not applicable in a wide range of bird lineages. Here, we developed a novel molecular sexing method based on the comparison of gene copy number variation by quantitative real-time PCR (qPCR) in conserved Z-specific genes (CHRNA6, DDX4, LPAR1, TMEM161B, VPS13A), i.e. genes linked to Z but absent from W chromosomes. We tested the method across three paleognath and 70 neognath species covering the avian phylogeny. In addition, we designed primers for four Z-specific genes (DOCK8, FUT10, PIGG and PSD3) for qPCR-based molecular sexing in three paleognath species. We have demonstrated that the genes DOCK8, FUT10, PIGG and PSD3 can identify sex in paleognath birds and the genes CHRNA6, DDX4, TMEM161B, and VPS13A can reveal sex in neognath birds. The gene LPAR1 can be used to accurately identify sex in both paleognath and neognath species. Along with outlining a novel method of practical importance for molecular sexing in birds, our study also documents in detail the conservation of sex chromosomes across the avian phylogeny.

• Klíčová slova
• birds, molecular sexing, ostrich, qPCR, rhea, sex identification,
• MeSH
• analýza určování pohlaví * MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• pohlavní chromozomy * genetika   MeSH
• ptáci * genetika   MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Thermotolerant Campylobacter jejuni, coli and lari are recognized as leading food-borne pathogens causing an acute bacterial enteritis worldwide. Due to narrow spectrum of their biochemical activity, it is very complicated to distinguish between individual species. For reliable risk assessment, proper incidence evaluation or swift sample analysis regarding individual species, a demand for simple and rapid method for their distinguishing is reasonable. In this study, we evaluated a reliable and simple approach for their simultaneous detection, species identification and quantification using multiplex qPCR. RESULTS: Species specific primers and hydrolysis probes are directed to hippuricase gene of C. jejuni, serine hydroxymethyltransferase gene of C. coli and peptidase T gene of C. lari. Efficiencies of reactions were 90.85% for C. jejuni, 96.97% for C. coli and 92.89% for C. lari. At 95.00% confidence level and when cut off is set to 38 cycles, limits of detection are in all cases under 10 genome copies per reaction which is very appreciated since it is known that infectious doses are very low. CONCLUSIONS: Proposed assay was positively validated on different food matrices (chicken wing rinses, chicken juice and homogenized fried chicken strips). No inhibition of PCR reaction occurred. Assay was evaluated in accordance with MIQE handbook.

• Klíčová slova
• MIQE, Multiplex qPCR, Quantification, Thermotolerant Campylobacter spp,
• Publikační typ
• časopisecké články MeSH