Validation and Optimization of qPCR Method for Identification of Actaea racemosa (Black Cohosh) NHPs

BACKGROUND

Actaea racemosa (black cohosh) herbal dietary supplements are commonly used to treat menopausal symptoms in women. However, there is a considerable risk of contamination of A. racemosa herbal products in the natural health product (NHP) industry, impacting potential efficacy. Authentication of A. racemosa products is challenging because of the standard, multi-part analytical chemistry methods that may be too costly and not appropriate for both raw and finished products.

OBJECTIVE

In this paper, we discuss developing and validating quick alternative biotechnology methods to authenticate A. racemosa herbal dietary supplements, based on the use of a species-specific hydrolysis PCR probe assay.

METHODS

A qPCR-based species-specific hydrolysis probe assay was designed, validated, and optimized for precisely identifying the species of interest using the following analytical validation criteria: (1) specificity (accuracy) in determining the target species ingredient, while not identifying other non-target species; (2) sensitivity in detecting the smallest amount of the target material; and (3) reliability (repeatability and reproducibility) in detecting the target species in raw materials on a real-time PCR platform.

RESULTS

The results show that the species-specific hydrolysis probe assay was successfully developed for the raw materials and powders of A. racemosa. The specificity of the test was 100% to the target species. The efficiency of the assay was observed to be 99%, and the reliability of the assay was 100% for the raw/starting and powder materials.

CONCLUSION

The method developed in this study can be used to authenticate and perform qualitative analysis of A. racemosa supplements.

Quantification of Actaea racemosa L. (black cohosh) from some of its potential adulterants using qPCR and dPCR methods

The demand for popular natural health products (NHPs) such as Black Cohosh is increasing considerably, which in turn challenges quality assurance (QA) throughout the supply chain. To detect and quantify the target species present in a given NHP, DNA-based molecular techniques such as Real-time quantitative PCR (qPCR) and digital PCR (dPCR) are standard tools in the food and pathogen testing industries. There is a gap in the literature concerning validated quantitative PCR methods for botanicals that can be utilized for QA and good manufacturing practices. The objective of this study is to develop an efficient quantification method using qPCR and dPCR techniques for the detection and quantification of Actaea racemosa (Black cohosh) NHPs from its potential adulterants. These developed methods are validated for applicability on commercial NHPs. Species-specific hydrolysis probe assays were designed to analyze the black cohosh NHPs using qPCR and dPCR techniques. The results confirmed that the developed qPCR and dPCR methods are highly precise for identifying and quantifying black cohosh NHPs, indicating their potential applicability in future routine industrial and laboratory testing. This enables a single qPCR test to determine not only the presence of a specific botanical, but also the amount when mixed with an adulterant.

Thomas J Henry, as viewed by his son, daughter, and wife

When Al Wheeler told me that he was organizing a Festschrift to honor Tom, I (K.H.) thought, how is it possible that it could be time for a Festschrift already? It seems like I just met Tom yesterday. When Al asked me to write an introductory article for the journal, I wondered if I could manage that and called Tom’s children, Tommy (T.A.H.) and Angela (A.H.T.), asking for their help. They both agreed and we began a wonderful collaboration to honor their Dad. As with any life, certain stories and remembrances stand out, and that person’s characteristics and traits are known to some people, but perhaps not to others. We thought about how he enriched our lives through his generosity and guidance and how he influenced our professional lives with sound advice and counsel. We thought about his childhood and the special bond he had with his family, one steeped in the traditions of hard work and a drive to achieve desired goals. We (T.A.H. and A.H.T.) have chosen to focus on some of the highlights of our Dad’s remarkable career and events that show his love of natural history. Included are certain early events, as recounted by our Grandmother.

Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing

Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.

A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits

Genome size (C-value) and endopolyploidy (endoreduplication index, EI) are known to correlate with various morphological and ecological traits, in addition to phylogenetic placement. A phylogenetically controlled multivariate analysis was used to explore the relationships between DNA content and phenotype in angiosperms. Seeds from 41 angiosperm species (17 families) were grown in a common glasshouse experiment. Genome size (2C-value and 1Cx-value) and EI (in four tissues: leaf, stem, root, petal) were determined using flow cytometry. The phylogenetic signal was calculated for each measure of DNA content, and phylogenetic canonical correlation analysis (PCCA) explored how the variation in genome size and EI was correlated with 18 morphological and ecological traits. Phylogenetic signal (λ) was strongest for EI in all tissues, and λ was stronger for the 2C-value than the 1Cx-value. PCCA revealed that EI was correlated with pollen length, stem height, seed mass, dispersal mechanism, arbuscular mycorrhizal association, life history and flowering time, and EI and genome size were both correlated with stem height and life history. PCCA provided an effective way to explore multiple factors of DNA content variation and phenotypic traits in a phylogenetic context. Traits that were correlated significantly with DNA content were linked to plant competitive ability.

Quantitative and depth-resolved deep level defect distributions in InGaN/GaN light emitting diodes

Deep level defects in the multi-quantum well (MQW) region of InGaN/GaN light emitting diodes (LEDs) were investigated. InGaN quantum well and GaN quantum barrier defect states were distinguished using bias-dependent steady-state photocapacitance and deep level optical spectroscopy, and their possible physical origin and potential impact on LED performance is considered. Lighted capacitance-voltage measurements provided quantitative and nanoscale depth profiling of the deep level concentration within the MQW region. The concentration of every observed deep level varied strongly with depth in the MQW region, which indicates evolving mechanisms for defect incorporation during MQW growth.

Epistasis can increase multivariate trait diversity in haploid non-recombining populations

We evaluate the effect of epistasis on genetically-based multivariate trait variation in haploid non-recombining populations. In a univariate setting, past work has shown that epistasis reduces genetic variance (additive plus epistatic) in a population experiencing stabilizing selection. Here we show that in a multivariate setting, epistasis also reduces total genetic variation across the entire multivariate trait in a population experiencing stabilizing selection. But, we also show that the pattern of variation across the multivariate trait can be more even when epistasis occurs compared to when epistasis is absent, such that some character combinations will have more genetic variance when epistasis occurs compared to when epistasis is absent. In fact, a measure of generalized multivariate trait variation can be increased by epistasis under weak to moderate stabilizing selection conditions, as well as neutral conditions. Likewise, a measure of conditional evolvability can be increased by epistasis under weak to moderate stabilizing selection and neutral conditions. We investigate the nature of epistasis assuming a multivariate-normal model genetic effects and investigate the nature of epistasis underlying the biophysical properties of RNA. Increased multivariate diversity occurs for populations that are infinite in size, as well as populations that are finite in size. Our model of finite populations is explicitly genealogical and we link our findings about the evenness of eigenvalues with epistasis to prior work on the genealogical mapping of epistatic effects.