Herbal medicinal products (HMPs) have grown increasingly popular in the United States, many of them with imported raw materials and sold online. Yet due to the lack of regulation from the US Food and ...Drug Administration (FDA), manufacturers of the products can substitute or add in other herbs that are not advertised on the label. In this study, as part of the Urban Barcode Research Program (UBRP), an education initiative to engage New York City high school students in science, we aimed to taxonomically authenticate single-ingredient online-sold HMPs containing non-native plants through DNA barcoding of the internal transcribed spacer 2 region (ITS2) and
. We were able to successfully barcode 20 HMPs, but four of these did not match the expected species. It was concluded that the four HMPs advertising astragalus, epazote, ginseng, and chanca piedra were contaminated/ substituted because their ITS2 and
DNA sequences did not match the expected taxonomy in GenBank, a government database. Our study highlights the importance of herbal pharmacovigilance in the absence of strict government regulation of herbal supplements and motivates crowd-sourced DNA barcoding to enable American consumers make informed choices and be more empowered to safeguard their health.
Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon ...was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The large-flowered parasitic genus Rafflesia R.Br. (Rafflesiaceae) has long fascinated naturalists and scientists and is an iconic symbol for plant conservation. Techniques to effectively propagate ...members of the genus outside of their natural habitat are sparse, and grafting infected Tetrastigma K.Schum.(Vitaceae) host plants has previously been reported as a successful strategy for ex situ conservation of Rafflesia. Here we report our attempts in the United States to propagate host cuttings infected with Rafflesia speciosa Barcelona & Fernando and R. lagascae Blanco collectedfrom the Philippines, as well as uninfected host material. We also describe efforts to germinate R. speciosa seeds in vitro using various plant growth regulators (PGRs). After rooting, infected host cuttings survived for a maximum of 11 months, but did not produce shoots. However, an uninfected cutting of T. cf. magnum grafted onto an established Malaysian species of Tetrastigma in June 2017 has succeeded in the commencement of new growth. Three propagules of a second potential host, T. harmandii Planch., have also been vigorously growing at the United States Botanic Garden since June 2017. However, Rafflesia seeds did not germinate with the application of PGRs, even though the seeds were viable according to tetrazolium (TZ) testing.These ex situ propagation attempts have revealed challenges in propagating these species outside of their native ranges, but our incremental success in rooting infected Tetrastigma, as well as grafting interspecific Tetrastigma species, bodes well for further advances. With Philippine host species, T. harmandii and T. cf. magnum in cultivation, we can begin using these specimens for future experimentation involving grafting of infected material and Rafflesia seed inoculation trials.Furthermore, we describe new avenues of propagation techniques for Rafflesia as practised by Marius Gabin, one of the owners of the Vivian Rafflesia garden, which contains a natural Rafflesia forest habitat at Poring Springs, Sabah, Malaysia. Gabin openly shared his successes in artificially inoculating Rafflesia seeds into a mature Tetrastigma vine. Gabin’s willingness to share his experience highlights the importance of collaborating with practitioners who have developed local knowledge of Rafflesia horticulture and conservation.
New York City (NYC) has a diverse range of immigrant populations that consequently brought to the city their traditional herbal knowledge. Medicinal plants have been used by different cultures ...worldwide, long before the development of pharmaceuticals. Studying the traditional uses of plants in a phylogenetic framework can help determine pharmacologically important plant families. A phylogeny of common medicinal plant species sold in NYC and traditionally used in Ayurvedic/Indian, Chinese, Latin/Caribbean, Middle Eastern/Islamic, and African cultures has been reconstructed, and the traditional medicinal function of each plant was mapped on the phylogeny. The results showed that the plant families Apiaceae, Burseraceae, Combretaceae, Fabaceae, Lamiaceae, Lauraceae, Malvaceae, Meliaceae, Rubiaceae, and Zingiberaceae have disproportionate importance to herbal medicine in NYC, and collectively, show applications for gastrointestinal, cardiovascular, respiratory, musculoskeletal, gynecological conditions, and as antibiotic/anti-parasitic agents. Our study has demonstrated that different immigrant groups converge on related plants for similar ailments. This cultural convergence, possibly through independent discoveries of these plants' medicinal uses, suggests that there may be underlying bioactivity that should be further explored. Our study also highlights the utility of phylogenetic analysis in uncovering new medicinal applications and novel therapeutic sources. Addition of more plant species to the phylogeny may uncover plant families that could be medicinally important for other applications or health conditions.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The goal of this study was to use phylogenetic evidence to determine plant families with high representation of antibacterial activity and identify potential sources to focus on for antibacterial ...drug discovery.
We reconstructed the molecular phylogeny of plant taxa with antibacterial activity and mapped antibacterial mechanisms of action on the phylogeny.
The phylogeny highlighted seven plant families (Combretaceae, Cupressaceae, Fabaceae, Lamiaceae, Lauraceae, Myrtaceae and Zingiberaceae) with disproportionately represented antibacterial activity. Phytochemicals produced were primarily involved in the disruption of the bacterial cell wall/membrane and inhibition of quorum sensing/biofilm production.
The study provides phylogenetic evidence of seven plant families that should be examined as promising leads for novel antibacterial development.
Antibiotic resistance is a growing worldwide problem. However, discovery and development of new antibacterial compounds are currently lacking. For this study, we examined published literature to identify plant groups that disproportionately produce antibacterial compounds. Additionally, we examined the evolutionary basis for these chemicals by determining relatedness of antibacterial-producing plants and their common antibacterial mode of action due to shared ancestry. This study has increased our understanding of plants with inherent antibacterial properties and plant families to target in antibiotic drug discovery studies.
•Herbal products (HMPs) from New York City were DNA barcoded for rbcl, matK and ITS2.•We found that ITS2 was easier to amplify and can discriminate species on its own.•We were more successful in ...barcoding leaf and root HMPs than barks.•4 of 47 herbal products barcoded did not contain the species declared on the label.•ITS2 DNA barcoding is a practical tool to authenticate herbal products.
With the development of DNA barcoding methods and databases, misidentification may be easily caught. However, this technique has presented challenges with regard to the tissue type and marker locus variation. In this study, DNA barcoding was used to investigate the taxonomic accuracy of herbal medicines sold in the New York City (NYC) area using the plastid markers rbcL, matK and the nuclear ribosomal region ITS2. Forty-seven (47) samples (single-ingredient herbal medicinal products or HMPs) were purchased from eight herbal stores, and represented different structures: 22 leaf samples, 11 roots, 9 barks, and 5 samples that were ground beyond recognition. MEGABLAST sequence comparison was performed to verify the taxonomic identity of the samples. Maximum likelihood trees were constructed for sequence queries with equivocal multiple high-scoring MEGABLAST hits. Of the barcodes, ITS2 had the most success being amplified and sequenced (barcoded) in 38 of the 47 HMPs (81%), mostly leaf and root samples as barks were difficult to barcode. This is in contrast to 26/47 (55%) and 15/47 (32%) successful barcoding for rbcL and matK, respectively. ITS2 alone was accurate enough to match 88% of ITS2 sequences to the expected species, while only 59% of sequenced rbcL and 45% of matK was able to match with the expected species. All four HMPs obtained from one store did not match the declared species on the label based on ITS2, and this result was echoed by the rbcL and matK barcodes. However, all other herbal stores appeared to be selling accurately labeled HMPs. Our study showed that DNA barcoding is a worthwhile effort to test HMP authenticity, which may help build reputation of quality brands and ensure consumer safety. ITS2 is a practical DNA barcode that regulatory agencies may propose to NYC herbal medicine manufacturers and merchants to ensure quality.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The gentians (Gentianaceae, Asteridae) form a morphologically and ecologically diverse group of plants with interesting phytochemical and medicinal properties. The family contains six tribes, but ...phylogenetic relationships among the three more derived tribes (Gentianeae, Helieae, and Potalieae) are considered ambiguous. In an attempt to resolve alignment ambiguity and provide better scientific support for relationships, the internal transcribed spacer (ITS) of the nuclear ribosomal DNA was aligned for several gentian sequences with reference to the ITS secondary structure proposed for Anvillen radiata (Asteraceae) using Dynalign. We present here the first secondary structure of ITS for Gentianaceae, which may guide alignment of ITS data in other asterids taxa. The study included 42 species, with representatives from tribes Chironieae, Gentianeae, Helieae, and Potalieae, and with the majority of species from Potalieae. Phylogenetic analyses based on secondary structure alignment using parsimony and Bayesian methods provided additional support for Gentianeae plus Helieae as the sister group to Potalieae. Prepusa (Helieae) showed ambivalent associations. Within tribe Potalieae, the subtribes Potaliinae and Lisianthiinae were supported as monophyletic. Bisgoeppertia (Chironieae) was placed unambiguously inside Lisianthius (Potalieae-Lisianthiinae) in all analyses. Neurotheca (Potalieae-Faroinae) was positioned as sister to Lisianthiinae, making subtribe Faroinae paraphyletic.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These ...relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill-Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species.
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