Molecular Verification of the UK National Collection of Cultivated Liriope and Ophiopogon Plants

open access articleA collection of cultivated Liriope and Ophiopogon plants was established in 1996–1998 and subsequently hosted at a horticultural college. Uncertainties about the identification of the accessions, compounded by potential errors in propagation and labelling have led to waning confidence in the identities of the plants in the collection. The potential for using DNA barcoding to determine the species identities of the accessions was investigated. The DNA barcode regions of the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene (rbcL) and nuclear ribosomal internal transcribed spacer (nrITS) were amplified. DNA sequence analysis allowed the sequences of the accessions to be compared to reference sequences in public databases. A simple haplotype map of the characteristic polymorphic positions in the rbcL regions was used to clearly distinguish between the two genera and assign Ophiopogon accessions to individual species or sub-groups of species. The ITS sequence data confirmed these genus and species assignations and provided greater resolution to distinguish between closely related species. The combination of two DNA barcodes allowed most of the accessions to be assigned to individual species. This molecular verification confirmed the identity of about 70% of the accessions, with the remaining 30% demonstrating a range of mistaken identities at the species and genus level

RNA synthesis and processing in isolated HeLa cell nuclei

Isolated HeLa cell nuclei have been characterised in terms of their ability to transcribe, process and transport RNA. In terms of transcription, it was found that all three RNA polymerases were active in the isolated nuclei. The size and nuclear location of the products of RNA polymerase I and III suggested that transcription by these polymerases was occurring normally in vitro. However, the RNA synthesised by RNA polymerase II was found to be much smaller than expected from the reported size of HeLa cell transcription units, when analysed in denaturing gradients. This was in contrast to the results of Sarma et al (1976) which showed that the size of RNA synthesised by RNA polymerase II in isolated HeLa cell nuclei is large when analysed under non-denaturing conditions. A number of possible reasons for this small size of RNA were examined. The results obtained indicate that this small size of RNA polymerase II product was probably not due to;- i. A slow elongation rate by RNA polymerase II resulting in a "nascent transcript profile." ii. Degradation of RNA in the isolated nuclei. iii. The absence of nuclear and cytoplasmic factors during incubation of the nuclei. iv. Degradation of the DM template during isolation and incubation of nuclei. It was found, however, that the state of the chromatin template was important in determining the size of RM transcribed. Thus, addition of acetyl CoA to isolated nuclei, which acetylated the histones, caused an increase in the size of RNA polymerase II product. On the other hand methylation of histones with Ado-Met vitro was correlated with a decrease in the size of RM. It was also found that the ionic content of the incubation medium affected the size of RNA transcript synthesised by RNA polymerase II. In particular, substituting 90 mM (NH4)2SO4 for 75 mM KCl in the incubation medium increased the size of RNA. This effect is discussed in terms of recent results which suggest that the small size of RNA polymerase II transcript commonly observed in vitro might be due to premature termination of transcription. The small RNA transcribed by RNA polymerase II in vitro appears to be stable. However, hnRNA prelabelled in vivo reduced in size during incubation of isolated nuclei. Some of this RNA is released from the nuclei during incubation. This release of RNA was examined to determine whether it represented the specific transport of mRNA. Although the size of released RNA particles, their ability, and the size of released RNA were consistent with mRNA transport, other features were more consistent with the leakage of hnRNP particles. The released RNA resembled hnRNA in terms of binding to poly(U) Sepharose, and the protein associated with the released RNA were similar to hnRHP particle proteins. Although the released RNA had messenger activitiy in a wheat germ cell free translation system, it is not possible to rule out mRNA contamination as the cause of this stimulation. It therefore appears that the isolated nuclei system of Sarma et al (1976) may not be ideal either for examining the transcription or the processing and transport of mRNA. On the other hand, the results obtained in the present study suggest ways in which this system might be modified in order to achieve full length transcription by RNA polymerase II in vitro, and study the processing and transport of these transcripts

Applied Barcoding: The Practicalities of DNA Testing for Herbals

open access articleDNA barcoding is a widely accepted technique for the identification of plant materials, and its application to the authentication of commercial medicinal plants has attracted significant attention. The incorporation ofDNA-based technologies into the quality testing protocols of international pharmacopoeias represents a step-change in status, requiring the establishment of standardized, reliable and reproducible methods. The process by which this can be achieved for any herbal medicine is described, using Hypericum perforatum L. (St John’sWort) and potential adulterant Hypericum species as a case study. A range of practical issues are considered including quality control of DNA sequences from public repositories and the construction of individual curated databases, choice of DNA barcode region(s) and the identification of informative polymorphic nucleotide sequences. A decision tree informs the structure of the manuscript and provides a template to guide the development of future DNA barcode tests for herbals

PlantID – DNA-based identification of multiple medicinal plants in complex mixtures

Background An efficient method for the identification of medicinal plant products is now a priority as the global demand increases. This study aims to develop a DNA-based method for the identification and authentication of plant species that can be implemented in the industry to aid compliance with regulations, based upon the economically important Hypericum perforatum L. (St John’s Wort or Guan ye Lian Qiao). Methods The ITS regions of several Hypericum species were analysed to identify the most divergent regions and PCR primers were designed to anneal specifically to these regions in the different Hypericum species. Candidate primers were selected such that the amplicon produced by each species-specific reaction differed in size. The use of fluorescently labelled primers enabled these products to be resolved by capillary electrophoresis. Results Four closely related Hypericum species were detected simultaneously and independently in one reaction. Each species could be identified individually and in any combination. The introduction of three more closely related species to the test had no effect on the results. Highly processed commercial plant material was identified, despite the potential complications of DNA degradation in such samples. Conclusion This technique can detect the presence of an expected plant material and adulterant materials in one reaction. The method could be simply applied to other medicinal plants and their problem adulterants

Structure and magnetic properties of the cubic oxide fluoride BaFeO2F

Fluorination of the parent oxide, BaFeO3- δ, with polyvinylidine fluoride gives rise to a cubic compound with a = 4.0603(4) Å at 298K. 57Fe Mössbauer spectra confirmed that all the iron is present as Fe3+. Neutron diffraction data showed complete occupancy of the anion sites indicating a composition BaFeO2F, with a large displacement of the iron off-site. The magnetic ordering temperature was determined as TN = 645±5K. Neutron diffraction data at 4.2K established G-type antiferromagnetism with a magnetic moment per Fe3+ ion of 3.95μB. However, magnetisation measurements indicated the presence of a weak ferromagnetic moment which is assigned to the canting of the antiferromagnetic structure. 57Fe Mössbauer spectra in the temperature range 10 to 300K were fitted with a model of fluoride ion distribution that retains charge neutrality of the perovskite unit cel

On the size of identifying codes in triangle-free graphs

In an undirected graph $G$, a subset $C\subseteq V(G)$ such that $C$ is a dominating set of $G$, and each vertex in $V(G)$ is dominated by a distinct subset of vertices from $C$, is called an identifying code of $G$. The concept of identifying codes was introduced by Karpovsky, Chakrabarty and Levitin in 1998. For a given identifiable graph $G$, let \M(G) be the minimum cardinality of an identifying code in $G$. In this paper, we show that for any connected identifiable triangle-free graph $G$ on $n$ vertices having maximum degree $\Delta\geq 3$, \M(G)\le n-\tfrac{n}{\Delta+o(\Delta)}. This bound is asymptotically tight up to constants due to various classes of graphs including $(\Delta-1)$-ary trees, which are known to have their minimum identifying code of size $n-\tfrac{n}{\Delta-1+o(1)}$. We also provide improved bounds for restricted subfamilies of triangle-free graphs, and conjecture that there exists some constant $c$ such that the bound \M(G)\le n-\tfrac{n}{\Delta}+c holds for any nontrivial connected identifiable graph $G$

Challenges in Medicinal and Aromatic Plants DNA Barcoding—Lessons from the Lamiaceae

open access articleThe potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples

Radiocarbon dating of the historic Livingstone Tree at Chiramba, Mozambique

Author Posting. © Studia Chemia, 2020. Studia Universitatis Babes-Bolyai Seria Chemia is an Open Access Journal (read, download, copy, distribute, print for research use, search, or link to the full texts of articles). The definitive version was published in Studia Universitatis Babes-Bolyai, Seria Chemia 65, no. 3 (2020): 149-156, doi:10.24193/subbchem.2020.3.11.The article reports the AMS (accelerator mass spectrometry) radiocarbon dating results of the Livingstone Tree, a large African baobab on the right bank of the Zambezi, near Chiramba, Mozambique. In 1858, David Livingstone, who discovered the baobab, carved his monogram on the walls of its inner cavity. In 1996, the historic baobab was uprooted when a cyclone struck the area. Several wood fragments were extracted from the remains of the toppled tree. Five samples which originate from these fragments were subsequently dated by radiocarbon. The oldest sample had a radiocarbon date of 1598 ± 17 BP, that corresponded in 1996 to a calibrated age of 1490 ± 35 calendar years. According to this value, the Livingstone Tree at Chiramba becomes one of the oldest known African baobabs, with an age of over 1500 years. The Livingstone Tree had a closed ring-shaped structure, that consisted of 4 fused stems around a false cavity and also 2 additional stems outside the ring.The research was funded by the Romanian Ministry of National Education CNCS-UEFISCDI under grants PN-II-ID-PCE-2013-76 and PN-III-P4-ID-PCE-2016-0776, Nr. 90/2017

A neutron diffraction study and mode analysis of compounds of the system La_1−xSr_xFeO_3−xF_x (x=1, 0.8, 0.5, 0.2) and an investigation of their magnetic properties

AbstractWe report here a detailed study of the system La1−xSrxFeO3−xFx, by neutron powder diffraction- and magnetic-measurements. All the compounds are robust antiferromagnetics with ordering temperatures well above room temperature. Magnetic moments are shown to align parallel to the c-axis. FC-ZFC measurements indicate a small canting of the magnetic moments, resulting in a ferromagnetic component with a maximum for La0.5Sr0.5FeO2.5F0.5. We show that the system exhibits a composition-driven transition from a phase, for low fluorination levels (x≤0.5), with Pnma symmetry and the usual system of octahedral tiltings, to a phase with space group Imma for higher fluorine contents, where a correlated distortion of the oxygen octahedra plays a significant role. The consistency of the structural models, with respect to the expected continuity of the amplitudes of the different distortion modes and the invariance of their internal form, was monitored through the symmetry mode decomposition of the structures