DNA barcoding is a relatively new method developed to provide rapid, accurate and automatable species identification using standardized DNA sequences as tags. Species identification in this way is usually achieved by the repossession of a... more
DNA barcoding is a relatively new method developed to provide rapid, accurate and automatable species identification using standardized DNA sequences as tags. Species identification in this way is usually achieved by the repossession of a short DNA sequence, the “barcode” from a standard part of the genome of a given species. An experiment was conducted to identify three species of genus Allium using five barcode regions including ndhJ, rpoC1, rpoB, YCF5 and rbcL. Results indicated that A. ampeloprasum persicum was the only identified species. Barcode region of YCF5 had the highest SRSP with 93.33%. The highest interspecific diversity and intraspecific divergence with 0.8% and 0.4% were observed in region of ndhJ which was the most sufficient barcode region for species identification.
DNA barcoding is a relatively new method developed to provide rapid, accurate and automatable species identification using standardized DNA sequences as tags. Species identification in this way is usually achieved by the repossession of a... more
DNA barcoding is a relatively new method developed to provide rapid, accurate and automatable species identification using standardized DNA sequences as tags. Species identification in this way is usually achieved by the repossession of a short DNA sequence, the "barcode" from a standard part of the genome of a given species. An experiment was conducted to identify three species of genus Allium using five barcode regions including ndhJ, rpoC1, rpoB, YCF5 and rbcL. Results indicated that A. ampeloprasum persicum was the only identified species. Barcode region of YCF5 had the highest SRSP with 93.33%. The highest interspecific diversity and intraspecific divergence with 0.8% and 0.4% were observed in region of ndhJ which was the most sufficient barcode region for species identification.
DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus... more
DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Secale. In this study the plant material consisted of 10 cultivated and non-cultivated species and subspecies of rye genus. Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions. Universal primers were used, and sequenced products were analyzed using Neighbor Joining and the Maximum Likelihood in the MEGA 7.1 program. We did not observe high variability in nucleotide sequences within the matK and rbcL regions. Only 2.2% of the sequences showed polymorphism in the rbcL region, while 6.5% in the matK region. The most variable trnH-psbA (15.6%) intergenic region was the most useful for rye barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of rye species and subspecies according to the adopted classification of the genus Secale. The results confirm that the use of matK and rbcL is insufficient for DNA barcoding in rye species, and better discrimination within the genus Secale can be obtained only in combination with the non-coding trnH-psbA sequence. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in Genbank.
Taxonomy represents the baseline for biological characterization and naming for endangered plant species. Phlomis aurea has never been a subject of comprehensive biosystematics assessment. Phlomis aurea is an endangered species suffering... more
Taxonomy represents the baseline for biological characterization and naming for endangered plant species. Phlomis aurea has never been a subject of comprehensive biosystematics assessment. Phlomis aurea is an endangered species suffering from global changes which lead to population decline. It is important to rediscover critical biological traits related to endemic species to help set up conservation plan(s). The current study represents a comprehensive morphological and anatomical characterization of the endangered Phlomis aurea endemic to Sinai Peninsula, Egypt. Phylogenetic placement and DNA barcoding were done using two molecular markers (rbcL and psb-A/trn-H).
Elaeocarpus blascoi Weibel. A relative species of Rudraksha, of Elaeocarpaceae is an endemic and endangered evergreen forest tree from Palni hills, Southern Western Ghats. In vitro regeneration protocol from nodal segments of E. blascoi... more
Elaeocarpus blascoi Weibel. A relative species of Rudraksha, of Elaeocarpaceae is an endemic and endangered evergreen forest tree from Palni hills, Southern Western Ghats. In vitro regeneration protocol from nodal segments of E. blascoi for clonal propagation was developed by employing different tissue culture media. Woody plant medium (WPM) was found to be suitable for E. blascoi shoot multiplication and regenerations. Phenolic secretion makes the explants recalcitrant and was overcome by supplement of 0. 3% charcoal / 0.5% polyvinylpyrrolidone (PVP). Nodal segments were cultured in WPM medium supplemented with cytokinins including Thidiazuron (TDZ), 6-Benzylaminopurine (BAP), and Kinetin (KIN). Among the three plant growth regulators, TDZ induced multiple shoots. Shoot elongation was achieved by addition of 10 mg/l silver nitrate in the shoot elongation medium, and an average of 6 ± 0.47 shoots are produced per explants. The regenerated micro shoots were subsequently rooted in half-strength WPM supplemented with 2 mg/l Indole-3 Butyric Acid (IBA). Thus the protocol developed is utilised for successful conservation of the IUCN red listed species E. blascoi.
This review revealed a new mechanism for gene regulation through “gene silencing” at the transcriptional level (TGS) or at the post -transcriptional level (PTGS), which play a key role in many essential cellular processes. Today dsRNA... more
This review revealed a new mechanism for gene regulation through
“gene silencing” at the transcriptional level (TGS) or at the post -transcriptional level (PTGS), which play a key role in many essential
cellular processes. Today dsRNA is used as a powerful tool to
experimentally elucidate the function of essentially any gene in a
cell. The immense impact of the discovery of RNA interference
(RNAi) on biomedical research and its novel medical applications in
the future are reviewed in this article, with particular stress on
therapeutic applications of radio -labeled antisense oligonucleotides
(RASONs) for diagnosis and treatment of various cancers and
neurodegenerative diseases by “gene silencing”. Antisense
oligonucleotides (ASONs) can also modulate alternative splicing
which 74% of all human genes undergo. Epigenetic changes affect
chromatin structure and thus regulate processes such as transcription,
X-chromosome inactivation, allele-specific expression of imprinted
genes, and inactivation of tumor suppressor genes. Treatment with
inhibitors of DNA methylation and histone deacetylation can
reactivate epigenetically silenced genes and has been shown to
restore normal gene function. In cancer cells, this results in
expression of tumor suppressor genes and other regulatory functions,
inducing growth arrest and apoptosis.
DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus... more
DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Secale. In this study the plant material consisted of 10 cultivated and non-cultivated species and subspecies of rye genus. Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions. Universal primers were used, and sequenced products were analyzed using Neighbor Joining and the Maximum Likelihood in the MEGA 7.1 program. We did not observe high variability in nucleotide sequences within the matK and rbcL regions. Only 2.2% of the sequences showed polymorphism in the rbcL region, while 6.5% in the matK region. The most variable trnH-psbA (15.6%) intergenic region was the most useful for rye barcoding. Individual application of the studied regions did not provide the expected results. None of the ...
Combretaceae is an angiosperm family of high economic value. However, there is dearth of information on the phylogenetic relationship of the members of this family using ribulose biphosphate carboxylase (rcbL) gene. Previous studies with... more
Combretaceae is an angiosperm family of high economic value. However, there is dearth of information on the phylogenetic relationship of the members of this family using ribulose biphosphate carboxylase (rcbL) gene. Previous studies with electrophoretic-based and morphological markers revealed that this family is phylogenetically complex. In the present study, 79 sequences of rbcL were used to study the phylogenetic relationship among the members of Combretaceae of African origin with a view to provide more information required for the utilization and management of this family. Multiple Sequence alignment was executed using the MUSCLE component of Molecular Evolutionary Genetics Version X Analysis (MEGA X). Transition/Transversion ratio, Consistency index, Retention Index and Composite Index were also determined. Phylogenetic trees were constructed using Maximum parsimony (MP) and Neighbor joining methods. The alignment of rcbL in the family Combretaceae shows 0.59 for both variation and parsimony sites with the overall mean distance of 0.71. Result shows that the genera Combretum, Terminalia are polyphyletic, while Conocarpus, Quisqualis and Meiostemon are monophyletic. Findings from this study can be applied to the scientific classification of the African Combretaceae, especially where morphological and electrophoretic-based molecular delimitation have failed. rbcL from this family can also be used as barcodes against drug adulteration of the medicinal species.
The nomenclature of Eucalyptus camaldulensis Dehnh. (Myrtaceae) has been muchdiscussed since modern studies suggested that Dehnhardt, the author of the species, employed this name for a plant different from that indicated today with this... more
The nomenclature of Eucalyptus camaldulensis Dehnh. (Myrtaceae) has been muchdiscussed since modern studies suggested that Dehnhardt, the author of the species, employed this name for a plant different from that indicated today with this named. A recent work carried out by a multidisciplinary approach based on examination of illustrations and herbaria specimens as well as on consultation of documents in historical archives, showed that Dehnhardt’s original description applies to the taxon currently indicated as E. camaldulensis subsp. camaldulensis. In order to support this previous conclusion, a DNA barcoding analysis was carried on both historical specimens and cultivated and wild material of E. camaldulensis. Results confirmed that there is no substantial taxonomical difference between the plant on which Dehnhardt established E. camaldulensis and the plants now indicated by this name.
There have been a wide variety of approaches for handling the pieces of DNA as the "unplugged" tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based... more
There have been a wide variety of approaches for handling the pieces of DNA as the "unplugged" tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given "passwords" and/or secret numbers using DNA sequences. The "passwords" of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the non-coding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original "passwords." The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the chains. Lastly, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed.
Direct somatic embryogenesis from in vitro-cultured leaf segments of multiple disease-resistant pepper, Piper colubrinum Link is reported. Somatic embryos were initiated on Murashige and Skoog's (1962) basal medium containing 2.2 μM... more
Direct somatic embryogenesis from in vitro-cultured leaf segments of multiple disease-resistant pepper, Piper colubrinum Link is reported. Somatic embryos were initiated on Murashige and Skoog's (1962) basal medium containing 2.2 μM benzyladenine+0.46 μM kinetin and multiplied profusely through secondary embryogenesis on the same medium. Some 91% somatic embryos converted into plantlets on MS medium supplemented with 4.4 μM benzyladenine+0.23 μM kinetin and plantlets developed on half-strength MS+2.4 μM indole-3-butyric acid. Plantlets were hardened, transferred to soil, and 100% of plants survived. Various developmental stages of somatic embryogenesis were studied using histological methods.
Background: Memecylon species are commonly used in Indian ethnomedical practices. The accurate identification 20 is vital to enhance the drug's efficacy and biosafety. In the present study, PCR based techniques like RAPD, ISSR 21 and DNA... more
Background: Memecylon species are commonly used in Indian ethnomedical practices. The accurate identification 20 is vital to enhance the drug's efficacy and biosafety. In the present study, PCR based techniques like RAPD, ISSR 21 and DNA barcoding regions, such as 5s, psbA-trnH, rpoC1, ndh and atpF-atpH, were used to authenticate and 22 analyze the diversity of five Memecylon species collected from Western Ghats of India. 23 Results: Phylogenetic analysis clearly distinguished Memecylon malabaricum from Memecylon wightii and 24 Memecylon umbellatum from Memecylon edule and clades formed are in accordance with morphological keys. 25 In the RAPD and ISSR analyses, 27 accessions representing five Memecylon species were distinctly separated 26 into three different clades. M. malabaricum and M. wightii grouped together and M. umbellatum, M. edule and 27 Memecylon talbotianum grouped in the same clade with high Jaccard dissimilarity coefficient and bootstrap 28 support between each node, indicating that these grouped species are phylogenetically similar. 29 Conclusion: Data from the present study reveals that chloroplast psbA-trnH region could be used as a potential 30 candidate region for identifying Memecylon species, and ISSR marker system could be used for estimating 31 genetic diversity since it has high percent polymorphism compared to RAPD marker.
Herbal plants play a major role in the development of modern civilization. Justicia gendarussa is an interesting example for traditional plant with medicinal values and have been proved by many research works. The present study which is... more
Herbal plants play a major role in the development of modern civilization. Justicia gendarussa is an interesting example for traditional plant with medicinal values and have been proved by many research works. The present study which is focused on the Molecular characterization for the plant Justicia Gendarussa using Matk gene shows that the DNA isolated from was isolated from Justicia gendarussa has purity of purity 1.8. The purified DNA obtained was amplified using a matK primer. The amplified product of matK gene was found in the region of 750 – 1000 base pairs corresponding to the ladder. The PCR product using two sets of reverse primers were obtained and the result showed that reverse 1 primer was able to amplify the CO I gene better than reverse 2 primer. This plant is found to have a broad spectrum of activities due to the presence of active constituents like alkaloids, flavus compounds, phenolic compounds, steroids, carbohydrate, carotenoids and terpenoids. Various studies e...
Sapindaceae Jussieu is a family of flowering plants in the Order Sapindales. Members of the family exist as trees and shrubs, and tendril-bearing vines with about 140-150 genera and 1400-2000 species worldwide. They are economically,... more
Sapindaceae Jussieu is a family of flowering plants in the Order Sapindales. Members of the family exist as trees and shrubs, and tendril-bearing vines with about 140-150 genera and 1400-2000 species worldwide. They are economically, medicinally and aesthetically useful. This research aimed at exploring the diversity of Sapindaceae in West and Central Africa with particular emphasis on identification of the plant samples as well as generation of DNA barcodes with a view to sharing the DNA barcode sequence(s) in a public database. These were achieved following standard protocols. Extracted DNA samples (119) were deposited at the DNA Bank of the Royal Botanic Gardens, Kew, Richmond and voucher specmens were deposited at the University of Lagos Herbarium, Lagos, Nigeria. Silica gel dried specimens yielded good quality DNA unlike the old dried herbarium leaf samples. DNA samples were sent to International Barcode of Life (IBOL) Centre in Guelph, Canada for analysis of the barcode region and sixty-nine (69) DNA barcodes were generated. Barcode data which was hinged on matK and rbcL sequence data have been deposited at the Barcode of Life database (BOLD) website and GenBank for public use. This research therefore forms a basis for further taxonomic work on the family Sapindaceae especially in Africa. ABSTRACT 391
El Ecuador es un país considerado megabiodiverso por su alta riqueza de especies en varios grupos biológicos; sin embargo, aún se desconoce el número total de estas especies, en parte debido a la falta de fondos de investigación,... more
El Ecuador es un país considerado megabiodiverso por su alta riqueza de especies en varios grupos biológicos; sin embargo, aún se desconoce el número total de estas especies, en parte debido a la falta de fondos de investigación, complejidad taxonómica de algunos grupos y el relativo aislamiento del país en relación a iniciativas científicas mundiales. Solamente la creación de un sistema de identificación de especies que incluya las características del espécimen voucher, muestras de tejidos y la secuencia de Barcodes permitiría llegar a determinar la verdadera riqueza biológica del Ecuador. El presente trabajo aborda algunos aspectos sobre la iniciativa mundial del «Código de Barras del ADN», se hace hincapié en sus potenciales aplicaciones en torno a la investigación para la conservación de la diversidad biológica del Ecuador. Esta iniciativa propone emplear información dentro de una misma región génica (gen mitocondrial del Citocromo c Oxidasa I = COI), en todas las especies vivientes y con condiciones de secuenciación universalmente aceptadas y estandarizadas. Esta herramienta científica no pretende sustituir la taxonomía alfa y la filogenia, sino más bien agilizar las tareas de identificación, especialmente en el campo de la Biomedicina (identificación de patógenos, parásitos y vectores), el control de plagas (cualquiera sea su estado de desarrollo ontogenético), detección de especies invasivas, estudios sobre conservación de la biodiversidad y sanción de delitos ambientales. La integración del «Código de barras del ADN», el trabajo de campo, las colecciones de museos y la investigación científica resultan imprescindibles para que esta herramienta redunde en avances significativos en la generación de bioconocimiento en el Ecuador
DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a... more
DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions ( atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL + matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
Herbal plants play a major role in the development of modern civilization. Justicia gendarussa is an interesting example for traditional plant with medicinal values and have been proved by many research works. The present study which is... more
Herbal plants play a major role in the development of modern civilization. Justicia gendarussa is an interesting example for traditional plant with medicinal values and have been proved by many research works. The present study which is focused on the Molecular characterization for the plant Justicia Gendarussa using Matk gene shows that the DNA isolated from was isolated from Justicia gendarussa has purity of purity 1.8. The purified DNA obtained was amplified using a matK primer. The amplified product of matK gene was found in the region of 750 – 1000 base pairs corresponding to the ladder. The PCR product using two sets of reverse primers were obtained and the result showed that reverse 1 primer was able to amplify the CO I gene better than reverse 2 primer. This plant is found to have a broad spectrum of activities due to the presence of active constituents like alkaloids, flavus compounds, phenolic compounds, steroids, carbohydrate, carotenoids and terpenoids. Various studies explored this plant has various pharmacological actions like antioxidant, analgesic, anti-inflammatory, anti-anxiety, antiangiogenic, antiarthritic, prevent damage to the liver, anticancer, active against bacteria, destroying fungi and anthelmintic. The study on the mechanism of action of this plant leaves could be useful for the development of commercial drugs.
Ethnopharmacology relevance: Galphimia glauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses. Aim of the study:... more
Ethnopharmacology relevance: Galphimia glauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses. Aim of the study: The aim of this investigation is to find out if populations of Galphimia glauca collected in different regions and ecosystems in Mexico actually belong to the same species by using the contemporary technique of DNA barcodes. Our previous metabolic profiling study demonstrates that different collections of this plant obtained from various geographical areas exhibited diverse chemical profiles in terms of the active compounds named Galphimines. We expected the DNA barcodes apart from indicating the different species of Galphimia would indicate the active populations. Materials and methods: We employed matK, rpoC1 and rbcL DNA barcodes to indicate the different species. Furthermore to investigate the possible impact of the several different ecosystems where the seven populations were collected, thin layer chromatography was employed to create a partial chemical profile, which was then compared with the metabolic profiles obtained by 1 H-NMR and multivariate data analysis. Results and conclusions: This study showed that the seven populations here analyzed contain at least three different species of the genus Galphimia, although each individual population is homogeneous. Interestingly our TLC analysis clearly showed that the active populations displayed a distinctively unique chemical profile. This work also showed that the use of DNA barcodes combined with chemical profile analysis is an excellent approach to solve the problems of quality control in the development of Galphimia-based medicines as well as for any breeding programs for this species.
The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that... more
The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region - ITS) in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122), followed by trnH-psbA (0.019), matK (0.008) and rbcL (0.002). For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest.
Low rates of shoot multiplication, clonal instability, poor rooting frequency and high cost of production are major impediments challenging the micropropagation of orchids and other ornamental plants. These problems can be solved with the... more
Low rates of shoot multiplication, clonal instability, poor rooting frequency and high cost of production are major impediments challenging the micropropagation of orchids and other ornamental plants. These problems can be solved with the proper usage of plant growth regulators (PGRs) in the medium. The highest shoot proliferation rate of 21 shoots/explant was recorded in Murashige and Skoog (MS) medium containing 1 mg/l meta-topolin and 0.8mg/l Putrescine. Till date, this is the best frequency of shoot induction for D. nobile and one of the highest amongst other orchids. Higher rooting frequency was also recorded with the highest rooting of 10.1 roots/shoot achieved in plants grown in half strength MS media supplemented with 2mg/l of indole butyric acid and 0.5mg/l of phloroglucinol. The plantlets were successfully acclimatized in the greenhouse with a survival rate of 82.3% exhibiting normal developmental patterns. The regenerated plantlets were assessed for genetic stability using the molecular markers namely SCoT and IRAP revealing high degree of genetic stability within the micropropagated plants of D. nobile. Being a highly medicinal orchid, the antioxidant potentials of the mother and the micropropagated plants were assessed using DPPH, FRAP and Metal chelating assays which revealed a significantly higher antioxidant activity in the micropropagated plants. Rapid multiplication rate, higher genetic stability and significantly higher antioxidant power reported in the present study on D. nobile ensure the use of this micropropagation protocol for ex-situ conservation and commercial exploitation which could also be extended to other important orchid species.
