Search

Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

Medicinal plants are used in traditional medicine since the prehistoric period. They are considered a rich resource for developing single drugs and formulations due to a wide variety of bioactive phytochemicals present. Bitter gourd (Momordica charantia L.) is an important tropical and subtropical medicinal plant commonly cultivated in Asian and African countries for its health and nutritional properties. The bitter gourd fruits possess antidiabetic, anticancer, anti-obesity, antimicrobial, antioxidant, anti-inflammatory, anti-helminthic, and anti-HIV properties. In this study, we extracted the phytochemicals from the rind, pulp, and seeds of the two botanical varieties of bitter gourd, Momordica charantia var. charantia and Momordica charantia var. muricata in methanol, and subjected them to gas chromatography-mass spectrometry (GC-MS) analysis. Phytochemical analysis revealed several important bioactive compounds such as n-Hexadecanoic acid, Linolenic acid, Vitamin E, Sitosterol, Stigmasterol, and Phytol. Biological activities were reported for some of these compounds. Identification of these compounds validates the medicinal value of bitter gourd. Further studies are to be carried out to isolate, characterize, and study the individual compound's mechanism of action.

The predicted increase in global mean temperature and its variability is a significant challenge for sustainable crop productivity under current and future climates. Research on understanding heat stress responses, identifying physiological processes, developing phenotyping protocols and unraveling molecular pathways that can help breed heat stress resilient crops is prominent in the crop science community. Research teams and laboratories contributing to this special issue title ‘Heat Stress on Crop Growth and Development’ have consolidated information on multiple dimensions of heat stress. The collection of reviews and research papers provides an excellent platform for developing future research objectives and is a valuable reference for students and researchers working on the heat stress response in crops.

Andrographolide and related compounds are effective against several viral diseases, including dengue, COVID-19, influenza, and chikungunya. Andrographis paniculata is the primary source for these compounds, but its availability is limited. A. alata is a potential alternative source, and neoandrographolide (NAG) is the major antiviral compound in this species. Since molecular studies in A. alata are scarce, we sequenced its leaf transcriptome to identify the full-length genes involved in neoandrographolide biosynthesis. We assembled 13.6 Gb RNA-Seq data and generated 81,361 transcripts with 1007 bp average length and 1,810 bp N50. The transcripts were categorized under biological processes (2,707), cellular components (678), and molecular functions (2,036). KEGG analysis mapped 975 transcripts to the secondary metabolite pathways. Among the 420 transcripts mapped to terpenoids and polyketides pathways, 142 transcripts were related to the biosynthesis of andrographolide and its derivatives. After a detailed analysis of these transcripts, we identified 32 full-length genes coding for all the 22 enzymes needed for andrographolide biosynthesis. Among them, 15 full-length genes were identified for the first time from Andrographis species. These full-length genes and the transcripts shall serve as an invaluable resource for the metabolic engineering of andrographolides and neoandrographolide in Andrographis and other species.

Ocimum tenuiflorum L. subtype Rama Tulsi is an important aromatic perennial herb. It belongs to the family of Lamiaceae. In this study, the complete chloroplast genome sequence of O. tenuiflorum subtype Rama Tulsi was assembled and annotated using Illumina paired-end sequencing data. The length of the complete circular chloroplast genome was 151,722 bp. It comprises an inverted repeat (IR) region with a repeat length of 25,677 bp, a large single-copy (LSC) region of 82,781 bp, and a small single-copy (SSC) region of 17,587 bp. The GC content of complete chloroplast genome, LSC, SSC, IR regions is 37.9%, 36.0%, 31.8%, and 43.1%, respectively. The chloroplast genome contains 134 genes, including 88 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis with the complete chloroplast genomes of other related species revealed that the O. tenuiflorum L. subtype Rama Tulsi is fully resolved in a clade with other Ocimum species classified under the Lamiaceae family.

As in many other countries, the field of genetic counseling is in its initial stages of development in India, where there are efforts to streamline the profession and to implement graduate-level training programs. We implemented an elective course on genetic counseling at the undergraduate level in a private university in India to assess students' interest, to provide early exposure for students interested in pursuing the career, and to aid recruitment. To assess satisfaction with the course and recruitment outcomes, we sent a course evaluation survey to 332 students and received 134 responses. Familiarity with genetic counseling topics increased significantly after completing the course. Of the 42 respondents who reported they were planning to pursue formal genetic counseling training, 21% (n = 9/42) became interested in the profession as a result of taking this course. Survey respondents who were prospective applicants to genetic counseling training programs referred mostly to the websites of the National Society of Genetic Counselors and the American Board of Genetic Counseling for information on genetic counseling and training. Barriers to entry into the field included lack of shadowing opportunities, inadequate coursework, and limited opportunities to interact with practicing genetic counselors. Respondents stated that additional case studies as well as observation of patient interactions would elucidate the role of a genetic counselor and help define the scope of the practice in India and other countries. Overall, genetic counseling education at the undergraduate level is a scalable way to improve understanding of genetic counseling topics, increase professional interest in the field, and support workforce development.

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide., Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide.

Ocimum gratissimum L. is an important medicinal species with several therapeutic applications. It is used in traditional medicine as a single drug and in formulations. We generated the complete chl...

Exposure to poisonous plants is hazardous to health; thus, reliable species identification is required to decide the most appropriate treatment. Since ingested plants are too much degraded for visual observation, DNA barcoding can be used as a molecular tool for species identification. Considering the universal primers, PCR and sequencing success rate, and diversity of the poisonous plants, the rbcL DNA marker was selected for molecular identification. A reference DNA barcode library for 100 poisonous plant species was created using rbcL DNA barcodes. For the poisonous plants represented in the library, 100% and 89% species differentiation was observed at the genus and species level, respectively. All the undifferentiated species were congeneric species. Mapping the metabolites of the poisonous plants to the DNA based phylogenetic tree indicated that the phylogenetically related species also had related toxic compounds. Therefore, genus-level identification may be sufficient in the practical application of DNA barcoding in poisoning cases. We conclude that rbcL can be used as a primary marker, and if required, ITS2 or trnH-psbA may be used as a secondary marker to identify the poisonous plants. The present study provides the foundation to develop a reliable molecular method to identify the poisonous species from the vomit samples of poisoning cases.

Summary The current pandemic of severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) has quickly emerged as a global health concern with government bodies worldwide taking drastic control measures. Understanding the virology of SARS‐CoV‐2, its molecular mechanisms, and its pathogenesis are required for a targeted therapeutic approach. In this review, we highlight the current molecular and drug advances that target SARS‐CoV‐2 at the genome level. We also summarize studies that therapeutically target the host angiotensin‐converting enzyme 2 and proteases. Finally, we summarize antibody‐mediated therapeutic approaches, as well as recent trends in vaccine development. Hence, the purpose of this study is to investigate different molecular targets in SARS‐CoV‐2 pathogenesis and their usefulness in developing strategies for drug development.

Plant-derived compounds are used to manage dyslipidemia and oxidative stress in type 2 diabetic condition. In this study, anti-lipidemic and antioxidant properties of the protein extracts from "Charantia" (PEC) and "Muricata" (PEM) varieties of Momordica charantia were analyzed by quantifying lipids, hepatic, renal, and oxidative stress markers, and histopathological examination of liver and kidney tissues. Protein extracts were orally administered at 10 (PEC10, PEM10) or 20 mg/kg body weight (PEC20, PEM20). Levels of cholesterol, low-density lipoprotein, and triglycerides decreased but high-density lipoprotein increased significantly in treated rats as compared to untreated diabetic rats (p < .01), and attained normal physiological range in both doses. Levels of superoxide dismutase, catalase, glutathione peroxidase, and reduced glutathione increased but thiobarbituric acid reactive substances decreased significantly in treated rats as compared to untreated diabetic rats (p < .01), and attained normal physiological range in PEM20 only. Histopathological examinations supported a protective role for the protein extracts against oxidative stress. PRACTICAL APPLICATIONS: Momordica charantia, a well-known medicinal plant is traditionally used for treating diabetes in India as well as other countries. The whole plant was shown to have medicinal importance. Anti-diabetic potential of this plant was scientifically established largely using organic extracts and water extract mainly from the fruits of this plant. However, protein extracts from the seeds and fruit pulp of this plant were also proven to have anti-diabetic activity. The present study illustrates the anti-lipidemic and antioxidant effect of protein extracts from the fruit pulp of two varieties of M. charantia (Charantia and Muricata) in Streptozotocin-induced type 2 diabetic rats. This study provides experimental evidence in support of its use in the management of type 2 diabetes-related complications.

ITS2 marker is highly efficient in species discrimination but its application in DNA barcoding is limited due to huge variations in the PCR success rate. We have hypothesized that higher GC content and the resultant secondary structures formed during annealing might hinder the PCR amplification of ITS2. To test this hypothesis, we selected 12 species from 12 different families in which ITS2 was not amplified under standard PCR reaction conditions. In these samples, DMSO, formamide, betaine, and 7-deaza-dGTP were evaluated for their ability to improve the PCR success rate. The highest PCR success rate (91.6%) was observed with 5% DMSO, followed by 1 M betaine (75%), 50 μM 7-deaza-dGTP (33.3%), and 3% formamide (16.6%). The one sample that did not amplify with DMSO was amplified by adding 1 M betaine. However, combining DMSO and betaine in the same reaction did not improve the PCR. Therefore, to achieve the highest PCR success rate for ITS2, it is recommended to include 5% DMSO by default and substitute it with 1 M betaine only in the case of failed reactions. When this strategy was tested in 50 species from 43 genera and 29 families, the PCR success rate of ITS2 increased from 42% to 100%.

Additional file of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

Additional file 2:Reference mapping statistics. Reference assembly with the partial genomic sequence of jatropha showed mapping of 95.87% of the reads and consensus accuracy was 99.15%. (DOC 32 KB)

Background and objectives To analyse the audiometric profile and the pedigree of a large family with otosclerosis to understand the inheritance pattern and its implication in clinical management of the disease. Subjects and. Methods Pedigree analysis was performed on the basis of family history and audiometric tests. Pure tone audiometry, tympanometry, and acoustic reflexes were evaluated for the family members. Audiometric analysis was also carried out for the individuals who have already underwent corrective surgery at the time of study. Results Out of 112 family members, 17 were affected individuals, and 11 of them were surgically confirmed. Hearing loss (HL) started unilaterally and progressed to bilateral form. Otosclerosis was presented in early 20's in the first and second generations but it was delayed to mid-late 30's in the fourth generation. An affected female was diagnosed with otosclerosis during her pregnancy. Though the disease was familial, a mother of four affected offspring in this family did not develop otosclerosis until she died at the age of 84. Conclusions The five-generation family, which was analysed in the present study, exhibited autosomal dominant inheritance of otosclerosis with reduced penetrance. Bilateral HL and pregnancy-aggravated otosclerosis were observed in this family. It was found for the first time that the age of onset of the disease delayed in the successive generations. The current study indicated the importance of detailed pedigree analysis for better clinical management of otosclerosis.

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

The genus Melia L., which belongs to the “Mahogany” family Meliaceae, is a source of important phytochemicals with marked medicinal properties. Species identification in Melia is complex due to the existence of overlapping morphological features. Although Melia dubia Cav. is listed as a synonym of Melia azedarach L., it is not clear from the available literature whether they are the same species or different, and the species complexity still remains unresolved. In the present study, 10 accessions of M. dubia and M. azedarach were analysed by DNA barcoding using three chloroplast DNA markers (rbcL, matK, and trnH–psbA), and one nuclear marker (ITS2). Intraspecific divergence was not found in any of the four markers. However, the interspecific divergence between M. azedarach and M. dubia ranged between 0.3% (rbcL) and 4.7% (ITS2) for individual markers, and for the combined dataset, it was 8.5%. Among the four markers, ITS2 was found to be the most suitable marker for differentiating M. azedarach and M. dubia. Parsimony analysis of the DNA barcoding data showed a clear segregation between M. azedarach and M. dubia as distinct monophyletic clades in all the markers, except the rbcL marker. Our results based on Bayesian analysis of the concatenated dataset strongly support the view that M. dubia be considered a distinct species; not a synonym of M. azedarach.

Background & objectives: New Delhi metallo-β-lactamase 1 (NDM-1) cleaves the beta-lactam ring, and confers bacterial resistance against most of the beta-lactam antibiotics, except tigecycline and colistin. Among these two antibiotics, colistin is considered toxic, and therefore, its clinical use and dosage need cautious approach. In the present study, six organic acids were screened individually and in combination of two acids for their effectiveness against NDM-1 Escherichia coli and a combination of colistin and oxalic or succinic acid was tested to find out the potential of combination therapy for reducing the dose of toxic colistin. Methods: Antibacterial activity of the organic acid and their combinations was tested by disc diffusion method against NDM-1 E. coli, and minimum inhibitory concentration (MIC) was determined by broth dilution method. Synergistic effect between organic acids and colistin was tested by checkerboard method. Results: Oxalic acid showed the highest zone of inhibition (15±1 mm) followed by succinic acid, tartaric acid, fumaric acid, citric acid and malic acid. The combination of two acids did not increase the zone of inhibition significantly. MIC was found to be the lowest with oxalic acid and succinic acid (320 μg/ml). In the presence of 160 μg/ml oxalic acid or succinic acid, MIC of colistin was reduced from 8 to 4 μg/ml, indicating synergistic effect. Interpretation & conclusions: Our findings showed that combination therapy using colistin and oxalic acid or succinic acid might find safe clinical application of this antibiotic in controlling infections due to NDM-1 bacteria.

Streptozotocin-induced diabetic rats were orally treated with protein extract from Momordica dioica fruit pulp for 30 days. Treated rats showed reduced blood glucose levels, greater oral carbohydrate tolerance, and ameliorated weight loss. Glucose, urea, triglycerides, cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase levels were significantly decreased, while high-density lipoprotein levels were significantly increased in treated diabetic rats, compared to untreated diabetic rats (P

Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.

The genus Terminalia L. belongs to the Combretaceae family, which includes several medicinal and threatened species with high trade value. Species of Terminalia in India belong to four sections and species identification within the sections is considered to be complex due to the lack of sufficient taxonomical characters and the existence of morphotypes. Therefore, we tested the effectiveness of three chloroplast DNA barcodes ( rbcL , matK , and trnH - psbA ) and a nuclear DNA barcode (ITS2) for the discrimination of Terminalia species. A reference DNA barcode library consisting of 120 DNA barcodes from ten species of Terminalia was created. Intra-specific divergence was not observed among the accessions for any marker. Inter-specific divergence was highest in trnH - psbA (10.6%), followed by ITS2, matK and rbcL markers. The success of species differentiation by DNA barcodes was 100% with trnH - psbA , 80% with matK and ITS2, and 10% with rbcL . In the phylogenetic trees, the rbcL marker did not differentiate the species in any section. Two species from the section Catappa were not differentiated by matK and ITS2 markers. Only trnH - psbA resolved all the species and ranked the best among four markers for species identification. However, regarding species relationship studies, ITS2 was found to be better than other markers because it formed a separate clade for each section.

Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.

Nanoengineered biomaterials have dramatically expanded the range of tools used for infection control and to accelerate wound healing. This review thoroughly describes the developments that are shaping this emerging field and evaluates the potential wound healing applications of recently developed engineered nanomaterials for both acute and chronic wounds. Specifically, we will assess the unique characteristics of engineered nanomaterials that render them applicable for wound healing and infection control. A range of engineered nanomaterials, including polymeric-, metallic- and ceramic-based nanomaterials, that could be used as therapeutic delivery agents to accelerate regeneration of damaged dermal and epidermal tissues are also detailed. Finally, we will detail the current state of engineered nanomaterials for wound regeneration and will identify promising new research directions in infection control.

Ethnopharmacological relevance Ashwagandha, also known as Indian Ginseng, is a highly traded medicinal plant, which is used in Ayurveda, Siddha and Unani systems of medicine to improve cognitive function, decrease inflammation, and to counter the ill-effects of aging. Withanolide A and Withaferin A from Ashwagandha were shown to improve immunity and have anti-cancer property, respectively. Aim of the study Here, we aimed to create reference DNA barcodes for W. somnifera and to authenticate root and powder samples of Ashwagandha collected from markets. Materials and methods Three plant specimen of W. somnifera were collected, and reference DNA barcodes were generated using rbcL, matK, trnH-psbA, and ITS2 DNA barcode markers. Market samples in the form of root (n = 33) and powder (n = 70) were collected and authenticated using ITS2 and trnH-psbA DNA barcodes. Results Genomic DNA was successfully isolated from all plant specimens and market samples. DNA barcoding showed that 77% of samples were authentic. About 22% of non-authentic samples were powder samples and only 1% were root samples. Among the non-authentic samples, 18% were completely substituted with single species (Mucuna pruriens (L.) DC., Trigonella foenum-graceum L., or Senna auriculata (L.) Roxb.) and 82% were mixed samples containing more than one species. About 63% of the mixed samples contained Ashwagandha as the major ingredient. Furthermore, we identified that six taxonomically divergent plant species from four families were present as adulterants in the mixed samples. Conclusion DNA barcoding revealed that botanical adulteration in the market samples of Ashwagandha is significant. Powder samples are more prone to adulteration than root samples. The adulterated samples contained plant material that is not related to Ashwagandha, which warrants strict quantity control and market surveillance to derive the true medicinal benefits of this medicinal plant.