Quality evaluation of different black rice varieties of northeastern region of India.

INTRODUCTION: Black rice (Oryza sativa L.), which is rich in polyphenols and flavonoids, is indigenous to Northeast India, specifically Manipur, and traditionally consumed for its protective effects on human health. Due to its economic value, it is crucial to evaluate the quality of different black rice varieties to authenticate their therapeutic and nutritional properties. OBJECTIVE: We aimed to evaluate the quality of pre- and post-marketed black rice samples by a validated high-performance thin layer chromatography method and determine variations of total phenolics and total flavonoids with antioxidant potential. MATERIAL AND METHODS: The ferulic acid, gallic acid, quercetin, and caffeic acid contents of three black rice varieties-Poireiton, Amubi, and Sempak-along with two marketed samples of Amubi from Manipur, India, were quantified based on standards. Antioxidant potential was measured by the 2,2-diphenyl-1-picryl-hydrazyl hydrate free radical scavenging assay. RESULTS: The highest and lowest relative biomarker contents were found in hydroalcoholic extracts of Amubi [caffeic acid (1.43% w/w), ferulic acid (1.15% w/w), quercetin (0.6% w/w), and gallic acid (0.39% w/w)] and the marketed sample Var. Amubi from Kakching District, respectively. Pearson's correlation coefficient of antioxidant potential with phenolic and flavonoid content showed a moderate to strong correlation for all samples. CONCLUSION: This validated, rapid, accurate standardization method for black rice varieties will be beneficial for the quality evaluation of black rice and its derived products. It will also be helpful to authenticate the nutritional benefits for the consumers.

Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species.

BACKGROUND: Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions. RESULTS: A large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants. CONCLUSIONS: We reveal P. sikkimensis's capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers.

BACKGROUND: The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. RESULTS: One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. CONCLUSIONS: The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.

Cochliobolus lunatus down-regulates proteome at late stage of colonization and transiently alters StNPR1 expression in Solanum tuberosum L.

Cochliobolus lunatus abundantly produces four-celled conidia at high temperatures (>30 °C) and under suitable conditions; the fungus colonizes potato (Solanum tuberosum L.) cultivars by adopting different invasion strategies at the microscopic level. Long-lasting defence during infection requires an upsurge in proteome changes particularly pathogenesis-related proteins chiefly under the control of nonexpresser of pathogenesis-related proteins. In order to gain molecular insights, we profiled the changes in proteome and potato nonexpresser of pathogenesis-related proteins (StNPR1) during the infection process. It is found that C. lunatus significantly (P < 0.05) suppressed the host functional proteome by 96 h after infection (hai), principally, affecting the expression of ribulose bisphosphate carboxylase enzyme, plastidic aldolase enzyme, alcohol dehydrogenase 2 and photosystem II protein prior to the formation of brown-to-black leaf spot disease. Strongest host response was observed at 24 hai hallmarked by 307 differentially expressed peptide spots concurring with the active phase of production of penetrating hyphae. Additionally, C. lunatus differentially down-regulated StNPR1 transcript by 8.19 fold by 24 hai. This study is the first to elucidate that C. lunatus transiently down-regulates the expression of StNPR1 at the onset of infection, and as a whole, infection negatively affects the expression of proteome components involved in photosynthesis, carbon fixation and light assimilation. This study contributes towards better understanding of the mechanism underlining the invasion strategies of C. lunatus.

Secretome weaponries of Cochliobolus lunatus interacting with potato leaf at different temperature regimes reveal a CL[xxxx]LHM - motif.

BACKGROUND: Plant and animal pathogenic fungus Cochliobolus lunatus cause great economic damages worldwide every year. C. lunatus displays an increased temperature dependent-virulence to a wide range of hosts. Nonetheless, this phenomenon is poorly understood due to lack of insights on the coordinated secretome weaponries produced by C. lunatus under heat-stress conditions on putative hosts. To understand the mechanism better, we dissected the secretome of C. lunatus interacting with potato (Solanum tuberosum L.) leaf at different temperature regimes. RESULTS: C. lunatus produced melanized colonizing hyphae in and on potato leaf, finely modulated the ambient pH as a function of temperature and secreted diverse set of proteins. Using two dimensional gel electrophoresis (2-D) and mass spectrometry (MS) technology, we observed discrete secretomes at 20°C, 28°C and 38°C. A total of 21 differentially expressed peptide spots and 10 unique peptide spots (that did not align on the gels) matched with 28 unique protein models predicted from C. lunatus m118 v.2 genome peptides. Furthermore, C. lunatus secreted peptides via classical and non-classical pathways related to virulence, proteolysis, nucleic acid metabolism, carbohydrate metabolism, heat stress, signal trafficking and some with unidentified catalytic domains. CONCLUSIONS: We have identified a set of 5 soluble candidate effectors of unknown function from C. lunatus secretome weaponries against potato crop at different temperature regimes. Our findings demonstrate that C. lunatus has a repertoire of signature secretome which mediates thermo-pathogenicity and share a leucine rich "CL[xxxx]LHM"-motif. Considering the rapidly evolving temperature dependent-virulence and host diversity of C. lunatus, this data will be useful for designing new protection strategies.

2-Cys peroxiredoxin responds to low temperature and other cues in Caragana jubata, a plant species of cold desert of Himalaya.

A 2-Cys peroxiredoxin cDNA (CjPrx) was isolated and characterized from Caragana jubata, a temperate/alpine plant species of high altitude cold desert of Himalaya and Eurasia. The cDNA obtained was 1,064 bp long consisting of an open reading frame of 789 bp encoding 262 amino acids. The calculated molecular mass of the mature protein was 28.88 kDa and pI was 5.84. Deduced amino acid sequence of CjPrx shared a high degree homology with 2-CysPrx proteins from other plants. CjPrx had both the PRX_type 2-Cys domain and thioredoxin-like superfamily domains. CjPrx contained 26.72% α-helices, 6.87% ß-turns, 20.61% extended strands and 45.80% random coils, and was a hydrophilic protein. Expression of CjPrx was modulated by low temperature, methyl jasmonate (MJ), salicylic acid and drought stress, but no significant change was observed in response to abscisic acid treatment. Among all the treatments, a strong up-regulation of CjPrx was observed in response to MJ treatment.

Bioeconomy and ethnopharmacology - Translational perspective and sustainability of the bioresources of northeast region of India.

ETHNOPHARMACOLOGICAL RELEVANCE: The ecological environment of Northeast region of India (NER), with its high humidity, has resulted in greater speciation and genetic diversity of plant, animal, and microbial species. This region is not only rich in ethnic and cultural diversity, but it is also a major biodiversity hotspot. The sustainable use of these bioresources can contribute to the region's bioeconomic development. AIM OF THE STUDY: The review aimed to deliver various perspectives on the development of bioeconomy from NER bioresources under the tenets of sustainable utilization and socioeconomic expansion. MATERIALS AND METHODS: Relevant information related to prospects of the approaches and techniques pertaining to the sustainable use of ethnomedicine resources for the growth of the bioeconomy were retrieved from PubMed, ScienceDirect, Google Scholar, Scopus, and Springer from 1984 to 2023. All the appropriate abstracts, full-text articles and various book chapters on bioeconomy and ethnopharmacology were conferred. RESULT: As the population grows, so does the demand for basic necessities such as food, health, and energy resources, where insufficient resource utilization and unsustainable pattern of material consumption cause impediments to economic development. On the other hand, the bioeconomy concept leads to "the production of renewable biological resources and the conversion of these resources and waste streams into value-added products. CONCLUSIONS: In this context, major emphasis should be placed on strengthening the economy's backbone in order to ensure sustainable use of these resources and livelihood security; in other words, it can boost the bio-economy by empowering the local people in general.

Identification and expression analysis of CjLTI, a novel low temperature responsive gene from Caragana jubata.

Using rapid amplification of cDNA ends, a full length cDNA (CjLTI) was cloned from apical buds of Caragana jubata, a plant species that grows under extreme cold. The cDNA obtained was 573 bp long consisting of an open reading frame of 351 bp encoding 116 amino acids. Homology analysis did not exhibit significant similarity with any sequence at NCBI database, therefore it was deduced as a novel gene. Secondary structure analysis suggested that the deduced CjLTI contained 25.86% α-helices, 4.31% ß-turns, 6.90% extended strands, and 62.93% random coils. The hydropathy profile suggested CjLTI to be a hydrophobic protein having characteristic features of signal peptides at N-terminus. The gene exhibited down-regulation at 5 min of exposure to low temperature (LT, 4 ± 3 °C) followed by a strong up-regulation after 15 min and onwards. Methyl jasmonate (MJ) lead to up-regulation of CjLTI starting at 5 min onwards. The gene exhibited up- and down-regulation of expression pattern in response to abscisic acid (ABA) and salicylic acid (SA). Mild drought stress slightly up-regulated gene expression and at severe drought (up to 115% reduction in leaf water potential) slight down-regulation of gene expression was observed. These results suggested CjLTI to be a LT responsive gene wherein MJ, ABA and SA pathways might be involved in regulating the gene expression.

Role of medicinal plants in inhibiting SARS-CoV-2 and in the management of post-COVID-19 complications.

BACKGROUND: The worldwide corona virus disease outbreak, generally known as COVID-19 pandemic outbreak resulted in a major health crisis globally. The morbidity and transmission modality of COVID-19 appear more severe and uncontrollable. The respiratory failure and following cardiovascular complications are the main pathophysiology of this deadly disease. Several therapeutic strategies are put forward for the development of safe and effective treatment against SARS-CoV-2 virus from the pharmacological view point but till date there are no specific treatment regimen developed for this viral infection. PURPOSE: The present review emphasizes the role of herbs and herbs-derived secondary metabolites in inhibiting SARS-CoV-2 virus and also for the management of post-COVID-19 related complications. This approach will foster and ensure the safeguards of using medicinal plant resources to support the healthcare system. Plant-derived phytochemicals have already been reported to prevent the viral infection and to overcome the post-COVID complications like parkinsonism, kidney and heart failure, liver and lungs injury and mental problems. In this review, we explored mechanistic approaches of herbal medicines and their phytocomponenets as antiviral and post-COVID complications by modulating the immunological and inflammatory states. STUDY DESIGN: Studies related to diagnosis and treatment guidelines issued for COVID-19 by different traditional system of medicine were included. The information was gathered from pharmacological or non-pharmacological interventions approaches. The gathered information sorted based on therapeutic application of herbs and their components against SARSCoV-2 and COVID-19 related complications. METHODS: A systemic search of published literature was conducted from 2003 to 2021 using different literature database like Google Scholar, PubMed, Science Direct, Scopus and Web of Science to emphasize relevant articles on medicinal plants against SARS-CoV-2 viral infection and Post-COVID related complications. RESULTS: Collected published literature from 2003 onwards yielded with total 625 articles, from more than 18 countries. Among these 625 articles, more than 95 medicinal plants and 25 active phytomolecules belong to 48 plant families. Reports on the therapeutic activity of the medicinal plants belong to the Lamiaceae family (11 reports), which was found to be maximum reported from 4 different countries including India, China, Australia, and Morocco. Other reports on the medicinal plant of Asteraceae (7 reports), Fabaceae (8 reports), Piperaceae (3 reports), Zingiberaceae (3 reports), Ranunculaceae (3 reports), Meliaceae (4 reports) were found, which can be explored for the development of safe and efficacious products targeting COVID-19. CONCLUSION: Keeping in mind that the natural alternatives are in the priority for the management and prevention of the COVID-19, the present review may help to develop an alternative approach for the management of COVID-19 viral infection and post-COVID complications from a mechanistic point of view.

Characterization of gene expression of QM from Caragana jubata, a plant species that grows under extreme cold.

Caragana [Caragana jubata (Pall.) Poir] is a temperate plant that thrives well under extremes of cold in high altitude of Himalaya and hence the plant is expected to be a source of genes that might play an important role in tolerance to low temperature (LT). In order to identify LT inducible gene(s), differential display of mRNA (DD) was performed using the apical buds growing under snow as well as growing in the near vicinity without snow, and a LT inducible QM gene (CjQM) homologue was identified. Realizing the importance of QM gene (which encodes human Wilms' tumor suppressor QM protein) in aggregation of 40 and 60S ribosomal subunit and that not much has been reported on this gene in plant systems in relation to its relationship with LT, full length cDNA of CjQM was cloned through rapid amplification of cDNA ends. The gene (977 bp), encoded by small gene family, had an open reading frame of 651 bp and was found to be intronless. The gene exhibited up-regulation within 20 min of exposure to LT and abscisic acid (ABA), but no significant change in gene expression was observed in response to drought stress (DS), salicylic acid (SA) and methyl jasmonate (MJ) application. Up-regulation of CjQM was obtained in the tissues growing in situ under snow. Non-responsiveness of CjQM towards DS, SA and MJ, but up-regulation in response to LT and ABA suggested a specific regulation of the gene in Caragana under varied cues.

Major ginsenoside contents in rhizomes of Panax sokpayensis and Panax bipinnatifidus.

This study compared eight major ginsenosides (Rg1, Rg2, Rf, Re, Rd, Rc, Rb1 and Rb2) between Panax sokpayensis and Panax bipinnatifidus collected from Sikkim Himalaya, India. High-performance liquid chromatographic analysis revealed that all major ginsenosides were present in the rhizomes of P. sokpayensis except ginsenoside Rc, whereas ginsenoside Rf, Rc and Rb2 were not detected in P. bipinnatifidus.

Invasion of Solanum tuberosum L. by Aspergillus terreus: a microscopic and proteomics insight on pathogenicity.

BACKGROUND: Aspergillus terreus is one of the most harmful filamentous fungal pathogen of humans, animals and plants. Recently, researchers have discovered that A. terreus can cause foliar blight disease in potato (Solanum tuberosum L.). We used light and scanning electron microscopy, and performed proteomics analysis in an attempt to dissect the invasion process of A. terreus in this important crop. RESULTS: Microscopic study revealed that invasion of leaf tissue is marked by rapid germination of A. terreus phialidic conidia (PC) by 4 h after inoculation. By 8 h after inoculation, primary germ tubes from PC differentiated into irregular protuberance, often displayed stomata atropism, and failed to penetrate via the epidermal cells. Colonization of leaf tissues was associated with high rate of production of accessory conidia (AC). These analyses showed the occurrence of a unique opposing pattern of AC, tissue-specific and produced on melanized colonizing hyphae during the infection of leaf tissue. A significant proteome change hallmarked by differential expression of class I patatin, lipoxygenase, catalase-peroxidase complex, and cysteine proteinase inhibitor were observed during tuber colonization. These proteins are often involved in signal transduction pathways and crosstalk in pathogenic responses. CONCLUSION: A. terreus abundantly produced AC and multipolar germinating PC to invade potato leaf tissue. Additionally, A. terreus differentially induced enzymes in potato tuber during colonization which facilitates rapid disease development.

Host-range dynamics of Cochliobolus lunatus: from a biocontrol agent to a severe environmental threat.

We undertook an investigation to advance understanding of the host-range dynamics and biocontrol implications of Cochliobolus lunatus in the past decade. Potato (Solanum tuberosum L) farms were routinely surveyed for brown-to-black leaf spot disease caused by C. lunatus. A biphasic gene data set was assembled and databases were mined for reported hosts of C. lunatus in the last decade. The placement of five virulent strains of C. lunatus causing foliar necrosis of potato was studied with microscopic and phylogenetic tools. Analysis of morphology showed intraspecific variations in stromatic tissues among the virulent strains causing foliar necrosis of potato. A maximum likelihood inference based on GPDH locus separated C. lunatus strains into subclusters and revealed the emergence of unclustered strains. The evolving nutritional requirement of C. lunatus in the last decade is exhibited by the invasion of vertebrates, invertebrates, dicots, and monocots. Our results contribute towards a better understanding of the host-range dynamics of C. lunatus and provide useful implications on the threat posed to the environment when C. lunatus is used as a mycoherbicide.

Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya.

The present work was conducted to understand the basis of adaptation in Caragana jubata in its niche environment at high altitude cold desert of Himalaya. Molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (LT), a major cue operative at high altitude. Importantly, these genes expressed in C. jubata in its natural habitat. Their homologues in Arabidopsis thaliana, Oryza sativa, and Glycine max did not exhibit similar trend of gene expression at LT. Constitutive expression and a quick up-regulation of the above genes suggested the ability of C. jubata to adjust its cellular machinery to maintain growth and development in its niche. This was reflected in LT(50 )(the temperature at which 50% injury occurred) and LT mediated photosynthetic acclimatory response. Such molecular and physiological plasticity enables C. jubata to thrive in the high altitude cold desert of Himalayas.

Lipoxygenase in Caragana jubata responds to low temperature, abscisic acid, methyl jasmonate and salicylic acid.

Lipoxygenase (LOX) catalyses oxygenation of free polyunsaturated fatty acids into oxylipins, and is a critical enzyme of the jasmonate signaling pathway. LOX has been shown to be associated with biotic and abiotic stress responses in diverse plant species, though limited data is available with respect to low temperature and the associated cues. Using rapid amplification of cDNA ends, a full-length cDNA (CjLOX) encoding lipoxygenase was cloned from apical buds of Caragana jubata, a temperate plant species that grows under extreme cold. The cDNA obtained was 2952bp long consisting of an open reading frame of 2610bp encoding 869 amino acids protein. Multiple alignment of the deduced amino acid sequence with those of other plants demonstrated putative LH2/ PLAT domain, lipoxygenase iron binding catalytic domain and lipoxygenase_2 signature sequences. CjLOX exhibited up- and down-regulation of gene expression pattern in response to low temperature (LT), abscisic acid (ABA), methyl jasmonate (MJ) and salicylic acid (SA). Among all the treatments, a strong up-regulation was observed in response to MJ. Data suggests an important role of jasmonate signaling pathway in response to LT in C. jubata.

Structure of a superoxide dismutase and implications for copper-ion chelation.

Superoxide dismutase (SOD) plays a central role in cellular defence against oxidative stress and is of pharmaceutical importance. The SOD from Potentilla atrosanguinea (Pa-SOD) is a unique enzyme as it possesses free-radical scavenging capability at temperatures ranging between 263 and 353 K. The crystal structure of recombinant Pa-SOD has been determined to 2.3 A resolution. The active-site residues are well ordered and additional water molecules are present in place of a bound copper ion. There is a significant difference in the relative orientation of the two subunits of Pa-SOD and asymmetry is also present in numerous hydrogen-bonding interactions. Structures of SODs, both bound with copper and unbound, have been compared with respect to the orientation of the electrostatic and Greek-key loops. This analysis provides new insights into the copper-chelation process in SODs. Several new structural features in Pa-SOD which may be responsible for its unique properties of thermostability and expanded range of antioxidant activity are also highlighted.