The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of ...rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies.
High-fat diets (HFDs) induce systemic inflammation, gut microbial derangements and disturb metabolic homeostasis, resulting in weight gain, insulin resistance and nonalcoholic fatty liver (NAFL). ...Numerous antioxidants and prebiotic/probiotics per se may prevent HFD-associated comorbidities, but there are no reports related to their combination.
In the present study, we aim to evaluate a cobiotic combination of lycopene (antioxidant) and isomalto-oligosaccharides (IMOs, a prebiotic) for prevention of HFD-induced alterations.
Male Swiss albino mice were fed either normal pellet diet (NPD) or HFD and lycopene (5 and 10 mg kg(-1)), IMOs (0.5 and 1 g kg(-1)) or their combination for 12 weeks. Systemic adiposity, glucose tolerance, insulin sensitivity, feeding regulators in hypothalamus, hepatosteatosis and liver inflammation, cecal short chain fatty acids (SCFAs), serum inflammatory cytokines, gut morphology and alterations in selected gut microbes were studied.
Lycopene, IMOs and their combination prevented weight gain, adiposity, improved adipose tissue fat mobilization and reduced insulin resistance. Hypothalamic orexigenic and anorectic genes have also been modulated by these treatments. Dietary interventions prevented NAFL-like symptoms and improved glucose homeostasis. Improvement in selected gut microbial abundance and SCFA concentration along with reduced systemic inflammation, metabolic endotoxemia and improved ileal and colonic health were observed in mice supplemented with lycopene, IMOs and their combination. Interestingly, cobiotic combination synergistically improved many of the HFD-induced alterations.
The present work provide evidence that new approach based on cobiotic combination (antioxidant plus prebiotic) can be employed to develop novel class of functional foods for their application against HFD-associated pathological complications.
Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The ...relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume'. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.
Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population ...structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.
Summary
Canine distemper (CD) is one of the highly contagious and invariably fatal viral diseases of dogs and other carnivores. Despite the widespread use of modified live vaccines to control CD, the ...prevalence of disease has increased at an alarming rate in recent years. Although a number of factors may be ascribed for vaccine failure, antigenic differences among the vaccine and wild‐type strains have gained the interest of researchers. Considering the high genetic variability of haemagglutinin gene (H gene) and its role in eliciting the immune response to canine distemper virus (CDV), we have generated nine full‐length CDV H gene sequences from infected dogs including three vaccinated cases. Bayesian analysis was performed using 102 full‐length H gene nucleotide sequences over a time frame of 76 years (1940–2016) from 18 countries. The time to the most recent common ancestor (tMRCA) of CDV was estimated to be 1696 AD. Phylogenetic reconstruction clustered Indian wild‐type viruses into a distinct monophyletic group clearly separated from the previously established CDV lineages. This signifies the presence of a novel genetic variant (proposed as “Lineage India‐1/Asia‐5”) circulating among dog population in India. To investigate the importance of substitutions at amino acid residues 530 and 549 of CDV H protein in determining the host switches from canid to non‐canid hosts, we analysed 125 H gene sequences including nine sequences generated in this study. Selection pressure analysis and analysis of amino acid sequences revealed a trend towards adaptation of 549H variants in non‐canid hosts although no role of G/E530R/D/N substitution could be identified. This is the first comprehensive study about the nature and ecology of CDV circulating among dog population in India. Outbreaks in vaccinated animals as observed in this study have raised a concern towards the effectiveness of current vaccine strains warranting detailed investigation.
Graphene coating on copper (Cu) is shown to increase the resistance of the metal to electrochemical degradation by one and half orders of magnitude. Detailed electrochemical characterization in ...aggressive chloride environment shows the impedance of Cu increasing dramatically and the anodic and cathodic current densities of the coated Cu becoming nearly 1–2 orders of magnitude smaller when coated with graphene. The observations are counterintuitive as graphite in contact with metals increases metallic corrosion. The results can bring paradigm changes in the development of anti-corrosion coatings using conformal, ultrathin graphene films.
Aims
To study the biocontrol potential of nematode‐trapping fungus Arthrobotrys oligospora in protecting tomato (Lycopersicon esculentum Mill.) against Meloidogyne incognita and Rhizoctonia solani ...under greenhouse and field conditions.
Methods and Results
Five isolates of the nematode‐trapping fungus Arthrobotrys oligospora isolated from different parts of India were tested against Meloidogyne incognita and Rhizoctonia solani in tomato (Lycopersicon esculentum Mill.) plants grown under greenhouse and field conditions. Arthrobotrys oligospora‐treated plants showed enhanced growth in terms of shoot and root length and biomass, chlorophyll and total phenolic content and high phenylalanine ammonia lyase activity in comparison with M. incognita‐ and R. solani‐inoculated plants. Biochemical profiling when correlated with disease severity and intensity in A. oligospora‐treated and untreated plants indicate that A. oligospora VNS‐1 offered significant disease reduction in terms of number of root galls, seedling mortality, lesion length, disease index, better plant growth and fruit yield as compared to M. incognita‐ and R. solani‐challenged plants.
Conclusion
The result established that A. oligospora VNS‐1 has the potential to provide bioprotection agents against M. incognita and R. solani.
Significance and Impact of the Study
Arthrobotrys oligospora can be a better environment friendly option and can be incorporated in the integrated disease management module of crop protection. Application of A. oligospora not only helps in the control of nematodes but also increases plant growth and enhances nutritional value of tomato fruits. Thus, it proves to be an excellent biocontrol as well as plant growth promoting agent.
One of the main concerns about the fast spreading coronavirus disease 2019 (Covid-19) pandemic is how to intervene. We analysed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) isolates ...data using the multifractal approach and found a rich in viral genome diversity, which could be one of the root causes of the fast Covid-19 pandemic and is strongly affected by pressure and health index of the hosts inhabited regions. The calculated mutation rate (mr) is observed to be maximum at a particular pressure, beyond which mr maintains diversity. Hurst exponent and fractal dimension are found to be optimal at a critical pressure (Pm), whereas, for P > Pm and P < Pm, we found rich genome diversity relating to complicated genome organisation and virulence of the virus. The values of these complexity measurement parameters are found to be increased linearly with health index values.
Graphene and graphene oxide have become the base of many advanced biosensors due to their exceptional characteristics. However, lack of some properties, such as inertness of graphene in organic ...solutions and non-electrical conductivity of graphene oxide, are their drawbacks in sensing applications. To compensate for these shortcomings, various methods of modifications have been developed to provide the appropriate properties required for biosensing. Efficient modification of graphene and graphene oxide facilitates the interaction of biomolecules with their surface, and the ultimate bioconjugate can be employed as the main sensing part of the biosensors. Graphene nanomaterials as transducers increase the signal response in various sensing applications. Their large surface area and perfect biocompatibility with lots of biomolecules provide the prerequisite of a stable biosensor, which is the immobilization of bioreceptor on transducer. Biosensor development has paramount importance in the field of environmental monitoring, security, defense, food safety standards, clinical sector, marine sector, biomedicine, and drug discovery. Biosensor applications are also prevalent in the plant biology sector to find the missing links required in the metabolic process. In this review, the importance of oxygen functional groups in functionalizing the graphene and graphene oxide and different types of functionalization will be explained. Moreover, immobilization of biomolecules (such as protein, peptide, DNA, aptamer) on graphene and graphene oxide and at the end, the application of these biomaterials in biosensors with different transducing mechanisms will be discussed.
The present rate of economic growth is unsustainable without saving of fossil energy like crude oil, natural gas or coal. Thus mankind has to rely on the alternate/renewable energy sources like ...biomass, hydropower, geothermal energy, wind energy, solar energy, nuclear energy, etc. On the other hand, suitable waste management strategy is another important aspect of sustainable development. The growth of welfare levels in modern society during the past decades has brought about a huge increase in the production of all kinds of commodities, which indirectly generate waste. Plastics have been one of the materials with the fastest growth because of their wide range of applications due to versatility and relatively low cost. Since the duration of life of plastic products is relatively small, there is a vast plastics waste stream that reaches each year to the final recipients creating a serious environmental problem. Again, because disposal of post consumer plastics is increasingly being constrained by legislation and escalating costs, there is considerable demand for alternatives to disposal or land filling. Advanced research in the field of green chemistry could yield biodegradable/green polymers but is too limited at this point of time to substitute the non-biodegradable plastics in different applications. Once standards are developed for degradable plastics they can be used to evaluate the specific formulations of materials which will find best application in this state as regards their performance and use characteristics. Among the alternatives available are source reduction, reuse, recycling, and recovery of the inherent energy value through waste-to-energy incineration and processed fuel applications. Production of liquid fuel would be a better alternative as the calorific value of the plastics is comparable to that of fuels, around 40Â MJ/kg. Each of these options potentially reduces waste and conserves natural resources. Plastics recycling, continues to progress with a wide range of old and new technologies. Many research projects have been undertaken on chemical recycling of waste plastics to fuel and monomer. This is also reflected by a number of pilot, demonstration, and commercial plants processing various types of plastic wastes in Germany, Japan, USA, India, and elsewhere. Further investigations are required to enhance the generation of value added products (fuel) with low investments without affecting the environment. The paper reviews the available literature in this field of active research and identifies the gaps that need further attention.
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