Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications.

BACKGROUND: Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species. METHODS AND RESULTS: Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220 bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH. CONCLUSION: We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.

A plastid-localized bona fide geranylgeranyl diphosphate synthase plays a necessary role in monoterpene indole alkaloid biosynthesis in Catharanthus roseus.

In plants, geranylgeranyl diphosphate (GGPP, C20 ) synthesized by GGPP synthase (GGPPS) serves as precursor for vital metabolic branches including specialized metabolites. Here, we report the characterization of a GGPPS (CrGGPPS2) from the Madagascar periwinkle (Catharanthus roseus) and demonstrate its role in monoterpene (C10 )-indole alkaloids (MIA) biosynthesis. The expression of CrGGPPS2 was not induced in response to methyl jasmonate (MeJA), and was similar to the gene encoding type-I protein geranylgeranyltransferase_ß subunit (CrPGGT-I_ß), which modulates MIA formation in C. roseus cell cultures. Recombinant CrGGPPS2 exhibited a bona fide GGPPS activity by catalyzing the formation of GGPP as the sole product. Co-localization of fluorescent protein fusions clearly showed CrGGPPS2 was targeted to plastids. Downregulation of CrGGPPS2 by virus-induced gene silencing (VIGS) significantly decreased the expression of transcription factors and pathway genes related to MIA biosynthesis, resulting in reduced MIA. Chemical complementation of CrGGPPS2-vigs leaves with geranylgeraniol (GGol, alcoholic form of GGPP) restored the negative effects of CrGGPPS2 silencing on MIA biosynthesis. In contrast to VIGS, transient and stable overexpression of CrGGPPS2 enhanced the MIA biosynthesis. Interestingly, VIGS and transgenic-overexpression of CrGGPPS2 had no effect on the main GGPP-derived metabolites, cholorophylls and carotenoids in C. roseus leaves. Moreover, silencing of CrPGGT-I_ß, similar to CrGGPPS2-vigs, negatively affected the genes related to MIA biosynthesis resulting in reduced MIA. Overall, this study demonstrated that plastidial CrGGPPS2 plays an indirect but necessary role in MIA biosynthesis. We propose that CrGGPPS2 might be involved in providing GGPP for modifying proteins of the signaling pathway involved in MIA biosynthesis.

Assessment of nutritional status using anthropometric variables by multivariate analysis.

BACKGROUND: Undernutrition is a serious health problem and highly prevalent in developing countries. There is no as such confirmatory test to measure undernutrition. The objective of the present study is to determine a new Composite Score using anthropometric measurements. Composite Score was then compared with other methods like body mass index (BMI) and mid-upper arm circumference (MUAC) classification, to test the significance of the method. METHODS: Anthropometric data were collected from 780 adult Oraon (Male = 387, Female = 393) labourers of Alipurduar district of West Bengal, India, following standard instruments, and protocols. Nutritional status of the study participants were assessed by conventional methods, BMI and MUAC. Confirmatory factor analysis was carried out to reduce 12 anthropometric variables into a single Composite Score (C) and classification of nutritional status was done on the basis of the score. Furthermore, all the methods (BMI, MUAC and C) were compared and discriminant function analysis was adopted to find out the percentage of correctly classified individuals by each of the three methods. RESULT: The frequency of undernutrition was 45.9% according to BMI category, 56.7% according to MUAC category and 51.8% according to newly computed Composite Score. Further analysis showed that Composite Score has a higher strength of correct classification (98.7%), compared to BMI (95.9%) and MUAC (96.2%). CONCLUSION: Therefore, anthropometric measurements can be used to identify nutritional status in the population more correctly by calculating Composite Score of the measurements and it is a non-invasive and relatively correct way of identification.

Synergism of fungal and bacterial cellulases and hemicellulases: a novel perspective for enhanced bio-ethanol production.

The complex structure of lignocellulose requires the involvement of a suite of lignocellulolytic enzymes for bringing about an effective de-polymerization. Cellulases and hemicellulases from both fungi and bacteria have been studied extensively. This review illustrates the mechanism of action of different cellulolytic and hemi-cellulolytic enzymes and their distinctive roles during hydrolysis. It also examines how different approaches can be used to improve the synergistic interaction between fungal and bacterial glycosyl hydrolases with a focus on fungal cellulases and bacterial hemicellulases. The approach entails the role of cellulosomes and their improvement through incorporation of novel enzymes and evaluates the recent break-through in the construction of designer cellulosomes and their extension towards improving fungal and bacterial synergy. The proposed approach also advocates the incorporation and cell surface display of designer cellulosomes on non-cellulolytic solventogenic strains along with the innovative application of combined cross-linked enzyme aggregates (combi-CLEAs) as an economically feasible and versatile tool for improving the synergistic interaction through one-pot cascade reactions.

De novo sequencing and comparative analysis of holy and sweet basil transcriptomes.

BACKGROUND: Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing. RESULTS: The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes. CONCLUSION: This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum.

Nanoparticle-induced morphological transition of Bombyx mori nucleopolyhedrovirus: a novel method to treat silkworm grasserie disease.

Grasserie, a polyorganotrophic disease caused by Bombyx mori nucleopolyhedrovirus (BmNPV), accounts for lethal infection to fifth instar silkworm larvae. It was found that nanoparticle (NP)-induced morphological transformation of BmNPV polyhedra could reduce the infectivity of BmNPV both in cell line and in silkworm larvae. Initially, 11 NPs were screened for evaluation of their nature of interaction with polyhedra surface through scanning electron microscopy. Amongst these NPs, lipophilically coated silica nanoparticle (SNPL), alumina nanoparticles in the hexagonal close-packed α structure and aspartate capped gold nanoparticle transformed polyhedra were tested for their infectivity in B. mori cell line using cytopathic effect and plaque reduction assay. SNPL was evaluated for its bio-efficacy in fifth instar silkworm larvae. The study of polyhedra morphology as a function of NP concentration showed severe 'roughening' of the polyhedra with replacement of the regular facets by a large number of irregular ones by SNPL, and this caused transition of highly infectious polyhedra into a nearly spherical, non-infectious structure. A moderate polyhedra roughening was observed for alumina NPs, and no roughening was noticed for gold NPs. The morphological changes could be correlated with reduction of virus-induced cytopathic effect and plaque formation, and increased survival rate of SNPL transformed polyhedra infected silkworm larvae to 70.09±6.61% after 96 h. In this group, 61.04±8.03% larvae formed normal cocoons from which moths eclosed, laid eggs and larvae emerged. This study could lead to open up newer pathways for designing nano pharmaceuticals to combat other viral diseases.

Rice transcriptome upon infection with Xanthomonas oryzae pv. oryzae relative to its avirulent T3SS-defective strain exposed modulation of many stress responsive genes.

Xanthomonas oryzae pv. oryzae (Xoo) is a destructive pathogen that causes bacterial blight disease of rice worldwide. Xoo uses T3SS (type III secretion system) effectors to subvert rice innate immunity. However, the comprehensive knowledge of rice genes involved in T3SS effectors-mediated interaction remains unclear. In this study, the transcriptome profiles of rice infected with a virulent Xoo strain from North-eastern region of India relatives to its avirulent strain (that lacks functional T3SS) were analyzed at early (2-6 hpi) and late (16-24 hpi) hours of infection. Out of total 255 differentially expressed genes (DEGs), during early infection, 62 and 70 genes were upregulated and downregulated, respectively. At late infection, 70 and 53 genes were upregulated and downregulated, respectively. The transcriptomic data identified many differentially expressed resistant genes, transposons, transcription factors, serine/threonine protein kinase, cytochrome P450 and peroxidase genes that are involved in plant defense. Pathway analysis revealed that these DEGs are involved in hormone signaling, plant defense, cellular metabolism, growth and development processes. DEGs associated with plant defense were also validated through quantitative real-time PCR. Our study brings a comprehensive picture of the rice genes that are being differentially expressed during bacterial blight infection. Nevertheless, the DEG-associated pathways would provide sensible targets for developing resistance to bacterial blight. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03193-4.

Blue Sheep Resource Selection in Alpine Grasslands of a Western Himalayan Landscape - A Point Process Approach.

In-depth knowledge of distribution and factors influencing it is important for species conservation and management. Many forms of such data have led to the development of new analytical techniques for better interpretation. For mountainous terrains with certain limitations, species data are obtained in the presence-only form. The point process model is one of the recent approaches for modelling such data, taking care of pseudo-absences and spatial independence. For conservation in regions with limited resources and species with similar ecological requirements, it is important to properly assess the extent of competition extent between wild and domestic species. We attempted to use point process framework to estimate the function of resource selection in blue sheep (Pseudois nayaur) in areas influenced by pastoralism in a western Himalayan region. Our study is the first attempt to use this framework to estimate resource selection on a dataset not collected using radio-telemetry. Spatial locations of blue sheep and livestock and a background sample of random points with six topographic covariates were used to model resource selection probability via intensity function. Blue sheep showed its predicted presence in areas with open vegetation coinciding with alpine meadows, influenced by southern aspect keeping a threshold distance of 600-1000 m from cliffs (escape terrain). Livestock, also showed presence probability in open vegetation, but at lower altitudes, mainly on valley floors. Our results suggest that though blue sheep continued to use the same habitat type after livestock arrival, they selected different resources based on topographic factors. Livestock were in areas where it was convenient for pastoralists to establish campsites and where nutritious grasses were present, making it feasible to graze. Thus, we argue that the probable shift in habitat for blue sheep from optimal areas occurs due to livestock presence, which might disturb their nutritional balance. Our study provides helpful insights for managing rangelands, which when tied with dietary patterns will give a better idea for proper conservation measures in the future.

Halo-tolerant plant growth promoting rhizobacteria for improving productivity and remediation of saline soils.

BACKGROUND: The collective impact of climate change and soil salinity is continuously increasing the degraded lands across the globe, bringing agricultural productivity and food security under stress. The high concentration of salts in saline soils impose osmotic, ionic, oxidative and water stress in plants. Biological solutions can be the most reliable and sustainable approach to ensure food security and limit the use of agro-chemicals. AIM OF REVIEW: Halo-tolerant plant growth promoting rhizobacteria (HT-PGPR) are emerging as efficient biological tools to mitigate the toxic effects of high salt concentrations and improve the growth of plants, simultaneously remediating the degraded saline soils. The review explains the role of HT-PGPR in mitigating the salinity stress in plants through diverse mechanisms and concurrently leading to improvement of soil quality. KEY SCIENTIFIC CONCEPTS OF REVIEW: HT-PGPR are involved in alleviating the salinity stress in plants through a number of mechanisms evoking multipronged physiological, biochemical and molecular responses. These include changes in expression of defense-related proteins, exopolysaccharides synthesis, activation of antioxidant machinery, accumulation of osmolytes, maintaining the Na+ kinetics and improving the levels of phytohormones and nutrient uptake in plants. The modification of signaling by HT-PGPR inoculation under stress conditions elicits induced systemic resistance in plants which further prepares them against salinity stress. The role of microbial-mechanisms in remediating the saline soil through structural and compositional improvements is also important. Development of novel bioinoculants for saline soils based on the concepts presented in the review can be a sustainable approach in improving productivity of affected agro-ecosystems and simultaneously remediating them.

Metabolic engineering of Acinetobacter baylyi ADP1 for removal of Clostridium butyricum growth inhibitors produced from lignocellulosic hydrolysates.

BACKGROUND: Pretreatment of lignocellulosic biomass can produce inhibitory compounds that are harmful for microorganisms used in the production of biofuels and other chemicals from lignocellulosic sugars. Selective inhibitor removal can be achieved with biodetoxification where microorganisms catabolize the inhibitors without consuming the sugars. We engineered the strictly aerobic Acinetobacter baylyi ADP1 for detoxification of lignocellulosic hydrolysates by removing the gene for glucose dehydrogenase, gcd, which catalyzes the first step in its glucose catabolism. RESULTS: The engineered A. baylyi ADP1 strain was shown to be incapable of consuming the main sugar components of lignocellulosic hydrolysates, i.e., glucose, xylose, and arabinose, but rapidly utilized acetate and formate. Formate was consumed during growth on acetate and by stationary phase cells, and this was enhanced in the presence of a common aromatic inhibitor of lignocellulosic hydrolysates, 4-hydroxybenzoate. The engineered strain tolerated glucose well up to 70 g/l, and the consumption of glucose, xylose, or arabinose was not observed in prolonged cultivations. The engineered strain was applied in removal of oxygen, a gaseous inhibitor of anaerobic fermentations. Co-cultivation with the A. baylyi ADP1 gcd knockout strain under initially aerobic conditions allowed the strictly anaerobic Clostridium butyricum to grow and produce hydrogen (H2) from sugars of the enzymatic rice straw hydrolysate. CONCLUSIONS: We demonstrated that the model organism of bacterial genetics and metabolism, A. baylyi ADP1, could be engineered to be an efficient biodetoxification strain of lignocellulosic hydrolysates. Only one gene knockout was required to completely eliminate sugar consumption and the strain could be used in production of anaerobic conditions for the strictly anaerobic hydrogen producer, C. butyricum. Because of these encouraging results, we believe that A. baylyi ADP1 is a promising candidate for the detoxification of lignocellulosic hydrolysates for bioprocesses.

High throughput electron transfer from carbon dots to chloroplast: a rationale of enhanced photosynthesis.

A biocompatible amine functionalized fluorescent carbon dots were developed and isolated for gram scale applications. Such carbogenic quantum dots can strongly conjugate over the surface of the chloroplast and due to that strong interaction the former can easily transfer electrons towards the latter by assistance of absorbed light or photons. An exceptionally high electron transfer from carbon dots to the chloroplast can directly effect the whole chain electron transfer pathway in a light reaction of photosynthesis, where electron carriers play an important role in modulating the system. As a result, carbon dots can promote photosynthesis by modulating the electron transfer process as they are capable of fastening the conversion of light energy to the electrical energy and finally to the chemical energy as assimilatory power (ATP and NADPH).