291 results on '"Pratyoosh, Shukla"'
Search Results
2. Editorial: Engineering microalgal chassis cells
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Xuefeng Lu, Martin Hagemann, Jin Liu, Pratyoosh Shukla, and Xiaoming Tan
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microalgae ,chassis cell ,synthetic biology ,metabolic engineering ,photosynthetic production ,Microbiology ,QR1-502 - Published
- 2023
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3. Synthetic Biology and Biocomputational Approaches for Improving Microbial Endoglucanases toward Their Innovative Applications
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Mandeep, Hao Liu, and Pratyoosh Shukla
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Chemistry ,QD1-999 - Published
- 2021
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4. Computational tools for modern vaccine development
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Sunita, Andaleeb Sajid, Yogendra Singh, and Pratyoosh Shukla
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vaccine ,reverse vaccinology ,rational design ,antibodyomics tools ,epitope prediction ,multi-graft scaffolding ,Immunologic diseases. Allergy ,RC581-607 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Vaccines play an essential role in controlling the rates of fatality and morbidity. Vaccines not only arrest the beginning of different diseases but also assign a gateway for its elimination and reduce toxicity. This review gives an overview of the possible uses of computational tools for vaccine design. Moreover, we have described the initiatives of utilizing the diverse computational resources by exploring the immunological databases for developing epitope-based vaccines, peptide-based drugs, and other resources of immunotherapeutics. Finally, the applications of multi-graft and multivalent scaffolding, codon optimization and antibodyomics tools in identifying and designing in silico vaccine candidates are described.
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- 2020
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5. Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance
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Mohit Kumar, Shweta Jaiswal, Kushneet Kaur Sodhi, Pallee Shree, Dileep Kumar Singh, Pawan Kumar Agrawal, and Pratyoosh Shukla
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Environmental sciences ,GE1-350 - Abstract
Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms. Keywords: Antibiotics, Bioremediation, Biofilm, Microbial consortium, Degradation
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- 2019
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6. Synthetic Organic Compounds From Paper Industry Wastes: Integrated Biotechnological Interventions
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Shweta Jaiswal, Guddu Kumar Gupta, Kusum Panchal, Mandeep, and Pratyoosh Shukla
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synthetic organic compounds ,bioremediation ,xenobiotics ,pollution ,pulp and paper industry ,Biotechnology ,TP248.13-248.65 - Abstract
Synthetic organic compounds (SOCs) are reported as xenobiotics compounds contaminating the environment from various sources including waste from the pulp and paper industries: Since the demand and production of paper is growing increasingly, the release of paper and pulp industrial waste consisting of SOCs is also increasing the SOCs’ pollution in natural reservoirs to create environmental pollution. In pulp and paper industries, the SOCs viz. phenol compounds, furans, dioxins, benzene compounds etc. are produced during bleaching phase of pulp treatment and they are principal components of industrial discharge. This review gives an overview of various biotechnological interventions for paper mill waste effluent management and elimination strategies. Further, the review also gives the insight overview of various ways to restrict SOCs release in natural reservoirs, its limitations and integrated approaches for SOCs bioremediation using engineered microbial approaches. Furthermore, it gives a brief overview of the sustainable remediation of SOCs via genetically modified biological agents, including bioengineering system innovation at industry level before waste discharge.
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- 2021
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7. Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile
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Harish Chandra, Krishna Kant Sharma, Olli H. Tuovinen, Xingmin Sun, and Pratyoosh Shukla
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dysbiosis ,toxins ,inflammasome ,pseudomembranous colitis ,inflammatory bowel disease ,innate lymphoid cells ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion. Their proliferations can aggravate inflammatory manifestations, trigger autoimmune diseases, and lead to severe life-threatening conditions. Current surge in microbiome research is unwinding these complex interplays between disease development and protection against pathobionts. This review summarizes the current knowledge of pathobiont emergence with a focus on Clostridioides difficile and the recent findings on the roles of immune cells such as iTreg cells, Th17 cells, innate lymphoid cells, and cytokines in protection against pathobionts. The review calls for adoption of innovative tools and cutting-edge technologies in clinical diagnostics and therapeutics to provide insights in identification and quantification of pathobionts.
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- 2021
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8. Deciphering the Potential of Rhizobium pusense MB-17a, a Plant Growth-Promoting Root Endophyte, and Functional Annotation of the Genes Involved in the Metabolic Pathway
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Twinkle Chaudhary, Rajesh Gera, and Pratyoosh Shukla
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endophyte ,plant growth-promoting rhizobacteria (PGPR) ,Rhizobium pusense MB-17a ,ACC deaminase ,Vigna radiata ,siderophore ,Biotechnology ,TP248.13-248.65 - Abstract
Plant growth-promoting rhizobacteria (PGPR) are root endophytic bacteria used for growth promotion, and they have broader applications in enhancing specific crop yield as a whole. In the present study, we have explored the potential of Rhizobium pusense MB-17a as an endophytic bacterium isolated from the roots of the mung bean (Vigna radiata) plant. Furthermore, this bacterium was sequenced and assembled to reveal its genomic potential associated with plant growth-promoting traits. Interestingly, the root endophyte R. pusense MB-17a showed all essential PGPR traits which were determined by biochemical and PGPR tests. It was noted that this root endophytic bacterium significantly produced siderophores, indole acetic acid (IAA), ammonia, and ACC deaminase and efficiently solubilized phosphate. The maximum IAA and ammonia produced were observed to be 110.5 and 81 μg/ml, respectively. Moreover, the PGPR potential of this endophytic bacterium was also confirmed by a pot experiment for mung bean (V. radiata), whose results show a substantial increase in the plant's fresh weight by 76.1% and dry weight by 76.5% on the 60th day after inoculation of R. pusense MB-17a. Also, there is a significant enhancement in the nodule number by 66.1% and nodule fresh weight by 162% at 45th day after inoculation with 100% field capacity after the inoculation of R. pusense MB-17a. Besides this, the functional genomic annotation of R. pusense MB-17a determined the presence of different proteins and transporters that are responsible for its stress tolerance and its plant growth-promoting properties. It was concluded that the unique presence of genes like rpoH, otsAB, and clpB enhances the symbiosis process during adverse conditions in this endophyte. Through Rapid Annotation using Subsystem Technology (RAST) analysis, the key genes involved in the production of siderophores, volatile compounds, indoles, nitrogenases, and amino acids were also predicted. In conclusion, the strain described in this study gives a novel idea of using such type of endophytes for improving plant growth-promoting traits under different stress conditions for sustainable agriculture.
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- 2021
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9. Lignocellulosic Biomass for the Synthesis of Nanocellulose and Its Eco-Friendly Advanced Applications
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Guddu Kumar Gupta and Pratyoosh Shukla
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cellulose ,flexible supercapacitor ,energy harvesting device ,nanocellulose ,composite materials ,water treatment ,Chemistry ,QD1-999 - Abstract
Nanocellulose is a unique and natural compound extracted from native cellulose using different extraction techniques. Nanocellulose is currently attracting attention due to its excellent properties such as special surface chemistry, exceptional physical and chemical strength, and rich hydroxyl groups for modification. In addition, its significant biological properties, like biodegradability, biocompatibility, and non-toxicity, accompanied by being environmentally friendly, are added advantages. The current review is focused on the lignocellulosic biomass processing methods for nanocellulose production and their usage for eco-friendly and environmental sustainability. We have also described insights into different techniques by which cellulosic materials can be changed into cellulose nanofibers (CNFs) and cellulose nanocrystals (CNCs). Lastly, we further discussed how nano-cellulosic materials are being used in a variety of industries such as the food sector, biomedical hygiene products, health care, water purification, and sensors. In the review, the unique uses of nanocelluloses in the production of nanocomposite materials, like flexible supercapacitor and polymer matrix, toward minimizing the utilization of global fossil energy and environmental pollution are envisaged. Finally, the significant application of nanomaterials in the areas of packaging industries, health and hygienic sector, cosmetics, and other important sectors are discussed. In the aspect of techno-economically feasibility, nano-cellulose-based materials may prove to be outstanding, environment friendly, and mitigate effluent load.
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- 2020
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10. Microbial Nanotechnology for Bioremediation of Industrial Wastewater
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Mandeep and Pratyoosh Shukla
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microbial nanotechnology ,nanoparticles ,bioremediation ,carbon nanotubes ,industrial effluents ,green technology ,Microbiology ,QR1-502 - Abstract
Pollutant removal from industrial effluents is a big challenge for industries. These pollutants pose a great risk to the environment. Nanotechnology can reduce the expenditure made by industries to mitigate these pollutants through the production of eco-friendly nanomaterials. Nanomaterials are gaining attention due to their enhanced physical, chemical, and mechanical properties. Using microorganisms in the production of nanoparticles provides an even greater boost to green biotechnology as an emerging field of nanotechnology for sustainable production and cost reduction. In this mini review, efforts are made to discuss the various aspects of industrial effluent bioremediation through microbial nanotechnology integration. The use of enzymes with nanotechnology has produced higher activity and reusability of enzymes. This mini review also provides an insight into the advantages of the use of nanotechnology as compared to conventional practices in these areas.
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- 2020
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11. Systems Biology Approaches for Therapeutics Development Against COVID-19
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Shweta Jaiswal, Mohit Kumar, Mandeep, Sunita, Yogendra Singh, and Pratyoosh Shukla
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systems biology ,multiomics ,in silico ,database (DB) ,COVID-19 ,coronavirus ,Microbiology ,QR1-502 - Abstract
Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host–virus interactions in search of therapeutic targets against the COVID-19.
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- 2020
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12. Molecular Analysis of Disease-Responsive Genes Revealing the Resistance Potential Against Fusarium Wilt (Fusarium udum Butler) Dependent on Genotype Variability in the Leguminous Crop Pigeonpea
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Koushik Biswas, Avijit Tarafdar, Roshan Kumar, Nirjara Singhvi, Parthadeb Ghosh, Mamta Sharma, Sunil Pabbi, and Pratyoosh Shukla
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disease incidence ,Fusarium udum ,gene expression ,innate resistance ,pathogenesis ,pigeonpea ,Genetics ,QH426-470 - Abstract
Fusarium wilt (FW), caused by Fusarium udum Butler (FU), is among the challenging factors in the production of pigeonpea. Therefore, exploring a superior pigeonpea genotype from landraces or local cultivars through the selection of innate resistance to FW using different biological and molecular approaches, and validating its resistance response, could be an alternative to sustainable crop improvement. Five distinct pigeonpea genotypes, with resistant (ICP2894) and susceptible (ICP2376) controls, were selected on the basis of the incidence percentage of FW, from three different states of India. Among them, the cultivar Richa, which displayed low incidence of FW (10.0%) during the genotype evaluation, was further examined for its innate resistance to FW. Molecular characterization of antioxidant (AO) enzyme [APX and SOD] and pathogenesis-related (PR) protein [CHS and β-1, 3-glucanase] families were performed. The obtained results of reverse transcription-polymerase chain reaction-based expression study and in silico analysis showed a higher level of induction of PR and AO genes, and the strong interaction of their putative proteins with fungal cellobiohydrolase-c protein established their antifungal activity, conferring early plant defense responses to FU in Richa. Our study demonstrated a strong and combinatorial approach involving biological assay, molecular experiments, and in silico analysis to identify a superior pigeonpea genotype that was resistant to FW across a major biogeographic region.
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- 2020
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13. Quest for cardiovascular interventions: precise modeling and 3D printing of heart valves
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Rajat Vashistha, Prasoon Kumar, Arun Kumar Dangi, Naveen Sharma, Deepak Chhabra, and Pratyoosh Shukla
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Cardiovascular fluid mechanics ,Image processing ,Biomaterials ,3D bioprinting ,Mechanobiology ,Biology (General) ,QH301-705.5 - Abstract
Abstract Digitalization of health care practices is substantially manifesting itself as an effective tool to diagnose and rectify complex cardiovascular abnormalities. For cardiovascular abnormalities, precise non-invasive imaging interventions are being used to develop patient specific diagnosis and surgical planning. Concurrently, pre surgical 3D simulation and computational modeling are aiding in the effective surgery and understanding of valve biomechanics, respectively. Consequently, 3D printing of patient specific valves that can mimic the original one will become an effective outbreak for valvular problems. Printing of these patient-specific tissues or organ components is becoming a viable option owing to the advances in biomaterials and additive manufacturing techniques. These additive manufacturing techniques are receiving a full-fledged support from burgeoning field of computational fluid dynamics, digital image processing, artificial intelligence, and continuum mechanics during their optimization and implementation. Further, studies at cellular and molecular biomechanics have enriched our understanding of biomechanical factors resulting in valvular heart diseases. Hence, the knowledge generated can guide us during the design and synthesis of biomaterials to develop superior extra cellular matrix, mimicking materials that can be used as a bioink for 3D printing of organs and tissues. With this notion, we have reviewed current opportunities and challenges in the diagnosis and treatment of heart valve abnormalities through patient-specific valve design via tissue engineering and 3D bioprinting. These valves can replace diseased valves by preserving homogeneity and individuality of the patients.
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- 2019
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14. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology
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Shweta Jaiswal and Pratyoosh Shukla
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synthetic biology ,bioremediation ,xenobiotics ,genetic circuit ,biosensor ,Microbiology ,QR1-502 - Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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- 2020
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15. Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production
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Sheeja Jagadevan, Avik Banerjee, Chiranjib Banerjee, Chandan Guria, Rameshwar Tiwari, Mehak Baweja, and Pratyoosh Shukla
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Synthetic biology ,Microalgae ,Biofuel ,Optimization models ,Genome-scale reconstruction ,Biorefinery ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract In the wake of the uprising global energy crisis, microalgae have emerged as an alternate feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell factories in terms of producing key chemicals, recombinant proteins, enzymes, lipid, hydrogen and alcohol. Abstraction of such high-value products (algal biorefinery approach) facilitates to make microalgae-based renewable energy an economically viable option. Synthetic biology is an emerging field that harmoniously blends science and engineering to help design and construct novel biological systems, with an aim to achieve rationally formulated objectives. However, resources and tools used for such nuclear manipulation, construction of synthetic gene network and genome-scale reconstruction of microalgae are limited. Herein, we present recent developments in the upcoming field of microalgae employed as a model system for synthetic biology applications and highlight the importance of genome-scale reconstruction models and kinetic models, to maximize the metabolic output by understanding the intricacies of algal growth. This review also examines the role played by microalgae as biorefineries, microalgal culture conditions and various operating parameters that need to be optimized to yield biofuel that can be economically competitive with fossil fuels.
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- 2018
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16. Bioprospecting of novel thermostable β-glucosidase from Bacillus subtilis RA10 and its application in biomass hydrolysis
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Rameshwar Tiwari, Puneet Kumar Singh, Surender Singh, Pawan K. S. Nain, Lata Nain, and Pratyoosh Shukla
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Thermotolerant ,Thermostable β-glucosidase ,Saccharification ,Cloning and expression ,Molecular modelling ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background Saccharification is the most crucial and cost-intensive process in second generation biofuel production. The deficiency of β-glucosidase in commercial enzyme leads to incomplete biomass hydrolysis. The decomposition of biomass at high temperature environments leads us to isolate thermotolerant microbes with β-glucosidase production potential. Results A total of 11 isolates were obtained from compost and cow dung samples that were able to grow at 50 °C. On the basis of qualitative and quantitative estimation of β-glucosidase enzyme production, Bacillus subtilis RA10 was selected for further studies. The medium components and growth conditions were optimized and β-glucosidase enzyme production was enhanced up to 19.8-fold. The β-glucosidase from B. subtilis RA10 retained 78% of activity at 80 °C temperature and 68.32% of enzyme activity was stable even at 50 °C after 48 h of incubation. The supplementation of β-glucosidase from B. subtilis RA10 into commercial cellulase enzyme resulted in 1.34-fold higher glucose release. Furthermore, β-glucosidase was also functionally elucidated by cloning and overexpression of full length GH1 family β-glucosidase gene from B. subtilis RA10. The purified protein was characterized as thermostable β-glucosidase enzyme. Conclusions The thermostable β-glucosidase enzyme from B. subtilis RA10 would facilitate efficient saccharification of cellulosic biomass into fermentable sugar. Consequently, after saccharification, thermostable β-glucosidase enzyme would be recovered and reused to reduce the cost of overall bioethanol production process.
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- 2017
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17. Lipid production and molecular dynamics simulation for regulation of accD gene in cyanobacteria under different N and P regimes
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Roshan Kumar, Koushik Biswas, Puneet Kumar Singh, Pankaj Kumar Singh, Sanniyasi Elumalai, Pratyoosh Shukla, and Sunil Pabbi
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Cyanobacteria ,Nitrogen ,Phosphorus limitation ,Lipid production ,accD gene expression ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background Microalgae grown under different nutrient deficient conditions present a good source of natural lipids with applications for several types of biofuels. The expression of acetyl-CoA carboxylase gene can further provide an insight to the mechanisms leading to enhanced lipid production under such stresses. In this study, two nutrients viz. nitrogen and phosphorus were modulated to see its effect on lipid productivity in selected cyanobacteria and its correlation with Accase followed by molecular dynamics simulation. Results Selected cyanobacteria viz. Oscillatoria sp. (SP8), Anabaena sp. (SP12), Anabaena sp. (SP13), Microcoleus sp. (SP18), and Nostoc sp. (SP20) varied in their ability to accumulate lipids which ranged from a lowest of 0.13% in Anabaena sp. (SP13) to the maximum of 7.24% in Microcoleus sp. (SP18). Microcoleus sp. (SP18) also recorded highest lipid accumulation at both N (6 mM NaNO3) and P (0.20 mM K2HPO4) limiting conditions. The overall expression of accD was found to be upregulated in both Oscillatoria sp. (SP8) and Microcoleus sp. (SP18) for all nitrogen concentrations but was differentially regulated with both positive and negative induction under phosphorus stress conditions. Maximum induction was observed in Microcoleus sp. (SP18) at 0.20 mM K2HPO4. The obtained 3D structure of SP8 protein (21.8 kDa) showed six alpha helices, while SP18 protein (16.7 kDa) exhibited four alpha helices and four beta sheets. The phi (ϕ)/psi(ψ) angles of the amino acid residues observed in Ramachandran plot analysis showed that both SP8 and SP18 proteins were highly stable with more than 90% amino acids in allowed regions. The molecular dynamics simulation results also indicated the stability of ligand-bound protein complexes. Conclusion It has been demonstrated that cyanobacterial isolates are affected differently by nutrient limitation leading to variation in their lipid productivity. The same has been revealed by the behavior of accD gene expression which was regulated more by nutrients concentrations rather than the organism. However, the ligand-bound protein complexes were stable throughout MD simulations.
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- 2017
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18. Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications
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Amit Srivastava, Shobit Thapa, Hillol Chakdar, Piyoosh Kumar Babele, and Pratyoosh Shukla
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General Medicine ,Applied Microbiology and Biotechnology ,Biotechnology - Abstract
Cyanobacteria safeguard their photosynthetic machinery from oxidative damage caused by adverse environmental factors such as high-intensity light. Together with many photoprotective compounds, they contain myxoxanthophylls, a rare group of glycosidic carotenoids containing a high number of conjugated double bonds. These carotenoids have been shown to: have strong photoprotective effects, contribute to the integrity of the thylakoid membrane, and upregulate in cyanobacteria under a variety of stress conditions. However, their metabolic potential has not been fully utilized in the stress biology of cyanobacteria and the pharmaceutical industry due to a lack of mechanistic understanding and their insufficient biosynthesis. This review summarizes current knowledge on: biological function, genetic regulation, biotechnological production, and pharmaceutical potential of myxoxanthophyll, with a focus on strain engineering and parameter optimization strategies for increasing their cellular content. The summarized knowledge can be utilized in cyanobacterial metabolic engineering to improve the stress tolerance of useful strains and enhance the commercial-scale synthesis of myxoxanthophyll for pharmaceutical uses.
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- 2022
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19. Microbiome engineering for bioremediation of emerging pollutants
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L. Paikhomba Singha and Pratyoosh Shukla
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Bioengineering ,General Medicine ,Biotechnology - Published
- 2022
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20. Bio-Based Formulations for Sustainable Applications in Agri-Food-Pharma
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Minaxi Sharma, Rajeev Bhat, Zeba Usmani, David Julian McClements, Pratyoosh Shukla, Vinay B. Raghavendra, and Vijai Kumar Gupta
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n/a ,Microbiology ,QR1-502 - Abstract
Currently, there is a strong enduring interest towards obtaining high-value, sustainable bio-based bioactive compounds from natural resources, as there is great demand for these compounds in various market sectors such as agriculture, food, pharma, cosmeceuticals, and others [...]
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- 2021
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21. Computational Approaches for the Structure-Based Identification of Novel Inhibitors Targeting Nucleoid-Associated Proteins in Mycobacterium Tuberculosis
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null Sunita, Nirjara Singhvi, Vipin Gupta, Yogendra Singh, and Pratyoosh Shukla
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Bioengineering ,Molecular Biology ,Applied Microbiology and Biotechnology ,Biochemistry ,Biotechnology - Published
- 2023
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22. Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review
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Shweta Jaiswal, Dileep Kumar Singh, and Pratyoosh Shukla
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systems biology ,xenobiotics ,bioremediation ,metabolomics ,pollutant ,metabolic network ,Microbiology ,QR1-502 - Abstract
Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.
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- 2019
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23. Cell Line Techniques and Gene Editing Tools for Antibody Production: A Review
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Arun K. Dangi, Rajeshwari Sinha, Shailja Dwivedi, Sanjeev K. Gupta, and Pratyoosh Shukla
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cell line engineering ,antibodies ,CRISPR-Cas ,gene editing ,RNAi ,ribozymes ,Therapeutics. Pharmacology ,RM1-950 - Abstract
The present day modern formulation practices for drugs are based on newer tools and techniques toward effective utilization. The methods of antibody formulations are to be revolutionized based on techniques of cell engineering and gene editing. In the present review, we have discussed innovations in cell engineering toward production of novel antibodies for therapeutic applications. Moreover, this review deciphers the use of RNAi, ribozyme engineering, CRISPR-Cas-based techniques for better strategies for antibody production. Overall, this review describes the multidisciplinary aspects of the production of therapeutic proteins that has gained more attention due to its increasing demand.
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- 2018
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24. Algal genomics tools: technological updates and progress
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Niwas Kumar, Srabani Kar, Amit Srivastava, Chiranjib Banerjee, and Pratyoosh Shukla
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- 2023
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25. Bioinoculants development for sustainable agriculture by innovative optimization processes: a future roadmap to commercialization
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Twinkle Chaudhary and Pratyoosh Shukla
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- 2023
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26. Microbial enzyme bioprocesses in biobleaching of pulp and paper: technological updates
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Guddu Kumar Gupta, Mandeep Dixit, Dharini Pandey, Rajeev Kumar Kapoor, Naveen Kango, and Pratyoosh Shukla
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- 2023
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27. Bioresources, environmental aspects, and patent scenario for biobleaching in pulp and paper industry
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Guddu Kumar Gupta, Gaurav Pathak, Pratyoosh Shukla, and Rajeev Kumar Kapoor
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- 2023
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28. Multi-efficient thermostable endoxylanase from Bacillus velezensis AG20 and its production of xylooligosaccharides as efficient prebiotics with anticancer activity
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Pratyoosh Shukla, Debabrat Baishya, Anshuman Chandra, Avinash Dhar, and Arabinda Ghosh
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biology ,Substrate (chemistry) ,Bioengineering ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Biochemistry ,Enzyme assay ,chemistry.chemical_compound ,chemistry ,Catalytic cycle ,Enzymatic hydrolysis ,biology.protein ,Xylobiose ,Xylanase ,Food science ,Bagasse ,Bifidobacterium - Abstract
In this study, we have unveiled the novel potential of xylanase production by Bacillus velezensis, previously known only for its PGPR traits. According to our investigations, Bacillus velezensis AG20 produced extracellular xylanase with a fold purification of 5.3 and a yield of 21 %. The purified xylanase (45 kDa) aptly cleaved linear β-(1→4)-xylan with a maximum velocity of 21.0 ± 3.0 U/mL, a turnover of 1.75/s, and a catalytic cycle of 0.571 at optimum pH 7. The temperature of 50 °C was found optimum for enzyme activity. Purified endoxylanase was thermostable and retained its significant residual activities at 50 °C and 60 °C. Metal cations such as Ca2+ and Mg2+ enhanced the substrate catalysis up to 1.5 fold. The purified endoxylanase also demonstrated multi-substrate hydrolyzing properties. However, the enzymatic hydrolysis of sugarcane bagasse produced xylooligosaccharides (XOS), including xylobiose, xylotriose, and xylotetrose. The mixture of released XOS has profound stability in gastric juice, intestinal fluid, and α-amylase and facilitates probiotic bacteria Bifidobacterium. The mixed XOS (300 μg/mL) significantly inhibited the HT-29 and Caco-2 cell proliferation by 90 % and 75 %, respectively, at 48 h. The possible mechanism of XOS uptake through the BIAXP receptor of Bifidobacterium has been contemplated and established using the caver analysis, Molecular Dynamics (MD) simulation, and Density Functional Theory (DFT) studies. Thus, here we reveal the utility of this novel bacterial strain in industries as high-temperature catalysts.
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- 2021
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29. Xylanolytic Enzymes in Pulp and Paper Industry: New Technologies and Perspectives
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Rajeev Kumar Kapoor, Pratyoosh Shukla, Guddu Kumar Gupta, and Mandeep Dixit
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Laccase ,chemistry.chemical_classification ,biology ,Biomass ,Bioengineering ,Cellulase ,Raw material ,Biodegradation ,Pulp and paper industry ,Applied Microbiology and Biotechnology ,Biochemistry ,Xylan ,Enzyme ,chemistry ,biology.protein ,Xylanase ,Molecular Biology ,Biotechnology - Abstract
The pulp and paper industry discharges massive amount of wastewater containing hazardous organochlorine compounds released during different processing stages. Therefore, some cost-effective and nonpolluting practices such as enzymatic treatments are required for the potential mitigation of effluents released in the environment. Various xylanolytic enzymes such as xylanases, laccases, cellulases and hemicellulases are used to hydrolyse raw materials in the paper manufacturing industry. These enzymes are used either individually or in combination, which has the efficient potential to be considered for bio-deinking and bio-bleaching components. They are highly dynamic, renewable, and high in specificity for enhancing paper quality. The xylanase act on the xylan and cellulases act on the cellulose fibers, and thus increase the bleaching efficacy of paper. Similarly, hemicellulase enzyme like endo-xylanases, arabinofuranosidase and β-d-xylosidases have been described as functional properties towards the biodegradation of biomass. In contrast, laccase enzymes act as multi-copper oxidoreductases, bleaching the paper by the oxidation and reduction process. Laccases possess low redox potential compared to other enzymes, which need some redox mediators to catalyze. The enzymatic process can be affected by various factors such as pH, temperature, metal ions, incubation periods, etc. These factors can either increase or decrease the efficiency of the enzymes. This review draws attention to the xylanolytic enzyme-based advanced technologies for pulp bleaching in the paper industry.
- Published
- 2021
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30. Understanding the Xylooligosaccharides Utilization Mechanism of Lactobacillus brevis and Bifidobacterium adolescentis: Proteins Involved and Their Conformational Stabilities for Effectual Binding
- Author
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Ishu Khangwal, Aditi G Muddebihalkar, Pratyoosh Shukla, Sinosh Skariyachan, Akshay Uttarkar, and Vidya Niranjan
- Subjects
chemistry.chemical_classification ,biology ,Hydrogen bond ,Lactobacillus brevis ,Bioengineering ,Bifidobacterium adolescentis ,Xylose ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Biochemistry ,Molecular dynamics ,chemistry.chemical_compound ,Enzyme ,chemistry ,Xylulokinase ,Xylobiose ,Molecular Biology ,Biotechnology - Abstract
Xylooligosaccharides having various degrees of polymerization such as xylobiose, xylotriose, and xylotetraose positively affect human health by interacting with gut proteins. The present study aimed to identify proteins present in gut microflora, such as xylosidase, xylulokinase, etc., with the help of retrieved whole-genome annotations and find out the mechanistic interactions of those with the above substrates. The 3D structures of proteins, namely Endo-1,4-beta-xylanase B (XynB) from Lactobacillus brevis and beta-d-xylosidase (Xyl3) from Bifidobacterium adolescentis, were computationally predicted and validated with the help of various bioinformatics tools. Molecular docking studies identified the effectual binding of these proteins to the xylooligosaccharides, and the stabilities of the best-docked complexes were analyzed by molecular dynamic simulation. The present study demonstrated that XynB and Xyl3 showed better effectual binding toward Xylobiose with the binding energies of − 5.96 kcal/mol and − 4.2 kcal/mol, respectively. The interactions were stabilized by several hydrogen bonding having desolvation energy (− 6.59 and − 7.91). The conformational stabilities of the docked complexes were observed in the four selected complexes of XynB–xylotriose, XynB–xylotetraose, Xyl3–xylobiose, and Xyn3–xylotriose by MD simulations. This study showed that the interactions of these four complexes are stable, which means they have complex metabolic activities among each other. Extending these studies of understanding, the interaction between specific probiotics enzymes and their ligands can explore the detailed design of synbiotics in the future.
- Published
- 2021
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31. Sophisticated Cloning, Fermentation, and Purification Technologies for an Enhanced Therapeutic Protein Production: A Review
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Sanjeev K. Gupta and Pratyoosh Shukla
- Subjects
monoclonal antibody (mAb) ,cloning ,therapeutic protein ,drug development ,quality by design (QbD) ,gene editing ,Therapeutics. Pharmacology ,RM1-950 - Abstract
The protein productions strategies are crucial towards the development of application based research and elucidating the novel purification strategies for industrial production. Currently, there are few innovative avenues are studies for cloning, upstream, and purification through efficient bioprocess development. Such strategies are beneficial for industries as well as proven to be vital for effectual therapeutic protein development. Though, these techniques are well documented, but, there is scope of addition to current knowledge with novel and new approaches and it will pave new avenues in production of recombinant microbial and non-microbial proteins including secondary metabolites. In this review, we have focussed on the recent development in clone selection, various modern fermentation and purification technologies and future directions in these emerging areas. Moreover, we have also highlighted notable perspectives and challenges involved in the bioengineering of such proteins, including quality by design, gene editing and pioneering ideas. The biopharmaceutical industries continue to shift towards more flexible, automated platforms and economical product development, which in turn can help in developing the cost effective processes and affordable drug development for a large community.
- Published
- 2017
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32. Over-expression of a Codon Optimized Yeast Cytosolic Pyruvate Carboxylase (PYC2) in CHO Cells for an Augmented Lactate Metabolism
- Author
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Sanjeev K. Gupta, Ankit Sharma, Hiralal Kushwaha, and Pratyoosh Shukla
- Subjects
monoclonal antibody ,super-transfection ,codon optimization ,yeast pyruvate carboxylase ,Chinese hamster ovary cells ,stable pool ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Monoclonal antibodies are the most demanding biotherapeutic drugs now a days used for the cure of various critical illnesses. Chinese hamster ovary (CHO) cells are one of the main hosts used for the large scale production of these antibodies. However, the cell line and production processes are the key factors to determine the cost and affordability of these antibodies. The metabolic waste lactic acid and ammonium are accumulated during a cell culture process and adversely affects productivity as well as product quality. To control the lactate metabolism of mAb (IgG1-kappa) producing CHO clones, we super-transfected the cells with a mammalian construct bearing codon optimized yeast cytosolic pyruvate carboxylase (PYC2) and a strong fusion promoter for optimal expression of PYC2 enzyme. A pool study was also performed for the assessment of cell’s performance, post-translational modification of a mAb and its expression in a CHO clone. The current study resulted an improved mAb titer up to 5%, galactosylation up to 2.5-folds, mannosylation up to twofold and marginal improved main and basic peaks in the charge variant profile at the cell pool stage. Such, approach may be suitable for the implementation in CHO cells producing recombinant protein for a better process control for the production of biotherapeutics.
- Published
- 2017
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33. Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review
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Dinesh K. Dahiya, Renuka, Monica Puniya, Umesh K. Shandilya, Tejpal Dhewa, Nikhil Kumar, Sanjeev Kumar, Anil K. Puniya, and Pratyoosh Shukla
- Subjects
gut microbiota ,prebiotic ,probiotics ,obesity ,nanotechnology ,Microbiology ,QR1-502 - Abstract
In the present world scenario, obesity has almost attained the level of a pandemic and is progressing at a rapid rate. This disease is the mother of all other metabolic disorders, which apart from placing an added financial burden on the concerned patient also has a negative impact on his/her well-being and health in the society. Among the various plausible factors for the development of obesity, the role of gut microbiota is very crucial. In general, the gut of an individual is inhabited by trillions of microbes that play a significant role in host energy homeostasis by their symbiotic interactions. Dysbiosis in gut microbiota causes disequilibrium in energy homeostasis that ultimately leads to obesity. Numerous mechanisms have been reported by which gut microbiota induces obesity in experimental models. However, which microbial community is directly linked to obesity is still unknown due to the complex nature of gut microbiota. Prebiotics and probiotics are the safer and effective dietary substances available, which can therapeutically alter the gut microbiota of the host. In this review, an effort was made to discuss the current mechanisms through which gut microbiota interacts with host energy metabolism in the context of obesity. Further, the therapeutic approaches (prebiotics/probiotics) that helped in positively altering the gut microbiota were discussed by taking experimental evidence from animal and human studies. In the closing statement, the challenges and future tasks within the field were discussed.
- Published
- 2017
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34. An efficient endoglucanase and lipase enzyme consortium (ELEC) for deinking of old newspaper and ultrastructural analysis of deinked pulp
- Author
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Mandeep Dixit, Guddu Kumar Gupta, Puneet Pathak, Nishi K. Bhardwaj, and Pratyoosh Shukla
- Subjects
Renewable Energy, Sustainability and the Environment - Published
- 2022
- Full Text
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35. Multi-Objective Optimization Through Machine Learning Modeling for Production of Xylooligosaccharides from Alkali-Pretreated Corn-Cob Xylan Via Enzymatic Hydrolysis
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Pratyoosh Shukla, Ishu Khangwal, and Deepak Chhabra
- Subjects
business.industry ,Xylose ,Machine learning ,computer.software_genre ,Microbiology ,Multi-objective optimization ,Xylan ,chemistry.chemical_compound ,chemistry ,Yield (chemistry) ,Enzymatic hydrolysis ,Xylanase ,Xylobiose ,Hemicellulose ,Original Research Article ,Artificial intelligence ,business ,computer - Abstract
The hemicellulose content present in corn cobs can help in producing a high amount of xylooligosaccharides (XOS) in an eco-friendly manner. In this work, the XOS was produced from alkali pre-treated corn-cobs having a true yield of 38 ± 1.4% via enzymatic hydrolysis with the help of xylanase from T. lanuginosus VAPS-24. The production process was optimized to achieve a high concentration of XOS using innovative multi-objective optimization through machine learning modeling and finding out the most suitable parameters where xylobiose production is higher than xylose. The Multi-objective connected neural networks (MOCNN) model with tangent sigmoid activation function yielded a correlation coefficient of 96.51%; there were six optimal sets where xylobiose concentration was higher than xylose. The best-optimized conditions yielded 3.03 mg/ml of xylobiose and 1.31 mg/ml of xylose. Therefore, this novel approach of machine learning can target the increasing demand for xylooligosaccharides in the growing industrial market of prebiotics.
- Published
- 2021
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36. Metabolic sink engineering in cyanobacteria: Perspectives and applications
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Riya Bongirwar and Pratyoosh Shukla
- Subjects
Environmental Engineering ,Renewable Energy, Sustainability and the Environment ,Bioengineering ,General Medicine ,Waste Management and Disposal - Published
- 2023
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37. Robotics for enzyme technology: innovations and technological perspectives
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Dharini Pandey, Pratyoosh Shukla, Kusum Panchal, Nikolaos E. Labrou, and Mandeep Dixit
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0303 health sciences ,Engineering ,030306 microbiology ,business.industry ,Research areas ,technology, industry, and agriculture ,Robotics ,General Medicine ,Biocompatible material ,Applied Microbiology and Biotechnology ,Monitoring and control ,03 medical and health sciences ,Systems engineering ,High throughput technology ,Robot ,Artificial intelligence ,business ,030304 developmental biology ,Biotechnology - Abstract
The use of robotics in the life science sector has created a considerable and significant impact on a wide range of research areas, including enzyme technology due to their immense applications in enzyme and microbial engineering as an indispensable tool in high-throughput screening applications. Scientists are experiencing the advanced applications of various biological robots (nanobots), fabricated based on bottom-up or top-down approaches for making nanotechnology scaffolds. Nanobots and enzyme-powered nanomotors are particularly attractive because they are self-propelled vehicles, which consume biocompatible fuels. These smart nanostructures are widely used as drug delivery systems for the efficient treatment of various diseases. This review gives insights into the escalating necessity of robotics and nanobots and their ever-widening applications in enzyme technology, including biofuel production and biomedical applications. It also offers brief insights into high-throughput robotic platforms that are currently being used in enzyme screening applications for monitoring and control of microbial growth conditions. • Robotics and their applications in biotechnology are highlighted. • Robotics for high-throughput enzyme screening and microbial engineering are described. • Nanobots and enzyme-powered nanomotors as controllable drug delivery systems are reviewed.
- Published
- 2021
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38. Sigma Factor Modulation for Cyanobacterial Metabolic Engineering
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Rajeev K. Varshney, Pratyoosh Shukla, and Amit Srivastava
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Microbiology (medical) ,0303 health sciences ,030306 microbiology ,Gene regulatory network ,Microbial metabolism ,Sigma Factor ,Gene Expression Regulation, Bacterial ,Computational biology ,Biology ,Cyanobacteria ,ENCODE ,Microbiology ,Genome ,Metabolic engineering ,03 medical and health sciences ,Infectious Diseases ,Bacterial Proteins ,Metabolic Engineering ,Sigma factor ,Transcription (biology) ,Virology ,Gene ,030304 developmental biology - Abstract
Sigma (σ) factors are key regulatory proteins that control the transcription initiation in prokaryotes. In response to environmental or developmental cues, σ factors initiate the transcription of necessary genes responsible for maintaining a life-sustaining metabolic balance. Due to the significant role of σ factors in bacterial metabolism, their rational engineering for commercial metabolite production in photoautotrophic, cyanobacterial cells is a desirable venture. As cyanobacterial genomes typically encode multiple σ factors, effective execution of metabolic engineering efforts largely relies on uncovering the complicated gene regulatory network and further characterization of the members of σ factor regulatory circuits. This review outlines the prospects of σ factor in metabolic engineering of cyanobacteria, summarizes the challenges in the path towards an efficient strain construction and highlights the genomic context of putative regulators of cyanobacterial σ factors.
- Published
- 2021
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39. Cellulase-assisted deinking approach for the recycling of mixed office waste papers and its quality improvement
- Author
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Puneet Pathak, Chakarvati Sango, Anshul Sabharwal, Rajeev Kapoor, Pratyoosh Shukla, and Nishi Kant Bhardwaj
- Abstract
This study involves the evaluation of the potential of commercial cellulase enzyme for the deinking of mixed office waste paper. The pH and temperature optima for the enzyme were 6.0 and 50°C. Enzyme dose and reaction time for the deinking process were optimized. An optimum dose of 300 g/t and reaction time of 90 min for commercial cellulase enzyme significantly improved deinking efficiency (79.3%) than the control set (59.4%) and chemical deinking (75.7%). Strength properties (except tear index) like tensile index, breaking length, burst factor and double fold were improved at optimized conditions. Cleanliness of pulp in terms of dirt and specks contents was also improved up to a significant level after cellulase treatment. Thus, it was concluded that commercial cellulase enzyme-based deinking was better than chemical deinking of mixed office waste in terms of improved pulp and paper quality.
- Published
- 2022
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40. Explication of interactions between HMGCR isoform 2 and various statins through In silico modeling and docking.
- Author
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M. V. K. Karthik, M. V. K. N. Satya Deepak, and Pratyoosh Shukla
- Published
- 2012
- Full Text
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41. Metabolic engineering of CHO cells for the development of a robust protein production platform.
- Author
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Sanjeev Kumar Gupta, Santosh K Srivastava, Ankit Sharma, Vaibhav H H Nalage, Darshita Salvi, Hiralal Kushwaha, Nikhil B Chitnis, and Pratyoosh Shukla
- Subjects
Medicine ,Science - Abstract
Chinese hamster ovary (CHO) cells are the most preferred mammalian host used for the bio-pharmaceutical production. A major challenge in metabolic engineering is to balance the flux of the tuned heterogonous metabolic pathway and achieve efficient metabolic response in a mammalian cellular system. Pyruvate carboxylase is an important network element for the cytoplasmic and mitochondrial metabolic pathway and efficiently contributes in enhancing the energy metabolism. The lactate accumulation in cell culture can be reduced by re-wiring of the pyruvate flux in engineered cells. In the present work, we over-expressed the yeast cytosolic pyruvate carboxylase (PYC2) enzyme in CHO cells to augment pyruvate flux towards the TCA cycle. The dual selection strategy is adopted for the screening and isolation of CHO clones containing varying number of PYC2 gene load and studied their cellular kinetics. The enhanced PYC2 expression has led to enhanced pyruvate flux which, thus, allowed reduced lactate accumulation up to 4 folds and significant increase in the cell density and culture longevity. With this result, engineered cells have shown a significant enhanced antibody expression up to 70% with improved product quality (~3 fold) as compared to the parental cells. The PYC2 engineering allowed overall improved cell performance with various advantages over parent cells in terms of pyruvate, glucose, lactate and cellular energy metabolism. This study provides a potential expression platform for a bio-therapeutic protein production in a controlled culture environment.
- Published
- 2017
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42. Emerging Molecular Tools for Engineering Phytomicrobiome
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Twinkle Chaudhary, Pratyoosh Shukla, and Rajesh Gera
- Subjects
0106 biological sciences ,0303 health sciences ,030306 microbiology ,Cas9 ,fungi ,food and beverages ,Plant Immunity ,Review Article ,Computational biology ,Biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,Quorum sensing ,Genome editing ,010608 biotechnology ,Metabolome ,CRISPR ,Identification (biology) ,Microbiome - Abstract
Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.
- Published
- 2021
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43. Allele mining and selective patterns of Pi9 gene in a set of rice landraces from India
- Author
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Jahangir Imam, Nimai Prasad Mandal, Mukund Variar, and Pratyoosh Shukla
- Subjects
polymorphism ,Allele mining ,Selection pressure ,blast resistance genes ,rice land races ,Plant culture ,SB1-1110 - Abstract
Allelic variants of the broad-spectrum blast resistance gene, Pi9 (NBS-LRR region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups. All the blast resistance Pi9 alleles were grouped into one cluster, whereas Pi9 alleles of susceptible landraces formed another cluster even though these landraces have a low level of DNA polymorphisms. A total number of 136 polymorphic sites comprising of transitions, transversions and InDels were identified in the 2.9kb sequence of Pi9 alleles. Lower variation in the form of mutations (77) (Transition + Transversion), and InDels (59) were observed in the Pi9 alleles isolated from rice landraces studied. The results showed that the Pi9 alleles of the selected rice landraces were less variable, suggesting that the rice landraces would have been exposed to less number of pathotypes across the country. The positive Tajima’s D (0.33580), P > 0.10 (not significant) was observed among the seven rice landraces, which suggests the balancing selection of Pi9 alleles. The value of synonymous substitution (-0.43337) was less than the non-synonymous substitution (0.78808). The greater non-synonymous substitution than the synonymous means that the coding region, mainly the LRR domain was under diversified selection. In this study, the Pi9 gene has been subjected to balancing selection with low nucleotide diversity which is different from the earlier reports, this may be because of the closeness of the rice landraces, cultivated in the same region and under low pathotype pressure.
- Published
- 2016
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- View/download PDF
44. Probiotic properties of Lactobacillus plantarum RYPR1 from an indigenous fermented beverage Raabadi
- Author
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Ruby Yadav, Anil Kumar Puniya, and Pratyoosh Shukla
- Subjects
Lactobacillus plantarum ,Probiotics ,Cell surface hydrophobicity ,Hypocholesterolemic effect ,Raabadi ,Microbiology ,QR1-502 - Abstract
Present study documents the potential probiotic Lactobacillus isolated from indigenous fermented beverage Raabadi, consumed during summers in Haryana and Rajasthan regions of India. A total of 5 Raabadi samples were collected aseptically and 54 isolates were purified using MRS medium. All the isolates were assessed for tolerance to low pH and bile salts. It was observed that out of 54 only 24 isolates could survive the simulated gastric conditions. These isolates were further evaluated in vitro for cell surface hydrophobicity, cell surface hydrophobicity, hypocholesteramic activity, anti-oxidative potential, BSH activity, antagonistic activity and antibiotic resistance profile. In addition, the confirmation of phenol resistance was also done. On the basis of results obtained, the survival rate of isolates was noted and 6 isolates were finally selected for further studies. Among them Lactobacillus plantarum RYPR1 and RYPC7 showed good survival at pH 2 which shows good acid tolerance. Moreover, Lactobacillus plantarum RYPR1 showed the highest hydrophobicity (79.13%) and represented the deconjugation of bile salts, which help in their adhesion to epithelial cells and colonization. Furthermore, RYPR1 also exhibited highest cholesterol reduction (59%) and subsequent analysis of results revealed that the above mentioned isolates further exhibit a good hypocholesterolemic effect and could be possibly used to prevent hypercholesterolemia. The present study divulges that Lactobacillus plantarum RYPR1 has an excellent probiotic potential.
- Published
- 2016
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- View/download PDF
45. Molecular detection and environment-specific diversity of glycosyl hydrolase family 1 β-glucosidase in different habitats
- Author
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Rameshwar Tiwari, Kanika Kumar, Surender Singh, Lata Nain, and Pratyoosh Shukla
- Subjects
Metagenomics ,microbial community ,metabolic profiling ,Operational taxonomic units ,GH1 β-glucosidase ,Microbiology ,QR1-502 - Abstract
β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulphur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.
- Published
- 2016
- Full Text
- View/download PDF
46. Recent developments in systems biology and metabolic engineering of plant microbe interactions
- Author
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Vishal Kumar, Mehak Baweja, Puneet Kumar Singh, and Pratyoosh Shukla
- Subjects
Systems Biology ,signaling ,Plant-Microbe Interactions ,CRISPR-Cas ,gene editing. ,Plant culture ,SB1-1110 - Abstract
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant microbe interactions using gene editing and system biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP) detection, RNA-seq, proteomics) and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.
- Published
- 2016
- Full Text
- View/download PDF
47. Plant microbe interactions in post genomic era: perspectives and applications
- Author
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Jahangir Imam, Puneet Kumar Singh, and Pratyoosh Shukla
- Subjects
Plant-Microbe Interactions ,emerging pathogens ,Plant immune response ,Genome-scale metabolic modeling ,PHI-base ,beneficial interactions ,Microbiology ,QR1-502 - Abstract
Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.
- Published
- 2016
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- View/download PDF
48. An Alkaline Protease from Bacillus pumilus MP 27: Functional Analysis of its Binding Model towards its Applications as Detergent Additive
- Author
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Mehak Baweja, Rameshwar Tiwari, Puneet Kumar Singh, Lata Nain, and Pratyoosh Shukla
- Subjects
Protease ,Docking ,Molecular modeling ,surfactant ,Bacillus pumilus ,De-staining ,Microbiology ,QR1-502 - Abstract
A proteolytic strain of Bacillus pumilus MP 27 was isolated from water samples of Southern ocean produced alkaline protease. Since protease production need expensive ingredients, an economically viable process was developed by using low cost carbon source, wheat straw, supplemented with peptone. This protease was active within temperature ranges 10˚C -70˚C at pH 9. This process was optimized by response surface methodology using a Box Bekhman design by Design Expert 7.0 software that increased the protease activity to 776.5 U/ml. Moreover, the enzyme was extremely stable at a broad range of temperature and pH retaining 69% of its activity at 50 ºC and 70% at pH 11. The enzyme exhibited excellent compatibility with surfactants and commercial detergents, showing 87% stability with triton X-100 and ̴ 100% stability with Tide commercial detergent. The results of the wash performance analysis demonstrated considerably good de-staining at 50ºC and 4ºC with low supplementation (109 U/ml). Molecular modeling of the protease revealed the presence of serine proteases, subtilase family and serine active site and further docking supported the association of catalytic site with the various substrates. Certainly, such protease can be considered as a good detergent additive in detergent industry with a possibility to remove the stains effectively even in a cold wash.
- Published
- 2016
- Full Text
- View/download PDF
49. Futuristic avenues of metabolic engineering techniques in bioremediation
- Author
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Pratyoosh Shukla and Babita Sharma
- Subjects
Gene Editing ,0106 biological sciences ,0303 health sciences ,Process Chemistry and Technology ,Biomedical Engineering ,Bioengineering ,General Medicine ,Biology ,01 natural sciences ,Applied Microbiology and Biotechnology ,Metabolic engineering ,03 medical and health sciences ,Biodegradation, Environmental ,Bioremediation ,Metabolic Engineering ,Genome editing ,010608 biotechnology ,Drug Discovery ,Molecular Medicine ,Environmental Pollutants ,Biochemical engineering ,CRISPR-Cas Systems ,030304 developmental biology ,Biotechnology - Abstract
Bioremediation is a promising technology for the treatment of environmental contaminants and paving new avenues for the betterment of the environment. Over the last some years, several approaches have been employed to optimize the genetic machinery of microorganisms relevant to bioremediation. Metabolic engineering is one of them that provides a new insight for bioremediation. This review envisages the critical role of these techniques toward exploring the possibilities of the creation of a new pathway, leading to pathway expansion to new substrates by assembling of catabolic modules from different origins in the same microbial cell. The recombinant DNA technology and gene editing tools were also explored for the construction of metabolically engineered microbial strains for the degradation of complex pollutants. Moreover, the importance of CRISPR-Cas system for knock-in and knock-out of genes was described by using recent studies. Further, the idea of the cocultivation of more than one metabolic engineered microbial communities is also discussed, which can be crucial in the bioremediation of multiple and complex pollutants. Finally, this review also elucidates the effective application of metabolic engineering in bioremediation through these techniques and tools.
- Published
- 2020
- Full Text
- View/download PDF
50. Artificial intelligence and synthetic biology approaches for human gut microbiome
- Author
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Pratyoosh Shukla, Prasoon Kumar, and Rajeshwari Sinha
- Subjects
030309 nutrition & dietetics ,Health benefits ,Biology ,Industrial and Manufacturing Engineering ,03 medical and health sciences ,Synthetic biology ,0404 agricultural biotechnology ,Human gut ,Genome editing ,Artificial Intelligence ,Humans ,CRISPR ,Microbiome ,Gene Editing ,0303 health sciences ,business.industry ,Microbiota ,04 agricultural and veterinary sciences ,General Medicine ,040401 food science ,Gut microbiome ,Gastrointestinal Microbiome ,Metagenomics ,Synthetic Biology ,Artificial intelligence ,business ,Food Science - Abstract
The gut microbiome comprises a variety of microorganisms whose genes encode proteins to carry out crucial metabolic functions that are responsible for the majority of health-related issues in human beings. The advent of the technological revolution in artificial intelligence (AI) assisted synthetic biology (SB) approaches will play a vital role in the modulating the therapeutic and nutritive potential of probiotics. This can turn human gut as a reservoir of beneficial bacterial colonies having an immense role in immunity, digestion, brain function, and other health benefits. Hence, in the present review, we have discussed the role of several gene editing tools and approaches in synthetic biology that have equipped us with novel tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) systems to precisely engineer probiotics for diagnostic, therapeutic and nutritive value. A brief discussion over the AI techniques to understand the metagenomic data from the healthy and diseased gut microbiome is also presented. Further, the role of AI in potentially impacting the pace of developments in SB and its current challenges is also discussed. The review also describes the health benefits conferred by engineered microbes through the production of biochemicals, nutraceuticals, drugs or biotherapeutics molecules etc. Finally, the review concludes with the challenges and regulatory concerns in adopting synthetic biology engineered microbes for clinical applications. Thus, the review presents a synergistic approach of AI and SB toward human gut microbiome for better health which will provide interesting clues to researchers working in the area of rapidly evolving food and nutrition science.
- Published
- 2020
- Full Text
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