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Gupta PK, Acharya A, Khanna V, Mourya A. Intra-femoral tunnel graft lengths less than 20 mm do not predispose to early graft failure, inferior outcomes or poor function. A prospective clinico-radiological comparative study. Musculoskelet Surg 2023; 107:179-186. [PMID: 35288845 DOI: 10.1007/s12306-022-00740-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/21/2022] [Indexed: 05/18/2023]
Abstract
PURPOSE Increasing demands on skills with mounting pressures from expectations from arthroscopic anterior cruciate ligament (ACL) reconstructions requires precise knowledge of technical details by surgeons. One such element is the minimum length of graft in femoral tunnel to allow for adequate tendon-to-bone healing and early return to activities and sports. This has, however, remained an unanswered question. PURPOSE To study and compare clinico-radiological outcomes of ACL reconstructions in patients with < 20 mm of intra-femoral tunnel graft length with those measuring ≥ 20 mm. METHODS All eligible patients undergoing arthroscopic ACL reconstruction were sequentially divided into two groups based on the intra-femoral tunnel graft lengths (A: < 20 mm, n = 27; and B: ≥ 20 mm, n = 25). Exclusions were made for those > 45 years of age, with chondral and/or multi-ligamentous injuries and with systemic pathologies. All patients were postoperatively evaluated in clinics by physical examination and functional scoring (Lysholm and modified Cincinnati scores) at 3, 6 and 12-month intervals. Graft vascularity was assessed by signal-to-noise quotient ratio (SNQR) using magnetic resonance imaging (MRI) at 3 and 12 months. RESULTS No significant differences were noted in mean Lysholm and modified Cincinnati scores between the two groups at the end of 1 year. There were also no significant differences in graft maturation over time and SNQR at 3 and 12 months in the region of interest (ROI). CONCLUSIONS Intra-femoral tunnel graft length of less than 20 mm does not compromise early clinical and functional outcomes of ACL reconstructions.
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Affiliation(s)
- P K Gupta
- Department of Sports Medicine, Sir Ganga Ram Hospital, New Delhi, India.
| | - A Acharya
- Department of Sports Medicine, Sir Ganga Ram Hospital, New Delhi, India
| | - V Khanna
- University Hospital Dorset, Dorset, UK
| | - A Mourya
- Department of Orthopaedics, Sir Ganga Ram Hospital, New Delhi, India
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Jain N, Shiv A, Sinha N, Singh PK, Prasad P, Balyan HS, Gupta PK. Leaf rust responsive miRNA and their target genes in wheat. Funct Integr Genomics 2022; 23:14. [PMID: 36550370 DOI: 10.1007/s10142-022-00928-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - P K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Pramod Prasad
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Pal N, Jan I, Saini DK, Kumar K, Kumar A, Sharma PK, Kumar S, Balyan HS, Gupta PK. Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.). Theor Appl Genet 2022; 135:2385-2405. [PMID: 35699741 DOI: 10.1007/s00122-022-04119-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/28/2022] [Indexed: 05/20/2023]
Abstract
In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.
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Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
- Murdoch's Centre for Crop & Food Innovation, Murdoch University, Murdoch, Perth, WA 6150, Australia.
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Saini DK, Srivastava P, Pal N, Gupta PK. Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.). Theor Appl Genet 2022; 135:1049-1081. [PMID: 34985537 DOI: 10.1007/s00122-021-04018-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/10/2021] [Indexed: 05/03/2023]
Abstract
In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder's MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified. Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999-2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder's MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
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Sumithra TG, Chaturvedi VK, Gupta PK, Bincy J, Siju SJ, Sunita SC, Reshma KJ, Patel CL, Rai AK. A novel bicistronic DNA vaccine with enhanced protective immune response against Bacillus anthracis through DNA prime-protein boost vaccination approach. Microb Pathog 2021; 158:105104. [PMID: 34298126 DOI: 10.1016/j.micpath.2021.105104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/26/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022]
Abstract
Anthrax, by Bacillus anthracis, remains a dreadful fatal hazard worldwide. The currently used anthrax vaccines are plagued by numerous issues that limit their widespread use. As an immunization approach targeting both extracellular antigens and toxins of B. anthracis may achieve better sterile immunity, the present investigation designed a bicistronic secretory anti-anthrax DNA vaccine targeting immune response against toxin and cells. The efficacy of the vaccine was compared with monocistronic DNA vaccines and the currently used anthrax vaccine. For this, mice were immunized with the developed vaccine containing pag (encoding protective antigen to block toxin) and eag genes (encoding EA1 to target cells) of B. anthracis through DNA-prime/Protein-boost (D/P) and DNA prime/DNA-boost (D/D) approaches. There was a >2 and > 5 fold increase in specific antibody level by D/D and D/P approaches respectively, on 42nd days post-immunization (dpi). Serum cytokine profiling showed that both Th1 and Th2 immune responses were elicited, with more Th2 responses in D/P strategy. More importantly, challenge with 100 times LD50 of B. anthracis at 42nd dpi exhibited maximum cumulative survival (83.33 %) by bicistronic D/P approach. Remarkably, immunization with EA1 delayed mortality onset in infection. The study forms the first report on complement-dependent bactericidal activity of antiEA1 antibodies. In short, co-immunization of PA and EA1 through the developed bicistronic DNA vaccine would be an effective immunization approach in anthrax vaccination. Further, D/P strategy could enhance vaccine-induced immunity against B. anthracis. Altogether, the study generates certain critical insights having direct applications in next-generation vaccine development against anthrax.
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Affiliation(s)
- T G Sumithra
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India.
| | - V K Chaturvedi
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India.
| | - P K Gupta
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
| | - J Bincy
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
| | - S J Siju
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
| | - S C Sunita
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
| | - K J Reshma
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
| | - C L Patel
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
| | - A K Rai
- ICAR-Indian Veterinary Research Institute, Izatnagar, UP, 243122, India
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Bhardwaj P, Gupta PK, Panwar H, Siddiqui MK, Morales-Menendez R, Bhaik A. Application of Deep Learning on Student Engagement in e-learning environments. Comput Electr Eng 2021; 93:107277. [PMID: 36567679 PMCID: PMC9757737 DOI: 10.1016/j.compeleceng.2021.107277] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 04/14/2021] [Accepted: 06/14/2021] [Indexed: 05/07/2023]
Abstract
The drastic impact of COVID-19 pandemic is visible in all aspects of our lives including education. With a distinctive rise in e-learning, teaching methods are being undertaken remotely on digital platforms due to COVID-19. To reduce the effect of this pandemic on the education sector, most of the educational institutions are already conducting online classes. However, to make these digital learning sessions interactive and comparable to the traditional offline classrooms, it is essential to ensure that students are properly engaged during online classes. In this paper, we have presented novel deep learning based algorithms that monitor the student's emotions in real-time such as anger, disgust, fear, happiness, sadness, and surprise. This is done by the proposed novel state-of-the-art algorithms which compute the Mean Engagement Score (MES) by analyzing the obtained results from facial landmark detection, emotional recognition and the weights from a survey conducted on students over an hour-long class. The proposed automated approach will certainly help educational institutions in achieving an improved and innovative digital learning method.
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Affiliation(s)
- Prakhar Bhardwaj
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - P K Gupta
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - Harsh Panwar
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | | | | | - Anubha Bhaik
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
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Gupta PK, Balyan HS, Sharma S, Kumar R. Biofortification and bioavailability of Zn, Fe and Se in wheat: present status and future prospects. Theor Appl Genet 2021; 134:1-35. [PMID: 33136168 DOI: 10.1007/s00122-020-03709-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/13/2020] [Indexed: 05/02/2023]
Abstract
Knowledge of genetic variation, genetics, physiology/molecular basis and breeding (including biotechnological approaches) for biofortification and bioavailability for Zn, Fe and Se will help in developing nutritionally improved wheat. Biofortification of wheat cultivars for micronutrients is a priority research area for wheat geneticists and breeders. It is known that during breeding of wheat cultivars for productivity and quality, a loss of grain micronutrient contents occurred, leading to decline in nutritional quality of wheat grain. Keeping this in view, major efforts have been made during the last two decades for achieving biofortification and bioavailability of wheat grain for micronutrients including Zn, Fe and Se. The studies conducted so far included evaluation of gene pools for contents of not only grain micronutrients as above, but also for phytic acid (PA) or phytate and phytase, so that, while breeding for the micronutrients, bioavailability is also improved. For this purpose, QTL interval mapping and GWAS were carried out to identify QTLs/genes and associated markers that were subsequently used for marker-assisted selection (MAS) during breeding for biofortification. Studies have also been conducted to understand the physiology and molecular basis of biofortification, which also allowed identification of genes for uptake, transport and storage of micronutrients. Transgenics using transgenes have also been produced. The breeding efforts led to the development of at least a dozen cultivars with improved contents of grain micronutrients, although land area occupied by these biofortified cultivars is still marginal. In this review, the available information on different aspects of biofortification and bioavailability of micronutrients including Zn, Fe and Se in wheat has been reviewed for the benefit of those, who plan to start work or already conducting research in this area.
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Affiliation(s)
- P K Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India.
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
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Rana V, Malik S, Joshi G, Rajput NK, Gupta PK. Preparation of alpha cellulose from sugarcane bagasse and its cationization: Synthesis, characterization, validation and application as wet-end additive. Int J Biol Macromol 2020; 170:793-809. [PMID: 33387544 DOI: 10.1016/j.ijbiomac.2020.12.165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/13/2020] [Accepted: 12/21/2020] [Indexed: 11/26/2022]
Abstract
Paper industry uses cationic polymers for imparting strong bonds with pulp furnish to enhance strength properties. Due to environmental reasons, emphasis is on utilization of biobased polymers in place of synthetic. Sugarcane bagasse, an agro-industrial waste, was processed for extraction of alpha cellulose and preparation of cationic derivative. Reaction conditions were optimized to achieve highly substituted cationic derivative with insertion of 2-hydroxy-3-(trimethylammonium) propyl group. Artificial neural network (ANN) was applied to analyze the experimental data for cationization modeling. Maximum degree of substitution 0.66, was achieved at 5.0 M NaOH/anhydro glucose unit (AGU), 20 °C alkalization temperature, 8 min alkalization time, 3.5 M/AGU etherification agent concentration, 45 min time and 60 °C etherification reaction temperature. The experimental results showed that mean square error values for input parameters were significantly low. The ANN based regression values of the output, and computed values of target were close to unity. ANN based fitting indicates better performance level to predict the degree of substitution. The synthesized cationic cellulose was characterized through FTIR, XRD, NMR, FESEM and TGA. The activity of cationized cellulose as wet-end additive was tested for bagasse, wheat straw and recycled pulps due to their shorten fiber and feeble pulp characters than wood pulp.
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Affiliation(s)
- Vikas Rana
- Cellulose & Paper Discipline, Forest Products Division, Forest Research Institute, P.O. New Forest, Dehradun, Uttarakhand 248006, India.
| | - Shuank Malik
- Cellulose & Paper Discipline, Forest Products Division, Forest Research Institute, P.O. New Forest, Dehradun, Uttarakhand 248006, India
| | - Gyanesh Joshi
- Cellulose & Paper Discipline, Forest Products Division, Forest Research Institute, P.O. New Forest, Dehradun, Uttarakhand 248006, India.
| | - Nikhil Kumar Rajput
- Department of Computer Science, Ramanujan College, University of Delhi, New Delhi, India
| | - P K Gupta
- Cellulose & Paper Discipline, Forest Products Division, Forest Research Institute, P.O. New Forest, Dehradun, Uttarakhand 248006, India.
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Upadhyay L, Chaturvedi VK, Gupta PK, Sunita SC, Sumithra TG, Prusty BR, Yadav AK. Development of a visible loop mediated isothermal amplification assay for rapid detection of Bacillus anthracis. Biologicals 2020; 69:59-65. [PMID: 33309531 DOI: 10.1016/j.biologicals.2020.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022] Open
Abstract
Distressing effects on animal and human health with lethal progression, being used as bioweapon and shared features with non-pathogenic bacteria demands sensitive, specific, safe, cost effective and rapid detection methods for anthrax causing organisms. Conventional microbiology based diagnostics for anthrax are time consuming and need sophisticated equipment, while molecular diagnostics require less time and labor. The Loop mediated isothermal amplification assay (LAMP) is rapid, sensitive and specific assay and requires no specialized equipment. In the present study, we developed a LAMP assay for rapid as well as specific detection of Bacillus anthracis. The optimized assay produced positive results with the Sterne strain and one field isolate of B. anthracis and, negative results with other bacteria of the same and different genera within 2 h. Sensitivity was 500 fg of total DNA of B. anthracis, which was 100 times more sensitive than conventional PCR. The present study also demonstrated that the simple method of total DNA extraction by repeated boiling and freezing will not adversely affect the LAMP results. In conclusion, the optimized LAMP assay is a promising tool for the specific, sensitive, less time-consuming diagnosis for anthrax causing bacteria and also, for detecting the virulence of suspected B. anthracis cultures.
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Affiliation(s)
- L Upadhyay
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India.
| | - V K Chaturvedi
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India.
| | - P K Gupta
- Division of Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India.
| | - S C Sunita
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - T G Sumithra
- ICAR-Central Marine Fisheries Research Institute, Kochi, 682 018, India.
| | - B R Prusty
- Division of Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - A K Yadav
- ICAR-National Research Centre on Pig, Rani, Guwahati, 781131, Assam, India.
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Anele U, Singh S, Kushwaha BP, Gupta PK, Bhattacharya S. PSII-5 Chemical composition, in vitro dry matter digestibility, gas production and methane emission of maintenance, growth and production diets/rations of buffaloes. J Anim Sci 2020. [DOI: 10.1093/jas/skaa278.715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ten types of diets were prepared to meet the nutrient requirements of buffaloes for maintenance (MD1 to MD10), growth (GD1 to GD10) and production/lactation (PD1 to PD10). A total of 30 diets were evaluated for chemical composition, in vitro gas and methane production, and dry matter (DM) disappearance using buffalo rumen liquor. The CNCPS was used to estimate the carbohydrate and protein fractions. Protein fractions PB1 and PB2 of maintenance diets were lower (P < 0.05) than growth and production diets, while protein fractions (PB3) and Pc were (P < 0.05) higher in maintenance than in growth and production diets. Mean values of PA was (P < 0.05) higher in growth diets (136.9) than production (114.8) and maintenance diets (105.6 g/kg DM). Maintenance diets had (P < 0.05) higher structural carbohydrate contents (586.2 g/kg DM) than production diets (513.0 g/kg DM). Carbohydrate fraction (CB1) was highest (P < 0.05) in production diets (187.2 g/kg DM) followed by growth (129.5 g/kg DM) and maintenance diets (96.1 g/kg DM). In vitro gas production at different time periods (12, 24 and 48 h) was similar for maintenance (63.04, 51.98 and 48.15 ml/g DM), growth (63.83, 52.73 and 48.250) and production diets (63.51, 52.54 and 47.21 ml/g DM). Cumulative methane production was numerically lower for maintenance (28.40 ml/g DM) than growth (29.58 ml/g DM) and production diets (33.13 ml/g DM). In vitro methane production as a proportion of degraded DM (ml/g DDM and g/kg DDM) was similar for maintenance (14.21 and 29.53), growth (42.19 and 30.25) and production diets (41.26 and 29.58). Dietary chemical constituents such as EE, lignin, NDIN, ADIN and PB3 and Cc were (P < 0.05) negatively associated with methane production, while OM, NPN, SP, PA and PB1, TCHO and CB2 were positively (P < 0.05) correlated with methane production.
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Affiliation(s)
- Uchenna Anele
- North Carolina Agricutural & Technical State University
| | - Sultan Singh
- ICAR-Indian Grassland and Fodder Research Institute
| | - B P Kushwaha
- ICAR-Indian Grassland and Fodder Research Institute
| | - P K Gupta
- Plant Animal Relationship Division Indian Grassland and Fodder Research Institute
| | - S Bhattacharya
- Plant Animal Relationship Division Indian Grassland and Fodder Research Institute
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Panwar H, Gupta PK, Siddiqui MK, Morales-Menendez R, Bhardwaj P, Singh V. A deep learning and grad-CAM based color visualization approach for fast detection of COVID-19 cases using chest X-ray and CT-Scan images. Chaos Solitons Fractals 2020; 140:110190. [PMID: 32836918 PMCID: PMC7413068 DOI: 10.1016/j.chaos.2020.110190] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/04/2020] [Indexed: 05/17/2023]
Abstract
The world is suffering from an existential global health crisis known as the COVID-19 pandemic. Countries like India, Bangladesh, and other developing countries are still having a slow pace in the detection of COVID-19 cases. Therefore, there is an urgent need for fast detection with clear visualization of infection is required using which a suspected patient of COVID-19 could be saved. In the recent technological advancements, the fusion of deep learning classifiers and medical images provides more promising results corresponding to traditional RT-PCR testing while making detection and predictions about COVID-19 cases with increased accuracy. In this paper, we have proposed a deep transfer learning algorithm that accelerates the detection of COVID-19 cases by using X-ray and CT-Scan images of the chest. It is because, in COVID-19, initial screening of chest X-ray (CXR) may provide significant information in the detection of suspected COVID-19 cases. We have considered three datasets known as 1) COVID-chest X-ray, 2) SARS-COV-2 CT-scan, and 3) Chest X-Ray Images (Pneumonia). In the obtained results, the proposed deep learning model can detect the COVID-19 positive cases in ≤ 2 seconds which is faster than RT-PCR tests currently being used for detection of COVID-19 cases. We have also established a relationship between COVID-19 patients along with the Pneumonia patients which explores the pattern between Pneumonia and COVID-19 radiology images. In all the experiments, we have used the Grad-CAM based color visualization approach in order to clearly interpretate the detection of radiology images and taking further course of action.
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Affiliation(s)
- Harsh Panwar
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - P K Gupta
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - Mohammad Khubeb Siddiqui
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. E. Garza Sada 2501, Monterrey, N.L, 64,489, Mexico
| | - Ruben Morales-Menendez
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. E. Garza Sada 2501, Monterrey, N.L, 64,489, Mexico
| | - Prakhar Bhardwaj
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - Vaishnavi Singh
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
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Panwar H, Gupta PK, Siddiqui MK, Morales-Menendez R, Singh V. Application of deep learning for fast detection of COVID-19 in X-Rays using nCOVnet. Chaos Solitons Fractals 2020; 138:109944. [PMID: 32536759 PMCID: PMC7254021 DOI: 10.1016/j.chaos.2020.109944] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 05/26/2020] [Indexed: 05/18/2023]
Abstract
Presently, COVID-19 has posed a serious threat to researchers, scientists, health professionals, and administrations around the globe from its detection to its treatment. The whole world is witnessing a lockdown like situation because of COVID-19 pandemic. Persistent efforts are being made by the researchers to obtain the possible solutions to control this pandemic in their respective areas. One of the most common and effective methods applied by the researchers is the use of CT-Scans and X-rays to analyze the images of lungs for COVID-19. However, it requires several radiology specialists and time to manually inspect each report which is one of the challenging tasks in a pandemic. In this paper, we have proposed a deep learning neural network-based method nCOVnet, an alternative fast screening method that can be used for detecting the COVID-19 by analyzing the X-rays of patients which will look for visual indicators found in the chest radiography imaging of COVID-19 patients.
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Affiliation(s)
- Harsh Panwar
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - P K Gupta
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | | | | | - Vaishnavi Singh
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
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Saripalli G, Singh K, Gautam T, Kumar S, Raghuvanshi S, Prasad P, Jain N, Sharma PK, Balyan HS, Gupta PK. Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum). Plant Mol Biol 2020; 104:113-136. [PMID: 32627097 DOI: 10.1007/s11103-020-01029-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.
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Affiliation(s)
- Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - Kalpana Singh
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pramod Prasad
- Regional Station, Indian Institute of Wheat and Barley Research (IIWBR), Flowerdale, Shimla, HP, 171002, India
| | - Neelu Jain
- Division of Genetics and Plant Breeding, ICAR-IARI, Pusa, New Delhi, 110012, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India.
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Prasad P, Savadi S, Bhardwaj SC, Gupta PK. The progress of leaf rust research in wheat. Fungal Biol 2020; 124:537-550. [PMID: 32448445 DOI: 10.1016/j.funbio.2020.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/25/2023]
Abstract
Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.
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Affiliation(s)
- Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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15
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Gahlaut V, Jaiswal V, Singh S, Balyan HS, Gupta PK. Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes. Sci Rep 2019; 9:19486. [PMID: 31862891 PMCID: PMC6925107 DOI: 10.1038/s41598-019-55520-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/29/2019] [Indexed: 11/20/2022] Open
Abstract
Multi-locus genome wide association study was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel was grown in replicated trials in four environments [two each in irrigated (IR) and rainfed (RF) environments], and phenotypic data were recorded for five traits including days to heading, days to maturity, plant height, thousand grain weight and grain yield. Forty-six significant marker-trait associations (MTAs) were identified for five traits. These included 20 MTAs in IR and 19 MTAs in RF environments; seven additional MTAs were common to both the environments. Five of these MTAs were co-localized with previously known QTL/MTAs and the remaining MTAs were novel and add to the existing knowledge. Three desirable haplotypes for agronomic traits, one for improvement in RF environment and two for improvement in IR environment were identified. Eighteen (18) promising candidate genes (CGs) involved in seven different biological activities were also identified. The expression profiles of four (Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger and Gibberellin-dioxygenases) of the 18 genes showed that they were induced by drought stress in the wheat seedlings. The MTAs, haplotypes and CG-based markers may be used in marker-assisted breeding for drought tolerance in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
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Gupta PK, Lal P, Tiwari A. A case report of carcinoma of uterine cervix throwing heterochronous metastasis to the skin, spleen, and pancreas: the role of multimodality treatment approach. J Egypt Natl Canc Inst 2019; 31:8. [PMID: 32372163 DOI: 10.1186/s43046-019-0009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cancer of cervix often fails locally and/or within the pelvis. One to two percent of cervical squamous cell carcinoma patients have lung metastases at presentation, and 5-35% develop pulmonary metastases later on. Common sites of metastases are the liver, bone, and bowel. We report a rare case presentation of cervical squamous cell cancer where heterochronous metastasis occurred in the skin, spleen, and pancreas without loco-regional recurrence and skipping of visceral organs such as the lung, liver, and brain. CASE PRESENTATION A 55-year-old, postmenopausal lady presented with a complaint of bleeding of the vagina for 2 months duration. Cervical biopsy revealed squamous cell carcinoma of the cervix, and she was staged as a case of FIGO stage IIIB. She received external beam-beam radiotherapy of 50 Gy in 25 fractions along with concurrent weekly cisplatin at 35 mg/m2 followed by 3 fractions of intracavitary brachytherapy of 6 Gy each. After 30 months of follow-up, she presented with a skin lesion of 6 × 5 cm2 in the infrascapular region for 2 months duration. Biopsy revealed metastatic squamous cell carcinoma. Her metastatic work-up revealed no other lesions. Palliative radiotherapy to local site of 8 Gy in single fraction was delivered. The lesion disappeared within 4 weeks. She was given 6 cycles of cisplatin and paclitaxel salvage chemotherapy. After 30 months of follow-up, she presented with a skin lesion of 6 × 5 cm2 in the infrascapular region. Biopsy revealed metastatic squamous cell carcinoma. Her metastatic work-up revealed no other lesions. Palliative radiotherapy to the local site was planned, and a dose of 8 Gy in a single fraction was delivered. The lesion disappeared within 4 weeks. She was given 6 cycles of cisplatin and paclitaxel salvage chemotherapy. Six months after the completion of salvage therapy, she reported with the complaints of recurrent bouts of hematemesis and melena. Her CECT scan revealed 2 × 1.5 cm2 growth in the body of the pancreas and a subcentric splenic hilum node. She underwent open splenectomy with distal pancreatectomy. Histopathology report showed metastatic infiltration in pancreatic tissue by squamous cell carcinoma and one metastatic node in the splenic hilum. Post-treatment, 6 months, the patient was asymptomatic with no recurrence. CONCLUSIONS This is a rare heterochronous metastatic presentation of cervical cancer without loco-regional recurrence and visceral organs such as the lung, liver, and brain. The optimal treatment remains undefined for these patients. Multimodality treatment is necessary to manage the patients.
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Affiliation(s)
- P K Gupta
- Department of Radiation Oncology, Super Speciality Cancer Institute and Hospital, C.G. City, Lucknow, Uttar Pradesh, 226002, India.
| | - P Lal
- Department of Radiotherapy, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - A Tiwari
- Royal Cancer Institute and Research Centre, Kanpur, Uttar Pradesh, India
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Gautam T, Saripalli G, Gahlaut V, Kumar A, Sharma PK, Balyan HS, Gupta PK. Further studies on sugar transporter (SWEET) genes in wheat (Triticum aestivum L.). Mol Biol Rep 2019; 46:2327-2353. [PMID: 30830588 DOI: 10.1007/s11033-019-04691-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
SWEET proteins represent one of the largest sugar transporter family in the plant kingdom and play crucial roles in plant development and stress responses. In the present study, a total of 108 TaSWEET genes distributed on all the 21 wheat chromosomes were identified using the latest whole genome sequence (as against 59 genes reported in an earlier report). These 108 genes included 14 of the 17 types reported in Arabidopsis and also included three novel types. Tandem duplications (22) and segmental duplications (5) played a significant role in the expansion of TaSWEET family. A number of cis-elements were also identified in the promoter regions of TaSWEET genes, indicating response of TaSWEET genes during development and also during biotic/abiotic stresses. The TaSWEET proteins carried 4-7 trans-membrane helices (TMHs) showing diversity in structure. Phylogenetic analysis using SWEET proteins of wheat and 8 other species gave four well-known clusters. Expression analysis involving both in silico and in planta indicated relatively higher expression of TaSWEET genes in water/heat sensitive and leaf rust resistant genotypes. The results provided insights into the functional role of TaSWEETs in biotic and abiotic stresses, which may further help in planning strategies to develop high yielding wheat varieties tolerant to environmental stresses.
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Affiliation(s)
- Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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18
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Sharma C, Kumar S, Saripalli G, Jain N, Raghuvanshi S, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. H3K4/K9 acetylation and Lr28-mediated expression of six leaf rust responsive genes in wheat (Triticum aestivum). Mol Genet Genomics 2018; 294:227-241. [PMID: 30298213 DOI: 10.1007/s00438-018-1500-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose. The proximal and distal promoters of these genes contained a number of motifs that are known to respond to biotic stresses. The enrichment of two acetylation marks changed with passage of time; changes in expression of two of the six genes (N-acetyltransferase and peroxidase12), largely matched with changes in H3K4/H3K9 acetylation patterns of the two promoter regions. For example, enrichment of both the marks matched with higher expression of N-acetyltransferase gene in susceptible NIL and the deacetylation (H3K4ac) largely matched with reduced gene expression in resistant NIL. In peroxidase12, enrichment of H3K4ac and H3K9ac largely matched with higher expression in both the NILs. In the remaining four genes, changes in H3 acetylation did not always match with gene expression levels. This indicated complexity in the regulation of the expression of these remaining four genes, which may be controlled by other epigenetic/genetic regulatory mechanisms that need further analysis.
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Affiliation(s)
- Chanchal Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.,Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan, Gyeongbuk, 38453, South Korea
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - J B Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - K V Prabhu
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Sharma C, Saripalli G, Kumar S, Gautam T, Kumar A, Rani S, Jain N, Prasad P, Raghuvanshi S, Jain M, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. A study of transcriptome in leaf rust infected bread wheat involving seedling resistance gene Lr28. Funct Plant Biol 2018; 45:1046-1064. [PMID: 32291004 DOI: 10.1071/fp17326] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 04/09/2018] [Indexed: 05/02/2023]
Abstract
Leaf rust disease causes severe yield losses in wheat throughout the world. During the present study, high-throughput RNA-Seq analysis was used to gain insights into the role of Lr28 gene in imparting seedling leaf rust resistance in wheat. Differential expression analysis was conducted using a pair of near-isogenic lines (NILs) (HD 2329 and HD 2329+Lr28) at early (0h before inoculation (hbi), 24 and 48h after inoculation (hai)) and late stages (72, 96 and 168 hai) after inoculation with a virulent pathotype of pathogen Puccinia triticina. Expression of a large number of genes was found to be affected due to the presence/absence of Lr28. Gene ontology analysis of the differentially expressed transcripts suggested enrichment of transcripts involved in carbohydrate and amino acid metabolism, oxidative stress and hormone metabolism, in resistant and/or susceptible NILs. Genes encoding receptor like kinases (RLKs) (including ATP binding; serine threonine kinases) and other kinases were the most abundant class of genes, whose expression was affected. Genes involved in reactive oxygen species (ROS) homeostasis and several genes encoding transcription factors (TFs) (most abundant being WRKY TFs) were also identified along with some ncRNAs and histone variants. Quantitative real-time PCR was also used for validation of 39 representative selected genes. In the long term, the present study should prove useful in developing leaf rust resistant wheat cultivars through molecular breeding.
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Affiliation(s)
- Chanchal Sharma
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Avneesh Kumar
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Sushma Rani
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Pramod Prasad
- Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - J B Sharma
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - K V Prabhu
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
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Shakya R, Hoque MK, Sapkota AS, Gupta PK. Differential Hepatotoxic Effects of Sodium Valproate at Different Doses in Albino Rats. Kathmandu Univ Med J (KUMJ) 2018; 16:78-82. [PMID: 30631023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Background Liver plays an essential role for transforming and clearing chemicals that may cause harmful effects to it. Sodium Valproate, renowned to be a potent antiepileptic drug, when taken in overdose may cause toxic effects to liver and other organs as well. Liver damage can be assessed with histological changes and measurement of enzymes produced by it. Objective To investigate the histological changes induced by different doses of Sodium Valproate ranging from 100-500 mg/kg/day and observe its correlation with liver enzymes level in serum. Method Three-months old albino rats were divided into six groups, five in each. Control group was treated with normal saline and rest five groups with Sodium Valproate in different doses 100, 200, 300, 400 and 500 mg/kg/day respectively. Then, liver of those experimented rats were examined histologically under the light microscope. Furthermore, Liver enzymes; Alanine Transaminase and Aspartate transaminase were measured to assess the micro-anatomical changes in liver. Result Distorted hepatic lobular architecture with aggregations of nuclei at certain interval was observed in the groups of higher doses; 300 mg/kg/day and above. However, accumulation of adipocytes was observed in all the Sodium Valproate treated rats unlike the control group. When compared the enzyme levels among the groups, it was found to be significantly increased in dose dependent manner. Besides, it also showed skin lesions in all rats treated with the dose 400 mg/kg/day and above. Conclusion Higher doses of Sodium Valproate; 300 mg/kg/day and above induces hepatotoxicity and skin lesions in adult albino rats.
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Affiliation(s)
- R Shakya
- Department of Anatomy, Kathmandu University School of Medical Sciences, Dhulikhel, Kavre, Nepal
| | - M K Hoque
- Department of Anatomy, Kathmandu University School of Medical Sciences, Dhulikhel, Kavre, Nepal
| | - A S Sapkota
- Department of Anatomy, Kathmandu University School of Medical Sciences, Dhulikhel, Kavre, Nepal
| | - P K Gupta
- Department of Anatomy, Kathmandu University School of Medical Sciences, Dhulikhel, Kavre, Nepal
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Sharma P, Sahu K, Kushwaha PK, Kumar S, Swami MK, Kumawat J, Patel HS, Kher S, Sahani PK, Haridas G, Gupta PK. Noninvasive assessment of cutaneous alterations in mice exposed to whole body gamma irradiation using optical imaging techniques. Lasers Med Sci 2017; 32:1535-1544. [PMID: 28699043 DOI: 10.1007/s10103-017-2276-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/25/2017] [Indexed: 10/25/2022]
Abstract
We report the results of a study carried out to investigate the potential of optical techniques such as optical coherence tomography, Mueller matrix spectroscopy, and cross-polarization imaging for noninvasive monitoring of the ionizing radiation exposure-induced alterations in cutaneous tissue of mice. Radiation dose-dependent changes were observed in tissue microvasculature and tissue optical parameters like retardance and depolarization as early as 1 h post radiation exposure. Results suggest that these optical techniques may allow early detection of radiation dose-dependent alterations which could help in screening of population exposed to radiation.
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Affiliation(s)
- P Sharma
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India.,Homi Bhabha National Institute, Mumbai, India
| | - K Sahu
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India.
| | - P K Kushwaha
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - S Kumar
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - M K Swami
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - J Kumawat
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - H S Patel
- Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - S Kher
- Solid State Lasers Division, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - P K Sahani
- Indus Operations, Beam Dynamics & Diagnostics Division, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - G Haridas
- Indus Operations, Beam Dynamics & Diagnostics Division, Raja Ramanna Centre for Advanced Technology, Indore, India
| | - P K Gupta
- Homi Bhabha National Institute, Mumbai, India
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Abstract
We have fabricated pliable, porous, biodegradable scaffolds with poly(lactic-co-glycolic acid) (PLGA) and poly(ethylene glycol) (PEG) blends using a solvent-casting and particulate-leaching technique. Our study investigated the effects of four different processing parameters on pliability and pore morphology of the biodegradable scaffolds. The parameters investigated were the PLGA copolymer ratio, the PLGA/PEG blend ratio, the initial salt weight fraction, and the salt particle size. A wide range of shear moduli (0.59 to 9.55 MPa), porosities (0.798 to 0.942), and median pore diameters (71 to 154 μm) was able to be achieved by varying the combination of these parameters. Our study indicates that initial salt weight fraction and PLGA/PEG blend ratio have the most significant effects on the physico-mechanical properties of the scaffolds. Enhanced pliability of the three dimensional foams made with blends of PLGA and PEG is evidenced by the ability to roll them into a tube without macroscopic damage to the scaffold. Pliable polymer substrates hold great promise for regeneration of soft tissues such as skin, or those requiring a tubular conformation such as intestine or vascular grafts.
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Affiliation(s)
- M C Wake
- Department of Chemical Engineering, Cox Laboratory for Biomedical Engineering, Rice University, Houston TX 77251-1892, USA
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Soharab M, Bhaumik I, Bhatt R, Saxena A, Karnal AK, Gupta PK. Effect of Yb doping on the refractive index and thermo-optic coefficient of YVO 4 single crystals. Appl Opt 2017; 56:1682-1688. [PMID: 28234377 DOI: 10.1364/ao.56.001682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single crystals of YVO4 with different doping concentrations of Yb (1.5, 3.0, 8.0, and 15.0 at. %) and with good crystalline quality (FWHM ∼43-55 arc sec of rocking curve) were grown by the optical floating zone technique. Refractive index measurements were carried out at four wavelengths as a function of temperature. The measurements show that as the doping concentration of Yb is increased, the refractive index varies marginally for ne whereas there is a significant change in the value of no. The thermo-optic coefficient (dn/dT) was found to be positive with a value ∼10-5/°C, which is 1 order higher than that for the undoped YVO4 crystal. The thermo-optic coefficient is higher for ne compared to that of no. Also, a set of relations describing the wavelength dependence of the thermo-optic coefficient were established that are useful for calculating the thermo-optic coefficient at any temperature in the range 30°C-150°C and at any wavelength in the range 532-1551 nm.
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Varshney GK, Kintali SR, Gupta PK, Das K. A comparative study on the effect of Curcumin and Chlorin-p 6 on the transport of the LDS cation across a negatively charged POPG bilayer: Effect of pH. Spectrochim Acta A Mol Biomol Spectrosc 2017; 173:132-138. [PMID: 27619975 DOI: 10.1016/j.saa.2016.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/28/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
We report the use of interface selective Second Harmonic generation technique to investigate the transport of the LDS cation across POPG liposomes in the pH range of 4.0 to 8.0 in the presence and absence of two amphiphilic drugs, Curcumin and Chlorin-p6 (Cp6). Our results show that bilayer permeability of liposomes is significantly affected by the presence of the drugs and pH of the medium as evidenced by significant changes in the transport kinetics of the LDS. Studies carried out in the pH range 4.0-8.0 show that while Cp6 significantly enhanced the transport of LDS at pH4.0, the transport of the cation was seen to increase with increasing pH, with maximum effect at pH7.4 for Curcumin. The pH dependent bilayer localization of both the drugs was investigated by conducting steady state FRET studies using DPH labeled lipids as donors. The FRET results and the relative population of the various ionic/nonionic species of the drugs at different pH suggest that distance dependent interaction between the various ionic species of the drugs and polar head groups of the lipid is responsible for the observed pH dependence enhancement of the drug induced membrane permeability. Another interesting observation was that the stability of Curcumin in presence of POPG liposomes was observed to degrade significantly near physiological pH (7.4 and 8.0). Although this degradation did not affect the liposome integrity, interestingly this was observed to enhance the transport of the LDS cation across the bilayer. That the degradation products of Curcumin are equally effective as the drug itself in enhancing the membrane permeability lends additional support to the current opinion that the bioactive degradation products of the drug may have a significant contribution to its observed pharmacological effects.
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Affiliation(s)
- G K Varshney
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, M.P. 452013, India
| | - S R Kintali
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, M.P. 452013, India
| | - P K Gupta
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, M.P. 452013, India
| | - K Das
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, M.P. 452013, India.
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Gupta PK, Kukreja R, Mital M, Rathee N. A case series of tuberous sclerosis complex: Clinico-radiological study and review of the literature. West Afr J Radiol 2017. [DOI: 10.4103/1115-3474.198155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Varshney GK, Kintali SR, Gupta PK, Das K. Effect of Bilayer Partitioning of Curcumin on the Adsorption and Transport of a Cationic Dye Across POPG Liposomes Probed by Second-Harmonic Spectroscopy. Langmuir 2016; 32:10415-10421. [PMID: 27636651 DOI: 10.1021/acs.langmuir.6b02797] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The effect of Curcumin partitioning into the bilayer during the adsorption and transport of a cationic dye, LDS, across a negatively charged POPG bilayer was investigated by the interface-selective second-harmonic (SH) spectroscopic technique. The intensity of SH electric field (E2ω) arising due to LDS adsorbed on the outer bilayer of the POPG liposome was observed to increase instantaneously (<1 s) following the addition of Curcumin. The fractional increase in the SH electric field (Ef2ω) and the bilayer transport rates (kT) of LDS were studied with respect to the pH of the solution and also with the Curcumin content in the lipid bilayer. Results obtained indicate that compared with the anionic form of the drug, its neutral form is more conducive of increasing the Ef2ω of LDS. With increasing Curcumin content in the lipid bilayer, two distinct regimes could be observed in terms of Ef2ω and kT values of LDS. For Curcumin:Lipid (C/L) ratio ≤0.02, the Ef2ω of LDS increases rapidly, while kT remains unchanged; and for C/L ratio ≥0.02, the Ef2ω values remains more or less constant, while there is a significant (∼40 times) increase followed by a modest increase in the kT values of LDS. The observed results support an earlier two-state binding model of Curcumin with the POPG bilayer. In addition, it is further proposed that at low C/L ratio Curcumin binds to the surface of the bilayer replacing the counterions (Na+) bound to the lipid head groups, which changes the bilayer surface charge density, thereby causing more LDS cations to adsorb on the bilayer surface. At high C/L ratio, Curcumin intercalates within the hydrophobic domain of the bilayer, altering its hydrophobicity and inducing enhanced transport of the LDS cation. Results presented in this work provide further insights into how Curcumin alters bilayer properties when it partitions from the aqueous to the bilayer phase.
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Affiliation(s)
- G K Varshney
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - S R Kintali
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - P K Gupta
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - K Das
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
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Gupta PK, Appannanavar SB, Mohan B, Taneja N. Improved detection of Shigella using Escherichia coli medium enrichment: Polymerase chain reaction from stool samples. Indian J Med Microbiol 2016; 34:526-528. [DOI: 10.4103/0255-0857.195355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Chandra S, Singh D, Pathak J, Kumari S, Kumar M, Poddar R, Balyan HS, Gupta PK, Prabhu KV, Mukhopadhyay K. De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection. PLoS One 2016; 11:e0148453. [PMID: 26840746 PMCID: PMC4739524 DOI: 10.1371/journal.pone.0148453] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/17/2016] [Indexed: 11/20/2022] Open
Abstract
Pathogens like Puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. The interaction at molecular level between wheat and the pathogen is complex and less explored. The pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene Lr28). Four Serial Analysis of Gene Expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to Sequencing by Oligonucleotide Ligation and Detection, which generated a total of 165,767,777 reads, each 35 bases long. The reads were processed and multiple k-mers were attempted for de novo transcript assembly; 22 k-mers showed the best results. Altogether 21,345 contigs were generated and functionally characterized by gene ontology annotation, mining for transcription factors and resistance genes. Expression analysis among the four libraries showed extensive alterations in the transcriptome in response to pathogen infection, reflecting reorganizations in major biological processes and metabolic pathways. Role of auxin in determining pathogenesis in susceptible and resistant lines were imperative. The qPCR expression study of four LRR-RLK (Leucine-rich repeat receptor-like protein kinases) genes showed higher expression at 24 hrs after inoculation with pathogen. In summary, the conceptual model of induced resistance in wheat contributes insights on defense responses and imparts knowledge of Puccinia triticina-induced defense transcripts in wheat plants.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Dharmendra Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Jyoti Pathak
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Supriya Kumari
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Puspendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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Joshi G, Naithani S, Varshney VK, Bisht SS, Rana V, Gupta PK. Synthesis and characterization of carboxymethyl cellulose from office waste paper: a greener approach towards waste management. Waste Manag 2015; 38:33-40. [PMID: 25543195 DOI: 10.1016/j.wasman.2014.11.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/17/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Abstract
In the present study, functionalization of mixed office waste (MOW) paper has been carried out to synthesize carboxymethyl cellulose, a most widely used product for various applications. MOW was pulped and deinked prior to carboxymethylation. The deinked pulp yield was 80.62 ± 2.0% with 72.30 ± 1.50% deinkability factor. The deinked pulp was converted to CMC by alkalization followed by etherification using NaOH and ClCH2COONa respectively, in an alcoholic medium. Maximum degree of substitution (DS) (1.07) of prepared CMC was achieved at 50 °C with 0.094 M and 0.108 M concentrations of NaOH and ClCH2COONa respectively for 3h reaction time. The rheological characteristics of 1-3% aqueous solution of optimized CMC product showed the non-Newtonian pseudoplastic behavior. Fourier transform infra red (FTIR), nuclear magnetic resonance (NMR) and scanning electron microscope (SEM) study were used to characterize the CMC product.
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Affiliation(s)
- Gyanesh Joshi
- Cellulose and Paper Division, Forest Research Institute, Dehradun 248006, India.
| | - Sanjay Naithani
- Chemistry of Forest Products Division, Institute of Wood Science & Technology, Bangalore 560003, India
| | - V K Varshney
- Chemistry Division, Forest Research Institute, Dehradun 248006, India
| | - Surendra S Bisht
- Chemistry of Forest Products Division, Institute of Wood Science & Technology, Bangalore 560003, India
| | - Vikas Rana
- Cellulose and Paper Division, Forest Research Institute, Dehradun 248006, India
| | - P K Gupta
- Cellulose and Paper Division, Forest Research Institute, Dehradun 248006, India
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Gupta S, Sexana S, Bhagwat S, Aggarwal P, Gupta PK. Clinicopathological characteristics of ameloblastomas in Western Uttar Pradesh population: An institutional study. Indian J Cancer 2015; 52:57-60. [DOI: 10.4103/0019-509x.175557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Singhal L, Gupta PK, Kale P, Gautam V, Ray P. Trends in antimicrobial susceptibility of Salmonella Typhi from North India (2001-2012). Indian J Med Microbiol 2014; 32:149-52. [PMID: 24713900 DOI: 10.4103/0255-0857.129799] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Enteric fever is endemic in India with Salmonella Typhi being the major causative agent. Antibiotic therapy constitutes the mainstay of management. The present study was undertaken to find the susceptibility profile of Salmonella enterica var Typhi (S. Typhi) blood isolates in a tertiary care hospital between January 2001 and December 2012. MATERIALS AND METHODS A retrospective analysis of laboratory records was carried out. Conventional blood culture method was used until 2009; from January 2010 onwards BACTEC 9240 system has been in use. Salmonella were confirmed by serotyping using group and type specific antisera. Antibiotic susceptibility was performed using the disk diffusion method. In addition 116 isolates were subjected to minimum inhibitory concentration testing for chloramphenicol, ciprofloxacin, amoxicillin and nalidixic acid (NA) using agar dilution and for ceftriaxone and azithromycin using E-strips (Biomerieux). RESULT A total of 1016 typhoidal salmonellae were obtained. The predominant serotype obtained was S. Typhi (852, 83.8%) followed by Salmonella enterica var Paratyphi A (164, 16.2%). We observed a re-emergence of susceptibility to first line antibiotics and a notable decline in multidrug resistant (MDR) strains. We also found all recent isolates resistant to NA and susceptible to third generation cephalosporins and 84.5% of isolates having decreasing ciprofloxacin susceptibility using revised criteria as per Clinical and Laboratory Standards Institute 2012 guidelines. CONCLUSION There has been re-emergence of susceptibility to first line antibiotics and a notable decline in MDR strains of S. Typhi. We have a very high resistance to NA and decreasing susceptibility to ciprofloxacin. Third generation cephalosporins and azithromycin seem to be effective therapeutic options. Judicious use of these antibiotics is mandatory to prevent emergence of resistant strains.
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Affiliation(s)
- L Singhal
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Handa R, Jain RS, Nagpal K, Prakash S, Bhana I, Sisodiya MS, Gupta PK. EHMTI-0261. Idiopathic intracranial hypertension presenting as acute onset bilateral visual loss. J Headache Pain 2014. [PMCID: PMC4180373 DOI: 10.1186/1129-2377-15-s1-c21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Yadav SK, Swami D, Kumar P, Meena MK, Maurya CK, Gupta PK, Ganesan K, Jain AK, Bhattacharya R. Acute inhalation toxicity of smoke of fentanyl and its 1-substituted analogs in Swiss albino mice. Cell Mol Biol (Noisy-le-grand) 2014; 60:1-9. [PMID: 25208041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/03/2014] [Indexed: 06/03/2023]
Abstract
Fentanyl (N-(1-phenethyl-4-piperidinyl)propionanilide) is a synthetic, potent narcotic analgesic agent. However, it is known to have several side effects, which led to synthesis and evaluation of its new analogs for the management of pain. We have earlier reported the comparative bioassay of fentanyl and its eight 1-substituted analogs (1-8) in mice. Three compounds, viz., N-(1-(2-phenoxyethyl)-4-piperidinyl)propionanilide (2), N-isopropyl-3-(4-(N-phenylpropionamido)piperidin-1-yl)propanamide (5), and N-t-butyl-3-(4-(N-phenylpropionamido)piperidin-1-yl)propanamide (6) were found to be more effective and less toxic compared to fentanyl. The present study reports the comparative acute inhalation toxicity of smoke of fentanyl and its three analogs, viz., 2, 5, and 6 in mice. Animals were exposed to different concentrations of smoke generated by heating the compounds. Exposure was performed in a head only all glass static exposure assembly for 15 min to determine the median lethal concentration (LC50). The breathing pattern and various respiratory parameters of the animals were also monitored online using a polygraph. Out of three compounds tested, analog 5 was found to be most toxic (LC50 = 2820 mg/m3) while 2 was least toxic (LC50 = >8000 mg/m3). All the compounds caused long lasting respiratory depression in a dose-dependent manner, which did not completely resolve even after discontinuation of exposure. Aerodynamic median diameter and geometric standard deviation of smoke particles was determined employing eight-stage Andersen sampler. The particles were found to be within the respirable range. The study, however, concludes that due to possible decomposition of the compounds by heating or its poor absorption by the alveolar surface, the present inhalation technique cannot be employed to generate smoke of fentanyl and its analogs for any medical or surreptitious use.
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Affiliation(s)
- S K Yadav
- Defence Research and Development Establishment Pharmacology and Toxicology Division Gwalior India
| | - D Swami
- Defence Research and Development Establishment Pharmacology and Toxicology Division Gwalior India
| | - P Kumar
- Defence Research and Development Establishment Pharmacology and Toxicology Division Gwalior India
| | - M K Meena
- Defence Research and Development Establishment Pharmacology and Toxicology Division Gwalior India
| | - C K Maurya
- Defence Research and Development Establishment Synthetic Chemistry Division Gwalior India
| | - P K Gupta
- Defence Research and Development Establishment Synthetic Chemistry Division Gwalior India
| | - K Ganesan
- Defence Research and Development Establishment Synthetic Chemistry Division Gwalior India
| | - A K Jain
- Jiwaji University School of Studies in Zoology Gwalior India
| | - R Bhattacharya
- Defence Research and Development Establishment Pharmacology and Toxicology Division Gwalior India rahul@drde.drdo.in
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Sumithra TG, Chaturvedi VK, Gupta PK, Siju SJ, Susan C, Bincy J, Laxmi U, Sunita SC, Rai AK. Development of a simple method for the rapid identification of organisms causing anthrax by coagglutination test. Biologicals 2014; 42:316-21. [PMID: 25151655 DOI: 10.1016/j.biologicals.2014.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 07/30/2014] [Indexed: 11/28/2022] Open
Abstract
A protective antigen (PA) based coagglutination test was optimized in the present study for the specific and sensitive identification of bacteria causing anthrax in a cost effective and less risky manner. The test showed 100% specificity and sensitivity up to 9 × 10(3) formalinized vegetative cells or 11 ng of PA. The optimized test also detected anthrax toxin directly from the serum as well as blood of anthrax infected animals indicating the potential application for direct diagnosis of anthrax under field conditions.
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Affiliation(s)
- T G Sumithra
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - V K Chaturvedi
- Principal Scientist & Head, Division of Biological Products, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - P K Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - S J Siju
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - C Susan
- Division of Pathology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - J Bincy
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - U Laxmi
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - S C Sunita
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
| | - A K Rai
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, U.P. 243122, India.
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Dash P, Sahoo PK, Gupta PK, Garg LC, Dixit A. Immune responses and protective efficacy of recombinant outer membrane protein R (rOmpR)-based vaccine of Aeromonas hydrophila with a modified adjuvant formulation in rohu (Labeo rohita). Fish Shellfish Immunol 2014; 39:512-523. [PMID: 24937805 DOI: 10.1016/j.fsi.2014.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
Despite the importance and success of developing a candidate vaccine against Aeromonas hydrophila infection in fish, little is known about the molecular mechanisms of the vaccine-induced immunoprotection in Indian major carp, Labeo rohita, primarily due to lack of information on most of the immune related genes of the species. In this study, a novel candidate antigen recombinant outer membrane protein R (rOmpR) of A. hydrophila was evaluated as a vaccine candidate along with a modified adjuvant formulation. Protective efficacy of the rOmpR immunization was assessed in terms of survival against A. hydrophila challenge as well as modulation of immune response in vaccinated fish after 1, 3, 6, 12, 24, 72 h and 10 days post-injection (using immune gene expression analysis) and 10, 28, 56 and 140 days post-injection (serum immune parameter analysis). The generated immune response was compared with a formalin-killed A. hydrophila antigen preparation using mineral oil only and modified adjuvant alone. We report a variable up-regulation of the immune-related genes viz., lysozyme G, complement factor 4, immunoglobulin M, β2-microglobulin, major histocompatibility complex I and II, and interleukin-1β in anterior kidney and spleen tissues at early time points post-immunization in all the groups, when compared to the control fish. The vaccinated fish also showed an increase in serum natural hemolysin titer, lysozyme and myeloperoxidase activities, and antibody titer irrespective of vaccine formulations as compared to control fish on days 10, 28 and 56. However, the increase in the serum parameters was more pronounced on day 140 in rOmpR-modified adjuvant injected group, indicating the modulatory role of this new vaccine formulation. Upon challenge with live A. hydrophila on days 56 and 140 post-immunization, significantly reduced percent mortality was noted in the group immunized with modified adjuvant based rOmpR vaccine formulation. Taken together, our results suggest that rOmpR along with modified adjuvant could potentially be used as a vaccine formulation to handle A. hydrophila infection on a long-term basis.
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Affiliation(s)
- P Dash
- Fish Health Management Division, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, India
| | - P K Sahoo
- Fish Health Management Division, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, India.
| | - P K Gupta
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India
| | - L C Garg
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - A Dixit
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India
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Das K, Uppal A, Saini RK, Varshney GK, Mondal P, Gupta PK. Hyper-Rayleigh scattering from gold nanoparticles: effect of size and shape. Spectrochim Acta A Mol Biomol Spectrosc 2014; 128:398-402. [PMID: 24682054 DOI: 10.1016/j.saa.2014.02.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 06/03/2023]
Abstract
We report hyper-Rayleigh scattering (HRS) properties of gold nanoparticles (GNPs) of five different shapes, quasi-spherical (∼10 and ∼20 nm diameter), rod (aspect ratio ∼2), and branched shapes, tetrapod, flower and star with 800 nm, 150 fs laser excitation. Using ∼10 nm spherical GNPs as reference, the first hyperpolarizability (β) values were calculated for all other shapes. Star and flower shaped GNPs have the highest hyperpolarizability (∼130 and ∼52 times higher, respectively), while rod and tetrapod shaped GNPs only have modest enhancement (∼7 times), which is similar to ∼20 nm size quasi-spherical particles. These enhancements are attributed to reduced symmetry as well as the presence of sharp tips on GNP surface. When the β values are normalized with respect to the number of atoms per particle, the flower and star shaped GNPs still have the highest hyperpolarizability values. The polar plots of vertically polarized HRS signal as a function of the angle of polarization of the incoming incident light shows two lobes, indicating that excitation is predominantly dipolar in nature although the size of some GNPs are big enough to show a quadrupolar response. It is believed that the presence of sharp tips at the surface of these large sized GNPs is responsible for the observed dipolar response. This study shows that GNPs having sharp tips might be a better candidate when their nonlinear properties are used for sensing applications.
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Affiliation(s)
- K Das
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore 452013, MP, India.
| | - A Uppal
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore 452013, MP, India
| | - R K Saini
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore 452013, MP, India
| | - G K Varshney
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore 452013, MP, India
| | - P Mondal
- Indus Synchrotrons Utilization Division, Raja Ramanna Center for Advanced Technology, Indore 452013, MP, India
| | - P K Gupta
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore 452013, MP, India
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Gupta PK, Gupta RK, Garg RK, Rai Y, Roy B, Pandey CM, Malhotra HS, Narayana PA. DTI correlates of cognition in conventional MRI of normal-appearing brain in patients with clinical features of subacute combined degeneration and biochemically proven vitamin B(12) deficiency. AJNR Am J Neuroradiol 2013; 35:872-7. [PMID: 24263693 DOI: 10.3174/ajnr.a3785] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Vitamin B12 deficiency may cause neural injury that results in cognitive deficits. The main purpose of our study was to evaluate morphometric and microstructural changes in the brain and relate them to cognition in subacute combined degeneration of the spinal cord and patients with biochemically deficient vitamin B12. MATERIALS AND METHODS Fifty-one patients were recruited and underwent nerve-conduction velocity tests and routine hematologic examinations. Serum vitamin B12 and homocystine levels were also measured. All patients and 46 age- and sex-matched controls underwent cervical spine and brain MR imaging along with cognition tests. MR imaging included conventional scans and DTI. Voxel-based morphometry was performed for determining the WM and GM volumes, based on T1-weighted images. DTI measures that included fractional anisotropy, ADC, radial diffusivity, and axial diffusivity were determined by using tract-based statistics. RESULTS None of the patients showed any abnormality on conventional MR imaging. No significant changes in GM and WM volumes were observed in patients compared with controls. Significant reductions in the fractional anisotropy and an increase in ADC and radial diffusivity values were observed in multiple brain regions in patients compared with controls. These changes were confirmed on the region-of-interest analysis. Neuropsychological scores were significantly different in patients compared with controls and showed significant correlation with fractional anisotropy and radial diffusivity in a few brain regions. CONCLUSIONS Microstructural changes are seen in WM regions on DTI in patients with vitamin B12 deficiency and correlate with cognition scores. DTI can be used for objective assessment of microstructural changes in the brain in vitamin B12 deficiency.
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Affiliation(s)
- P K Gupta
- From the Department of Neurology (P.K.G., R.K.Garg, H.S.M.), King George's Medical University, Lucknow, Uttar Pradesh, India
| | - R K Gupta
- Department of Radiology and Imaging (R.K.Gupta, B.R.), Fortis Memorial Research Institute, Gurgaon, Haryana, India
| | - R K Garg
- From the Department of Neurology (P.K.G., R.K.Garg, H.S.M.), King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Y Rai
- Department of Radiodiagnosis (Y.R.)
| | - B Roy
- Department of Radiology and Imaging (R.K.Gupta, B.R.), Fortis Memorial Research Institute, Gurgaon, Haryana, India
| | - C M Pandey
- Biostatistics (C.M.P.), Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - H S Malhotra
- From the Department of Neurology (P.K.G., R.K.Garg, H.S.M.), King George's Medical University, Lucknow, Uttar Pradesh, India
| | - P A Narayana
- Department of Diagnostic and Interventional Imaging (P.A.N.), University of Texas Medical School at Houston, Houston, Texas
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Kanafi MM, Ramesh A, Gupta PK, Bhonde RR. Dental pulp stem cells immobilized in alginate microspheres for applications in bone tissue engineering. Int Endod J 2013; 47:687-97. [PMID: 24127887 DOI: 10.1111/iej.12205] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/12/2013] [Indexed: 01/09/2023]
Abstract
AIM To immobilize dental pulp stem cells (DPSC) in alginate microspheres and to determine cell viability, proliferation, stem cell characteristics and osteogenic potential of the immobilized DPSCs. METHODOLOGY Human DPSCs isolated from the dental pulp were immobilized in 1% w/v alginate microspheres. Viability and proliferation of immobilized DPSCs were determined by trypan blue and MTT assay, respectively. Stem cell characteristics of DPSCs post immobilization were verified by labelling the cells with CD73 and CD90. Osteogenic potential of immobilized DPSCs was assessed by the presence of osteocalcin. Alizarin red staining and O-cresolphthalein complexone method confirmed and quantified calcium deposition. A final reverse transcriptase PCR evaluated the expression of osteogenic markers - ALP, Runx-2 and OCN. RESULTS More than 80% of immobilized DPSCs were viable throughout the 3-week study. Proliferation appeared controlled and consistent unlike DPSCs in the control group. Presence of CD73 and CD90 markers confirmed the stem cell nature of immobilized DPSCs. The presence of osteocalcin, an osteoblastic marker, was confirmed in the microspheres on day 21. Mineralization assays showed high calcium deposition indicating elevated osteogenic potential of immobilized DPSCs. Osteogenic genes- ALP, Runx-2 and OCN were also upregulated in immobilized DPSCs. Surprisingly, immobilized DPSCs in the control group cultured in conventional stem cell media showed upregulation of osteogenic genes and expressed osteocalcin. CONCLUSION Dental pulp stem cells immobilized in alginate hydrogels exhibit enhanced osteogenic potential while maintaining high cell viability both of which are fundamental for bone tissue regeneration.
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Affiliation(s)
- M M Kanafi
- Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, India
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Swami MK, Patel HS, Geethu P, Uppal A, Kushwaha PK, Gupta PK. Effect of gold nanoparticles on depolarization characteristics of Intralipid tissue phantom. Opt Lett 2013; 38:2855-7. [PMID: 23903162 DOI: 10.1364/ol.38.002855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report results of studies on the effect of different shapes and sizes of gold nanoparticles (GNPs) on the depolarization characteristics of Intralipid tissue phantoms. For a given extinction coefficient, the absorption characteristics of the GNPs contributed more to the depolarization of the turbid medium, and the contribution of scattering was significant only for the larger-sized particles. For rod-shaped GNPs, their depolarization plays an important role in the low scattering regime in which the depolarization properties of the nanoparticles (NPs) dominate in the turbid medium even if the contribution of the scattering from the NPs is about an order of magnitude less. For highly scattering samples, GNP absorption significantly modulates the depolarization spectra of the turbid medium.
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Affiliation(s)
- M K Swami
- Laser Biomedical Applications and Instrumentations Division, Raja Ramanna Centre for Advanced Technology, Indore, India
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Biswal M, Singh G, Jain V, Appannanavar SB, Hallur V, Gupta PK, Malvi S, Taneja N, Sethi S. P201: First report in the world of Mycobacterium bacteremicum causing a cluster of postlaparotomy surgical wound infections. Antimicrob Resist Infect Control 2013. [PMCID: PMC3688203 DOI: 10.1186/2047-2994-2-s1-p201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
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Topdar N, Kundu A, Sinha MK, Sarkar D, Das M, Banerjee S, Kar CS, Satya P, Balyan HS, Mahapatra BS, Gupta PK. A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.). Tsitol Genet 2013; 47:3-13. [PMID: 23821949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report the first complete microsatellite genetic map of jute (Corchorus olitorius L.; 2n = 2x = 14) using an F6 recombinant inbred population. Of the 403 microsatellite markers screened, 82 were mapped on the seven linkage groups (LGs) that covered a total genetic distance of 799.9 cM, with an average marker interval of 10.7 cM. LG5 had the longest and LG7 the shortest genetic lengths, whereas LG1 had the maximum and LG7 the minimum number of markers. Segregation distortion of microsatellite loci was high (61%), with the majority of them (76%) skewed towards the female parent. Genomewide non-parametric single-marker analysis in combination with multiple quantitative trait loci (QTL)-models (MQM) mapping detected 26 definitive QTLs for bast fibre quality, yield and yield-related traits. These were unevenly distributed on six LGs, as colocalized clusters, at genomic sectors marked by 15 microsatellite loci. LG1 was the QTL-richest map sector, with the densest colocalized clusters of QTLs governing fibre yield, yield-related traits and tensile strength. Expectedly, favorable QTLs were derived from the desirable parents, except for nearly all of those of fibre fineness, which might be due to the creation of new gene combinations. Our results will be a good starting point for further genome analyses in jute.
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Affiliation(s)
- N Topdar
- Biotechnology Unit, Division of Crop Improvement, Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata 700120, West Bengal, India
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Gupta RK, Awasthi R, Garg RK, Kumar N, Gupta PK, Singh AK, Sahoo P, Paliwal VK, Prasad KN, Pandey CM, Rathore RKS. T1-weighted dynamic contrast-enhanced MR evaluation of different stages of neurocysticercosis and its relationship with serum MMP-9 expression. AJNR Am J Neuroradiol 2013. [PMID: 23179648 DOI: 10.3174/ajnr.a3346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Epileptogenesis in NCC is associated with perilesional inflammation and disruption in BBB. We quantified BBB in different stages of NCC by using DCE-MR imaging to look for the differences in perfusion indices and to correlate these indices with serum MMP-9 expression. MATERIALS AND METHODS DCE-MR imaging along with conventional MR imaging was performed in 57 single cysticercous brain lesions to quantify the kep, K(trans), and ve around the lesions, which were in different stages of evolution. There were 6 lesions in the vesicular stage and 17 lesions each in the colloidal, granular-nodular, and calcified stages. Serum MMP-9 was quantified from all patients, whereas perfusion indices were quantified from all stages except for the vesicular stage. RESULTS We observed significant differences among the 3 stages of NCC in serum MMP-9 expression as well as DCE-derived kep values. In addition, kep showed a strongly significant positive correlation with MMP-9 expression when modeled with the individual stage of the disease as well as with all stages when pooled together. Other DCE-derived hemodynamic and pharmacokinetic parameters showed inconsistent differences with each stage of the disease. The correlation of DCE-derived parameters with serum MMP-9 expression and edema volume also showed inconsistency with the stage of the disease. CONCLUSIONS We conclude that kep correlates best with serum MMP-9 expression among the pharmacokinetic indices and most closely represents the degree of BBB breakdown, which is highest in the colloidal stage and lowest in the calcified stage. kep may be used as a noninvasive image biomarker of BBB breakdown in different stages of NCC.
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Affiliation(s)
- R K Gupta
- Department of Radiodiagnosis, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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Varshney GK, Saini RK, Gupta PK, Das K. Effect of curcumin on the diffusion kinetics of a hemicyanine dye, LDS-698, across a lipid bilayer probed by second harmonic spectroscopy. Langmuir 2013; 29:2912-8. [PMID: 23391287 DOI: 10.1021/la304778d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The diffusion kinetics of a hemicyanine dye, LDS-698, across model membrane bilayers was studied in real time by the surface specific second harmonic technique. Using liposomes made from different headgroups, it has been established that the diffusion is initiated by electrostatic adsorption of the positively charged dye to the outer surface of negatively charged liposomes and its time constant is affected by the rigidity of the bilayer. In the presence of the liphophilic drug curcumin (curcumin/lipid mole ratio ~ 0.2), the diffusion of LDS-698 was observed to be faster by ~56 times (from 780 to 14 s) at 25 °C. Under similar curcumin concentration, when cholesterol containing liposomes are used at 2 °C, the observed diffusion time constant increases from 14 to 65 s, showing that the effect of curcumin is superior to the effect of increasing bilayer rigidity on the diffusion process. Control experiments with other lipophilic molecules such as DPH and Nile Red showed that the effect of liposomal curcumin is superior. Consistent with previous reports of curcumin affecting the bilayer organization, this study additionally demonstrates increased permeability of liposomal curcumin, in particular against organic cations. It is speculated that origin of this enhanced membrane permeability by lipophilic molecules may depend upon the interaction of the molecule with the polar headgroup region of the lipid which, in turn, is expected to depend on the chemical structure of the molecule.
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Affiliation(s)
- G K Varshney
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, M.P., India
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Sharma K, Gupta N, Sharma A, Singh G, Gupta PK, Rajwanshi A, Varma SC, Sharma M. Multiplex polymerase chain reaction using insertion sequence 6110 (IS6110) and mycobacterial protein fraction from BCG of Rm 0.64 in electrophoresis target genes for diagnosis of tuberculous lymphadenitis. Indian J Med Microbiol 2013; 31:24-8. [DOI: 10.4103/0255-0857.108714] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
It is shown that by appropriately choosing the periodicity of a blinking optical trap only larger sized colloidal spheres can be selectively trapped out of a mixed population. This happens because smaller sized, more agile, spheres escape out of the trap volume during the off period of the trap beam. Therefore, by scanning an array of blinking traps over a mixed sample, bigger spheres can be forced to move with the traps and eventually could be taken to the output side. Experimental demonstration of sorting between 1 µm and 2 µm diameter silica spheres is presented.
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Affiliation(s)
- R Dasgupta
- Laser Biomedical Applications and Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, India.
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Saini RK, Dube A, Gupta PK, Das K. Diffusion of chlorin-p6 across phosphatidyl choline liposome bilayer probed by second harmonic generation. J Phys Chem B 2012; 116:4199-205. [PMID: 22414064 DOI: 10.1021/jp205335z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have investigated the diffusion of the photosensitizer Chlorin-p(6) (Cp(6)) across a egg lecithin lipid bilayer at different pH by the Second Harmonic Generation (SHG) method. Cp(6) has three ionizable carboxylic acid groups, and consequently, neutral and several ionic forms of Cp(6) are expected to be present in the pH range 3-8. The absorption spectra of Cp(6) get considerably modified in the presence of liposomes as the pH is decreased indicating that the drug liposome binding is pH dependent. The first pK(a) of interconversion (D-C) has been identified at pH ~7.0 by fluorescence measurement in an earlier work. In this work, the second pK(a) of interconversion (C-B) has been identified at pH ~4.8 by the hyper-Rayleigh scattering method. At acidic pH (3, 4, and 5), where species A, B, and C are dominant, the addition of liposomes to a Cp(6) solution generates an instantaneous rise (less than 1 s) in the second harmonic (SH) signal followed by decays whose time constants ranged from ten to hundreds of seconds. The instantaneous rise is attributed to the adsorption of Cp(6) to the outer lipid bilayer, and the decay is attributed to the diffusion of the neutral and charged (A and B) species of the drug. The observed fast and slow time constants for diffusion in the pH range 3-5 are attributed to the neutral (A) and ionic form (B) of Cp(6), respectively. At pH 6, the intensity of the generated SH signals on the addition of liposome reduced, and at physiological pH, it was too weak to be detected. These results are consistent with previous studies that show that the interaction between Cp(6) and egg-PC liposomes is pH dependent. At lower pH due to the presence of the hydrophobic species (A and B) of Cp(6), its interaction with liposomes is strong, and at higher pH, the abundance of the negatively charged hydrophilic species (C and D) decreases the interaction with the like charged liposomes. We have also studied the effect of increasing the bilayer rigidity by decreasing the temperature of the medium or by incorporating 50 mol % cholesterol in the lipid bilayer and observed that lowering of temperature has more profound effect on the diffusion rates. The characteristics of the SH signal changed significantly when liposomes incorporating 50 mol % cholesterol were used at a low (3 °C) temperature. Under these conditions, the SH signal consisted of an instantaneous (<1s) followed by a slower rise (10-90s), and then, it decayed on a much longer time scale. This slow rise of the SH signal at pH 3 and 4 may be attributed to the temperature dependent adsorption of the anionic species (B) of Cp(6) with the liposomes. Further investigations are required in order to understand clearly the pH dependent diffusion of this drug across lipid bilayers.
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Affiliation(s)
- R K Saini
- Laser Bio-Medical Applications & Instrumentation Division, Raja Ramanna Center for Advanced Technology, Indore, MP 452013, India
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Denry I, Holloway JA, Gupta PK. Effect of crystallization heat treatment on the microstructure of niobium-doped fluorapatite glass-ceramics. J Biomed Mater Res B Appl Biomater 2012; 100:1198-205. [PMID: 22454333 DOI: 10.1002/jbm.b.32684] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/04/2012] [Accepted: 01/14/2012] [Indexed: 11/09/2022]
Abstract
Our goal was to study the effect of heat treatment temperature and heating rate on the microstructure and crystalline phases and assess the domain of existence of submicrometer fluorapatite crystals in niobium-doped fluorapatite glass-ceramics for biomedical applications. Glass-ceramic specimens were prepared by casting and heat treatment between 700 and 1200°C using a fast or a slow heating rate. The microstructure was characterized by atomic force microscopy and scanning electron microscopy. Crystalline phases were analyzed by x-ray diffraction. AFM of the as-cast glass revealed that amorphous phase separation occurred in this system. XRD confirmed the presence of fluorapatite in all specimens, together with forsterite and enstatite at higher temperatures. Both heating rate and heat treatment temperature strongly influenced microstructure and crystallinity. A dual microstructure with submicrometer fluorapatite crystals and polygonal forsterite crystals was obtained when slow heating rates and crystallization temperatures between 950 and 1100°C were used. Needle-shaped fluorapatite crystals appeared after heat treatment above 1100°C. Fast heating rates led to an increase in crystal size. Heat treatment temperatures should remain below 1100°C, together with slow heating rates, to prevent crystal dissolution, and preserve a dual microstructure of finely dispersed submicrometer crystals without growth of needle-shaped crystals.
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Affiliation(s)
- I Denry
- Department of Prosthodontics, and Dows Institute for Dental Research, College of Dentistry, The University of Iowa, Iowa City, Iowa 52242-1010, USA.
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Gupta PK, Ramanan B, Lynch TG, Gupta H, Fang X, Balters M, Johanning JM, Longo GM, MacTaggart JN, Pipinos II. Endovascular repair of abdominal aortic aneurysm does not improve early survival versus open repair in patients younger than 60 years. Eur J Vasc Endovasc Surg 2012; 43:506-12. [PMID: 22386386 DOI: 10.1016/j.ejvs.2012.02.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 02/01/2012] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Multiple randomised trials have demonstrated lower perioperative mortality after endovascular aneurysm repair (EVAR) compared to open surgical repair for infrarenal abdominal aortic aneurysms (AAAs). However, in these trials the mortality advantage for EVAR is being lost within 2 years of repair and the patients evaluated are relatively older with no study specifically comparing EVAR and open repair for patients younger than 60 years of age. DESIGN A retrospective analysis of prospectively collected data. MATERIALS AND METHODS Patients younger than 60 years of age who underwent EVAR and open surgical repair for elective infrarenal AAA were identified from the 2007-09 National Surgical Quality Improvement Program (NSQIP) - a prospective database maintained at 237 centres across the United States. Univariate and multivariate analyses were performed. RESULTS Of the 651 patients, 369 (56.7%) underwent EVAR and 282 (43.3%) underwent open repair. Thirty-day mortality for EVAR and open repair were 1.1% and 0.4%, respectively. This was not significantly different on univariate (P = 0.22) as well as multivariate (P = 0.69) analysis after controlling for other co-morbidities. On multivariate analysis, body mass index, history of stroke and bleeding disorder prior to surgery were associated with a higher 30-day mortality after AAA repair (combined open and EVAR). CONCLUSIONS These contemporary results demonstrate that the 30-day mortality rate after open repair is similar to that after EVAR in patients younger than 60 years with infrarenal AAA.
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Affiliation(s)
- P K Gupta
- Department of Surgery, Creighton University, Omaha, NE 68131, USA
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Affiliation(s)
- P Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
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Bhaumik I, Bhatt R, Ganesamoorthy S, Saxena A, Karnal AK, Gupta PK, Sinha AK, Deb SK. Temperature-dependent index of refraction of monoclinic Ga2O3 single crystal. Appl Opt 2011; 50:6006-6010. [PMID: 22086027 DOI: 10.1364/ao.50.006006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present temperature-dependent refractive index along crystallographic b[010] and a direction perpendicular to (100)-plane for monoclinic phase (β) Ga(2)O(3) single crystal grown by the optical floating zone technique. The experimental results are consistent with the theoretical result of Litimein et al.1. Also, the Sellmeier equation for wavelengths in the range of 0.4-1.55 μm is formulated at different temperatures in the range of 30-175 °C. The thermal coefficient of refractive index in the above specified range is ~10(-5)/°C.
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Affiliation(s)
- Indranil Bhaumik
- Laser Materials Development and Devices Division, Raja Ramanna Centre for Advanced Technology, Indore-452 013, India.
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