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Son SE, Gupta PK, Hur W, Choi H, Lee HB, Park Y, Seong GH. Determination of glycated albumin using a Prussian blue nanozyme-based boronate affinity sandwich assay. Anal Chim Acta 2020; 1134:41-49. [DOI: 10.1016/j.aca.2020.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/04/2020] [Accepted: 08/10/2020] [Indexed: 01/07/2023]
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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, AND FRACTALS 2020; 138:109944. [PMID: 32536759 PMCID: PMC7254021 DOI: 10.1016/j.chaos.2020.109944] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [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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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 MOLECULAR BIOLOGY 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] [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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Pachauri N, Lakshmi GBVS, Sri S, Gupta PK, Solanki PR. Silver molybdate nanoparticles based immunosensor for the non-invasive detection of Interleukin-8 biomarker. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 113:110911. [PMID: 32487373 DOI: 10.1016/j.msec.2020.110911] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/14/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
In this study, we report the silver molybdate nanoparticles (β-Ag2MoO4 NPs) based non-invasive and sensitive electrochemical immunosensor for label-free detection of Interleukin-8 (IL-8) biomarker. The X-ray diffraction and Raman spectroscopy studies confirm the cubic spinel structures of β-Ag2MoO4 NPs. High-resolution transmission electron microscopy study depicted average size of β-Ag2MoO4 NPs as 27.15 nm. The cleaned indium tin oxide coated glass substrates were coated with spin-coated thin films of Ag2MoO4 NPs. These electrodes used for covalently immobilization of antibodies specific to IL-8 (Anti-IL-8) using EDC-NHS chemistry and unbound activated sites blocked by bovine serum albumin. Electrochemical response was obtained in the range of 1 fg mL-1 to 40 ng mL-1 and the sensitivity was found to be 7.03 μA ng-1mL cm-2 with LOD of 90 pg mL-1. Spiked samples prepared by human saliva were tested and found efficient detection with this immunoelectrode.
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Jahagirdar PS, Gupta PK, Kulkarni SP, Devarajan PV. Intramacrophage Delivery of Dual Drug Loaded Nanoparticles for Effective Clearance of Mycobacterium tuberculosis. J Pharm Sci 2020; 109:2262-2270. [PMID: 32240695 DOI: 10.1016/j.xphs.2020.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/28/2020] [Accepted: 03/18/2020] [Indexed: 12/26/2022]
Abstract
The escalating global burden of tuberculosis necessitates radical strategies to curb its spread. In this study, rifampicin (RIF), a first line anti-tubercular antibiotic and curcumin (CUR), a promising antimycobacterial compound were co-encapsulated in polymeric nanoparticles to achieve intramacrophage delivery and improved Mycobacterium tuberculosis clearance. The dual loaded nanoparticles revealed average size ∼400 nm, low polydispersity and zeta potential of -26.89 ± 2.9 mV. Near complete release of both drugs from nanoparticles in artificial lysosomal fluid proposed drug release after macrophage internalisation. Nanoparticles were nontoxic to RAW 264.7 macrophages and aided 1.5-fold higher drug internalisation compared to free drugs. Enriched intracellular internalisation and lysosomal presence of nanoparticles was ascertained by confocal microscopy. Comparable minimum inhibitory concentration (MIC) of free RIF and CUR and nanoparticle encapsulated RIF and CUR confirmed retention of drug properties. High efficacy against Mycobacterium tuberculosis infected macrophages with RIF-CUR nanoparticles at 25× MIC (98.03 ± 2.5%), with complete clearance above 50× MIC suggests the dual loaded nanoparticles as a promising new nanosystem for tackling tuberculosis.
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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] [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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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] [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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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] [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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Gupta PK, Misra S, Verma R, Soni N, Lamin JC, Mishra RK, Behari S, Kumar S. Primary intradural cervical spine melanocytoma: A rare tumor and review of literature. Neurol India 2019; 65:653-657. [PMID: 28488646 DOI: 10.4103/neuroindia.ni_171_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Vaishnavi C, Gupta PK, Sharma M, Kochhar R. Pancreatic disease patients are at higher risk for Clostridium difficile infection compared to those with other co-morbidities. Gut Pathog 2019; 11:17. [PMID: 31044014 PMCID: PMC6480607 DOI: 10.1186/s13099-019-0300-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/13/2019] [Indexed: 12/29/2022] Open
Abstract
Background Surveillance of Clostridium difficile infection (CDI) in patients with underlying diseases is important because use of prophylactic antibiotics makes them prone to CDI. Epidemiology of CDI in this high-risk population is poorly understood. A study was conducted to evaluate the impact of CDI in patients with specific underlying co-morbidities. Method A total of 2036 patients, whose fecal samples were processed for C. difficile toxin A and B assay by ELISA formed the basis of study. Patients with underlying diseases were classified based on the organ/kind of disease as pancreatic (n = 340), renal (n = 408), hepatic (n = 245), malignant (n = 517) and miscellaneous disease (n = 526). Laboratory records of clinical and demographic details were reviewed. The association of CDI with age, gender, antibiotic receipt, clinical symptoms and underlying co-morbidities was analyzed. Variation in CDI cases based on age groups was also investigated. Result Clostridium difficile toxin positivity was 21.6% in general, whereas it was 30.6% in the pancreatic, 17.9% in the renal, 19.6%, in the hepatic, 21.3% in the malignancy and 20.0% in the miscellaneous disease groups. Toxin positivity was the lowest (14.8%) for female gender under renal disease and the highest (31.8%) for patients aged 40 to < 60 years, under pancreatic disease. Bloody diarrhea was a significant predictor for C. difficile toxin positivity. C. difficile toxin status irrespective to the underlying diseases was neither dependent on gender, age-groups or the number of antibiotics used. Association between patients’ gender, age and antibiotics receipt with underlying disease conditions, respective to C. difficile toxin status showed significance in relation to male gender (p < 0.05), age 40 to < 60 years (p = 0.03) and those receiving single (p = 0.09) or multiple antibiotics (p = 0.07). Conclusion Pancreatic disease patients are at a higher risk for developing CDI, and particularly male gender, age 40 to < 60 years and those receiving antibiotics are at significant risk.
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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: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [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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Jahagirdar PS, Gupta PK, Kulkarni SP, Devarajan PV. Polymeric curcumin nanoparticles by a facile in situ method for macrophage targeted delivery. Bioeng Transl Med 2019; 4:141-151. [PMID: 30680325 PMCID: PMC6336664 DOI: 10.1002/btm2.10112] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/22/2018] [Accepted: 08/22/2018] [Indexed: 01/05/2023] Open
Abstract
Targeting macrophages is a promising strategy for improved therapy of intracellular infections as macrophages exhibit rapid phagocytosis of particles >200 nm. Entrapment of Curcumin (CUR) in nanocarriers could provide bioenhancement and macrophage targeting. We present a simple and facile in situ nanoprecipitation approach for instantaneous and on-site generation of curcumin nanoparticles (ISCurNP). ISCurNP optimised by Box-Behnken design exhibited average size of 208.25 ± 7.55 nm and entrapment efficiency of 90.16 ± 1.17%. Differential scanning calorimetry and X-Ray diffraction confirmed amorphization of CUR in ISCurNP. Sustained release was observed over 72 hr in vitro at lysosomal pH 4.5. Rapid and high uptake in RAW 264.7 macrophages was confirmed by flow cytometry and high performance liquid chromatography. Confocal microscopy established localisation of ISCurNP in lysosomal compartment. The facile in situ nanoprecipitation method provides simple, scalable technology to enable macrophage targeted delivery of CUR, with great promise for improved therapy of intracellular infections.
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Avasthi A, Basu D, Subodh BN, Gupta PK, Goyal BL, Sidhu BS, Gargi PD, Sharma A, Ghosh A. Epidemiology of dependence on illicit substances, with a special focus on opioid dependence, in the State of Punjab, India: Results from two different yet complementary survey methods. Asian J Psychiatr 2019; 39:70-79. [PMID: 30593987 DOI: 10.1016/j.ajp.2018.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/21/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND We used two different yet complementary methods to capture the 'hidden population' of illicit substance users in the state of Punjab, India: Rapid Assessment Survey (RAS) and Punjab Drug Use Monitoring Survey (P-DUMS). METHODOLOGY For the RAS component, following a pilot study, Respondent Driven Sampling was used to recruit 6600 community-dwelling substance dependent persons aged 11-60 years from all the 22 districts of Punjab. Size was estimated using benchmark-multiplier method, and prevalence was calculated by projecting these data to the source population. For the P-DUMS component, data were collected on 7421 inpatients from 75 government de-addiction centres from 19 districts of Punjab. RESULTS Subjects In both RAS and P-DUMS were primarily opioid dependent (88% in RAS and 83% in P-DUMS). Heroin (inhaled/injected) emerged as the commonest opioid in both RAS (46%) and P-DUMS (52%), though 30.5% of the RAS sample also used the prescription opioid tramadol. Using the benchmark-multiplier method, 0.27 million (2.5% of the source population) were estimated to be opioid dependent, of which nearly 78,000 (0.7% of the source population) were injecting opioid users (IDUs), predominantly heroin (62%) but also buprenorphine (32.5%). High-risk behaviour was reported by nearly 60% of IDUs. Only 14% of the RAS sample had ever visited any de-addiction centre, and only 2.8% individuals had been admitted to a de-addiction centre in the past year. CONCLUSION There is a substantive problem of opioid dependence in this difficult-to-reach population of Punjab, with low treatment access. Misuse of prescription opioids along with IDU also raises concern.
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Chauhan D, Gupta PK, Solanki PR. Electrochemical immunosensor based on magnetite nanoparticles incorporated electrospun polyacrylonitrile nanofibers for Vitamin-D3 detection. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2018; 93:145-156. [DOI: 10.1016/j.msec.2018.07.036] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
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Gupta PK, Khan ZH, Solanki PR. Improved electrochemical performance of metal doped Zirconia nanoparticles for detection of Ochratoxin-A. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [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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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. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1046-1064. [PMID: 32291004 DOI: 10.1071/fp17326] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [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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Vaishnavi C, Gupta PK, Sharma M, Kochhar R. Quantification of major constituents of biofilms in occluded pancreatic stents. J Med Microbiol 2018; 67:1225-1231. [PMID: 30051805 DOI: 10.1099/jmm.0.000805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Biofilms comprise bacterial populations enclosed in a matrix that attaches to surfaces such as medical stents. We characterized the biofilm components in occluding pancreatic stents and investigated potential factors for the formation of the biofilms. METHODOLOGY The clinical details of 24 patients (M : F, 15 : 9) undergoing pancreatic stent retrieval were noted and the retrieved stents were processed for the quantification of biofilm proteins and polysaccharides and the molecular identification of bacteria. RESULTS The patients' ages ranged from 16 to 62 years. The underlying indications for stent insertion were bile duct stone prophylaxis against post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (n=7; 29.1 %) and pancreatic ductal leaks (n=17; 70.9 %). The retrieved stent sizes were 5 Fr (n=5; 20.8 %) and 7 Fr (n=19; 79.2 %), with a mean insertion duration of 103 days. The polybacteria detected by PCR in 95.8 % of the stents were Pseudomonas (n=8), Staphylococcus (n=8), Serratia (n=5), Aeromonas (n=4), Proteus (n=4), Klebsiella (n=4), Escherichia coli (n=4), Enterococcus (n=4), Streptococcus (n=4), Citrobacter (n=3), Bacillus (n=2), Enterobacter (n=1), Vibrio (n=1) and Clostridium (n=1). Several other organisms were identified by sequencing. The mean protein concentration was 0.585±0.29 mg ml-1 and the mean polysaccharide concentration was 0.054±0.03 mg ml-1. No significant differences were observed in the quantity of proteins and polysaccharides (P=0.933) for various factors, namely gender, presence of cholangitis, indications for stenting, stent sizes and duration of indwelling stents. Age was found to be a significant (P=0.013) factor for protein deposition for those aged >50 years. CONCLUSION The majority of the pancreatic stents grew polymicro-organisms, and those from patients aged >50 years showed significant deposition of protein, which is a key element in biofilm formation. Understanding the constituents of the biofilms in pancreatic stents could be very useful in developing future strategies for the prevention of biofilm formation.
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Sharma PP, Gupta PK, Solanki PR. Effect of pH on the Structural Properties and Bioactivity of Zirconia Nanoparticles. ACTA ACUST UNITED AC 2018. [DOI: 10.1166/asl.2018.10864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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] [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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Gupta PK, Pachauri N, Khan ZH, Solanki PR. One pot synthesized zirconia nanoparticles embedded in amino functionalized amorphous carbon for electrochemical immunosensor. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.11.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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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] [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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Avasthi A, Basu D, Subodh BN, Gupta PK, Malhotra N, Rani P, Sharma S. Pattern and prevalence of substance use and dependence in the Union Territory of Chandigarh: Results of a rapid assessment survey. Indian J Psychiatry 2017; 59:284-292. [PMID: 29085086 PMCID: PMC5659077 DOI: 10.4103/psychiatry.indianjpsychiatry_327_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Substance misuse is a matter of major public health concern in India. House-to-house survey, though an appealing method to generate population-level estimates, has limitations for estimating prevalence rates of use of illicit and rare substances. MATERIALS AND METHODS In this rapid assessment survey (RAS), respondent-driven sampling was used to recruit substance-using individuals from the field. Size of the substance-using population was estimated using the "benchmark-multiplier" method. This figure was then projected to the entire population of the Union Territory (U.T) of Chandigarh. Focused group discussions were used to study the perceptions and views of the substance users regarding various aspects of substance use. RESULTS Prevalence of any substance dependence in the U.T of Chandigarh was estimated to be 4.65%. Dependence rates on opioids, cannabinoids, and sedative hypnotics were found to be 1.53%, 0.52%, and 0.015%, respectively. Prevalence of injectable opioids was calculated to be 0.91%. Injectable buprenorphine was the most commonly used opioid, followed by bhukhi/doda/opium and heroin. A huge gap was found between the prevalence rates of substance-using population and those seeking treatment. CONCLUSION RAS can be a useful method to determine the prevalence of illicit and rare substances. Our survey shows that the use of substance including that of opioids is highly prevalent in the U.T of Chandigarh. The findings of this survey can have implications for policymaking.
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Avasthi A, Basu D, Subodh BN, Gupta PK, Malhotra N, Rani P, Sharma S. Substance use and dependence in the Union Territory of Chandigarh: Results of a household survey using a multistage stratified random sample. Indian J Psychiatry 2017; 59:275-283. [PMID: 29085085 PMCID: PMC5659076 DOI: 10.4103/psychiatry.indianjpsychiatry_326_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Substance misuse is a global health and social problem with major adverse consequences. A number of regional studies on prevalence of substance use and dependence have been carried out in India; but methodologically robust data from Chandigarh are sparse. METHODOLOGY A house-to-house survey was carried out to estimate the prevalence of substance use and dependence in an adequate multistage-stratified random sample in the Union Territory (UT) of Chandigarh, using standardized instruments and predefined measures. Two thousand individuals (1000 each from urban and rural sites) from 743 households were interviewed. RESULTS Lifetime use of any substance was reported in 21.26% households (8.01% of all respondents; 13.6% males and 1.01% females). Current use was reported in 6.55% of respondents. Prevalence rates of both lifetime and annual/current substance dependence were 2.96% (4.74% for males and 0.72% for females). Alcohol (6.72%) was the most common substance to be ever used by respondents, followed by tobacco (3.34%), opioids (0.17%), and hypnotics (0.04%). Lifetime dependence rates were found to be 1.76%, 2.28%, 0.04% and 0.17% for alcohol, tobacco, hypnotics, and opioids, respectively. None reported the use of cannabinoids, inhalants, or stimulants. Substance users were more likely to be married, employed, and in higher income group as compared to those who never used substance. Only 3.78% substance users had ever sought treatment for the same. CONCLUSION Substance use is prevalent in the UT of Chandigarh, with a higher prevalence in males. Substance users hardly ever seek treatment for substance use. This highlights the need of awareness and community-level services for the treatment of substance use disorders.
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Wake MC, Gupta PK, Mikos AG. Fabrication of Pliable Biodegradable Polymer foams to Engineer Soft Tissues. Cell Transplant 2017; 5:465-73. [PMID: 8800514 DOI: 10.1177/096368979600500405] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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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