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Aftab R, Akbar F, Afroz A, Asif A, Khan MR, Rehman N, Zeeshan N. Mentha piperita silver nanoparticle-loaded hydrocolloid film for enhanced diabetic wound healing in rats. J Wound Care 2024; 33:xlviii-lx. [PMID: 38457268 DOI: 10.12968/jowc.2024.33.sup3a.xlviii] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
OBJECTIVE To investigate the role of Mentha piperita silver nanoparticle-loaded carbopol gel for enhanced wound healing in a diabetic rat model. This research further aims to explore bioactive compounds derived from Mentha piperita obtained from high altitude. METHOD Methanolic extracts of Mentha piperita (MP), Mentha spicata (MS) and Mentha longifolia (ML) were used to synthesise silver nanoparticles (AgNP). AgNP synthesis was confirmed by ultraviolet-visible (UV-Vis) spectroscopy, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The antioxidant activity was assessed by 2, 2-diphenyl-1-picrylhydrazyl (DDPH) assay. Antiglycation potential was determined by measuring the fluorescent advanced glycation end products. The bioactive compound identified in the Mentha piperita methanolic (MPM) fraction through electrospray ionisation tandem mass spectrometric analysis (ESI-MS) was responsible for the highest antiglycation. The effects of MPM and MPM.AgNP-loaded Carbopol (Sanare Lab, India) on wound healing were compared in male, alloxan-induced, diabetic albino rats (200-250g), divided into control and treated groups. Effects on wound healing were assessed via histopathology. RESULTS UV-Vis and FTIR confirmed NP synthesis with peaks for flavonoids and polyphenols. SEM and XRD explored the cubical, 30-63nm crystalline NP. The maximum antioxidant and antiglycation potential was observed in order of; MP.AgNP>MS.AgNP>ML.AgNP. The highest antioxidant activity was observed by methanolic and aqueous MP.AgNPs (88.55% and 83.63%, respectively) at 2mg.ml-1, and (75.16% and 69.73%, respectively) at 1mg.ml-1, compared to ascorbic acid (acting as a positive control, 90.01%). MPM.AgNPs demonstrated the best antiglycation potential of 75.2% and 83.3% at 1mg.ml-1 and 2mg.ml-1, respectively, comparable to positive control (rutin: 88.1%) at 14 days post-incubation. A similar trend was observed for antimicrobial activity against Bacillus subtilis, Micrococcus luteus and Escherichia coli with an inhibition zone of 21mm, 21.6mm and 24.6mm. Rosmarinic acid was the active compound present in Mentha piperita, as identified by ESI-MS. MPM.AgNP-loaded Carbopol resulted in 100% wound closure compared with control at 20 days post-wounding. In the treatment group, re-epithelialisation was achieved by day 18, compared with 25 days for the positive control group. CONCLUSION MPM.AgNP-loaded Carbopol demonstrated safer and more effective biological properties, hence accelerating the diabetic excision wound healing process in alloxan-induced diabetic rats.
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Affiliation(s)
- Reema Aftab
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Punjab, Pakistan
| | - Fatima Akbar
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Punjab, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Punjab, Pakistan
| | - Awais Asif
- Nawaz Sharif Medical College, University of Gujrat, Hafiz Hayat Campus Gujrat, Punjab, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Nadia Zeeshan
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus Gujrat, Punjab, Pakistan
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Maqbool Z, Shahbaz Farooq M, Rafiq A, Uzair M, Yousuf M, Ramzan Khan M, Huo S. Unlocking the potential of biochar in the remediation of soils contaminated with heavy metals for sustainable agriculture. Funct Plant Biol 2024; 51:FP23257. [PMID: 38310926 DOI: 10.1071/fp23257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/20/2023] [Indexed: 02/06/2024]
Abstract
Agricultural soils contaminated with heavy metals (HMs) impose a threat to the environmental and to human health. Amendment with biochar could be an eco-friendly and cost-effective option to decrease HMs in contaminated soil. This paper reviews the application of biochar as a soil amendment to immobilise HMs in contaminated soil. We discuss the technologies of its preparation, their specific properties, and effect on the bioavailability of HMs. Biochar stabilises HMs in contaminated soil, enhance the overall quality of the contaminated soil, and significantly reduce HM uptake by plants, making it an option in soil remediation for HM contamination. Biochar enhances the physical (e.g. bulk density, soil structure, water holding capacity), chemical (e.g. cation exchange capacity, pH, nutrient availability, ion exchange, complexes), and biological properties (e.g. microbial abundance, enzymatic activities) of contaminated soil. Biochar also enhances soil fertility, improves plant growth, and reduces the plant availability of HMs. Various field studies have shown that biochar application reduces the bioavailability of HMs from contaminated soil while increasing crop yield. The review highlights the positive effects of biochar by reducing HM bioavailability in contaminated soils. Future work is recommended to ensure that biochars offer a safe and sustainable solution to remediate soils contaminated with HMs.
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Rubab M, Jannat S, Freeg H, Abbas H, Attia KA, Fiaz S, Zahra N, Uzair M, Inam S, Shah AH, Kimiko I, Naeem MK, Khan MR. Evaluation of functional kompetitive allele-specific PCR (KASP) markers for selection of drought-tolerant wheat ( Triticum aestivum) genotypes. Funct Plant Biol 2024; 51:NULL. [PMID: 37308134 DOI: 10.1071/fp23032] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/06/2023] [Indexed: 06/14/2023]
Abstract
Wheat (Triticum aestivum ) is a major crop around the globe and different techniques are being used for its productivity enhancement. Germplasm evaluation to improve crop productivity mainly depends on accurate phenotyping and selection of genotypes with a high frequency of superior alleles related to the trait of interest. Therefore, applying functional kompetitive allele-specific PCR (KASP) markers for drought-related genes is essential to characterise the genotypes for developing future climate-resilient wheat crop. In this study, eight functional KASP markers and nine morphological traits were employed to evaluate the 40 wheat genotypes for drought tolerance. Morphological traits showed significant variation (P ≤0.05) among the genotypes, except tiller count (TC), fresh root weight (FRW) and dry root weight (DRW). PCA biplot showed that 63.3% phenotypic variation was explained by the first two PCs under control treatment, while 70.8% variation was explained under drought treatment. It also indicated that root length (RL) and primary root (PR) have considerable variations among the genotypes under both treatments and are positively associated with each other. Hence, the findings of this study suggested that both these traits could be used as a selection criterion to classify the drought-tolerant wheat genotypes. KASP genotyping accompanied by morphological data revealed that genotypes Markaz, Bhakar Star, China 2, Aas and Chakwal-50 performed better under drought stress. These outperforming genotypes could be used as parents in developing drought-tolerant wheat genotypes. Hence, KASP genotyping assay for functional genes or significant haplotypes and phenotypic evaluation are prerequisites for a modern breeding program.
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Affiliation(s)
- Marya Rubab
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan; and Department of Biotechnology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Summiya Jannat
- Department of Biotechnology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Haytham Freeg
- Rice Biotechnology Lab., Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh 33717, Egypt
| | - Hina Abbas
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, POX 2455-11451, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan
| | - Asad Hussain Shah
- Department of Biotechnology, University of Kotli, Kotli, Azad Jammu and Kashmir, Pakistan
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata 950-2181, Japan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad 45500, Pakistan
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Zaman Z, Iqbal R, Jabbar A, Zahra N, Saleem B, Kiran A, Maqbool S, Rasheed A, Naeem MK, Khan MR. Genetic Signature Controlling Root System Architecture in Diverse Spring Wheat Germplasm. Physiol Plant 2024; 176:e14183. [PMID: 38343301 DOI: 10.1111/ppl.14183] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 02/15/2024]
Abstract
Roots are the main sensing organ, initiating multiple signaling pathways in response to abiotic factors, including nutrients, drought, and salt stress. A focus on improving the root system architecture is a key strategy to mitigate these stresses in wheat crop. In the present study, a diversity panel comprising indigenous landraces and historical cultivars from Pakistan was characterized for the root system architecture (RSA) and important loci were identified using a genome-wide association study (GWAS). RSA of the diversity panel was characterized 30 days after sowing in brunch tubes, and root images were taken. A high-throughput root imaging analysis using Rhizovision software was performed by setting the scale to extract the eight RSA traits and four plant biomass-related traits. GWAS identified 323 association signals for 12 root and biomass traits present on all wheat chromosomes, while the most important and reliable genetic loci (based on pleotropic loci and candidate genes) were identified on chromosomes 2A, 2B, 5A, 5D, 6A, 7B, and 7D for RSA. SNP annotation and transcriptome profiling identified nine candidate genes regulating the RSA and plant biomass traits, including ROOTLESS WITH UNDETECTABLE MERISTEM1, MYB TRANSCRIPTION FACTOR4, BRASSINOSTEROID INSENSITIVE1, SLENDER RICE1, AUXIN-RESPONSIVE FACTOR25, SCARECROW, NARROW LEAF2, PIN-FORMED1 AND PHOSPHATE TRANSCRIPTION FACTOR1. This study provided pre-breeding information for deep-rooting genotypes and associated markers that will accelerate the incorporation of such traits in breeding.
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Affiliation(s)
- Zahra Zaman
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Rubab Iqbal
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
- Department of Botany, University of Agriculture, Faisalabad
| | - Abdul Jabbar
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Pakistan
| | - Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Aysha Kiran
- Department of Botany, University of Agriculture, Faisalabad
| | - Saman Maqbool
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
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Zahra N, Uzair M, Zaid IU, Attia KA, Inam S, Fiaz S, Abdallah RM, Naeem MK, Farooq U, Rehman N, Ali GM, Xu J, Li Z, Khan MR. The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress. Mol Biol Rep 2023; 51:22. [PMID: 38110786 DOI: 10.1007/s11033-023-08998-x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars. METHODS AND RESULTS In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data. CONCLUSION These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.
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Affiliation(s)
- Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Imdad Ullah Zaid
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan.
| | - Rizk M Abdallah
- Department of Rice, Field Crops Research Institute, ARC, Sakha, Kafrelshiekh, 33717, Egypt
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | | | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan.
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Maqbool S, Naseer S, Zahra N, Rasool F, Qayyum H, Majeed K, Jahanzaib M, Sajjad M, Fayyaz M, Naeem MK, Khan MR, Zhang H, Rasheed A, Li H. RNAseq of diverse spring wheat cultivars released during last 110 years. Sci Data 2023; 10:884. [PMID: 38065977 PMCID: PMC10709563 DOI: 10.1038/s41597-023-02769-w] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Here, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson's correlation coefficients between root phenotypes and expression of root-specific genes varied from -0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.
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Affiliation(s)
- Saman Maqbool
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Samar Naseer
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nageen Zahra
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Fatima Rasool
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Humaira Qayyum
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Khawar Majeed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Jahanzaib
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Oilseeds Research Program, Crop Sciences Institute (CSI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Sajjad
- Department of BioSciences, COMSATS University, Islamabad, Pakistan
| | - Muhammad Fayyaz
- Crop Disease Research Institute, National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Hao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Awais Rasheed
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Huihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China.
- Nanfan Research Institute, CAAS, Sanya, Hainan, China.
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Rehman OU, Uzair M, Farooq MS, Saleem B, Attacha S, Attia KA, Farooq U, Fiaz S, El-Kallawy WH, Kimiko I, Khan MR. Comprehensive insights into the regulatory mechanisms of lncRNA in alkaline-salt stress tolerance in rice. Mol Biol Rep 2023; 50:7381-7392. [PMID: 37450076 DOI: 10.1007/s11033-023-08648-2] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Alkaline-salt is one of the abiotic stresses that slows plant growth and developmental processes and threatens crop yield. Long non-coding RNAs (lncRNAs) are endogenous RNA found in plants that engage in a variety of cellular functions and stress responses. METHOD lncRNAs act as competing endogenous RNAs (ceRNA) and constitute a new set of gene control. The precise regulatory mechanism by which lncRNAs function as ceRNAs in response to alkaline-salt stress remains unclear. We identified alkaline-salt responsive lncRNAs using transcriptome-wide analysis of two varieties including alkaline-salt tolerant [WD20342 (WD)] and alkaline-salt sensitive [Caidao (CD)] rice cultivar under control and alkaline-salt stress treated [WD20342 (WDT, and Caidao (CDT)] conditions. RESULTS Investigating the competitive relationships between mRNAs and lncRNAs, we next built a ceRNA network involving lncRNAs based on the ceRNA hypothesis. Expression profiles revealed that a total of 65, 34, and 1549 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs were identified in alkaline-salt tolerant WD (Control) vs. WDT (Treated). Similarly, 75 DE-lncRNAs, 34 DE-miRNAs, and 1725 DE-mRNAs (including up-regulated and down-regulated) were identified in alkaline-salt sensitive CD (Control) vs. CDT (Treated), respectively. An alkaline-salt stress ceRNA network discovered 321 lncRNA-miRNA-mRNA triplets in CD and CDT, with 32 lncRNAs, 121 miRNAs, and 111 mRNAs. Likewise, 217 lncRNA-miRNA-mRNA triplets in WD and WDT revealed the NONOSAT000455-osa_miR5809b-LOC_Os11g01210 triplet with the highest degree as a hub node with the most significant positive correlation in alkaline-salt stress response. CONCLUSION The results of our investigation indicate that osa-miR5809b is dysregulated and plays a part in regulating the defense response of rice against alkaline-salt stress. Our study highlights the regulatory functions of lncRNAs acting as ceRNAs in the mechanisms underlying alkaline-salt resistance in rice.
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Affiliation(s)
- Obaid Ur Rehman
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
| | - Muhammad Shahbaz Farooq
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Safira Attacha
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, Science College, King Saud University, POX, Riyadh, 2455-11451, Saudi Arabia.
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Wael H El-Kallawy
- Agriculture Research Center, (ARC), Rice Research and Training Center, (RRTC) Sakha, Field Crop Research Institute, Sakha, Egypt
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
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Saleem B, Uzair M, Noman M, Attia KA, Zhang M, Alwahaibi MS, Zahra N, Naeem MK, Mohammed AA, Fiaz S, Kimiko I, Khan MR. Evaluation of sugarcane promising clones based on the morphophysiological traits developed from fuzz. PeerJ 2023; 11:e15646. [PMID: 37456879 PMCID: PMC10340094 DOI: 10.7717/peerj.15646] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023] Open
Abstract
Sugarcane is one of the critical commercial crops and principal sources of ethanol and sugar worldwide. Unfavorable conditions and poor seed setting rates hinder variety development in sugarcane. Countries like Pakistan directly import fuzz (true seed) and other propagation material from the USA, China, Brazil, etc. In this study, we imported fuzz from China, developed 29 genotypes germinating in the glasshouse, and evaluated at field conditions along with two local checks (CPF-251 and HSF-240). Morphophysiological data were recorded, including plant height (PH), cane length (CL), internodal length (IL), tiller number (TN), brix percentage (B), cane diameter (CD), chlorophyll a (Chl. a), chlorophyll b (Chl. b), and total chlorophyll (T. Chl). Results showed highly significant (p < 0.001) differences among the sugarcane accessions for all the studied traits. High broad-sense heritability (81.89% to 99.91%) was recorded for all the studied parameters. Genetic Advance (GA) ranges from 4.6% to 65.32%. The highest GA was observed for PH (65.32%), followed by CL (63.28%). Chlorophyll leaching assay was also performed at different time points (0, 50, 100, 150, and 200 min). All the genotypes showed the same leaching trend at all times, and better performing genotypes showed less leaching compared to poor performing, indicating the high amount of cutin and wax on the leaf surface. Correlation analysis showed that PH, CL, IL, and TN had significant associations. Principal components analysis (PCA) further confirms these results. Based on PCA and correlation results, PH, CL, IL, and TN can be utilized as a selection criterion for sugarcane improvement. Genotypes such as NS-4a, NS-5, NS-6, NS-8, NS-9, and NS-15 are recommended for future breeding programs related to sugarcane variety development.
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Affiliation(s)
- Bilal Saleem
- Functional Genomics and Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Uzair
- Functional Genomics and Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Noman
- Functional Genomics and Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
- Plant Molecular Physiology Laboratory, Department of Biology, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muqing Zhang
- Guangxi Key Lab for Sugarcane Biology, State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Mona S. Alwahaibi
- Department of Botany and Microbiology, College of Science, King Saud University, Al-Riyadh, Saudi Arabia
| | - Nageen Zahra
- Functional Genomics and Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- Functional Genomics and Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Arif A. Mohammed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Niigata, Japan
| | - Muhammad Ramzan Khan
- Functional Genomics and Bioinformatics Lab, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
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Errum A, Rehman N, Uzair M, Inam S, Ali GM, Khan MR. CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits. Funct Integr Genomics 2023; 23:66. [PMID: 36840774 DOI: 10.1007/s10142-023-00989-2] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023]
Abstract
Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T0-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T1 and T2 progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.
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Affiliation(s)
- Aliya Errum
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
- PARC Institute of Advanced Studies in Agriculture (PIASA), Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | | | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.
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10
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Rafique A, Afroz A, Zeeshan N, Rashid U, Khan MAU, Irfan M, Chatha W, Khan MR, Rehman N. Production of Sitobion avenae-resistant Triticum aestivum cvs using laccase as RNAi target and its systemic movement in wheat post dsRNA spray. PLoS One 2023; 18:e0284888. [PMID: 37163535 PMCID: PMC10171587 DOI: 10.1371/journal.pone.0284888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023] Open
Abstract
Among the wheat biotic stresses, Sitobion avenae is one of the main factors devastating the wheat yield per hectare. The study's objective was to find out the laccase (lac) efficacy; as a potential RNAi target against grain aphids. The Sitobion avenae lac (Salac) was confirmed by Reverse Transcriptase-PCR. Gene was sequenced and accession number "ON703252" was allotted by GenBank. ERNAi tool was used to design 143 siRNA and one dsRNA target. 69% mortality and 61% reduction in lac expression were observed 8D-post lac DsRNA feeding. Phylogenetic analysis displayed the homology of grain aphid lac gene with peach potato, pea, and Russian wheat aphids. While Salac protein was found similar to the Russian grain, soybean, pea, and cedar bark aphid lac protein multi-copper oxidase. The dsRNAlac spray-induced silencing shows systematic translocation from leaf to root; with maximum lac expression found in the root, followed by stem and leaf 9-13D post-spray; comparison to control. RNAi-GG provides the Golden Gate cloning strategy with a single restriction ligation reaction used to achieve lac silencing. Agrobacterium tumefaciens mediated in planta and in-vitro transformation was used in the study. In vitro transformation, Galaxy 2012 yielded a maximum transformation efficiency (1.5%), followed by Anaj 2017 (0.8%), and Punjab (0.2%). In planta transformation provides better transformation efficiencies with a maximum in Galaxy 2012 (16%), and a minimum for Punjab (5%). Maximum transformation efficiency was achieved for all cultivars with 250 μM acetosyringone and 3h co-cultivation. Galaxy 2012 exhibited maximum transformation efficiency, and aphid mortality post-feeding transgenic wheat.
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Affiliation(s)
- Asma Rafique
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - Nadia Zeeshan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - Umer Rashid
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | | | - Muhammad Irfan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - Waheed Chatha
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
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11
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Bashir S, Rehman N, Fakhar Zaman F, Naeem MK, Jamal A, Tellier A, Ilyas M, Silva Arias GA, Khan MR. Genome-wide characterization of the NLR gene family in tomato ( Solanum lycopersicum) and their relatedness to disease resistance. Front Genet 2022; 13:931580. [PMID: 36544493 PMCID: PMC9760929 DOI: 10.3389/fgene.2022.931580] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Nucleotide-binding leucine-rich-repeat receptors (NLR), the largest group of genes associated with plant disease resistance (R), have attracted attention due to their crucial role in protecting plants from pathogens. Genome-wide studies of NLRs have revealed conserved domains in the annotated tomato genome. The 321 NLR genes identified in the tomato genome have been randomly mapped to 12 chromosomes. Phylogenetic analysis and classification of NLRs have revealed that 211 genes share full-length domains categorized into three major clades (CNL, TNL, and RNL); the remaining 110 NLRs share partial domains and are classified in CN, TN, and N according to their motifs and gene structures. The cis-regulatory elements of NLRs exhibit the maximum number of these elements and are involved in response to biotic and abiotic stresses, pathogen recognition, and resistance. Analysis of the phylogenetic relationship between tomato NLRs and orthologs in other species has shown conservation among Solanaceae members and variation with A. thaliana. Synteny and Ka/Ks analyses of Solanum lycopersicum and Solanum tuberosum orthologs have underscored the importance of NLR conservation and diversification from ancestral species millions of years ago. RNA-seq data and qPCR analysis of early and late blight diseases in tomatoes revealed consistent NLR expression patterns, including upregulation in infected compared to control plants (with some exceptions), suggesting the role of NLRs as key regulators in early blight resistance. Moreover, the expression levels of NLRs associated with late blight resistance (Solyc04g007060 [NRC4] and Solyc10g008240 [RIB12]) suggested that they regulate S. lycopersicum resistance to P. infestans. These findings provide important fundamental knowledge for understanding NLR evolution and diversity and will empower the broader characterization of disease resistance genes for pyramiding through speed cloning to develop disease-tolerant varieties.
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Affiliation(s)
- Sehrish Bashir
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan,*Correspondence: Nazia Rehman, ; Muhammad Ramzan Khan,
| | - Fabia Fakhar Zaman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Atif Jamal
- Crop Disease Research Institute, National Agricultural Research Center, Islamabad, Pakistan
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Muhammad Ilyas
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Gustavo Adolfo Silva Arias
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan,*Correspondence: Nazia Rehman, ; Muhammad Ramzan Khan,
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12
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Saleem B, Farooq U, Rehman OU, Aqeel M, Farooq MS, Naeem MK, Inam S, Ajmal W, Rahim AA, Chen M, Kalsoom R, Uzair M, Fiaz S, Attia K, Alafari HA, Khan MR, Yu G. Genome-wide and molecular characterization of the DNA replication helicase 2 ( DNA2) gene family in rice under drought and salt stress. Front Genet 2022; 13:1039548. [PMID: 36506305 PMCID: PMC9728955 DOI: 10.3389/fgene.2022.1039548] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
Rice plants experience various biotic (such as insect and pest attack) and abiotic (such as drought, salt, heat, and cold etc.) stresses during the growing season, resulting in DNA damage and the subsequent losses in rice production. DNA Replication Helicase/Nuclease2 (DNA2) is known to be involved in DNA replication and repair. In animals and yeast DNA2 are well characterized because it has the abilities of both helicase and nuclease, it plays a crucial role in DNA replication in the nucleus and mitochondrial genomes. However; they are not fully examined in plants due to less focused on plants damage repair. To fill this research gap, the current study focused on the genome-wide identification and characterization of OsDNA2 genes, along with analyses of their transcriptional expression, duplication, and phylogeny in rice. Overall, 17 OsDNA2 members were reported to be found on eight different chromosomes (2, 3, 4, 6, 7, 9, 10, and 11). Among these chromosomes (Chr), Chr4 contained a maximum of six OsDNA2 genes. Based on phylogenetic analysis, the OsDNA2 gene members were clustered into three different groups. Furthermore, the conserved domains, gene structures, and cis-regulatory elements were systematically investigated. Gene duplication analysis revealed that OsDNA2_2 had an evolutionary relationship with OsDNA2_14, OsDNA2_5 with OsDNA2_6, and OsDNA2_1 with OsDNA2_8. Moreover, results showed that the conserved domain (AAA_11 superfamily) were present in the OsDNA2 genes, which belongs to the DEAD-like helicase superfamily. In addition, to understand the post-transcriptional modification of OsDNA2 genes, miRNAs were predicted, where 653 miRNAs were reported to target 17 OsDNA2 genes. The results indicated that at the maximum, OsDNA2_1 and OsDNA2_4 were targeted by 74 miRNAs each, and OsDNA2_9 was less targeted (20 miRNAs). The three-dimensional (3D) structures of 17 OsDNA2 proteins were also predicted. Expression of OsDNA2 members was also carried out under drought and salt stresses, and conclusively their induction indicated the possible involvement of OsDNA2 in DNA repair under stress when compared with the control. Further studies are recommended to confirm where this study will offer valuable basic data on the functioning of DNA2 genes in rice and other crop plants.
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Affiliation(s)
- Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Shahbaz Farooq
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Amna Abdul Rahim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rabia Kalsoom
- School of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Kotb Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hayat Ali Alafari
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| | - Guoping Yu
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China,China National Rice Research Institute, Hangzhou, China,Hainan Yazhou Bay Seed Lab, Sanya, China,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
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13
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Farooq MS, Khaskheli MA, Uzair M, Xu Y, Wattoo FM, Rehman OU, Amatus G, Fatima H, Khan SA, Fiaz S, Yousuf M, Ramzan Khan M, Khan N, Attia KA, Ercisli S, Golokhvast KS. Inquiring the inter-relationships amongst grain-filling, grain-yield, and grain-quality of Japonica rice at high latitudes of China. Front Genet 2022; 13:988256. [PMID: 36338987 PMCID: PMC9635508 DOI: 10.3389/fgene.2022.988256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
The widespread impacts of projected global and regional climate change on rice yield have been investigated by different indirect approaches utilizing various simulation models. However, direct approaches to assess the impacts of climatic variabilities on rice growth and development may provide more reliable evidence to evaluate the effects of climate change on rice productivity. Climate change has substantially impacted rice production in the mid-high latitudes of China, especially in Northeast China (NEC). Climatic variabilities occurring in NEC since the 1970s have resulted in an obvious warming trend, which made this region one of the three major rice-growing regions in China. However, the projections of future climate change have indicated the likelihood of more abrupt and irregular climatic changes, posing threats to rice sustainability in this region. Hence, understanding the self-adaptability and identifying adjustive measures to climate variability in high latitudes has practical significance for establishing a sustainable rice system to sustain future food security in China. A well-managed field study under randomized complete block design (RCBD) was conducted in 2017 and 2018 at two study sites in Harbin and Qiqihar, located in Heilongjiang province in NEC. Four different cultivars were evaluated: Longdao-18, Longdao-21 (longer growth duration), Longjing-21, and Suijing-18 (shorter growth duration) to assess the inter-relationships among grain-filling parameters, grain yield and yield components, and grain quality attributes. To better compare the adaptability mechanisms between grain-filling and yield components, the filling phase was divided into three sub-phases (start, middle, and late). The current study evaluated the formation and accumulation of the assimilates in superior and inferior grains during grain-filling, mainly in the middle sub-phase, which accounted for 59.60% of the yield. The grain yields for Suijing-18, Longjing-21, Longdao-21, and Longdao-18 were 8.02%, 12.78%, 17.19%, and 20.53% higher in Harbin than those in Qiqihar, respectively in 2017, with a similar trend observed in 2018. At Harbin, a higher number of productive tillers was noticed in Suijing-18, with averages of 17 and 15 in 2017 and 2018, respectively. The grain-filling parameters of yield analysis showed that the filling duration in Harbin was conducive to increased yield but the low dry weight of inferior grains was a main factor limiting the yield in Qiqihar. The average protein content values in Harbin were significantly higher (8.54% and 9.13%) than those in Qiqihar (8.34% and 9.14%) in 2017 and 2018, respectively. The amylose content was significantly higher in Harbin (20.03% and 22.27%) than those in Qiqihar (14.44% and 14.67%) in 2017 and 2018, respectively. The chalkiness percentage was higher in Qiqihar, indicating that Harbin produced good quality rice. This study provides more direct evidence of the relative changes in rice grain yield due to changes in grain-filling associated with relative changes in environmental components. These self-adaptability mechanisms to climatic variability and the inter-relationships between grain-filling and grain yield underscore the urgent to investigate and explore measures to improve Japonica rice sustainability, with better adaptation to increasing climatic variabilities. These findings may also be a reference for other global rice regions at high latitudes in addressing the impacts of climate change on future rice sustainability.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maqsood Ahmed Khaskheli
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Muhammad Ramzan Khan, ; Maqsood Ahmed Khaskheli, ; Kirill S. Golokhvast,
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Yinlong Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fahad Masood Wattoo
- Department of Plant Breeding and Genetics, PMAS- Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Gyilbag Amatus
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sher Aslam Khan
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- *Correspondence: Muhammad Ramzan Khan, ; Maqsood Ahmed Khaskheli, ; Kirill S. Golokhvast,
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, Florida University, Gainesville, FL, United States
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Kirill S. Golokhvast
- Siberian Federal Scientific Center of Agrobiotechnology RAS, Krasnoobsk, Russia
- *Correspondence: Muhammad Ramzan Khan, ; Maqsood Ahmed Khaskheli, ; Kirill S. Golokhvast,
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14
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Afridi M, Ahmad K, Malik SS, Rehman N, Yasin M, Khan SM, Hussain A, Khan MR. Correction: Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants. J Genet Eng Biotechnol 2022; 20:139. [PMID: 36156165 PMCID: PMC9512943 DOI: 10.1186/s43141-022-00419-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mahideen Afridi
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University, Islamabad, 44000, Pakistan
| | - Shahana Seher Malik
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
| | - Muhammad Yasin
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
| | - Shujaul Mulk Khan
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Adil Hussain
- Food and Biotechnology Research Centre (FBRC), Pakistan Council of Scientific and Industrial Research (PCSIR) Laboratories Complex, Ferozepur Road, Lahore, Punjab, 56400, Pakistan
| | - Muhammad Ramzan Khan
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.,National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
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15
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Nazir N, Imran M, Bodlah I, Mahmood K, Khan MR, Osman K, Rasool A, Usman M, Din AU. Distribution, host range and toxicity assessment of different insecticides on Bactrocera diversa Coquillett, 1904 (Diptera: Tephritidae). BRAZ J BIOL 2022; 84:e263261. [PMID: 36102373 DOI: 10.1590/1519-6984.263261] [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: 04/20/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023] Open
Abstract
The present study was conducted to investigate the array of hosts, distribution and to evaluate the toxicity of four insecticides: imidacloprid, fipronil, cypermethrin and chlorpyrifos alone and in combination against 3rd instar maggot and adult stage of fruit fly Bactrocera diversa Coquillett, 1904 (Diptera: Tephritidae) during 2021. B. diversa maggots were found vigorously feeding inside the cucurbit hosts (pumpkin, cucumber, bitter gourd, watermelon, round melon, bottle gourd) collected from different localities of Poonch division of Azad Jammu & Kashmir, Pakistan, and this species is reported for the first time as new record to this region. Susceptibilities of B. diversa to insecticides were evaluated using topical method. Mortality was checked after 3, 6, 8 and 24h of exposure. Cypermethrin was most effective to kill 50% of both larval and adult stage with least LC50 [7.2(1.040±0.214), 17.4(0.748±0.193)], respectively followed by imidacloprid. Imidacloprid most effectively killed 90% of both larval and adult population with least LC90 value [73.2 (3.013±0.708) 16.9 (1.886±0.437)] respectively after 24 hours. Cypermethrin with chlorpyrifos most effectively killed 50 and 90 percent of both larval and adult stage of B. diversa with least LC50 value [11.3 (1.085±0.245), 2.5 (0.759±0.252)] and least LC90 value [171.3 (1.085±0.245), 121.9 (0.759±0.252)], respectively after 24h of exposure. Toxicity of each insecticide increased with exposure for longer time and increased dose. Cypermethrin is suggested as most effective against both larval and adult stages of B. diversa in combination with chlorpyrifos followed by imidacloprid.
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Affiliation(s)
- N Nazir
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Rawalakot, Azad Jammu & Kashmir, Pakistan
| | - M Imran
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Rawalakot, Azad Jammu & Kashmir, Pakistan
| | - I Bodlah
- Pir Mehr Ali Shah Arid Agriculture University, Department of Entomology, Rawalpindi, Pakistan
| | - K Mahmood
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Rawalakot, Azad Jammu & Kashmir, Pakistan
| | - M R Khan
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Rawalakot, Azad Jammu & Kashmir, Pakistan
| | - K Osman
- Alexandria University, Faculty of Agriculture, Department of Pesticide Chemistry & Toxicology, Alexandria, Egypt
| | - A Rasool
- University of Swat, Centre for Biotechnology and Microbiology, Charbagh, Pakistan
| | - M Usman
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Rawalakot, Azad Jammu & Kashmir, Pakistan
| | - A U Din
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Rawalakot, Azad Jammu & Kashmir, Pakistan
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16
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Farooq MS, Wang X, Uzair M, Fatima H, Fiaz S, Maqbool Z, Rehman OU, Yousuf M, Khan MR. Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system. Front Plant Sci 2022; 13:960641. [PMID: 36092421 PMCID: PMC9453445 DOI: 10.3389/fpls.2022.960641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3 -), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
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Afridi M, Ahmad K, Malik SS, Rehman N, Yasin M, Khan SM, Hussain A, Khan MR. Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants. J Genet Eng Biotechnol 2022; 20:124. [PMID: 35980545 PMCID: PMC9388710 DOI: 10.1186/s43141-022-00408-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/05/2022] [Indexed: 11/22/2022]
Abstract
Background Non-synchronized pods shattering in the Brassicaceae family bring upon huge yield losses around the world. The shattering process was validated to be controlled by eight genes in Arabidopsis, including SHP1, SHP2, FUL, IND, ALC, NAC, RPL, and PG. We performed genome-wide identification, characterization, and expression analysis of shattering genes in B.napus and B. juncea to gain understanding into this gene family and to explain their expression patterns in fresh and mature siliques. Results A comprehensive genome investigation of B.napus and B.juncea revealed 32 shattering genes, which were identified and categorized using protein motif structure, exon-intron organization, and phylogeny. The phylogenetic study revealed that these shattering genes contain little duplications, determined with a distinct chromosome number. Motifs of 32 shattering proteins were observed where motifs1 and 2 were found to be more conserved. A single motif was observed for other genes like Br-nS7, Br-nS9, Br-nS10, Br-jS21, Br-jS23, Br-jS24, Br-jS25, and Br-jS26. Synteny analysis was performed that validated a conserved pattern of blocks among these cultivars. RT-PCR based expressions profiles showed higher expression of shattering genes in B. juncea as compared to B.napus. SHP1, SHP2, and FUL gene were expressed more in mature silique. ALC gene was upregulated in fresh silique of B. napus but downregulation of ALC were observed in fresh silique of B. juncea. Conclusion This study authenticates the presence of shattering genes in the local cultivars of Brassica. It has been validated that the expression of shattering genes were more in B. juncea as compared to B.napus. The outcomes of this study contribute to the screening of more candidate genes for further investigation.
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Affiliation(s)
- Mahideen Afridi
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University, Islamabad, 44000, Pakistan
| | - Shahana Seher Malik
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
| | - Muhammad Yasin
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Shujaul Mulk Khan
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Adil Hussain
- Food and Biotechnology Research Centre (FBRC), Pakistan Council of Scientific and Industrial Research (PCSIR) Laboratories Complex, Ferozepur Road, Lahore, Punjab, 56400, Pakistan
| | - Muhammad Ramzan Khan
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.,National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
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Farooq MS, Uzair M, Raza A, Habib M, Xu Y, Yousuf M, Yang SH, Ramzan Khan M. Uncovering the Research Gaps to Alleviate the Negative Impacts of Climate Change on Food Security: A Review. Front Plant Sci 2022; 13:927535. [PMID: 35903229 PMCID: PMC9315450 DOI: 10.3389/fpls.2022.927535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/15/2022] [Indexed: 05/05/2023]
Abstract
Climatic variability has been acquiring an extensive consideration due to its widespread ability to impact food production and livelihoods. Climate change has the potential to intersperse global approaches in alleviating hunger and undernutrition. It is hypothesized that climate shifts bring substantial negative impacts on food production systems, thereby intimidating food security. Vast developments have been made addressing the global climate change, undernourishment, and hunger for the last few decades, partly due to the increase in food productivity through augmented agricultural managements. However, the growing population has increased the demand for food, putting pressure on food systems. Moreover, the potential climate change impacts are still unclear more obviously at the regional scales. Climate change is expected to boost food insecurity challenges in areas already vulnerable to climate change. Human-induced climate change is expected to impact food quality, quantity, and potentiality to dispense it equitably. Global capabilities to ascertain the food security and nutritional reasonableness facing expeditious shifts in biophysical conditions are likely to be the main factors determining the level of global disease incidence. It can be apprehended that all food security components (mainly food access and utilization) likely be under indirect effect via pledged impacts on ménage, incomes, and damages to health. The corroboration supports the dire need for huge focused investments in mitigation and adaptation measures to have sustainable, climate-smart, eco-friendly, and climate stress resilient food production systems. In this paper, we discussed the foremost pathways of how climate change impacts our food production systems as well as the social, and economic factors that in the mastery of unbiased food distribution. Likewise, we analyze the research gaps and biases about climate change and food security. Climate change is often responsible for food insecurity issues, not focusing on the fact that food production systems have magnified the climate change process. Provided the critical threats to food security, the focus needs to be shifted to an implementation oriented-agenda to potentially cope with current challenges. Therefore, this review seeks to have a more unprejudiced view and thus interpret the fusion association between climate change and food security by imperatively scrutinizing all factors.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Ali Raza
- College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Yinlong Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
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Rahim AA, Uzair M, Rehman N, Rehman OU, Zahra N, Khan MR. Genome-Wide Identification and Characterization of Receptor-Like Protein Kinase 1 (RPK1) Gene Family in Triticum aestivum Under Drought Stress. Front Genet 2022; 13:912251. [PMID: 35860467 PMCID: PMC9289140 DOI: 10.3389/fgene.2022.912251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/24/2022] [Indexed: 01/08/2023] Open
Abstract
Receptor-like protein kinase1 (RPK1) genes play crucial roles in plant growth and development processes, root architecture, and abiotic stress regulation. A comprehensive study of the RPK1 gene family has not been reported in bread wheat (Triticum aestivum). Here, we reported the genome-wide identification, characterization, and expression patterns of the RPK1 gene family in wheat. Results confirmed 15 TaRPK1 genes, classified mainly into three sub-clades based on a phylogenetic tree. The TaRPK1 genes were mapped on chromosomes 1–3 in the respective A, B, and D genomes. Gene structure, motif conservation, collinearity prediction, and synteny analysis were carried out systematically. A Gene ontology study revealed that TaRPK1 genes play a vital role during molecular and biological processes. We also identified 18 putative miRNAs targeting TaRPK1 genes, suggesting their roles in growth, development, and stress responses. Cis-Regulatory elements interpreted the presence of light-related elements, hormone responsiveness, and abiotic stress-related motifs in the promoter regions. The SWISS_MODEL predicted the successful models of TaRPK1 proteins with at least 30% identity to the template, a widely accepted threshold for successful modeling. In silico expression analysis in different tissues and stages suggested that TaRPK1 genes exhibited the highest expression in root tissues. Moreover, qRT-PCR further validated the higher expression of TaRPK1 genes in roots of drought-tolerant varieties compared to the drought-susceptible variety. Collectively, the present study renders valuable information on the functioning of TaRPK1 genes in wheat that will be useful in further functional validation of these genes in future studies.
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Affiliation(s)
- Amna Abdul Rahim
- National Centre for Bioinformatics (NCB), Quaid-e-Azam University, Islamabad, Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Centre for Bioinformatics (NCB), Quaid-e-Azam University, Islamabad, Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
- *Correspondence: Muhammad Ramzan Khan,
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20
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Rehman O, Uzair M, Chao H, Khan MR, Chen M. Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress. Front Plant Sci 2022; 13:892729. [PMID: 35812946 PMCID: PMC9260663 DOI: 10.3389/fpls.2022.892729] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.
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Affiliation(s)
- Obaid Rehman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Rasool F, Khan MR, Schneider M, Uzair M, Aqeel M, Ajmal W, Léon J, Naz AA. Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes. Plant Physiol Biochem 2022; 178:20-30. [PMID: 35247694 DOI: 10.1016/j.plaphy.2022.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 09/27/2021] [Revised: 01/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Drought is a big challenge for agricultural production. Root attributes are the important target traits for breeding high-yielding sustainable wheat varieties against ever changing climatic conditions. However, the transcriptomic of wheat concerning root architecture remained obscure. Here, we explored RNA-Seq based transcriptome to dissect putative genes involved in root system variations in naturally occurring six genotypes (drought-tolerant and sensitive) of wheat. Global RNA-Seq based root transcriptome analysis revealed single nucleotide polymorphisms (SNPs) variations and differentially expressed genes. Putative 56 SNPs were identified related to 15 genes involved in root architecture. Enrichment of these genes using GO terms demonstrated that differentially expressed genes (DEGs) are divided into sub-categories implicated in molecular functions, cellular components and biological processes. The KEGG analysis of DEGs in each comparison of genotype include metabolic, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and biosynthesis of antibiotics. A deeper insight into DEGs unveiled various pathways involved in drought response and positive gravitropism. These genes belong to various transcription factor families such as DOF, C3H, MYB, and NAC involved in root developmental and stress-related pathways. Local White and UZ-11-CWA-8, which are drought-tolerant genotypes, harbor over-representation of most of DEGs or transcription factors. Notably, a microtubule-associated protein MAPRE1 belonging to RP/EB family recruited in positive gravitropism was enriched. Real-time PCR analysis revealed expression of MAPRE1 and PAL genes is consistent with RNA-seq data. The presented data and genetic resources seem valuable for providing genes involved in the root system architecture of drought-tolerant and susceptible genotypes.
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Affiliation(s)
- Fatima Rasool
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
| | - Michael Schneider
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Ali Ahmed Naz
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany.
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22
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Rehman OU, Uzair M, Chao H, Fiaz S, Khan MR, Chen M. Role of the type-B authentic response regulator gene family in fragrant rice under alkaline salt stress. Physiol Plant 2022; 174:e13696. [PMID: 35502736 DOI: 10.1111/ppl.13696] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Globally, rice is being consumed as a main staple food and faces different kinds of biotic and abiotic stresses such drought, salinity, and pest attacks. Through the cytokinin signaling, Type-B authentic response regulators (ARR-Bs) respond positively towards the environmental stimuli. ARR-Bs are involved in abiotic stress tolerance and plant development but their molecular mechanisms in fragrant rice are still not fully explored. The current study showed the genome-wide characterization of OsARR-B genes under alkaline salt stress. Results showed that in total, 24 OsARR-B genes were found and divided into four subgroups on the basis of a phylogenetic analysis. These genes were located on all rice chromosomes except 8 and 10. Analysis of gene duplications, gene structure, cis-elements, protein-protein interactions, and miRNA were performed. Gene ontology analysis showed that OsARR-B genes are involved in plant development through the regulation of molecular functions, biological processes, and cellular components. Furthermore, 117 and 192 RNA editing sites were detected in chloroplast and mitochondrial genes, respectively, encoding proteins of OsARR-B. In chloroplast and mitochondrial genes, six and nine types of amino acid changes, respectively, were caused by RNA editing, showing that RNA editing has a role in the alkaline salt stress tolerance in fragrant rice. We also used a comparative transcriptome approach to study the gene expression changes in alkaline tolerant and susceptible genotypes. Under alkaline salt stress, OsARR-B5, OsARR-B7, OsARR-B9, OsARR-B10, OsARR-B16, OsARR-B22, and OsARR-B23 showed higher transcript levels in alkaline salt tolerant genotypes as compared to susceptible ones. Quantitative RT-PCR showed upregulation of gene expression in the alkaline tolerant genotypes under alkaline stress. Our study explored the gene expression profiling and RESs of two rice contrasting genotypes, which will help to understand the molecular mechanisms of alkaline salt tolerance in fragrant rice.
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Affiliation(s)
- Obaid Ur Rehman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Uzair M, Ali M, Fiaz S, Attia K, Khan N, Al-Doss AA, Ramzan Khan M, Ali Z. The Characterization of Wheat Genotypes for Salinity Tolerance Using Morpho-Physiological Indices under Hydroponic Conditions. Saudi J Biol Sci 2022; 29:103299. [PMID: 35574282 PMCID: PMC9092983 DOI: 10.1016/j.sjbs.2022.103299] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/14/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
Salinity affects plant growth, development, yield, and is a big challenge for wheat growth across the globe. Possible feasible solution is creation of salt-tolerant material, genetic variation is a criterion to developing genetically superior individuals. To assess the genetic variation for salt tolerance, nationally and internationally-derived 81 wheat genotypes were selected and evaluated in 0- and 150-mM salt in nutritional culture at seedling stage. Results indicate that salinity levels reveal significant (p ≤ 0.01) differences for fresh root weight (RW), shoot length (SL), fresh shoot weight (SW), total plant length (TL), total fresh weight (TW), root/shoot weight ratio (RSWR), root/shoot length ratio (RSLR), and relative growth rate for weight (RGR-Wt). While, there was no difference for root length (RL). Hierarchical Clustering and Pairwise correlation analysis showed TW, RGR-Wt, SL, SW, and RW were positively correlated among themselves, whereas RL had poor correlations with all the traits except TL and RSLR. Hence, selection of SL can improve the performance of other parameters. Based on PCA analysis, SW and RGR-Wt were the major discriminative components for wheat genotypes. Present study explained that shoot related parameters could be used as a selection criterion to categorize salt-tolerant genotypes. Outperforming genotypes 1104 and 1106 in saline conditions could be used as parents in creation of salt-tolerant wheat genotypes, and parameters such as SL, SW, TW, and RGR-Wt for early screening will be important for creating salt-tolerant and high yielding wheat genotypes.
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Affiliation(s)
- Muhammad Uzair
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad 45500, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad 38000, Pakistan
- Corresponding authors at: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China (M. Uzair). Department of Plant Breeding and Genetics, University of Agriculture Faisalabad 38000, Pakistan (Z. Ali).
| | - Mohsin Ali
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Haripur 22620, Khyber Pakhtunkhwa, Pakistan
| | - Kotb Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Abdullah A. Al-Doss
- Biotechnology Lab, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 2455-11451, Saudi Arabia
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad 45500, Pakistan
| | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad 38000, Pakistan
- Institute of Plant Breeding and Biotechnology, MNS-University of Agriculture, Multan 60000, Pakistan
- Corresponding authors at: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China (M. Uzair). Department of Plant Breeding and Genetics, University of Agriculture Faisalabad 38000, Pakistan (Z. Ali).
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Ahmad H, Zafar SA, Naeem MK, Shokat S, Inam S, Rehman MAU, Naveed SA, Xu J, Li Z, Ali GM, Khan MR. Impact of Pre-Anthesis Drought Stress on Physiology, Yield-Related Traits, and Drought-Responsive Genes in Green Super Rice. Front Genet 2022; 13:832542. [PMID: 35401708 PMCID: PMC8987348 DOI: 10.3389/fgene.2022.832542] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022] Open
Abstract
Optimum soil water availability is vital for maximum yield production in rice which is challenged by increasing spells of drought. The reproductive stage drought is among the main limiting factors leading to the drastic reduction in grain yield. The objective of this study was to investigate the molecular and morphophysiological responses of pre-anthesis stage drought stress in green super rice. The study assessed the performance of 26 rice lines under irrigated and drought conditions. Irrigated treatment was allowed to grow normally, while drought stress was imposed for 30 days at the pre-anthesis stage. Three important physiological traits including pollen fertility percentage (PFP), cell membrane stability (CMS), and normalized difference vegetative index (NDVI) were recorded at anthesis stage during the last week of drought stress. Agronomic traits of economic importance including grain yield were recorded at maturity stage. The analysis of variance demonstrated significant variation among the genotypes for most of the studied traits. Correlation and principal component analyses demonstrated highly significant associations of particular agronomic traits with grain yield, and genetic diversity among genotypes, respectively. Our study demonstrated a higher drought tolerance potential of GSR lines compared with local cultivars, mainly by higher pollen viability, plant biomass, CMS, and harvest index under drought. In addition, the molecular basis of drought tolerance in GSR lines was related to upregulation of certain drought-responsive genes including OsSADRI, OsDSM1, OsDT11, but not the DREB genes. Our study identified novel drought-responsive genes (LOC_Os11g36190, LOC_Os12g04500, LOC_Os12g26290, and LOC_Os02g11960) that could be further characterized using reverse genetics to be utilized in molecular breeding for drought tolerance.
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Affiliation(s)
- Hassaan Ahmad
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Syed Adeel Zafar
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Malik Attique ur Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Shahzad Amir Naveed
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ghulam Muhammad Ali
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
- *Correspondence: Muhammad Ramzan Khan,
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Bashir S, Naqvi SMS, Muhammad A, Hussain I, Ali K, Khan MR, Farrakh S, Yasmin T, Hyder MZ. Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes. PLoS One 2022; 17:e0263875. [PMID: 35255085 PMCID: PMC8901069 DOI: 10.1371/journal.pone.0263875] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/30/2022] [Indexed: 11/30/2022] Open
Abstract
Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.
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Affiliation(s)
- Sana Bashir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aish Muhammad
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Iqbal Hussain
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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Inam S, Abbas Z, Noor S, Rehman N, Adeel Zafar S, Ramzan Khan M, Ali Kaimkhani Z, Al-Misned F, Shah M, Mahboob S, Muhammad Ali G. Isolation, cloning and transgenic expression of hepatitis B surface antigen (HBsAg) in Solanum lycopersicum L. Saudi J Biol Sci 2022; 29:1559-1564. [PMID: 35280581 PMCID: PMC8913426 DOI: 10.1016/j.sjbs.2021.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan Agriculture Research Council, Pakistan
| | - Zaheer Abbas
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan Agriculture Research Council, Pakistan
| | - Sabahat Noor
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan Agriculture Research Council, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan Agriculture Research Council, Pakistan
| | - Syed Adeel Zafar
- Department of Botany and Plant Sciences, University of California, Reiverside, USA
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan Agriculture Research Council, Pakistan
| | | | - F. Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Masaud Shah
- School of Medicine, Department of Physiology, Ajou University, Suwon 16499, Korea
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
- Corresponding authors.
| | - Ghulam Muhammad Ali
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan Agriculture Research Council, Pakistan
- Corresponding authors.
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Ullah MF, Ali Y, Khan MR, Khan IU, Yan B, Ijaz Khan M, Malik M. A review of COVID-19: Treatment strategies and CRISPR/Cas9 gene editing technology approaches to the coronavirus disease. Saudi J Biol Sci 2022; 29:860-871. [PMID: 34658640 PMCID: PMC8511869 DOI: 10.1016/j.sjbs.2021.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/12/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
The new coronavirus SARS-CoV-2 pandemic has put the world on lockdown for the first time in decades. This has wreaked havoc on the global economy, put additional burden on local and global public health resources, and, most importantly, jeopardised human health. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, and the CRISPR associated (Cas) protein (CRISPR/Cas) was identified to have structures in E. coli. The most modern of these systems is CRISPR/Cas. Editing the genomes of plants and animals took several years and cost hundreds of thousands of dollars until the CRISPR approach was discovered in 2012. As a result, CRISPR/Cas has piqued the scientific community's attention, particularly for disease diagnosis and treatment, because it is faster, less expensive, and more precise than previous genome editing technologies. Data from gene mutations in specific patients gathered using CRISPR/Cas can aid in the identification of the best treatment strategy for each patient, as well as other research domains such as coronavirus replication in cell culture, such as SARS-CoV2. The implications of the most prevalent driver mutations, on the other hand, are often unknown, making treatment interpretation difficult. For detecting a wide range of target genes, the CRISPR/Cas categories provide highly sensitive and selective tools. Genome-wide association studies are a relatively new strategy to discovering genes involved in human disease when it comes to the next steps in genomic research. Furthermore, CRISPR/Cas provides a method for modifying non-coding portions of the genome, which will help advance whole genome libraries by speeding up the analysis of these poorly defined parts of the genome.
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Affiliation(s)
- Muhammad Farhat Ullah
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan
| | - Yasir Ali
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan
| | - Inam Ullah Khan
- University of Sheffield, Department of Chemical and Biological Engineering, Arts Tower Western Bank, Sheffield, S102TN, The University of Sheffield, Manchester, UK
| | - Bing Yan
- Department of Pharmacy, The First Affiliated Hospital of Huzhou University, Huzhou 313000, PR China
| | - M. Ijaz Khan
- Department of Mathematics and Statistics, Riphah International University, I-14, Islamabad 44000, Pakistan
| | - M.Y. Malik
- Department of Mathematics, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. Front Plant Sci 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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Farhat Ullah M, Ali A, Majeed A, Ijaz A, Albastaki A, Ijaz Khan M, Ramzan Khan M, Ahmed Alghamdi H, Abdulrahman Alshahrani M. Population and Mutational Assessment of Novel Repeats in 13RM Y-STRs in Unrelated Males Born in Gilgit, Pakistan. Saudi J Biol Sci 2022; 29:3177-3183. [PMID: 35844379 PMCID: PMC9280172 DOI: 10.1016/j.sjbs.2022.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
Because they are totally transferred to the future generations until mutations occur, Y chromosome genetic markers are commonly utilised in forensics for the classification of male lineages for criminal justice purposes. The mutation rate of Rapidly Mutating Y-STRs (RM Y-STRs) markers is high. That is not seen in other Y-STRs markers, and they appear to be effective in distinguishing paternally related men. This study aimed to estimate the population and mutational parameters of 13 RM Y-STRs in 13 unrelated males born in Gilgit, Pakistan. Repeat there was no population substructure and strong discriminating capacity in the counts. In this population, there were higher mutation rates with the unusual structure of repeats. More research is needed to better characterize these loci in diverse Pakistani groups.
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Nath NC, Saha M, Khan MR, Debi MR, Shil BC, Amiruzzaman M. Helicobacter Pylori Infection and Endoscopic Findings in Bangladeshi Dyspeptic Patients. Mymensingh Med J 2022; 31:161-164. [PMID: 34999697] [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: 06/14/2023]
Abstract
Helicobacter Pylori (H Pylori) that infects about 90% people of developing countries causes dyspepsia and upper gastrointestinal lesions. The aim of this study was to detect the trend of H Pylori active infection and to investigate the endoscopic findings of H Pylori infected dyspeptic patient of Bangladesh. In this prospective study, 360 dyspeptic patients (Male-251, Female-109) were recruited. Patients having alarm features, history of gastrectomy and malignancy were excluded from this study. Non-invasive fecal antigen test for H Pylori was done of all patients. All selected patients were sent for upper gastrointestinal endoscopy. Helicobacter Pylori fecal antigen was found positive in 134(37.2%) from 360 dyspeptic patients (age 14-80 years). Among 360 patients 303 (80.16%) had macroscopic endoscopic mucosal lesions. H Pylori infected 114 patients had endoscopic mucosal abnormality. H Pylori non-infected 189 patients also had mucosal lesion. Twenty patients (35.08%) had H Pylori infection among the 57 patients having endoscopic normal looking mucosa. This study revealed that active H Pylori infection rate is declining in Bangladesh. Risk of endoscopic mucosal lesion is more expected in H Pylori active infection.
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Affiliation(s)
- N C Nath
- Dr Nikhil Chandra Nath, Associate Professor & Head, Department of Gastroenterology, Mugda Medical College, Dhaka, Bangladesh; E-mail:
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31
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Raza H, Khan MR, Zafar SA, Kirch HH, Bartles D. Aldehyde dehydrogenase 3I1 gene is recruited in conferring multiple abiotic stress tolerance in plants. Plant Biol (Stuttg) 2022; 24:85-94. [PMID: 34670007 DOI: 10.1111/plb.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/12/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Plant growth and productivity is restricted by a multitude of abiotic stresses. These stresses negatively affect physiological and metabolic pathways, leading to the production of many harmful substances like ROS, lipid peroxides and aldehydes. This study was conducted to investigate the role of Arabidopsis ALDH3I1 gene in multiple abiotic stress tolerance. Transgenic tobacco plants were generated that overexpress the ALDH3I1 gene driven by the CaMV35S promoter and evaluated under different abiotic stresses, namely salt, drought, cold and oxidative stress. Tolerance to stress was evaluated based on responses of various growth and physiological traits under stress condition. Transgenic plants displayed elevated ALDH3I1 transcript levels compared to WT plants. The constitutive ectopic expression of ALDH3I1 conferred increased tolerance to salt, drought, cold and oxidative stresses in transgenic plants, along with improved plant growth. Transgenic plants overexpressing ALDH3I1 had higher chlorophyll content, photosynthesis rate and proline, and less accumulation of ROS and malondialdehyde compared to the WT, which contributed to stress tolerance in transgenic plants. Our results further revealed that ALDH3I1 had a positive effect on CO2 assimilation rate in plants under abiotic stress conditions. Overall, this study revealed that ALDH3I1 positively regulates abiotic stress tolerance in plants, and has future implications in producing transgenic cereal and horticultural plants tolerant to abiotic stresses.
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Affiliation(s)
- H Raza
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - M R Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - S A Zafar
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - H H Kirch
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - D Bartles
- Institute for Molecular Physiology & Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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Khan MB, Irshad N, Ahmed B, Khan MR, Minhas RA, Ali U, Mahmood M, Muhammad A, Sheikh AA, Ashraf N. Food habits of indian crested porcupine (Hystrix indica) (Kerr 1792), in district Bagh, Azad Jammu and Kashmir. BRAZ J BIOL 2021; 82:e243063. [PMID: 34287526 DOI: 10.1590/1519-6984.243063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/06/2020] [Indexed: 11/22/2022] Open
Abstract
The Indian Crested Porcupine (Hystrix indica) is classified as an agricultural pest species. It feeds on plants and crops; hence, it is responsible for massive financial losses worldwide. The current study was conducted to assess the diet composition of Indian Crested Porcupine in District Bagh, Azad Jammu and Kashmir (AJ&K). Thus, fecal samples were collected and examined from different sampling sites. Reference slides of the material collected from the study area were prepared for identification of dietary components in fecal pellets. A total of 80 fecal samples were collected and processed. Percent relative frequencies (P.R.F.) were calculated for each plant species recovered from pellets. Data revealed that Indian Crested Porcupine consumed 31 plant species in its diet, among them Zea mays (34.31±7.76) was the most frequently selected species followed by Rumex obtusifolius (15.32±2.57) and Melia azedarach (12.83±4.79). The study revealed that the greatest diversity of (n=20) plant species were consumed in summer season while minimum (n=13) species were used during winter. Among the parts of plants, stem was highly consumed in spring (57.2%) as compared to seed in fall (36.7%) while spikes and leaf were the least recovered parts from the fecal matter. The Berger-Parker diversity index showed highly diversified food (10.92) in the summer time of the year as compared to the autumn season (2.95). This study provides a baseline for the diet preference of this pest in the study area. Based on current findings, a detailed investigation on damage assessment, exploration, habitat use and management of Indian Crested Porcupine in AJ&K has been recommended.
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Affiliation(s)
- M B Khan
- Department of Zoology, University of Poonch, Rawalakot, AJ&K Pakistan
| | - N Irshad
- Department of Zoology, University of Poonch, Rawalakot, AJ&K Pakistan
| | - B Ahmed
- Department of Zoology, University of Azad Jammu and Kashmir Muzaffarabad, AJ&K Pakistan
| | - M R Khan
- Department of Zoology, University of Poonch, Rawalakot, AJ&K Pakistan
| | - R A Minhas
- Department of Zoology, University of Azad Jammu and Kashmir Muzaffarabad, AJ&K Pakistan
| | - U Ali
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, AJ&K Pakistan
| | - M Mahmood
- Department of Zoology, University of Poonch, Rawalakot, AJ&K Pakistan
| | - A Muhammad
- Department of Zoology, University of Poonch, Rawalakot, AJ&K Pakistan
| | - A A Sheikh
- Department of Zoology, University of Poonch, Rawalakot, AJ&K Pakistan
| | - N Ashraf
- Department of Zoology, University of Azad Jammu and Kashmir Muzaffarabad, AJ&K Pakistan
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Holman ME, Chang G, Ghatas MP, Saha PK, Zhang X, Khan MR, Sima AP, Adler RA, Gorgey AS. Bone and non-contractile soft tissue changes following open kinetic chain resistance training and testosterone treatment in spinal cord injury: an exploratory study. Osteoporos Int 2021; 32:1321-1332. [PMID: 33443609 DOI: 10.1007/s00198-020-05778-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/04/2020] [Indexed: 01/30/2023]
Abstract
UNLABELLED Twenty men with spinal cord injury (SCI) were randomized into two 16-week intervention groups receiving testosterone treatment (TT) or TT combined with resistance training (TT + RT). TT + RT appears to hold the potential to reverse or slow down bone loss following SCI if provided over a longer period. INTRODUCTION Persons with SCI experience bone loss below the level of injury. The combined effects of resistance training and TT on bone quality following SCI remain unknown. METHODS Men with SCI were randomized into 16-week treatments receiving TT or TT + RT. Magnetic resonance imaging (MRI) of the right lower extremity before participation and post-intervention was used to visualize the proximal, middle, and distal femoral shaft, the quadriceps tendon, and the intermuscular fascia of the quadriceps. For the TT + RT group, MRI microarchitecture techniques were utilized to elucidate trabecular changes around the knee. Individual mixed models were used to estimate effect sizes. RESULTS Twenty participants completed the pilot trial. A small effect for yellow marrow in the distal femur was indicated as increases following TT and decreases following TT + RT were observed. Another small effect was observed as the TT + RT group displayed greater increases in intermuscular fascia length than the TT arm. Distal femur trabecular changes for the TT + RT group were generally small in effect (decreased trabecular thickness variability, spacing, and spacing variability; increased network area). Medium effects were generally observed in the proximal tibia (increased plate width, trabecular thickness, and network area; decreased trabecular spacing and spacing variability). CONCLUSIONS This pilot suggests longer TT + RT interventions may be a viable rehabilitation technique to combat bone loss following SCI. CLINICAL TRIAL REGISTRATION Registered with clinicaltrials.gov : NCT01652040 (07/27/2012).
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Affiliation(s)
- M E Holman
- Spinal Cord Injury and Disorders, Hunter Holmes McGuire VAMC, Richmond, VA, 23249, USA
| | - G Chang
- Department of Radiology, NYU School of Medicine, New York, NY, 10016, USA
| | - M P Ghatas
- Spinal Cord Injury and Disorders, Hunter Holmes McGuire VAMC, Richmond, VA, 23249, USA
| | - P K Saha
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, 52242, USA
- Department of Radiology, University of Iowa, Iowa City, IA, 52242, USA
| | - X Zhang
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - M R Khan
- Department of Radiology, Hunter Holmes McGuire VAMC, Richmond, VA, 23249, USA
| | - A P Sima
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - R A Adler
- Spinal Cord Injury and Disorders, Hunter Holmes McGuire VAMC, Richmond, VA, 23249, USA
| | - A S Gorgey
- Spinal Cord Injury and Disorders, Hunter Holmes McGuire VAMC, Richmond, VA, 23249, USA.
- Department of Physical Medicine & Rehabilitation, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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Sharma NK, Gautam DK, Sahu LK, Khan MR. First wave of covid-19 in India using IoT for identification of virus. Mater Today Proc 2021:S2214-7853(21)04094-3. [PMID: 34123732 PMCID: PMC8182415 DOI: 10.1016/j.matpr.2021.05.492] [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] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 11/26/2022]
Abstract
Internet of Things (IoT) are evolving rapidly and making it possible for many uses, such as manufacturing, military, education and health, to link different intelligent objects. Coronavirus has recently spread widely around the globe and no effective therapies are currently available. It is also very necessary to avoid infection and to control the symptoms, such as fever and shortness of breath. As Coronavirus is a disease that is circulating very rapidly and the social distancing to deter an outbreak is very significant, it is essential to provide a system that is intelligent enough to monitor the effects of individuals with little direct contact. This document contains an IoT-based and wireless sensor network architecture and simulation of the COVID-19 Monitoring Mechanism (CSMM) for the monitoring of people in their quarantine, particularly the elderly who are living under chronic diseases and immune failure, and are therefore more likely to contract severe diseases. The mechanism relies on patient health data remotely. A doctor or care practitioner may carry out the monitoring process. For starters, where there is high fire or trouble breathing, this can conveniently be used for a detected urgent or irregular situation. The process will then give a warning to the health care provider or practitioner, sending urgent SMS with time and condition to act without any delays to save the patient's life.
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Affiliation(s)
- Nitesh Kumar Sharma
- Electronics and Communication Engineering, Dr. C.V. Raman University, Bilaspur, India
| | - Deepesh Kumar Gautam
- Electronics and Telecommunication Engineering, Government Girls Polytechnic, Jagdalpur, India
| | | | - M R Khan
- Electronics and Telecommunication Engineering, Government Engineering College, Jagdalpur, India
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Errum A, Rehman N, Khan MR, Ali GM. Genome-wide characterization and expression analysis of pseudo-response regulator gene family in wheat. Mol Biol Rep 2021; 48:2411-2427. [PMID: 33782785 DOI: 10.1007/s11033-021-06276-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/11/2021] [Indexed: 11/29/2022]
Abstract
Pseudo-response regulator (PRR) gene family members play a significant role in plant circadian clocks, flowering time inflorescence architecture development during transition from vegetative growth phase to reproductive phase. In current study, we analyzed the expression profiling, phylogenetic relationship, and molecular characterization of PRR gene family members of common wheat by using IWGSC Ref seq v1.1 wheat genome database with a coverage rate of 90%. By using bioinformatic approach total 20 candidate gene sequences were identified and divided into six groups and four clades. It was found that mostly genes have same number of exons and introns showed similar features because they originated through duplication events during evolution processes. Although all the proteins have conserved PRR domains, but some are distinct in their sequences suggesting functional divergence. By comparative synteny analysis it was revealed that Group 1, 2, 3 and 11-D of group 4 have duplication events while group 5 and TaPRR9-B,10-D showed conservation with previously identified PRR members from rice. While expression variation of six groups from each analysis matches with each other. Five groups highly expressed in leaf, spike, and roots in pattern like leaf > spike > root at all three stages booting, heading and anthesis of spike development. This suggests that TaPRR genes play important roles in different photoperiod signaling pathways in different organs at different stages of spike development and flowering via unknown pathway. These findings will also provide comprehensive knowledge about future investigations on wheat PRR family members involved in complex network of circadian system for plant development.
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Affiliation(s)
- Aliya Errum
- Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
| | - Nazia Rehman
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan. .,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan.
| | - Muhammad Ramzan Khan
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan. .,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan.
| | - Ghulam Muhammad Ali
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan.,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
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Adeel Zafar S, Uzair M, Ramzan Khan M, Patil SB, Fang J, Zhao J, Lata Singla‐Pareek S, Pareek A, Li X. DPS1
regulates cuticle development and leaf senescence in rice. Food Energy Secur 2021. [DOI: 10.1002/fes3.273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Syed Adeel Zafar
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Muhammad Uzair
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology National Agricultural Research Centre Islamabad Pakistan
| | - Suyash B. Patil
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Sneh Lata Singla‐Pareek
- Plant Stress BiologyInternational Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
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Sethy PK, Behera SK, Anitha K, Pandey C, Khan MR. Computer aid screening of COVID-19 using X-ray and CT scan images: An inner comparison. J Xray Sci Technol 2021; 29:197-210. [PMID: 33492267 DOI: 10.3233/xst-200784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The objective of this study is to conduct a critical analysis to investigate and compare a group of computer aid screening methods of COVID-19 using chest X-ray images and computed tomography (CT) images. The computer aid screening method includes deep feature extraction, transfer learning, and machine learning image classification approach. The deep feature extraction and transfer learning method considered 13 pre-trained CNN models. The machine learning approach includes three sets of handcrafted features and three classifiers. The pre-trained CNN models include AlexNet, GoogleNet, VGG16, VGG19, Densenet201, Resnet18, Resnet50, Resnet101, Inceptionv3, Inceptionresnetv2, Xception, MobileNetv2 and ShuffleNet. The handcrafted features are GLCM, LBP & HOG, and machine learning based classifiers are KNN, SVM & Naive Bayes. In addition, the different paradigms of classifiers are also analyzed. Overall, the comparative analysis is carried out in 65 classification models, i.e., 13 in deep feature extraction, 13 in transfer learning, and 39 in the machine learning approaches. Finally, all classification models perform better when applying to the chest X-ray image set as comparing to the use of CT scan image set. Among 65 classification models, the VGG19 with SVM achieved the highest accuracy of 99.81%when applying to the chest X-ray images. In conclusion, the findings of this analysis study are beneficial for the researchers who are working towards designing computer aid tools for screening COVID-19 infection diseases.
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Affiliation(s)
| | | | - Komma Anitha
- Department of Electronics and Communication Engineering, Prasad V Potluri Siddhartha Institute of Technology, Vijayawada, Andrapradesh, India
| | - Chanki Pandey
- Department of Electronics and Telecommunication Engineering, GEC, Jagdalpur, CG, India
| | - M R Khan
- Department of Electronics and Telecommunication Engineering, GEC, Jagdalpur, CG, India
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Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Dev Dyn 2021; 250:669-683. [PMID: 33381902 PMCID: PMC9292287 DOI: 10.1002/dvdy.291] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/03/2022] Open
Abstract
Background The zinc finger‐containing transcription factor Gli2, is a key mediator of Hedgehog (Hh) signaling and participates in embryonic patterning of various organs including the central nervous system (CNS) and limbs. Abnormal expression of Gli2 can impede the transcription of Hh target genes through disruption of proper balance between Gli2 and Gli3 functions. Therefore, delineation of enhancers that are required for complementary roles of Glis would allow the interrogation of those pathogenic variants that cause gene dysregulation, and a corresponding abnormal phenotype. Previously, we reported tissue‐specific enhancers for Gli family including Gli2 through direct tetrapod‐teleost comparisons. Results Here, we employed the sequence alignments of slowly evolving spotted gar and elephant shark and have identified six novel conserved noncoding elements in human GLI2 containing locus. Zebrafish‐based transgenic assays revealed that combined action of these autonomous CNEs reflects many aspects of Gli2 specific endogenous transcriptional activity, including CNS and pectoral fins. Conclusion Taken together with our previous findings, this study suggests that Hh‐signaling controlled deployment of Gli2 activity in embryonic patterning arose in the common ancestor of gnathostomes. These GLI2 specific cis‐regulatory modules will help to identify DNA variants that probably reside outside of coding intervals and are associated with congenital anomalies. We performed a phylogenetic footprint analyses of human GLI2 containing locus by incorporating relatively slowly evolving gar and elephant shark genomes and have identified multiple novel conserved non‐coding elements (CNEs) that were not predicted by direct human‐teleostcomparisons. Comparative analyses suggest that majority of the GLI2 associated CNEs identified in the present data and reported previously arose in the common ancestor of gnathostomes but lost in teleosts, presumably because of fast teleost sequence evolution. Functional testing of GLI2 associated CNEs by employing zebrafish based transgenic reporter assays revealed their tissue specific cis‐regulatory potential that corresponds with the results based on whole‐mount in situ hybridization analysis of gli2 mRNA in zebrafish. The delineated set of GLI2 associated enhancers can be further interrogated to determine their role in canonical Hh signaling, gene dysregulation, and a corresponding congenital anomaly.
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Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irum Arif
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Ayesha Iqbal
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Islamabad, Pakistan
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
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Ahmad N, Ali GM, Khan MR. Molecular Identification and Characterization of Bacillus sp. NIGAB-1 for Phenol Degradation Under Saline Conditions. Iran J Biotechnol 2020; 18:e2275. [PMID: 32884957 PMCID: PMC7461705 DOI: 10.30498/ijb.2020.133622.2275] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Phenol is an aromatic pollutant in industrial wastes that in combination with salts is highly toxic for all forms of life. Phenol elimination is the foremost challenge to meet the goal of pollutant-free environment. Objective The present study was carried out to isolate phenol degrading bacteria which can degrade phenol under saline conditions and to identify the isolated strains using 16S rRNA gene sequence analysis. Material and Methods Sediment samples were collected from Rawal Lake, Islamabad, Pakistan and enriched in mineral salt medium (MSM) containing phenol (150 mg.L-1). Isolated strains were identified on the basis of 16S rRNA gene sequence analysis. Growth of strains were tested at different pH, NaCl concentrations and temperature using Tryptic Soy Agar (TSA). Tolerance to phenol (0-750 mg.L-1) was checked at 5% NaCl and phenol degrading experiment was performed at 4% NaCl, pH 7 and 30 oC. In both, phenol tolerance and degradation study, phenol was used a sole source of carbon and energy. Results Thirteen bacterial strains were isolated after enrichment among which, NIGAB-1 was found capable of degrading phenol in saline conditions. This strain was identified as Bacillus sp. NIGAB-1 on the basis of 16S rRNA gene sequence analysis and the closest match was Bacillus marisflavi with 99.71% sequence identity. The Bacillus sp. NIGAB-1 exhibited best growth at 30 oC at pH 7 with 10% NaCl. The optimum phenol concentration for growth was recorded as 300 mg.L-1. This strain degraded 300 mg.L-1 of phenol at 4% NaCl in 120 hours with the average degradation rate of 2.63 mg.L-1.h. Conclusion These findings suggest that this strain could be efficient in phenol degradation at adverse environmental conditions and helpful in remediation of phenol where the salt concentration is high.
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Affiliation(s)
- Nazir Ahmad
- PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad-45500, Pakistan
| | - Ghulam Muhammad Ali
- PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad-45500, Pakistan
| | - Muhammad Ramzan Khan
- PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad-45500, Pakistan
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Khan MR, Haque Z, Ahamad F, Zaidi B. Biomanagement of rice root-knot nematode Meloidogyne graminicola using five indigenous microbial isolates under pot and field trials. J Appl Microbiol 2020; 130:424-438. [PMID: 32686259 DOI: 10.1111/jam.14788] [Citation(s) in RCA: 3] [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: 02/01/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 11/30/2022]
Abstract
AIMS To ascertain the effectiveness of Aspergillus niger, Trichoderma harzianum, Pochonia chlamydosporia, Bacillus subtilis and Pseudomonas fluorescens against rice root-knot nematode, Meloidogyne graminicola, and to optimize their application methods. METHODS AND RESULTS The relative effectiveness of five indigenous biocontrol agents (BCA) against M. graminicola on rice cv. PS-5 was tested initially in pot culture. The BCAs, A. niger, P. chlamydosporia and P. fluorescens proved more effective, and significantly reduced the nematode disease. It is hypothesized that success of a biocontrol module may vary with the BCA and application methods. Hence, the effectiveness of the above three BCAs as well as seven different treatment schemes were evaluated in naturally infested farmer's fields during 2 consecutive years. In nematode-infested plots without any BCA treatments, terminal galls formed on the roots, and plants suffered a 19-31% decrease in the growth and yield. The treatments with P. chlamydosporia or A. niger through root-dip (RD) plus one soil application (SA) at 15 days after planting were found to be highly effective against the nematode. CONCLUSIONS Relatively greater nematode control was achieved with RD plus two SAs (15 + 30 DAP) but statistically the effect was on par with RD + one SA at 15 DAP. These treatments significantly reduced galling (22-25%), egg mass production (21-29%) and reproduction factor (63-70%) of M. graminicola, and subsequently increased the grain yield (11-21%). SIGNIFICANCE AND IMPACT OF THE STUDY Application methods enhanced the effectiveness of BCAs against M. graminicola. The RD plus one SA at 15 DAP proved to be most effective treatment to control root-knot disease in rice. Use of multiple treatments (root dip and SA) appears cumbersome, but in view of effectiveness and limitation of chemical control in rice paddies, farmers may adopt the above module that may lead to 11-21% yield improvement.
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Affiliation(s)
- M R Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Z Haque
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - F Ahamad
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - B Zaidi
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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Sarkar SK, Shah MS, Begum M, Yunus AM, Aziz MA, Kabir AL, Khan MR, Rahman F, Rahman A. Red Cell Alloantibodies in Thalassaemia Patients Who Received Ten or More Units of Transfusion. Mymensingh Med J 2019; 28:364-369. [PMID: 31086152] [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
Thalassaemia patients are the highest consumers of blood. Recurrent exposure to allogenic red cell antigen puts this population at increased risk of alloimmunization. This causes delayed hemolytic transfusion reactions. So transfusion requirement increases. But no data regarding alloimmunization was available in Bangladesh. Aim of this study was to estimate the prevalence of alloimmunization and to find out the potential factors associated with its development. This analytical cross sectional study was done by enrolling 97 patients, received at least 10 units transfusions, through convenient sampling. Indirect and direct antiglobulin tests were done to detect immunization by spin tube technique keeping an autocontrol and carried out in the Department of Haematology & Department of Transfusion Medicine, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from March 2016 to March 2017. Polyclonal anti-AHG reagent was used. A total 21 patients developed alloimmunization (21.6%) and 4 patients (4.1%) developed autoimmunization. Age, gender, splenectomy and number of transfusion are shown significant risk factors for alloimmunization. Data from this study demonstrate that the RBC alloimmunization is significantly high in our country. So, pretransfusion antibody screening needs to be initiated in order to ensure safe transfusion and RBC phenotyping should be started before starting first transfusion to prevent alloimmunization.
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Affiliation(s)
- S K Sarkar
- Dr Surozit Kumar Sarkar, Resident, Department of Haematology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh; E-mail:
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Khan MR, Saha M, Mamun MA, Salam KS, Chowdhury MS, Haque MM, Nath NC, Chowdhury WA. Upper GIT Endoscopic Evaluation and Psychological State Assessment of Patients with Globus Sensation. Mymensingh Med J 2019; 28:405-409. [PMID: 31086158] [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
Globus sensation is a subjective feeling of a lump or foreign body in the throat without interfering swallowing of food. It is a persistent and distressing sensation in throat. It affects about 6% of population. But cause of globus is still unknown. Exact aetiology of globus is considered to be multifactorial. Some other studies also show association between globus and psychological distress including anxiety and depression. As there is no established pharmacological treatment, adequate investigations with negative result could reassure patients and improve their symptoms. In this prospective study consecutive patients with globus symptoms examined by upper GIT endoscopy with attention to larynx, epiglottis, base of tongue, both pyriform fossa and hypo-pharynx using Olympus forward viewing video Gastroscope (GIF Q-150 & GIF Q-170) to exclude organic lesion and was conducted in the department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University (BSMMU) and North East Medical College, Sylhet from 1st July 2014 to 31 December 2016. Their psychological status and epidemiological information including personal and family history were noted in a pre-designed data sheet. Total 104 patients were examined, among them definite anxiety was found in 36(34.95%) and borderline feature of anxiety was found in 19(18.44%) and 48(46.60%) were free of anxiety. Incidence of anxiety was significantly higher among females and was more prevalent among housewife, married people and people from rural community. In this series, 13(12.5%) patients had definite depression and 29(27.9%) patients had borderline depression, while 61(59.2%) patients had no feature of depression. Incidence of depression was significantly higher among females, housewife and married people. Organic lesion is rare in patients with globus symptoms. Globus sensation is more common among females. Psychological factors like anxiety and depression are frequently associated with globus sensation.
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Affiliation(s)
- M R Khan
- Dr Md Masudur Rahman Khan, Associate Professor, Department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh;
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Sarkar AM, Akhter S, Khan MR, Saha M, Alam MR, Ghosh CK, Ahmed DS, Miah AR, Roy PK. Evaluation of Duodenal Eosinophil Count in Adult Patients with Functional Dyspepsia. Mymensingh Med J 2019; 28:150-156. [PMID: 30755564] [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
Several mechanisms have been proposed to explain the symptoms of functional dyspepsia but actual pathogenesis is still poorly understood. Recent studies support duodenal abnormality to be the most important causal link to explain symptoms and to understand abnormal pathophysiology of functional dyspepsia. The aim of this prospective observational study is to compare eosinophil count in duodenal mucosa between patients with functional dyspepsia and control subjects without dyspepsia and was done at the department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh from December 2015 to December 2016. Total 42 patients of functional dyspepsia based on Bangla validated version of ROME III criteria and 42 controls who were referred for upper gastrointestinal endoscopy for reasons other than dyspepsia were included. Biopsy specimens were collected from the second part (D2) of the duodenum of all participants. Eosinophil count was quantitatively evaluated by hematoxylin and eosin staining and expressed in numbers per 5 HPF. Significantly increased duodenal eosinophil count was found in functional dyspepsia group than non dyspeptic patients (22.78±08.78 vs. 14.90±10.70, p=0.001). Higher duodenal eosinophil count was found in patients with postprandial distress syndrome. Increased duodenal eosinophil count was found in patient of functional dyspepsia. It requires further large scale multicenter studies to establish duodenal eosinophilia as a biomarker of functional dyspepsia.
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Affiliation(s)
- A M Sarkar
- Dr Md Abdul Mumit Sarkar, Resident, Department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
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Choudhury R, Nath B, Khan MR, Mahanta C, Ellis T, van Geen A. The Impact of Aquifer Flushing on Groundwater Arsenic Across a 35-km Transect Perpendicular to the Upper Brahmaputra River in Assam, India. Water Resour Res 2018; 54:8160-8173. [PMID: 30906078 PMCID: PMC6424526 DOI: 10.1029/2017wr022485] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/24/2018] [Indexed: 05/27/2023]
Abstract
Well testing in the floodplain of the Brahmaputra River in Golaghat and Jorhat districts of Assam, India, shows that groundwater arsenic (As) concentrations increase with distance from the river. To establish the origin of this pattern, an additional 900 wells <60 m deep were tested for As and 9 sites were drilled along a 35-km transect perpendicular to the river. The field data show no relation between groundwater As concentrations ranging from <1 to 660 μg/L along the transect and (a) As concentrations of <1-5 mg/kg in cuttings of aquifer sand recovered while drilling or (b) the degree of reduction of iron oxides in these cuttings. The drilling indicates, however, a marked increase in the thickness of a clay layer capping the aquifer starting from <1-5 m near the river to over 60 m at the most distant site towards the base of the Naga foothills. Organic radiocarbon ages of 18-46 kyr obtained from all but one of 13 clay samples indicate pre-Holocene deposition of the underlying sands across the entire transect. Radiocarbon ages of dissolved inorganic carbon of 0.2, 4.7, and 17.8 kyr were measured in groundwater from 3 monitoring wells installed to 30-60 m depth at distances of 10, 20, and 40 km from the river, respectively. A conceptual groundwater flow model consistent with monitored heads and groundwater ages suggests that thick clay layers capping the aquifer further from the river inhibited flushing of the aquifer and, as a result, preserved higher As levels in groundwater.
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Affiliation(s)
- R Choudhury
- Department of Civil Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
- Now at Department of Geological Sciences, Gauhati University, Gauhati 781014, Assam, India
| | - B Nath
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964, USA
| | - M R Khan
- Department of Geology, University of Dhaka, Dhaka 1000, Bangladesh
| | - C Mahanta
- Department of Civil Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - T Ellis
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964, USA
| | - A van Geen
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964, USA
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Habib SA, Islam MN, Rahman MF, Ullah M, Pasha K, Alam SN, Mohsin K, Fatema N, Khan MR, Shakil SS, Hasan MN. Study of Angiographic Relationship between Peripheral Arterial Diseases with the Involvement of Specific Coronary Artery Lesion. Mymensingh Med J 2018; 27:126-129. [PMID: 29459603] [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: 06/08/2023]
Abstract
The purpose of this study was to investigate magnitude, pattern and involvement of previously unheralded coronary artery disease in patients suffering from clinically significant peripheral artery disease of lower limbs. This cross sectional study was carried out in National Institute of Cardiovascular Diseases, Dhaka, Bangladesh from January 2014 to February 2015. Total 58 patients with clinically diagnosed peripheral arterial disease of lower limb undergoing angiographic evaluation. Selective CAG in addition to peripheral arteriography was performed in all the study population as per ACC/AHA guidelines for CAG (class IIa recommendation).In this study, it was documented that the proportion of coronary arterial disease was highest in LAD (63.9%) followed by LCX (55.6%), RCA (52.8%), and lowest LM (11.1%) in lesion with aorto-iliac segment. But the proportion of coronary arterial disease was highest in LCX (41.9%) followed by LAD (38.7%), RCA (35.5%), and lowest LM (12.9%) in lesion with femero-popliteal blood vessels. Similarly, the proportion of coronary arterial disease was highest in LCX (36.4%) followed by RCA (27.3%) and equal percentage in LAD and lowest in LM (9.1%) in tibioperoneal segment. Patients of peripheral arterial disease (PAD) having no symptoms of coronary artery disease (CAD) are more likely to have severe coronary artery involvement. Coronary angiogram should be done in patient with PAD to detect previously undetected CAD and pattern of PAD reflects the severity and involvement of coronary arteries.
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Affiliation(s)
- S A Habib
- Dr SM Ahsan Habib, Associate Professor, Department of Cardiology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
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Aziz MA, Singh NK, Rahman MH, Khan MR, Kabir AL, Begum M. A Young Boy with L-asparaginase-Induced Seizure. Mymensingh Med J 2017; 26:459-461. [PMID: 28588188] [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: 06/07/2023]
Abstract
L-Asparaginase is a critical component in the treatment of acute lymphoblastic leukemia in children. It is known to cause coagulation abnormalities, thrombosis and hemorrhage in the central nervous system in addition to vasculitis and hypersensitivity reactions. This syndrome generally occurs after a few weeks of therapy and may occur after L-asparaginase therapy is completed. Seizures are uncommon symptoms. We report a case of seizure associated with L-asparaginase therapy but no evidence of hemorrhagic or thrombotic cerebrovascular events, completed in the department of Hematology of Bangabandhu Sheikh Mujib Medical University during March & April 2016.
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Affiliation(s)
- M A Aziz
- Dr Md Abdul Aziz, Associate Professor, Department of Haematology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh; E-mail:
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Ghosh CK, Khan MR, Alam F, Shil BC, Kabir MS, Mahmuduzzaman M, Das SC, Masud H, Roy PK. Peptic Ulcer Disease in Bangladesh: A Multi-centre Study. Mymensingh Med J 2017; 26:141-144. [PMID: 28260768] [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: 06/06/2023]
Abstract
The incidence of peptic ulcer has steadily declined through out the world. This decreasing trend is also noticeable in this subcontinent. The point prevalence of peptic ulcer (PUD) in Bangladesh was around 15% in eighties. The aim of this study was to see the present prevalence of peptic ulcer at endoscopy and to identify changing trends in the occurrence of peptic ulcer in Bangladesh. This retrospective analysis of the endoscopic records of multiple tertiary referral centres of Dhaka city were done from January 2012 to July 2013. A total of 5608 subjects were the study samples. We included those patients having peptic ulcer in the form of duodenal ulcer, benign gastric ulcer including pre-pyloric ulcer and gastric outlet obstruction due to peptic ulcer. Duodenal ulcer and benign gastric ulcer were found in 415(7.4%) and 184(3.28%) patients respectively and gastric outlet obstruction due to peptic ulcer was found in 23(0.40%) patients.
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Affiliation(s)
- C K Ghosh
- Dr Chanchal Kumar Ghosh, Associate Professor, Department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbagh, Dhaka, Bangladesh; E-mail:
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Khan MR, Ihsan H, Ali GM. WSA206, a paralog of duplicated MPF2-like MADS-box family is recruited in fertility function in Withania. Plant Sci 2016; 253:215-228. [PMID: 27968991 DOI: 10.1016/j.plantsci.2016.10.004] [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: 04/24/2016] [Revised: 09/03/2016] [Accepted: 10/08/2016] [Indexed: 06/06/2023]
Abstract
Best known for their implication in calyx inflation, MPF2-like genes pertinent to the STMADS11 clade of the MADS-box family exert their functions in leaf development, flowering time, inflorescence architecture and floral reversion to just name but a few. However, our knowledge about their involvement in fertility function remained obscure. Therefore the major thrust of this study was to probe the recruitment of WSA206 (MPF2-like) protein in fertility function. The WSA206 functions were revealed by knocking down and overexpressing this protein in Withania somnifera. The WSA206 promoter functions were defined by stable integration in Arabidopsis using GUS tag. The interactions of WSA206 were investigated by screening Arabidopsis Oligo-dT yeast library and YFP-split analysis. WSA206 knockdown plants revealed fewer flowers, abortion in seed set, reduction in pollen number and deformed non-viable pollen in comparison with wild type counterparts. Overexpression of WSA206 in Withania generated more berries/seeds and healthier viable pollen grains. Remarkably, along with fertility control, the impairment in calyx inflation in knockdown Withania plants and extraordinary growth of sepals in overexpression lines is observed. Thus, fertility and calyx inflation are tightly coupled traits under the control of WSA206. Coding sequence revealed SNP mutations from arginine to lysine as well as a leucine-rich motif duplication at the C-terminus, a characteristic feature of pollen specific and fertility function proteins. The protein-protein interaction spectrum of WSA206 comprises 40% of those MADS and non-MADS-box proteins implicated in floral/anther expression and embryogenesis. Predominant WSA206 promoter:GUS expression accrued in the anthers/pollen may be attributed to of the presence of GAAATTGTTA pollen specific proximal motifs along with several other anther specific homotypic cis-clusters. MPF2-like protein WSA206 through interactions with MADS-box and non-MADS-domain proteins confers male fertility in Withania regulated by anther/pollen specific promoter motif GAAATTGTTA.
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Affiliation(s)
- Muhammad Ramzan Khan
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan; National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan.
| | - Humera Ihsan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
| | - Ghulam Muhammad Ali
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan
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Bostan N, Naeem M, Afzal MS, Shah ZH, Mustafa I, Arshad M, Haider W, Khan AA, Asif S, Khan MR, Ahmad SS, Ali S, Naveed M, Ahmed H. Sero-prevalence of Hepatitis B and C Virus from rural areas of northern Punjab (Sargodha District), Pakistan. Trop Biomed 2016; 33:599-607. [PMID: 33579055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pakistan is endemic for hepatitis B virus (HBV) and hepatitis C virus (HCV) infections with 10 and 11 million infections, respectively. The epidemiological studies of these virus showed that the information is only from few cities of the country and is relevant to high risk groups. It is of great importance to have an idea about the prevalence of infectious agents in general population to help in identification of hot spot for infections. Identification of hot spots will help in disease management for future. As the there is no report form district Sargodha (Punjab Province) so this study was designed to analyze the prevalence of HBV and HCV in general population. Blood samples of 2373 randomly selected individuals from six different tehsils were collected and were analyzed for HBV and HCV sero-positivity. An overall prevalence of both HBV and HCV in district Sargodha was 28.10% (667/2373). HCV prevalence was (20.01%) and HBV seropositivity was (8.09%). Males were more infected than females, and a significant difference was found in positive cases between male (58.77%) and female (41.22%). The most common routes of transmission of hepatitis virus in present study were shaving assisted by barbers in male patients 143 (21.43%), non sterile or used needles and syringes 127 (19.04%), dental surgical procedures 88 (13.19%), and sharing razors in males 49 (7.34%). In female patients a significant factor is labor and child birth process. Most cases of hepatitis were seen in mesons, farmers and house wives. The prevalence of HBV and HCV in general population of district Sargodha is very high. The study will help for better management of disease to contain the disease spread. The study highlighted that District Sargodha is endemic for these viral infections and it is highly warranted to carry out more studies to get better idea about the infection spread. Community education campaigns are also highly warranted to general population as well as high risk population to control future disease spread.
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Affiliation(s)
- N Bostan
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chakh Shazad, Islamabad, Pakistan
| | - M Naeem
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - M S Afzal
- School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Z H Shah
- School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - I Mustafa
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - M Arshad
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - W Haider
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chakh Shazad, Islamabad, Pakistan
| | - A A Khan
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chakh Shazad, Islamabad, Pakistan
| | - S Asif
- Department of Botany, PMAS-University of Arid Agriculture, Rawalpindi, Pakistan
| | - M R Khan
- Department of Remote Sensing and GIS/ University Institute of Information Technology, PMAS-University of Arid Agriculture, Rawalpindi, Pakistan
| | - S S Ahmad
- Department of Remote Sensing and GIS, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - S Ali
- Department of Biotechnology, University of Gujrat, Sialkot Campus, Pakistan
| | - M Naveed
- Department of Biotechnology, University of Gujrat, Sialkot Campus, Pakistan
| | - H Ahmed
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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Ghosh CK, Khan MR, Alam F, Shil BC, Kabir MS, Mahmuduzzaman M, Das SC, Roy PK. Pattern of Changes in the Findings among the Patients Undergoing Diagnostic Esophagogastroduodenoscopy in Bangladesh. Mymensingh Med J 2016; 25:726-729. [PMID: 27941738] [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: 06/06/2023]
Abstract
This cross-sectional observational study was conducted in the Department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University, Sir Salimullah Medical College and Mitford Hospital, Holy family Red Crescent Medical College and Hospital and Popular Diagnostic Centre, Shantinagar branch, Dhaka, Bangladesh from January 2012 to July 2013. Study subjects were included in the study irrespective of age and sex having different upper GI tract. Complaints like dysphagia, heart burn, abdominal pain/dyspepsia, nausea, vomiting, haematemesis and/or malena, anorexia, unexplained anemia, weight loss etc. All the findings of oesophagus, stomach and duodenal lesions were observed and data were recorded. The results were considered positive based on the macroscopic appearance using standard diagnostic criteria. During the study period endoscopy was performed in 5608 subjects. Among which 2968(52.92%) were male and 2640(47.07%) were female. The patients age range from 7 years to 108 years. The majority of the patients were from 40-50 years. Normal findings were observed among 3321(59.21%) cases. Gastroduodenal erosions were present among 684(12.19%) cases, Oesophageal varices in 444(7.91%) cases, duodenal ulcer diseases in 415(7.40%) cases and gastric ulcer in 184(3.28%) cases. Ca stomach was found among 165(2.94%) cases. A number of diseases were identified through this procedure. Current study observed a large proportion of patients (40.79%) had positive upper GI endoscopy.
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Affiliation(s)
- C K Ghosh
- Dr Chanchal Kumar Ghosh, Associate Professor, Department of gastroenterology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbagh, Dhaka, Bangladesh
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