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Khan RU, Ullah I, Khurshid G, Suboktagin S, Khan AR, Zeb I, Khan ZA, Jamil M, Rha ES, Muhammad Ali H, Ahmad R. Stimulatory effects of smoke solution and biogas digestate slurry application on photosynthesis, growth, and methylation profiling of solanum tuberosum. Plant Signal Behav 2024; 19:2336724. [PMID: 38600704 PMCID: PMC11017950 DOI: 10.1080/15592324.2024.2336724] [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] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Biostimulants are obtained from various sources like plants, animals, microorganisms, and industrial by-products as well as waste material. Their utilization in agriculture practices is being increased that is giving positive results. The purpose of the current study was to use plant-derived smoke (SMK) solution and biogas digestate (BGD) slurry as biostimulant to elucidate their impact on potato (Solanum tuberosum) performance. The experiment was conducted in lab as well as field conditions, and SMK and BGD solutions were prepared in varying concentrations such as SMK 1:500, SMK 1:250, BGD 50:50, and BGD 75:25. Foliar applications were performed thrice during experiments and data were collected related to photosynthesis, growth, pigments, and genome-wide methylation profiling. Net photosynthesis rate (A) and water use efficiency (WUE) were found higher in SMK- and BGD-treated lab and field grown plants. Among pigments, BGD-treated plants depicted higher levels of Chl a and Chl b while SMK-treated plants showed higher carotenoid levels. Alongside, enhancement in growth-related parameters like leaf number and dry weight was also observed in both lab- and field-treated plants. Furthermore, DNA methylation profile of SMK- and BGD-treated plants depicted variation compared to control. DNA methylation events increased in all the treatments compared to control except for SMK 1:500. These results indicate that smoke and slurry both act as efficient biostimulants which result in better performance of plants. Biostimulants also affected the genome-wide DNA methylation profile that resultantly might have changed the plant gene expression profiling and played its role in plant responsiveness to these biostimulants. However, there is need to elucidate a possible synergistic effect of SMK and BGD on plant growth along with gene expression profiling.
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Affiliation(s)
- Rafi Ullah Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Irfan Ullah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Ghazal Khurshid
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Sultan Suboktagin
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Abdul Rehman Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Iftikhar Zeb
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Zahid Ahmad Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Muhammad Jamil
- Department of Biotechnology and Genetic Engineering, Kohat University, Kohat, Pakistan
| | - Eui Shik Rha
- Department of Wellbeing Resources, Sunchon National University, Sunchon, South Korea
| | - Hayssam Muhammad Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Raza Ahmad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
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Jamil M, Margueritte O, Yonli D, Wang JY, Navangi L, Mudavadi P, Patil RH, Bhoge SE, Traore H, Runo S, Al-Babili S. Evaluation of granular formulated strigolactone analogs for Striga suicidal germination. Pest Manag Sci 2024. [PMID: 38634513 DOI: 10.1002/ps.8136] [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] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/24/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Striga hermonthica, an obligate root parasitic weed, poses significant threat to cereal production in sub-Saharan Africa. Lowering Striga seed bank in infested soils is a promising strategy to mitigate infestation levels. The dependency of Striga seed germination on strigolactones opens up the possibility of a "suicidal germination" approach, where synthetic germination stimulants induce lethal germination in the absence of a host. Implementing this approach requires active germination stimulants with a suitable formulation for field application. Here, we describe the development of slow-releasing granular formulation of two potent germination stimulants 'Methyl Phenlactonoate 3' and 'Nijmegen-1' and the assessment of their activity under Lab, greenhouse, mini-field, and field conditions. RESULTS Under laboratory conditions, the granular formulation of either of the two germination stimulants (1.25 mg per plate, corresponding to 0.09 mg a.i.) induced Striga seed germination at a rate of up to 43%. With 10 mg granular product (0.75 mg a.i.) per pot, we observed 77-83% reduction in Striga emergence under greenhouse pot conditions. Application of the formulated stimulants under artificially or naturally infested fields resulted in approximately 56%, 60%, and 72% reduction in Striga emergence in maize, sorghum, and millet fields in Kenya and Burkina Faso, respectively. CONCLUSION Our findings on the newly designed granular formulation of Methyl Phenlactonoate 3 and Nijmegen-1 reveal encouraging prospects for addressing the Striga problem in Africa. These findings underscore several significant advantages of the formulated stimulants, including suitability for the African agricultural context, and, most importantly, their effectiveness in reducing Striga infection. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi, Arabia
| | - Ouedraogo Margueritte
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, 04, Burkina Faso
| | - Djibril Yonli
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, 04, Burkina Faso
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi, Arabia
| | - Lynet Navangi
- Kenya Agricultural and Livestock Research Organisation, Alupe Center, Busia, 399-50400, Kenya
| | - Patrick Mudavadi
- Kenya Agricultural and Livestock Research Organisation, Alupe Center, Busia, 399-50400, Kenya
| | - Rohit H Patil
- UPL House, Express Highway, Bandra-East, Mumbai, 400 051, Maharashtra, India
| | | | - Hamidou Traore
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, 04, Burkina Faso
| | - Steven Runo
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, 00100, Nairobi, Kenya
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi, Arabia
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Kanwal R, Maqsood MF, Shahbaz M, Naz N, Zulfiqar U, Ali MF, Jamil M, Khalid F, Ali Q, Sabir MA, Chaudhary T, Ali HM, Alsakkaf WAA. Exogenous ascorbic acid as a potent regulator of antioxidants, osmo-protectants, and lipid peroxidation in pea under salt stress. BMC Plant Biol 2024; 24:247. [PMID: 38575856 PMCID: PMC10996094 DOI: 10.1186/s12870-024-04947-3] [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] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Pea (Pisum sativum L.), a globally cultivated leguminous crop valued for its nutritional and economic significance, faces a critical challenge of soil salinity, which significantly hampers crop growth and production worldwide. A pot experiment was carried out in the Botanical Garden, The Islamia University of Bahawalpur to alleviate the negative impacts of sodium chloride (NaCl) on pea through foliar application of ascorbic acid (AsA). Two pea varieties Meteor (V1) and Sarsabz (V2) were tested against salinity, i.e. 0 mM NaCl (Control) and 100 mM NaCl. Three levels of ascorbic acid 0 (Control), 5 and 10 mM were applied through foliar spray. The experimental design was completely randomized (CRD) with three replicates. Salt stress resulted in the suppression of growth, photosynthetic activity, and yield attributes in pea plants. However, the application of AsA treatments effectively alleviated these inhibitory effects. Under stress conditions, the application of AsA treatment led to a substantial increase in chlorophyll a (41.1%), chl. b (56.1%), total chl. contents (44.6%) and carotenoids (58.4%). Under salt stress, there was an increase in Na+ accumulation, lipid peroxidation, and the generation of reactive oxygen species (ROS). However, the application of AsA increased the contents of proline (26.9%), endogenous AsA (23.1%), total soluble sugars (17.1%), total phenolics (29.7%), and enzymatic antioxidants i.e. SOD (22.3%), POD (34.1%) and CAT (39%) in both varieties under stress. Salinity reduced the yield attributes while foliarly applied AsA increased the pod length (38.7%), number of pods per plant (40%) and 100 seed weight (45.2%). To sum up, the application of AsA alleviated salt-induced damage in pea plants by enhancing photosynthetic pigments, both enzymatic and non-enzymatic activities, maintaining ion homeostasis, and reducing excessive ROS accumulation through the limitation of lipid peroxidation. Overall, V2 (Sarsabz) performed better as compared to the V1 (Meteor).
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Affiliation(s)
- Rehana Kanwal
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | | | - Muhammad Shahbaz
- Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Nargis Naz
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Muhammad Fraz Ali
- College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China
| | - Muhammad Jamil
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Faizan Khalid
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Qasim Ali
- Department of Soil Science, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Azeem Sabir
- Institute of Forest Sciences, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Talha Chaudhary
- Faculty of Agricultural and Environmental Sciences, Hungarian University of Agriculture and Life Sciences 2100, Godollo, Hungary.
| | - Hayssam M Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Waleed A A Alsakkaf
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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Rashid A, Siddiqui NA, Ahmed N, Wahid A, Jamil M, Sankoh AA, Olutoki JO. Geochemical and mineralogical characteristics of shales from the early to middle Permian Dohol Formation in Peninsular Malaysia: Implications for organic matter enrichment, provenance, tectonic setting, palaeoweathering and paleoclimate. Heliyon 2024; 10:e27553. [PMID: 38524595 PMCID: PMC10958216 DOI: 10.1016/j.heliyon.2024.e27553] [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: 12/01/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
The early to middle Permian Dohol Formation is characterized by a significant presence of shale deposits. While these shales exhibit a low potential to generate hydrocarbons, there is a need to ascertain the possible reasons for the low hydrocarbon generation potential. Also, there are several unidentified properties and attributes associated with these shales in terms of their inorganic geochemical characteristics and their mineralogy. This study is focused on using XRF, ICPMS, and SEM with EDX to determine the mineralogical and geochemical characteristics of these shales and use these data to discuss their provenance history and tectonic setting and interpret the paleoclimatic and paleoweathering conditions. The inorganic geochemical analysis shows that the shales from the Dohol Formation are from a felsic igneous source. The shales were also identified to be from a passive margin based on the bivariate plot of SiO2 vs log (K2O/Na2O) and several multidimensional diagram plots. The CIA and CIW data, as well as the A-CN-K plot, all point to a significant degree of chemical weathering, ranging from mild to intense. The Sr/Cu ratio and C-value, combined with various other geochemical proxies, indicate that the shales were formed in warm-humid climatic conditions. The SEM analysis shows that the samples are mainly composed of kaolinite and illite, and this result was supported by the EDX elemental composition. The high terrigenous influx of sediments, the oxic to sub-oxic conditions in which the sediments were deposited, and finally low marine productivity were found to be the reasons for the low TOC in the shales from the Dohol Formation.
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Affiliation(s)
- Alidu Rashid
- Department of Geoscience, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia
| | - Numair Ahmed Siddiqui
- Department of Geoscience, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia
| | - Nisar Ahmed
- Department of Geoscience, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia
| | - Ali Wahid
- Institute of Geology, University of Azad Jammu and Kashmir, Muzaffarabad, AJK, Pakistan
| | - Muhammad Jamil
- Department of Earth Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Abdul Aziz Sankoh
- Department of Civil and Environmental Engineering, University of Energy and Natural Resources, P.O. Box 214, Sunyani, Ghana
- College of Engineering and Computing, George Mason University, 4400 University Dr, Fairfax, VA, 22030, USA
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Khan T, Jamil M, Ali A, Rasheed S, Irshad A, Maqsood MF, Zulfiqar U, Chaudhary T, Ali MA, Elshikh MS. Exploring water-absorbing capacity: a digital image analysis of seeds from 120 wheat varieties. Sci Rep 2024; 14:6757. [PMID: 38514746 PMCID: PMC10957954 DOI: 10.1038/s41598-024-57193-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
Wheat is a staple food crop that provides a significant portion of the world's daily caloric intake, serving as a vital source of carbohydrates and dietary fiber for billions of people. Seed shape studies of wheat typically involve the use of digital image analysis software to quantify various seed shape parameters such as length, width, area, aspect ratio, roundness, and symmetry. This study presents a comprehensive investigation into the water-absorbing capacity of seeds from 120 distinct wheat lines, leveraging digital image analysis techniques facilitated by SmartGrain software. Water absorption is a pivotal process in the early stages of seed germination, directly influencing plant growth and crop yield. SmartGrain, a powerful image analysis tool, was employed to extract precise quantitative data from digital images of wheat seeds, enabling the assessment of various seed traits in relation to their water-absorbing capacity. The analysis revealed significant transformations in seed characteristics as they absorbed water, including changes in size, weight, shape, and more. Through statistical analysis and correlation assessments, we identified robust relationships between these seed traits, both before and after water treatment. Principal Component Analysis (PCA) and Agglomerative Hierarchical Clustering (AHC) were employed to categorize genotypes with similar trait patterns, providing insights valuable for crop breeding and genetic research. Multiple linear regression analysis further elucidated the influence of specific seed traits, such as weight, width, and distance, on water-absorbing capacity. Our study contributes to a deeper understanding of seed development, imbibition, and the crucial role of water absorption in wheat. These insights have practical implications in agriculture, offering opportunities to optimize breeding programs for improved water absorption in wheat genotypes. The integration of SmartGrain software with advanced statistical methods enhances the reliability and significance of our findings, paving the way for more efficient and resilient wheat crop production. Significant changes in wheat seed shape parameters were observed after imbibition, with notable increases in area, perimeter, length, width, and weight. The length-to-width ratio (LWR) and circularity displayed opposite trends, with higher values before imbibition and lower values after imbibition.
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Affiliation(s)
- Tooba Khan
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Jamil
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Aamir Ali
- Department of Botany, University of Sargodha, Sargodha, Pakistan
| | - Sana Rasheed
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Asma Irshad
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Talha Chaudhary
- Faculty of Agricultural and Environmental Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Godollo, Hungary.
| | - M Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
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Mao G, Xu W, Jamil M, Zhang W, Jiao N, Liu Y. Exploring the Diagnostic and Prognostic Predictive Values of Ferroptosis- Related Markers in Lung Adenocarcinoma. Curr Pharm Biotechnol 2024; 25:CPB-EPUB-139318. [PMID: 38523537 DOI: 10.2174/0113892010293337240312051931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Lung Adenocarcinoma (LUAD), a common and aggressive form of lung cancer, poses significant treatment challenges due to its low survival rates. AIM To better understand the role of ferroptosis driver genes in LUAD, this study aimed to explore their diagnostic and prognostic significance, as well as their impact on treatment approaches and tumor immune function in LUAD. METHOD To accomplish the defined goals, a comprehensive methodology incorporating both in silico and wet lab experiments was employed. A comprehensive analysis was conducted on a total of 233 ferroptosis driver genes obtained from the FerrDB database. Utilizing various TCGA databases and the RT-qPCR technique, the expression profiles of 233 genes were examined. Among them, TP53, KRAS, PTEN, and HRAS were identified as hub genes with significant differential expression. Notably, TP53, KRAS, and HRAS exhibited substantial up-regulation, while PTEN demonstrated significant down-regulation at both the mRNA and protein levels in LUAD samples. The dysregulation of hub genes was further associated with poor overall survival in LUAD patients. Additionally, targeted bisulfite-sequencing (bisulfite-seq) analysis revealed aberrant promoter methylation patterns linked to the dysregulation of hub genes. RESULT & DISCUSSION Furthermore, hub genes were found to participate in diverse oncogenic pathways, highlighting their involvement in LUAD tumorigenesis. By leveraging the diagnostic and prognostic potential of ferroptosis driver hub genes (TP53, KRAS, PTEN, and HRAS), significant advancements can be made in the understanding and management of LUAD pathogenesis. CONCLUSION Therapeutic targeting of these genes using specific drugs holds great promise for revolutionizing drug discovery and improving the overall survival of LUAD patients.
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Affiliation(s)
- Guoliang Mao
- Department of Pathology, Wannan Medical College First Affiliated Hospital, Yijishan Hospital
| | - Wuqin Xu
- Department of Pathology, Wannan Medical College First Affiliated Hospital, Yijishan Hospital
| | | | - Wei Zhang
- Department of Pathology, Wannan Medical College First Affiliated Hospital, Yijishan Hospital
| | - Nanlin Jiao
- Department of Pathology, Wannan Medical College First Affiliated Hospital, Yijishan Hospital
| | - Yinhua Liu
- Department of Pathology, Wannan Medical College First Affiliated Hospital, Yijishan Hospital
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Jamil M, Alagoz Y, Wang JY, Chen GTE, Berqdar L, Kharbatia NM, Moreno JC, Kuijer HNJ, Al-Babili S. Abscisic acid inhibits germination of Striga seeds and is released by them likely as a rhizospheric signal supporting host infestation. Plant J 2024; 117:1305-1316. [PMID: 38169533 DOI: 10.1111/tpj.16610] [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] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Seeds of the root parasitic plant Striga hermonthica undergo a conditioning process under humid and warm environments before germinating in response to host-released stimulants, particularly strigolactones (SLs). The plant hormone abscisic acid (ABA) regulates different growth and developmental processes, and stress response; however, its role during Striga seed germination and early interactions with host plants is under-investigated. Here, we show that ABA inhibited Striga seed germination and that hindering its biosynthesis induced conditioning and germination in unconditioned seeds, which was significantly enhanced by treatment with the SL analog rac-GR24. However, the inhibitory effect of ABA remarkably decreased during conditioning, confirming the loss of sensitivity towards ABA in later developmental stages. ABA measurement showed a substantial reduction of its content during the early conditioning stage and a significant increase upon rac-GR24-triggered germination. We observed this increase also in released seed exudates, which was further confirmed by using the Arabidopsis ABA-reporter GUS marker line. Seed exudates of germinated seeds, containing elevated levels of ABA, impaired the germination of surrounding Striga seeds in vitro and promoted root growth of a rice host towards germinated Striga seeds. Application of ABA as a positive control caused similar effects, indicating its function in Striga/Striga and Striga/host communications. In summary, we show that ABA is an essential player during seed dormancy and germination processes in Striga and acts as a rhizospheric signal likely to support host infestation.
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Affiliation(s)
- Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yagiz Alagoz
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Guan-Ting Erica Chen
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Najeh M Kharbatia
- Analytical Chemistry Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Juan C Moreno
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Hendrik N J Kuijer
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Wang JY, Chen GTE, Balakrishna A, Jamil M, Berqdar L, Al-Babili S. Strigolactone biosynthesis in rice can occur via a 9-cis-3-OH-10'-apo-β-carotenal intermediate. FEBS Lett 2024; 598:571-578. [PMID: 38373744 DOI: 10.1002/1873-3468.14828] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024]
Abstract
Strigolactones (SLs) play a crucial role in regulating plant architecture and mediating rhizosphere interactions. They are synthesized from all-trans-β-carotene converted into the intermediate carlactone (CL) via the intermediate 9-cis-β-apo-10'-carotenal. Recent studies indicate that plants can also synthesize 3-OH-CL from all-trans-β-zeaxanthin via the intermediate 9-cis-3-OH-β-apo-10'-carotenal. However, the question of whether plants can form bioactive SLs from 9-cis-3-OH-β-apo-10'-carotenal remains elusive. In this study, we supplied the 13 C-labeled 9-cis-3-OH-β-apo-10'-carotenal to rice seedlings and monitored the synthesis of SLs using liquid chromatography-mass spectrometry (LC-MS) and Striga bioassay. We further validated the biological activity of 9-cis-3-OH-β-apo-10'-carotenal-derived SLs using the ccd7/d17 SL-deficient mutant, which demonstrated increased Striga seed-germinating activity and partial rescue of tiller numbers and plant height. Our results establish 9-cis-3-OH-β-apo-10'-carotenal as a significant SL biosynthetic intermediate with implications for understanding plant hormonal functions and potential applications in agriculture.
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Affiliation(s)
- Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Guan-Ting Erica Chen
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Aparna Balakrishna
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Wang M, Liu C, Wang Y, Jamil M, Alhomrani M, Alamri AS, Alsanie WF, Alsharif A, Ali M, Jabeen N. Bone morphogenetic protein 1: a prognostic indicator and potential biomarker in three cancer types. Am J Transl Res 2024; 16:400-414. [PMID: 38463598 PMCID: PMC10918118] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/10/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Bone morphogenetic protein 1 (BMP1) is a metalloprotease that plays a role in activating both transforming growth factor-β (TGF-β) and BMP signaling pathways. TGF-β has been identified as a factor initiating and facilitating cancer development. Consequently, we propose the hypothesis that dysregulation of BMP1 could potentially contribute to the onset and advancement of human cancers. METHODS In this research, we aimed to analyze BMP1 expression level and the associated clinical outcomes across various cancers using online cancer OMICS databases, advanced Bioinformatics tools, and molecular analyses. RESULTS The outcomes of our web server-based expression analysis indicated an up-regulation of BMP1 in a majority of the human cancers examined. External validation using clinical samples also showed higher expression of BMP1. Moreover, heightened BMP1 expression exhibited a noteworthy correlation with reduced overall survival (OS) duration in Bladder Cancer (BLCA), Kidney Renal Clear Cell Carcinoma (KIRC), and Lung Adenocarcinoma (LUAD) patients. This suggests a substantial involvement of the BMP1 gene in the development and progression of these three types of cancers. The major signaling pathways related with BMP1 enriched genes were "ECM-receptor interaction, Amoebiasis, Focal adhesion, Protein digestion and absorption, progesterone-mediated, PI3K-Akt signaling pathway, and platelet activation". Moreover, we also explored some interesting correlations among BMP1 expression and its DNA promoter methylation level, CD8+ T immune cells level, and genetic variations. CONCLUSION In conclusion, our study has provided some solid basis for BMP1 to be used as a reliable common biomarker for BLCA, KIRC, and LUAD patients.
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Affiliation(s)
- Ming Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Chunmei Liu
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Yingjie Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Majid Alhomrani
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulhakeem S Alamri
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Walaa F Alsanie
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulaziz Alsharif
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of Agriculture FaisalabadFaisalabad 38040, Punjab, Pakistan
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10
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Alhusari L, Abdallah M, Dakkak B, Bsiso T, Jamil M. Anaplastic Large Cell Lymphoma (ALCL) With a Sarcomatoid Variant Presenting As Distributive Shock in a 41-Year-Old Female: A Case Report. Cureus 2024; 16:e55235. [PMID: 38558574 PMCID: PMC10981390 DOI: 10.7759/cureus.55235] [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] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
The sarcomatoid variant is considered a rare subtype of anaplastic large cell lymphoma. We present a 40-year-old diabetic female who was evaluated in the ER for distributive shock, requiring vasopressors and mechanical ventilation. An extensive workup was negative for infection. A serial CT scan of the abdomen and pelvis showed evolving lymphadenopathy, and a biopsy revealed malignant anaplastic lymphoma cells with a sarcomatous variant. The oncology team recommended the initiation of inpatient chemotherapy; however, the family opted to proceed with comfort care measures.
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Affiliation(s)
- Leena Alhusari
- Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Mahmoud Abdallah
- Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Bassel Dakkak
- Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Taysir Bsiso
- Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Muhammad Jamil
- Hematology and Medical Oncology, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
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11
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Lou J, Chu X, Yang X, Jamil M, Zhu H. Deciphering DNA repair gene mutational landscape in uterine corpus endometrial carcinoma patients using next generation sequencing. Am J Cancer Res 2024; 14:210-226. [PMID: 38323278 PMCID: PMC10839304] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
Uterine Corpus Endometrial Carcinoma (UCEC) is a significant health concern with a complex genetic landscape impacting disease susceptibility and progression. This study aimed to unravel the spectrum of DNA repair gene mutations in Pakistani UCEC patients through Next Generation Sequencing (NGS) and explore their potential functional consequences via downstream analyses. NGS analysis of genomic DNA from 30 UCEC patients was conducted to identify clinically significant pathogenic mutations in DNA repair genes. This analysis revealed mutations in 4 key DNA repair genes: BRCA1, BRCA2, APC, and CDH1. Kaplan-Meier (KM) analysis was employed to assess the prognostic value of these mutations on patient overall survival (OS) in UCEC. To delve into the functional impact of these mutations, we performed RT-qPCR, immunohistochemistry (IHC), and western blot analyses on the mutated UCEC samples compared to their non-mutated counterparts. These results unveiled the up-regulation in the expression of the mutated genes, suggesting a potential association between the identified mutations and enhanced gene activity. Additionally, targeted bisulfite sequencing analysis was utilized to evaluate DNA methylation patterns in the promoters of the mutated genes. Strikingly, hypomethylation in the promoters of BRCA1, BRCA2, APC, and CDH1 was observed in the mutated UCEC samples relative to the non-mutated, indicating the involvement of epigenetic mechanisms in the altered gene expression. In conclusion, this study offers insights into the genetic landscape of DNA repair gene mutations in Pakistani UCEC patients. The presence of pathogenic mutations in BRCA1, BRCA2, APC, and CDH1, coupled with their down-regulation and hypermethylation, suggests a convergence of genetic and epigenetic factors contributing to genomic instability in UCEC cells. These findings enhance our understanding of UCEC susceptibility and provide potential avenues for targeted therapeutic interventions in Pakistani UCEC patients.
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Affiliation(s)
- Jun Lou
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Key Laboratory of Translational Research for CancerNanchang 330029, Jiangxi, China
| | - Xiaoyan Chu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Xiaorong Yang
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Hong Zhu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
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12
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Irshad K, Ramzan B, Qazi SNA, Areeb F, Rasheed A, Jamil M. Continuous solutions of cosmic-rays and waves in astrophysical environments. Sci Rep 2023; 13:22850. [PMID: 38129432 PMCID: PMC10739817 DOI: 10.1038/s41598-023-48223-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
The propagation of energetic charged particles and cosmic rays in magnetized thermal plasma is focused. We consider a four-fluid system that consists of thermal plasma, cosmic rays, and two opposite propagating Alfvén waves to investigate the dynamics and energy exchange mechanisms of the system. Additionally, cosmic rays diffusion within the plasma is considered along the magnetic field lines whereas neglected the cross field line diffusion effects. This study is important for understanding of pressure gradients and their impact on the feedback in astrophysical environment. Over the last few decades, this problem becomes important when we discuss the interaction of cosmic rays with plasma in space, such as interstellar clouds or interstellar medium.
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Affiliation(s)
- K Irshad
- Department of Physics, University of Management and Technology, Lahore, 54770, Pakistan
| | - B Ramzan
- Department of Physics, University of Management and Technology, Lahore, 54770, Pakistan.
| | - S N A Qazi
- Department of Physics, University of Management and Technology, Lahore, 54770, Pakistan
| | - F Areeb
- Department of Physics, Govt. College University, Faislabad, 38000, Pakistan
| | - A Rasheed
- Department of Physics, Govt. College University, Faislabad, 38000, Pakistan.
| | - M Jamil
- Department of Physics, COMSATS University Islamabad, Lahore Campus, Lahore, 54000, Pakistan
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13
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Lan H, Jamil M, Ke G, Dong N. The role of nanoparticles and nanomaterials in cancer diagnosis and treatment: a comprehensive review. Am J Cancer Res 2023; 13:5751-5784. [PMID: 38187049 PMCID: PMC10767363] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Cancer's pathological processes are complex and present several challenges for current chemotherapy methods. These challenges include cytotoxicity, multidrug resistance, the proliferation of cancer stem cells, and a lack of specificity. To address these issues, researchers have turned to nanomaterials, which possess distinct optical, magnetic, and electrical properties due to their size range of 1-100 nm. Nanomaterials have been engineered to improve cancer treatment by mitigating cytotoxicity, enhancing specificity, increasing drug payload capacity, and improving drug bioavailability. Despite a growing corpus of research on this subject, there has been limited progress in permitting nanodrugs for medical use. The advent of nanotechnology, particularly advances in intelligent nanomaterials, has transformed the field of cancer diagnosis and therapy. Nanoparticles' large surface area allows them to successfully encapsulate a large number of molecules. Nanoparticles can be functionalized with various bio-based substrates like RNA, DNA, aptamers, and antibodies, enhancing their theranostic capabilities. Biologically derived nanomaterials offer economical, easily producible, and less toxic alternatives to conventionally manufactured ones. This review offers a comprehensive overview of cancer theranostics methodologies, focusing on intelligent nanomaterials such as metal, polymeric, and carbon-based nanoparticles. I have also critically discussed their benefits and challenges in cancer therapy and diagnostics. Utilizing intelligent nanomaterials holds promise for advancing cancer theranostics, and improving tumor detection and treatment. Further research should optimize nanocarriers for targeted drug delivery and explore enhanced permeability, cytotoxicity, and retention effects.
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Affiliation(s)
- Hongwen Lan
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Gaotan Ke
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
| | - Nianguo Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
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14
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Wei X, Tian Z, Zhao F, Sun A, Zhao S, Jamil M, Yan W. Unveiling pathogenic mutations in BRCA1 and BRCA2 genes across head and neck squamous cell carcinoma patients via next generation sequencing. Am J Cancer Res 2023; 13:6099-6112. [PMID: 38187047 PMCID: PMC10767334] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSC) presents a formidable challenge in the field of oncology due to its aggressive nature and the limited therapeutic options available. In this study, our primary focus was on the Pakistani HNSC patient population, aiming to investigate germline oncogenic mutations within the BRCA1 and BRCA2 genes via Next Generation Sequencing (NGS) and explore their clinical implications. We sought to understand the functional consequences of these mutations via RT-qPCR and Immunohistochemistry (IHC) techniques. The key discovery of our research lies in the identification of three pathogenic mutations, including two within BRCA1 (p.Cys274Ter and p.Glu272Ter) and one within BRCA2 (p.Met1Val), among Pakistani HNSC patients. These mutations previously associated with an increased risk of various cancers. What sets our study apart is the uniqueness of these pathogenic mutations, absent in HNSC patients from other populations. This suggests a distinct genetic profile in Pakistani HNSC patients, possibly contributing to their susceptibility to this malignancy. Furthermore, our research revealed elevated expression levels of BRCA1 and BRCA2 genes in HNSC samples harboring pathogenic mutations, offering insights into mechanisms driving tumor progression in HNSC. Importantly, we identified significant enrichment of BRCA1/2 genes in pathways related to cancer development within the KEGG database. Finally, in our quest to explore therapeutic avenues, we systematically analyzed drugs targeting up-regulated and mutated BRCA1/2 genes, identifying promising candidates for tailored treatment modalities in HNSC. In conclusion, our study reveals the unique genetic profile of HNSC in Pakistani patients, featuring unique pathogenic mutations in BRCA1 and BRCA2 genes. These mutations offer promise as valuable diagnostic markers and potential therapeutic targets.
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Affiliation(s)
- Xiaotong Wei
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Zhizhengrong Tian
- Department of Ultrasound, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Fengyun Zhao
- Department of Ultrasound, Cangzhou Maternal and Child Health Care HospitalCangzhou 061000, Hebei, China
| | - Anjun Sun
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Shujuan Zhao
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Wei Yan
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
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15
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Alhusari L, Tahboub I, Masoudi M, Lawrence LM, Jamil M. Unusual Presentation of Primary Pulmonary Sarcomatous Cancer With Brain Metastasis: A Case Report. Cureus 2023; 15:e51361. [PMID: 38292953 PMCID: PMC10825077 DOI: 10.7759/cureus.51361] [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] [Accepted: 12/30/2023] [Indexed: 02/01/2024] Open
Abstract
Pulmonary sarcomatous carcinoma is a rare subtype of non-small cell lung cancer (NSCLC). This cancer has very low survival rates primarily due to its aggressive nature and propensity for early spread to abdominal organs and the skeletal system. Remarkably, brain metastasis is observed at later stages of the disease, likely attributing to the high fatality rate after the disease progresses to the brain tissue. In our case, a 79-year-old female with a 45-pack-year smoking history sought medical attention at a primary care clinic due to a 3-month history of recurrent right-sided chest pain. Notably, she denied cough, sputum production, palpitations, or syncope. CT chest revealed a 6.8 x 3.5 cm mass in the right upper lobe (RUL) of the lung, with evidence of obstruction and infiltration of the adjacent chest wall. A PET scan indicated increased uptake in the mass and the presence of smaller pulmonary nodules in both lungs, and multiple nodules in the upper left arm, abdomen, right inguinal region, left thigh, and cecum. Importantly, no intracranial lesions were detected. A subsequent colonoscopy yielded normal findings. Histopathologic examination of the lung mass and cell markers was consistent with a diagnosis of sarcomatous carcinoma of the lung. Only three days after the initial clinic visit, the patient presented with numbness and tingling in her lower extremities. Brain MRI revealed multiple bilateral brain metastases accompanied by significant vasogenic edema, prompting treatment with steroid therapy and brain radiation therapy. Subsequent chemotherapy/immunotherapy with Nab-paclitaxel /carboplatin/atezolizumab was initiated but led to significant treatment-related toxicities. Consequently, the treatment plan was adjusted to a single dose of single-agent immunotherapy using pembrolizumab. Unfortunately, the patient chose to discontinue treatment and eventually passed away after 13 days of palliative care. Compared to other lung cancer subtypes, brain metastasis in sarcomatous lung cancer is infrequent due to its lower prevalence among all lung cancer cases. Furthermore, sarcomatous lung cancer has a reduced propensity for developing brain metastasis when compared to other forms of non-small cell lung cancer (NSCLC). Regrettably, the prognosis for sarcomatous lung cancer with brain metastasis remains generally unfavorable, signaling an advanced stage of the disease with limited treatment options.
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Affiliation(s)
- Leena Alhusari
- Internal Medicine Residency Program, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Ihab Tahboub
- Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Moh'd Masoudi
- Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Edwards Comprehensive Cancer Center, Huntington, USA
| | - Logan M Lawrence
- Pathology, Marshall University School of Medicine, Clinical Laboratories of the Mountain Health Network, Huntington, USA
| | - Muhammad Jamil
- Hematology and Medical Oncology, Marshall University Joan C. Edwards School of Medicine, Edwards Comprehensive Cancer Center, Huntington, USA
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16
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Kirschner GK, Xiao TT, Jamil M, Al-Babili S, Lube V, Blilou I. A roadmap of haustorium morphogenesis in parasitic plants. J Exp Bot 2023; 74:7034-7044. [PMID: 37486862 PMCID: PMC10752351 DOI: 10.1093/jxb/erad284] [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] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/23/2023] [Indexed: 07/26/2023]
Abstract
Parasitic plants invade their host through their invasive organ, the haustorium. This organ connects to the vasculature of the host roots and hijacks water and nutrients. Although parasitism has evolved independently in plants, haustoria formation follows a similar mechanism throughout different plant species, highlighting the developmental plasticity of plant tissues. Here, we compare three types of haustoria formed by the root and shoot in the plant parasites Striga and Cuscuta. We discuss mechanisms underlying the interactions with their hosts and how different approaches have contributed to major understanding of haustoria formation and host invasion. We also illustrate the role of auxin and cytokinin in controlling this process.
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Affiliation(s)
- Gwendolyn K Kirschner
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ting Ting Xiao
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Jamil
- BESE Division, The BioActives Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Salim Al-Babili
- BESE Division, The BioActives Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Vinicius Lube
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ikram Blilou
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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17
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Wang P, Khan AM, Alkahtani M, Alasim F, Jamil M, Hussain G. Introducing new green machining technology to enhance process performance and reduce environmental pollution in the metal processing industry. Environ Sci Pollut Res Int 2023; 30:111552-111569. [PMID: 37816967 DOI: 10.1007/s11356-023-30238-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023]
Abstract
The pursuit of enhanced cooling and lubrication methods for machining processes that are energy-efficient, environmentally friendly, and cost-effective is receiving significant attention from both academia and industry. The reduction of CO2 emissions is closely tied to electrical and embodied energy consumption. This study introduces a novel LN2 oil-on-water (LNOoW) cooling/lubrication (lubricooling) approach for the machining of Ti-6Al-4V alloy. Machinability aspects, energy-related aspects, environmental-related aspects, and economic aspects are measured and compared. More specifically, surface quality, electrical energy, cutting forces, and tool wear were measured in machinability aspects. Similarly, specific total energy and specific cumulative Energy Demand (S_CED), specific carbon emission, and production costs were measured to investigate the energy and environmental and economic aspects, respectively. The LNOoW provided the best machinability results compared with other approaches. Result found that LNOoW produced 37.5% better surface quality, removed 159.17% more material, and reduced 50.56% specific cutting energy and 53.63% specific costs as compared to traditional dry cutting conditions. The 39% increment in specific carbon emissions observed in the LN2 oil-on-water (LNOoW) approach in comparison to the dry-cutting method can be mitigated through the implementation of sustainable practices in the production of liquid nitrogen (LN2). The information provided in this study serves as a valuable resource for the development of environmentally friendly machining processes. The study also helps get the sustainable development goals (SDGs) of the United Nations.
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Affiliation(s)
- Pengwen Wang
- College of Design and Art, Xijing University, Xi'an, Shaanxi, 710123, China
| | - Aqib Mashood Khan
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Mohammed Alkahtani
- Department of Industrial Engineering, College of Engineering, King Saud University, P.O. Box 800, Riyadh, 11421, Saudi Arabia
| | - Fahad Alasim
- Department of Industrial Engineering, College of Engineering, King Saud University, P.O. Box 800, Riyadh, 11421, Saudi Arabia
| | - Muhammad Jamil
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Ghulam Hussain
- Department of Mechanical Engineering, College of Engineering, University of Bahrain, Isa Town, 32038, Kingdom of Bahrain
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18
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Chen GTE, Wang JY, Votta C, Braguy J, Jamil M, Kirschner GK, Fiorilli V, Berqdar L, Balakrishna A, Blilou I, Lanfranco L, Al-Babili S. Disruption of the rice 4-DEOXYOROBANCHOL HYDROXYLASE unravels specific functions of canonical strigolactones. Proc Natl Acad Sci U S A 2023; 120:e2306263120. [PMID: 37819983 PMCID: PMC10589652 DOI: 10.1073/pnas.2306263120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Strigolactones (SLs) regulate many developmental processes, including shoot-branching/tillering, and mediate rhizospheric interactions. SLs originate from carlactone (CL) and are structurally diverse, divided into a canonical and a noncanonical subfamily. Rice contains two canonical SLs, 4-deoxyorobanchol (4DO) and orobanchol (Oro), which are common in different plant species. The cytochrome P450 OsMAX1-900 forms 4DO from CL through repeated oxygenation and ring closure, while the homologous enzyme OsMAX1-1400 hydroxylates 4DO into Oro. To better understand the biological function of 4DO and Oro, we generated CRISPR/Cas9 mutants disrupted in OsMAX1-1400 or in both OsMAX1-900 and OsMAX1-1400. The loss of OsMAX1-1400 activity led to a complete lack of Oro and an accumulation of its precursor 4DO. Moreover, Os1400 mutants showed shorter plant height, panicle and panicle base length, but no tillering phenotype. Hormone quantification and transcriptome analysis of Os1400 mutants revealed elevated auxin levels and changes in the expression of auxin-related, as well as of SL biosynthetic genes. Interestingly, the Os900/1400 double mutant lacking both Oro and 4DO did not show the observed Os1400 architectural phenotypes, indicating their being a result of 4DO accumulation. Treatment of wild-type plants with 4DO confirmed this assumption. A comparison of the Striga seed germinating activity and the mycorrhization of Os900, Os900/1400, and Os1400 loss-of-function mutants demonstrated that the germination activity positively correlates with 4DO content while disrupting OsMAX1-1400 has a negative impact on mycorrhizal symbiosis. Taken together, our paper deciphers the biological function of canonical SLs in rice and reveals their particular contributions to establishing architecture and rhizospheric communications.
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Affiliation(s)
- Guan-Ting Erica Chen
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
| | - Cristina Votta
- Department of Life Sciences and Systems Biology, University of Torino, Torino10125, Italy
| | - Justine Braguy
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
| | - Gwendolyn K. Kirschner
- Biological and Environmental Science and Engineering (BESE) Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal23955-6900, Saudi Arabia
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Torino10125, Italy
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
| | - Aparna Balakrishna
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
| | - Ikram Blilou
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
- Biological and Environmental Science and Engineering (BESE) Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal23955-6900, Saudi Arabia
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Torino10125, Italy
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal23955-6900, Kingdom of Saudi Arabia
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Minbo J, Feng C, Wen H, Jamil M, Zhang H, Abdel-Maksoud MA, Zakri AM, Almanaa TN, Alfuraydi AA, Almunqedhi BM. Up-regulated and hypomethylated genes are causative factors and diagnostic markers of osteoporosis. Am J Transl Res 2023; 15:6042-6057. [PMID: 37969207 PMCID: PMC10641362] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND Due to the lack of sensitive diagnostic biomarkers for osteoporosis (OP), there is an urgent need to identify and uncover biomarkers associated with the disease in order to facilitate early clinical diagnosis and effective intervention strategies. METHODS GEO2R was employed to conduct a screening of differentially expressed genes (DEGs) within the transcriptome sequencing data obtained from blood samples of OP patients within the GSE163849 dataset. Subsequently, we conducted expression confirmation of the identified DEGs using an additional dataset, GSE35959. To further explore Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, MicroRNA (miRNA) interactions, and drug predictions, we employed the DAVID, miRTarBase, and DrugBank databases. For validation purposes, clinical OP samples paired with normal controls were collected from the Pakistani population. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was employed to assess the expression levels of DEGs and miRNA, while targeted bisulfite sequencing (bisulfite-seq) analysis was used to investigate methylation patterns. DNA and RNA from clinical OP and normal control samples were extracted using appropriate methods. RESULTS Out of total identified 269 DEGs, EGFR (epidermal growth factor receptor), HMOX1 (heme oxygenase-1), PGR (progesterone receptor), CXCL10 (C-X-C motif chemokine ligand 10), CCL5 (C-C motif chemokine ligand 5), and IL12B (interleukin 12B) were prioritized as top DEGs in OP patients. Expression validation of these genes on additional Gene Expression Omnibus (GEO) dataset and Pakistani OP patients revealed consistent significant up-regulation of these genes in OP patients. Receiver operating characteristic (ROC) analysis demonstrated that these DEGs displayed considerable diagnostic accuracy for detecting OP. Targeted bisulfite-seq analysis further revealed that EGFR, HMOX1, PGR, CXCL10, CCL5, and IL12B were hypomethylated in OP patients. Moreover, has-miR-27a-5p, a common expression regulator of the EGFR, HMOX1, PGR, CXCL10, CCL5, and IL12B was also significantly down-regulated in OP patients. CONCLUSION The DEGs that have been identified hold significant potential for the future development of diagnostic and treatment approaches for OP in preclinical and clinical applications.
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Affiliation(s)
- Jiang Minbo
- Department of Orthopedic, Shanghai Songjiang District Central HospitalShanghai 201699, China
| | - Chen Feng
- Department of Orthopedics, Hongqi HospitalMuDanjiang 157011, Heilongjiang, China
| | - Hongli Wen
- Department of Foreign Language, MuDanjiang Medical UniversityMuDanjiang 157011, Heilongjiang, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Heng Zhang
- Department of Orthopedic, Shanghai Songjiang District Central HospitalShanghai 201699, China
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Akram A Alfuraydi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bandar M Almunqedhi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
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Mi J, Luo J, Zeng H, Zhang H, Jamil M, Abdel-Maksoud MA, Zakri AM, Alfuraydi AA, Zhang N, Xiao M. Elucidating cuproptosis-related gene SLC31A1 diagnostic and prognostic values in cancer. Am J Transl Res 2023; 15:6026-6041. [PMID: 37969191 PMCID: PMC10641336] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/28/2023] [Indexed: 11/17/2023]
Abstract
OBJECTIVES Cancer remains a global health challenge, necessitating the identification of novel biomarkers and therapeutic targets. Cuproptosis, a recently recognized form of cell death linked to copper metabolism, presents a promising avenue for anticancer strategies. We investigated the clinical significance of SLC31A1, a key regulator of cuproptosis, in multiple cancer types, aiming to elucidate its potential as a diagnostic biomarker, prognostic, indicator and therapeutic target. METHODS We conducted a pan-cancer analysis through TIMER2.0, evaluating SLC31A1 expression across multiple cancer types. Survival analysis was performed using KM plotter. Expression validation was carried out using UALCAN and Human Protein Atlas (HPA) databases. Methylation analysis was conducted with the help of ULACAN and OncoDB. Mutational analysis was performed using cBioPortal database. Immune infiltration analysis via the TIMER2.0 and gene enrichment analysis via the Metascape were performed to gain insights into the potential mechanisms underlying SLC31A1's role in cancer. Finally, Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was employed to confirm SLC31A1 expression in clinical samples. RESULTS Out of analyzed cancer, SLC31A1 exhibited significant up-regulation and correlation with worse overall survival (OS) across Breast Cancer (BRCA), Cervical Squamous Cell Carcinoma (CESC), Head and Neck Squamous Cell Carcinoma (HNSC), and Esophageal Carcinoma (ESCA). Mutational and promoter methylation analyses further revealed that hypomethylation is the major cause of SLC31A1 overexpression among BRCA, CESC, HNSC, and ESCA. Immune infiltration analysis showed significant associations between SLC31A1 expression and the presence of CD8+ T cells, CD4+ T cells, and macrophages in the tumor microenvironment. Gene enrichment analysis provided valuable insights into potential molecular pathways in context to BRCA, CESC, HNSC, and ESCA. Furthermore, when SLC31A1 was analyzed using clinical samples through RT-qPCR, this gene showed promising diagnostic potential, reflected by high Area Under the Curve (AUC) values. CONCLUSION Our pan-cancer study highlights the up-regulation of SLC31A1 and its correlation with worse OS in BRCA, CESC, HNSC, and ESCA. In sum, outcomes of this study showed that SLC31A1 could be a potential biomarker and novel therapeutic target of BRCA, CESC, HNSC, and ESCA.
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Affiliation(s)
- Jiaoping Mi
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, Guangdong, PR China
- Department of Otolaryngology Head and Neck Surgery, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Juncong Luo
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Huanwen Zeng
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Hongyu Zhang
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Akram A Alfuraydi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ning Zhang
- Internal Medicine Oncology, Minhang Brunch Fudan University Shanghai Cancer CenterShanghai 200240, PR China
| | - Mei Xiao
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityZhuhai 519000, Guangdong, PR China
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Zia T, Bangfan L, Nadeem A, Hussain A, Abdel-Maksoud MA, Zakri AM, Bashir MK, Ali M, Jabeen N, Jamil M, Al-Qahtani WH, Almanaa TN. Comprehensive multi-level expression profiling of key biomarkers in breast cancer patients. Am J Transl Res 2023; 15:6058-6070. [PMID: 37969199 PMCID: PMC10641354] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 10/11/2023] [Indexed: 11/17/2023]
Abstract
OBJECTIVES In this comprehensive breast cancer (BC) study, we aimed to identify, validate, and characterize key biomarkers with significant implications in BC diagnosis, prognosis, and as therapeutic targets. METHODS Our research strategy involved a multi-level methodology, combining bioinformatic analysis with experimental validation. RESULTS Initially, we conducted an extensive literature search to identify BC biomarkers, selecting those with reported accuracies exceeding 20% in specificity and sensitivity. This yielded nine candidate biomarkers, which we subsequently analyzed using Cytoscape to identify a few key biomarkers. Based on the degree method, we denoted four key biomarkers, including progesterone receptor (PGR), epidermal growth factor receptor (EGFR), estrogen receptor 1 (ESR1), and Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2). Expression analysis using The Cancer Genome Atlas (TCGA) dataset revealed that PGR and EGFR exhibited significant (p-value < 0.05) down-regulation in BC samples when compared to controls, while ESR1 and ERBB2 showed up-regulation. To strengthen our findings, we collected clinical BC tissue samples from Pakistani patients and performed expression verification using real-time quantitative polymerase chain reaction (RT-qPCR). The results aligned with our initial TCGA dataset analysis, further validating the differential expression of these key biomarkers in BC. Furthermore, we utilized receiver operating characteristic (ROC) curves to demonstrate the diagnostic use of these biomarkers. Our analysis underscored their accuracy and sensitivity as diagnostic markers for BC. Survival analysis using the Kaplan-Meier Plotter tool revealed a prognostic significance of PGR, ESR1, EGFR, and ERBB2. Their expression levels were associated with poor overall survival (OS) of BC patients, shedding light on their roles as prognostic indicators in BC. Lastly, we explored DrugBank to identify drugs that may reverse the expression patterns , and estradiol, decitabine, and carbamazepine were singled out. CONCLUSION Our study gives valuable insight into BC biomarkers, for diagnosis and prognosis. These findings have implications for BC management using personalized and targeted therapeutic approaches for BC patients.
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Affiliation(s)
- Tayyaba Zia
- School of Public Management, Yanshan UniversityQinhuangdao 066000, Hebei, China
| | - Liu Bangfan
- School of Public Administration, Yanshan UniversityQinhuangdao 066000, Hebei, China
| | - Amun Nadeem
- Department of Pathology, Gujranwala Medical College Teaching Hospital and DHQ Teaching HospitalGujranwala 52250, Punjab, Pakistan
| | - Abid Hussain
- APMO Nishter HospitalMultan 60000, Punjab, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversitySaudi Arabia
| | - Muhammad Kazim Bashir
- Shaukat Khanum Memorial Cancer Hospital and Research CentreLahore 13014, Punjab, Pakistan
| | - Mubarak Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of Agriculture FaisalabadFaisalabad 38000, Punjab, Pakistan
| | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Wahidah H Al-Qahtani
- Department of Food Sciences & Nutrition, College of Food and Agricultural Sciences, King Saud UniversitySaudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
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Wang L, Ma Y, Han W, Yang Q, Jamil M. Whole Exome Sequencing reveals clinically important pathogenic mutations in DNA repair genes across lung cancer patients. Am J Cancer Res 2023; 13:4989-5004. [PMID: 37970346 PMCID: PMC10636674] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/24/2023] [Indexed: 11/17/2023] Open
Abstract
Lung cancer remains a substantial health challenge, with distinct genetic factors influencing disease susceptibility and progression. This study aimed to decipher the landscape of DNA repair gene mutations in Pakistani lung cancer patients using Whole Exome Sequencing (WES) and to investigate their potential functional implications through downstream analyses. WES analysis of genomic DNA from 15 lung cancer patients identified clinically important pathogenic mutations in 6 DNA repair genes, including, BReast CAncer gene 1 (BRCA1), BReast CAncer gene 2 (BRCA2), Excision Repair Cross Complementing rodent repair deficiency, complementation group 6 (ERCC6), Checkpoint Kinase 1 (CHEK1), mutY DNA glycosylase (MUTYH), and RAD51D (RAD51 Paralog D). Kaplan-Meier (KM) analysis showed that pathogenic mutations in BRCA1, BRCA2, ERCC6, CHEK1, MUTYH, and RAD51D genes were the prognostic biomarkers of worse OS in lung cancer patients. To explore the functional impact of these mutations, we performed Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Immunohistochemistry (IHC) analyses. Our results revealed a down-regulation in the expression of the mutated genes, indicating a potential link between the identified mutations and reduced gene activity. This down-regulation could contribute to compromised DNA repair efficiency, thereby fostering genomic instability in lung cancer cells. Furthermore, targeted bisulfite sequencing analysis was employed to assess the DNA methylation status of the mutated genes. Strikingly, hypermethylation in the promoters of BRCA1, BRCA2, ERCC6, CHEK1, MUTYH, and RAD51D was observed across lung cancer samples harboring pathogenic mutations, suggesting the involvement of epigenetic mechanism underlying the altered gene expression. In conclusion, this study provides insights into the genetic landscape of DNA repair gene mutations in Pakistani lung cancer patients. The observed pathogenic mutations in BRCA1, BRCA2, ERCC6, CHEK1, MUTYH, and RAD51D, coupled with their down-regulation and hypermethylation, suggest a potential convergence of genetic and epigenetic factors driving genomic instability in lung cancer cells. These findings contribute to our understanding of lung cancer susceptibility and highlight potential avenues for targeted therapeutic interventions in Pakistani lung cancer patients.
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Affiliation(s)
- Lanlan Wang
- Department of Medicine, The First People’s Hospital of ShangqiuShangqiu 476100, Henan, China
| | - Yali Ma
- Department of Oncology, Shangqiu First People’s HospitalShangqiu 476000, Henan, China
| | - Wenjie Han
- Department of Oncology, Shangqiu First People’s HospitalShangqiu 476000, Henan, China
| | - Qiumin Yang
- Department of Oncology, Shangqiu First People’s HospitalShangqiu 476000, Henan, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
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Wang JY, Jamil M, AlOtaibi TS, Abdelaziz ME, Ota T, Ibrahim OH, Berqdar L, Asami T, Ahmed Mousa MA, Al-Babili S. Zaxinone mimics (MiZax) efficiently promote growth and production of potato and strawberry plants under desert climate conditions. Sci Rep 2023; 13:17438. [PMID: 37838798 PMCID: PMC10576822 DOI: 10.1038/s41598-023-42478-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/16/2023] Open
Abstract
Climate changes and the rapid expanding human population have become critical concerns for global food security. One of the promising solutions is the employment of plant growth regulators (PGRs) for increasing crop yield and overcoming adverse growth conditions, such as desert climate. Recently, the apocarotenoid zaxinone and its two mimics (MiZax3 and MiZax5) have shown a promising growth-promoting activity in cereals and vegetable crops under greenhouse and field conditions. Herein, we further investigated the effect of MiZax3 and MiZax5, at different concentrations (5 and 10 µM in 2021; 2.5 and 5 µM in 2022), on the growth and yield of the two valuable vegetable crops, potato and strawberry, in the Kingdom of Saudi of Arabia. Application of both MiZax significantly increased plant agronomic traits, yield components and total yield, in five independent field trials from 2021 to 2022. Remarkably, the amount of applied MiZax was far less than humic acid, a widely applied commercial compound used here for comparison. Hence, our results indicate that MiZax are very promising PGRs that can be applied to promote the growth and yield of vegetable crops even under desert conditions and at relatively low concentrations.
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Affiliation(s)
- Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Turki S AlOtaibi
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University (KAU), 21589, Jeddah, Saudi Arabia
| | - Mohamed E Abdelaziz
- Department of Vegetable Crops, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- The National Research and Development Center for Sustainable Agriculture (Estidamah), Riyadh, Kingdom of Saudi Arabia
| | - Tsuyoshi Ota
- Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Omer H Ibrahim
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University (KAU), 21589, Jeddah, Saudi Arabia
- Department of Ornamental Crops, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Tadao Asami
- Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Magdi Ali Ahmed Mousa
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University (KAU), 21589, Jeddah, Saudi Arabia
- Department of Vegetable Crops, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia.
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia.
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Usman R, Jamil M, Fatima R, Mazhar M, Majeed S, Shahab A. Efficacy of Revision Using Distal Inflow in Patients with Symptomatic Dialysis Access-Associated Steal Syndrome. Ann Vasc Dis 2023; 16:205-209. [PMID: 37779643 PMCID: PMC10539131 DOI: 10.3400/avd.oa.23-00043] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/21/2023] [Indexed: 10/03/2023] Open
Abstract
Objectives: In this study, we aim to assess the efficacy of revision using distal inflow (RUDI) in patients with symptomatic dialysis access-associated steal syndrome (DASS). Materials and Methods: All consecutive patients who were diagnosed with grade 3 or 4 DASS and have undergone RUDI in 4 years were included in this study. Results: In total, 35 patients were included in this study; participants had a mean age of 47.5±7.52 years and 54% (n=19) were males. As per our findings, significant improvement was noted in terms of paresthesia (81.2%, p-value: 0.012), coolness (79.4%, p-value: 0.006), pain (78.1%, p-value: 0.006), discoloration (76.4%, p-value: 0.044), paresis (71.4%, p-value: 0.016), and ulcer healing (50%, p-value: 0.044). Gangrene did not further progress in all patients (n=35). Reduction in fistula flow rate after RUDI was 57.5% (682±121 ml/min, p-value: 0.001). Digital systolic pressure was noted to improve by 71.4% (60±9.2 mmHg, p-value: 0.002) after RUDI. Peak systolic velocity increased in both ulnar (66.1±8.2 cm/s, p-value: 0.04) and radial (64.2±7.6 cm/s, p-value: 0.024) arteries of the wrist. Cumulative patency of RUDI graft was 100%, 91.4%, and 85.7% at 3, 6, and 12 months, respectively. Conclusion: RUDI has resulted in significant improvements in terms of DASS symptoms. Using a native vein as conduit, RUDI should be considered a procedure of choice for patients with high-flow DASS.
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Affiliation(s)
- Rashid Usman
- Department of Surgery, Combined Military Hospital, Lahore Cantt, Pakistan
| | - Muhammad Jamil
- Department of Surgery, Combined Military Hospital, Multan Cantt, Pakistan
| | - Rabail Fatima
- Department of Surgery, CMH Lahore Medical College, Lahore Cantt, Pakistan
| | - Minahil Mazhar
- Department of Surgery, CMH Lahore Medical College, Lahore Cantt, Pakistan
| | - Shahid Majeed
- Department of Surgery, Combined Military Hospital, Lahore Cantt, Pakistan
| | - Amna Shahab
- Department of Surgery, Combined Military Hospital, Lahore Cantt, Pakistan
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Zhao T, Li X, Li M, Jamil M, Zhang J. Characterization and verification of MMP family members as potential biomarkers in kidney clear cell renal carcinoma. Am J Cancer Res 2023; 13:3941-3962. [PMID: 37818055 PMCID: PMC10560920] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/13/2023] [Indexed: 10/12/2023] Open
Abstract
Renal cell carcinoma can arise from lesions in the renal epithelium. This particular type of cancer is prevalent in the realm of renal cancers and is associated with an unfavorable prognosis. Among these cases, over 70% are classified as kidney renal clear cell carcinoma (KIRC). Since the underlying causes of KIRC haven't been fully understood, there is an urgent need for deeper investigation into its pathogenesis. Various tools, software, and molecular analysis was used, including Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Cytoscape, University of ALabama at Birmingham CANcer data analysis Portal (UALCAN), muTarget, Gene Expression Profiling Interactive Analysis (GEPIA), OncoDB, Human Protein Atlas (HPA), cBioPortal, Kaplan-Meier (KM) plotter, Gene Set Enrichment Analysis (GSEA), Tumor IMmune Estimation Resource (TIMER), Encyclopedia of RNA Interactomes (ENCORI), DrugBank, Encyclopedia of RNA Interactomes (RT-qPCR), targeted bisulfide sequencing (bisulfide-seq), and receiver operating curve (ROC) to matrix metallopeptidase (MMP) gene family constituents, with the precise objective of identifying a small set of hub genes. These hub genes hold the potential to be harnessed as molecular biomarkers for KIRC. By performing STRING and CytoHubba analyses of the 24 MMP gene family members, MMP2 (matrix metallopeptidase 2), MMP9 (matrix metallopeptidase 9), MMP14 (matrix metallopeptidase 14), and MMP16 (matrix metallopeptidase 16) were recognized as hub genes having highest degree scores. After conducting an in-depth expression analysis of MMP2, MMP9, MMP14, and MMP16 using various The Cancer Genome Atlas (TCGA) databases and RT-qPCR techniques, these displayed a significant increase in expression at both the mRNA and protein levels within KIRC samples when compared to control samples. The impact of the over expression of MMP2, MMP9, MMP14, and MMP16 also left a distinct mark on the worst overall survival (OS) rates of KIRC patients. Furthermore, a targeted bisulfide-seq investigation unveiled a correlation between promoter hypomethylation patterns and the up-regulation of these key genes in KIRC patients. Additionally, hub genes were involved in various diverse oncogenic pathways. In conclusion, four MMP gene family members, including MMP2, MMP9, MMP14, and MMP16 may serve as therapeutic target and molecular biomarker in KIRC.
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Affiliation(s)
- Tianyu Zhao
- Central People’s Hospital of ZhanjiangZhanjiang 524000, Guangdong, China
| | - Xue Li
- Central People’s Hospital of ZhanjiangZhanjiang 524000, Guangdong, China
| | - Mingfeng Li
- Central People’s Hospital of ZhanjiangZhanjiang 524000, Guangdong, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Jingyu Zhang
- Central People’s Hospital of ZhanjiangZhanjiang 524000, Guangdong, China
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Sheikh K, Memon KN, Usman H, Abdel-Maksoud MA, Ullah S, Almanaa TN, Chaudhary A, Jamil M, Gill OBQ, Yar MA, Hussein AM, Zakri AM. Identification of useful biomolecular markers in kidney renal clear cell carcinoma: an in silico and in vitro analysis-based study. Am J Transl Res 2023; 15:5574-5593. [PMID: 37854221 PMCID: PMC10579006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/28/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is the most prevalent type of renal cell carcinoma (RCC), with a high incidence and mortality rate. There is a lack of sensitive biomarkers. Therefore, the discovery of accurate biomarkers for KIRC patients is critical to improve prognosis. METHODS We determined hub genes and their associated pathways involved in the pathogenesis of KIRC from the GSE66272 dataset consisting of KIRC (n = 26) and corresponding control (n = 26) samples and later validated the expression and methylation level of the identified hub genes on The Cancer Genomic Atlas (TCGA) datasets and Human RCC 786-O and normal HK-2 cell lines through RNA sequencing (RNA-seq), Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and targeted bisulfite sequencing (bisulfite-seq) analyses. RESULTS The identified up-regulated four hub genes include TYROBP (Transmembrane Immune Signaling Adaptor TYROBP), PTPRC (Protein tyrosine phosphatase, receptor type, C), LCP2 (Lymphocyte cytosolic protein 2), and ITGB2 (Integrin Subunit Beta 2). Moreover, the higher expression of TYROBP, PTPRC, LCP2, and ITGB2 in KIRC patients insignificantly correlates with a poor prognosis in KIRC patients. In addition, hub genes were involved in the "Fc epsilon RI signaling pathway, asthma, natural cell killer mediated cytotoxicity, T cell receptor signaling pathway, primary immunodeficiency, Fc gamma R-mediated phagocytosis, malaria, leukocyte transendothelial migration, and legionellosis" pathways and associated with the infiltration level of CD8+ T, CD4+ T, and macrophage cells. CONCLUSION Our integrated in silico and in vitro analysis identified important hub genes (TYROBP, PTPRC, LCP2, and ITGB2) involved in the pathogenesis of KIRC as possible diagnostic biomarkers.
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Affiliation(s)
- Khalida Sheikh
- Liaquat University of Medical and Health Sciences (LUMHS)Jamshoro 76090, Pakistan
| | | | - Humera Usman
- Fazaia Medical College, Air UniversityIslamabad 44000, Pakistan
| | | | | | | | - Aqsa Chaudhary
- Department of Biochemistry, University of Central PunjabLahore, Pakistan
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | | | - Muhammad Ahmed Yar
- Mufti Mehmood Memorial Teaching HospitalDera Ismail Khan 29050, KPK, Pakistan
| | - Ahmed M Hussein
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of ViennaVienna 1090, Austria
| | - Adel M Zakri
- Plant Production Department, College of Food and Agricultural Sciences, King Saud UniversityRiyadh 11451, Saudi Arabia
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Li J, Shaikh SN, Uqaili AA, Nasir H, Zia R, Akram MA, Jawad FA, Sohail S, AbdelGawwad MR, Almutairi SM, Elshikh MS, Jamil M, Rasheed RA. A pan-cancer analysis of pituitary tumor-transforming 3, pseudogene. Am J Transl Res 2023; 15:5408-5424. [PMID: 37692950 PMCID: PMC10492052] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Although evidence regarding pituitary tumor-transforming 3, pseudogene (PTTG3P) involvement in human cancers has been acquired via human and animal model-based molecular studies, there is a lack of pan-cancer analysis of this gene in human tumors. METHODS Tumor-causing effects of PTTG3P in 24 human tumors were explored using The Cancer Genome Atlas (TCGA) datasets from different bioinformatics databases and applying in silico tools such as The University of ALabama at Birmingham CANcer (UALCAN), Human Protein Atlas (HPA), Kaplan Meier (KM) plotter, cBioPortal, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Cytoscape, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Tumor IMmune Estimation Resource (TIMER), and Comparative Toxicogenomics Database (CTD). Then, via in vitro experiments, including RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq), expression and promoter methylation levels of PTTG3P were verified in cell lines. RESULTS The PTTG3P expression was overexpressed across 23 malignancies and its overexpression was further found significantly effecting the overall survival (OS) durations of the esophageal carcinoma (ESCA) and head and neck cancer (HNSC) patients. This important information helps us to understand that PTTG3P plays a significant role in the development and progression of ESCA and HNSC. As for PTTG3P functional mechanisms, this gene along with its other binding partners was significantly concentrated in "Oocyte meiosis", "Cell cycle", "Ubiquitin mediated proteolysis", and "Progesterone-mediated oocyte maturation". Moreover, ESCA and HNSC tissues having the higher expression of PTTG3P were found to have lower promoter methylation levels of PTTG3P and higher CD8+ T immune cells level. Additionally, PTTG3P expression-regulatory drugs were also explored in the current manuscript for designing appropriate treatment strategies for ESCA and HNSC with respect to PTTG3P expression. CONCLUSION Our pan-cancer based findings provided a comprehensive account of the oncogenic role and utilization of PTTG3P as a novel molecular biomarker of ESCA and HNSC.
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Affiliation(s)
- Jie Li
- The Second Affiliated Hospital of Hainan Medical University Health Management CenterHaikou 570311, Hainan, China
| | - Saima Naz Shaikh
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro, Sindh 76090, Pakistan
| | - Arsalan Ahmed Uqaili
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro, Sindh 76090, Pakistan
| | - Hilal Nasir
- Clinical and Translational Oncology, Scuola Superiore Meridionale, Naples Federico II UniversityNapoli 80138, Italy
| | - Rabeea Zia
- Pakistan Kidney and Liver Institute and ResearchLahore, Punjab 54000, Pakistan
| | - Muhammad Aitzaz Akram
- University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Fahim Ali Jawad
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture FaisalabadFaisalabad 38000, Pakistan
| | - Salman Sohail
- Registrar Ophthalmology, Al Shifa Trust Eye HospitalRawalpindi 46000, Pakistan
| | - Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of SarajevoSarajevo 71210, Bosnia and Herzegovina
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Rabab Ahmed Rasheed
- Histology & Cell Biology Department, Faculty of Medicine, King Salman International UniversitySouth Sinai, Egypt
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Jamil M, Lin PY, Berqdar L, Wang JY, Takahashi I, Ota T, Alhammad N, Chen GTE, Asami T, Al-Babili S. New Series of Zaxinone Mimics (MiZax) for Fundamental and Applied Research. Biomolecules 2023; 13:1206. [PMID: 37627271 PMCID: PMC10452442 DOI: 10.3390/biom13081206] [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: 06/23/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
The apocarotenoid zaxinone is a recently discovered regulatory metabolite required for proper rice growth and development. In addition, zaxinone and its two mimics (MiZax3 and MiZax5) were shown to have a remarkable growth-promoting activity on crops and a capability to reduce infestation by the root parasitic plant Striga through decreasing strigolactone (SL) production, suggesting their potential for application in agriculture and horticulture. In the present study, we developed a new series of MiZax via structural modification of the two potent zaxinone mimics (MiZax3 and MiZax5) and evaluated their effect on plant growth and Striga infestation. In general, the structural modifications to MiZax3 and MiZax5 did not additionally improve their overall performance but caused an increase in certain activities. In conclusion, MiZax5 and especially MiZax3 remain the likely most efficient zaxinone mimics for controlling Striga infestation.
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Affiliation(s)
- Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
| | - Pei-Yu Lin
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
| | - Ikuo Takahashi
- Applied Biological Chemistry, The University of Tokyo, Tokyo 113-8657, Japan; (I.T.); (T.O.); (T.A.)
| | - Tsuyoshi Ota
- Applied Biological Chemistry, The University of Tokyo, Tokyo 113-8657, Japan; (I.T.); (T.O.); (T.A.)
| | - Noor Alhammad
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
| | - Guan-Ting Erica Chen
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Tadao Asami
- Applied Biological Chemistry, The University of Tokyo, Tokyo 113-8657, Japan; (I.T.); (T.O.); (T.A.)
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.J.); (P.-Y.L.); (L.B.); (J.Y.W.); (N.A.); (G.-T.E.C.)
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Wang JY, Chen GTE, Braguy J, Jamil M, Berqdar L, Al-Babili S. Disruption of the cytochrome CYP711A5 gene reveals MAX1 redundancy in rice strigolactone biosynthesis. J Plant Physiol 2023; 287:154057. [PMID: 37531662 DOI: 10.1016/j.jplph.2023.154057] [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] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/04/2023]
Abstract
Strigolactones (SLs) inhibit shoot branching/tillering and are secreted by plant roots as a signal to attract symbiotic mycorrhizal fungi in the rhizosphere, particularly under phosphate starvation. However, SLs are also hijacked by root parasitic weeds as inducer for the germination of their seeds. There are around 35 natural SLs divided, based on their structures, into canonical and non-canonical SLs. Cytochrome P450 enzymes of the 711 clade, such as MORE AXILLARY GROWTH1 (MAX1) in Arabidopsis, are a major driver of SL structural diversity. Monocots, such as rice, contain several MAX1 homologs that participate in SL biosynthesis. To investigate the function of OsMAX1-1900 in planta, we generated CRISPR/Cas9 mutants disrupted in the corresponding gene. Characterizing of the generated mutants at metabolite and phenotype level suggests that OsMAX1-1900 loss-of-function does neither affect the SL pattern nor rice architecture, indicating functional redundancy among rice MAX1 homologs.
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Affiliation(s)
- Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Saudi Arabia
| | - Guan-Ting Erica Chen
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Saudi Arabia; The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Justine Braguy
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Saudi Arabia
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Saudi Arabia; The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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Shaikh K, Iqbal Y, Abdel-Maksoud MA, Murad A, Badar N, Alarjani KM, Siddiqui K, Chandio K, Almanaa TN, Jamil M, Ali M, Jabeen N, Hussein AM. Characterization of ferroptosis driver gene signature in head and neck squamous cell carcinoma (HNSC). Am J Transl Res 2023; 15:4829-4850. [PMID: 37560204 PMCID: PMC10408515] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSC), a prevalent malignant tumor with a low survival rate, is often accompanied by ferroptosis, which is a recently-described type ofprogrammed cell death. Investigating the significance of ferroptosis driver genes in HNSC, this study aimed to assess their diagnostic and prognostic values, as well as their impact on treatment and tumor immune function. The results of this investigation provide novel insight into using ferroptosis-related genes as molecular biomarkers as well as precise chemotherapeutic targets for the therapy of HNSC. METHODOLOGY A detailed in silico and in vitro experiment-based methodology was adopted to achieve the goals. RESULTS A total of 233 ferroptosis driver genes were downloaded from the FerrDB database. After comprehensively analyzing these 233 ferroptosis driver genes by various TCGA databases, RNA-sequencing (RNA-seq), and Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) techniques, TP53 (tumor protein 53), PTEN (Phosphatase and TENsin homolog deleted on chromosome 10), KRAS (Ki-ras2 Kirsten rat sarcoma viral oncogene homolog), and HRAS (Harvey Rat sarcoma virus) were identified as differentially expressed hub genes. Interestingly, these hub genes were found to have significant (P < 0.05) variations in their mRNA and protein expressions and effects on overall survival of the HNSC patients. Moreover, targeted bisulfite-sequencing (bisulfite-seq) analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes (TP53, PTEN, KRAS, and HRAS). In addition to this, hub genes were involved in diverse oncogenic pathways. CONCLUSION Since HNSC pathogenesis is a complex process, using ferroptosis driver hub genes (TP53, PTEN, KRAS, and HRAS) as a diagnostic and prognostic tool, and therapeutically targeting those genes through appropriate drugs could bring a milestone change in the drug discovery and management and survival in HNSC.
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Affiliation(s)
- Khalida Shaikh
- Liaquat University of Medical and Health SciencesJamshoro, Pakistan
| | - Yusra Iqbal
- Continental Medical College LahoreLahore 54660, Pakistan
| | - Mostafa A Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Amina Murad
- Department of Bioscience, Comsats UniversityIslamabad, Pakistan
| | - Nadia Badar
- Department of Medical Oncology Allied HospitalFaisalabad, Pakistan
| | - Khaloud Mohammed Alarjani
- Botany and Microbiology Department, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Komal Siddiqui
- Institute of Biotechnology and Genetic Engineering University of SindhJamshoro, Pakistan
| | | | | | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of AgricultureFaisalabad 38000, Pakistan
| | - Ahmed M Hussein
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna1090 Vienna, Austria
- Programme for Proteomics, Paracelsus Medical UniversitySalzburg, Austria
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Ali L, Raza AA, Zaheer AB, Alhomrani M, Alamri AS, Alghamdi SA, Almalki AA, Alghamdi AA, Khawaja I, Alhadrami M, Ramzan F, Jamil M, Ali M, Jabeen N. In vitro analysis of PI3K pathway activation genes for exploring novel biomarkers and therapeutic targets in clear cell renal carcinoma. Am J Transl Res 2023; 15:4851-4872. [PMID: 37560222 PMCID: PMC10408522] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVES The regulation of various cellular functions such as growth, proliferation, metabolism, and angiogenesis, is dependent on the PI3K pathway. Recent evidence has indicated that kidney renal clear cell carcinoma (KIRC) can be triggered by the deregulation of this pathway. The objective of this research was to investigate 25 genes associated with activation of the PI3K pathway in KIRC and control samples to identify four hub genes that might serve as novel molecular biomarkers and therapeutic targets for treating KIRC. METHODS Multi-omics in silico and in vitro analysis was employed to find hub genes related to the PI3K pathway that may be biomarkers and therapeutic targets for KIRC. RESULTS Using STRING software, a protein-protein interaction (PPI) network of 25 PI3K pathway-related genes was developed. Based on the degree scoring method, the top four hub genes were identified using Cytoscape's Cytohubba plug-in. TCGA datasets, KIRC (786-O and A-498), and normal (HK2) cells were used to validate the expression of hub genes. Additionally, further bioinformatic analyses were performed to investigate the mechanisms by which hub genes are involved in the development of KIRC. Out of a total of 25 PI3K pathway-related genes, we developed and validated a diagnostic and prognostic model based on the up-regulation of TP53 (tumor protein 53) and CCND1 (Cyclin D1) and the down-regulation of PTEN (Phosphatase and TENsin homolog deleted on chromosome 10), and GSK3B (Glycogen synthase kinase-3 beta) hub genes. The hub genes included in our model may be a novel therapeutic target for KIRC treatment. Additionally, associations between hub genes and infiltration of immune cells can enhance comprehension of immunotherapy for KIRC. CONCLUSION We have created a new diagnostic and prognostic model for KIRC patients that uses PI3K pathway-related hub genes (TP53, PTEN, CCND1, and GSK3B). Nevertheless, further experimental studies are required to ascertain the efficacy of our model.
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Affiliation(s)
- Liaqat Ali
- Department of Urology, Institute of Kidney Diseases, Hayatabad Medical ComplexPeshawar 25000, Pakistan
| | - Abbas Ali Raza
- Surgery Department, Bacha Khan Medical College, MTI Mardan Medical ComplexMardan 23200, Pakistan
| | | | - Majid Alhomrani
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif UniversityTaif 21944, Saudi Arabia
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif UniversityTaif 21944, Saudi Arabia
| | - Abdulhakeem S Alamri
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif UniversityTaif 21944, Saudi Arabia
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif UniversityTaif 21944, Saudi Arabia
| | - Saleh A Alghamdi
- Department of Clinical Laboratory Since, Medical Genetics, College of Applied Medical Sciences, Taif UniversityTaif 21944, Saudi Arabia
| | - Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityTaif 21944, Saudi Arabia
| | - Ahmad A Alghamdi
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
| | - Imran Khawaja
- Department of Medicine, Ayub Teaching HospitalAbbottabad 22010, Pakistan
| | - Mai Alhadrami
- Department of Pathology, Faculty of Medicine, Umm Alqura UniversityMakkah 24373, Saudi Arabia
| | - Faiqah Ramzan
- Department of Animal and Poultry Production, Faculty of Veterinary and Animal Sciences, Gomal UniversityDera Ismail Khan 29050, Pakistan
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of AgricultureFaisalabad 38040, Pakistan
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Ullah G, Ibrahim M, Nawaz G, Khatoon A, Jamil M, Rehman SU, Ali EA, Tariq A. Plant-Derived Smoke Mitigates the Inhibitory Effects of the Auxin Inhibitor 2,3,5-Triiodo Benzoic Acid (TIBA) by Enhancing Root Architecture and Biochemical Parameters in Maize. Plants (Basel) 2023; 12:2604. [PMID: 37514219 PMCID: PMC10383894 DOI: 10.3390/plants12142604] [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] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
The present study was designed to investigate and compare the effects of plant-derived smoke (PDS) and auxin (IAA and IBA) on maize growth under the application of 2,3,5-triiodo benzoic acid (TIBA). For this purpose, indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA), each at a concentration of 10 ppm, along with PDS at a ratio of 1:500 (v/v) were used alone and in combination with 10 ppm of TIBA. The results indicate that the germination percentage (%) of maize seeds was enhanced under IAA, IBA and PDS treatment. However, IAA and IBA resulted in reduced germination when applied in combination with TIBA. Importantly, the germination percentage (%) was improved by PDS under TIBA treatment. The analysis of seedling height, length of leaves, and number of primary, seminal and secondary/lateral roots showed improvement under individual treatments of IAA and IBA, PDS and PDS + TIBA treatment, while these values were reduced under IAA + TIBA and IBA + TIBA application. Chlorophyll content, total soluble sugars and antioxidative enzymatic activity including POD and SOD increased in seedlings treated with PDS alone or both PDS and TIBA, while in seedlings treated with IAA and TIBA or IBA and TIBA, their levels were decreased. APX and CAT responded in the opposite way-under IAA, IBA and PDS treatment, their levels were found to be lower than the control (simple water treatment), while TIBA treatment with either IAA, IBA or PDS enhanced their levels as compared to the control. These results reveal that PDS has the potential to alleviate the inhibitory effects of TIBA. This study highlights the role of PDS in preventing TIBA from blocking the auxin entry sites.
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Affiliation(s)
- Gulfan Ullah
- Department of Botany, Kohat University of Science and Technology, Kohat 2600, Pakistan
| | - Muhammad Ibrahim
- Department of Botany, Kohat University of Science and Technology, Kohat 2600, Pakistan
| | - Ghazala Nawaz
- Department of Botany, Kohat University of Science and Technology, Kohat 2600, Pakistan
| | - Amana Khatoon
- Department of Botany, Kohat University of Science and Technology, Kohat 2600, Pakistan
| | - Muhammad Jamil
- Department of Botany, Kohat University of Science and Technology, Kohat 2600, Pakistan
| | - Shafiq Ur Rehman
- Department of Biology, The University of Haripur, Haripur 2262, Pakistan
| | - Essam A Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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Javed MS, Zubair M, Rizwan K, Jamil M. In Vitro Anti-Microbial Activity and Anti-Cancer Potential of Novel Synthesized Carbamothioyl-Furan-2-Carboxamide Derivatives. Molecules 2023; 28:4583. [PMID: 37375137 DOI: 10.3390/molecules28124583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
A series of carbamothioyl-furan-2-carboxamide derivatives were synthesized using a one-pot strategy. Compounds were obtained in moderate to excellent yields (56-85%). Synthesized derivatives were evaluated for their anti-cancer (HepG2, Huh-7, and MCF-7 human cancer cell lines) and anti-microbial potential. Compound p-tolylcarbamothioyl)furan-2-carboxamide showed the highest anti-cancer activity at a concentration of 20 μg/mL against hepatocellular carcinoma, with a cell viability of 33.29%. All compounds showed significant anti-cancer activity against HepG2, Huh-7, and MCF-7, while indazole and 2,4-dinitrophenyl containing carboxamide derivatives were found to be less potent against all tested cell lines. Results were compared with the standard drug doxorubicin. Carboxamide derivatives possessing 2,4-dinitrophenyl showed significant inhibition against all bacterial and fungal strains with inhibition zones (I.Z) in the range of 9-17 and MICs were found to be 150.7-295 μg/mL. All carboxamide derivatives showed significant anti-fungal activity against all tested fungal strains. Gentamicin was used as the standard drug. The results showed that carbamothioyl-furan-2-carboxamide derivatives could be a potential source of anti-cancer and anti-microbial agents.
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Affiliation(s)
- Muhammad Salman Javed
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Zubair
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Komal Rizwan
- Department of Chemistry, University of Sahiwal, Sahiwal 57000, Pakistan
| | - Muhammad Jamil
- Department of Chemistry, Government Post Graduate College, Sahiwal 57000, Pakistan
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Aguliar Perez KM, Alagoz Y, Maatouk B, Wang J, Berqdar L, Qutub S, Jamil M, AlNasser S, BinSaleh N, Lin P, Almarwaey L, Asami T, Al-Babili S, Khashab NM. Biomimetic Mineralization for Smart Biostimulant Delivery and Crop Micronutrients Fortification. Nano Lett 2023. [PMID: 37272543 DOI: 10.1021/acs.nanolett.2c04506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sustainable and precise fortification practices are necessary to ensure food security for the increasing human population. Precision agriculture aims to minimize the use of fertilizers and pesticides by developing smart materials for real-life agricultural practices. Here, we show that biomimetic mineralization can be efficiently employed to encapsulate and controllably release plant biostimulants (MiZax-3) to improve the quality and yield of capsicum (Capsicum annum) crops in field experiments. ZIF-8 encapsulation of MiZax-3 (MiZIFs) could significantly enhance its stability up to around 679 times (6p value = 0.0072) at field conditions. Our results demonstrate that the coordinating Zn ions and the MiZax-3 play a vital role in improving Zn content in the produced fruits by 2-fold, which is the first report of this nature on Zn content in fruits. We envision this platform as a starting point to investigate other biocompatible coordination-based platforms for micronutrient delivery in precision agriculture.
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Affiliation(s)
- Katya M Aguliar Perez
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yagiz Alagoz
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Batoul Maatouk
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jiangyou Wang
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Lamis Berqdar
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Somayah Qutub
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Sara AlNasser
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Nouf BinSaleh
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Peiyu Lin
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Lamyaa Almarwaey
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 1138657, Japan
| | - Salim Al-Babili
- The BioActives Lab. Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Niveen M Khashab
- Smart Hybrid Materials Laboratory (SHMs), Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Ahmad F, Cheema TA, Rehman K, Ullah M, Jamil M, Park CW. Hemodynamic performance evaluation of neonatal ECMO double lumen cannula using fluid-structure interaction. Int J Numer Method Biomed Eng 2023; 39:e3706. [PMID: 37039384 DOI: 10.1002/cnm.3706] [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] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 12/30/2022] [Accepted: 03/19/2023] [Indexed: 06/07/2023]
Abstract
Extra corporeal membrane oxygenation (ECMO) is an artificial oxygenation facility, employed in situations of cardio-pulmonary failure. Some diseases i.e., acute respiratory distress syndrome, pulmonary hypertension, corona virus disease (COVID-19) etc. affect oxygenation performance of the lungs thus requiring the need of artificial oxygenation. Critical care teams used ECMO technique during the COVID-19 pandemic to support the heart and lungs of COVID-19 patients who had an acute respiratory or cardiac failure. Double Lumen Cannula (DLC) is one of the most critical components of ECMO as it resides inside the patient and, connects patient with external oxygenation circuit. DLC facilitates delivery and drainage of blood from the patient's body. DLC is characterized by delicate balance of internal and external flows inside a limited space of the right atrium (RA). An optimal performance of the DLC necessitates structural stability under biological and hemodynamic loads, a fact that has been overlooked by previously published studies. In the past, many researchers experimentally and computationally investigated the hemodynamic performance of DLC by employing Eulerian approach, which evaluate instantaneous blood damage without considering blood shear exposure history (qualitative assessment only). The present study is an attempt to address the aforementioned limitations of the previous studies by employing Lagrangian (quantitative assessment) and incorporating the effect of fluid-structure interaction (FSI) to study the hemodynamic performance of neonatal DLC. The study was performed by solving three-dimensional continuity, momentum, and structural mechanics equation(s) by numerical methods for the blood flow through neonatal DLC. A two-way coupled FSI analysis was performed to analyze the effect of DLC structural deformation on its hemodynamic performance. Results show that the return lumen was the most critical section with maximum pressure drop, velocity, shear stresses, and blood damage. Recirculation and residence time of blood in the right atrium (RA) increases with increasing blood flow rates. Considering the structural deformation has led to higher blood damage inside the DLC-atrium system. Maximum Von-Mises stress was present on the side edges of the return lumen that showed direct proportionality with the blood flow rate.
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Affiliation(s)
- Faiq Ahmad
- Faculty of Mechanical Engineering, GIK Institute of Engineering Sciences and Technology, Topi, 23460, KPK, Pakistan
| | - Taqi Ahmad Cheema
- Faculty of Mechanical Engineering, GIK Institute of Engineering Sciences and Technology, Topi, 23460, KPK, Pakistan
| | - Khawar Rehman
- Department of Civil and Environmental Engineering, Hanyang University, Seoul, 04763, South Korea
- Department of Civil Engineering, GIK Institute of Engineering Sciences and Technology, Topi, 23460, KPK, Pakistan
| | - Minhaj Ullah
- Faculty of Mechanical Engineering, GIK Institute of Engineering Sciences and Technology, Topi, 23460, KPK, Pakistan
| | - Muhammad Jamil
- Analysis Group, Starfish Medical, 455 Boleskine Rd, Victoria, British Columbia, Canada
- Department of Mechanical Engineering, KoÇ University, Sariyar, Istanbul, 34450, Turkey
| | - Cheol Woo Park
- School of Mechanical Engineering, Kyungpook National University, 80 Daehak-Ro, Buk-Gu, Daegu, 41566, South Korea
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Sarwar S, Ashraf S, Shafiq M, Malik A, Akhtar S, Arshad R, Jamil M, Gul H, Ullah N. SEC24D gene as a biomarker in human cancers and its association with CD8+ T cell immune cell infiltration. Am J Transl Res 2023; 15:3115-3130. [PMID: 37303662 PMCID: PMC10251021] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 04/21/2023] [Indexed: 06/13/2023]
Abstract
OBJECTIVE The SEC24D (SEC24 Homolog D, COPII Coat Complex Component) gene belongs to the SEC24 subfamily of genes. The protein encoded by this gene, along with its other binding partners, mediates the transport of newly-synthesized proteins from the endoplasmic reticulum to the Golgi apparatus. METHODS A pan-cancer analysis of this gene, as well as its diagnostic and prognostic implications, are lacking in the medical literature. First, we analyzed SEC24D gene expression, its prognostic effect, promoter methylation level, genetic alteration landscape, pathways, CD8+ T immune cell infiltration, and gene-drug network in various types of cancer through various online databases and bioinformatic tools. Then, we performed the expression and methylation validation analysis of the SEC24D gene on cell lines using RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq) techniques. RESULTS Bioinformatic analysis showed that the SEC24D gene was overexpressed in metastasis across Kidney Renal Clear Cell Carcinoma (KIRC), Lung Squamous Cell Carcinoma (LUSC), and Stomach Adenocarcinoma (STAD) patients and was a prognostic risk factor. Then, using RNA sequencing and targeted bisulfite sequencing analysis, it was validated in cell lines that SEC24D was overexpressed and hypomethylated in KIRC patients. Mutational analysis revealed that SEC24D was mutated less frequently in KIRC, LUSC, and STAD patients. It was further observed that CD8+ T cell infiltration levels were increased in SEC24D-overexpressed KIRC, LUSC, and STAD samples. Pathway enrichment analysis of SEC24D-associated genes revealed their participation in two important pathways. Moreover, we suggested a few valuable drugs for treating KIRC, LUSC, and STAD patients with respect to overexpressed SEC24D. CONCLUSION This is the first pan-cancer study that details the oncogenic roles of SEC24D among different cancers.
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Affiliation(s)
| | | | | | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud UniversityRiyadh, Saudi Arabia
| | - Suhail Akhtar
- Department of Biochemistry, A.T. Still University of Health SciencesKirksville, Missouri, USA
| | - Rabia Arshad
- Faculty of Pharmacy, The University of LahorePakistan
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan, Pakistan
| | - Hadia Gul
- Institute of Biological Sciences Gomal UniversityD. I. Khan, Pakistan
| | - Naimat Ullah
- Institute of Biological Sciences Gomal UniversityD. I. Khan, Pakistan
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Zhu Q, Zhang L, Sadiq FM, Abdel-Maksoud MA, Almutairi SM, Al-Qahtani WH, Gul J, Jamil M, Fatima I, Zia S. Integrative bioinformatics and RNA sequencing based methodology results in the exploration of breast invasive carcinoma biomarkers. Am J Transl Res 2023; 15:3067-3091. [PMID: 37303632 PMCID: PMC10251034] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/03/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND Previously reported breast invasive carcinoma (BRIC) biomarkers have compromised utility because of their heterogeneity-specific behaviors. The goal of this study was to find BRIC biomarkers that could be used in spite of the heterogeneity barrier. METHODS Previously reported BRIC-linked hub genes were obtained from the literature via a search technique. A protein-protein interaction (PPI) network of the extracted hub genes was constructed, visualized, and analyzed to explore the top six real hub genes. Following this, real hub genes' expression profiling was carried out using various TCGA data sources and RNA sequencing (RNA-seq) of BT 20 and HMEC cell lines to uncover the tumor-driver roles of the real hub genes. RESULTS In total, 124 BRIC-linked hub genes were collected from the literature via the search technique. From these collected hub genes, a total of 6 genes, including Centrosomal protein of 55 kDa (CEP55), Kinesin Family Member 2C (KIF2C), kinesin family member 20A (KIF20A), Ribonucleotide Reductase Regulatory Subunit M2 (RRM2), Aurora A Kinase (AURKA), and Protein Regulator of cytokinesis 1 (PRC1) were determined to be the real hub genes. Via expression profiling and validation analyses, we documented the overexpression of CEP55, KIF2C, KIF20A, RRM2, AURKA, and PRC1 real hub genes in BRIC patients with different clinical variables. Further correlational analyses showed diverse associations among real hub genes' expression and other important parameters, including promoter methylation status, genetic alteration, overall survival (OS), relapse-free survival (RFS), tumor purity, CD8+ T, CD4+ T immune cell infiltration, and different mutant genes across BRIC samples. Finally, in this work, we investigated several transcription factors (TFS), microRNAs, and therapeutic medicines related to the real hub genes that have great therapeutic potential. CONCLUSION In conclusion, we discovered six real hub genes, which may be employed as novel potential biomarkers for BRIC patients with different clinical parameters.
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Affiliation(s)
- Qiang Zhu
- Department of Breast Surgery, Beijing Tiantan Hospital, Capital Medical UniversityNo. 119 South Fourth Ring West Road, Fengtai District, Beijing 100070, The People’s Republic of China
| | - Luyan Zhang
- Department of Oncology, Binzhou People’s HospitalBinzhou 256600, Shandong, The People’s Republic of China
| | | | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud University RiyadhP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University RiyadhP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Wahidah H Al-Qahtani
- Department of Food Sciences & Nutrition, College of Food and Agricultural Sciences, King Saud UniversityP.O. Box 270677, Riyadh 11352, Saudi Arabia
| | - Jaweria Gul
- Department of Biotechnology, Shaheed Benazir Bhutto UniversitySheringal, Dir Upper, Pakistan
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan, Pakistan
| | - Isha Fatima
- Akhtar Saeed Medical and Dental CollegeLahore, Pakistan
| | - Sikandar Zia
- Department of Biochemistry, Gajju Khan Medical CollegeSwabi, Pakistan
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Jamil M. Taxonomical and epidemiological study of tick species on domesticated animals. PAB 2023. [DOI: 10.19045/bspab.2023.120054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Yang Y, Abuauf H, Song S, Wang JY, Alagoz Y, Moreno JC, Mi J, Ablazov A, Jamil M, Ali S, Zheng X, Balakrishna A, Blilou I, Al-Babili S. The Arabidopsis D27-LIKE1 is a cis/cis/trans-β-carotene isomerase that contributes to Strigolactone biosynthesis and negatively impacts ABA level. Plant J 2023; 113:986-1003. [PMID: 36602437 DOI: 10.1111/tpj.16095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The enzyme DWARF27 (D27) catalyzes the reversible isomerization of all-trans- into 9-cis-β-carotene, initiating strigolactone (SL) biosynthesis. Genomes of higher plants encode two D27-homologs, D27-like1 and -like2, with unknown functions. Here, we investigated the enzymatic activity and biological function of the Arabidopsis D27-like1. In vitro enzymatic assays and expression in Synechocystis sp. PCC6803 revealed an unreported 13-cis/15-cis/9-cis- and a 9-cis/all-trans-β-carotene isomerization. Although disruption of AtD27-like1 did not cause SL deficiency phenotypes, overexpression of AtD27-like1 in the d27 mutant restored the more-branching phenotype, indicating a contribution of AtD27-like1 to SL biosynthesis. Accordingly, generated d27 d27like1 double mutants showed a more pronounced branching phenotype compared to d27. The contribution of AtD27-like1 to SL biosynthesis is likely a result of its formation of 9-cis-β-carotene that was present at higher levels in AtD27-like1 overexpressing lines. By contrast, AtD27-like1 expression correlated negatively with the content of 9-cis-violaxanthin, a precursor of ABA, in shoots. Consistently, ABA levels were higher in shoots and also in dry seeds of the d27like1 and d27 d27like1 mutants. Transgenic lines expressing GUS driven by the AtD27LIKE1 promoter and transcript analysis of hormone-treated Arabidopsis seedlings revealed that AtD27LIKE1 is expressed in different tissues and affects ABA and auxin. Taken together, our work reports a cis/cis-β-carotene isomerase that affects the content of both cis-carotenoid-derived plant hormones, ABA and SLs.
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Affiliation(s)
- Yu Yang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, 23955, Saudi Arabia
| | - Haneen Abuauf
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, 8XH2+XVP, Mecca, 24382, Saudi Arabia
| | - Shanshan Song
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Yagiz Alagoz
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Juan C Moreno
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Jianing Mi
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Abdugaffor Ablazov
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, 23955, Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Shawkat Ali
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main Street, Kentville, NS, B4N 1J5, Canada
| | - Xiongjie Zheng
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Aparna Balakrishna
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Ikram Blilou
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, 23955, Saudi Arabia
- The Laboratory of Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, 23955, Saudi Arabia
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Ramzan M, Naz G, Shah AA, Parveen M, Jamil M, Gill S, Sharif HMA. Synthesis of phytostabilized zinc oxide nanoparticles and their effects on physiological and anti-oxidative responses of Zea mays (L.) under chromium stress. Plant Physiol Biochem 2023; 196:130-138. [PMID: 36706692 DOI: 10.1016/j.plaphy.2023.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 10/12/2022] [Revised: 12/15/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Chromium (Cr) is a hazardous metal that has a significant risk of transfer from soil to edible parts of food crops, including shoot tissues. Reduction of Cr accumulation is required to lower the risk of Cr-exposed in humans and animals feeding on metal-contaminated parts of such plant. Zea mays is a global staple crop irrigated intensively with Cr-contaminated water. Consequently, the objective of this study was to investigate that FI-stabilized ZnO NPs could be used as an eco-friendly and efficient amendment to reduced Cr uptake and toxicity in Zea mays. To investigate the growth parameters, physiological, oxidative stress and biochemical parameters under different Cr-VI concentrations (10.0, 15.0, and 20.0 ppm). Cr exposed Z. mays plants exhibited substantially reduced plant biomass, chlorophyll contents, and altered antioxidant enzyme activity compared to untreated control. The results revealed that foliar application of Fagonia-ZnO-NPs helps eliminate the harmful effects of Cr (VI), which can enter plants through soil pollution. Increased levels of proline, soluble sugars and various antioxidant enzymes reflected this. Mean comparisons showed that Cr stress led to a 33-50% reduction in fresh shoot weight, 73-170% in fresh root weight, 16-34% shoot length, 9.5-129% root length, Chlorophyll contents 20-33% (Chl a), 18-27% (Chl b) and 17-27% (car), 14-33% total soluble sugars, 54-170% proline content, 7-7.5% POD, 0.66-75% CAT and 32-77% APX enzyme activities compared to untreated plants. Application of FI-stabilized ZnO NPs led to an increase 21-77% in fresh shoot weight, 22-45%, fresh root weight, 3-35% shoot length, 24-154% root length, Chlorophyll contents 39-60% (Chl a), 15-79% (Chl b) and 28-82% (car), 19-52% total soluble sugars, 21-55% proline content, 14-43% POD, 34-95% CAT and 130-186% APX enzyme activities under 10, 15 and 20 ppm Cr stress respectively, compared to Cr-treated plants. However, the principal component analysis revealed that chlorophyll contents, carotenoid, CAT, APX and length were in the same group and showed a positive correlation. These data collectively suggest that phytostabilized zinc oxide NPs may be an eco-friendly solution to mitigate Cr toxicity in agricultural soils and crop plants.
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Affiliation(s)
- Musarrat Ramzan
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Gul Naz
- Institute of Physics, Faculty of Physical & Mathematical Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Misbah Parveen
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Muhammad Jamil
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Sidra Gill
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Hafiz M Adeel Sharif
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China.
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Mahmood F, Zehra SS, Hasan M, Zafar A, Tariq T, Abdullah M, Nazir MA, Jamil M, Hassan SG, Huang X, Javed HU, Shu X. Bioinspired Cobalt Oxide Nanoball Synthesis, Characterization, and Their Potential as Metal Stress Absorbants. ACS Omega 2023; 8:5836-5849. [PMID: 36816675 PMCID: PMC9933469 DOI: 10.1021/acsomega.2c07545] [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] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Massive accumulation of heavy metals in agricultural land as a result of enhanced levels of toxicity in the soil is an emerging global concern. Among various metals, zinc contamination has severe effects on plant and human health through the food chain. To remove such toxicity, a nanotechnological neutralizer, cobalt oxide nanoballs (Co3O4 Nbs) were synthesized by using the extract of Cordia myxa. The Co3O4 Nbs were well characterized via UV-vis spectrophotometry, scanning electron microscopy, and X-ray diffraction techniques. Green-synthesized Co3O4 Nbs were exposed over Acacia jacquemontii and Acacia nilotica at different concentrations (25, 50, 75, and 100 ppm). Highly significant results were observed for plant growth by the application of Co3O4 Nbs at 100 ppm, thereby increasing the root length (35%), shoot length (48%), fresh weight (44%), and dry weight (40%) of the Acacia species with respect to the control. Furthermore, physiological parameters including chlorophyll contents, relative water contents, and osmolyte contents like proline and sugar showed a prominent increase. The antioxidant activity and atomic absorption supported and justified the positive response to using Co3O4 Nbs that mitigated the heavy-metal zinc stress by improving the plant growth. Hence, the biocompatible Co3O4 Nbs counteract the zinc toxicity for governing and maintaining plant growth. Such nanotechnological tools can therefore step up the cropping system and overcome toxicity to meet the productivity demand along with the development of agricultural management strategies.
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Affiliation(s)
- Faisal Mahmood
- Department
of Botany, The Islamia University, Bahawalpur63100, Pakistan
| | - Syeda Sadaf Zehra
- Department
of Botany, The Islamia University, Bahawalpur63100, Pakistan
| | - Murtaza Hasan
- Department
of Biotechnology, The Islamia University
of Bahawalpur, Bahawalpur63100, Pakistan
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou510225, China
| | - Ayesha Zafar
- Department
of Biotechnology, The Islamia University
of Bahawalpur, Bahawalpur63100, Pakistan
- Department
of Biomedical Engineering, College of Future Technology, Peking University, Beijing100871, China
| | - Tuba Tariq
- Department
of Biotechnology, The Islamia University
of Bahawalpur, Bahawalpur63100, Pakistan
| | - Muhammad Abdullah
- Cholistan
Institute of Desert Studies, The Islamia
University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muniba Anum Nazir
- Department
of Biotechnology, The Islamia University
of Bahawalpur, Bahawalpur63100, Pakistan
| | - Muhammad Jamil
- Department
of Botany, The Islamia University, Bahawalpur63100, Pakistan
| | - Shahbaz Gul Hassan
- College of
Information Science and Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou510225, China
| | - Xue Huang
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou510225, China
| | - Hafiz Umer Javed
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou510225, China
| | - Xugang Shu
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou510225, China
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Grossmann N, Soria F, Juvet T, Potretzka A, Djaladat H, Kikuchi E, Mari A, Khene Z, Fujita K, Raman J, Breda A, Sfakianos J, Pfail J, Laukhtina E, Rajwa P, Pallauf M, Cacciamani G, Poyet C, Van Doeveren T, Boormans J, Antonelli A, Jamil M, Ploussard G, Shariat S, Pradere B. Comparing oncological and perioperative outcomes of open versus laparoscopic versus robotic radical nephroureterectomy for the treatment of upper tract urothelial carcinoma: A multicenter, multinational, propensity score-matched analysis. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Jamil M, Sweed H, Abou-Hashem R, Hamed H, Ali K. 1283 MEDICATION-RELATED HARM (MRH) IN OLDER PEOPLE AFTER LEAVING HOSPITAL - AN UNDER-REPORTED EGYPTIAN CHALLENGE. Age Ageing 2023. [DOI: 10.1093/ageing/afac322.055] [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] [Indexed: 01/18/2023] Open
Abstract
Abstract
Introduction
Ageing is associated with multimorbidity, polypharmacy and medication-related harm (MRH). A 2013 systematic review reported only one study of medication errors (MEs) in older Egyptian patients. Our study investigated MRH (adverse drug reactions (ADR), drug errors, and non-adherence) in older Egyptian adults after hospital-discharge.
Methods
Between 2018 and 2020, we recruited 400 Egyptian patients, aged ≥60 years on discharge from Geriatrics and Internal Medicine wards from 3 hospitals, and followed them up for 8 weeks. Study procedures adopted a modified PRIME trial methodology (1).
Results
The average age of study participants was 71 (range 60 to 93, SD +/- 6.29) years with 53% females. In the cohort of 325 patients completing follow up, MRH occurred in 99 patients (incidence of 30.5%), with 5 patients (5.1%) experiencing a fatal MRH. Almost two thirds (65.7%) of MRH events were secondary to ADRs, 2 % related to non-adherence, 18.2 % due to both ADR and non-adherence, and 14% related to MEs. Multivariate logistic regression analysis showed that non-adherence (p-value 0.000, OR- 95% CI: 36.029), inappropriate prescription using Beer’s criteria (p 0.000, OR- 95% CI: 6.589), length of stay >7days (p 0.001, OR- 95% CI: 6.176), presence of Ischaemic Heart Disease (IHD) (p 0.000,OR- 95% CI: 5.695), Platelets count ≤ 245X 109/L (p 0.021, OR- 95% CI: 2.640), and dementia medications (p 0.017, OR- 95% CI: 4.616) were all significantly associated with MRH.
Conclusions
Medication-related harm in older Egyptian adults is common after hospital discharge. An integrated care pathway is required targeting high-risk older patients.
Reference
1. Stevenson J, Parekh N, Ali K et al. Protocol for a Prospective (P) study to develop a model to stratify the risk (RI) of medication (M) related harm in hospitalized elderly (E) patients in the UK (The PRIME study). BMC Geriatrics 2016; 16: 22. https://doi.org/10.1186/s12877-016-0191-8.
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Affiliation(s)
- M Jamil
- Ain Shams University Geriatrics and Gerontology Department, , Egypt
| | - H Sweed
- Ain Shams University Geriatrics and Gerontology Department, , Egypt
| | - R Abou-Hashem
- Ain Shams University Geriatrics and Gerontology Department, , Egypt
| | | | - K Ali
- Brighton and Sussex Medical School Academic Department of Geriatrics, , UK
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Ablazov A, Votta C, Fiorilli V, Wang JY, Aljedaani F, Jamil M, Balakrishna A, Balestrini R, Liew KX, Rajan C, Berqdar L, Blilou I, Lanfranco L, Al-Babili S. ZAXINONE SYNTHASE 2 regulates growth and arbuscular mycorrhizal symbiosis in rice. Plant Physiol 2023; 191:382-399. [PMID: 36222582 PMCID: PMC9806602 DOI: 10.1093/plphys/kiac472] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/09/2022] [Indexed: 05/24/2023]
Abstract
Carotenoid cleavage, catalyzed by CAROTENOID CLEAVAGE DIOXYGENASEs (CCDs), provides signaling molecules and precursors of plant hormones. Recently, we showed that zaxinone, a apocarotenoid metabolite formed by the CCD ZAXINONE SYNTHASE (ZAS), is a growth regulator required for normal rice (Oryza sativa) growth and development. The rice genome encodes three OsZAS homologs, called here OsZAS1b, OsZAS1c, and OsZAS2, with unknown functions. Here, we investigated the enzymatic activity, expression pattern, and subcellular localization of OsZAS2 and generated and characterized loss-of-function CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and associated protein 9)-Oszas2 mutants. We show that OsZAS2 formed zaxinone in vitro. OsZAS2 was predominantly localized in plastids and mainly expressed under phosphate starvation. Moreover, OsZAS2 expression increased during mycorrhization, specifically in arbuscule-containing cells. Oszas2 mutants contained lower zaxinone content in roots and exhibited reduced root and shoot biomass, fewer tillers, and higher strigolactone (SL) levels. Exogenous zaxinone application repressed SL biosynthesis and partially rescued the growth retardation of the Oszas2 mutant. Consistent with the OsZAS2 expression pattern, Oszas2 mutants displayed a lower frequency of arbuscular mycorrhizal colonization. In conclusion, OsZAS2 is a zaxinone-forming enzyme that, similar to the previously reported OsZAS, determines rice growth, architecture, and SL content, and is required for optimal mycorrhization.
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Affiliation(s)
| | | | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10125, Italy
| | - Jian You Wang
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), The BioActives Lab, Thuwal, 23955-15 6900, Saudi Arabia
| | - Fatimah Aljedaani
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Jamil
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), The BioActives Lab, Thuwal, 23955-15 6900, Saudi Arabia
| | - Aparna Balakrishna
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), The BioActives Lab, Thuwal, 23955-15 6900, Saudi Arabia
| | - Raffaella Balestrini
- National Research Council, Institute for Sustainable Plant Protection, Turin 10135, Italy
| | - Kit Xi Liew
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), The BioActives Lab, Thuwal, 23955-15 6900, Saudi Arabia
| | - Chakravarthy Rajan
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), The BioActives Lab, Thuwal, 23955-15 6900, Saudi Arabia
| | - Lamis Berqdar
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), The BioActives Lab, Thuwal, 23955-15 6900, Saudi Arabia
| | - Ikram Blilou
- The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Plant Cell and Developmental Biology, Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10125, Italy
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Malik MS, Rehman A, Khan IU, Khan TA, Jamil M, Rha ES, Anees M. Thermo-neutrophilic cellulases and chitinases characterized from a novel putative antifungal biocontrol agent: Bacillus subtilis TD11. PLoS One 2023; 18:e0281102. [PMID: 36706132 PMCID: PMC9882894 DOI: 10.1371/journal.pone.0281102] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Cellulose and chitin are the most abundant naturally occurring biopolymers synthesized in plants and animals and are used for synthesis of different organic compounds and acids in the industry. Therefore, cellulases and chitinases are important for their multiple uses in industry and biotechnology. Moreover, chitinases have a role in the biological control of phytopathogens. A bacterial strain Bacillus subtilis TD11 was previously isolated and characterized as a putative biocontrol agent owing to its significant antifungal potential. In this study, cellulase and chitinase produced by the strain B. subtilis TD11 were purified and characterized. The activity of the cellulases and chitinases were optimized at different pH (2 to 10) and temperatures (20 to 90°C). The substrate specificity of cellulases was evaluated using different substances including carboxymethyl cellulose (CMC), hydroxyethyl cellulose (HEC), and crystalline substrates. The cellulase produced by B. subtilis TD11 had a molecular mass of 45 kDa while that of chitinase was 55 kDa. The optimal activities of the enzymes were found at neutral pH (6.0 to 7.0). The optimum temperature for the purified cellulases was in the range of 50 to 70°C while, purified chitinases were optimally active at 50°C. The highest substrate specificity of the purified cellulase was found for CMC (100%) followed by HEC (>50% activity) while no hydrolysis was observed against the crystalline substrates. Moreover, it was observed that the purified chitinase was inhibitory against the fungi containing chitin in their hyphal walls i.e., Rhizoctonia, Colletotrichum, Aspergillus and Fusarium having a dose-effect relationship.
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Affiliation(s)
- Muhammad Saqib Malik
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Abdul Rehman
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Irfan Ullah Khan
- Vaccine Development Group, Animal Sciences Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Taj Ali Khan
- Department of Microbiology, Khyber Medical University Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Jamil
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - Eui Shik Rha
- Department of Well-Being Resources, Sunchon National University, Suncheon, Republic of Korea
- * E-mail: (MA); (ESR)
| | - Muhammad Anees
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
- * E-mail: (MA); (ESR)
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46
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Jamil M, Latif N, Gul J, Ali M, Jabeen N, Khan I, Qazi I, Ullah F. Identification of Tick Species on Angora Rabbits in Sothern's Areas of Khyber Pakhtunkhwa, Pakistan. Egyptian Academic Journal of Biological Sciences A, Entomology 2022. [DOI: 10.21608/eajbsa.2022.284169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
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47
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Shah G, Tu J, Fayyaz M, Masood S, Ullah H, Jamil M. Moringa oleifera smoke induced positive changes in biochemical, metabolic, and antioxidant profile of rice seedling under cadmium stress. Int J Phytoremediation 2022:1-11. [PMID: 36573355 DOI: 10.1080/15226514.2022.2157793] [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] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Cadmium as a heavy metal contaminates the agricultural soil and effect plant growth due to rapid increases in industrialization and anthropogenic activities. Smoke water of Moringa oleifera was used in the current study to alleviate the effect of cadmium on the physiological, biochemical, metabolic, and antioxidant profile of Basmati 385 and Shaheen Basmati seedling. Cadmium stress of 100, 200, and 400 µM were given to 28 days-old seedlings along with smoke water (1:1,000) for one week in hydroponic culture. As a result, Cd+2 toxicity negatively affects the seedling length, fresh and dry weight, photosynthetic pigment, and electrolytes leakage, while the application of smoke water alleviated those effects. Furthermore, Cd+2 content, cell injury, metabolic parameters (proline, total soluble sugar), and antioxidants (peroxidase, catalase) were increased with increasing Cd+2 concentration while smoke water-treated seedlings showed reduction at high concentration. From present study, it can be concluded that smoke water had some regulatory compound which could reduce the Cd+2 stress level in rice seedlings and improve plant growth.
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Affiliation(s)
- Gulmeena Shah
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Biotechnology & Genetic Engineering, Kohat University of Science & Technology, Kohat, Pakistan
| | - Jumin Tu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Fayyaz
- Department of Biotechnology & Genetic Engineering, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sadaf Masood
- Department of Biotechnology & Genetic Engineering, Kohat University of Science & Technology, Kohat, Pakistan
| | - Habib Ullah
- Department of Plant Breeding and Genetics, The University of Agriculture Peshawar, Pakistan
| | - Muhammad Jamil
- Department of Biotechnology & Genetic Engineering, Kohat University of Science & Technology, Kohat, Pakistan
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48
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Saleem Y, Ali A, Naz S, Jamil M, Naveed NH. Amelioration of lead toxicity by ascorbic acid in sugarcane (Saccharum officinarum L.) under in vitro condition. Environ Sci Pollut Res Int 2022; 29:85160-85171. [PMID: 35793025 DOI: 10.1007/s11356-022-21882-8] [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] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Agricultural sites are polluted with various metal ions worldwide. Ascorbic acid (AA) plays diverse roles in plant growth, development, and the regulation of cellular mechanisms against environmental stress. This study provides the relationship between morphological and biochemical parameters involved in the amelioration of Pb toxicity in three sugarcane (Saccharum officinarum L.) genotypes (YT-53, CP-77-400, NSG-59) by using six concentrations of Pb(NO3)2 under in vitro conditions. Morphological and biochemical parameters of ascorbic acid pretreated and non-pretreated calli were compared at each Pb(NO3)2 concentration. Ascorbic acid-pretreated calli have better callus growth and regeneration potential than non-treated calli under increased Pb concentration. Biochemical parameters such as antioxidant enzyme activity (peroxidase (POD), superoxide dismutase (SOD), catalase (CAT)) increased under increased Pb concentration. Ascorbic acid pretreatment further enhanced the POD and SOD activity, while CAT activity and total soluble protein contents of pretreated calli did not change significantly. Ascorbic acid ameliorated the Pb toxicity morphologically but showed uneven behavior towards biochemical parameters. Different genotypic behaviors versus different treatments were also observed. In the future, information from this study can be used to develop the metal-resistant sugarcane genotype against metal stress under in vitro conditions.
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Affiliation(s)
- Yasmeen Saleem
- Department of Botany, University of Sargodha, Sargodha, Pakistan.
| | - Aamir Ali
- Department of Botany, University of Sargodha, Sargodha, Pakistan
| | - Shagufta Naz
- Department of Biotechnology, Lahore College for Women University Lahore, Punjab, Pakistan
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Wang JY, Braguy J, Chen GTE, Jamil M, Balakrishna A, Berqdar L, Al-Babili S. Perspectives on the metabolism of strigolactone rhizospheric signals. Front Plant Sci 2022; 13:1062107. [PMID: 36507392 PMCID: PMC9729874 DOI: 10.3389/fpls.2022.1062107] [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: 10/05/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Strigolactones (SLs) are a plant hormone regulating different processes in plant development and adjusting plant's architecture to nutrition availability. Moreover, SLs are released by plants to communicate with beneficial fungi in the rhizosphere where they are, however, abused as chemical cues inducing seed germination of root parasitic weeds, e.g. Striga spp., and guiding them towards host plants in their vicinity. Based on their structure, SLs are divided into canonical and non-canonical SLs. In this perspective, we describe the metabolism of root-released SLs and SL pattern in rice max1-900 mutants, which are affected in the biosynthesis of canonical SLs, and show the accumulation of two putative non-canonical SLs, CL+30 and CL+14. Using max1-900 and SL-deficient d17 rice mutants, we further investigated the metabolism of non-canonical SLs and their possible biological roles. Our results show that the presence and further metabolism of canonical and non-canonical SLs are particularly important for their role in rhizospheric interactions, such as that with root parasitic plants. Hence, we proposed that the root-released SLs are mainly responsible for rhizospheric communications and have low impact on plant architecture, which makes targeted manipulation of root-released SLs an option for rhizospheric engineering.
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Affiliation(s)
- Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Justine Braguy
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guan-Ting Erica Chen
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Muhammad Jamil
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aparna Balakrishna
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lamis Berqdar
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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50
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Ito S, Braguy J, Wang JY, Yoda A, Fiorilli V, Takahashi I, Jamil M, Felemban A, Miyazaki S, Mazzarella T, Chen GTE, Shinozawa A, Balakrishna A, Berqdar L, Rajan C, Ali S, Haider I, Sasaki Y, Yajima S, Akiyama K, Lanfranco L, Zurbriggen MD, Nomura T, Asami T, Al-Babili S. Canonical strigolactones are not the major determinant of tillering but important rhizospheric signals in rice. Sci Adv 2022; 8:eadd1278. [PMID: 36322663 PMCID: PMC9629705 DOI: 10.1126/sciadv.add1278] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/14/2022] [Indexed: 05/09/2023]
Abstract
Strigolactones (SLs) are a plant hormone inhibiting shoot branching/tillering and a rhizospheric, chemical signal that triggers seed germination of the noxious root parasitic plant Striga and mediates symbiosis with beneficial arbuscular mycorrhizal fungi. Identifying specific roles of canonical and noncanonical SLs, the two SL subfamilies, is important for developing Striga-resistant cereals and for engineering plant architecture. Here, we report that rice mutants lacking canonical SLs do not show the shoot phenotypes known for SL-deficient plants, exhibiting only a delay in establishing arbuscular mycorrhizal symbiosis, but release exudates with a significantly decreased Striga seed-germinating activity. Blocking the biosynthesis of canonical SLs by TIS108, a specific enzyme inhibitor, significantly lowered Striga infestation without affecting rice growth. These results indicate that canonical SLs are not the determinant of shoot architecture and pave the way for increasing crop resistance by gene editing or chemical treatment.
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Affiliation(s)
- Shinsaku Ito
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Justine Braguy
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf 40225, Germany
| | - Jian You Wang
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Akiyoshi Yoda
- Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Ikuo Takahashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Muhammad Jamil
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abrar Felemban
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sho Miyazaki
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Teresa Mazzarella
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Guan-Ting Erica Chen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Akihisa Shinozawa
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
- Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Aparna Balakrishna
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lamis Berqdar
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chakravarty Rajan
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Shawkat Ali
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Kentville Research and Development Centre, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Imran Haider
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
| | - Yasuyuki Sasaki
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Kohki Akiyama
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Matias D. Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf 40225, Germany
| | - Takahito Nomura
- Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
- Center for Bioscience Research and Education, Utsunomiya University, 350 Minemachi, Utsunomiya, Tochigi 321-8505, Japan
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Salim Al-Babili
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, The BioActives Lab, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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