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Azab O, Ben Romdhane W, El-Hendawy S, Ghazy A, Zakri AM, Abd-ElGawad AM, Al-Doss A. Ectopic Expression of a Wheat R2R3-Type MYB Gene in Transgenic Tobacco Enhances Osmotic Stress Tolerance via Maintaining ROS Balance and Improving Root System Architecture. Biology (Basel) 2024; 13:128. [PMID: 38392346 PMCID: PMC10886976 DOI: 10.3390/biology13020128] [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: 12/12/2023] [Revised: 01/29/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024]
Abstract
Water scarcity is a critical cause of plant yield loss and decreased quality. Manipulation of root system architecture to minimize the impact of water scarcity stresses may greatly contribute towards an improved distribution of roots in the soil and enhanced water and nutrient uptake abilities. In this study, we explored the potential of TaMYB20 gene, a wheat gene belonging to the R2R3-MYB transcription factor family, to improve root system architecture in transgenic tobacco plants. The full-length TaMYB20 gene was isolated from Triticum aestivum.cv. Sakha94 and used to produce genetically engineered tobacco plants. The transgenic plants exhibited enhanced tolerance to extended osmotic stress and were able to maintain their root system architecture traits, including total root length (TRL), lateral root number (LRN), root surface area (RSa), and root volume (RV), while the wild-type plants failed to maintain the same traits. The transgenic lines presented greater relative water content in their roots associated with decreased ion leakage. The oxidative stress resulted in the loss of mitochondrial membrane integrity in the wild-type (WT) plants due to the overproduction of reactive oxygen species (ROS) in the root cells, while the transgenic lines were able to scavenge the excess ROS under stressful conditions through the activation of the redox system. Finally, we found that the steady-state levels of three PIN gene transcripts were greater in the TaMYB20-transgenic lines compared to the wild-type tobacco. Taken together, these findings confirm that TaMYB20 is a potentially useful gene candidate for engineering drought tolerance in cultivated plants.
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Affiliation(s)
- Omar Azab
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Walid Ben Romdhane
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Salah El-Hendawy
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Abdelhalim Ghazy
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Adel M Zakri
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Ahmed M Abd-ElGawad
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Abdullah Al-Doss
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Abdel-Maksoud MA, Ullah S, Nadeem A, Shaikh A, Zia MK, Zakri AM, Almanaa TN, Alfuraydi AA, Mubarak A, Hameed Y. Unlocking the diagnostic, prognostic roles, and immune implications of BAX gene expression in pan-cancer analysis. Am J Transl Res 2024; 16:63-74. [PMID: 38322551 PMCID: PMC10839381] [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: 07/29/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVES Cancer, a formidable disease, continues to challenge our understanding and therapeutic approaches. This study delves into the pan-cancer analysis of BCL2 Associated X (BAX) gene expression, seeking to unravel its significance in cancer development, prognosis, and potential therapeutic strategies. METHODS A combination of bioinformatics and molecular experiments. RESULTS Our pan-cancer investigation into BAX expression encompassed 33 distinct cancer types, revealing a remarkable and uniform increase in BAX expression. This groundbreaking finding emphasizes the potential universality of BAX's role in cancer development and progression. Further, our study explored the prognostic implications of BAX expression, highlighting a consistent association between up-regulated BAX and poor overall survival (OS) in Liver Hepatocellular Carcinoma (LIHC) and Skin Cutaneous Melanoma (SKCM). These results suggest that BAX may serve as an adverse prognostic indicator in these malignancies, emphasizing the importance of personalized treatment strategies. Epigenetic and genetic analyses of BAX provided valuable insights. Hypomethylation of the BAX promoter region was evident in LIHC and SKCM, which likely contributes to the up-regulation of BAX, while genetic mutations in the BAX gene itself were infrequent in these cancers. Our exploration of BAX-associated signaling pathways and the correlation between BAX expression and CD8+ T cell infiltration shed light on the intricate molecular landscape of cancer. BAX's interaction with key apoptotic and immune-related pathways reinforces its role as a central player in tumor development and the immune microenvironment. Moreover, our drug prediction analysis identified potential therapeutic agents for modulating BAX expression in the context of LIHC and SKCM, bridging the gap between research and clinical application. CONCLUSION In sum, our comprehensive BAX study not only enhances our understanding of its significance as a biomarker gene but also offers novel avenues for therapeutic interventions, contributing to the ongoing quest for more effective cancer treatments and improved patient care.
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Affiliation(s)
- Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Amun Nadeem
- Department of Pathology, Gujranwala Medical College Teaching Hospital GujranwalaPakistan
| | | | - Muhammad Khurram Zia
- Department of Surgery, Liaquat College of Medicine and Dentistry and Darul Sehat HospitalKarachi, Pakistan
| | - 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
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
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AbdElgawad H, Magdy Korany S, Hagagy N, Yaghoubi Khanghahi M, Reyad AM, Crecchio C, Zakri AM, Alsherif EA, Bakkar MR. Biochemical and pharmaceutical traits of Marrubium vulgare L. plants treated with plant growth-promoting bacteria and elevated CO 2. 3 Biotech 2023; 13:412. [PMID: 37997597 PMCID: PMC10663420 DOI: 10.1007/s13205-023-03836-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
The present research aimed to understand the influence of plant growth-promoting bacteria (PGPB) on various biochemical, nutritional, and pharmaceutical characteristics of Marrubium vulgare plants grown under elevated carbon dioxide (eCO2). To achieve this objective, a pot experiment was carried out, consisting of two treatments, namely: (i) biofertilization (Bf) by a PGPB strain (Micromonospora sp.) and (ii) two different air CO2 levels, including ambient CO2 (aCO2) and eCO2 concentrations (410 and 710 μmol CO2 mol-1, respectively). The improvement in the photosynthesis rate of eCO2 and Bf-treated plants can explain the increase in the production of carbohydrate. This is evidenced by a substantial rise, reaching up to + 75% and 25% in the total sugar and starch content in plants subjected to eCO2 treatment, respectively. Additionally, eCO2-treated plants exhibited a remarkable 102% increase in soluble sugar synthesis, while plants subjected to Bf treatment showed a notable increase of 66%. Such modifications could be the main factor affecting plants carbon and nitrogen metabolism. Although the level of certain amino acids (such as glycine, tyrosine, and phenylalanine) in plants exhibited significant increases in response to eCO2 and Bf, the levels of other amino acids demonstrated enhancements in plants grown under eCO2 (e.g., histidine) or under treatments containing Bf (e.g., alanine and ornithine). Improvements in primary metabolites led to more benefits in plants treated with Bf and CO2 by boosting secondary metabolites accumulation, including phenolics (+ 27-100%), flavonoids (+ 30-92%), and essential oils (up to + 296%), as well as improved antioxidant capacity (FRAP). This remarkable effectiveness was evident in the significant increase in the biomass production, highlighting the synergistic impact of the treatments. Therefore, the interaction of Bf and eCO2 not only induced plant biomass accumulation but also improved the nutritional and pharmaceutical value of M. vulgare plants.
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Affiliation(s)
- Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni Suef, 62521 Egypt
| | - Shereen Magdy Korany
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo, 11795 Egypt
| | - Nashwa Hagagy
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Mohammad Yaghoubi Khanghahi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Ahmed Mohamed Reyad
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni Suef, 62521 Egypt
| | - Carmine Crecchio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Adel M. Zakri
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Emad A. Alsherif
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni Suef, 62521 Egypt
| | - Marwa Reda Bakkar
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo, 11795 Egypt
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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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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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Hussain K, Khalid Z, Amer MA, Zaman M, Amir M, Al-Shahwan IM, Zakri AM, Al-Saleh MA. Identification and molecular characterization of cotton leaf curl Gezira betasatellite and two distinct begomoviruses infecting papaya trees in the Kingdom of Saudi Arabia. Cell Mol Biol (Noisy-le-grand) 2022; 68:129-134. [PMID: 36905263 DOI: 10.14715/cmb/2022.68.9.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Indexed: 03/12/2023]
Abstract
Begomovirus is the largest genus in the family Geminiviridae and constitutes more than 445 virus species. Begomoviruses are characterized by single-stranded circular genomes with monopartite or bipartite components and transmitted by whitefly (Bemisia tabaci). Begomoviruses cause severe diseases in many economically important crops throughout the world. Typical symptoms of a begomovirus infection including severe leaf curling, vein thickening, vein darkening and reduced leaf size were observed in papaya plants in the Dammam district of the Eastern Province of Saudi Arabia during the growing season in 2022. A total of 10 samples were collected, and total genomic DNA was isolated from naturally infected papaya tree samples and subjected to PCR amplification using universal diagnostic primers for begomoviruses and associated satellites. Three PCR-amplified genomic components of begomoviruses and betasatellite namely P61Begomo (645 bp), P62Begomo (341 bp) and P62Beta (563 bp) were sent for Sanger DNA sequencing to Macrogen Inc. These partial viral genome sequences were submitted to Genbank database and accession numbers ON206051, ON206052 and ON206050 were assigned to P61Begomo, P62Begomo and P62Beta respectively. Phylogenetic analysis and pairwise nucleotide sequence identity studies identified P61Begomo was identified as Tomato yellow leaf curl virus, P62Begomo as DNA A component of a bipartite begomovirus Watermelon chlorotic stunt virus and P62Beta as begomovirus associated betasatellite; Cotton leaf curl Gezira betasatellite. To the best of our knowledge, this is the first report of a begomovirus complex infecting papaya (Carica papaya) in the Kingdom of Saudi Arabia.
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Affiliation(s)
- Khadim Hussain
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
| | - Zaheer Khalid
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
| | - Mahmoud A Amer
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
| | - Muhammad Zaman
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
| | - Muhammad Amir
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
| | - Ibrahim M Al-Shahwan
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia.
| | - Mohammed A Al-Saleh
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia.
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Zakri AM, Al-Doss AA, Ali AA, Samara EM, Ahmed BS, Al-Saleh MA, Idris AM, Abdalla OA, Sack M. Generation and Characterization of Nanobodies Against Tomato Leaf Curl Sudan Virus. Plant Dis 2021; 105:2410-2417. [PMID: 33599515 DOI: 10.1094/pdis-11-20-2407-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Begomoviruses infect food, fiber, and vegetable crop plants, including tomato, potato, bean, cotton, cucumber, and pumpkin, and damage many economically important crop plants worldwide. Tomato leaf curl Sudan virus (ToLCSDV) is the most widespread tomato-infecting begomovirus in Saudi Arabia. Using phage display technology, this study isolated two camel-derived nanobodies against purified ToLCSDV virions from a library of antigen-binding fragments (VHH or nanobody) of heavy-chain antibodies built from an immunized camel. The isolated nanobodies also cross-reacted with purified tomato yellow leaf curl virus virions and showed significant enzyme-linked immunosorbent assay reactivity with extracts from plants with typical begomovirus infection symptoms. The results can pave the way to developing diagnostics for begomovirus detection, design, and characterization of novel nanomaterials based on virus-like particles, in addition to nanobody-mediated begomovirus resistance in economically important crops, such as tomato, potato, and cucumber.
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Affiliation(s)
- Adel M Zakri
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A Al-Doss
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed A Ali
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Emad M Samara
- Department of Animal Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Basem S Ahmed
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed A Al-Saleh
- Department of Plant Protection, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali M Idris
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, U.S.A
| | - Omar A Abdalla
- Department of Plant Protection, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
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Saheb Sharif-Askari F, Saheb Sharif-Askari N, Goel S, Mahboub B, Ansari AW, Temsah MH, Zakri AM, Ratemi E, Hamoudi R, Hamid Q, Halwani R. Upregulation of interleukin-19 in severe asthma: a potential saliva biomarker for asthma severity. ERJ Open Res 2021; 7:00984-2020. [PMID: 34322544 PMCID: PMC8311130 DOI: 10.1183/23120541.00984-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/08/2021] [Indexed: 11/30/2022] Open
Abstract
Interleukin (IL)-19, a designated IL-20 subfamily cytokine, has been implicated in inflammatory disorders including rheumatoid arthritis, psoriasis and, lately, asthma. Here, through the analysis of transcriptomic datasets of lung tissue of large asthma cohorts, we report that IL-19 expression is upregulated in asthma and correlates with disease severity. The gene expression of IL-19 was significantly higher in lung tissue from patients with severe and mild/moderate asthma compared to healthy controls. IL-19 protein level, however, was significantly higher in the blood and saliva of patients with severe asthma compared to mild/moderate subgroups as measured by ELISA assay. IL-19 protein level was not affected by corticosteroid treatment in plasma. Our data provide insights into the potential use of IL-19 as a saliva marker for asthma severity and a potential therapeutic target. Plasma and saliva IL-19 are significantly upregulated in asthma and correlate with disease severity. Plasma IL-19 is not affected by steroid treatment. This suggests that IL-19 can be used as a biomarker of asthma severity.https://bit.ly/2QfYwpc
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Affiliation(s)
- Fatemeh Saheb Sharif-Askari
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Narjes Saheb Sharif-Askari
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Swati Goel
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Abdul Wahid Ansari
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohamad-Hani Temsah
- Immunology Research Lab, Dept of Pediatrics, College of Medicine, King Saud University, Sharjah, Saudi Arabia
| | - Adel M Zakri
- Dept of Plant Production, Faculty of Agriculture and Food Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Elaref Ratemi
- Dept of Chemical and Process Engineering Technology, Jubail Industrial College, Jubail Industrial City, Saudi Arabia
| | - Rifat Hamoudi
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Dept of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Qutayba Hamid
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Dept of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Rabih Halwani
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Dept of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Dept of Pediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
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11
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Nour I, Hanif A, Alanazi F, Zakri AM, Al-Ashkar I, Alhetheel A, Eifan S. Evaluation of three different concentration and extraction methods for recovery efficiency of human adenovirus and human rotavirus virus A. J Virol Methods 2021; 295:114212. [PMID: 34126107 DOI: 10.1016/j.jviromet.2021.114212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Routine wastewater treatment plants (WWTPs) effluents monitoring is essential because of enteric viruses' low infectious dose beyond molecular detectability. In current study methods for concentration and extraction, inter-method compatibility and recovery efficiency of spiked human adenovirus (HAdV) and human rotavirus A (RVA) were evaluated. For virus concentration, polyethylene glycol precipitation (PEG), charged membrane-based adsorption/elution (CMAE), and glass wool-based concentration (GW) methods were used. Nucleic acid was extracted by PowerViral™ Environmental RNA/DNA Isolation (POW), ZymoBIOMICS™ RNA extraction (ZYMO) and Wizard® Genomic DNA Purification (WGDP) and samples were analyzed by Real-Time PCR. CMAE method yielded significantly higher concentrations for both ARQ (Armored-RNA Quant) and RVA compared to PEG (P = 0.001 and 0.003) and GW (P < 0.0001). Highest HAdV concentration was obtained by PEG (P = 0.001 and < 0.0001) in relation to CMAE and GW. ZYMO yielded a significantly higher ARQ and RVA concentrations (P = 0.03 and 0.0057), whereas significantly higher concentration was obtained by POW for HAdV (P = 0.032). CMAE × ZYMO achieved the highest recovery efficiencies for ARQ (69.77 %) and RVA (64.25, respectively, while PEG × POW present efficiency of 9.7 % for HAdV. These findings provide guidance for understanding of method-related biases for viral recovery efficiency.
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Affiliation(s)
- Islam Nour
- Botany and Microbiology Department, College of Science, King Saud University, Saudi Arabia
| | - Atif Hanif
- Botany and Microbiology Department, College of Science, King Saud University, Saudi Arabia.
| | - Fahd Alanazi
- Botany and Microbiology Department, College of Science, King Saud University, Saudi Arabia
| | - Adel M Zakri
- Biotechnology Laboratory, Plant Production Department, Faculty of Agriculture and Food Sciences, King Saud University, Saudi Arabia
| | - Ibrahim Al-Ashkar
- Biotechnology Laboratory, Plant Production Department, Faculty of Agriculture and Food Sciences, King Saud University, Saudi Arabia
| | - Abdulkarim Alhetheel
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Saudi Arabia
| | - Saleh Eifan
- Botany and Microbiology Department, College of Science, King Saud University, Saudi Arabia
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12
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Saadeldin IM, Swelum AAA, Zakri AM, Tukur HA, Alowaimer AN. Effects of Acute Hyperthermia on the Thermotolerance of Cow and Sheep Skin-Derived Fibroblasts. Animals (Basel) 2020; 10:ani10040545. [PMID: 32218166 PMCID: PMC7222367 DOI: 10.3390/ani10040545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary We compared the thermotolerance of cow and sheep fibroblasts after exposure to acute hyperthermia (45 °C for 4 h). The primary culture, first passage, and cryopreserved cow fibroblasts resisted acute hyperthermia in terms of cell viability, proliferation, and migration to close cell scratch, in addition to increased expression of heat shock protein (HSP70 and HSP90) mRNA transcripts. Abstract This study was conducted to compare the effects of acute hyperthermia (45 °C for 4 h) on the viability, proliferation, and migratory activity through wound-healing assays of cow and sheep fibroblasts. The study examined the effects on primary cultures and first passage skin-derived fibroblasts. Relative quantification of HSP70, HSP90, P53, BAX, BCL2, and BECN1 was investigated after normalization to housekeeping genes GAPDH and beta-actin. The results revealed that cultured cow primary fibroblasts exhibited increased viability and reinitiated cell migration to close the cell monolayer scratch earlier than sheep cells. Similar patterns were observed in the first passage fibroblasts, with severe effects on sheep cells. Both cow and sheep cells exhibited decreased cell viability and failed to regain migratory activity after re-exposure of recovered heat-shocked cells. Effects of hyperthermia on sheep cells were potentiated by cell cryopreservation. The qPCR results showed that cow cells significantly increased HSP70 and HSP90 expression, which decreased the elevation of P53, and ameliorated the effects of the increased BAX/BCL2 ratio. The results provide a paradigm to compare thermotolerance among different animal species and revealed that trypsin could be an additional stress, which potentiates the effects of heat shock in in vitro experiments.
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Affiliation(s)
- Islam M Saadeldin
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
- Department of Physiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Ayman Abdel-Aziz Swelum
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
- Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Adel M Zakri
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hammed A Tukur
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah N Alowaimer
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
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Idris AM, Al-Saleh MA, M Zakri A, Brown JK. Minimal genomic variability in Merremia mosaic virus isolates endemic in Merremia spp and cultivated tomato in Puerto Rico. Virusdisease 2019; 30:84-94. [PMID: 31143835 DOI: 10.1007/s13337-017-0412-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/15/2017] [Indexed: 11/24/2022] Open
Abstract
Merremia mosaic virus (MerMV), a bipartite begomovirus, was identified for the first time as a pathogen of commercial tomato plantings. Infection of tomato by MerMV caused mild leaf curling and yellow foliar mosaic symptoms. Herein, the MerMV was identified in symptomatic Merremia quinquefolia and M. aegyptia (Convolvulaceae) plants exhibiting bright yellow or yellow-green foliar mosaic symptoms, respectively. The full-length begomoviral components were amplified from total DNA isolated from two wild species of Merremia and commercial tomato plants during 1991-1998. The DNA was subjected to rolling circle amplification, restriction digestion, and DNA sequencing. The resultant 19 and 26 apparently full-length DNA-A and DNA-B components were ~ 2557 and ~ 2492 bases, respectively. The 140-base common region was 97.9% identical between DNA-A and -B components, a predictive evidence for cognate DNA-A and -B components. Although the DNA-A components were highly conserved at 96-100%, the DNA-B components diverged at ~ 89 to 100%, respectively. The overall clonal genomic features strongly suggested that MerMV lineage has been under host-selection for some time, and only recently, has undergone a host-shift, putatively, from wild convolvulaceous species to tomato (Solanaceae). Phylogenetically, MerMV grouped with other bipartite begomoviruses indigenous to the Caribbean region, with MerMV DNA-A components forming three clusters, and the DNA-B components grouped in one clade. Both clades contained only one closet relative, an isolate of MerMV from Venezuela, MerMV-VE. Biolistic inoculation of M. quinquefolia and tomato seedlings with the DNA-A and -B components of PR68 and PR80 resulted in development of symptoms like those observed in naturally-infected species, respectively.
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Affiliation(s)
- Ali M Idris
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
| | - M A Al-Saleh
- 2Plant Protection Department, King Saud University, Riyadh, Saudi Arabia
| | - A M Zakri
- 2Plant Protection Department, King Saud University, Riyadh, Saudi Arabia
| | - J K Brown
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
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Umar M, Amer MA, Al-Saleh MA, Al-Shahwan IM, Shakeel MT, Zakri AM, Katis NI. Characterization of lettuce big-vein associated virus and Mirafiori lettuce big-vein virus infecting lettuce in Saudi Arabia. Arch Virol 2017; 162:2067-2072. [PMID: 28299485 DOI: 10.1007/s00705-017-3319-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
During 2014 and 2015, 97 lettuce plants that showed big-vein-disease-like symptoms and seven weed plants were collected from the Riyadh region. DAS-ELISA revealed that 25% and 9% of the lettuce plants were singly infected with LBVaV and MiLBVV, respectively, whereas 63% had a mixed infection with both viruses. The results were confirmed by multiplex reverse transcription polymerase chain reaction using primers specific for LBVaV and MiLBVV. LBVaV and MiLBVV were also detected in Sonchus oleraceus and Eruca sativa, respectively. The nucleotide sequence of LBVaV and MiLBVV Saudi isolates ranged from 94.3-100%, and their similarities to isolates with sequences in the GenBank database ranged from 93.9 to 99.6% and 93.8 to 99.3%, respectively. Olpidium sp. was present in the roots of lettuce plants with big-vein disease and it was shown to facilitate transmission of both viruses.
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Affiliation(s)
- M Umar
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M A Amer
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.
- Viruses and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt.
| | - M A Al-Saleh
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - I M Al-Shahwan
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M T Shakeel
- Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - A M Zakri
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - N I Katis
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, P.O. Box 269, 54124, Thessaloniki, Greece
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Al-Arfaj AA, Ali MS, Hessain AM, Zakri AM, Dawoud TM, Al-Maary KS, Moussa IM. Phenotypic and genotypic analysis of pathogenic Escherichia coli virulence genes recovered from Riyadh, Saudi Arabia. Saudi J Biol Sci 2016; 23:713-717. [PMID: 27872566 PMCID: PMC5109281 DOI: 10.1016/j.sjbs.2015.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/17/2015] [Accepted: 11/11/2015] [Indexed: 11/29/2022] Open
Abstract
The current study was carried out to evaluate the phenotypic and genotypic characterization of avian pathogenic Escherichia coli recovered from Riyadh, Saudi Arabia. During the period of 10th February–30th May 2015, 70 E. coli strains were isolated from chicken farms located in Riyadh, Saudi Arabia. All strains were tested phenotypically by standard microbiological techniques, serotyped and the virulence genes of such strains were detected by polymerase chain reaction (PCR). Most of the recovered strains from chickens belonged to serotype O111:K58 25 strains (35.7%), followed by serotype O157:H7 13 strains (18.57%), followed by serotype O114:K90 10 strains (14.29%), then serotype O126:K71 9 strains (12.9%), serotype O78:K80 8 strains (11.43%) and in lower percentage serotype O114:K90 and O119:K69 5 strains (7.14%). The virulence genotyping of E. coli isolates recovered from broilers revealed the presence of the uidA gene in all the field isolates (6 serovars) examined in an incidence of 100%, as well as the cvaC gene was also present in all field isolates (6 serovars), while the iutA gene and the iss gene were detected in 5 out of 6 field serovars in an incidence of 81.43% and 64.29%, respectively. Phenotypical examination of the other virulence factors revealed that 65 isolates were hemolytic (92.9%), as well as 15 isolates (21.42%) were positive for enterotoxin production. Meanwhile, 21 isolates (30%) were positive for verotoxin production, 58 isolates (82.86%) for the invasiveness and 31 isolates (44.29%) for Congo red binding activities of the examined serotypes.
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Affiliation(s)
- Abdullah A Al-Arfaj
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed S Ali
- Department of Microbiology and Immunology, College of Pharmacy, AL Azhar University, Cairo, Egypt
| | - Ashgan M Hessain
- Department of Health Science, College of Applied Studies and Community Service, King Saud University, P.O. Box 22459, Riyadh 11495, Saudi Arabia; Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, P.O. 2446, Cairo 14242, Giza, Egypt
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, P.O. Box 2466, Riyadh 11451, Saudi Arabia
| | - Turki M Dawoud
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Khalid S Al-Maary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ihab M Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, P.O. 2446, Cairo 14242, Giza, Egypt
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Hessain AM, Al-Arfaj AA, Zakri AM, El-Jakee JK, Al-Zogibi OG, Hemeg HA, Ibrahim IM. Molecular characterization of Escherichia coli O157:H7 recovered from meat and meat products relevant to human health in Riyadh, Saudi Arabia. Saudi J Biol Sci 2015; 22:725-9. [PMID: 26587000 PMCID: PMC4625360 DOI: 10.1016/j.sjbs.2015.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/31/2015] [Accepted: 06/10/2015] [Indexed: 11/17/2022] Open
Abstract
Raw meat can harbor pathogenic bacteria, potentially harmful to humans such as Escherichia coli O157:H7 causing diarrhea and hemolytic-uremic syndrome (HS). Therefore, the current study was carried out to evaluate the prevalence and the molecular detection characterization of E. coli serotype O157:H7 recovered from raw meat and meat products collected from Saudi Arabia. During the period of 25th January 2013 to 25th March 2014, 370 meat samples were collected from abattoirs and markets located in Riyadh, Saudi Arabia "200 raw meat samples and 170 meat products". Bacteriological analysis of the meat samples and serotyping of the isolated E. coli revealed the isolation of 11 (2.97%) strains of E. coli O157:H7. Isolation of E. coli O157:H7 in raw beef, chicken and mutton were 2%, 2.5%, and 2.5%, respectively, however, there was no occurrence in raw turkey. The incidences of E. coli O157:H7 in ground beef, beef burgers, beef sausage, ground chicken and chicken burgers were 5%, 10%, 0.0%, 5% and 0.0%, respectively. The multiplex PCR assay revealed that 3 (27.27%) out of 11 E. coli O157:H7 isolates from raw beef, chicken and mutton had stx1, stx2, and eae while 5 (45.45%) E. coli O157:H7 isolates from ground beef, ground chicken, and raw beef had both stx1 and stx2. However, from beef burgers, only one E. coli O157:H7 isolate had stx1 while two were positive for hlyA gene. These results call for urgent attention toward appropriate controls and good hygienic practices in dealing with raw meat.
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Affiliation(s)
- Ashgan M. Hessain
- Department of Health Science, College of Applied Studies and Community Service, King Saud University, P.O. Box 22459, Riyadh 11495, Saudi Arabia
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, P.O. Box 2446, Cairo 14242, Giza, Egypt
| | - Abdullah A. Al-Arfaj
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Adel M. Zakri
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, P.O. Box 2466, Riyadh 11451, Saudi Arabia
| | - Jakeen K. El-Jakee
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, P.O. Box 2446, Cairo 14242, Giza, Egypt
| | - Onizan G. Al-Zogibi
- Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Hassan A. Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Science, Taibah University, Madinah, Saudi Arabia
| | - Ihab M. Ibrahim
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Zakri AM, Ziegler A, Commandeur U, Fischer R, Torrance L. In vivo expression and binding activity of scFv-RWAV, which recognizes the coat protein of tomato leaf curl New Delhi virus (family Geminiviridae). Arch Virol 2012; 157:1291-9. [PMID: 22491815 DOI: 10.1007/s00705-012-1310-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 03/15/2012] [Indexed: 11/26/2022]
Abstract
Recombinant antibodies expressed in plants have the potential to interrupt virus infections by blocking essential stages of the infection cycle. Here, we show that the expression of a recombinant single-chain variable fragment (scFv) that recognizes the coat protein of tomato leaf curl New Delhi virus (ToLCNDV) in vitro can also bind to a recombinant coat protein in vivo in the reducing environment of the plant cytosol. The scFv and its target were both expressed as fluorescent protein fusions, one incorporating green fluorescent protein (GFP) and the other DsRed. We found that the incorporation of a nuclear localization signal into the scFv construct resulted in the nuclear import of the antibody-antigen complex, as shown by colocalization of the two fluorescent signals. This demonstrates that recombinant antibodies can be targeted to the nucleus and will bind to geminivirus coat proteins therein, allowing the virus infection cycle to be interrupted during its critical replicative phase.
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Affiliation(s)
- Adel M Zakri
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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