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Rahman L, Sarwar Y, Khaliq S, Inayatullah, Abbas W, Mobeen A, Ullah A, Hussain SZ, Khan WS, Kyriazi ME, Hussain I, Kanaras AG, Rehman A. Surfactin-Conjugated Silver Nanoparticles as an Antibacterial and Antibiofilm Agent against Pseudomonas aeruginosa. ACS Appl Mater Interfaces 2023; 15:43321-43331. [PMID: 37668507 DOI: 10.1021/acsami.3c07071] [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] [Indexed: 09/06/2023]
Abstract
The emergence of antimicrobial resistance is an alarming global health concern and has stimulated the development of novel functional nanomaterials to combat multi-drug-resistant (MDR) bacteria. In this work, we demonstrate for the first time the synthesis and application of surfactin-coated silver nanoparticles as an efficient antibacterial and antibiofilm agent against the drug-resistant bacteria Pseudomonas aeruginosa for safe dermal applications. Our in vivo studies showed no significant superficial dermal irritation, edema, and erythema, while microscopic analysis revealed that surfactin-coated silver nanoparticles caused no pathological alterations at the applied concentrations. These results support the potential use of surfactin-coated silver nanoparticles against drug-resistant bacterial biofilm infections and in skin wound dressing applications.
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Affiliation(s)
- Lutfur Rahman
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Yasra Sarwar
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Inayatullah
- Department of Anatomy, Saidu Medical and Dental College, Saidu Sharif 19130, Mingora, Swat, Pakistan
| | - Wasim Abbas
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Ameena Mobeen
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Ata Ullah
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Syed Zajif Hussain
- Department of Chemistry and Chemical Engineering, SBA School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), DHA, Lahore Cantt 54792, Pakistan
| | - Waheed S Khan
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Maria-Eleni Kyriazi
- College of Engineering and Technology, American University of the Middle East, 15453 Egaila, Kuwait
| | - Irshad Hussain
- Department of Chemistry and Chemical Engineering, SBA School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), DHA, Lahore Cantt 54792, Pakistan
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO171BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO171BJ, United Kingdom
| | - Asma Rehman
- National Institute for Biotechnology & Genetic Engineering College Pakistan Institute of Engineering & Applied Sciences (NIBGE-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan
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Jawad I, Bin Tawseen H, Irfan M, Ahmad W, Hassan M, Sattar F, Awan FR, Khaliq S, Akhtar N, Akhtar K, Anwar MA, Munawar N. Dietary Supplementation of Microbial Dextran and Inulin Exerts Hypocholesterolemic Effects and Modulates Gut Microbiota in BALB/c Mice Models. Int J Mol Sci 2023; 24:ijms24065314. [PMID: 36982388 PMCID: PMC10049499 DOI: 10.3390/ijms24065314] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023] Open
Abstract
Microbial exopolysaccharides (EPSs), having great structural diversity, have gained tremendous interest for their prebiotic effects. In the present study, mice models were used to investigate if microbial dextran and inulin-type EPSs could also play role in the modulation of microbiomics and metabolomics by improving certain biochemical parameters, such as blood cholesterol and glucose levels and weight gain. Feeding the mice for 21 days on EPS-supplemented feed resulted in only 7.6 ± 0.8% weight gain in the inulin-fed mice group, while the dextran-fed group also showed a low weight gain trend as compared to the control group. Blood glucose levels of the dextran- and inulin-fed groups did not change significantly in comparison with the control where it increased by 22 ± 5%. Moreover, the dextran and inulin exerted pronounced hypocholesterolemic effects by reducing the serum cholesterol levels by 23% and 13%, respectively. The control group was found to be mainly populated with Enterococcus faecalis, Staphylococcus gallinarum, Mammaliicoccus lentus and Klebsiella aerogenes. The colonization of E. faecalis was inhibited by 59–65% while the intestinal release of Escherichia fergusonii was increased by 85–95% in the EPS-supplemented groups, respectively, along with the complete inhibition of growth of other enteropathogens. Additionally, higher populations of lactic acid bacteria were detected in the intestine of EPS-fed mice as compared to controls.
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Affiliation(s)
- Iqra Jawad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Husam Bin Tawseen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Irfan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Waqar Ahmad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad 22020, Pakistan
| | - Mujtaba Hassan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Fazal Sattar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Fazli Rabbi Awan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
- Correspondence: or (M.A.A.); (N.M.); Tel.: +92-41-920-1316 (M.A.A.); +971-3-713-6168 (N.M.); Fax: +92-41-920-1322 (M.A.A.)
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University (UAEU), Al Ain 15551, United Arab Emirates
- Correspondence: or (M.A.A.); (N.M.); Tel.: +92-41-920-1316 (M.A.A.); +971-3-713-6168 (N.M.); Fax: +92-41-920-1322 (M.A.A.)
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Haq AU, Majeed MI, Nawaz H, Rashid N, Javed MR, Raza A, Shakeel M, Zahra ST, Meraj L, Perveen A, Murtaza S, Khaliq S. Surface-enhanced Raman spectroscopy for monitoring antibacterial activity of imidazole derivative (1-benzyl-3-(sec‑butyl)-1H-imidazole-3-ium bromide) against Bacillus subtilis and Escherichia coli. Photodiagnosis Photodyn Ther 2023; 42:103533. [DOI: 10.1016/j.pdpdt.2023.103533] [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] [Received: 09/09/2022] [Revised: 02/17/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
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Mahreen N, Yasmin S, Asif M, Yahya M, Ejaz K, Mehboob-ur-Rahman, Yousaf S, Amin I, Zulfiqar S, Imran A, Khaliq S, Arif M. Mitigation of water scarcity with sustained growth of Rice by plant growth promoting bacteria. Front Plant Sci 2023; 14:1081537. [PMID: 36755700 PMCID: PMC9900138 DOI: 10.3389/fpls.2023.1081537] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/02/2023] [Indexed: 11/03/2023]
Abstract
Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, we isolated, identified, and well-characterized eight drought-tolerant bacteria from the rice rhizosphere that are tolerant to 20% PEG-8000. These strains exhibited multiple plant growth-promoting traits, i.e., 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, exopolysaccharide production, phosphate (P)-solubilizing activity (51-356 µg ml-1), indole-3 acetic acid (IAA) production (14.3-46.2 µg ml-1), and production of organic acids (72-178 µg ml-1). Inoculation of bacterial consortium (Bacillus subtilis NM-2, Brucella haematophilum NM-4, and Bacillus cereus NM-6) significantly improved seedling growth and vigor index (1009.2-1100) as compared to non-inoculated stressed plants (630-957). Through rhizoscanning, efficiency of the consortium was validated by improved root parameters such as root length (17%), diameter, and surface area (18%) of all tested genotypes as compared with respective non-inoculated stressed treatments. Furthermore, the response of consortium inoculation on three rice genotypes was positively correlated with improved plant growth and drought stress ameliorating traits by the accumulation of osmoprotectant, i.e., proline (85.8%-122%), relative water content (51%), membrane stability index (64%), and production of antioxidant enzymes to reduce oxidative damage by reactive oxygen species. A decrease in temperature and improved chlorophyll content of inoculated plants were found using infrared thermal imaging and soil plant analyzer development (SPAD), respectively. The key supporting role of inoculation toward stress responses was validated using robust techniques like infrared thermal imaging and an infrared gas analyzer. Furthermore, principal component analysis depicts the contribution of inoculation on stress responses and yield of tested rice genotypes under water stress. The integration of drought-tolerant rice genotype (NIBGE-DT02) and potential bacterial strains, i.e., NM-2, NM-4, and NM-6, can serve as an effective bioinoculant to cope with water scarcity under current alarming issues related to food security in fluctuating climate.
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Affiliation(s)
- Naima Mahreen
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mahreen Yahya
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Khansa Ejaz
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mehboob-ur-Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB) College, Pakistan Institute for Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sana Zulfiqar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
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Jawad I, Khaliq S, Akhtar N, Saleem M, Akhtar K, Ghauri K, Anwar MA. Genome analysis of novel Apilactobacillus sp. isolate from butterfly (Pieris canidia) gut reveals occurrence of unique glucanogenic traits and probiotic potential. Lett Appl Microbiol 2023; 76:6953797. [PMID: 36688789 DOI: 10.1093/lambio/ovac024] [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: 07/28/2022] [Revised: 10/19/2022] [Accepted: 11/10/2022] [Indexed: 01/24/2023]
Abstract
This study was conducted with a perception that fructose-rich niches may inhabit novel species of lactic acid bacteria that are gaining importance as probiotics and for the production of exopolysaccharides that have applications in food and pharmaceuticals. Recently, some Lactobacillus species have been reclassified as fructophilic lactic acid bacteria due to their preference for fructose over glucose as a carbon source. These bacteria are likely to be found in fructose rich niches such as flower nectar and insects that feed on it. We explored the butterfly gut and acquired a new isolate, designated as F1, of fructophilic lactic acid bacteria, which produces a glucan-type exopolysaccharide. Whole genome sequencing and in silico analysis revealed that F1 has significantly lower average nucleotide identity and DNA-DNA hybridization values as compared to its closest Apilactobacillus neighbors in phylogenetic analysis. Therefore, we declare the isolate F1 as a novel Apilactobacillus species with the proposed name of Apilactobacillus iqraium F1. Genome mining further revealed that F1 harbors genes for exopolysaccharide synthesis and health-promoting attributes. To this end, F1 is the only Apilactobacillus species harboring three diverse α-glucan-synthesis genes that cluster with different types of dextransucrases in the dendrogram. Moreover, many nutritional marker genes, as well as genes for epithelial cell adhesion and antimicrobial synthesis, were also detected suggesting the probiotic attributes of F1. Overall analysis suggests A. iqraium sp. F1 be a potential candidate for various health beneficial and pharmaceutical applications.
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Affiliation(s)
- Iqra Jawad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Saleem
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Komal Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Munir A Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
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Ashraf N, Zafar S, Makitrynskyy R, Bechthold A, Spiteller D, Song L, Anwar MA, Luzhetskyy A, Khan AN, Akhtar K, Khaliq S. Revealing Genome-Based Biosynthetic Potential of Streptomyces sp. BR123 Isolated from Sunflower Rhizosphere with Broad Spectrum Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11081057. [PMID: 36009926 PMCID: PMC9405382 DOI: 10.3390/antibiotics11081057] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Actinomycetes, most notably the genus Streptomyces, have great importance due to their role in the discovery of new natural products, especially for finding antimicrobial secondary metabolites that are useful in the medicinal science and biotechnology industries. In the current study, a genome-based evaluation of Streptomyces sp. isolate BR123 was analyzed to determine its biosynthetic potential, based on its in vitro antimicrobial activity against a broad range of microbial pathogens, including gram-positive and gram-negative bacteria and fungi. A draft genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 was attained, containing a GC content of 72.63% and 8103 protein coding genes. Many antimicrobial, antiparasitic, and anticancerous compounds were detected by the presence of multiple biosynthetic gene clusters, which was predicted by in silico analysis. A novel metabolite with a molecular mass of 1271.7773 in positive ion mode was detected through a high-performance liquid chromatography linked with mass spectrometry (HPLC-MS) analysis. In addition, another compound, meridamycin, was also identified through a HPLC-MS analysis. The current study reveals the biosynthetic potential of Streptomyces sp. isolate BR123, with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study compared the isolate BR123 with other Streptomyces strains, which may expand the knowledge concerning the mechanism involved in novel antimicrobial metabolite synthesis.
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Affiliation(s)
- Neelma Ashraf
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
| | - Sana Zafar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Roman Makitrynskyy
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Dieter Spiteller
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Lijiang Song
- Department of Chemistry, University of Warwick Coventry, Coventry CV4 7AL, UK
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology Campus, Saarland University, Building C2.3, 66123 Saarbrucken, Germany
| | - Ali Nisar Khan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
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Nasir A, Ahmad W, Sattar F, Ashfaq I, Lindemann SR, Chen MH, Van den Ende W, Ӧner ET, Kirtel O, Khaliq S, Ghauri MA, Anwar MA. Production of a high molecular weight levan by Bacillus paralicheniformis, an industrially and agriculturally important isolate from the buffalo grass rhizosphere. Antonie Van Leeuwenhoek 2022; 115:1101-1112. [PMID: 35840814 DOI: 10.1007/s10482-022-01760-6] [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: 02/08/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
A new exopolysaccharide (EPS) producing Gram-positive bacterium was isolated from the rhizosphere of Bouteloua dactyloides (buffalo grass) and its EPS product was structurally characterized. The isolate, designated as LB1-1A, was identified as Bacillus paralicheniformis based on 16S rRNA gene sequence and phylogenetic tree analysis. The EPS produced by LB1-1A was identified as a levan, having β(2 → 6) linked backbone with β(2 → 1) linkages at the branch points (4.66%). The isolate LB1-1A yielded large amount (~ 42 g/l) of levan having high weight average molecular weight (Mw) of 5.517 × 107 Da. The relatively low degree of branching and high molecular weight of this levan makes B. paralicheniformis LB1-1A a promising candidate for industrial applications.
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Affiliation(s)
- Anam Nasir
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan
| | - Waqar Ahmad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan
- Department of Microbiology, Abbottabad University of Science and Technology, Havelian, Abbottabad, Pakistan
| | - Fazal Sattar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan
| | - Iram Ashfaq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan
| | - Stephen R Lindemann
- Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN, 47907, USA
| | - Ming-Hsu Chen
- Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN, 47907, USA
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Leuven, Belgium
| | - Ebru Toksoy Ӧner
- IBSB-Industrial Biotechnology and Systems Biology Research Group, Department of Bioengineering, Marmara University, Göztepe Campus, Istanbul, Turkey
| | - Onur Kirtel
- IBSB-Industrial Biotechnology and Systems Biology Research Group, Department of Bioengineering, Marmara University, Göztepe Campus, Istanbul, Turkey
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan
| | - Muhammad A Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan
| | - Munir A Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Punjab, 38000, Faisalabad, Pakistan.
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Anwar S, Wahla AQ, Ali T, Khaliq S, Imran A, Tawab A, Afzal M, Iqbal S. Biodegradation and Subsequent Toxicity Reduction of Co-contaminants Tribenuron Methyl and Metsulfuron Methyl by a Bacterial Consortium B2R. ACS Omega 2022; 7:19816-19827. [PMID: 35721981 PMCID: PMC9202245 DOI: 10.1021/acsomega.2c01583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
AllyMax is a widely used herbicide formulation in wheat-rice cropping areas of the world. The residues of its active ingredients, tribenuron methyl (TBM) and metsulfuron methyl (MET), persist in soil and water as co-contaminants, and cause serious threats to nontarget organisms. This study was performed to assess the potential of a bacterial consortium for the degradation and detoxification of TBM and MET individually and as co-contaminants. A bacterial consortium (B2R), comprising Bacillus cereus SU-1, Bacillus velezensis OS-2, and Rhodococcus rhodochrous AQ1, capable of degrading TBM and MET in liquid cultures was developed. Biodegradation of TBM and MET was optimized using the Taguchi design of experiment. Optimum degradation of both TBM and MET was obtained at pH 7 and 37 °C. Regarding media composition, optimum degradation of TBM and MET was obtained in minimal salt medium (MSM) supplemented with glucose, and MSM without glucose, respectively. The consortium simultaneously degraded TBM and MET (94.8 and 80.4%, respectively) in cultures containing the formulation AllyMax, where TBM and MET existed as co-contaminants at 2.5 mg/L each. Mass spectrometry analysis confirmed that during biodegradation, TBM and MET were metabolized into simpler compounds. Onion (Allium cepa) root inhibition and Comet assays revealed that the bacterial consortium B2R detoxified TBM and MET separately and as co-contaminants. The consortium B2R can potentially be used for the remediation of soil and water co-contaminated with TBM and MET.
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Affiliation(s)
- Samina Anwar
- Soil
& Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College,
Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Abdul Qadeer Wahla
- Soil
& Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College,
Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Tayyaba Ali
- Department
of Zoology, Government College University, Allama Iqbal Road, Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial
Biotechnology Division, National Institute
for Biotechnology and Genetic Engineering College, Pakistan Institute
of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Asma Imran
- Soil
& Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College,
Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Abdul Tawab
- Health
Biotechnology Division, National Institute
for Biotechnology and Genetic Engineering College, Pakistan Institute
of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Afzal
- Soil
& Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College,
Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Samina Iqbal
- Soil
& Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College,
Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
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Ahmad W, Khaliq S, Akhtar N, El Arab J, Akhtar K, Prakash S, Anwar MA, Munawar N. Whole Genome Sequence Analysis of a Novel Apilactobacillus Species from Giant Honeybee (Apis dorsata) Gut Reveals Occurrence of Genetic Elements Coding Prebiotic and Probiotic Traits. Microorganisms 2022; 10:microorganisms10050904. [PMID: 35630349 PMCID: PMC9147854 DOI: 10.3390/microorganisms10050904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Apilactobacillus spp. are classified as obligate fructophilic lactic acid bacteria (FLAB) that inhabit fructose-rich niches such as honeybee gut. Lactic acid bacteria are an important component of the gut microbiome and play a crucial role in maintaining gut health. In this study, a new FLAB strain HBW1, capable of producing glucan-type exopolysaccharide, was isolated from giant honeybee (Apis dorsata) gut and subjected to whole genome sequencing (WHS) to determine its health-beneficial traits. The genome size of the isolate was 1.49 Mb with a GC content of 37.2%. For species level identity, 16S rDNA sequence similarity, genome to genome distance calculator (dDDH), and average nucleotide identity (ANI) values were calculated. Phylogenetic analysis showed that the isolate HBW1 belongs to the Apilactobacillus genus. The dDDH and ANI values in comparison with closely clustered Apilactobacillus kunkeei species were 52% and 93.10%, respectively. Based on these values, we concluded that HBW1 is a novel species of Apilactobacillus, and we propose the name Apilactobacillus waqarii HBW1 for it. Further, WHS data mining of HBW1 revealed that it harbors two glucosyltransferase genes for prebiotic glucan-type exopolysaccharide synthesis. Moreover, chaperon (clp) and methionine sulfoxide reductase (msrA, msrB, and msrC) genes as well as nutritional marker genes for folic acid (folD) and riboflavin biosynthesis (rib operon), important for conferring probiotic properties, were also detected. Occurrence of these genetic traits make HBW1 an excellent candidate for application to improve gut function.
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Affiliation(s)
- Waqar Ahmad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan; (W.A.); (S.K.); (N.A.); (K.A.)
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University, 3775 University Street, Montreal, QC H3A 2B4, Canada;
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan; (W.A.); (S.K.); (N.A.); (K.A.)
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan; (W.A.); (S.K.); (N.A.); (K.A.)
| | - Jamilah El Arab
- Department of Chemistry, College of Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates;
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan; (W.A.); (S.K.); (N.A.); (K.A.)
| | - Satya Prakash
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University, 3775 University Street, Montreal, QC H3A 2B4, Canada;
| | - Munir A. Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan; (W.A.); (S.K.); (N.A.); (K.A.)
- Correspondence: (M.A.A.); (N.M.)
| | - Nayla Munawar
- Department of Chemistry, College of Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates;
- Correspondence: (M.A.A.); (N.M.)
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10
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Ahmad W, Khaliq S, Akhtar N, El Arab J, Akhtar K, Prakash S, Anwar MA, Munawar N. Whole Genome Sequence Analysis of a Novel Apilactobacillus Species from Giant Honeybee (Apis dorsata) Gut Reveals Occurrence of Genetic Elements Coding Prebiotic and Probiotic Traits. Microorganisms 2022. [DOI: https://doi.org/10.3390/microorganisms10050904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Apilactobacillus spp. are classified as obligate fructophilic lactic acid bacteria (FLAB) that inhabit fructose-rich niches such as honeybee gut. Lactic acid bacteria are an important component of the gut microbiome and play a crucial role in maintaining gut health. In this study, a new FLAB strain HBW1, capable of producing glucan-type exopolysaccharide, was isolated from giant honeybee (Apis dorsata) gut and subjected to whole genome sequencing (WHS) to determine its health-beneficial traits. The genome size of the isolate was 1.49 Mb with a GC content of 37.2%. For species level identity, 16S rDNA sequence similarity, genome to genome distance calculator (dDDH), and average nucleotide identity (ANI) values were calculated. Phylogenetic analysis showed that the isolate HBW1 belongs to the Apilactobacillus genus. The dDDH and ANI values in comparison with closely clustered Apilactobacillus kunkeei species were 52% and 93.10%, respectively. Based on these values, we concluded that HBW1 is a novel species of Apilactobacillus, and we propose the name Apilactobacillus waqarii HBW1 for it. Further, WHS data mining of HBW1 revealed that it harbors two glucosyltransferase genes for prebiotic glucan-type exopolysaccharide synthesis. Moreover, chaperon (clp) and methionine sulfoxide reductase (msrA, msrB, and msrC) genes as well as nutritional marker genes for folic acid (folD) and riboflavin biosynthesis (rib operon), important for conferring probiotic properties, were also detected. Occurrence of these genetic traits make HBW1 an excellent candidate for application to improve gut function.
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Hassam UA, Gulzar A, Rasool B, Zafar S, Younis T, Shakeel M, Khan D, Ullah S, Khaliq S, Ahmad SF, Hafeez M. Efficacy of Citrullus colocynthis seed extract on Earias vittella, Fabricius, (Lepidoptera: Noctuidae): environment sustainable approach. BRAZ J BIOL 2022; 84:e254479. [DOI: 10.1590/1519-6984.254479] [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: 07/21/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Abstract Earias vittellaFabricius, 1794 (Noctuidae: Lepidoptera) is deliberated to be one of the most destructive pests of cotton and okra vegetation in the world including Asia. The pest has established resistance to various synthetic insecticides. The use of bio-pesticide is one of the unconventional approaches to develop a vigorous ecosystem without harming non- target pests and beneficial natural insect fauna. In the present study, the toxicity levels of Citrullus colocynthis seed extract have been evaluated against the populations of E. vittellaunder standardized laboratory conditions. The toxic effects of C. colocynthis on development periods, protein contents and esterase activity of the life stages of E. vittella were also evaluated. The toxicity levels of methanol, ethanol, hexane, water and profenofos were evaluated on the 1st instar larvae of E. vittella. LC30 and LC80 concentrations exhibited the effectiveness of methanol-based C. colocynthis seed extract against 1st instar larvae of E. vitella. The enhanced larval and pupal periods were revealed in treated samples during the comparison with untreated samples. The intrinsic rate of increase, net reproductive rate in the LC30 and LC80 concentrations exposed larvae remained less than the control treatment. Fecundity, the esterase activity and protein contents were declined in LC30 and LC80 treated samples as compared to the control. The present findings suggest that C. colosynthis extracts based botanical insecticides are beneficial, ecosystem sustainable and can be integrated with insect management programs from environment safety perspective.
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Affiliation(s)
- U. A. Hassam
- Pir-Meher Ali Shah Arid Agriculture University, Pakistan
| | - A. Gulzar
- Pir-Meher Ali Shah Arid Agriculture University, Pakistan
| | - B. Rasool
- Government College University Faisalabad, Pakistan
| | - S. Zafar
- University of Education, Pakistan
| | - T. Younis
- Government College University Faisalabad, Pakistan
| | - M. Shakeel
- Pakistan Agricultural Research Council, Pakistan
| | - D. Khan
- Pir-Meher Ali Shah Arid Agriculture University, Pakistan
| | - S. Ullah
- Pir-Meher Ali Shah Arid Agriculture University, Pakistan
| | - S. Khaliq
- Pir-Meher Ali Shah Arid Agriculture University, Pakistan
| | - S. F. Ahmad
- Pir-Meher Ali Shah Arid Agriculture University, Pakistan
| | - M. Hafeez
- Zhejiang Academy of Agricultural Sciences, China
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12
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13
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Khan AQ, Khaliq S, Tunç O, Khaliq A, Javaid MB, Ahmed I. Bifurcation analysis and chaos of a discrete-time Kolmogorov model. Journal of Taibah University for Science 2021. [DOI: 10.1080/16583655.2021.2014679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- A. Q. Khan
- Department of Mathematics, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - S. Khaliq
- Department of Mathematics, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - O. Tunç
- Department of Computer Programing Baskale Vocational School, Van Yuzuncu Yil University, Van, Turkey
| | - A. Khaliq
- Department of Mathematics, Riphah International University, Lahore, Pakistan
| | - M. B. Javaid
- Department of Mathematics, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - I. Ahmed
- Department of Mathematics, Mirpur University of Science and Technology (MUST), Mirpur, Pakistan
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Aftab K, Akhtar K, Kausar A, Khaliq S, Nisar N, Umbreen H, Iqbal M. Fungal strains isolation, identification and application for the recovery of Zn(II) ions. J Photochem Photobiol B 2017; 175:282-290. [PMID: 28923600 DOI: 10.1016/j.jphotobiol.2017.08.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 01/08/2023]
Abstract
Fungal biomass proves to be highly efficient for the treatment of wastewater as well as recovery of metal ions from wastewater. Present investigation was aimed to evaluate the efficiency of indigenous fungal isolates for the sequestration of Zn(II) ions aqueous solution. Among twenty five fungal isolates, Aspergillus oryzae SV/09 (AO SV/09), Aspergillus flavus NA9 (AF NA9) and Paecilomyces formosus DTO 63f4 (PF DTO-63f4) were identified by gene sequencing of ITS regions of the ribosomal DNA (rDNA). The AO SV/09, AF NA9 and PF DTO-63f4 showed promising efficiency for the biosorption of Zn(II) ions. Zn(II) ions adsorption was endothermic in nature and data fitted will to the Freundlich isotherm with correlation coefficients values of 0.99, 0.98 and 0.99 for AO SV/09, AF NA9 and PF DTO-63f4, respectively. Pseudo-second order kinetic model explained well the Zn(II) adsorption kinetic of Zn(II) ions onto biosorbents. The adsorbed Zn(II) ions were desorbed using HCl and 85.5, 75.3, 73.7 (%) Zn(II) ions were recovered from AO SV/09, AF NA9 and PF DTO-63f4 sorbents, respectively. The fungal biosorbents were successfully recycled up to five cycles. Based on sorption, recovery and regeneration, the application of fungal bio-sorbents for the sequestration and recovery of Zn(II) ions is suggested from wastewater and could possibly be extended for the recovery of other heavy metal ions from wastewater.
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Affiliation(s)
- Kiran Aftab
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Abida Kausar
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Numrah Nisar
- Department of Environmental Sciences, Lahore College for Women University, Lahore, Pakistan
| | - Huma Umbreen
- Department of Home economics, Government College Women University Faisalabad, Pakistan
| | - Munawar Iqbal
- Department of Chemistry, The University of Lahore, Lahore, Pakistan.
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15
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Wahid A, Khaliq S. Architectural and biochemical changes in embryonic tissues of maize under cadmium toxicity. Plant Biol (Stuttg) 2015; 17:1005-1012. [PMID: 25732002 DOI: 10.1111/plb.12326] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Heavy metals greatly alter plant morphology and architecture, however detailed mechanisms of such changes are not fully explored. Two experiments were conducted to investigate the influence of cadmium (CdCl2 · 2.5H2 O) on some germination, morphological, biochemical and histological characteristics of developing embryonic tissue of maize. In the first experiment, maize seeds were germinated in increasing levels of CdCl2 (200-2000 μm) in sand and measurements were taken of changes in germination and seedling development attributes. Based on these parameters, 1000 μM CdCl2 was chosen for detailed biochemical and histological measurements. In the second experiment, seeds were germinated in Petri dishes and supplied with 0 (control) or 1000 μM CdCl2 (Cd-treated). Radicle, plumule, coleoptile and coleorhiza were measured for biochemical and histological changes. The highest amount of Cd was in the coleorhiza and radicle. Free proline, soluble sugars, anthocyanin, soluble phenolics, ascorbic acid, H2 O2 and MDA were significantly higher in coleorhizae, followed by the coleoptile, radicle and plumule. Although the radicle and coleorhiza were relatively poor targets of Cd than the other tissues, Cd stress reduced cortical cell size and vascular tissues, and deformed xylem and phloem parenchyma in all plant parts. In conclusion, the main reason for reduced germination was the influence of Cd on architecture of the coleorhiza and coleoptile, which was the result of oxidative stress and other physiological changes taking place in these tissues.
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Affiliation(s)
- A Wahid
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - S Khaliq
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
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16
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Hussain S, Amar A, Najeeb MN, Khaliq S. Two novel mutations in theNR5A1gene as a cause of disorders of sex development in a Pakistani cohort of 46,XY patients. Andrologia 2015; 48:509-17. [DOI: 10.1111/and.12470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 11/29/2022] Open
Affiliation(s)
- S. Hussain
- Department of Biochemistry; University of Health Sciences; Lahore Pakistan
| | - A. Amar
- Department Human Genetics & Molecular Biology; University of Health Sciences; Lahore Pakistan
| | - M. N. Najeeb
- Department of Biochemistry; Quaid-e-Azam Medical Collage; Bahawalpur Pakistan
| | - S. Khaliq
- Department Human Genetics & Molecular Biology; University of Health Sciences; Lahore Pakistan
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17
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M. Khan A, Khaliq S, Sadiq R. Investigation of waste banana peels and radish leaves for their biofuels potentialInvestigation of waste banana peels and radish leaves for their biofuels potential. B CHEM SOC ETHIOPIA 2015. [DOI: 10.4314/bcse.v29i2.7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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18
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Khaliq S, Ghauri MA, Akhtar K. Characterization of mutations in regulatory genes of Tyl cluster leading to overexpression of tylosin in mutant γ-1 of Streptomyces fradiae NRRL-2702. Appl Microbiol Biotechnol 2013; 98:785-93. [DOI: 10.1007/s00253-013-5317-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/02/2013] [Accepted: 10/03/2013] [Indexed: 10/26/2022]
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19
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Walsh DM, Shah SH, Simpson MA, Morgan NV, Khaliq S, Trembath RC, Mehdi SQ, Maher ER. A Novel ABCA12 Mutation in Two Families with Congenital Ichthyosis. Scientifica (Cairo) 2012; 2012:649090. [PMID: 24278723 PMCID: PMC3820470 DOI: 10.6064/2012/649090] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/19/2012] [Indexed: 06/02/2023]
Abstract
Autosomal recessive congenital ichthyosis (ARCI) is a rare genetically heterogeneous disorder characterized by hyperkeratosis in addition to dry, scaly skin. There are six genes currently known to be associated with the disease. Exome sequencing data for two affected individuals with ichthyosis from two apparently unrelated consanguineous Pakistani families was analysed. Potential candidate mutations were analysed in additional family members to determine if the putative mutation segregated with disease status. A novel mutation (c.G4676T, p.Gly1559Val) in ABCA12 occurred at a highly conserved residue, segregated with disease status in both families, and was not detected in 143 control chromosomes. Genotyping with microsatellite markers demonstrated a partial common haplotype in the two families, and a common founder mutation could not be excluded. Comparison to previously reported cases was consistent with the hypothesis that severe loss of function ABCA12 mutations are associated with Harlequin Ichthyosis and missense mutations are preferentially associated with milder phenotypes. In addition to identifying a possible founder mutation, this paper illustrates how advances in genome sequencing technologies could be utilised to rapidly elucidate the molecular basis of inherited skin diseases which can be caused by mutations in multiple disease genes.
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Affiliation(s)
- D. M. Walsh
- Centre for Rare Diseases and Personalised Medicine, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - S. H. Shah
- Centre for Human Genetics, Sindh Institute of Urology and Transplantation, Karachi 74200, Pakistan
| | - M. A. Simpson
- Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London, UK
| | - N. V. Morgan
- Centre for Rare Diseases and Personalised Medicine, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - S. Khaliq
- University of Health Sciences, Lahore, Pakistan
| | - R. C. Trembath
- Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London, UK
| | - S. Q. Mehdi
- Centre for Human Genetics, Sindh Institute of Urology and Transplantation, Karachi 74200, Pakistan
| | - E. R. Maher
- Centre for Rare Diseases and Personalised Medicine, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TT, UK
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Jahan S, Khaliq S, Afzal N, Mahmood S, Malik IA. Effect of HCV core gene of genotype 3a on HCV induced oxidative stress, steatosis and Apoptosis leading to HCC. Z Gastroenterol 2012. [DOI: 10.1055/s-0032-1324007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Khaliq S, Rashid N, Akhtar K, Ghauri MA. Production of tylosin in solid-state fermentation byStreptomyces fradiaeNRRL-2702 and its gamma-irradiated mutant (γ-1). Lett Appl Microbiol 2009; 49:635-40. [DOI: 10.1111/j.1472-765x.2009.02720.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Khaliq S, Akhtar K, Afzal Ghauri M, Iqbal R, Mukhtar Khalid A, Muddassar M. Change in colony morphology and kinetics of tylosin production after UV and gamma irradiation mutagenesis of Streptomyces fradiae NRRL-2702. Microbiol Res 2007; 164:469-77. [PMID: 17475458 DOI: 10.1016/j.micres.2007.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [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: 11/17/2006] [Revised: 02/26/2007] [Accepted: 02/26/2007] [Indexed: 11/27/2022]
Abstract
Tylosin is a macrolide antibiotic used as veterinary drug and growth promoter. Attempts were made for hyper production of tylosin by a strain of Streptomyces fradiae NRRL-2702 through irradiation mutagenesis. Ultraviolet (UV) irradiation of wild-type strain caused development of six morphologically altered colony types on agar plates. After screening using Bacillus subtilis bioassay only morphological mutants indicated the production of tylosin. An increase of 2.7+/-0.22-fold in tylosin production (1500mg/l) in case of mutant UV-2 in complex medium was achieved as compared to wild-type strain (550mg/l). Gamma irradiation of mutant UV-2 using (60)Co gave one morphologically altered colony type gamma-1, which gave 2500mg/l tylosin yield in complex medium. Chemically defined media promoted tylosin production upto 3800mg/l. Maximum value of q(p) (3.34mg/gh) was observed by mutant gamma-1 as compared to wild strain (0.81mg/gh). Moreover, UV irradiation associated changes were unstable with loss of tylosin activity whereas mutant gamma-1 displayed high stability on subsequent culturing.
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Affiliation(s)
- Shazia Khaliq
- Bioprocess Technology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan
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Haider S, Khaliq S, Ahmed SP, Haleem DJ. Long-term tryptophan administration enhances cognitive performance and increases 5HT metabolism in the hippocampus of female rats. Amino Acids 2006; 31:421-5. [PMID: 16699826 DOI: 10.1007/s00726-005-0310-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 11/25/2005] [Indexed: 11/25/2022]
Abstract
It has been shown in various studies that increase in serotonergic neurotransmission is associated with increased memory consolidation whereas low brain 5HT impairs memory performance. In the first phase of our study we found that tryptophan (TRP) administration for 6 weeks increased plasma TRP and whole brain TRP, 5HT and 5HIAA levels. Many brain regions are involved in the learning process but particularly the hippocampus is known to have key role in learning and memory. The present study was therefore designed to investigate the effects of TRP loading particularly on hippocampal 5HT metabolism and cognitive performance in rats. TRP-treated rats demonstrated spatial enhancement as evidenced by a significant decrease in time to find the hidden food reward in radial arm maze test (RAM). The important finding of the present study was the greater increase in the 5HT metabolism in hippocampus than in any other brain region of the TRP-treated rats. This increased 5HT metabolism in the hippocampus emphasizes the involvement of this region in memory process.
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Affiliation(s)
- S Haider
- Department of Biochemistry, Neurochemistry and Biochemical Neuropharmacology Research Unit, University of Karachi, Karachi, Pakistan.
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Khaliq S, Abid A, Ismail M, Hameed A, Mohyuddin A, Lall P, Aziz A, Anwar K, Mehdi SQ. Novel association of RP1 gene mutations with autosomal recessive retinitis pigmentosa. J Med Genet 2006; 42:436-8. [PMID: 15863674 PMCID: PMC1736063 DOI: 10.1136/jmg.2004.024281] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Semaphorins are a large family of transmembrane proteins. The gene for SEMA4A encodes a transmembrane protein comprising 760 amino acids. To investigate its association with human retinal degeneration, mutation screening of the SEMA4A gene was carried out on 190 unrelated patients suffering from a variety of eye diseases. We report the first observation of the involvement of SEMA4A gene mutations causing retinitis pigmentosa (RP) and cone rod dystrophy (CRD). We screened the DNA of 135 patients with RP, 25 patients with CRD, and 30 with LCA using SSCP and direct DNA sequencing for mutations in the SEMA4A gene. Two mutations, p.D345H and p.F350C, were observed only in affected patients; they were not observed in any of the normal members or the 100 control subjects. Both mutations identified occur in the conserved semaphorin domain. Multiple sequence alignments using Clustal analysis showed that R713Q is a conserved substitution and D345H is a semi-conserved substitution. We conclude that these mutations are a cause of various retinal degenerations.
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Forshew T, Khaliq S, Tee L, Smith U, Johnson CA, Mehdi SQ, Maher ER. Identification of novel TYR and TYRP1 mutations in oculocutaneous albinism. Clin Genet 2005; 68:182-4. [PMID: 15996218 DOI: 10.1111/j.1399-0004.2005.00460.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Khaliq S, Abid A, Hameed A, Anwar K, Mohyuddin A, Ismail M, Mehdi SQ. Gene symbol: AIPL1. Disease: LCA4. Hum Genet 2005; 116:542. [PMID: 15991325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- S Khaliq
- Dr. A. Q. Khan Research Laboratories, Biomedical and Genetic Engineering Division, Islamabad, Pakistan.
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Mohyuddin A, Khaliq S, Ayub Q, Mehdi S. HLA-A, -B, -Cw, -DQB1 and -DRB1 allele frequencies in a Sindhi population from Pakistan. Hum Immunol 2004. [DOI: 10.1016/j.humimm.2004.08.098] [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: 10/26/2022]
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Mohyuddin A, Khaliq S, Ayub Q, Mehdi S. HLA-A, -B, -Cw, -DQB1 and -DRB1 allele frequencies in a Kalash population from Pakistan. Hum Immunol 2004. [DOI: 10.1016/j.humimm.2004.08.096] [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: 10/26/2022]
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Hameed A, Abid A, Aziz A, Ismail M, Mehdi SQ, Khaliq S. Evidence of RPGRIP1 gene mutations associated with recessive cone-rod dystrophy. J Med Genet 2003; 40:616-9. [PMID: 12920076 PMCID: PMC1735563 DOI: 10.1136/jmg.40.8.616] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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31
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Khaliq S, Hameed A, Ayub Q, Mazhar K, Mohyuddin A, Mansoor A, Mehdi SQ. Frequency of CCR5 Gene 32-bp deletion in Pakistani ethnic groups. Genet Test 2003; 6:123-7. [PMID: 12215252 DOI: 10.1089/10906570260199384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CCR5 is a G-protein-coupled chemokine receptor that is used as a co-factor by macrophage-tropic (M-tropic) isolates of human immunodeficiency virus-1 (HIV-1) to gain entry into host cells. A 32-bp deletion in the CCR5 gene (CCR5-Delta32) leads to the production of an altered gene product that prevents HIV-1 from entering the host cell. This study was carried out to determine prevalence of CCR5-Delta32 allele frequency in a large Pakistani population sample (n = 821) representing 10 ethnic groups. No individual was homozygous for the mutant allele and the frequency of the CCR5-Delta32 allele ranged from 0.62% to 3.57%. The CCR5-Delta32 allele frequency was generally lower in populations from southern Pakistan. The overall frequency of the CCR5-Delta32 allele in Pakistan was 2.31%, which is much lower than that found in European populations and similar to that in the Middle East. This is consistent with the historical records and genetic data that indicate a close genetic affinity among these populations. This study demonstrates that the Pakistani population is highly susceptible to M-tropic isolates of HIV-1 and public health measures need to be enforced with urgency if Pakistan is to avoid an HIV epidemic.
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Affiliation(s)
- S Khaliq
- Biomedical and Genetic Engineering Division, Dr. A.Q. Khan Research Laboratories, Islamabad 44000, Pakistan
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Abstract
The extreme polymorphism found at some of the loci of the HLA system has made it an invaluable tool for population genetic analyses. In this study the genetic polymorphism of six Pakistani ethnic groups was investigated at the HLA-A, -B, -C, -DRB and DQB1 loci using polymerase chain reaction with sequence specific primers. The groups included in this study are the Baloch, Brahui and Sindhi from the south and the Burusho, Kalash and Pathan from the north of Pakistan. The allele frequencies, three-locus haplotype frequencies for HLA-A, -C, -B and HLA-A, -B, -DRB1 are given. Variation in the allele and haplotype distribution between the six Pakistani ethnic groups was observed. A phylogenetic tree and correspondence analysis based on HLA-A, -B, -C, -DRB1 and -DQB1 allele frequencies revealed the Kalash population to be distinct from the remaining Pakistani populations. The Baloch and Brahui were closely related to one another. The Sindhi were closer to the Pathan and Burusho populations than to the neighboring Baloch and Brahui populations, indicating admixture between the northern and southern populations of Pakistan. A phylogenetic tree and correspondence analysis comparing the Pakistani populations with various other world populations showed that the Pakistani ethnic groups lie within the cluster of Asian Indian populations. The three-locus haplotypes found in the Pakistani populations suggest an influence from Caucasian and Oriental populations.
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Affiliation(s)
- A Mohyuddin
- Biomedical and Genetic Engineering Division, Dr A. Q. Khan Research Laboratories, PO Box 2891, Islamabad-44000, Pakistan.
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Alexander MR, Kitzman DW, Khaliq S, Darty SN, Hamilton CA, Herrington DM, Link KM, Hundley WG. Determination of femoral artery endothelial function by phase contrast magnetic resonance imaging. Am J Cardiol 2001; 88:1070-4. [PMID: 11704017 DOI: 10.1016/s0002-9149(01)01998-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- M R Alexander
- Department of Internal Medicine (Cardiology Section), The Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157-1045, USA
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35
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Khaliq S, Hameed A, Ismail M, Anwar K, Leroy B, Payne AM, Bhattacharya SS, Mehdi SQ. Locus for autosomal recessive nonsyndromic persistent hyperplastic primary vitreous. Invest Ophthalmol Vis Sci 2001; 42:2225-8. [PMID: 11527934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
PURPOSE To map the disease locus in a six-generation, consanguineous Pakistani family affected by nonsyndromic autosomal recessive persistent hyperplastic primary vitreous (arPHPV). All affected individuals had peripheral anterior synechiae and corneal opacities with variable degrees of cataract and a retrolenticular white mass behind the lens. METHODS Genomic DNA from family members was typed for alleles at more than 400 known polymorphic genetic markers, by polymerase chain reaction. Alleles were assigned to individuals, which allowed calculation of lod scores. RESULTS A maximum two-point lod score of 4.07 was obtained with marker D10S1225 with no recombination. Two recombinations with marker D10S208 and D10S537 localized the disease within a region of approximately 30 centimorgans (cM). However, homozygosity across the region refined the arPHPV locus to 13 cM. CONCLUSIONS Linkage analysis shows localization of nonsyndromic arPHPV to chromosome10q11-q21.
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Affiliation(s)
- S Khaliq
- Dr. A. Q. Khan Research Laboratories, Biomedical and Genetic Engineering Division, Islamabad, Pakistan.
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36
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Abstract
A liquid-level sensor based on the refractive-index sensitivity of long-period fiber-optic gratings is proposed and demonstrated. The form of the transmission spectrum of the long-period grating is dependent on the fraction of the length of the long-period grating that is surrounded by the liquid. The sensor shows a large linear range, with sensitivity of 4.8% change in transmission per millimeter, for a long-period grating with a length of 40 mm and a periodicity of 400mu;m .
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Hameed A, Khaliq S, Ismail M, Anwar K, Mehdi SQ, Bessant D, Payne AM, Bhattacharya SS. A new locus for autosomal recessive RP (RP29) mapping to chromosome 4q32-q34 in a Pakistani family. Invest Ophthalmol Vis Sci 2001; 42:1436-8. [PMID: 11381043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
PURPOSE To map the disease locus in a six-generation, consanguineous Pakistani family with autosomal recessive retinitis pigmentosa (arRP). All affected individuals had pigmentary retinopathy associated with symptoms of night blindness and the loss of peripheral visual fields by the age of 20 years, loss of central vision between the ages of 25 and 30 years, and complete blindness between the ages of 40 and 50 years. METHODS Genomic DNA from family members was typed for alleles at known polymorphic genetic markers using polymerase chain reaction. Alleles were assigned to individuals, which allowed calculation of LOD scores using the programs Cyrillic (http://www.cyrillicsoftware.com) and MLINK (Cherwell Scientific Publishing LTD:, Oxford, UK). The genes for membrane glycoprotein (M6a) and chloride channel 3 (CLCN3) were analyzed by direct sequencing for mutations. RESULTS A new locus for arRP (RP29) has been mapped to chromosome 4q32-q34. A maximum two-point LOD score of 3.76 was obtained for the marker D4S415, with no recombination. Two recombination events in the pedigree positioned this locus to a region flanked by markers D4S621 and D4S2417. A putative region of homozygosity by descent was observed between the loci D4S3035 and D4S2417, giving a probable disease interval of 4.6 cM. Mutation screening of two candidate genes, M6a and CLCN3, revealed no disease-associated mutations. CONCLUSIONS The results suggest that the arRP phenotype maps to a new locus and is due to a mutated gene within the 4q32-q34 chromosomal region.
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Affiliation(s)
- A Hameed
- Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad, Pakistan
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Payne A, Vithana E, Khaliq S, Hameed A, Deller J, Abu-Safieh L, Kermani S, Leroy BP, Mehdi SQ, Moore AT, Bird AC, Bhattacharya SS. RP1 protein truncating mutations predominate at the RP1 adRP locus. Invest Ophthalmol Vis Sci 2000; 41:4069-73. [PMID: 11095597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
PURPOSE Recent reports have shown that the autosomal dominant retinitis pigmentosa (adRP) phenotype linked to the pericentric region of chromosome 8 is associated with mutations in a gene designated RP1. Screening of the whole gene in a large cohort of patients has not been undertaken to date. To assess the involvement and character of RP1 mutations in adRP, the gene was screened in a panel of 266 unrelated patients of British origin and a Pakistani family linked to this locus. METHODS Patients exhibiting the adRP phenotype were screened for mutations in the four exons of the RP1 gene by heteroduplex analysis and direct sequencing. Linkage of the Pakistani family was achieved using microsatellite markers. Polymerase chain reaction (PCR) products were separated by nondenaturing polyacrylamide gel electrophoresis. Alleles were assigned to individuals, which allowed calculation of LOD scores. Microsatellite marker haplotyping was used to determine ancestry of patients carrying the same mutation. RESULTS In the 266 British patients and 1 Pakistani family analyzed, 21 loss-of-function mutations and 7 amino acid substitutions were identified, some of which may also be disease-causing. The mutations, many of which were deletion or insertion events, were clustered in the 5' end of exon 4. Most mutations resulted in a premature termination codon in the mRNA. Haplotype analysis of nine patients carrying an R677X mutation suggested that these patients are not ancestrally related. CONCLUSIONS RP1 mutations account for 8% to 10% of the mutations in our cohort of British patients. The most common disease-causing mechanism is deduced to be one involving the presence of a truncated protein. Mutations in RP1 have now been described in adRP patients of four ethnically diverse populations. The different disease haplotype seen in the nine patients carrying the same mutation suggests that this mutation has arisen independently many times, possibly due to a mutation hot spot in this part of the gene.
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Affiliation(s)
- A Payne
- Department of Molecular Genetics, Institute of Ophthalmology, Moorfields Eye Hospital, London, United Kingdom.
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Khaliq S, Hameed A, Ismail M, Anwar K, Leroy BP, Mehdi SQ, Payne AM, Bhattacharya SS. Novel locus for autosomal recessive cone-rod dystrophy CORD8 mapping to chromosome 1q12-Q24. Invest Ophthalmol Vis Sci 2000; 41:3709-12. [PMID: 11053266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
PURPOSE To map the disease locus of a two-generation, consanguineous Pakistani family with autosomal recessive cone-rod dystrophy (arCRD). All affected individuals had night blindness, deterioration of central vision, photophobia, epiphora in bright light, and problems with color distinction. Fundoscopy revealed marked macular degeneration and attenuation of retinal vessels. Mild pigmentary changes were present in the periphery. METHODS Genomic DNA was amplified across the polymorphic microsatellite poly-CA regions identified by markers. Alleles were assigned to individuals that allowed calculation of LOD scores using the Cyrillic (Cherwell Scientific, Oxford, UK) and MLINK (accessed from ftp://linkage. rockefeller.edu/softeware/linkage/) software programs. The cellular retinoic acid-binding protein 2 (CRABP2), cone transducin alpha-subunit (GNAT2), potassium inwardly rectifying channel, subfamily J, member 10 (KCNJ10), genes were analyzed by heteroduplex analysis and direct sequencing for mutations. RESULTS A new locus for arCRD (CORD8) has been mapped to chromosome 1q12-q24. A maximum two-point LOD score of 4.22 was obtained with marker D1S2635 at recombination fraction of theta = 0.00. Two critical recombinations in the pedigree positioned this locus to a region flanked by markers D1S457 and D1S2681. A region of homozygosity was observed within the loci D1S442 and D1S2681, giving a probable critical disease interval of 21 cM. Mutation screening of the three candidate genes CRABP2, GNAT2, and KCNJ10 revealed no disease-associated mutations. CONCLUSIONS The findings therefore suggest that this phenotype maps to a new locus and is due to an as yet uncharacterized gene within the 1q12-q24 chromosomal region.
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Affiliation(s)
- S Khaliq
- Dr. A.Q. Khan Research Laboratories, Biomedical and Genetic Engineering Division, Islamabad, Pakistan
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Khaliq S, Hameed A, Khaliq T, Ayub Q, Qamar R, Mohyuddin A, Mazhar K, Qasim-Mehdi S. P53 mutations, polymorphisms, and haplotypes in Pakistani ethnic groups and breast cancer patients. Genet Test 2000; 4:23-9. [PMID: 10794357 DOI: 10.1089/109065700316435] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Inactivation of the p53 gene has been found to be associated with the pathogenesis of several neoplasias. Three biallelic polymorphisms in the p53 gene have been linked to predisposition to the development of various malignancies. These include a 16-bp duplication in intron 3 and BstU I and Msp I restriction fragment length polymorphisms (RFLPs) in exon 4 and intron 6, respectively. The prevalence of these polymorphisms was studied in breast cancer patients and nine major ethnic groups of Pakistan. Differences in allele frequencies for all three polymorphisms were observed among the various ethnic groups and breast cancer patients. The absence of the 16-bp duplication was common among the northern ethnic groups, being highest in the Hazara (0.90). The Msp I A1 allele frequency in the southern Makrani population was significantly higher in comparison with the other ethnic groups. In the cancer patients, the absence of the 16-bp duplication in combination with the BstU I Pro and absence of Msp I restriction site were the most frequent. In these patients, ten substitution mutations were found in the p53 gene, seven of which have been reported previously for breast cancer. The remaining three mutations have been found in other malignancies, but not in carcinoma of the breast.
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Affiliation(s)
- S Khaliq
- Biomedical and Genetic Engineering Division, Islamabad, Pakistan
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Bessant DA, Khaliq S, Hameed A, Anwar K, Payne AM, Mehdi SQ, Bhattacharya SS. Severe autosomal dominant retinitis pigmentosa caused by a novel rhodopsin mutation (Ter349Glu). Mutations in brief no. 208. Online. Hum Mutat 2000; 13:83. [PMID: 10189219 DOI: 10.1002/(sici)1098-1004(1999)13:1<83::aid-humu12>3.0.co;2-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mutations in the rhodopsin gene are reported to be responsible for approximately 25% of all cases of autosomal dominant Retinitis pigmentosa (adRP). Affected individuals from a large family with an unusually severe form of adRP were screened for mutations in the rhodopsin gene. Direct sequencing of exon 5 revealed a TAA to GAA transversion at nucleotide 5276/codon 349, which was confirmed by Dde1 restriction digest analysis. This change would replace the normal termination codon with a glutamic acid residue (Ter-349-Glu, or X349E). The next predicted termination codon (TAA) lies 153bp downstream at nucleotides 5429 to 5431. Termination of transcription at this point would add an additional 51 amino-acid residues to the carboxy terminus of the rhodopsin molecule. This mutation is unique in producing a mutant rhodopsin in which all of the normal 348 amino-acid residues remain intact. It produces one of the most severe adRP phenotypes ever observed in a family with a rhodopsin mutation. In view of this the Ter-349-Glu mutation is worthy of further investigation to determine how the presence of this particular mutant opsin leads to rod photoreceptor degeneration.
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Affiliation(s)
- D A Bessant
- Department of Molecular Genetics, Institute of Ophthalmology, London, United Kingdom
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Sohoki MM, Browne SJ, Sullivan LS, Blackshaw S, Cepko CL, Payne AM, Bhattacharya SS, Khaliq S, Mehdi SQ, Birch DG, Harrison WR, Elder FF, Heckenlively JR, Daiger SP. Mutations in a new photoreceptor-pineal gene on 17p cause leber congenital amaurosis. Nat gen 2000;24:79-83. Am J Ophthalmol 2000; 129:834-5. [PMID: 10927016 PMCID: PMC2796558 DOI: 10.1016/s0002-9394(00)00517-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Leber congenital amaurosis (LCA, MIM 204000) accounts for at least 5% of all inherited retinal disease1 and is the most severe inherited retinopathy with the earliest age of onset2. Individuals affected with LCA are diagnosed at birth or in the first few months of life with severely impaired vision or blindness, nystagmus and an abnormal or flat electroretinogram (ERG). Mutations in GUCY2D (ref. 3), RPE65 (ref. 4) and CRX (ref. 5) are known to cause LCA, but one study identified disease-causing GUCY2D mutations in only 8 of 15 families whose LCA locus maps to 17p13.1 (ref. 3), suggesting another LCA locus might be located on 17p13.1. Confirming this prediction, the LCA in one Pakistani family mapped to 17p13.1, between D17S849 and D17S960—a region that excludes GUCY2D. The LCA in this family has been designated LCA4 (ref. 6). We describe here a new photoreceptor/pineal-expressed gene, AIPL1 (encoding arylhydrocarbon interacting protein-like 1), that maps within the LCA4 candidate region and whose protein contains three tetratricopeptide (TPR) motifs, consistent with nuclear transport or chaperone activity. A homozygous nonsense mutation at codon 278 is present in all affected members of the original LCA4 family. AIPL1 mutations may cause approximately 20% of recessive LCA, as disease-causing mutations were identified in 3 of 14 LCA families not tested previously for linkage.
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Hameed A, Khaliq S, Ismail M, Anwar K, Ebenezer ND, Jordan T, Mehdi SQ, Payne AM, Bhattacharya SS. A novel locus for Leber congenital amaurosis (LCA4) with anterior keratoconus mapping to chromosome 17p13. Invest Ophthalmol Vis Sci 2000; 41:629-33. [PMID: 10711674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
PURPOSE A two-generation consanguineous Pakistani family with autosomal recessive Leber congenital amaurosis (LCA, MIM 204,000) and keratoconus was identified. All affected individuals have bilateral keratoconus and congenital pigmentary retinopathy. The goal of this study was to link the disease phenotype in this family. METHODS Genomic DNA was amplified across the polymorphic microsatellite poly-CA regions identified by markers. Polymerase chain reaction (PCR) products were separated by nondenaturing polyacrylamide gel electrophoresis. Alleles were assigned to individuals, which allowed calculation of LOD scores using the Cyrillic and MLINK software program. The retinal guanylate cyclase (RETGC-1, GDB symbol GUC2D) and pigment epithelium-derived factor (PEDF) genes were analyzed by heteroduplex analysis and direct sequencing for mutations in diseased individuals. RESULTS Based on a whole genome linkage analysis the first locus for this combined phenotype has been mapped to chromosome 17p13. Linkage analysis gave a two point LOD score of 3.21 for marker D17S829. Surrounding this marker is a region of homozygosity of 15.77 cM, between the markers D17S1866 and D17S960; however, the crossover for the marker D17S1529 refines the region to 10.77 cM within which the disease gene is predicted to lie. Mutation screening of the nearby RETGC-1 gene, which has been shown to be associated with LCA1, revealed no mutations in the affected individuals of this family. Similarly, another prime candidate in the region PEDF was also screened for mutations. The factor has been shown to be involved in the photoreceptor differentiation and neuronal survival. No mutations were found in this gene either. Furthermore, RETGC-1 was physically excluded from the critical disease region based on the existing physical map. CONCLUSIONS It is therefore suggested that this combined phenotype maps to a new locus and is due to an as yet uncharacterized gene within the 17p13 chromosomal region.
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Affiliation(s)
- A Hameed
- Dr. A.Q. Khan Research Laboratories, Biomedical and Genetic Engineering Division, Islamabad, Pakistan
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Sohocki MM, Bowne SJ, Sullivan LS, Blackshaw S, Cepko CL, Payne AM, Bhattacharya SS, Khaliq S, Qasim Mehdi S, Birch DG, Harrison WR, Elder FF, Heckenlively JR, Daiger SP. Mutations in a new photoreceptor-pineal gene on 17p cause Leber congenital amaurosis. Nat Genet 2000; 24:79-83. [PMID: 10615133 PMCID: PMC2581448 DOI: 10.1038/71732] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Leber congenital amaurosis (LCA, MIM 204000) accounts for at least 5% of all inherited retinal disease and is the most severe inherited retinopathy with the earliest age of onset. Individuals affected with LCA are diagnosed at birth or in the first few months of life with severely impaired vision or blindness, nystagmus and an abnormal or flat electroretinogram (ERG). Mutations in GUCY2D (ref. 3), RPE65 (ref. 4) and CRX (ref. 5) are known to cause LCA, but one study identified disease-causing GUCY2D mutations in only 8 of 15 families whose LCA locus maps to 17p13.1 (ref. 3), suggesting another LCA locus might be located on 17p13.1. Confirming this prediction, the LCA in one Pakistani family mapped to 17p13.1, between D17S849 and D17S960-a region that excludes GUCY2D. The LCA in this family has been designated LCA4 (ref. 6). We describe here a new photoreceptor/pineal-expressed gene, AIPL1 (encoding aryl-hydrocarbon interacting protein-like 1), that maps within the LCA4 candidate region and whose protein contains three tetratricopeptide (TPR) motifs, consistent with nuclear transport or chaperone activity. A homozygous nonsense mutation at codon 278 is present in all affected members of the original LCA4 family. AIPL1 mutations may cause approximately 20% of recessive LCA, as disease-causing mutations were identified in 3 of 14 LCA families not tested previously for linkage.
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Affiliation(s)
- M M Sohocki
- Human Genetics Center, School of Public Health, The University of Texas-Houston Health Science Center, Houston, Texas, USA
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Mohyuddin A, Ayub Q, Qamar R, Khaliq S, Mansoor A, Mehdi SQ. HLA polymorphisms in ethnic groups from Pakistan. Transplant Proc 1999; 31:3350-1. [PMID: 10616502 DOI: 10.1016/s0041-1345(99)00821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- A Mohyuddin
- Biomedical & Genetic Engineering Division, AQ Khan Research Laboratories, Islamabad, Pakistan
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Qamar R, Ayub Q, Khaliq S, Mansoor A, Karafet T, Mehdi SQ, Hammer MF. African and Levantine origins of Pakistani YAP+ Y chromosomes. Hum Biol 1999; 71:745-55. [PMID: 10510568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-chromosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide polymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes carrying the YAP element (YAP+) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern populations appeared to lack YAP+ chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYS19*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all polymorphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, including YAP+ haplotypes 4-A, 4-B, 5-C, and 5-E. We hypothesize that the geographic distributions of YAP+ haplotypes 4 and 5 trace separate migratory routes to Pakistan: YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data suggesting that Pakistan's ethnic groups have been influenced by migrations from both African and Levantine source populations.
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Affiliation(s)
- R Qamar
- Biomedical and Genetic Engineering Division, Khan Research Laboratories, Islamabad, Pakistan
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Bessant DA, Anwar K, Khaliq S, Hameed A, Ismail M, Payne AM, Mehdi SQ, Bhattacharya SS. Phenotype of autosomal recessive congenital microphthalmia mapping to chromosome 14q32. Br J Ophthalmol 1999; 83:919-22. [PMID: 10413693 PMCID: PMC1723146 DOI: 10.1136/bjo.83.8.919] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Congenital microphthalmia (OMIM: 309700) may occur in isolation or in association with a variety of systemic malformations. Isolated microphthalmia may be inherited as an autosomal dominant, an autosomal recessive, or an X linked trait. METHODS Based on a whole genome linkage analysis, in a six generation consanguineous family with autosomal recessive inheritance, the first locus for isolated microphthalmia was mapped to chromosome 14q32. Eight members of this family underwent clinical examination to determine the nature of the microphthalmia phenotype associated with this locus. RESULTS All affected individuals in this family suffered from bilateral microphthalmia in association with anterior segment abnormalities, and the best visual acuity achieved was "perception of light". Corneal changes included partial or complete congenital sclerocornea, and the later development of corneal vascularisation and anterior staphyloma. Intraocular pressure, as measured by Schiotz tonometry, was greatly elevated in many cases. CONCLUSIONS This combination of ocular defects suggests an embryological disorder involving tissues derived from both the neuroectoderm and neural crest. Other families with defects in the microphthalmia gene located on 14q32 may have a similar ocular phenotype aiding their identification.
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Affiliation(s)
- D A Bessant
- Department of Molecular Genetics, Institute of Ophthalmology, London
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Khaliq S, Hameed A, Ismail M, Mehdi SQ, Bessant DA, Payne AM, Bhattacharya SS. Refinement of the locus for autosomal recessive Retinitis pigmentosa (RP25) linked to chromosome 6q in a family of Pakistani origin. Am J Hum Genet 1999; 65:571-4. [PMID: 10417302 PMCID: PMC1377958 DOI: 10.1086/302493] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Berry V, Mackay D, Khaliq S, Francis PJ, Hameed A, Anwar K, Mehdi SQ, Newbold RJ, Ionides A, Shiels A, Moore T, Bhattacharya SS. Connexin 50 mutation in a family with congenital "zonular nuclear" pulverulent cataract of Pakistani origin. Hum Genet 1999; 105:168-70. [PMID: 10480374 DOI: 10.1007/s004399900094] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Inherited cataract is a clinically and genetically heterogeneous disease that most often presents as a congenital autosomal dominant trait. Here we report linkage of a three-generation family of Pakistani origin with autosomal dominant cataract "zonular nuclear" pulverulent type (CZNP) on chromosome 1q21.1. Genome wide-linkage analysis excluded all the known cataract loci except on chromosome 1q. Significantly positive 2-point lod score values (Z=3.01 at theta=0) were obtained for markers D1S305 and D1S2721, which are known to flank the gene for connexin 50 (Cx50) or gap junction protein alpha-8 (Gja8). Previously a mutation in this gene has been reported in a British family with zonular pulverulent cataract (CZP). Here we describe a second mutation (E48K) in connexin 50 that confirms the involvement of this gene in cataractogenesis.
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Affiliation(s)
- V Berry
- Department of Molecular Genetics, Institute of Ophthalmology, London, UK.
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Bessant DA, Khaliq S, Hameed A, Anwar K, Mehdi SQ, Payne AM, Bhattacharya SS. A locus for autosomal recessive congenital microphthalmia maps to chromosome 14q32. Am J Hum Genet 1998; 62:1113-6. [PMID: 9545413 PMCID: PMC1377100 DOI: 10.1086/301843] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Congenital microphthalmia (CMIC) (OMIM 309700) may occur in isolation or in association with a variety of systemic malformations. Isolated CMIC may be inherited as an autosomal dominant, an autosomal recessive, or an X-linked trait. On the basis of a whole-genome linkage analysis, we have mapped the first locus for isolated CMIC, in a five-generation consanguineous family with autosomal recessive inheritance, to chromosome 14q32. All affected individuals in this family have bilateral CMIC. Linkage analysis gave a maximum two-point LOD score of 3.55 for the marker D14S65. Surrounding this marker is a region of homozygosity of 7.3 cM, between the markers D14S987 and D14S267, within which the disease gene is predicted to lie. The genes for several eye-specific transcription factors are located on human chromosome 14q and in the syntenic region of mouse chromosome 12. However, both CHX10 (14q24.3), mutations of which give rise to CMIC in mouse models, and OTX2 (14q21-22) can be excluded as candidates for autosomal recessive congenital microphthalmia (arCMIC), since they map outside the critical disease region defined by recombination events. This suggests that arCMIC is caused by defects in a novel developmental gene that may be important or even essential in eye development.
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Affiliation(s)
- D A Bessant
- Department of Molecular Genetics, Institute of Ophthalmology, University College, London, United Kingdom
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