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Zafar Z, Wood MJ, Fatima S, Bhatti MF, Shah FA, Saud Z, Loveridge EJ, Karaca I, Butt TM. Identification of the odorant binding proteins of Western Flower Thrips ( Frankliniella occidentalis), characterization and binding analysis of FoccOBP3 with molecular modelling, molecular dynamics simulations and a confirmatory field trial. J Biomol Struct Dyn 2024:1-16. [PMID: 38415377 DOI: 10.1080/07391102.2024.2317990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024]
Abstract
Olfactory systems are indispensable for insects as they, including Western Flower Thrips (Frankliniella occidentalis), use olfactory cues for ovipositing and feeding. F. occidentalis use odorant binding proteins (OBPs) to transport semiochemicals to odorant receptors to induce a behavioural response from the sensillum lymph of the insect's antennae. This study identifies four OBPs of F. occidentalis and analyses their expression at three stages of growth: larvae, adult males and adult females. Further, it investigates the presence of conserved motifs and their phylogenetic relationship to other insect species. Moreover, FoccOBP3 was in silico characterized to analyse its structure along with molecular docking and molecular dynamics simulations to understand its binding with semiochemicals of F. occidentalis. Molecular docking revealed the interactions of methyl isonicotinate, p-anisaldehyde and (S)-(-)-verbenone with FoccOBP3. Moreover, molecular dynamics simulations showed bonding stability of these ligands with FoccOBP3, and field trials validated that Lurem TR (commercial product) and p-anisaldehyde had greater attraction as compared to (S)-(-)-verbenone, given the compound's binding with FoccOBP3. The current study helps in understanding the tertiary structure and interaction of FoccOBP3 with lures using computational and field data and will help in the identification of novel lures of insects in the future, given the importance of binding with OBPs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zeeshan Zafar
- Research and Development, Razbio Limited, Bridgend, UK
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Martyn J Wood
- Research and Development, Razbio Limited, Bridgend, UK
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Sidra Fatima
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Farooq A Shah
- Research and Development, Razbio Limited, Bridgend, UK
| | - Zack Saud
- Department of Biosciences, Swansea University, Swansea, UK
| | | | - Ismail Karaca
- Faculty of Agriculture, Department of Plant Protection, Isparta University of Applied Sciences, Isparta, Turkey
| | - Tariq M Butt
- Department of Biosciences, Swansea University, Swansea, UK
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Yan Y, Yin X, Li J, Li H, Liu J, Liu Y, Tian G. NPAS4 Polymorphisms Contribute to Coronary Heart Disease (CHD) Risk. Cardiovasc Toxicol 2022; 22:515-527. [PMID: 35532855 DOI: 10.1007/s12012-022-09735-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
As genetic inheritance is an inevitable risk factor in the development of coronary heart disease (CHD), it is critical to identify the polymorphisms of CHD risk. This study explored whether the NPAS4 polymorphisms are related to the CHD risk in the Chinese Han population. Five SNPs in NPAS4 were genotyped using Agena Mass ARRAY from 499 CHD and 500 controls. RT-PCR detected the NPAS4 expression levels in peripheral blood mononuclear cells from 50 CHD and 50 controls. χ2 test compared the distributions of gender, allele and genotypes frequencies between cases and controls. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs). MDR analyzed the SNP-SNP interactions on risk of CHD. U test compared the differences in gene expression between different groups. The results showed that rs4466842 was correlated with an increased CHD risk in overall, males and age ≤ 60; rs117186164 and rs12785321 were significantly related to an increased CHD risk in male and age ≤ 60, respectively; haplotype Ars117186164Crs4466842 was significantly correlated with an increased CHD risk. SNP-SNP interactions results showed that the best model was the four-locus model was the combination of rs117770654, rs117957381, rs12785321, and rs4466842 (CVC = 10/10, Testing Sensitivity = 0.647). The expression levels of NPAS4 in the case group (0.365 ± 0.139) were significantly lower than that in the control group (0.782 ± 0.224) (P < 0.001). The results revealed that SNPs in NPAS4 may play an important role in the occurrence and development of CHD.
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Affiliation(s)
- Yuping Yan
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, #277 Yanta West Road, Xi'an, 710061, Shaanxi, China.,Department of Cardiovascular Medicine, Xi'an Daxing Hospital, Xi'an, 710016, Shaanxi, China
| | - Xiangli Yin
- Department of Pathology, Xi'an International Medical Center Hospital, Xi'an, 710100, Shaanxi, China
| | - Jingjie Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Haiyue Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Jianfeng Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yuanwei Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Gang Tian
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, #277 Yanta West Road, Xi'an, 710061, Shaanxi, China.
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Jabeen R, Iqbal A, Deeba F, Zulfiqar F, Mustafa G, Nawaz H, Habiba U, Nafees M, Zaid A, Siddique KHM. Isolation and characterization of peroxidase P7-like gene and Rab-GDI like gene from potential medicinal plants: A step toward understanding cell defense signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:975852. [PMID: 36119597 PMCID: PMC9478186 DOI: 10.3389/fpls.2022.975852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
Defensin genes form part of a plant's defense system and are activated when exposed to biotic or abiotic stress. They play a vital role in controlling many signaling pathways involved in various plant defense mechanisms. This research aimed to isolate and characterize novel defensin genes from selected medicinally important plants to explore their signaling mechanisms and defense associated roles for breeding. The DNA of Albizia lebbeck and Moringa oleifera was subjected to PCR amplification using gene-specific primers of defensin genes. Two novel defensin genes were isolated in each species, with sequence lengths of 300 bp in A. lebbeck and 150 bp in M. oleifera. In-silico analysis undertaken to retrieve and align their orthologous sequences revealed 100% similarity of the A. lebbeck gene with the Musa acuminate peroxidase P7-like gene and 85% similarity of the M. oleifera gene with the Manihot esculenta GDP dissociation inhibitor gene. The reliability, stability and physiochemical properties of homology models of these sequences was confirmed through online computational studies. This preliminary study confirmed the presence of novel genes with peroxidase P7 and Rab GDP dissociation inhibitor gene-like activity in A. lebbeck and M. oleifera, respectively, and their potential defense role in plants. Thus, the defensin genes of both species could be used in the synthesis of transgenic self-defensive plants with increased disease resistance and as potential candidates for improved crop production and thraputic formulation in the future.
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Affiliation(s)
- Raheela Jabeen
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
- *Correspondence: Raheela Jabeen,
| | - Atia Iqbal
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Punjab, Pakistan
| | - Farah Deeba
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Faisal Zulfiqar,
| | - Ghulam Mustafa
- Department of Biochemsitry, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Haq Nawaz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Ume Habiba
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Punjab, Pakistan
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Abbu Zaid
- Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Fu J, Guo O, Zhen Z, Zhen J. Essential Functions of the Transcription Factor Npas4 in Neural Circuit Development, Plasticity, and Diseases. Front Neurosci 2020; 14:603373. [PMID: 33335473 PMCID: PMC7736240 DOI: 10.3389/fnins.2020.603373] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022] Open
Abstract
Signaling from the synapse to nucleus is mediated by the integration and propagation of both membrane potential changes (postsynaptic potentials) and intracellular second messenger cascades. The electrical propagation of postsynaptic potentials allows for rapid neural information processing, while propagating second messenger pathways link synaptic activity to the transcription of genes required for neuronal survival and adaptive changes (plasticity) underlying circuit formation and learning. The propagation of activity-induced calcium signals to the cell nucleus is a major synapse-to-nucleus communication pathway. Neuronal PAS domain protein 4 (Npas4) is a recently discovered calcium-dependent transcription factor that regulates the activation of genes involved in the homeostatic regulation of excitatory–inhibitory balance, which is critical for neural circuit formation, function, and ongoing plasticity, as well as for defense against diseases such as epilepsy. Here, we summarize recent findings on the neuroprotective functions of Npas4 and the potential of Npas4 as a therapeutic target for the treatment of acute and chronic diseases of the central nervous system.
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Affiliation(s)
- Jian Fu
- Department of Emergency Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ouyang Guo
- Department of Biology, Boston University, Boston, MA, United States
| | - Zhihang Zhen
- Department of Neurology, Key Laboratory of Neurology of Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Junli Zhen
- Department of Neurology, Key Laboratory of Neurology of Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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