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Zhang M, Hong Y, Zhu J, Pan Y, Zhou H, Lv C, Guo B, Wang F, Xu R. Molecular insights into the responses of barley to yellow mosaic disease through transcriptome analysis. BMC PLANT BIOLOGY 2023; 23:267. [PMID: 37208619 DOI: 10.1186/s12870-023-04276-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Barley (Hordeum vulgare L.) represents the fourth most essential cereal crop in the world, vulnerable to barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), leading to the significant yield reduction. To gain a better understanding of the mechanisms regarding barley crop tolerance to virus infection, we employed a transcriptome sequencing approach and investigated global gene expression among three barley varieties under both infected and control conditions. RESULTS High-throughput sequencing outputs revealed massive genetic responses, reflected by the barley transcriptome after BaYMV and/or BaMMV infection. Significant enrichments in peptidase complex and protein processing in endoplasmic reticulum were clustered through Gene ontology and KEGG analysis. Many genes were identified as transcription factors, antioxidants, disease resistance genes and plant hormones and differentially expressed between infected and uninfected barley varieties. Importantly, general response genes, variety-specific and infection-specific genes were also discovered. Our results provide useful information for future barley breeding to resist BaYMV and BaMMV. CONCLUSIONS Our study elucidates transcriptomic adaptations in barley response to BaYMV/BaMMV infection through high-throughput sequencing technique. The analysis outcome from GO and KEGG pathways suggests that BaYMV disease induced regulations in multiple molecular-biology processes and signalling pathways. Moreover, critical DEGs involved in defence and stress tolerance mechanisms were displayed. Further functional investigations focusing on these DEGs contributes to understanding the molecular mechanisms of plant response to BaYMV disease infection, thereby offering precious genetic resources for breeding barley varieties resistant to BaYMV disease.
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Affiliation(s)
- Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuhan Pan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Hui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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2
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Garai T, Garg H. Multi-criteria decision making of COVID-19 vaccines (in India) based on ranking interpreter technique under single valued bipolar neutrosophic environment. EXPERT SYSTEMS WITH APPLICATIONS 2022; 208:118160. [PMID: 35873110 PMCID: PMC9288936 DOI: 10.1016/j.eswa.2022.118160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 06/01/2023]
Abstract
COVID-19 is a respiratory infection caused by a coronavirus that spreads from person to person. In the present situation, the COVID-19 pandemic is a swiftly rising phase. Now the time is the second wave ending phase of coronavirus and the third wave coming phase of coronavirus in India. The pandemic situation is moving forward all over India. Nowadays, the worldwide COVID-19 pandemic structure is a very hazardous situation. The COVID-19 vaccine can suppress this situation and gain preventive measures against coronavirus. In producing the COVID-19 vaccine, the Indian medical board plays a significant role. The COVID-19 vaccines have exhibited 90%-95% efficacy in preventing symptomatic COVID-19 infections. Against COVID-19, for emergency purposes, the Indian medical board has approved three vaccines: Covishield, Covaxin, and Sputnik V. Generally, the Indian people are embarrassed about the vaccination of COVID-19. All people are thinking about which vaccine is best for them. This labyrinth can be evaluated effectively using the multi-criteria decision-making (MCDM) technique. Therefore, we have proposed a novel MCDM technique for selecting COVID-19 vaccines. The main aim of this paper is to develop an MCDM technique based on a λ -weighted ranking interpreter ( R λ + , R λ - ). The first time, we have defined positive and negative λ -weighted rank interpreter for the ranking of single-valued bipolar neutrosophic (SVbN) number. Additionally, positive and negative λ -weighted values and positive and negative λ -weighted ambiguity of an SVbN-number are formulated here. Some important, valuable theorems and corollary of SVbN-number are formulated. To show the applicability of the proposed MCDM technique, we have considered a real decision-making problem where ratings of the alternatives are with SVbN-numbers.
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Affiliation(s)
- Totan Garai
- Department of Mathematics, Syamsundar College, Syamsundar, Purba Bardhaman 713424, West Bengal, India
| | - Harish Garg
- School of Mathematics, Thapar Institute of Engineering and Technology, Deemed University, Patiala 147004, Punjab, India
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3
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Transcriptomic Insight into Viviparous Growth in Water Lily. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8445484. [PMID: 35845943 PMCID: PMC9283058 DOI: 10.1155/2022/8445484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/30/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
Water lily is an important ornamental flower plant which is capable of viviparous plantlet development. But no study has been reported on the molecular basis of viviparity in water lily. Hence, we performed a comparative transcriptome study between viviparous water lily Nymphaea micrantha and a nonviviparous species Nymphaea colorata at four developmental stages. The higher expression of highly conserved AUX/IAA, ARF, GH3, and SAUR gene families in N. micrantha compared to N. colorata is predicted to have a major impact on the development and evolution of viviparity in water lily. Likewise, differential regulation of hormone signaling, brassinosteroid, photosynthesis, and energy-related pathways in the two species provide clues of their involvement in viviparity phenomenon. This study revealed the complex mechanism of viviparity trait in water lily. The transcriptomic signatures identified are important basis for future breeding and research of viviparity in water lily and other plant species.
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4
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Vekety B, Logemann A, Takacs ZK. Mindfulness Practice with a Brain-Sensing Device Improved Cognitive Functioning of Elementary School Children: An Exploratory Pilot Study. Brain Sci 2022; 12:103. [PMID: 35053846 PMCID: PMC8774020 DOI: 10.3390/brainsci12010103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/04/2022] Open
Abstract
This is the first pilot study with children that has assessed the effects of a brain-computer interface-assisted mindfulness program on neural mechanisms and associated cognitive performance. The participants were 31 children aged 9-10 years who were randomly assigned to either an eight-session mindfulness training with EEG-feedback or a passive control group. Mindfulness-related brain activity was measured during the training, while cognitive tests and resting-state brain activity were measured pre- and post-test. The within-group measurement of calm/focused brain states and mind-wandering revealed a significant linear change. Significant positive changes were detected in children's inhibition, information processing, and resting-state brain activity (alpha, theta) compared to the control group. Elevated baseline alpha activity was associated with less reactivity in reaction time on a cognitive test. Our exploratory findings show some preliminary support for a potential executive function-enhancing effect of mindfulness supplemented with EEG-feedback, which may have some important implications for children's self-regulated learning and academic achievement.
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Affiliation(s)
- Boglarka Vekety
- Doctoral School of Education, Faculty of Education and Psychology, ELTE Eötvös Loránd University, 1075 Budapest, Hungary;
- MTA-ELTE Lendület Adaptation Research Group, 1064 Budapest, Hungary
| | - Alexander Logemann
- Institute of Psychology, Faculty of Education and Psychology, ELTE Eötvös Loránd University, 1064 Budapest, Hungary;
| | - Zsofia K. Takacs
- Clinical Psychology, School of Health in Social Science, University of Edinburgh, Edinburgh EH8 9AG, UK
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5
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Xu C, Zhan C, Huang S, Xu Q, Tang T, Wang Y, Luo J, Zeng X. Resistance to Powdery Mildew in Qingke Involves the Accumulation of Aromatic Phenolamides Through Jasmonate-Mediated Activation of Defense-Related Genes. FRONTIERS IN PLANT SCIENCE 2022; 13:900345. [PMID: 35845698 PMCID: PMC9280689 DOI: 10.3389/fpls.2022.900345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/25/2022] [Indexed: 05/08/2023]
Abstract
Powdery mildew (PM) leads to severe yield reduction in qingke (Hordeum vulgare L. var. nudum). Although studies have focused on identifying PM-related resistance genes, mechanistic insights into the metabolic regulation networks of resistance against PM have rarely been explored in qingke. Here, we integrated transcriptomic, proteomic and metabolomic data using PM-susceptible (G72) and PM-resistant (K69) accessions to systemically explore the mechanisms of PM resistance. The integrated results show that a rapidly transduction of jasmonic acid (JA) and (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile), and importantly, a inducing accumulation of aromatic PAs conferred qingke-specific resistance for PM stress. Functional analysis revealed that the four BAHD N-acyltransferase genes were responsible for the synthesis of aliphatic and aromatic PAs. The expression of the four genes are induced by methyl jasmonate (MeJA) and PM treatment. Co-expression network analysis shows that a histone lysine demethylase, JMJ705 gene, also induced by MeJA and PM treatment, had highly correlation with PAs biosynthesis. Chromatin immunoprecipitation (ChIP)-seq assays revealed that the level of trimethylated histone H3 lysine 27 (H3K27me3) of the four genes in MeJA and PM-treated plants was significantly reduced. Overall, our results suggest that a novel strategy for jasmonic acid signal-mediated demethylation controlling the accumulation of aromatic PAs to enhance plant immune resistance through removal of H3K27me3 and activating defense-related gene expression.
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Affiliation(s)
- Congping Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet, China
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chuansong Zhan
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sishu Huang
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Jie Luo,
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet, China
- Plant Sciences College, Tibet Agriculture and Animal Husbandry University, Tibet, China
- Xingquan Zeng,
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6
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Chutia R. Ordering intuitionistic fuzzy numbers by a convex combination of values and multiple of ambiguity inclusion functions with ambiguities of membership and nonmembership functions. INT J INTELL SYST 2021. [DOI: 10.1002/int.22530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Rituparna Chutia
- Department of Mathematics Cotton University Guwahati Assam India
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7
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Diao J, Wang J, Zhang P, Hao X, Wang Y, Liang L, Zhang Y, Ma W, Ma L. Transcriptome Analysis Reveals the Important Role of WRKY28 in Fusarium oxysporum Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:720679. [PMID: 34490017 PMCID: PMC8418079 DOI: 10.3389/fpls.2021.720679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Root rot of Populus davidiana × P. alba var. pyramidalis Louche (Pdpap) is caused by Fusarium oxysporum. We used RNA sequencing to study the molecular mechanisms and response pattern of Pdpap infected by F. oxysporum CFCC86068. We cloned the PdpapWRKY28 transcription factor gene and transformed the recombinant vector pBI121-PdpapWRKY28 into Pdpap. The resistance function of PdpapWRKY28 was verified using physiological and biochemical methods. By means of RNA sequencing, we detected 1,403 differentially expressed genes (DEGs) that are common in the different treatments by F. oxysporum. Furthermore, we found that overexpression of the PdpapWRKY28 gene may significantly improve the resistance of Pdpap plants to F. oxysporum. Our research reveals a key role for PdpapWRKY28 in the resistance response of Pdpap to F. oxysporum. Additionally, our results provide a theoretical basis for in-depth research on resistance breeding to combat root rot.
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Affiliation(s)
- Jian Diao
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Jiaqi Wang
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Ping Zhang
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xin Hao
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Yang Wang
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Liwei Liang
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Yue Zhang
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
| | - Wei Ma
- Medicinal Plant, College of Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ling Ma
- Forest Protection, College of Forestry, Northeast Forestry University, Harbin, China
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8
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Misiak P, Markiewicz KH, Szymczuk D, Wilczewska AZ. Polymeric Drug Delivery Systems Bearing Cholesterol Moieties: A Review. Polymers (Basel) 2020; 12:E2620. [PMID: 33172152 PMCID: PMC7694753 DOI: 10.3390/polym12112620] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
This review aims to provide an overview of polymers comprising cholesterol moiety/ies designed to be used in drug delivery. Over the last two decades, there have been many papers published in this field, which are summarized in this review. The primary focus of this article is on the methods of synthesis of polymers bearing cholesterol in the main chain or as side chains. The data related to the composition, molecular weight, and molecular weight distribution of polymers are presented. Moreover, other aspects, such as forms of carriers, types of encapsulated drugs, encapsulation efficiency and capacity, are also included.
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Affiliation(s)
- Paweł Misiak
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1k, 15-245 Bialystok, Poland; (K.H.M.); (D.S.)
| | | | | | - Agnieszka Z. Wilczewska
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1k, 15-245 Bialystok, Poland; (K.H.M.); (D.S.)
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9
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Jeong JH, Shim KH, Kim DJ, Lee SW. Brain-Controlled Robotic Arm System Based on Multi-Directional CNN-BiLSTM Network Using EEG Signals. IEEE Trans Neural Syst Rehabil Eng 2020; 28:1226-1238. [DOI: 10.1109/tnsre.2020.2981659] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Tarmudi Z, Abd Rahman N. Diverse Ranking Approach in MCDM Based on Trapezoidal Intuitionistic Fuzzy Numbers. PROCEEDINGS OF THE TENTH INTERNATIONAL CONFERENCE ON SOFT COMPUTING AND PATTERN RECOGNITION (SOCPAR 2018) 2020:11-21. [DOI: 10.1007/978-3-030-17065-3_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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11
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Dutta P, Saikia B. Arithmetic operations on normal semi elliptic intuitionistic fuzzy numbers and their application in decision-making. GRANULAR COMPUTING 2019. [DOI: 10.1007/s41066-019-00175-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Suratanee A, Chokrathok C, Chutimanukul P, Khrueasan N, Buaboocha T, Chadchawan S, Plaimas K. Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice. Genes (Basel) 2018; 9:E594. [PMID: 30501128 PMCID: PMC6316690 DOI: 10.3390/genes9120594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/08/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022] Open
Abstract
Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.
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Affiliation(s)
- Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok 10800, Thailand.
| | - Chidchanok Chokrathok
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Panita Chutimanukul
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | | | - Teerapong Buaboocha
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Supachitra Chadchawan
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Kitiporn Plaimas
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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13
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Habachi-Houimli Y, Khalfallah Y, Mezghani-Khemakhem M, Makni H, Makni M, Bouktila D. Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley. 3 Biotech 2018; 8:453. [PMID: 30370194 DOI: 10.1007/s13205-018-1478-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/11/2018] [Indexed: 12/29/2022] Open
Abstract
In this study, a systematic analysis of Nucleotide-Binding Site (NBS) disease resistance (R) gene family in the barley, Hordeum vulgare L. cv. Bowman, genome was performed. Using multiple computational analyses, we could identify 96 regular NBS-encoding genes and characterize them on the bases of structural diversity, conserved protein signatures, genomic distribution, gene duplications, differential expression, selection pressure, codon usage, regulation by microRNAs and phylogenetic relationships. Depending on the presence or absence of CC and LRR domains; the identified NBS genes were assigned to four distinct groups; NBS-LRR (53.1%), CC-NBS-LRR (14.6%), NBS (26%), and CC-NBS (6.3%). NBS-associated domain analysis revealed the presence of signal peptides, zinc fingers, diverse kinases, and other structural features. Eighty-five of the identified NBS-encoding genes were mapped onto the seven barley chromosomes, revealing that 50% of them were located on chromosomes 7H, 2H, and 3H, with a tendency of NBS genes to be clustered in the distal telomeric regions of the barley chromosomes. Nine gene clusters, representing 22.35% of total mapped barley NBS-encoding genes, were found, suggesting that tandem duplication stands for an important mechanism in the expansion of this gene family in barley. Phylogenetic analysis determined 31 HvNBS orthologs from rice and Brachypodium. 87 out of 96 HvNBSs were supported by expression evidence, exhibiting various and quantitatively uneven expression patterns across distinct tissues, organs, and development stages. Fourteen potential miRNA-R gene target pairs were further identified, providing insight into the regulation of NBS genes expression. These findings offer candidate target genes to engineer disease-resistant barley genotypes, and promote our understanding of the evolution of NBS-encoding genes in Poaceae crops.
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Affiliation(s)
- Yosra Habachi-Houimli
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Yosra Khalfallah
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani-Khemakhem
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Hanem Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 2Université de Tunis, Institut Supérieur de l'Animation pour la Jeunesse et la Culture (ISAJC), Bir El Bey, Tunisia
| | - Mohamed Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Dhia Bouktila
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 3Université de Jendouba, Institut Supérieur de Biotechnologie de Béja (ISBB), 9000 Béja, Tunisia
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14
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Nasef SM, M TM, Mahmoud GA. Characterization and in vitro drug release properties of core–shell hydrogel prepared by gamma irradiation. INT J POLYM MATER PO 2017. [DOI: 10.1080/00914037.2017.1362642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shaimaa M. Nasef
- Department of Polymer chemistry, National Center for Radiation Research and Technology, Nasr City, Cairo, Egypt
| | - Tarek M. M
- Department of Polymer chemistry, National Center for Radiation Research and Technology, Nasr City, Cairo, Egypt
| | - Ghada A. Mahmoud
- Department of Polymer chemistry, National Center for Radiation Research and Technology, Nasr City, Cairo, Egypt
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15
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Adnan MN, Islam MZ. Optimizing the number of trees in a decision forest to discover a subforest with high ensemble accuracy using a genetic algorithm. Knowl Based Syst 2016. [DOI: 10.1016/j.knosys.2016.07.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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