1
|
Anjam MS, Siddique S, Marhavy P. RNA Isolation from Nematode-Induced Feeding Sites in Arabidopsis Roots Using Laser Capture Microdissection. Methods Mol Biol 2022; 2494:313-324. [PMID: 35467217 DOI: 10.1007/978-1-0716-2297-1_22] [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] [Indexed: 06/14/2023]
Abstract
Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1-J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host's roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.
Collapse
Affiliation(s)
- Muhammad Shahzad Anjam
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
- Institute of Molecular Biology and Biotechnology (IMBB), Bahauddin Zakariya University, Multan, Pakistan
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - Peter Marhavy
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
| |
Collapse
|
2
|
Anjam MS, Shah SJ, Matera C, Różańska E, Sobczak M, Siddique S, Grundler FMW. Host factors influence the sex of nematodes parasitizing roots of Arabidopsis thaliana. Plant Cell Environ 2020; 43:1160-1174. [PMID: 32103526 DOI: 10.1111/pce.13728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/02/2018] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 05/23/2023]
Abstract
Plant-parasitic cyst nematodes induce hypermetabolic syncytial nurse cells in the roots of their host plants. Syncytia are their only food source. Cyst nematodes are sexually dimorphic, with their differentiation into male or female strongly influenced by host environmental conditions. Under favourable conditions with plenty of nutrients, more females develop, whereas mainly male nematodes develop under adverse conditions such as in resistant plants. Here, we developed and validated a method to predict the sex of beet cyst nematode (Heterodera schachtii) during the early stages of its parasitism in the host plant Arabidopsis thaliana. We collected root segments containing male-associated syncytia (MAS) or female-associated syncytia (FAS), isolated syncytial cells by laser microdissection, and performed a comparative transcriptome analysis. Genes belonging to categories of defence, nutrient deficiency, and nutrient starvation were over-represented in MAS as compared with FAS. Conversely, gene categories related to metabolism, modification, and biosynthesis of cell walls were over-represented in FAS. We used β-glucuronidase analysis, qRT-PCR, and loss-of-function mutants to characterize FAS- and MAS-specific candidate genes. Our results demonstrate that various plant-based factors, including immune response, nutrient availability, and structural modifications, influence the sexual fate of the cyst nematodes.
Collapse
Affiliation(s)
- Muhammad Shahzad Anjam
- Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, INRES, Bonn, Germany
| | - Syed Jehangir Shah
- Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, INRES, Bonn, Germany
| | - Christiane Matera
- Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, INRES, Bonn, Germany
| | - Elżbieta Różańska
- Department of Botany, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Miroslaw Sobczak
- Department of Botany, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Shahid Siddique
- Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, INRES, Bonn, Germany
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - Florian M W Grundler
- Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, INRES, Bonn, Germany
| |
Collapse
|
3
|
Mehmood A, Baneen U, Zaheer A, Wasim Sajid M, Hussain A, Saleem S, Yousafi Q, Rashid H, Riaz H, Ihsan A, Jamil F, Sajjad Y, Zahid N, Shahzad Anjam M, Arshad M, Mirza Z, Karim S, Rasool M. Physical and chemical mutagens improved Sporotrichum thermophile, strain ST20 for enhanced Phytase activity. Saudi J Biol Sci 2019; 26:1485-1491. [PMID: 31762614 PMCID: PMC6864213 DOI: 10.1016/j.sjbs.2019.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 11/15/2022] Open
Abstract
Objective Phosphorous is an essential micronutrient of plants and involved in critical biological functions. In nature, phosphorous is mostly present in immobilized inorganic mineral and in the fixed organic form including phytic acid and phosphoesteric compounds. However, the bioavailability of bound phosphorous could be enhanced by the use of phosphate solubilizing microorganisms such as bacteria and fungi. The phytases are widespread in an environment and have been isolated from different sources comprising bacteria and fungi. Methodology In current studies, we show the successful use of gamma rays and EMS (Ethyl Methane Sulphonate) mutagenesis for enhanced activity of phytases in a fungal strain Sporotrichum thermophile. Results We report an improved strain ST2 that could produce a clear halo zone around the colony, up to 24 mm. The maximum enzymatic activity was found of 382 U/mL on pH 5.5. However, the phytase activity was improved to 387 U/ml at 45 °C. We also report that the mutants produced through EMS showed the greater potential for phytase production. Conclusion The current study highlights the potential of EMS mutagenesis for strain improvement over physical mutagens.
Collapse
Affiliation(s)
- Asim Mehmood
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Umal Baneen
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defence Road, Lahore, Pakistan
- Corresponding author.
| | | | - Abrar Hussain
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Shahzad Saleem
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Hamid Rashid
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Hassan Riaz
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Farrukh Jamil
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Yasar Sajjad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Nageena Zahid
- Institute of Molecular Biology and Biotechnology (IMBB), Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Shahzad Anjam
- Institute of Molecular Biology and Biotechnology (IMBB), Bahauddin Zakariya University, Multan, Pakistan
| | | | - Zeenat Mirza
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
4
|
Ali MA, Anjam MS, Nawaz MA, Lam HM, Chung G. Signal Transduction in Plant⁻Nematode Interactions. Int J Mol Sci 2018; 19:ijms19061648. [PMID: 29865232 PMCID: PMC6032140 DOI: 10.3390/ijms19061648] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022] Open
Abstract
To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.
Collapse
Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan.
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Muhammad Shahzad Anjam
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan 66000, Pakistan.
| | | | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
| |
Collapse
|
5
|
Anwer MA, Anjam MS, Shah SJ, Hasan MS, Naz AA, Grundler FMW, Siddique S. Genome-wide association study uncovers a novel QTL allele of AtS40-3 that affects the sex ratio of cyst nematodes in Arabidopsis. J Exp Bot 2018; 69:1805-1814. [PMID: 29378065 PMCID: PMC5889006 DOI: 10.1093/jxb/ery019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant-parasitic cyst nematodes are obligate sedentary parasites that infect the roots of a broad range of host plants. Cyst nematodes are sexually dimorphic, but differentiation into male or female is strongly influenced by interactions with the host environment. Female populations typically predominate under favorable conditions, whereas male populations predominate under adverse conditions. Here, we performed a genome-wide association study (GWAS) in an Arabidopsis diversity panel to identify host loci underlying variation in susceptibility to cyst nematode infection. Three different susceptibility parameters were examined, with the aim of providing insights into the infection process, the number of females and males present in the infected plant, and the female-to-male sex ratio. GWAS results suggested that variation in sex ratio is associated with a novel quantitative trait locus allele on chromosome 4. Subsequent candidate genes and functional analyses revealed that a senescence-associated transcription factor, AtS40-3, and PPR may act in combination to influence nematode sex ratio. A detailed molecular characterization revealed that variation in nematode sex ratio was due to the disturbed common promoter of AtS40-3 and PPR genes. Additionally, single nucleotide polymorphisms in the coding sequence of AtS40-3 might contribute to the natural variation in nematode sex ratio.
Collapse
Affiliation(s)
- Muhammad Arslan Anwer
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Karlrobert-Kreiten-Straße, Bonn, Germany
| | - Muhammad Shahzad Anjam
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Karlrobert-Kreiten-Straße, Bonn, Germany
- Institute of Molecular Biology and Biotechnology (IMBB), Bahauddin Zakariya University, Multan, Pakistan
| | - Syed Jehangir Shah
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Karlrobert-Kreiten-Straße, Bonn, Germany
| | - M Shamim Hasan
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Karlrobert-Kreiten-Straße, Bonn, Germany
| | - Ali A Naz
- Plant Breeding, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Florian M W Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Karlrobert-Kreiten-Straße, Bonn, Germany
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Karlrobert-Kreiten-Straße, Bonn, Germany
- Correspondence:
| |
Collapse
|
6
|
Radakovic ZS, Anjam MS, Escobar E, Chopra D, Cabrera J, Silva AC, Escobar C, Sobczak M, Grundler FMW, Siddique S. Arabidopsis HIPP27 is a host susceptibility gene for the beet cyst nematode Heterodera schachtii. Mol Plant Pathol 2018; 19:1917-1928. [PMID: 29470862 PMCID: PMC6638061 DOI: 10.1111/mpp.12668] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 05/23/2023]
Abstract
Sedentary plant-parasitic cyst nematodes are obligate biotrophs that infect the roots of their host plant. Their parasitism is based on the modification of root cells to form a hypermetabolic syncytium from which the nematodes draw their nutrients. The aim of this study was to identify nematode susceptibility genes in Arabidopsis thaliana and to characterize their roles in supporting the parasitism of Heterodera schachtii. By selecting genes that were most strongly upregulated in response to cyst nematode infection, we identified HIPP27 (HEAVY METAL-ASSOCIATED ISOPRENYLATED PLANT PROTEIN 27) as a host susceptibility factor required for beet cyst nematode infection and development. Detailed expression analysis revealed that HIPP27 is a cytoplasmic protein and that HIPP27 is strongly expressed in leaves, young roots and nematode-induced syncytia. Loss-of-function Arabidopsis hipp27 mutants exhibited severely reduced susceptibility to H. schachtii and abnormal starch accumulation in syncytial and peridermal plastids. Our results suggest that HIPP27 is a susceptibility gene in Arabidopsis whose loss of function reduces plant susceptibility to cyst nematode infection without increasing the susceptibility to other pathogens or negatively affecting the plant phenotype.
Collapse
Affiliation(s)
- Zoran S. Radakovic
- INRES–Molecular PhytomedicineRheinische‐Friedrich‐Wilhelms‐University of BonnD‐53115 BonnGermany
| | - Muhammad Shahzad Anjam
- INRES–Molecular PhytomedicineRheinische‐Friedrich‐Wilhelms‐University of BonnD‐53115 BonnGermany
| | - Elizabeth Escobar
- INRES–Molecular PhytomedicineRheinische‐Friedrich‐Wilhelms‐University of BonnD‐53115 BonnGermany
| | - Divykriti Chopra
- INRES–Molecular PhytomedicineRheinische‐Friedrich‐Wilhelms‐University of BonnD‐53115 BonnGermany
| | - Javier Cabrera
- Facultad de Ciencias Ambientales y BioquímicaUniversidad de Castilla‐La Mancha, Área de Fisiología VegetalAvda, Carlos III, s/n, 45071 ToledoSpain
| | - Ana Cláudia Silva
- Facultad de Ciencias Ambientales y BioquímicaUniversidad de Castilla‐La Mancha, Área de Fisiología VegetalAvda, Carlos III, s/n, 45071 ToledoSpain
| | - Carolina Escobar
- Facultad de Ciencias Ambientales y BioquímicaUniversidad de Castilla‐La Mancha, Área de Fisiología VegetalAvda, Carlos III, s/n, 45071 ToledoSpain
| | - Miroslaw Sobczak
- Department of BotanyWarsaw University of Life SciencesPL‐02787 WarsawPoland
| | - Florian M. W. Grundler
- INRES–Molecular PhytomedicineRheinische‐Friedrich‐Wilhelms‐University of BonnD‐53115 BonnGermany
| | - Shahid Siddique
- INRES–Molecular PhytomedicineRheinische‐Friedrich‐Wilhelms‐University of BonnD‐53115 BonnGermany
| |
Collapse
|
7
|
Shah SJ, Anjam MS, Mendy B, Anwer MA, Habash SS, Lozano-Torres JL, Grundler FMW, Siddique S. Damage-associated responses of the host contribute to defence against cyst nematodes but not root-knot nematodes. J Exp Bot 2017; 68:5949-5960. [PMID: 29053864 PMCID: PMC5854129 DOI: 10.1093/jxb/erx374] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 08/30/2017] [Accepted: 10/05/2017] [Indexed: 05/21/2023]
Abstract
When nematodes invade and subsequently migrate within plant roots, they generate cell wall fragments (in the form of oligogalacturonides; OGs) that can act as damage-associated molecular patterns and activate host defence responses. However, the molecular mechanisms mediating damage responses in plant-nematode interactions remain unexplored. Here, we characterized the role of a group of cell wall receptor proteins in Arabidopsis, designated as polygalacturonase-inhibiting proteins (PGIPs), during infection with the cyst nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita. PGIPs are encoded by a family of two genes in Arabidopsis, and are involved in the formation of active OG elicitors. Our results show that PGIP gene expression is strongly induced in response to cyst nematode invasion of roots. Analyses of loss-of-function mutants and overexpression lines revealed that PGIP1 expression attenuates infection of host roots by cyst nematodes, but not root-knot nematodes. The PGIP1-mediated attenuation of cyst nematode infection involves the activation of plant camalexin and indole-glucosinolate pathways. These combined results provide new insights into the molecular mechanisms underlying plant damage perception and response pathways during infection by cyst and root-knot nematodes, and establishes the function of PGIP in plant resistance to cyst nematodes.
Collapse
Affiliation(s)
- Syed Jehangir Shah
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
| | - Muhammad Shahzad Anjam
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
| | - Badou Mendy
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
| | - Muhammad Arslan Anwer
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
| | - Samer S Habash
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
| | | | - Florian M W Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES – Molecular Phytomedicine, Germany
- Correspondence:
| |
Collapse
|
8
|
Anjam MS, Ludwig Y, Hochholdinger F, Miyaura C, Inada M, Siddique S, Grundler FMW. An improved procedure for isolation of high-quality RNA from nematode-infected Arabidopsis roots through laser capture microdissection. Plant Methods 2016; 12:25. [PMID: 27123040 PMCID: PMC4847226 DOI: 10.1186/s13007-016-0123-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/19/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses. However, the inclusion of neighbouring cells dilutes the syncytium-specific mRNA population. Micro-sectioning coupled with laser capture microdissection (LCM) offers an opportunity for the isolation of feeding sites from heterogeneous cell populations. But recovery of intact RNA from syncytium dissected by LCM is complicated due to extended steps of fixation, tissue preparation, embedding and sectioning. RESULTS In the present study, we have optimized the procedure of sample preparation for LCM to isolate high quality of RNA from cyst nematode induced syncytia in Arabidopsis roots which can be used for transcriptomic studies. We investigated the effect of various sucrose concentrations as cryoprotectant on RNA quality and morphology of syncytial sections. We also compared various types of microscopic slides for strong adherence of sections while removing embedding material. CONCLUSION The use of optimal sucrose concentrations as cryoprotection plays a key role in RNA stability and morphology of sections. Treatment with higher sucrose concentrations minimizes the risk of RNA degradation, whereas longer incubation times help maintaining the morphology of tissue sections. Our method allows isolating high-quality RNA from nematode feeding sites that is suitable for downstream applications such as microarray experiments.
Collapse
Affiliation(s)
- Muhammad Shahzad Anjam
- />INRES - Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
- />Institute of Molecular Biology and Bio-technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Yvonne Ludwig
- />INRES - Crop Functional Genomics, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Frank Hochholdinger
- />INRES - Crop Functional Genomics, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Chisato Miyaura
- />Department of Biotechnology and Life Science, and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588 Japan
| | - Masaki Inada
- />Department of Biotechnology and Life Science, and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588 Japan
| | - Shahid Siddique
- />INRES - Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
| | - Florian M. W. Grundler
- />INRES - Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
| |
Collapse
|
9
|
Shaikh RS, Amir M, Masood AI, Sohail A, Athar HUR, Siraj S, Ali M, Anjam MS. Frequency distribution of GSTM1 and GSTT1 null allele in Pakistani population and risk of disease incidence. Environ Toxicol Pharmacol 2010; 30:76-79. [PMID: 21787632 DOI: 10.1016/j.etap.2010.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/17/2010] [Accepted: 04/19/2010] [Indexed: 05/31/2023]
Abstract
Glutathione-S-transferases, GSTM1 and GSTT1 play a significant role in detoxification and bioactivation of a broad range of xenobiotic compounds known to be mutagenic and/or carcinogenic. Deletion polymorphisms of these glutathione transferases (GSTM1 and GSTT1) predispose individuals to environmental carcinogenic compounds. Although a number of studies have shown the relationship between GSTM1 and/or GSTT1 deletion polymorphism and different cancers, these findings cannot be extrapolated to other populations due to intra- and inter-ethnic variability. In order to assess the impact of differential ethnicity on the occurrence of different cancers in local population due to GSTM1, or GSTT1 deletion polymorphism, 111 healthy male and female individuals of different age groups from Southern Punjab, Pakistan were genotyped using a multiplex polymerase chain reaction. From the results it is obvious that null alleles of GSTM1 and GSTT1 genes were found in 45% and 23% individuals, respectively. In 5% of individuals' simultaneous deletion of both GSTM1 and GSTT1 genes were observed. Frequency of GSTM1 null allele is in concordance with those documented for Chinese, Caucasians, Mongolian, and Japanese populations. However, a significantly higher frequency for GSTT1 null was reported in Chinese and Japanese population as compared to Pakistani population. It is the first ever report on frequency of GSTM1 and GSTT1 null allele in Pakistani population which demonstrate the impact of ethnicity and provide basis for future epidemiological and clinical studies.
Collapse
Affiliation(s)
- Rehan Sadiq Shaikh
- Institute of Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | | | | | | | | | | | | | | |
Collapse
|