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Janíček T, Hobza R, Hudzieczek V. Laser Capture Microdissection: From Genomes to Chromosomes, from Complex Tissue to Single-Cell Analysis. Methods Mol Biol 2023; 2672:163-175. [PMID: 37335475 DOI: 10.1007/978-1-0716-3226-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Laser microdissection (LM) is a powerful tool for various molecular analyses providing pure samples for genomic, transcriptomic, and proteomic studies. Cell subgroups, individual cells, or even chromosomes can be separated via laser beam from complex tissues, visualized under the microscope, and used for subsequent molecular analyses. This technique provides information on nucleic acids and proteins, keeping their spatiotemporal information intact. In short, the slide with tissue is placed under the microscope, imaged by a camera onto a computer screen, where the operator selects cells/chromosomes based on morphology or staining and commands the laser beam to cut the specimen following the selected path. Samples are then collected in a tube and subjected to downstream molecular analysis, such as RT-PCR, next-generation sequencing, or immunoassay.
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Affiliation(s)
- Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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2
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Xiao Y, Guo J, Dong Z, Richardson A, Patterson E, Mangrum S, Bybee S, Bertolini E, Bartlett M, Chuck G, Eveland AL, Scanlon MJ, Whipple C. Boundary domain genes were recruited to suppress bract growth and promote branching in maize. SCIENCE ADVANCES 2022; 8:eabm6835. [PMID: 35704576 PMCID: PMC9200273 DOI: 10.1126/sciadv.abm6835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling and genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and promote branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in nongrasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a nonautonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.
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Affiliation(s)
- Yuguo Xiao
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jinyan Guo
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Zhaobin Dong
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Annis Richardson
- Plant Gene Expression Center, Albany, CA 94710, USA
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland, UK
| | - Erin Patterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sidney Mangrum
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Seth Bybee
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | | | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | | | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Corresponding author.
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3
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Conklin PA, Johnston R, Conlon BR, Shimizu R, Scanlon MJ. Plant homeodomain proteins provide a mechanism for how leaves grow wide. Development 2020; 147:dev.193623. [PMID: 32994171 PMCID: PMC7595687 DOI: 10.1242/dev.193623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/13/2020] [Indexed: 01/24/2023]
Abstract
The mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf primordia, and is required for mediolateral outgrowth. To investigate the mechanisms of NS1 function, we used chromatin immunoprecipitation and laser-microdissection RNA-seq of leaf primordial margins to identify gene targets bound and modulated by NS1. Microscopic analyses of cell division and gene expression in expanding leaves, and reverse genetic analyses of homologous NS1 target genes in Arabidopsis, reveal that NS1 controls mediolateral outgrowth by repression of a growth inhibitor and promotion of cell division at primordial leaf margins. Intriguingly, homologous WOX gene products are expressed in stem cell-organizing centers and traffic to adjoining cells to activate stem-cell identity non-autonomously. In contrast, WOX3/NS1 does not traffic, and stimulates cell divisions in the same cells in which it is transcribed. Highlighted Article: The NS1 homeodomain transcription factor regulates lateral organ outgrowth from shoot meristems and leaf primordial margins by repressing the expression of negative growth regulators.
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Affiliation(s)
- Phillip A Conklin
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robyn Johnston
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,The Elshire Group Limited, Palmerston North 4472, New Zealand
| | - Brianne R Conlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Rena Shimizu
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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4
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Knauer S, Javelle M, Li L, Li X, Ma X, Wimalanathan K, Kumari S, Johnston R, Leiboff S, Meeley R, Schnable PS, Ware D, Lawrence-Dill C, Yu J, Muehlbauer GJ, Scanlon MJ, Timmermans MCP. A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. Genome Res 2019; 29:1962-1973. [PMID: 31744902 PMCID: PMC6886502 DOI: 10.1101/gr.250878.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.
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Affiliation(s)
- Steffen Knauer
- Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Marie Javelle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Xiaoli Ma
- Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Kokulapalan Wimalanathan
- Interdepartmental Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Robyn Johnston
- Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Samuel Leiboff
- Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Robert Meeley
- DuPont Pioneer, Agricultural Biotechnology, Johnston, Iowa 50131, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Carolyn Lawrence-Dill
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA.,Interdepartmental Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Verma S, Gautam V, Sarkar AK. Improved laser capture microdissection (LCM)-based method for isolation of RNA, including miRNA and expression analysis in woody apple bud meristem. PLANTA 2019; 249:2015-2020. [PMID: 30976910 DOI: 10.1007/s00425-019-03127-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
Isolation of high-quality RNA, including miRNA, from microscopic woody apple bud meristem using laser capture microdissection-based method. It is often challenging to study the expression of microRNAs (miRNAs) or genes in less accessible inner tissues of tree species rich in polyphenols or polysaccharides. Here, we report a laser capture microdissection (LCM)-based method for efficient and cost-effective isolation and expression analysis of miRNAs and genes in the meristem tissue of woody apple bud. The tissue fixation, processing, infiltration, and sectioning steps were optimized for LCM-based excision and subsequent RNA isolation. Further, we have confirmed that RNA isolated from LCM-derived apple bud meristem contained miRNAs and was of good quantity and quality, sufficient for downstream expression analysis.
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Affiliation(s)
- Swati Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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6
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Zhao W, Zhou X, Lei H, Fan J, Yang R, Li Z, Hu C, Li M, Zhao F, Wang S. Transcriptional evidence for cross talk between JA and ET or SA during root-knot nematode invasion in tomato. Physiol Genomics 2018; 50:197-207. [PMID: 29341868 DOI: 10.1152/physiolgenomics.00079.2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
studies have demonstrated that jasmonic acid (JA) reduces root-knot nematode (RKN) infections in tomato plants. RKN invasion is sensed by roots, and root-derived JA signaling activates systemic defense responses, though this is poorly understood. Here, we investigate variations in the RKN-induced transcriptome in scion phloem between two tomato plant grafts: CM/CM ( Lycopersicum esculentum Mill. cv. Castlemart) and CM/ spr2 (a JA-deficient mutant). A total of 8,716 genes were differentially expressed in the scion phloem of the plants with JA-deficient rootstock via RNA sequencing. Among these genes, 535 upregulated and 153 downregulated genes with high copy numbers were identified as significantly differentially expressed. Among them, 34 predicted transcription factor genes were identified. Additionally, we used real-time quantitative PCR to analyze the expression patterns of 42 genes involved in the JA, ethylene, or salicylic acid pathway in phloem under RKN infection. The results suggested that in the absence of JA signaling, the ET signaling pathway is enhanced after RKN infection; however, alterations in the SA signaling pathway were not observed.
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Affiliation(s)
- Wenchao Zhao
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Xiaoxuan Zhou
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Hui Lei
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jingwei Fan
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Rui Yang
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Zilong Li
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Canli Hu
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Mengyan Li
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Fukuan Zhao
- College of Biotechnology, Beijing University of Agriculture, Beijing, China
| | - Shaohui Wang
- Beijing Key Laboratory for Agricultural Applications and New Techniques, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
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7
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Gautam V, Singh A, Singh S, Sarkar AK. An Efficient LCM-Based Method for Tissue Specific Expression Analysis of Genes and miRNAs. Sci Rep 2016; 6:21577. [PMID: 26861910 PMCID: PMC4748277 DOI: 10.1038/srep21577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/26/2016] [Indexed: 12/26/2022] Open
Abstract
Laser Capture Microdissection (LCM) is a powerful tool to isolate and study gene expression pattern of desired and less accessible cells or tissues from a heterogeneous population. Existing LCM-based methods fail to obtain high quality RNA including small RNAs from small microdissected plant tissue and therefore, are not suitable for miRNA expression studies. Here, we describe an efficient and cost-effective method to obtain both high quality RNA and miRNAs from LCM-derived embryonic root apical meristematic tissue, which is difficult to access. We have significantly modified and improved the tissue fixation, processing, sectioning and RNA isolation steps and minimized the use of kits. Isolated RNA was checked for quality with bioanalyzer and used for gene expression studies. We have confirmed the presence of 19-24 nucleotide long mature miRNAs using modified stem-loop RT-PCR. This modified LCM-based method is suitable for tissue specific expression analysis of both genes and small RNAs (miRNAs).
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Affiliation(s)
- Vibhav Gautam
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Archita Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sharmila Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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8
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Single prokaryotic cell isolation and total transcript amplification protocol for transcriptomic analysis. Nat Protoc 2015; 10:974-84. [PMID: 26042386 DOI: 10.1038/nprot.2015.058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Until recently, transcriptome analyses of single cells have been confined to eukaryotes. The information obtained from single-cell transcripts can provide detailed insight into spatiotemporal gene expression, and it could be even more valuable if expanded to prokaryotic cells. Transcriptome analysis of single prokaryotic cells is a recently developed and powerful tool. Here we describe a procedure that allows amplification of the total transcript of a single prokaryotic cell for in-depth analysis. This is performed by using a laser-capture microdissection instrument for single-cell isolation, followed by reverse transcription via Moloney murine leukemia virus, degradation of chromosomal DNA with McrBC and DpnI restriction enzymes, single-stranded cDNA (ss-cDNA) ligation using T4 polynucleotide kinase and CircLigase, and polymerization of ss-cDNA to double-stranded cDNA (ds-cDNA) by Φ29 polymerase. This procedure takes ∼5 d, and sufficient amounts of ds-cDNA can be obtained from single-cell RNA template for further microarray analysis.
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9
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Laser Assisted Microdissection, an Efficient Technique to Understand Tissue Specific Gene Expression Patterns and Functional Genomics in Plants. Mol Biotechnol 2014; 57:299-308. [DOI: 10.1007/s12033-014-9824-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Frank MH, Scanlon MJ. Transcriptomic evidence for the evolution of shoot meristem function in sporophyte-dominant land plants through concerted selection of ancestral gametophytic and sporophytic genetic programs. Mol Biol Evol 2014; 32:355-67. [PMID: 25371433 DOI: 10.1093/molbev/msu303] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Alternation of generations, in which the haploid and diploid stages of the life cycle are each represented by multicellular forms that differ in their morphology, is a defining feature of the land plants (embryophytes). Anciently derived lineages of embryophytes grow predominately in the haploid gametophytic generation from apical cells that give rise to the photosynthetic body of the plant. More recently evolved plant lineages have multicellular shoot apical meristems (SAMs), and photosynthetic shoot development is restricted to the sporophyte generation. The molecular genetic basis for this evolutionary shift from gametophyte-dominant to sporophyte-dominant life cycles remains a major question in the study of land plant evolution. We used laser microdissection and next generation RNA sequencing to address whether angiosperm meristem patterning genes expressed in the sporophytic SAM of Zea mays are expressed in the gametophytic apical cells, or in the determinate sporophytes, of the model bryophytes Marchantia polymorpha and Physcomitrella patens. A wealth of upregulated genes involved in stem cell maintenance and organogenesis are identified in the maize SAM and in both the gametophytic apical cell and sporophyte of moss, but not in Marchantia. Significantly, meiosis-specific genetic programs are expressed in bryophyte sporophytes, long before the onset of sporogenesis. Our data suggest that this upregulated accumulation of meiotic gene transcripts suppresses indeterminate cell fate in the Physcomitrella sporophyte, and overrides the observed accumulation of meristem patterning genes. A model for the evolution of indeterminate growth in the sporophytic generation through the concerted selection of ancestral meristem gene programs from gametophyte-dominant lineages is proposed.
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11
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Artico S, Ribeiro-Alves M, Oliveira-Neto OB, de Macedo LLP, Silveira S, Grossi-de-Sa MF, Martinelli AP, Alves-Ferreira M. Transcriptome analysis of Gossypium hirsutum flower buds infested by cotton boll weevil (Anthonomus grandis) larvae. BMC Genomics 2014; 15:854. [PMID: 25280771 PMCID: PMC4234063 DOI: 10.1186/1471-2164-15-854] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/25/2014] [Indexed: 11/25/2022] Open
Abstract
Background Cotton is a major fibre crop grown worldwide that suffers extensive damage from chewing insects, including the cotton boll weevil larvae (Anthonomus grandis). Transcriptome analysis was performed to understand the molecular interactions between Gossypium hirsutum L. and cotton boll weevil larvae. The Illumina HiSeq 2000 platform was used to sequence the transcriptome of cotton flower buds infested with boll weevil larvae. Results The analysis generated a total of 327,489,418 sequence reads that were aligned to the G. hirsutum reference transcriptome. The total number of expressed genes was over 21,697 per sample with an average length of 1,063 bp. The DEGseq analysis identified 443 differentially expressed genes (DEG) in cotton flower buds infected with boll weevil larvae. Among them, 402 (90.7%) were up-regulated, 41 (9.3%) were down-regulated and 432 (97.5%) were identified as orthologues of A. thaliana genes using Blastx. Mapman analysis of DEG indicated that many genes were involved in the biotic stress response spanning a range of functions, from a gene encoding a receptor-like kinase to genes involved in triggering defensive responses such as MAPK, transcription factors (WRKY and ERF) and signalling by ethylene (ET) and jasmonic acid (JA) hormones. Furthermore, the spatial expression pattern of 32 of the genes responsive to boll weevil larvae feeding was determined by “in situ” qPCR analysis from RNA isolated from two flower structures, the stamen and the carpel, by laser microdissection (LMD). Conclusion A large number of cotton transcripts were significantly altered upon infestation by larvae. Among the changes in gene expression, we highlighted the transcription of receptors/sensors that recognise chitin or insect oral secretions; the altered regulation of transcripts encoding enzymes related to kinase cascades, transcription factors, Ca2+ influxes, and reactive oxygen species; and the modulation of transcripts encoding enzymes from phytohormone signalling pathways. These data will aid in the selection of target genes to genetically engineer cotton to control the cotton boll weevil. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-854) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Marcio Alves-Ferreira
- Department of Genetics, Universidade Federal do Rio de Janeiro - UFRJ Av, Prof, Rodolpho Paulo Rocco, s/n - Prédio do CCS Instituto de Biologia, 2° andar - sala 93, 219410-970 Rio de Janeiro, RJ, Brazil.
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12
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Abstract
Cellular context can be crucial when studying developmental processes as well as responses to environmental variation. Several different tools have been developed in recent years to isolate specific tissues or cell types. Laser-assisted microdissection (LAM) allows for the isolation of such specific tissue or single cell-types purely based on morphology and cytology. This has the advantage that (1) cell types that are rare can be isolated from heterogeneous tissue, (2) no marker line with cell type-specific expression needs to be established, and (3) the method can be applied to non-model species and species that are difficult to genetically transform. The rapid development of next-generation sequencing (NGS) approaches has greatly advanced the possibilities to perform molecular analyses in diverse organisms. However, there is a mismatch between currently available cell isolation tools and their applicability to non-model organisms. Therefore, LAM will become increasingly popular in the study of diverse agriculturally or ecologically relevant plant species. Here, we describe a protocol that has been successfully used for LAM to isolate either whole floral organs or even single cell types in plants, e.g., Arabidopsis thaliana, Boechera spp., or tomato.
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Affiliation(s)
- Samuel E Wuest
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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13
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Ma Z, Liu Q, Yang H, Runyan RB, Eisenberg CA, Xu M, Borg TK, Markwald R, Wang Y, Gao BZ. Laser patterning for the study of MSC cardiogenic differentiation at the single-cell level. LIGHT, SCIENCE & APPLICATIONS 2013; 2:68. [PMID: 24527266 PMCID: PMC3920285 DOI: 10.1038/lsa.2013.24] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 06/03/2023]
Abstract
Mesenchymal stem cells (MSCs) have been cited as contributors to heart repair through cardiogenic differentiation and multiple cellular interactions, including the paracrine effect, cell fusion, and mechanical and electrical couplings. Due to heart-muscle complexity, progress in the development of knowledge concerning the role of MSCs in cardiac repair is heavily based on MSC-cardiomyocyte coculture. In conventional coculture systems, however, the in vivo cardiac muscle structure, in which rod-shaped cells are connected end-to-end, is not sustained; instead, irregularly shaped cells spread randomly, resulting in randomly distributed cell junctions. Consequently, contact-mediated cell-cell interactions (e.g., the electrical triggering signal and the mechanical contraction wave that propagate through MSC-cardiomyocyte junctions) occur randomly. Thus, the data generated on the beneficial effects of MSCs may be irrelevant to in vivo biological processes. In this study, we explored whether cardiomyocyte alignment, the most important phenotype, is relevant to stem cell cardiogenic differentiation. Here, we report (i) the construction of a laser-patterned, biochip-based, stem cell-cardiomyocyte coculture model with controlled cell alignment; and (ii) single-cell-level data on stem cell cardiogenic differentiation under in vivo-like cardiomyocyte alignment conditions.
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Affiliation(s)
- Zhen Ma
- Department of Bioengineering and COMSET, Clemson University, Clemson, SC 29634, USA ; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiuying Liu
- Biomedical R&D Center, Jinan University, Guangzhou, China
| | - Huaxiao Yang
- Department of Bioengineering and COMSET, Clemson University, Clemson, SC 29634, USA
| | - Raymond B Runyan
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Carol A Eisenberg
- New York Medical College/Westchester Medical Center Stem Cell Laboratory, New York Medical College, Valhalla, New York, USA
| | - Meifeng Xu
- Department of Pathology and Laboratory Medicine, University of Cincinnati Medical Center, Cincinnati, OH, USA
| | - Thomas K Borg
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Roger Markwald
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Yifei Wang
- Biomedical R&D Center, Jinan University, Guangzhou, China
| | - Bruce Z Gao
- Department of Bioengineering and COMSET, Clemson University, Clemson, SC 29634, USA
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14
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Kang Y, Norris MH, Zarzycki-Siek J, Nierman WC, Donachie SP, Hoang TT. Transcript amplification from single bacterium for transcriptome analysis. Genome Res 2011; 21:925-35. [PMID: 21536723 PMCID: PMC3106325 DOI: 10.1101/gr.116103.110] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 03/10/2011] [Indexed: 11/24/2022]
Abstract
Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material, the lack of poly(A)-tails, and the fact that the messages can be polycistronic. Here, we describe a novel method for single-bacterium TTA using a model organism, Burkholderia thailandensis, exposed to a subinhibitory concentration of the antibacterial agent, glyphosate. Utilizing a B. thailandensis microarray to assess the TTA method showed low fold-change bias (less than twofold difference and Pearson correlation coefficient R ≈ 0.87-0.89) and drop-outs (4%-6% of 2842 detectable genes), compared with data obtained from the larger-scale nonamplified RNA samples. Further analysis of the microarray data suggests that B. thailandensis, when exposed to the aromatic amino acid biosynthesis inhibitor glyphosate, induces (or represses) genes to possibly recuperate and balance the intracellular amino acid pool. We validated our single-cell microarray data at the multi-cell and single-cell levels with lacZ and gfp reporter-gene fusions, respectively. Sanger sequencing of 192 clones generated from the TTA product of a single cell, with and without enrichment by elimination of rRNA and tRNA, detected only B. thailandensis sequences with no contamination. These data indicate that RNA-seq of TTA from a single cell is possible using this novel method.
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Affiliation(s)
- Yun Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Michael H. Norris
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Jan Zarzycki-Siek
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | | | - Stuart P. Donachie
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
| | - Tung T. Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
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