1
|
Ghanem N, Nasr NH, Elnaga NAA, Abou-Hashim F, Kamel S, Warda M, Dessouki SM, AbdRabou MA, Mehsien GK. Molecular and physiochemical evaluation of buck semen cryopreserved with antioxidants. Reprod Domest Anim 2023. [PMID: 37013810 DOI: 10.1111/rda.14354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/04/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
The current study evaluated the physiochemical quality and gene expression profile of post-thawed buck semen after supplementation with antioxidants [melatonin (M), L-carnitine (LC), cysteine (Cys), LC+M, M+Cys, LC+Cys, LC+Cys+M] in comparison with the non-treated control group. Physical as well as biochemical characteristics of semen were evaluated following freezing and thawing. Transcript abundance of six selected candidate gens was profile using quantitative real-time PCR. The data demonstrated significant enhancement of post-freezing total motility, progressive motility, percentage of live sperm, CASA parameters, plasma membrane and acrosome integrity in all groups supplemented with Cys, LC, M+Cys, and LC+Cys compared with the control group. The biochemical analysis of semen indicated that semen groups supplemented with LC and LC+Cys, recorded increased levels of GPX and SOD that were coupled with up-regulation of antioxidant genes (SOD1, GPX1, and NRF2) and mitochondrial transcripts (CPT2 and ATP5F1A). Moreover, H2O2 level and DNA fragmentation percentage were reduced compared to other groups. In conclusion, supplementation of Cys alone or in combination with LC positively improved the post-thaw physiochemical properties of rabbit semen through activation of bioenergetics-related mitochondrial genes and cellular antioxidant defense mechanism.
Collapse
Affiliation(s)
- Nasser Ghanem
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
- Cairo University, Research Park, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Norhan Hamdy Nasr
- Embryology Department, Faculty of Science, El- Azhar University, Egypt
| | | | - Fatma Abou-Hashim
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Shaimaa Kamel
- Department of Biochemistry and Molecular biology, Faculty of Veterinary Medicine, Cairo University, 12211, Giza, Egypt
| | - Mohamad Warda
- Department of Biochemistry and Molecular biology, Faculty of Veterinary Medicine, Cairo University, 12211, Giza, Egypt
| | - Sherif M Dessouki
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mervat Ahmed AbdRabou
- Biology Department, College of Science, Jouf University, P.O. Box: 2014, Sakaka, Saudi Arabia
| | - Gamal Kamel Mehsien
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| |
Collapse
|
2
|
Huang D, Liu AYN, Leung KS, Tang NLS. Direct Measurement of B Lymphocyte Gene Expression Biomarkers in Peripheral Blood Transcriptomics Enables Early Prediction of Vaccine Seroconversion. Genes (Basel) 2021; 12:genes12070971. [PMID: 34202032 PMCID: PMC8304400 DOI: 10.3390/genes12070971] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
Peripheral blood transcriptome is a highly promising area for biomarker development. However, transcript abundances (TA) in these cell mixture samples are confounded by proportions of the component leukocyte subpopulations. This poses a challenge to clinical applications, as the cell of origin of any change in TA is not known without prior cell separation procedure. We developed a framework to develop a cell-type informative TA biomarkers which enable determination of TA of a single cell-type (B lymphocytes) directly in cell mixture samples of peripheral blood (e.g., peripheral blood mononuclear cells, PBMC) without the need for subpopulation separation. It is applicable to a panel of genes called B cell informative genes. Then a ratio of two B cell informative genes (a target gene and a stably expressed reference gene) obtained in PBMC was used as a new biomarker to represent the target gene expression in purified B lymphocytes. This approach, which eliminates the tedious procedure of cell separation and directly determines TA of a leukocyte subpopulation in peripheral blood samples, is called the Direct LS-TA method. This method is applied to gene expression datasets collected in influenza vaccination trials as early predictive biomarkers of seroconversion. By using TNFRSF17 or TXNDC5 as the target genes and TNFRSF13C or FCRLA as the reference genes, the Direct LS-TA B cell biomarkers were determined directly in the PBMC transcriptome data and were highly correlated with TA of the corresponding target genes in purified B lymphocytes. Vaccination responders had almost a 2-fold higher Direct LS-TA biomarker level of TNFRSF17 (log 2 SMD = 0.84, 95% CI = 0.47–1.21) on day 7 after vaccination. The sensitivity of these Direct LS-TA biomarkers in the prediction of seroconversion was greater than 0.7 and area-under curves (AUC) were over 0.8 in many datasets. In this paper, we report a straightforward approach to directly estimate B lymphocyte gene expression in PBMC, which could be used in a routine clinical setting. Moreover, the method enables the practice of precision medicine in the prediction of vaccination response. More importantly, seroconversion could now be predicted as early as day 7. As the acquired immunology pathway is common to vaccination against influenza and COVID-19, these biomarkers could also be useful to predict seroconversion for the new COVID-19 vaccines.
Collapse
Affiliation(s)
- Dan Huang
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
| | - Alex Y. N. Liu
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
| | - Kwong-Sak Leung
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Nelson L. S. Tang
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
- Department of Chemical Pathology and Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence:
| |
Collapse
|
3
|
Hallikas O, Das Roy R, Christensen MM, Renvoisé E, Sulic AM, Jernvall J. System-level analyses of keystone genes required for mammalian tooth development. J Exp Zool B Mol Dev Evol 2020; 336:7-17. [PMID: 33128445 PMCID: PMC7894285 DOI: 10.1002/jez.b.23009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022]
Abstract
When a null mutation of a gene causes a complete developmental arrest, the gene is typically considered essential for life. Yet, in most cases, null mutations have more subtle effects on the phenotype. Here we used the phenotypic severity of mutations as a tool to examine system‐level dynamics of gene expression. We classify genes required for the normal development of the mouse molar into different categories that range from essential to subtle modification of the phenotype. Collectively, we call these the developmental keystone genes. Transcriptome profiling using microarray and RNAseq analyses of patterning stage mouse molars show highly elevated expression levels for genes essential for the progression of tooth development, a result reminiscent of essential genes in single‐cell organisms. Elevated expression levels of progression genes were also detected in developing rat molars, suggesting evolutionary conservation of this system‐level dynamics. Single‐cell RNAseq analyses of developing mouse molars reveal that even though the size of the expression domain, measured in the number of cells, is the main driver of organ‐level expression, progression genes show high cell‐level transcript abundances. Progression genes are also upregulated within their pathways, which themselves are highly expressed. In contrast, a high proportion of the genes required for normal tooth patterning are secreted ligands that are expressed in fewer cells than their receptors and intracellular components. Overall, even though expression patterns of individual genes can be highly different, conserved system‐level principles of gene expression can be detected using phenotypically defined gene categories. The phenotypic severity of mutations on mouse teeth is used to classify genes. Genes essential for the progression of odontogenesis are highly expressed at the organ and cell level. Many of the genes required for normal patterning are locally expressed ligands.
Collapse
Affiliation(s)
- Outi Hallikas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Elodie Renvoisé
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Lycée des Métiers Claude Chappe, Arnage, France
| | - Ana-Marija Sulic
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| |
Collapse
|
4
|
Rai N, Neugart S, Yan Y, Wang F, Siipola SM, Lindfors AV, Winkler JB, Albert A, Brosché M, Lehto T, Morales LO, Aphalo PJ. How do cryptochromes and UVR8 interact in natural and simulated sunlight? J Exp Bot 2019; 70:4975-4990. [PMID: 31100755 PMCID: PMC6760287 DOI: 10.1093/jxb/erz236] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/10/2019] [Indexed: 05/20/2023]
Abstract
Cryptochromes (CRYs) and UV RESISTANCE LOCUS 8 (UVR8) photoreceptors perceive UV-A/blue (315-500 nm) and UV-B (280-315 nm) radiation in plants, respectively. While the roles of CRYs and UVR8 have been studied in separate controlled-environment experiments, little is known about the interaction between these photoreceptors. Here, Arabidopsis wild-type Ler, CRYs and UVR8 photoreceptor mutants (uvr8-2, cry1cry2 and cry1cry2uvr8-2), and a flavonoid biosynthesis-defective mutant (tt4) were grown in a sun simulator. Plants were exposed to filtered radiation for 17 d or for 6 h, to study the effects of blue, UV-A, and UV-B radiation. Both CRYs and UVR8 independently enabled growth and survival of plants under solar levels of UV, while their joint absence was lethal under UV-B. CRYs mediated gene expression under blue light. UVR8 mediated gene expression under UV-B radiation, and in the absence of CRYs, also under UV-A. This negative regulation of UVR8-mediated gene expression by CRYs was also observed for UV-B. The accumulation of flavonoids was also consistent with this interaction between CRYs and UVR8. In conclusion, we provide evidence for an antagonistic interaction between CRYs and UVR8 and a role of UVR8 in UV-A perception.
Collapse
Affiliation(s)
- Neha Rai
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
- Correspondence:
| | - Susanne Neugart
- Research Area of Plant Quality and Food Security, Leibniz Institute of Vegetable and Ornamental Crops e. V., 14979 Grossbeeren, Germany
| | - Yan Yan
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Fang Wang
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Sari M Siipola
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | | | - Jana Barbro Winkler
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Ingolstädter Landstrasse, Neuherberg, Germany
| | - Andreas Albert
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Ingolstädter Landstrasse, Neuherberg, Germany
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Tarja Lehto
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Luis O Morales
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
- Current address: School of Science & Technology, Örebro Life Science Center, Örebro University, SE-70182 Örebro, Sweden
| | - Pedro J Aphalo
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| |
Collapse
|
5
|
Khan S, Thomas BR, de la Mata R, Randall MJ, Zhang W, Zwiazek JJ. Variation in Aquaporin and Physiological Responses Among Pinus contorta Families Under Different Moisture Conditions. Plants (Basel) 2019; 8:plants8010013. [PMID: 30621354 PMCID: PMC6359517 DOI: 10.3390/plants8010013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/22/2018] [Accepted: 12/31/2018] [Indexed: 01/05/2023]
Abstract
A population of eight open pollinated families of Pinus contorta was selected from sites varying in precipitation regimes and elevation to examine the possible role of aquaporins in adaptation to different moisture conditions. Five Pinus contorta aquaporins encoding PiconPIP2;1, PiconPIP2;2, PiconPIP2;3, PiconPIP1;2, and PiconTIP1;1 were cloned and detailed structural analyses were conducted to provide essential information that can explain their biological and molecular function. All five PiconAQPs contained hydrophilic aromatic/arginine selective filters to facilitate the transport of water. Transcript abundance patterns of PiconAQPs varied significantly across the P. contorta families under varying soil moisture conditions. The transcript abundance of five PiconPIPs remained unchanged under control and water-stress conditions in two families that originated from the sites with lower precipitation levels. These two families also displayed a different adaptive strategy of photosynthesis to cope with drought stress, which was manifested by reduced sensitivity in photosynthesis (maintaining the same rate) while exhibiting a reduction in stomatal conductance. In general, root:shoot ratios were not affected by drought stress, but some variation was observed between families. The results showed variability in drought coping mechanisms, including the expression of aquaporin genes and plant biomass allocation among eight families of Pinus contorta.
Collapse
Affiliation(s)
- Shanjida Khan
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB T6G 2E3, Canada.
| | - Barb R Thomas
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB T6G 2E3, Canada.
| | - Raul de la Mata
- Institut de Recerca i Tecnología Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain.
| | - Morgan J Randall
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB T6G 2E3, Canada.
| | - Wenqing Zhang
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB T6G 2E3, Canada.
| | - Janusz J Zwiazek
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB T6G 2E3, Canada.
| |
Collapse
|
6
|
Rai M, Rai A, Kawano N, Yoshimatsu K, Takahashi H, Suzuki H, Kawahara N, Saito K, Yamazaki M. De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids. Molecules 2017; 22:E2155. [PMID: 29206203 DOI: 10.3390/molecules22122155] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/18/2022] Open
Abstract
Aconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconitine-type diterpene alkaloids, its biosynthetic pathway remains largely unknown. Biosynthesis of these secondary metabolites is tightly controlled and mostly occurs in a tissue-specific manner; therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization. In order to understand the biosynthesis of secondary metabolites, Illumina-based deep transcriptome profiling and analysis was performed for four tissues (flower, bud, leaf, and root) of A. carmichaelii, resulting in 5.5 Gbps clean RNA-seq reads assembled into 128,183 unigenes. Unigenes annotated as possible rate-determining steps of an aconitine-type biosynthetic pathway were highly expressed in the root, in accordance with previous reports describing the root as the accumulation site for these metabolites. We also identified 21 unigenes annotated as cytochrome P450s and highly expressed in roots, which represent candidate unigenes involved in the diversification of secondary metabolites. Comparative transcriptome analysis of A. carmichaelii with A. heterophyllum identified 20,232 orthogroups, representing 30,633 unigenes of A. carmichaelii, gene ontology enrichment analysis of which revealed essential biological process together with a secondary metabolic process to be highly enriched. Unigenes identified in this study are strong candidates for aconitine-type diterpene alkaloid biosynthesis, and will serve as useful resources for further validation studies.
Collapse
|
7
|
Young EE, Bryant CD, Lee SE, Peng X, Cook B, Nair HK, Dreher KJ, Zhang X, Palmer AA, Chung JM, Mogil JS, Chesler EJ, Lariviere WR. Systems genetic and pharmacological analysis identifies candidate genes underlying mechanosensation in the von Frey test. Genes Brain Behav 2017; 15:604-15. [PMID: 27231153 DOI: 10.1111/gbb.12302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/05/2016] [Accepted: 05/24/2016] [Indexed: 12/22/2022]
Abstract
Mechanical sensitivity is commonly affected in chronic pain and other neurological disorders. To discover mechanisms of individual differences in punctate mechanosensation, we performed quantitative trait locus (QTL) mapping of the response to von Frey monofilament stimulation in BXD recombinant inbred (BXD) mice. Significant loci were detected on mouse chromosome (Chr) 5 and 15, indicating the location of underlying polymorphisms that cause heritable variation in von Frey response. Convergent evidence from public gene expression data implicates candidate genes within the loci: von Frey thresholds were strongly correlated with baseline expression of Cacna2d1, Ift27 and Csnk1e in multiple brain regions of BXD strains. Systemic gabapentin and PF-670462, which target the protein products of Cacna2d1 and Csnk1e, respectively, significantly increased von Frey thresholds in a genotype-dependent manner in progenitors and BXD strains. Real-time polymerase chain reaction confirmed differential expression of Cacna2d1 and Csnk1e in multiple brain regions in progenitors and showed differential expression of Cacna2d1 and Csnk1e in the dorsal root ganglia of the progenitors and BXD strains grouped by QTL genotype. Thus, linkage mapping, transcript covariance and pharmacological testing suggest that genetic variation affecting Cacna2d1 and Csnk1e may contribute to individual differences in von Frey filament response. This study implicates Cacna2d1 and Ift27 in basal mechanosensation in line with their previously suspected role in mechanical hypersensitivity. Csnk1e is implicated for von Frey response for the first time. Further investigation is warranted to identify the specific polymorphisms involved and assess the relevance of these findings to clinical conditions of disturbed mechanosensation.
Collapse
Affiliation(s)
- E E Young
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,School of Nursing, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - C D Bryant
- Department of Pharmacology and Experimental Therapeutics and Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - S E Lee
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - X Peng
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - B Cook
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - H K Nair
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - K J Dreher
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - X Zhang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - A A Palmer
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - J M Chung
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - J S Mogil
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - E J Chesler
- Mammalian Genetics & Genomics, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,The Jackson Laboratory, Bar Harbor, ME, USA
| | - W R Lariviere
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
8
|
Seeve CM, Cho IJ, Hearne LB, Srivastava GP, Joshi T, Smith DO, Sharp RE, Oliver MJ. Water-deficit-induced changes in transcription factor expression in maize seedlings. Plant Cell Environ 2017; 40:686-701. [PMID: 28039925 DOI: 10.1111/pce.12891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 09/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 05/15/2023]
Abstract
Plants tolerate water deficits by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. In this study, reverse transcription quantitative PCR (RT-qPCR) was used to examine the abundance of 618 transcripts from 536 TF genes in individual root and shoot tissues of maize seedlings grown in vermiculite under well-watered (water potential of -0.02 MPa) and water-deficit conditions (water potentials of -0.3 and -1.6 MPa). A linear mixed model identified 433 TF transcripts representing 392 genes that differed significantly in abundance in at least one treatment, including TFs that intersect growth and development and environmental stress responses. TFs were extensively differentially regulated across stressed maize seedling tissues. Hierarchical clustering revealed TFs with stress-induced increased abundance in primary root tips that likely regulate root growth responses to water deficits, possibly as part of abscisic acid and/or auxin-dependent signaling pathways. Ten of these TFs were selected for validation in nodal root tips of drought-stressed field-grown plants (late V1 to early V2 stage). Changes in abundance of these TF transcripts under a field drought were similar to those observed in the seedling system.
Collapse
Affiliation(s)
- Candace M Seeve
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - In-Jeong Cho
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA
| | - Leonard B Hearne
- Statistics Department, University of Missouri, Columbia, MO, 65211, USA
| | | | - Trupti Joshi
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
- Informatics Institute and Christopher S Bond Life Science Center, Columbia, MO, 65211, USA
| | - Dante O Smith
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert E Sharp
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Melvin J Oliver
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| |
Collapse
|
9
|
Clements J, Schoville S, Clements N, Chapman S, Groves RL. Temporal patterns of imidacloprid resistance throughout a growing season in Leptinotarsa decemlineata populations. Pest Manag Sci 2017; 73:641-650. [PMID: 27862872 PMCID: PMC5299531 DOI: 10.1002/ps.4480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 07/24/2016] [Revised: 10/12/2016] [Accepted: 11/06/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND The Colorado potato beetle, Leptinotarsa decemlineata (Say), is a major agricultural pest of commercial potatoes. Pest managers use a combination of control tactics to limit populations, including multiple insecticides. Finding a window of insecticide susceptibility and understanding genetic responses to insecticide exposure during a growing season may provide novel management recommendations for L. decemlineata. RESULTS We examined temporal changes (during one growing season) in phenotypic response between a susceptible population and an imidacloprid-resistant population. Beetles remained more susceptible to imidacloprid in the susceptible population throughout the growing season. Estimated mean LC50 values varied throughout the growing season in the resistant population, with increased susceptibility among overwintered and recently emerged adult beetles compared with a heightened level of resistance in the second generation. RNA transcript abundance was compared among multiple time points through the growing season, showing that cuticular proteins and cytochrome p450s were highly upregulated during peaks of measured resistance. CONCLUSION Temporal variation in imidacloprid susceptibility of L. decemlineata was observed, which included early time points of susceptibility and later peaks in resistance. Heightened resistance occurred during the second generation and correlated to increased transcript abundance of multiple mechanisms of resistance, including multiple cuticular protein and cytochrome p450 transcripts. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Justin Clements
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Sean Schoville
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Nathan Clements
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Scott Chapman
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Russell L Groves
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| |
Collapse
|
10
|
Abstract
RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality data and interpretable results. Important considerations for experimental design include number of replicates, whether to collect paired-end or single-end reads, sequence length, and sequencing depth. Common analysis steps in all RNA-seq experiments include quality control, read alignment, assigning reads to genes or transcripts, and estimating gene or transcript abundance. Our aims are two-fold: to make recommendations for common components of experimental design and assess tool capabilities for each of these steps. We also test tools designed to detect differential expression, since this is the most widespread application of RNA-seq. We hope that these analyses will help guide those who are new to RNA-seq and will generate discussion about remaining needs for tool improvement and development.
Collapse
|
11
|
Lv YH, Ma KJ, Zhang H, He M, Zhang P, Shen YW, Jiang N, Ma D, Chen L. A time course study demonstrating mRNA, microRNA, 18S rRNA, and U6 snRNA changes to estimate PMI in deceased rat's spleen. J Forensic Sci 2014; 59:1286-94. [PMID: 24611529 DOI: 10.1111/1556-4029.12447] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 05/26/2013] [Accepted: 06/13/2013] [Indexed: 11/28/2022]
Abstract
Determining the postmortem interval (PMI) is important in criminal, civil, and forensic cases. We examined the feasibility of using the transcript abundances of mRNAs, 18S rRNA, U6 snRNA, and microRNAs as a means to estimate the PMI. We removed spleen tissues from rats at different PMIs under 4°C or 25°C and examined gene transcript abundances in these samples by RT-qPCR. Using the algorithm geNorm, we found that microRNAs to be appropriate control markers because they were less affected by PMI and temperature. We also characterized relationships between observed PMI and the transcript levels of the above-mentioned RNAs. GAPDH1 and ACTB1 fluctuated slightly like cubic curves, while GAPDH2 and ACTB2 decreased rapidly. 18S rRNA transcript level exhibited a parabolic-like trend at 25°C and exponential growth at 4°C, while U6 transcript level exhibited exponential decay at 25°C and a parabolic-like trend at 4°C. Following validation, we conclude that GAPDH2, ACTB2, and 18S rRNA are suitable makers in the accurate determination of PMI.
Collapse
Affiliation(s)
- Ye-hui Lv
- Department of Forensic Medicine, Shanghai Medical School of Fudan University, 200032, Shanghai, China
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Tremblay A, Hosseini P, Li S, Alkharouf NW, Matthews BF. Analysis of Phakopsora pachyrhizi transcript abundance in critical pathways at four time-points during infection of a susceptible soybean cultivar using deep sequencing. BMC Genomics 2013; 14:614. [PMID: 24025037 PMCID: PMC3847679 DOI: 10.1186/1471-2164-14-614] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 08/31/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Phakopsora pachyrhizi, the causal agent responsible for soybean rust, is among the top hundred most virulent plant pathogens and can cause soybean yield losses of up to 80% when appropriate conditions are met. We used mRNA-Seq by Illumina to analyze pathogen transcript abundance at 15 seconds (s), 7 hours (h), 48 h, and 10 days (d) after inoculation (ai) of susceptible soybean leaves with P. pachyrhizi to gain new insights into transcript abundance in soybean and the pathogen at specific time-points during the infection including the uredinial stage. RESULTS Over three million five hundred thousand sequences were obtained for each time-point. Energy, nucleotide metabolism, and protein synthesis are major priorities for the fungus during infection and development as indicated by our transcript abundance studies. At all time-points, energy production is a necessity for P. pachyrhizi, as indicated by expression of many transcripts encoding enzymes involved in oxidative phosphorylation and carbohydrate metabolism (glycolysis, glyoxylate and dicarboxylate, pentose phosphate, pyruvate). However, at 15 sai, transcripts encoding enzymes involved in ATP production were highly abundant in order to provide enough energy for the spore to germinate, as observed by the expression of many transcripts encoding proteins involved in electron transport. At this early time-point, transcripts encoding proteins involved in RNA synthesis were also highly abundant, more so than transcripts encoding genes involved in DNA and protein synthesis. At 7 hai, shortly after germination during tube elongation and penetration, transcripts encoding enzymes involved in deoxyribonucleotide and DNA synthesis were highly abundant. At 48 hai, transcripts encoding enzymes involved in amino acid metabolism were highly abundant to provide for increased protein synthesis during haustoria maturation. During sporulation at 10 dai, the fungus still required carbohydrate metabolism, but there also was increased expression of transcripts encoding enzymes involved in fatty acid metabolism. CONCLUSION This information provides insight into molecular events and their timing throughout the life cycle of the P. pachyrhizi, and it may be useful in the development of new methods of broadening resistance of soybean to soybean rust.
Collapse
Affiliation(s)
- Arianne Tremblay
- Soybean Genomics & Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, BS411/412, Baltimore, MD 21250, USA
| | - Parsa Hosseini
- Bioinformatics/Computational Biology, George Mason University, 4400 University Dr. Manassas, Fairfax, VA 22030, USA
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxian Li
- USDA-ARS, Crop Genetics Research Unit, Stoneville, MS 38776, USA
| | - Nadim W Alkharouf
- Molecular Biology, Biochemistry and Bioinformatics, Fischer College of Science and Mathematics, Towson University, 8000 York Road, Towson, MD 21252, USA
| | - Benjamin F Matthews
- Soybean Genomics & Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA
| |
Collapse
|
13
|
Kaczmarczyk A, Bowra S, Elek Z, Vincze E. Quantitative RT-PCR based platform for rapid quantification of the transcripts of highly homologous multigene families and their members during grain development. BMC Plant Biol 2012; 12:184. [PMID: 23043496 PMCID: PMC3492166 DOI: 10.1186/1471-2229-12-184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/03/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND Cereal storage proteins represent one of the most important sources of protein for food and feed and they are coded by multigene families. The expression of the storage protein genes exhibits a temporal fluctuation but also a response to environmental stimuli. Analysis of temporal gene expression combined with genetic variation in large multigene families with high homology among the alleles is very challenging. RESULTS We designed a rapid qRT-PCR system with the aim of characterising the variation in the expression of hordein genes families. All the known D-, C-, B-, and γ-hordein sequences coding full length open reading frames were collected from commonly available databases. Phylogenetic analysis was performed and the members of the different hordein families were classified into subfamilies. Primer sets were designed to discriminate the gene expression level of whole families, subfamilies or individual members. The specificity of the primer sets was validated before successfully applying them to a cDNA population derived from developing grains of field grown Hordeum vulgare cv. Barke. The results quantify the number of moles of transcript contributed to a particular gene family and its subgroups. More over the results indicate the genotypic specific gene expression. CONCLUSIONS Quantitative RT-PCR with SYBR Green labelling can be a useful technique to follow gene expression levels of large gene families with highly homologues members. We showed variation in the temporal expression of genes coding for barley storage proteins. The results imply that our rapid qRT-PCR system was sensitive enough to identify the presence of alleles and their expression profiles. It can be used to check the temporal fluctuations in hordein expressions or to find differences in their response to environmental stimuli. The method could be extended for cultivar recognition as some of the sequences from the database originated from cv. Golden Promise were not expressed in the studied barley cultivar Barke although showed primer specificity with their cloned DNA sequences.
Collapse
Affiliation(s)
- Agnieszka Kaczmarczyk
- Department of Genetics and Biotechnology, Aarhus University, Research Centre Flakkebjerg, Forsøgsvej 1, Slagelse, DK-4200, Denmark
| | - Steve Bowra
- Verzyme (UK) Ltd., Plas Gogerddan, Aberystwyth, Wales, SY23 3EB, United Kingdom
| | - Zoltan Elek
- MTA-ELTE-MTM Ecology Research Group, Biological Institute, Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary
| | - Eva Vincze
- Department of Genetics and Biotechnology, Aarhus University, Research Centre Flakkebjerg, Forsøgsvej 1, Slagelse, DK-4200, Denmark
| |
Collapse
|
14
|
Paerl RW, Tozzi S, Kolber ZS, Zehr JP. VARIATION IN THE ABUNDANCE OF SYNECHOCOCCUS SP. CC9311 NARB MRNA RELATIVE TO CHANGES IN LIGHT, NITROGEN GROWTH CONDITIONS AND NITRATE ASSIMILATION(1). J Phycol 2012; 48:1028-1039. [PMID: 27009013 DOI: 10.1111/j.1529-8817.2012.01197.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Synechococcus- and Prochlorococcus-specific narB genes that encode for an assimilatory nitrate reductase are found in coastal to open-ocean waters. However, it remains uncertain if these picocyanobacteria assimilate nitrate in situ. This unknown can potentially be addressed by examining narB mRNA from the environment, but this requires a better understanding of the influence of environmental factors on narB gene transcription. In laboratory experiments with Synechococcus sp. CC9311 cultures exposed to diel light fluctuations and grown on nitrate or ammonium, there was periodic change in narB transcript abundance. This periodicity was broken in cultures subjected to a doubling of irradiance (40-80 μmol photons · m(-2) · s(-1) ) during the mid-light period. Therefore, the irradiance level, not circadian rhythm, was the dominant factor controlling narB transcription. In nitrate-grown cultures, diel change in narB transcript abundance and nitrate assimilation rate did not correlate; suggesting narB mRNA levels better indicate nitrate assimilation activity than assimilation rate. Growth history also affected narB transcription, as changes in narB mRNA levels in nitrogen-deprived CC9311 cultures following nitrate amendment were distinct from cultures grown solely on nitrate. Environmental sampling for narB transcripts should consider time, irradiance, and the growth status of cells to ecologically interpret narB transcript abundances.
Collapse
Affiliation(s)
- Ryan W Paerl
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street EMS D446, Santa Cruz, CA 95064, USA
| | - Sasha Tozzi
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street EMS D446, Santa Cruz, CA 95064, USA
| | - Zbigniew S Kolber
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street EMS D446, Santa Cruz, CA 95064, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street EMS D446, Santa Cruz, CA 95064, USA
| |
Collapse
|
15
|
Hung CY, Sun YH, Chen J, Darlington DE, Williams AL, Burkey KO, Xie J. Identification of a Mg-protoporphyrin IX monomethyl ester cyclase homologue, EaZIP, differentially expressed in variegated Epipremnum aureum 'Golden Pothos' is achieved through a unique method of comparative study using tissue regenerated plants. J Exp Bot 2010; 61:1483-93. [PMID: 20167611 PMCID: PMC2914579 DOI: 10.1093/jxb/erq020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Variegated plants provide a valuable tool for studying chloroplast biogenesis by allowing direct comparison between green and white/yellow sectors within the same leaf. While variegated plants are abundant in nature, the mechanism of leaf variegation remains largely unknown. Current studies are limited to a few mutants in model plant species, and are complicated by the potential for cross-contamination during dissection of leaf tissue into contrasting sectors. To overcome these obstacles, an alternative approach was explored using tissue-culture techniques to regenerate plantlets from unique sectors. Stable green and pale yellow plants were developed from a naturally variegated Epipremnum aureum 'Golden Pothos'. By comparing the gene expression between green and pale yellow plants using suppression subtractive hybridization in conjunction with homologous sequence search, nine down-regulated and 18 up-regulated genes were identified in pale yellow plants. Transcript abundance for EaZIP (Epipremnum aureum leucine zipper), a nuclear gene homologue of tobacco NTZIP and Arabidopsis CHL27, was reduced more than 4000-fold in qRT-PCR analysis. EaZIP encodes the Mg-protoporphyrin IX monomethyl ester cyclase, one of the key enzymes in the chlorophyll biosynthesis pathway. Examination of EaZIP expression in naturally variegated 'Golden Pothos' confirmed that EaZIP transcript levels were correlated with leaf chlorophyll contents, suggesting that this gene plays a major role in the loss of chlorophyll in the pale yellow sectors of E. aureum 'Golden Pothos'. This study further suggests that tissue-culture regeneration of plantlets from different coloured sectors of variegated leaves can be used to investigate the underlying mechanisms of variegation.
Collapse
Affiliation(s)
- Chiu-Yueh Hung
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA
| | - Ying-Hsuan Sun
- Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Jianjun Chen
- Environmental Horticulture Department and Mid-Florida Research and Education Center, Apopka, University of Florida, Apopka, FL 32703, USA
| | - Diane E. Darlington
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA
| | - Alfred L. Williams
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA
| | - Kent O. Burkey
- USDA-ARS Plant Science Research Unit and Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jiahua Xie
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC 27707, USA
- To whom correspondence should be addressed: E-mail:
| |
Collapse
|