7 results on '"Roya Campos"'
Search Results
2. A comparative analysis of RNA isolation methods optimized for high-throughput detection of viral pathogens in California’s regulatory and disease management program for citrus propagative materials
- Author
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Tyler Dang, Sohrab Bodaghi, Fatima Osman, Jinbo Wang, Tavia Rucker, Shih-Hua Tan, Amy Huang, Deborah Pagliaccia, Stacey Comstock, Irene Lavagi-Craddock, Kiran R. Gadhave, Paulina Quijia-Lamina, Arunabha Mitra, Brandon Ramirez, Gerardo Uribe, Alexandra Syed, Sarah Hammado, Iman Mimou, Roya Campos, Silva Abdulnour, Michael Voeltz, Jinhwan Bae, Emily Dang, Brittany Nguyen, Xingyu Chen, Noora Siddiqui, Yi Tien Hsieh, Shurooq Abu-Hajar, Joshua Kress, Kristina Weber, and Georgios Vidalakis
- Subjects
graft-transmissible pathogens of citrus ,magnetic bead-based RNA isolation ,RNA quality ,Citrus Clonal Protection Program (CCPP) ,National Clean Plant Network (NCPN) ,California Department of Food and Agriculture (CDFA) ,Agriculture ,Plant culture ,SB1-1110 - Abstract
Citrus germplasm programs can benefit from high-throughput polymerase chain reaction (PCR)-based methods for the detection of graft-transmissible pathogens in propagative materials. These methods increase diagnostic capacity, and thus contribute to the prevention of disease spread from nurseries to citrus orchards. High quality nucleic acids, as determined by purity, concentration, and integrity, are a prerequisite for reliable PCR detection of citrus pathogens. Citrus tissues contain high levels of polyphenols and polysaccharides, which can affect nucleic acid quality and inhibit PCR reactions. Various commercially available RNA isolation methods are used for citrus and include: phenol-chloroform (TRIzol®, Thermo Fisher Scientific); silica columns (RNeasy® Plant Mini Kit, Qiagen); and magnetic beads-based methods (MagMAX™-96 Viral RNA Isolation Kit, Thermo Fisher Scientific). To determine the quality of RNA and its impact on the detection of graft-transmissible citrus pathogens in reverse transcription (RT) PCR-based assays, we compared these three RNA isolation methods. We assessed RNA purity, concentration, and integrity from citrus inoculated with different viruses and viroids. All three RNA isolation methods produced high quality RNA, and its use in different RT-PCR assays resulted in the detection of all targeted citrus viruses and viroids with no false positive or negative results. TRIzol® yielded RNA with the highest concentration and integrity values but some samples required serial dilutions to remove PCR inhibitors and detect the targeted pathogens. The RNeasy® kit produced the second highest concentration and purity of RNA, and similar integrity to TRIzol®. MagMAX™ isolation also provided high quality RNA but most importantly produced RNA with consistent results clustered around a median value for concentration, purity, and integrity. Subsequently, MagMAX™-96 was combined with the semi-automated MagMAX™ Express-96 Deep Well Magnetic Particle Processor, for high-throughput sample processing. MagMAX™-96 enabled the diagnostic laboratory of the Citrus Clonal Protection Program-National Clean Plant Network at the University of California, Riverside to process over 16,500 samples from citrus budwood source trees between 2010 and 2019. This high-throughput approach dramatically reduced the incidence of viroids in citrus nurseries and was key to the successful implementation of the mandatory Citrus Nursery Stock Pest Cleanliness Program in California.
- Published
- 2022
- Full Text
- View/download PDF
3. Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay.
- Author
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Shih-Hua Tan, Fatima Osman, Sohrab Bodaghi, Tyler Dang, Greg Greer, Amy Huang, Sarah Hammado, Shurooq Abu-Hajar, Roya Campos, and Georgios Vidalakis
- Subjects
Medicine ,Science - Abstract
Citrus tatter leaf virus (CTLV) threatens citrus production worldwide because it induces bud-union crease on the commercially important Citrange (Poncirus trifoliata × Citrus sinensis) rootstocks. However, little is known about its genomic diversity and how such diversity may influence virus detection. In this study, full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside, were characterized using next generation sequencing. Genome structure and sequence for all CTLV isolates were similar to Apple stem grooving virus (ASGV), the type species of Capillovirus genus of the Betaflexiviridae family. Phylogenetic analysis highlighted CTLV's point of origin in Asia, the virus spillover to different plant species and the bottleneck event of its introduction in the United States of America (USA). A reverse transcription quantitative polymerase chain reaction assay was designed at the most conserved genome area between the coat protein and the 3'-untranslated region (UTR), as identified by the full genome analysis. The assay was validated with different parameters (e.g. specificity, sensitivity, transferability and robustness) using multiple CTLV isolates from various citrus growing regions and it was compared with other published assays. This study proposes that in the era of powerful affordable sequencing platforms the presented approach of systematic full-genome sequence analysis of multiple virus isolates, and not only a small genome area of a small number of isolates, becomes a guideline for the design and validation of molecular virus detection assays, especially for use in high value germplasm programs.
- Published
- 2019
- Full Text
- View/download PDF
4. Radial askew endodermal cell divisions reveal IRK functions in division orientation
- Author
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R. M. Imtiaz Karim Rony, Roya Campos, and Jaimie M. Van Norman
- Abstract
Oriented cell divisions produce different cell types and maintain tissue and organ patterning in plants; this is particularly true of the highly organized Arabidopsis root meristem. Because plant cells are encased by walls, the precise orientation of cell divisions is especially important for cell fate specification and tissue/organ organization. Mutant alleles of the transmembrane receptor kinase INFLORESCENCE AND ROOT APICES RECEPTOR KINASE (IRK) exhibit excess endodermal cell divisions, resulting in more cells in the radial axis ofirkroots. IRK localizes to the outer polar domain of endodermal cells, which suggests directional signal perception is necessary to repress endodermal cell proliferation. Here, we conducted a detailed examination of endodermal cell divisions inirkand identified a distinct cell division orientation defect. Many excess endodermal divisions inirk-4have outwardly skewed division planes, therefore we termed them ‘radial askew’ divisions. An IRK truncation lacking the kinase domain retains polar localization and rescues these radial askew divisions, but exhibits excess periclinal divisions, phenocopying the weakerirk-1allele. These results expand IRK’s function beyond repression of endodermal cell division activity showing it’s also required for division plane orientation. Based on its polarity, we propose that IRK at the outer lateral endodermal cell face interferes with division plane selection, maintenance, and/or cell plate attachment to influence endodermal cell division orientation.
- Published
- 2023
5. Confocal Analysis of Arabidopsis Root Cell Divisions in 3D: A Focus on the Endodermis
- Author
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Roya Campos and Jaimie M. Van Norman
- Subjects
Cell type ,Multicellular organism ,medicine.anatomical_structure ,Cell division ,biology ,Live cell imaging ,Arabidopsis ,Cell ,medicine ,Arabidopsis thaliana ,Endodermis ,biology.organism_classification ,Cell biology - Abstract
The development of multicellular organisms requires coordinated cell divisions for the production of diverse cell types and body plan elaboration and growth. There are two main types of cell divisions: proliferative or symmetric divisions, which produce more cells of a given type, and formative or asymmetric divisions, which produce cells of different types. Because plant cells are surrounded by cell walls, the orientation of plant cell divisions is particularly important in cell fate specification and tissue or organ morphology. The cellular organization of the Arabidopsis thaliana root makes an excellent tool to study how oriented cell division contributes to tissue patterning during organ development. To understand how division plane orientation in a specific genotype or growth condition may impact organ or tissue development, a detailed characterization of cell division orientation is required. Here we describe a confocal microscopy-based, live imaging method for Arabidopsis root tips to examine the 3D orientations of cell division planes and quantify formative, proliferative, and atypical endodermal cell divisions.
- Published
- 2021
6. The Arabidopsis Receptor Kinase IRK Is Polarized and Represses Specific Cell Divisions in Roots
- Author
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Cecilia Rodriguez-Furlan, Roya Campos, Jaimie M. Van Norman, and Jason Goff
- Subjects
Cell type ,Cell division ,Cell ,Meristem ,Arabidopsis ,Biology ,Plant Roots ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Gene Expression Regulation, Plant ,Cell polarity ,medicine ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Arabidopsis Proteins ,Cell Polarity ,Cell Differentiation ,Cell Biology ,biology.organism_classification ,Cell biology ,Multicellular organism ,medicine.anatomical_structure ,Stem cell ,030217 neurology & neurosurgery ,Intracellular ,Cell Division ,Developmental Biology ,Signal Transduction - Abstract
Development of multicellular organisms requires coordination of cell division and differentiation across tissues. In plants, directional signaling, and implicitly cell polarity, is proposed to participate in this coordination; however, mechanistic links between intercellular signaling, cell polarity, and cellular organization remain unclear. Here, we investigate the localization and function of INFLORESCENCE AND ROOT APICES RECEPTOR KINASE (IRK) in root development. We find that IRK-GFP localizes to the outer plasma membrane domain in endodermal cells but localizes to different domains in other cell types. Our results suggest that IRK localization is informed locally by adjacent cell types. irk mutants have excess cell divisions in the ground tissue stem cells and endodermis, indicating IRK functions to maintain tissue organization through inhibition of specific cell divisions. We predict that IRK perceives a directional cue that negatively regulates these cell divisions, thus linking intercellular signaling and cell polarity with the control of oriented cell divisions during development.
- Published
- 2019
7. Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay
- Author
-
Greg Greer, Shih-hua Tan, Sarah Hammado, Sohrab Bodaghi, Fatima Osman, Tyler Dang, Roya Campos, Amy Huang, Georgios Vidalakis, Shurooq Abu-Hajar, and Melcher, Ulrich
- Subjects
0106 biological sciences ,0301 basic medicine ,Citrus ,Artificial Gene Amplification and Extension ,Polymerase Chain Reaction ,01 natural sciences ,Genome ,Genome Size ,Phylogeny ,Conserved Sequence ,Genetics ,Viral Genomics ,Capillovirus ,Multidisciplinary ,biology ,Database and informatics methods ,Sequence analysis ,Eukaryota ,High-Throughput Nucleotide Sequencing ,food and beverages ,Genomics ,Plants ,Citrange ,Medicine ,Flexiviridae ,Infection ,Apple stem grooving virus ,Citrus × sinensis ,Research Article ,Biotechnology ,Citrus sinensis ,Human ,food.ingredient ,Bioinformatics ,Evolution ,General Science & Technology ,Science ,Nucleotide Sequencing ,Microbial Genomics ,Research and Analysis Methods ,Microbiology ,DNA sequencing ,Fruits ,Evolution, Molecular ,03 medical and health sciences ,food ,Virology ,Humans ,Poncirus ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,Genome size ,DNA sequence analysis ,Apples ,Whole Genome Sequencing ,Genome, Human ,Human Genome ,Organisms ,Biology and Life Sciences ,Computational Biology ,Molecular ,Genome Analysis ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,010606 plant biology & botany - Abstract
Citrus tatter leaf virus (CTLV) threatens citrus production worldwide because it induces bud-union crease on the commercially important Citrange (Poncirus trifoliata × Citrus sinensis) rootstocks. However, little is known about its genomic diversity and how such diversity may influence virus detection. In this study, full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside, were characterized using next generation sequencing. Genome structure and sequence for all CTLV isolates were similar to Apple stem grooving virus (ASGV), the type species of Capillovirus genus of the Betaflexiviridae family. Phylogenetic analysis highlighted CTLV's point of origin in Asia, the virus spillover to different plant species and the bottleneck event of its introduction in the United States of America (USA). A reverse transcription quantitative polymerase chain reaction assay was designed at the most conserved genome area between the coat protein and the 3'-untranslated region (UTR), as identified by the full genome analysis. The assay was validated with different parameters (e.g. specificity, sensitivity, transferability and robustness) using multiple CTLV isolates from various citrus growing regions and it was compared with other published assays. This study proposes that in the era of powerful affordable sequencing platforms the presented approach of systematic full-genome sequence analysis of multiple virus isolates, and not only a small genome area of a small number of isolates, becomes a guideline for the design and validation of molecular virus detection assays, especially for use in high value germplasm programs.
- Published
- 2019
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