Presenters
May 13 Symposium
City Center Campus 2nd Floor Auditorium
Gloria Muday, Wake Forest University
A Kinetic Analysis of the Auxin and Ethylene Transcriptomes Reveal Transcription Factor Networks and Cell Wall Remodeling Proteins that Modulate Lateral Root Development in Arabidopsis
Abstract
We are exploring the molecular mechanisms by which auxin and ethylene synergistically inhibit root elongation, while ethylene antagonizes the positive effect of auxin on lateral root formation. To expand our understanding of the transcriptional events that mediate crosstalk between these two hormones, we have identified genome-wide transcriptional changes in Arabidopsis roots over a time course of treatments with the endogenous auxin, IAA, and the ethylene precursor, ACC. We identified 1,246 and 449 genes that had consistent magnitude and pattern of expression in response to IAA or ACC, respectively, with an overlap of 139 genes. These include primary response genes, including transcription factors and signaling proteins, and the more slowly accumulated transcripts encoding proteins that control growth and development. We have identified groups of sequentially accumulating transcription factors and are building and testing models for networks of transcription factors that modulate root development. We are also examining transcripts whose abundance changes in response to IAA and ACC suggest a role in either the synergistic or the antagonistic actions of these hormones with a focus on functional groups of genes identified by conserved annotation of clusters of like responding genes, including genes linked to cell wall remodeling or division controls. We are testing the function of these genes by mutant analysis.
About Gloria
Dr. Gloria Muday teaches and does research in the Department of Biology at Wake Forest University and Director of the Center for Molecular Communication and Signaling. Her lab’s research is focused on crosstalk between auxin and ethylene and flavonoids that control root development in Arabidopsis and tomato.
Mark Johnson, Brown University and Ravi Palanivelu, University of Arizona
Caught in the act: Pollen-Pistil Transcriptomics
Abstract
Pollen tubes penetrate the stigma, extend through a specialized pistil transmitting tissue, are attracted to ovules and deliver two sperm to the female gametophyte so one can fuse with the egg to form the embryo and the other with the central cell to form endosperm. This double fertilization process depends on a series of complex cell:cell interactions and is central to seed crop production. Interestingly, pollen tubes grown in vitro are unable to respond to female attractants unless they are first grown through pistil tissue. These observations suggest that the pollen tube changes its gene expression patterns in response to interactions with the pistil and that these changes are critical for reproduction. Defining the pollen tube transcriptome as it interacts with pistil tissue would provide molecular insight into these changes. Our first approach was to use the ATH1 microarray to compare the transcriptomes of pollen tubes grown in vitro with those that had grown through a portion of the pistil tissue before they were collected from the surface of media. This led to the identification of hundreds of genes transcribed specifically in response to growth through the pistil. Additional analysis using ATH1 microarrays focused on characterizing in vivo interactions between pollen tubes and pistils by defining the transcriptomes of pistils containing actively growing pollen tubes and identifying the transcriptional regulators that mediated these changes and their potential target genes. Our current work is using RNA-seq, which enables identification of previously unannotated genes that may be essential for pollen-pistil signaling and holds the promise of being able to unambiguously distinguish pollen tube and pistil transcriptomes using an RNA sample from an intact pollinated pistil.
About Mark
Dr. Mark Johnson is a founding member of the Pollen Research Coordination Network. He teaches courses in plant biology and is co-organizing Frontiers in Plant Science at Cold Spring Harbor Lab in June 2014. His lab uses pollen tube growth and guidance as a model system to understand guidance of cellular migration, invasive cell growth, and determination of cellular polarity.
About Ravi
Dr. Ravi Palanivelu joined the Steering Committee of the Pollen Research Coordination Network in 2010 and has co-organized the annual Pollen RCN meetings in 2013 and 2014. His lab is interested in understanding how plant cells communicate with each other. To accomplish this goal, they are using pollen tube growth during Arabidopsis thaliana reproduction as a model system.
Colleen Doherty, NC State University
Want more out of high-throughput data? Change your perspective.
Abstract
More data is not always better data. This talk will explore what we have learned from microarrays, including how to combine disparate data sets to get new value from old experiments.
About Colleen
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Dr. Colleen Doherty received her PhD from Michigan State University in transcriptional networks of low temperature response in Arabidopsis. She did a post doc in the lab of Steve Kay examining the circadian regulatory networks in Arabidopsis and rice. Colleen recently started her position as an Assistant Professor in the department of Biochemistry at North Carolina State University where she investigates the intersection of circadian regulation and abiotic stress. She applies tools of statistical learning to mine datasets and explore changes in regulatory networks.
Jeff Harper, University of Nevada, Reno
Pollen - a model for calcium ion signaling and insights into stress tolerance
Abstract
Research in the Harper lab is focused on the role of Ca2+ signalling in pollen development. Ca2+ signals have been implicated in regulating pollen grain germination, tube growth, and sperm cell discharge in ovules. In Arabidopsis thaliana, there are at least 6 cyclic nucleotide-gated Ca2+-permeable ion channels (CNGCs) expressed in pollen. Gene knockouts have shown that three of these channels (CNGC18, 7, and 8) are essential for pollen tube tip growth. In contrast, a knockout of CNGC16 has no visible phenotype under normal growth conditions. However, cngc16 pollen are nearly sterile when plants are grown under conditions of hot days and cold nights. The most stress-sensitive time for cngc16 pollen development is during germination and the initiation of pollen tube tip growth. Using RNA-seq technology, the expression profiles of cngc16 pollen grains were compared to wild type. Under heat-stress conditions, pollen grains from both wild type and mutant plants showed nearly 5000 stress-dependent changes in their transcriptomes. However, more than 50% of these changes were different between wild type and mutant. This supports a model in which the mutant fails to develop a normal transcriptional stress response, and is therefore more sensitive to stress conditions. However, even under normal conditions, the two pollen types showed more than 1000 differences. Thus, it is also possible that cngc16 pollen have a “pre-existing condition” that make them more sensitive to death at the onset of a stress response. Consistent with this alternative model, the expression profiles reveal several mRNA differences of potential importance to the biogenesis of a normal cell wall. Defects in cell wall could make pollen more susceptible to bursting under conditions that either increase turgor or desynchronize growth processes during tip growth.
About Jeff
Dr. Jeff Harper is a Professor of Biology at the University of Nevada, Reno. The Harper lab is interested in how a plant can use as few as 28,000 genes to develop and survive under extreme environmental conditions, such as cold, heat, drought and salt stress. A primary focus is on calcium signaling. The lab employs genetic, cell, bioinformatic, and biochemical approaches, using Arabidopsis and yeast as model systems.
Beth Krizek, University of South Carolina
Regulation of flower development by two related AIL/PLT transcription factors
Abstract
Flowers initiate in the periphery of the shoot apical meristem, a dome-shaped structure at the apex of a plant that allows for the initiation of new organs throughout the plant’s life. After outgrowth of a flower primordium from the meristem, floral organ primordia appear in characteristic positions within the flower and undergo coordinated cellular behaviors and morphogenesis to develop into one of four organ types. Little is known about the mechanisms that dictate the positioning of floral organ primordia at precise locations within the flower and the means by which cell division, growth and differentiation are coordinated during floral organogenesis. Members of the Arabidopsis AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor family have partially overlapping functions in regulating floral organ initiation, growth and patterning. To better understand the cellular processes regulated by these transcription factors, we have performed RNA-Seq on ant ail6 double mutants inflorescences. In this talk, I will present our bioinformatic analyses of genes differentially expressed in the double mutant compared to wild type. In addition, I will present our examination of splicing differences between the mutant and wild type.
About Beth
Dr. Beth Krizek is a Professor in the Department of Biological Sciences at the University of South Carolina. Her lab’s research is focused on the transcriptional networks controlling the initiation and development of floral organs.
Jessica Schlueter, UNC Charlotte
Mapping the oat genome
Abstract
The hexaploid oat (Avena Sativa L.) is an important cereal crop worldwide, cultivated to produce grains for the food industry as well as animal feeding. For its importance, oat was chosen as one of the crops of the Plant Pathway Elucidation Project (P2EP), a groundbreaking program that engages college students from across North Carolina in an educational and research endeavor with the objective of the discovery of plant pathways aiming to help plant breeders to build better plants for the world. As demonstrated in model plants and other crops with great economic value, the power of having a genome available is tremendous and leads to new discoveries in shortened time. As such, I am reporting on the development of a pipeline for constructing the hexaploid oat genome zipper. First, a consensus linkage map in oat consisting of 12 individual mapping populations producing a final map of 7020 mapped markers and 2169 framework markers was produced. Linkage groups were assigned and anchored to physical chromosomes using monosomic hybrids. Two of these mapping populations were chased for shotgun sequencing using a POPSEQ approach, relying on population structure to aid in the assembly of the genome. Overall, current assemblies encompass 65x genomic coverage and the deep marker density of the linkage maps is allowing for contig anchoring to the genome. Our over all goal is to provide a functional genome of oats with an interactive browser system to allow for gene discovery and improvement in oats.
About Jessica
Dr. Jessica Schlueter teaches and does research in the Department of Bioinformatics and Genomics at UNC Charlotte. Her research interests include ozone sensitivity in soybean, oat genetics and genomics, and the biology of legumes. She also co-leads the Plant Pathways Elucidation Project based at the North Carolina Research Campus in Kannapolis.
Xiangqin Cui, University of Alabama at Birmingham
Three things you need to know about RNA-Seq data analysis
Abstract
RNA-seq is one of the most widely used applications of next generation sequencing technology. It has well-recognized advantages over its microarray predecessor. It also brings new challenges to data analysis. I will highlight major elements of RNA-seq analyses and key steps of the data processing, which will lay the foundation for part II of your hands-on workshop.
About Xiangqin
Dr. Xiangqin Cui is an Associate Professor of Biostatistics in the Section on Statistical Genetics at UAB. She is the author of multiple articles on microarray and RNA-Seq data analysis and teaches statistical bioinformatics, RNA-Seq data analysis, and other topics related to high-throughput biology. For more information about Dr. Cui, visit her Web site at UAB.
May 14 Workshop
City Center Campus Computer Classrooms 801 and 802
Naim Matasci, iPlant and University of Arizona
About Naim
Dr. Naim Matasci is the Scientific Lead for the Tree of Life Grant Challenge at the iPlant Collaborative and an Adjunct Assistant Professor in the Department of Ecology and Evolutionary Biology at the University of Arizona. The goal of the iPlant Tree of Life project is to produce a phylogenetic tree of all green plants and provide the scientific community with the tools to visualize and analyze trees of this magnitude. The challenges encountered range from designing new, more powerful computational methods to promote computational thinking among plant biologists. Naim has taught R and software carpentry to diverse audiences, including crop breeders, molecular biologists, and bioinformatics specialists. For more information, see http://www.matasci.info/.
Ann Loraine, UNC Charlotte
About Ann
Dr. Ann Loraine is an Associate Professor of Bioinformatics and Genomics at UNC Charlotte. She teaches and does research at the North Carolina Research Campus in Kannapolis, NC. Her lab studies regulation of alternative splicing, which enables one gene to produce multiple products with diverse functions. The Loraine Lab also develops software for biologists, including CressExpress and Integrated Genome Browser.
Ivory Clabaugh Blakley, UNC Charlotte
About Ivory
Ivory Clabaugh Blakley is a Research Specialist in the Loraine Lab at the North Carolina Research Campus and is Co-Organizer of the WiNGS 2014 meeting. A classically trained biologist, she developed expertise in R programming and data analysis while analyzing large-scale ChIP-Seq and RNA-Seq data sets. She enjoys teaching, bee-keeping, and helping biologists learn to use R in their research.
Xiangqin Cui, University of Alabama at Birmingham
About Xiangqin
Dr. Xiangqin Cui is an Associate Professor of Biostatistics in the Section on Statistical Genetics at UAB. She is the author of multiple articles on microarray and RNA-Seq data analysis and teaches statistical bioinformatics, RNA-Seq data analysis, and other topics related to high-throughput biology. For more information about Dr. Cui, visit her Web site at UAB.