Cell Biology & Molecular Genetics

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Author: search.filters.author.Bouten, Roxane

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    Ferret: a sentence-based literature scanning system
    (Springer Nature, 2015-06-20) Srinivasan, Padmini; Zhang, Xiao-Ning; Bouten, Roxane; Chang, Caren
    The rapid pace of bioscience research makes it very challenging to track relevant articles in one’s area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to see active research in building new document retrieval and sentence retrieval systems. We present Ferret, a prototype retrieval system, designed to retrieve and rank sentences (and their documents) conveying gene-centric relationships of interest to a scientist. The prototype has several features. For example, it is designed to handle gene name ambiguity and perform query expansion. Inputs can be a list of genes with an optional list of keywords. Sentences are retrieved across species but the species discussed in the records are identified. Results are presented in the form of a heat map and sentences corresponding to specific cells of the heat map may be selected for display. Ferret is designed to assist bio scientists at different stages of research from early idea exploration to advanced analysis of results from bench experiments. Three live case studies in the field of plant biology are presented related to Arabidopsis thaliana. The first is to discover genes that may relate to the phenotype of open immature flower in Arabidopsis. The second case is about finding associations reported between ethylene signaling and a set of 300+ Arabidopsis genes. The third case is on searching for potential gene targets of an Arabidopsis transcription factor hypothesized to be involved in plant stress responses. Ferret was successful in finding valuable information in all three cases. In the first case the bZIP family of genes was identified. In the second case sentences indicating relevant associations were found in other species such as potato and jasmine. In the third sentences led to new research questions about the plant hormone salicylic acid. Ferret successfully retrieved relevant gene-centric sentences from PubMed records. The three case studies demonstrate end user satisfaction with the system.
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    BOLT, AN AP2/ERF TRANSCRIPTION FACTOR, REGULATES ABIOTIC STRESS AND DEFENSE RESPONSES IN ARABIODPSIS THALIANA
    (2016) Bouten, Roxane; Chang, Caren; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Biotic and abiotic stresses negatively affect plant growth and development, hence decrease productivity. Many AP2/ERF family transcription factors in plants have important roles in stress response signaling although most have not yet been studied. Here I show that expression of an Arabidopsis thaliana AP2/ERF family member, which I call BOLT, is regulated by a MAPK pathway that includes MEKK1, MKK1, MKK2, and MPK4, and has roles in both biotic and abiotic stress response as well influencing growth and development. In this thesis, I examined BOLT’s gene expression pattern and protein localization, using GUS and YFP reporter genes respectively, measured its expression in response to biotic and abiotic stress and plant hormones using RT-qPCR, examined phenotypes by generating overexpressing and RNAi lines, and analyzed its effect on downstream gene expression using a microarray at time points after inducing BOLT expression. I found that BOLT is expressed in various plant tissues and the protein localizes to nuclear bodies as demonstrated in onion epidermal cells. Knockdown (RNAi) plants exhibit greater drought tolerance and are larger than wild type under low light conditions, while the overexpressors exhibit a dramatic early flowering phenotype and are small and weak under low light. Gene expression analysis suggests BOLT regulates genes involved in photosynthesis, hormone biosynthesis and signaling, and defense, many of which are also regulated in the MAPK pathway. Increased BOLT expression downregulates two discreet systems, cyclic electron flow and glycine cleavage, components of photosynthesis and photorespiration, respectively, which are two systems that are important under low light conditions. Taking these results together, I conclude that BOLT functions downstream of a stress responsive MAPK pathway and regulates a variety of growth- and stress-related genes necessary to balance growth and defense in response to biotic or abiotic stresses, or low light conditions.