A5042863536- Plant and animal studies
- Ecology and Vegetation Dynamics Studies
- Plant Molecular Biology Research
- Plant Gene Expression Analysis
- Plant Reproductive Biology
- Insect-Plant Interactions and Control
- Plant biochemistry and biosynthesis
- Genomics and Chromatin Dynamics
- Tree Root and Stability Studies
- Chromosomal and Genetic Variations
- Lichen and fungal ecology
- Plant tissue culture and regeneration
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Forest Insect Ecology and Management
- Horticultural and Viticultural Research
- Protist diversity and phylogeny
- Parasitic Infections and Diagnostics
- Technology Use by Older Adults
- Health Literacy and Information Accessibility
- Microbial Natural Products and Biosynthesis
- Wood and Agarwood Research
- Marine animal studies overview
- Plant Genetic and Mutation Studies
- Animal Ecology and Behavior Studies
Western Washington University
2018-2024
Pacific Southwest Research Station
2014-2020
Northern Arizona University
2010-2018
University of California, Davis
2016-2018
US Forest Service
2014-2017
University of Wisconsin–Madison
2011
Angiosperm trees reorient their woody stems by asymmetrically producing a specialized xylem tissue, tension wood, which exerts strong contractile force resulting in negative gravitropism of the stem. Here, we show, Populus trees, that initial gravity perception and response occurs cells through sedimentation starch-filled amyloplasts relocalization auxin transport protein, PIN3. Gibberellic acid treatment stimulates rate wood formation gravibending enhances tissue-specific expression an...
Altering gene dosage through variation in copy number is a powerful approach to addressing questions regarding regulation, quantitative trait loci, and heterosis, but one that not easily applied sexually transmitted species. Elite poplar (Populus spp) varieties are created interspecific hybridization, followed by clonal propagation. Altered relationships believed contribute hybrid performance. Clonal propagation allows for replication maintenance of meiotically unstable ploidy or structural...
Summary Community genetics studies frequently focus on individual communities associated with plant genotypes, but little is known about the genetically based relationships among taxonomically and spatially disparate communities. We integrate of a wide range living same genotypes to understand how ecological evolutionary dynamics one community may be constrained or modulated by its underlying genetic connections another community. use pre‐existing data sets collected from Populus...
One of the great advantages next generation sequencing is ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, apply advanced computational approaches these develop models biological processes. In a practical sense, working with organisms presents unique challenges. this paper we discuss some challenges ChIP-seq and RNA-seq experiments using undomesticated tree species genus Populus. We describe specific...
Summary Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate diverse conditions. In order identify relationships among genes expressed during formation, we integrated data from new publically available datasets Populus . These were generated tissue include transcriptome profiling, transcription factor binding, DNA accessibility genome‐wide...
Summary The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus . Currently, basic information lacking concerning the distribution, functional characteristics, evolution ARK1 binding genome. Here, we used chromatin immunoprecipitation sequencing (ChIP‐seq) technology to identify loci genome‐wide Computational analyses evaluated distribution loci, function genes associated with bound effect on...
Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative four Populus homeodomain factors expressed during secondary growth wood formation. Software code (programs scripts) processing ChIP-seq data are provided within publically available iPlant image, including tools...
Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer humans to yield plants. It is also expected affect important traits ecological agronomic importance forest trees, but this has not been systematically characterized or exploited. Here we performed comprehensive scan Populus genome for dosage-sensitive loci affecting quantitative trait spring fall phenology biomass production. The study population was large collection...
While monocots lack the ability to produce a vascular cambium or woody growth, some monocot lineages evolved novel lateral meristem, cambium, which supports secondary radial growth of stems. In contrast found in angiosperm and gymnosperm species, produces bundles, have an amphivasal organization tracheids encircling central strand phloem. Currently there is no information concerning molecular genetic basis development evolution cambium. Here we report high-quality transcriptomes for early...
Summary Numerous studies have explored plant strategies of resource allocation to growth and/or resistance traits within a single generation. In contrast, exceedingly little is known about whether such patterns hold across generations; that is, in seedlings plants experienced maternal herbivory. common garden study with clonally replicated genotypes three cottonwood taxa ( P opulus angustifolia , fremontii and their F 1 hybrids), we examined transgenerational response herbivory terms...
Understanding how genetic identity influences community structure is a major focus in evolutionary ecology, yet few studies examine interactions among organisms the same trophic level within this context. In common garden containing trees from hybrid system (Populus fremontii S. Wats. × Populus angustifolia James), we tested hypothesis that of establishing understory plant communities influenced by differences and explored foliar condensed tannins (CTs) photosynthetically active radiation...
Plants modify development in response to external stimuli, produce new growth that is appropriate for environmental conditions. For example, gravi-stimulation of leaning branches angiosperm trees results modifications wood development, tension pulls stems upright. Here, we use and dissect the temporal changes gene expression underlying formation Populus stems. Using time-series analysis seven time points over a 14-d experiment, identified 8,919 genes were differentially expressed between...
Elucidating the factors that determine abundance and distribution of species remains a central goal ecology. It is well recognized genetic differences among individual can affect interactions dependent taxa, but ecological effects on taxa same trophic level remain much less understood. Our was to test hypothesis between related overstory tree their hybrids influence understory plant community in wild settings.We conducted vegetation surveys riparian with dominated by Populus fremontii, P....
Insect galls are highly specialized structures arising from atypical development of plant tissue induced by insects. Galls provide the insect enhanced nutrition and protection against natural enemies environmental stresses. essentially organs formed an intimate biochemical interaction between gall-inducing its host plant. Because organs, their is likely to be governed phytohormones involved in normal organogenesis. We characterized concentrations both growth defensive ungalled control leaves...
Summary Wood formation was present in early angiosperms, but has been highly modified through evolution to generate the anatomical diversity seen extant angiosperm lineages. In this project, we modeled changes gene coexpression relationships associated with of wood a phylogenetic survey 13 tree species. Gravitropic stimulation used as an experimental treatment alter and also perturb expression. Gene transcript abundances were determined using RNA sequencing developing tissues from upright...
Alzheimer's disease is characterized by 2 pathological proteins, amyloid beta 42 and tau. The majority of cases in the population are sporadic late-onset disease, which exhibits high levels heritability. While several genetic risk factors for have been identified replicated independent studies, including ApoE ε4 allele, great heritability remains unexplained, likely due to aggregate effects a very large number genes with small effect size, as well biases sample collection statistical...
Pinniped predation on commercially and ecologically important prey has been a source of conflict for centuries. In the Salish Sea, harbor seals (Phoca vitulina) are suspected impeding recovery culturally critical Pacific salmon (Oncorhynchus spp.). Fall 2020, novel deterrent called Targeted Acoustic Startle Technology (TAST) was deployed at Whatcom Creek to deter from preying fall runs hatchery chum (O. keta) Chinook tshawytscha) in Bellingham, Washington, USA. Field observations were...
Abstract Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, for salicinoid phenolic glycosides ( SPG s)—ecologically compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We a linkage map derived from full‐sib population of hybrid cottonwoods Populus spp.) search quantitative trait loci QTL ) the s salicortin HCH ‐salicortin. SSR markers primer sequences were anchor V3.0 P....
Abstract Establishing efficient functional genomic systems for creating and characterizing genetic variation in forest trees is challenging. Here we describe protocols novel gene‐dosage Populus through gamma‐irradiation of pollen, followed by analysis to identify chromosomal regions that have been deleted or inserted each F1 individual. Irradiated pollen used a controlled, interspecific cross create progeny carry deletions insertions regions. These result changes gene dosage turn affect both...
Endogenous RNA interference (RNAi) pathways regulate a wide range of cellular processes in diverse eukaryotes, yet the ciliated eukaryote, Tetrahymena thermophila, purpose RNAi that generate ∼23-24 nucleotide (nt) small (s)RNAs has remained unknown. Here, we investigated phenotypic and gene expression impacts on vegetatively growing cells when genes involved nt sRNA biogenesis are disrupted. We observed slower proliferation increased DNA metabolism chromosome organization maintenance mutants...