A5053189630- Leaf Properties and Growth Measurement
- Plant Molecular Biology Research
- Plant Reproductive Biology
- Plant Gene Expression Analysis
- Entomopathogenic Microorganisms in Pest Control
- Insect symbiosis and bacterial influences
- Scientific Computing and Data Management
- Greenhouse Technology and Climate Control
- Plant tissue culture and regeneration
- Research Data Management Practices
- Genetic diversity and population structure
- Remote Sensing in Agriculture
- Genomics and Phylogenetic Studies
- Invertebrate Immune Response Mechanisms
- Chromosomal and Genetic Variations
- Rangeland and Wildlife Management
- Fire effects on ecosystems
- Light effects on plants
- Plant nutrient uptake and metabolism
- Species Distribution and Climate Change
- Recycling and Waste Management Techniques
- Microplastics and Plastic Pollution
- Municipal Solid Waste Management
- Plant Parasitism and Resistance
- Data Visualization and Analytics
University of California, Berkeley
2016-2024
University of California, Davis
2011-2015
University of Kansas
2011
John Innes Centre
2011
The developmental mechanisms regulating cell differentiation and patterning during the secondary growth of woody tissues are poorly understood. Class III HD ZIP transcription factors evolutionarily ancient play fundamental roles in various aspects plant development. Here we investigate role a factor, POPCORONA, stems. Transgenic Populus (poplar) trees expressing either miRNA-resistant POPCORONA or synthetic miRNA targeting were used to infer function growth. Whole plant, histological, gene...
Many microbes induce striking behavioral changes in their animal hosts, but how they achieve this is poorly understood, especially at the molecular level. Mechanistic understanding has been largely constrained by lack of an experimental system amenable to manipulation. We recently discovered a strain behavior-manipulating fungal pathogen Entomophthora muscae infecting wild Drosophila, and established methods infect D. melanogaster lab. Lab-infected flies manifest moribund behaviors...
Plastic production and plastic pollution have a negative effect on our environment, environmental justice, climate change. Using detailed global regional plastics datasets coupled with socioeconomic data, we employ machine learning to predict that, without intervention, annual mismanaged waste will nearly double 121 million metric tonnes (Mt) [100 139 Mt 95% confidence interval] by 2050. Annual greenhouse gas emissions from the system are projected grow 37% 3.35 billion CO 2 equivalent (3.09...
Leaf shape is mutable, changing in ways modulated by both development and environment within genotypes. A complete model of leaf phenotype would incorporate the changes during juvenile-to-adult phase transitions ontogeny each leaf. Here, we provide a morphometric description >33,000 leaflets from set tomato (Solanum spp) introgression lines grown under controlled conditions. We first compare these leaves, arising vegetative development, with >11,000 previously published field setting wild...
Leaf morphology and the pattern of shoot branching determine to a large extent growth habit seed plants. Until recently, developmental processes that led establishment these morphological structures seemed unrelated. Here, we show tomato Trifoliate ( Tf ) gene plays crucial role in both processes, affecting formation leaflets compound leaf initiation axillary meristems axil. encodes myeloblastosis oncoprotein (MYB)-like transcription factor related Arabidopsis thaliana LATERAL ORGAN FUSION1...
Angiosperms exhibit staggering diversity in floral form, and evolution of morphology is often correlated with changes pollination syndrome. The showy, bilaterally symmetrical flowers the model species Antirrhinum majus (Plantaginaceae) are highly specialized for bee pollination. In A. , CYCLOIDEA ( CYC ), DICHOTOMA DICH RADIALIS RAD DIVARICATA DIV ) specify development bilateral symmetry. However, it unclear to what extent these genes has resulted flower morphological divergence among...
In a majority of species, leaf development is thought to proceed in bilaterally symmetric fashion without systematic asymmetries. This despite the left and right sides an initiating primordium occupying niches that differ their distance from sinks sources auxin. Here, we revisit existing model auxin transport sufficient recreate spiral phyllotactic patterns find previously overlooked asymmetries between distribution centers primordia. We show it direction determines side these fall on....
Plants sense the foliar shade of competitors and alter their developmental programs through shade-avoidance response. Internode petiole elongation, changes in overall leaf area mass per area, are stereotypical architectural responses to shoot. However, shape complexity response remain incompletely, qualitatively, described. Using a meta-analysis more than 18,000 previously published leaflet outlines, we demonstrate that avoidance alters domesticated tomato (Solanum lycopersicum) wild...
The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One main contributors to is efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis has revealed that PIN1 genes are split into two sister clades; relatively uncharacterized Sister-Of-PIN1 (SoPIN1). In this paper we identify entire-2 loss-of-function SlSoPIN1a (Solyc10g078370) mutant in Solanum lycopersicum. plants unable specify proper initiation leading frequent...
Traditional data science education often omits training on research workflows: the process that moves a scientific investigation from raw to coherent question insightful contribution. In this paper, we elaborate basic principles of reproducible analysis workflow by defining three phases: Exploratory, Refinement, and Polishing Phases. Each phase is roughly centered around audience whom decisions, methodologies, results are being immediately communicated. Importantly, each can also give rise...
Novel wildfire regimes are rapidly changing global ecosystems and pose significant challenges for biodiversity conservation ecosystem management. In this study, we used DNA metabarcoding to assess the response of arthropod pollinator communities large-scale wildfires across diverse habitat types in California. We sampled six reserves within University California Natural Reserve System, each which was partially burned 2020 Lightning Complex Using yellow pan traps target pollinators, collected...
Abstract Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation a comparative genomic resource consisting 23 genomes from species-rich Drosophila montium group, 22 which presented here first time. The group is well-positioned clade genomics. Within clade, distances such that large numbers sequences can be accurately aligned while also recovering strong signals divergence; and distance between D....
Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of particular chirality are similarly asymmetric relative to each other. Models auxin flux capable recapitulating phyllotaxis predict handed asymmetries initiating leaf primordia empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend similar analysis asymmetry decussate and distichous phyllotaxy. We found our simulation models...
Abstract Leaf morphogenesis involves cell division, expansion, and differentiation in the developing leaf, which take place at different rates positions along medio-lateral proximal–distal leaf axes. The gene expression changes that control fate these axes remain elusive due to difficulties precisely isolating tissues. Here, we combined rigorous early characterization, laser capture microdissection, transcriptomic sequencing ask how patterns regulate wild-type tomato (Solanum lycopersicum)...
Plants sense foliar shade of competitors and alter their developmental programs through the avoidance response. Internode petiole elongation, changes in overall leaf area mass per area, are stereotypical architectural responses to shoot. However, shape complexity response remain incompletely, qualitatively, described. Using a meta-analysis >18,000 previously published leaflet outlines, we demonstrate that alters domesticated tomato wild relatives. The effects on subtle with respect...
What are the challenges and best practices for doing data-intensive research in teams, labs, other groups? This paper reports from a discussion which researchers many different disciplines departments shared their experiences on data science domains. The issues we discuss range technical to social, including with getting same computational stack, workflow pipeline management, handoffs, composing well-balanced team, dealing fluid membership, fostering coordination communication, not...
Abstract Plant morphology is inherently mathematical in that describes plant form and architecture with geometrical topological descriptors. The geometries topologies of leaves, flowers, roots, shoots their spatial arrangements have fascinated biologists mathematicians alike. Beyond providing aesthetic inspiration, quantifying has become pressing an era climate change a growing human population. Modifying morphology, through molecular biology breeding, aided by perspective, critical to...
ABSTRACT Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of particular chirality are similarly asymmetric relative to each other. Models auxin flux capable recapitulating phyllotaxis predict handed asymmetries initiating leaf primordia empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend similar analysis asymmetry decussate and distichous phyllotaxy. We found our simulation...
This multi-disciplinary case study details how a public web application combines information and game design to visualize effects of user-defined policies intended reduce plastic waste. Contextualizing this open source software within broader lineage digital media research, user experience exploration outlines potential directions for facilitating conversation between artificial intelligence, scientists, decision makers during an iterative policy building process. Furthermore, system...
Paraffin embedding and sectioning is a classic technique used in variety of biological disciplines. Though the fruit fly Drosophila melanogaster are one most commonly-employed model organisms, immense literature lacking current protocols for whole, adult flies. Here, we adopted plant histology protocol to embed entire flies thin present our performing FISH on subsequent sections. In interest reproducibility, have tried include details that normally omitted from published protocols.
Abstract The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One main contributors to is efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis has revealed that PIN1 genes are split into two sister clades; relatively uncharacterized Sister-Of-PIN1 (SoPIN1) . In this paper we identify entire-2 loss-of-function SlSoPIN1a (Solyc10g078370) mutant in Solanum lycopersicum plants unable specify proper initiation leading...
Abstract Many microbes induce striking behavioral changes in their animal hosts, but how they achieve this is poorly understood, especially at the molecular level. Mechanistic understanding has been largely constrained by lack of a model system with advanced tools for manipulation. We recently discovered strain behavior-manipulating fungal pathogen Entomophthora muscae infecting wild Drosophila , and established methods to infect D. melanogaster lab. Lab-infected flies manifest moribund...