The Mildred E. Mathias Botanical Garden is actively used as a research and teaching site by faculty from UCLA and other nearby colleges and universities. In addition to the Garden, MEMBG hosts the UCLA Herbarium, a collection of preserved plant specimens used for a variety of research activities.

UCLA faculty are at the forefront of botanical research. Explore the links below to learn about the diverse plant research being conducted at UCLA.

Peggy Fong -- Department of Ecology & Evolutionary Biology

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Our lab focuses on the ecology of marine systems. We work in a variety of habitats, from coral reefs to estuaries, and are especially interested in how human activities impact coastal ecosystems.

Bob Goldberg -- Department of Molecular, Cellular and Developmental Biology

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During the next 50 years, we need to produce more food than in the entire history of humankind on a decreasing amount of land for crop production. A major challenge for the 21st century is to increase the yields of major crop plants, such as soybean, using state-of-the-art genetic technologies. One way to accomplish this task is to use genomics to understand all of the genes required to ?make a seed? in order to engineer plants for yield traits such as more seeds, bigger seeds, and seeds with improved nutritional composition. Increasing seed yield should contribute significantly to enhancing our food supply, because over half of the major crops used for human consumption are seed crops. My laboratory has been investigating gene activity during seed development in order to identify the genes and gene regulatory networks required to program seed development. We have been using laser microdissection (LCM) and GeneChip microarray experiments to profile the mRNAs present in every soybean and Arabidopsis seed compartment (e.g., embryo, endosperm, seed coat), region (embryo proper, suspensor), and tissue (e.g., inner integument, endothelium, seed coat epidermis) throughout seed development. For example, what are the genes that are active in different embryonic regions shortly after fertilization (i.e., embryo proper, suspensor)? The genomes of both Arabidopsis and soybean have been sequenced and techniques to dissect gene function in both plants are well established. The focus of our experiments is to identify transcription factor genes that program differentiation events during seed formation. We are complementing our experiments by using high throughput sequencing, RNAi knock-down, promoter dissection, and bioinformatic experiments in order to determine how genes active in different seed parts are organized into regulatory networks that program seed development. The long-term goal of research being carried out in my laboratory is to understand ?how to make a seed? in order to use this information for the improvement of crop plants.

Ann Hirsch -- Department of Molecular, Cellular and Developmental Biology

Website

Research Interests

Earlier, we studied the interaction between nitrogen-fixing bacteria (alpha-rhizobia) and legumes such as alfalfa, pea, and soybean to learn why this interaction occurs exclusively with legumes. The roots of legume plants house the bacteria, usually in root nodules, in which the microbes convert atmospheric nitrogen into ammonia, thereby allowing the plant to live without added nitrogen fertilizer. In my early years at UCLA, I demonstrated the importance of phytohormones in nodule development, the significance of various plant and bacterial proteins for adherence to the root, and also showed the conservation of signal transduction pathways in nodulation and mycorrhization pathways based on common gene expression patterns. Later, we began to investigate what-are-known as “non-traditional” nitrogen fixers, the newly discovered beta-rhizobia, as well as the plants associated with them. Because many of these bacteria exhibit metabolic activities, such as cellulose degradation as well as nodulation and nitrogen fixation (in the case of the beta-rhizobia), they have the potential, not only to be used for enhancing nitrogen nutrition in crop plants, especially as increased energy costs result in greater fertilizer expenditures, but also in the production of biofuels. To this end, I coordinated the sequencing and annotation of four Burkholderia genomes, including a species that nodulates agronomically important legumes growing in arid and acidic soils. In addition, two Micromonospora (actinobacteria) genomes were sequenced and these data are published. Micromonospora is an important Plant Growth Promoting Bacterial (PGPB) species. My lab has also determined that symbiotic Burkholderia spp. are unlikely pathogens based on bioinformatics analyses and by employing HeLa cell and Caenorhabditis elegans assays to determine non-pathogenicity. We recently published on the different arrangement of nodulation and nitrogen fixation genes in the plant-associated Burkholderia versus the well-studied alpha rhizobial species. Because my research has always focused on the ?hidden half? of the plant, i.e. the root, and especially on the beneficial interactions that take place between plant roots and microbes in the rhizosphere microbiome, I made the transition early on to working on plant microbiomes. In so doing, we began to investigate a broader range of plant-growth promoting bacteria (PGPB), which are associated with roots, especially those isolated from arid environments. Our rationale is that as the climate changes, agricultural productivity will decline because crop-growing regions will become drier and less fertile. Novel drought-adapted, nitrogen-fixing bacteria are likely to provide genetic traits that increase both nutrient availability and environmental tolerance to salinity and drought brought about by reduced rainfall, higher soil acidity, and increased temperatures. In addition, many PGPB are effective at inhibiting plant pathogens, either directly by killing the pathogens or indirectly by making plants healthier so they can overcome pathogen infection. Moreover, a combination of nitrogen-fixing bacteria and one or more PGPB, such as Micromonospora or Bacillus spp., enhance plant growth and yield beyond single inoculation. The development of microbial consortia for plant inocula is the next direction of research that the Hirsch lab is pursuing. The microbes that inhabit nitrogen-fixing nodules grown in field conditions are the best way to determine which bacteria are compatible with another and could be used to establish consortia. My lab is also pursuing metagenomic and cultivation-dependent analysis of dryland soils as a means to find novel bacteria for inoculum development. We have licensed our discoveries from the Negev Desert (Israel) research, and we have a pending agreement with an agricultural company that is developing novel inocula to replace chemical amendments for certain crops. Studies in other deserts and dry environments are also in place.

Stephen Hubbell -- Department of Ecology & Evolutionary Biology

Nathan Kraft -- Department of Ecology & Evolutionary Biology

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Projects in the lab integrate aspects of community ecology, biogeography, ecophysiology, and phylogenetics. Recent projects have centered on the forests of lowland Amazonia and annual plant communities in California. In addition to a focus on species coexistence, research in the lab also addresses plant responses to climate change, the distribution of diversity at broad spatial scales, and the assembly of regional biotas.

Chentao Lin -- Department of Molecular, Cellular and Developmental Biology


Research Interests

We are interested in understanding a photosensory receptor called cryptochrome. Cryptochrome is a blue light receptor found in different organisms from a small weed Arabidopsis thaliana to a large animal Homo sapiens. Cryptochrome absorbs blue/UV-A light and it regulates various biological processes including biological clock in animals and flowering time in plants. We choose to work on an Arabidopsis cryptochrome, cry2 (cryptochrome 2), because Arabidopsis is relatively easy to work with. It is also a lot of fun to work with Arabidopsis because its genome has been completely sequenced so that we can use not only molecular genetics and biochemical techniques but also functional genomics approaches to solve our problems. We have found that cry2 regulates Arabidopsis flowering time, and we are trying to figure out how does cry2 do that (namely, what is the signal transduction mechanism of cry2)? We also try to understand how blue-light receptor cryptochromes work together with red-light receptor phytochromes in regulating cell elongation (namely, what is the co-action mechanism of different photoreceptors).

Jeffrey Long -- Department of Molecular, Cellular and Developmental Biology

Research Interests

The Long laboratory is interested in the transcriptional networks that control polarity and stem cell formation during plant embryonic development. We have focused our research on the transcriptional co-repressor TOPLESS (TPL) that is involved in almost all aspects of plant development, and use a variety of approaches including genetics, genomics, biochemistry and confocal imaging in our research. Our work on TPL has uncovered multiple transcription factors involved not just in embryogenesis, but also in polarity decisions in the leaves, patterning of floral organs, and the response to the hormone auxin. We also study the chromatin modifying enzymes that TPL uses to repress transcription, which are conserved between plants and animals.

Sabeeha Merchant -- Department of Biochemistry

Website

RESEARCH DESCRIPTION     

Dynamics of Fe and Cu metabolism

Plants require CO2, water, sunlight and a few minerals for growth and survival. Carbon contributes to biomass and sunlight the energy. The mineral requirement includes elements, found only at trace levels, like Fe, Zn, Cu and Mn, that enable the catalysis of an amazing repertoire of reactions, especially in the photosynthetic apparatus where biology’s most powerful oxidants and reductants are found. This structure is rich in metalloproteins and contributes to the high metal quota of some photosynthetic cells. Environmental factors can limit the availability of metals, especially Fe, but also Cu and Zn, and this naturally impacts photosynthetic performance and hence global primary productivity. The Merchant group has discovered mechanisms used by photosynthetic organisms to optimize performance in face of changing metal supply, especially limitation. Reduce, reuse and recycle! For instance, the Cu quota is dramatically reduced (to less than 5% relative to a Cu replete situation) by replacement of the copper-protein plastocyanin in photosynthesis with a functionally equivalent heme-containing cytochrome. This occurs through the action of a copper sensor and a transcription factor that recognizes copper response elements associated with the CYC6 gene. In parallel, plastocyanin is degraded, releasing the Cu cofactor, which is re-used for the biosynthesis of respiratory chain cytochrome oxidase. Similarly, Fe is recycled by degradation of ferredoxin to support the synthesis of an Fe-containing superoxide dismutase. The risk associated with the dynamics of metal ion metabolism is reduced by intracellular storage of these metals in a lysosome-related organelle. In ongoing work, the Merchant laboratory uses elemental and protein mass spectrometry in combination with live cell imaging of metal sensors and classical genetics to discover and dissect the biochemistry of the metal storing compartment.
Comparative genomics of algae
The Merchant group is also taking advantage of genome-sequencing based approaches for discovery of new components and functions related to photosynthesis and chloroplast biology. The group has amassed the largest collection of RNA-Seq data for Chlamydomonas and are presently creating co-expression networks with a view to deducing the functions of the many unannotated and uncharacterized proteins encoded in the algal genome. This work complements the prior and ongoing phylogenomics approaches for predicting functions for uncharacterized proteins in the plant lineage. Genomes of extremophile algae, isolated from acid mines or from the Svalbard archipelago, are being sequenced and assembled, with a view to discovering mechanisms for light sensing, photoprotection, CO2 concentration and pyrenoid structure and function.

Philip Rundel -- Department of Ecology & Evolutionary Biology

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Our laboratory maintains a breadth of interests centering on aspects of vascular plant adaptation to environmental water and nutrient stress. Within this context we have focused particularly on the interactions of physiological water stress and nutrient availability in limiting net primary production of arid zone plants. We are looking intensively at the relationship of seasonal changes in morphological, architectural and physiological components of plant form and function in woody desert legumes and evergreen shrubs. Our approaches in these investigations involve analysis of components of tissue water relations, photosynthetic capacity, foliar nutrient levels, leaf morphology and canopy architecture. We are very interested in applications of stable isotope ratios to ecological research studies as a means of developing integrated measurements of physiological response to environmental stress. Such measures will help us link physiological process studies to an ecosystem perspective. In addition to our work on desert ecosystems, my laboratory group maintains interests in several other areas. These include the physiological ecology of plant species in Mediterranean-type and tropical ecosystems, parallel with our desert research. We are also investigating the impact of air pollutants on photosynthetic capacity and productivity of coniferous forest trees in California.

Victoria Sork -- Department of Ecology and Evolutionary Biology

My research program examines evolutionary and ecological processes in tree populations. Gene flow and natural selection shape the genetic composition of populations that reflects evolutionary history and determines evolutionary response to future environmental change.

 Quercus lobata SW786, Sedgewick Reserve, CA

Quercus lobata SW786, Sedgewick Reserve, CA

Currently, a major thrust of my research utilizes genomic tools to document the extent to which candidate genes show environmental associations in range-wide samples of valley oak (Quercus lobata), an ecologically significant oak species that has lost the majority of its distribution in the last 300 years. This work takes a landscape genomic approach to understand adaptation, in the face of environmental change.

Our lab also investigates contemporary gene flow through pollen and seeds by developing new statistical tools for landscape scale analysis with long-term funding from the National Science Foundation. We currently have projects in a broad range of ecosystems, including oak-savanna in California, dry tropical fragmented forest in Mexico, desert communities of Africa and southern California, and tropical forest in Ecuador. These studies demonstrate the role of landscape factors and plant-animal interactions on genetic diversity within populations and connectivity among sites.

Elaine Tobin -- Department of Molecular, Cellular and Developmental Biology

Website

Research Interests

A transcription factor named CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) interacts with a phytochrome regulatory region of a photosynthetic gene of Arabidopsis thaliana. CCA1 is of particular interest because it is involved in both phytochrome and circadian regulation. Overexpression of the protein abolishes many different kinds of circadian rhythms including gene expression, leaf movements, photoperiodic flowering, and rhythmic growth of the hypocotyl. It is part of a negative feedback loop that suppresses its own synthesis. In fact, our work has shown that it is almost certainly part of the circadian oscillator itself. Our current work aims to define exactly how it interacts with other proteins and how the functioning of the oscillator is regulated. We have found that phosphorylation of CCA1 by the protein kinase CK2 is one way in which the clock is regulated. Other proteins that can interact with CCA1 are currently being investigated. We are also interested in the molecular basis of the interaction of the phytochrome photoreceptors and circadian rhythms.

Felipe Zapata -- Department of Ecology and Evolutionary Biology

Website

Most of our work is focused on flowering plants; however, research with other organisms is also welcome. Projects in the lab range from detailed evolutionary studies at the species level to broader comparative studies of large clades. To carry out our research, we use data, tools and approaches from different areas. The main motivation of our research is Natural History, so we always try to do field work to learn about the biology of the organisms we study and collect specimens for further study. We supplement our collections with Herbarium/Museum specimens to study spatial patterns of eco-phenotypic variation at different geographic scales. In the laboratory, we generate genetic and genomic data to study patterns of variation at the molecular level. Finally, we use and develop computational and statistical methods to analyze data in a comparative, quantitative framework. We aim to integrate all these approaches in our research, however some projects may emphasize one (or a few) approach more than the others. Thus, projects may involve data generation (e.g., field collections, phenotypic and ecological measurements, DNA/RNA sequencing), use publicly available data, and/or rely on computer simulations. In the future, we look forward to incorporating experimental approaches in our research.

Broad research areas that we are interested include: systematic biology, plant biology, phylogenetics, quantitative taxonomy, macroevolution, bio- and phylogeography, computational biology, evolutionary comparative genomics, adaptation, speciation, and tropical biology.

Current projects in the lab deal with questions emerging from:

  • Biosystematic studies on species discovery and species delimitation using multiple lines of evidence

  • Inference of the evolutionary history of different clades using genomic-level data

  • Inference of the evolutionary history of genes and phenotypes

  • Development of statistical methods to infer species boundaries, mainly using phenotypic and spatial data

  • Development of computational tools for phylogenomics and evolutionary comparative genomics