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Stacey Harmer | |
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Nationality | American |
Education | University of California, Berkeley (BA) University of California, San Francisco (PhD) |
Occupation | Professor · Researcher |
Awards | Howard Hughes Medical Institute Predoctoral Fellowship NIH National Research Service Award American Society for Photobiology New Investigator Award Fellow of American Society of Plant Biologists UC Davis College of Biological Sciences Faculty Research Award UC Davis Chancellor’s Fellowship Fellow of the American Association for the Advancement of Science |
Scientific career | |
Fields | Botany, Chronobiology, Cell Biology, Developmental Biology, Molecular Biology, Biochemistry, Genomics |
Institutions | University of California, Davis Scripps Research Institute Howard Hughes Medical Institute iPlant Collaborative |
Stacey Harmer is a chronobiologist whose work centers on the study of circadian rhythms in plants. Her research focuses on the molecular workings of the plant circadian clock and its influences on plant behaviors and physiology. She is a professor in the Department of Plant Biology at the University of California, Davis.
Harmer achieved her bachelor's degree in Biochemistry from the University of California, Berkeley in 1991, then earned a PhD at the University of California, San Francisco in 1998. At UC San Francisco, she was a Howard Hughes Predoctoral Fellow in Tony DeFranco's lab, while researching the systems involving signal transduction by the B-cell antigen receptor. [1] [2]
From 1998 to 2002, Harmer changed her post-doctoral studies from immunology to plant biology in order to research under Steve Kay at the Scripps Research Institute. Harmer received the NIH National Research Service Award and explored and analyzed the circadian rhythms in the lab with her in-depth knowledge in biochemistry and plant anatomy. When Harmer created her own lab, she started to investigate circadian rhythms in plants and the plant clock's function in plant physiology, which continues to be her primary scientific interest. [1] [2]
The Harmer Lab is a research group dedicated to studying the plant circadian clock, in particular the molecular processes and physiology underlying plant development and responses to environmental stimuli. The Harmer Lab was established when Harmer was recruited to the Department of Plant Biology at the University of California, Davis. [2]
By using Arabidopsis thaliana and the sunflower as models, the Harmer lab focuses on understanding how molecular mechanisms in plant circadian systems control responses to a variety of environmental cues through signaling pathways and physiological timing. Some of the lab's current research projects include investigating processes by which plants respond to fluctuations in light and identifying genes and pathways involved in regulating the plant circadian clock. [2] [3]
Over time, the Harmer Lab has made several important contributions to the field of plant chronobiology:
The Harmer Lab also collaborates with a number of outside research groups including:
At the forefront of the field, plants were used as models to establish the presence of circadian rhythms in organisms. With their accurate, endogenous clock to synchronize their physiology with the cycle of day and night, plants became model organisms to study within the field. [11] [12] Circadian rhythms enable plants to anticipate seasonal changes and adjust accordingly in order to promote survival and overall fitness through the facilitation of leaf movement, growth, pollination, and more. [13] A prime example of a model plant is Arabidopsis thaliana, also used by Harmer in many of her papers. Due to its relatively small and non-repetitive genome, Arabidopsis thaliana was also used to elucidate the existence of a TTFL (transcription-translation feedback loop) that facilitates the workings of an endogenous clock. [14] [15]
While research is still being conducted on the intricacies of the plant TFFL, many proteins and genes have been identified such as CCA1, TOC1, LHY. [13] [16] CCA1 and LHY are two, relatively well-researched transcription factors that work as repressors in the plant TFFL. These repressors target genes like ELF4, LUX, TOC1, GIGANTEA (GI), and more. The combination of activators and repressors and their oscillations within the plant circadian clock ultimately control phenotypic and physiological outputs. [13] [16] Such findings are foundational for Harmer's work on plant circadian rhythms and their subsequent effect on plant physiology. In many of her papers, Harmer utilizes implicated genes in the plant TFFL to conduct experiments.
Harmer found that circadian clock regulation within plants promoted physiological daily rhythms in root, leaf, and stem growth that were in direct response to a number of external cues including water availability, temperature, and light. Through various experiments and collaborations, Harmer discovered that this plant growth advantage revealed an underlying relationship with the genomic and metabolic makeup of the circadian clock—contributing to current models explaining plant optimization with the environment. [17]
The circadian mechanism within these plants involves numerous transcription factors that contribute to multiple transcriptional feedback loops that form a highly detailed, modeled network revolving around morning and evening outputs. Harmer suggests a simpler model that incorporates morning genes including CCA1 and LHY, and afternoon genes like RVE 4,6,8 within a regulatory system to investigate the robustness of plant rhythms in the face of changing environmental conditions. This central transcriptional feedback serves as a core part of the plant circadian clock and provides clues as to how solar tracking, water efficiency, and daily growth operate in plant systems. [5] [18]
The lab is currently exploring the role the eukaryote protein XCT to find out more about its role in stunting plant growth and regulating the circadian oscillator. With Harmer's work on the Arabidopsis thaliana,XCT has been found to rescue growth in yeast mutants. [2]
Auxin is a hormone essential to plant growth and development. Previous studies reported that the circadian clock coordinates plant growth to external environmental cues. Thus, the Harmer lab, in collaboration with another chronobiologist (Michael Covington), sought to investigate the clock regulation of auxin. In this investigation, Harmer and Covington conclude that auxin is clock-controlled in many aspects of its regulation (auxin production, auxin carriers, auxin sensors, etc.). Specifically, Harmer utilized Arabidopsis and its promoters of known clock-regulated genes in the plant TTFL (such as CCA1 and TOC1) to record expression of firefly reporter genes also known as a luciferase assay. [19] This method allows researchers to directly record and monitor the rhythmicity of circadian genes in plants.
Harmer investigated the effects of auxin dosage on the rhythmic expression in Arabidopsis. She found that exogenous application of the auxin IAA to plants causes a lengthening of the plants' free-running period. [19] This dosage was also consistent when the luciferase assay was applied to other clock-associated promoters such as Gigantea (GI), CAB2 , CCR2 , and ELF3 . Harmer then investigated circadian control over auxin signaling and its outputs such as plant growth. Harmer focused on the auxin-induced growth of the plant stem, specifically the hypocotyl. Under controlled conditions, Harmer recorded the rhythmic elongation of the stems in control and IAA-treated plants. She concluded that plants treated with exogenous auxin IAA had enhanced growth. [19] She further affirmed previous studies, stating that plant sensitivity to auxin varied with time of day, by displaying that the variable sensitivity is also a plant response regulated by circadian auxin transcriptional and growth responses. [19] Thus, by using these techniques, Harmer and Covington were able to conclude that plant responses to both endogenous auxin and exogenous auxin are regulated and controlled by the plant circadian clock. Such a link between the circadian clock and auxin signaling had never been documented before and broadened the field by connecting these two important mechanisms.
Harmer discovered that the circadian clock controls Arabidopsis seedlings’ sensitivity, which was influenced by auxin; sensitive reaction to auxin was different depending on the time of day. Building off this work, Harmer wondered about the significance of circadian clock and auxin signaling network on plant growth, so she studied circadian clock in sunflower heliotropism, or solar tracking. The sunflower's long stem made it easy to identify its heliotropism. Following the sun's location, the sunflower's leaves and stems moved from east to west during light. Anticipating sunrise, the flowers moved from west to east during dark; thus, the plant clock played a role in heliotropism. [20]
Since the sunflowers did not have pulvini, organs that controlled solar tracking for other plants, Harmer hypothesized that stem growth may cause heliotropism. She monitored growth of stems and solar tracking in '' dwarf2'' (dw2) sunflowers, which lack gibberellin growth hormones. Due to this deficiency, dw2 sunflowers have short stems and no heliotropism. After treating these flowers with gibberellin hormones, heliotropism was restored. As a result, this day and night movement was caused by the stem's elongation. [21]
Harmer further hypothesized that heliotropism occurs from the irregular growth rates on the opposite sides of the stem. On the east side, the stem had more growth during the day and less growth during the night, but on the west side, the stem experienced the opposite. This contrast indicated that the east side of the stem lengthened during day and the west side lengthened during night, which enabled it to move east to west during day and west to east at night. This uneven growth was controlled by genes influenced by light and circadian rhythm. Harmer's findings showed how circadian rhythms regulated the sunflowers movement during light and dark. [21]
Currently, Harmer is interested in understanding the molecular mechanism behind the sunflower's growth rates. Current reports suggest that certain pathways control the stem's movements during day and night. [20]
Harmer expanded her findings to search for the circadian clock's role in flower development and pollination. Sunflower heads are made up of hundreds or thousands of florets, or small individual flowers that are clustered to form a flower structure, which is a capitulum. To allow outcrossing, the florets constantly change their sex. From the outside to inside of the head, the florets are the oldest to youngest in development. In the capitulum, three to four rings of florets grow at the same time and day. [20]
Harmer hypothesized that the specific time of sunflower anthesis, the opening of the flower, could involve a circadian regulator. To test her theory, she monitored the sunflower capitula in constant darkness. The circadian rhythms of ovary and stamen continued to free run, while florets bloomed every 24 hours similar to their anthesis during light-dark cycles. The daily rhythms and floret growth without environmental distractions suggested the control from the circadian clock. [21] [22]
Circadian processes maintain temperature compensation. During constant darkness at 18 °C, 25 °C, and 30 °C, the ovary and stamen development maintained free-running rhythms. The general periods of these growths were similar across all temperatures. The internal, rhythmic activity that modulated floret's anthesis was temperature-compensated, further pushing the hypothesis on the plant clock. Based on her studies, Harmer concluded that the circadian clock, light, and temperature signals modulate the developmental timing of florets. Harmer continues to investigate the pathways that control when late-stage florets grow. Her findings opened up the possibility that the floret's anthesis may seduce pollinators, thus encouraging reproductive performance. [21] [22]
Harmer has also investigated the interplay of internal and external cues in Arabidopsis circadian rhythms. Specifically, Harmer discovered dual modes of regulation of the phytochrome-interacting proteins PIF4 and PIF5, which promote plant growth, by the internal circadian clock at the transcript level and external light at the protein level. Her findings provide a framework for explaining how internal and external cues regulate rhythmic phenotypes such as plant growth. [23]
Harmer is the recipient of several honors, both from professional societies and her institution:
A circadian rhythm, or circadian cycle, is a natural oscillation that repeats roughly every 24 hours. Circadian rhythms can refer to any process that originates within an organism and responds to the environment. Circadian rhythms are regulated by a circadian clock whose primary function is to rhythmically co-ordinate biological processes so they occur at the correct time to maximize the fitness of an individual. Circadian rhythms have been widely observed in animals, plants, fungi and cyanobacteria and there is evidence that they evolved independently in each of these kingdoms of life.
Helianthus is a genus comprising about 70 species of annual and perennial flowering plants in the daisy family Asteraceae commonly known as sunflowers. Except for three South American species, the species of Helianthus are native to North America and Central America. The best-known species is the common sunflower. This and other species, notably Jerusalem artichoke, are cultivated in temperate regions and some tropical regions, as food crops for humans, cattle, and poultry, and as ornamental plants. The species H. annuus typically grows during the summer and into early fall, with the peak growth season being mid-summer.
Heliotropism, a form of tropism, is the diurnal or seasonal motion of plant parts in response to the direction of the Sun.
A circadian clock, or circadian oscillator, also known as one’s internal alarm clock is a biochemical oscillator that cycles with a stable phase and is synchronized with solar time.
The repressilator is a genetic regulatory network consisting of at least one feedback loop with at least three genes, each expressing a protein that represses the next gene in the loop. In biological research, repressilators have been used to build cellular models and understand cell function. There are both artificial and naturally-occurring repressilators. Recently, the naturally-occurring repressilator clock gene circuit in Arabidopsis thaliana and mammalian systems have been studied.
In biology, phototropism is the growth of an organism in response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi. The cells on the plant that are farthest from the light contain a hormone called auxin that reacts when phototropism occurs. This causes the plant to have elongated cells on the furthest side from the light. Phototropism is one of the many plant tropisms, or movements, which respond to external stimuli. Growth towards a light source is called positive phototropism, while growth away from light is called negative phototropism. Negative phototropism is not to be confused with skototropism, which is defined as the growth towards darkness, whereas negative phototropism can refer to either the growth away from a light source or towards the darkness. Most plant shoots exhibit positive phototropism, and rearrange their chloroplasts in the leaves to maximize photosynthetic energy and promote growth. Some vine shoot tips exhibit negative phototropism, which allows them to grow towards dark, solid objects and climb them. The combination of phototropism and gravitropism allow plants to grow in the correct direction.
Timing of CAB expression 1 is a protein that in Arabidopsis thaliana is encoded by the TOC1 gene. TOC1 is also known as two-component response regulator-like APRR1.
Circadian Clock Associated 1 (CCA1) is a gene that is central to the circadian oscillator of angiosperms. It was first identified in Arabidopsis thaliana in 1993. CCA1 interacts with LHY and TOC1 to form the core of the oscillator system. CCA1 expression peaks at dawn. Loss of CCA1 function leads to a shortened period in the expression of many other genes.
Steve A. Kay is a British-born chronobiologist who mainly works in the United States. Dr. Kay has pioneered methods to monitor daily gene expression in real time and characterized circadian gene expression in plants, flies and mammals. In 2014, Steve Kay celebrated 25 years of successful chronobiology research at the Kaylab 25 Symposium, joined by over one hundred researchers with whom he had collaborated with or mentored. Dr. Kay, a member of the National Academy of Sciences, U.S.A., briefly served as president of The Scripps Research Institute. and is currently a professor at the University of Southern California. He also served on the Life Sciences jury for the Infosys Prize in 2011.
LUX or Phytoclock1 (PCL1) is a gene that codes for LUX ARRHYTHMO, a protein necessary for circadian rhythms in Arabidopsis thaliana. LUX protein associates with Early Flowering 3 (ELF3) and Early Flowering 4 (ELF4) to form the Evening Complex (EC), a core component of the Arabidopsis repressilator model of the plant circadian clock. The LUX protein functions as a transcription factor that negatively regulates Pseudo-Response Regulator 9 (PRR9), a core gene of the Midday Complex, another component of the Arabidopsis repressilator model. LUX is also associated with circadian control of hypocotyl growth factor genes PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PHYTOCHROME INTERACTING FACTOR 5 (PIF5).
Andrew John McWalter Millar, FRS, FRSE is a Scottish chronobiologist, systems biologist, and molecular geneticist. Millar is a professor at The University of Edinburgh and also serves as its chair of systems biology. Millar is best known for his contributions to plant circadian biology; in the Steve Kay lab, he pioneered the use of luciferase imaging to identify circadian mutants in Arabidopsis. Additionally, Millar's group has implicated the ELF4 gene in circadian control of flowering time in Arabidopsis. Millar was elected to the Royal Society in 2012 and the Royal Society of Edinburgh in 2013.
Pseudo-response regulator (PRR) refers to a group of genes that regulate the circadian oscillator in plants. There are four primary PRR proteins that perform the majority of interactions with other proteins within the circadian oscillator, and another (PRR3) that has limited function. These genes are all paralogs of each other, and all repress the transcription of Circadian Clock Associated 1 (CCA1) and Late Elongated Hypocotyl (LHY) at various times throughout the day. The expression of PRR9, PRR7, PRR5 and TOC1/PRR1 peak around morning, mid-day, afternoon and evening, respectively. As a group, these genes are one part of the three-part repressilator system that governs the biological clock in plants.
The Late Elongated Hypocotyl gene (LHY), is an oscillating gene found in plants that functions as part of their circadian clock. LHY encodes components of mutually regulatory negative feedback loops with Circadian Clock Associated 1 (CCA1) in which overexpression of either results in dampening of both of their expression. This negative feedback loop affects the rhythmicity of multiple outputs creating a daytime protein complex. LHY was one of the first genes identified in the plant clock, along with TOC1 and CCA1. LHY and CCA1 have similar patterns of expression, which is capable of being induced by light. Single loss-of-function mutants in both genes result in seemingly identical phenotypes, but LHY cannot fully rescue the rhythm when CCA1 is absent, indicating that they may only be partially functionally redundant. Under constant light conditions, CCA1 and LHY double loss-of-function mutants fail to maintain rhythms in clock-controlled RNAs.
Transcription-translation feedback loop (TTFL) is a cellular model for explaining circadian rhythms in behavior and physiology. Widely conserved across species, the TTFL is auto-regulatory, in which transcription of clock genes is regulated by their own protein products.
Carla Beth Green is an American neurobiologist and chronobiologist. She is a professor in the Department of Neuroscience and a Distinguished Scholar in Neuroscience at the University of Texas Southwestern Medical Center. She is the former president of the Society for Research on Biological Rhythms (SRBR), as well as a satellite member of the International Institute for Integrative Sleep Medicine at the University of Tsukuba in Japan.
Dmitri Nusinow is an American chronobiologist who studies plant circadian rhythms. He was born on November 7, 1976, in Inglewood, California. He currently resides in St. Louis, and his research focus includes a combination of molecular, biochemical, genetic, genomic, and proteomic tools to discover the molecular connections between signaling networks, circadian oscillators, and specific outputs. By combining these methods, he hopes to apply the knowledge elucidated from the Arabidopsis model to other plant species.
EARLY FLOWERING 3 (ELF3) is a plant-specific gene that encodes the hydroxyproline-rich glycoprotein and is required for the function of the circadian clock. ELF3 is one of the three components that make up the Evening Complex (EC) within the plant circadian clock, in which all three components reach peak gene expression and protein levels at dusk. ELF3 serves as a scaffold to bind EARLY FLOWERING 4 (ELF4) and LUX ARRHYTHMO (LUX), two other components of the EC, and functions to control photoperiod sensitivity in plants. ELF3 also plays an important role in temperature and light input within plants for circadian clock entrainment. Additionally, it plays roles in light and temperature signaling that are independent from its role in the EC.
Elaine Munsey Tobin is a professor of molecular, cell, and developmental biology at the University of California, Los Angeles (UCLA). Tobin is recognized as a Pioneer Member of the American Society of Plant Biologists (ASPB).
Professor Alex A.R. Webb is a plant biologist whose computational, genetic, and physiological studies center around plant chronobiology. He currently serves as the head of the Circadian Signal Transduction Group in the University of Cambridge's Department of Plant Sciences researching circadian pathways and what regulates them.
The chlorophyll a/b-binding protein gene, otherwise known as the CAB gene, is one of the most thoroughly characterized clock-regulated genes in plants. There are a variety of CAB proteins that are derived from this gene family. Studies on Arabidopsis plants have shed light on the mechanisms of biological clocks under the regulation of CAB genes. Dr. Steve Kay discovered that CAB was regulated by a circadian clock, which switched the gene on in the morning and off in the late afternoon. The genes code for proteins that associate with chlorophyll and xanthophylls. This association aids the absorption of sunlight, which transfers energy to photosystem II to drive photosynthetic electron transport.