DYNAMIC ENVIRONMENTAL PHOTOSYNTHETIC PHENOTYPING FOR MAPPING RESPONSES OF CROP PLANTS TO ENVIRONMENTAL FLUCTUATIONS

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1004797
• Project Start Date: Dec 1, 2014
• Project End Date: Nov 30, 2019
• Program Code: [(N/A)]- (N/A)

Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824

Performing Department
Plant Research Laboratory

Non Technical Summary
Our world is facing a confluence of unprecedented challenges that directly involve the plant sciences. The U.N. estimates that food production will have to increase by 50-70% over the next 30-50 years (http://www.un.org/waterforlifedecade/food_security.shtml), whereas the increases in plant productivity seen in the early years of the "green revolution" have flattened out (Ray et al., 2012), at least in part caused by rapid climate change, depletion of nonrenewable resources, eutrophication of waters etc. that may severely diminish plant productivity (Lobell and Gourdji, 2012). At the same time, plants and algae are increasingly viewed as sources of fuel to supplant fossil fuels, leading to potential competition for arable land (e.g. Rathmann et al., 2010). There is thus an urgent need to develop highly productive, environmentally robust and sustainable energy and food production under a rapidly changing environment. Traditional breeding of crops have focused on maximized many of the easily modifiable plant parameters (e.g., crop architecture, plant growth cycle), leaving the (more challenging) energy storing reactions of photosynthesis and plant responses to environmental changes as the remaining opportunities for improvement (Zhu et al., 2010). The long-term aim of this proposal is to accelerate development and deployment of crop lines with improved photosynthetic efficiency and robustness. We will focus on delineating the responses of photosynthesis to environmental conditions, in particular combinations of fluctuating light, temperature and CO2 levels. The project will take advantage of novel high throughput plant phenotyping technologies developed at MSU, including the Dynamic Environmental Phenotype Imager (DEPI) platform that captures "videos" of plant responses to environmental changes. Work over the past two years has shown that DEPI and related technologies can be used in model systems like Arabidopsis to discover new genes and biochemical processes that are critical for efficient and robust photosynthesis. The proposed work will attempt to expand the utility of the DEPI approach to agriculturally important crops. The work will focus on the large, unsolved issue that many varieties, mutants or other lines perform well under the artificially stable conditions of the greenhouse or growth chamber, but perform poorly under the dynamic conditions of the field. This is an emerging area of research and many phenotypes have been shown to have "beneficial" or minimal effects in the laboratory but large deleterious effects under dynamic conditions of the field. In other words, phenotypes observed under controlled greenhouse conditions are not always transferable to the field. In addition, there are many "hidden" phenotypes that are not revealed by the current laboratory screening protocols. Preliminary work has shown that these phenotypes (particularly those related to photosynthesis) are often dynamic and transient, and can only be observed by continuous non-invasive probes. This has been a major problem for gene discovery since field-testing is time-consuming, costly, and difficult to reproduce due to variable weather conditions. This issue is especially relevant to improving photosynthesis because this process must respond to very rapidly changing conditions, e.g. strong fluctuations in light and temperature. We propose to capture the dynamics of field conditions and replay them reproducibly in environmental chambers while measuring the dynamic responses of photosynthesis, photoinhibition, growth, seed yield and other fundamental phenotypes. We will screen association panels of highly diverse common bean varieties (in collaboration with Phil McLean, North Dakota State University and Wayne Loescher, Michigan State University) to test the feasibility of using DEPI for genome wide association (GWAS) mapping of dynamic photosynthetic responses. We will explore several environmental parameters including light intensity and fluctuation, temperature (both heat and chilling). Once established, we will apply for external funds to perform large-scale experiments to map quantitative trait loci that condition photosynthetic responses to environmental fluctuations, which may be used by plant breeders to generate more robust and productive production varieties.

Animal Health Component

10%

Research Effort Categories

Basic

50%

Applied

10%

Developmental

40%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
203	1410	1000	30%
201	1410	1060	30%
404	1410	1020	40%

Knowledge Area
203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 404 - Instrumentation and Control Systems; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1410 - Beans (dry);

Field Of Science
1060 - Biology (whole systems); 1000 - Biochemistry and biophysics; 1020 - Physiology;

Keywords

abiotic stress

common bean

genome wide association mapping

phenomics

phenotyping

photosynthesis

Goals / Objectives
Our world is facing a confluence of unprecedented challenges that directly involve the plant sciences. The U.N. estimates that food production will have to increase by 50-70% over the next 30-50 years (http://www.un.org/waterforlifedecade/food_security.shtml), whereas the increases in plant productivity seen in the early years of the "green revolution" have flattened out (Ray et al., 2012), at least in part caused by rapid climate change, depletion of nonrenewable resources, eutrophication of waters etc. that may severely diminish plant productivity (Lobell and Gourdji, 2012). At the same time, plants and algae are increasingly viewed as sources of fuel to supplant fossil fuels, leading to potential competition for arable land (e.g. Rathmann et al., 2010). There is thus an urgent need to develop highly productive, environmentally robust and sustainable energy and food production under a rapidly changing environment. Traditional breeding of crops have focused on maximized many of the easily modifiable plant parameters (e.g., crop architecture, plant growth cycle), leaving the (more challenging) energy storing reactions of photosynthesis and plant responses to environmental changes as the remaining opportunities for improvement (Zhu et al., 2010). The long-term aim of this proposal is to accelerate development and deployment of crop lines with improved photosynthetic efficiency and robustness. We will focus on delineating the responses of photosynthesis to environmental conditions, in particular combinations of fluctuating light, temperature and CO2 levels. The project will take advantage of novel high throughput plant phenotyping technologies developed at MSU, including the Dynamic Environmental Phenotype Imager (DEPI) platform that captures "videos" of plant responses to environmental changes. Work over the past two years has shown that DEPI and related technologies can be used in model systems like Arabidopsis to discover new genes and biochemical processes that are critical for efficient and robust photosynthesis. The proposed work will attempt to expand the utility of the DEPI approach to agriculturally important crops. The work will focus on the large, unsolved issue that many varieties, mutants or other lines perform well under the artificially stable conditions of the greenhouse or growth chamber, but perform poorly under the dynamic conditions of the field. This is an emerging area of research and many phenotypes have been shown to have "beneficial" or minimal effects in the laboratory but large deleterious effects under dynamic conditions of the field. In other words, phenotypes observed under controlled greenhouse conditions are not always transferable to the field. In addition, there are many "hidden" phenotypes that are not revealed by the current laboratory screening protocols. Preliminary work has shown that these phenotypes (particularly those related to photosynthesis) are often dynamic and transient, and can only be observed by continuous non-invasive probes. This has been a major problem for gene discovery since field-testing is time-consuming, costly, and difficult to reproduce due to variable weather conditions. This issue is especially relevant to improving photosynthesis because this process must respond to very rapidly changing conditions, e.g. strong fluctuations in light and temperature. We propose to capture the dynamics of field conditions and replay them reproducibly in environmental chambers while measuring the dynamic responses of photosynthesis, photoinhibition, growth, seed yield and other fundamental phenotypes. We will screen association panels of highly diverse common bean varieties (in collaboration with Phil McLean, North Dakota State University and Wayne Loescher, Michigan State University) to test the feasibility of using DEPI for genome wide association (GWAS) mapping of dynamic photosynthetic responses. We will explore several environmental parameters including light intensity and fluctuation, temperature (both heat and chilling). Once established, we will apply for external funds to perform large-scale experiments to map quantitative trait loci that condition photosynthetic responses to environmental fluctuations, which may be used by plant breeders to generate more robust and productive production varieties.

Project Methods
5.1.1. Design and construction of a full size crop DEPI system. Our current DEPI systems are well suited to models systems, but a larger platform is required to perform extensive experiments on crop plants. I am seeking funding to design and build a full size walk-in DEPI system to expand work to large crop plants over full growth cycles.The proposed new chamber systems should have the following features: i. The chamber will measure approximately 16 x 8 ft. and be as tall as 7.5 ft. high. This size will be able to accommodate up to the reproductive phase of the major crop species of rice and soybean. ii. The chamber will be outfitted with an automatic watering system using an ebb-flow bench system. The plants will be flooded for a determined period of time and the water and nutrients will be drained and not reused. iii. Wide ranges of light intensity allow us to examine photosynthesis potential of crop plants like beans or maize. The expected light intensity range would be 5 - 2000 mmol photons m-2 s-1. LED lights are used supplemented with far red (~730 nm) at virtual dusk. iv. Temperature control within the range of 10C - 45C. v. Relative humidity 20 - 80%. vi. Adjustable CO2 concentration within the range of 350 -550 ppm. vii. The chamber will be equipped with parallel cameras for video fluorescence imaging, which estimate whole plant photosynthesis and some plant growth ?parameters. viii. The chamber will be equipped with parallel RGB cameras for image analysis, ?which will be used to capture phenotypes such as growth rates. ix. The chamber will also be equipped two thermal imaging cameras to measure stomatal conductance and other transpiration related traits such as vapor pressure density (Optional: depends on cost at time of construction).5.1.2) Integrating high throughput canopy imaging and photosynthesis into DEPI Phenotyping the responses of crop plants requires measuring photosynthesis in 3D, dens and complex canopies. One of the accomplishments of the current ARPA-E supported work is the development of two new techniques for non-invasive, high throughput estimates of photosynthetic and other phenotypes in such complex canopies.5.1.3. Solar spectrum actinic illumination Our goal with DEPI is to incrementally impose key environmental parameters to reveal emergent photosynthetic properties. Currently, these parameters include light intensity, temperatures, humidity and CO2. The goal of this section is to add control of a key environmental property, light quality. We will assemble a DEPI lighting system(s) using recently available high CRI (color rendering index) LEDs and supplemental infrared (using the current DEPI system). We will assess the effects of these light improvements on growth, morphological and photosynthetic characteristics of Camelina and beans, which are highly sensitive to light quality. 5.1.4 Thermal Imaging We propose to incorporate a network thermal imaging cameras to an existing DEPI to allow high throughput screening for altered stomatal behaviors. We will then assess the genetic variability of stomatal dynamics (i.e the rates of stomatal opening and closing) in response to CO2 and light pulses. We will then compare these variations with field data for drought tolerance and water use efficiency in collaboration with Wayne Loescher (MSU, Department of Horticulture).5.2. Test the feasibility of mapping QTLs using GWAS in Common Bean using DEPI technology. Phaseolus vulgaris (Common Bean) Common bean researchers have developed a number of populations with high genetic diversity, making them extremely valuable for the proposed studies. The USDA funded BeanCAP project developed the Middle American Diversity Panel that contains approximately 300 cultivars from both the Durango (pinto, great northern, pink, and red market classes) and Mesoamerican (black, navy, small red) races. The value of such a panel is that it only needs to be genotyped once and then is available for mapping of any trait using genome-wide association studies (GWAS) approaches. The Middle American panel has already been genotyped using chip and genotype-by-sequencing (GBS) techniques, and a total of ~15,000 SNPs were discovered. This density of marker allows researchers to polymorphisms very near or even in potential candidate genes of interest. Currently there are several projects using this panel to identify loci for agronomic, root, micronutrient, and disease resistance traits. Given the abundant efforts already invested in this population, it is an ideal starting population for the research proposed here. Seed for this population would be available from Dr. Phil McClean, North Dakota State University. Based on our initial results, we may also explore a second population, the Durango Diversity Panel, of approximately 190 lines including pinto, great northern, pink, and red market classes. The high drought tolerance generally observed in genotypes from race Durango makes it an excellent system for studying response to drought and perhaps heat. This population is currently being genotyped in the McLean lab, or a ~6x coverage (>1 million SNPs) is expected for the population. This coverage should allow us to map important genetic factors close to or into individual genes. Dr. McClean will also be available to provide seed for this population. For these feasibility studies, association panel libraries will be grown in standard growth chambers from seed until a mid-vegetative stage. At this point in development, the plants will be transferred from the standard chambers into the DEPI prototype chamber for ~ one week. Throughout this week, the plants will be continually imaged for photosynthetic traits while exposed to the fluctuating environmental conditions of temperature, light intensity and humidity. Multiple photosynthetic parameters under multiple environmental conditions will be will analyzed with bioinformatics tools for strong GWAS signals in collaboration with Professor Phil McLean and Dr. Jin Chen (MSU, PRL). Strong leads will be pursued with external funding using larger plant populations to identify potential gene targets and follow up genetics and biochemical studies to determine the specific genes and mechanisms involved in differential responses.

Progress 12/01/14 to 11/30/19

Outputs
Target Audience:Plant scientists, local and global communities of farmers, researchers, extension agents, global modeling and big data efforts, and entrepreneurs Changes/Problems:We have constantly reassessed our research and development goals based on new knowledge. For our basic science goals, two new discoveries (the Dψ effects on photosystem II and the identification of the probably mechanism for regulating cyclic electron flow through the chloroplast NDH complex) have led us to refocus our efforts on certain processes. Also, the very exciting data from QTL analyses is leading us to explore new processes that may regulate certain photosynthetic responses. For our more outreach-oriented goals, experiences from the previous 3 years of PhotosynQ deployment has shown the effectiveness of on-the-ground training and technical support. To make these same tools available to a wider audience, at lower costs, we conducted 2-day workshops in MSU, Burkina Faso and Columbia, to provide hands-on training to representatives from a range of projects. In addition, based on the needs expressed by plant breeders, we have started development of an integrated system that automatically analyzes PhotosynQ data to produce high quality Quantitative Trait Loci (QTL) maps, making this sophisticated approach much easier to access. What opportunities for training and professional development has the project provided?The project has trained several graduate students (Donghee Hoh, Isaac Ossei-Bonsu, Chris Hall L. Ruby Carrillo and Geoffrey A. Davis), post-doctoral fellows (Dan TerAvest, Sebastian Kuhlgert, Ben Lucker) and many undergraduate students. The PhotosynQ web site is also a major educational platform, with over 3000 users, and is cited in over 82 publications How have the results been disseminated to communities of interest?Pulbications, web site, including www.photosynq.org, presentations at international meetings. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? New photosynthetic parameters, We developed and demonstrated (Tietz et al., 2017) a new method of measuring and imaging a key photosynthetic parameter (nonphotochemical quenching or NPQ). The new method overcomes certain limitations of the standard approach, allowing more rapid measurement and minimizing the impact certain artifacts. It also enables development of high throughput plant phenotyping approaches in both the lab and the field measurements, including high throughput and high resolution imaging of NPQ. In collaboration with the Osteryoung group at MSU, we developed methods for measuring and imaging chloroplast movements and accounting for their impact on photosynthesis (Dutta et al., 2017). There is considerable interest in improving plant productivity by altering the dynamic responses of photosynthesis in tune with natural conditions. This is exemplified by the 'energy-dependent' form of non-photochemical quenching (qE), the formation and decay of which can be considerably slower than natural light fluctuations, limiting photochemical yield. We recently reported (Davis et al., 2016) that rapidly fluctuating light can produce field recombination- induced photodamage (FRIP), where large spikes in electric field across the thylakoid membrane (delta.psi) induce photosystem II recombination reactions that produce damaging singlet oxygen. Using computational simulations as described in our publication (Davis et al., 2017), we explored the possibility of 'hacking' pmf partitioning as a target for improving photosynthesis. Under a range of illumination conditions, increasing the rate of counter-ion fluxes across the thylakoid membrane should lead to more rapid dissipation of delta.psi and formation of delta.pH. The results suggest that the partitioning of pmf into delta.psi and delta.pH are critical for responding to changes in the Calvin-Benson Cycle, illustrating the importance of integrating various levels of complexity. The central role of the chloroplast ATP synthase in regulating the light and dark reactions of photosynthesis. To optimize photosynthetic energy capture, while avoiding self-destruction, the light and dark reactions of photosynthesis must be finely co-regulated. Kanazawa et al. (Kanazawa et al., 2017) showed that the chloroplast ATP synthase, the enzyme that utilized thylakoid proton motive force (pmf) to drive the synthesis of ATP, plays a central role in the coordination of these processes. The cfq mutant of Arabidopsis, lacks the ability to downregulate the ATP synthase, resulting in uncontrolled fluxes of electrons to photosystem I, resulting in severe photodamage. These results support a critical role for ATP synthase regulation in maintaining photosynthetic control of electron transfer to prevent photodamage. A new regulatory component of the ATP synthase. ATP synthase is a major energy transducing enzyme in plants and an essential component of photosynthesis, acting as a key regulator in response to light and electron flow. We showed (Carrillo et al., 2016) that the NADPH thioredoxin reductase C (NTRC) is involved in redox regulation of the chloroplast ATP synthase specifically at low light, whereas the canonical thioredoxin-based system functions at higher light. Our results point to multiple roles for NTRC, maintaining photosynthesis under low light via its regulation of the ATP synthase, as well as playing a key role in regulation of photosynthesis under high and fluctuating light. The Energy Budget of Photosynthesis Strand et al. (Strand et al., 2017) describes the first ever demonstration that the chloroplast NDH complex is a thermodynamically reversible proton pump enables highly efficient ATP production by cyclic electron flow (CEF), and thus catalyzes very efficient ATP production by NDH-related cyclic electron flow (Strand et al., 2016). Fisher et al. (Fisher et al., 2016) describes the "final frontiers" of cytochrome bc1 and b6 f research, in particular recent discoveries in the mechanism of the Qo site "bifurcated" electron transfer that powers the translocation of protons across the energetic membrane. Strand et al. (Strand et al., 2016) presents our recent results demonstrating that the ferredoxin-quinone reductase (FQR) pathway for CEF is regulated by a redox (thiol) switch. This work may also explain some of the differences in the reported properties of the FQR pathway. Morales et al (Morales et al., 2017) describes recent advances in understanding the NDH complex and the thylakoid proton motive force (pmf) into a simulation of photosynthetic energy balance for C3 plants. Evidence that higher plant chloroplasts can rapidly exchange ATP, ADP+ Pi with the cytoplasm: Implications for the dynamic energy budget of photosynthesis. Early work suggested that exchange of ATP and ADP between the chloroplast and cytoplasm were slow, and thus the compartments likely have functionally independent adenylate pools, at least over the time scale of fluctuations in light intensity, thus requiring a self-contained photosynthetic regulatory system. However, our work showed that isolated, intact chloroplasts could apparently export ATP and follow up work showed that this activity is catalyzed by the chloroplast NTT transporters, and that it likely represents a mechanism for balancing ATP/NADPH over short time scales during fluctuating environmental conditions. MultispeQ Versions 1.0 and 2.0: In previous reports, I described out accomplishments of our PhotosynQ and MultispeQ phenotyping platforms (Kuhlgert et al. 2016). Recently, we developed, manufactured, tested and deployed the first mass produced versions 1 and 2 of MultispeQ, guided by feedback from our collaborators, including many local researchers in Malawi who have been supported by a variety of grants from USAID, McKnight Foundation etc. Version 2 is more independently produced by PhotosynQ, thus represents the culmination of one of our major goals: to produce a complete, independent and self-sustaining community resource for research. PhotosynQ Open Science Platform. We have continued development of the PhotosynQ platform to improve the collection, analyses and visualization of data more statistically powerful and more user friendly. Analyzing results from a large number of projects showed that most research teams were not capable of complex statistical analyses. We thus added tools to: 1) make accessible, integrated multivariate analyses and machine learning; 2) guide users for robust data collection; 3) automate field identification of plant genotypes and experimental conditions; 4) connect statistical packages to PhotosynQ; and 5) automated Quantitative Trait Loci (QTL) analyses using PhotosynQ. We have demonstrated the utility of these tools with our partners in Zambia, Uganda, Ghana, Nigeria and Malawi, showing successful application of the platform for identifying drought- and heat related QTLs in common bean and cowpeas. We also hosted these two researchers for a 2- week in-depth workshop at MSU to provide training on the analysis and interpretation of complex data and publish their results. Both projects showed solid, statistically significant results that are likely to be publishable in upper-tier journals. Currently there are 500 version1.0 units and more than 400 V2.0 units functioning in the world, more than 3000 users, 3600 projects and more than 982,000 experimental data sets. Key research questions being asked include assessing how crop productivity is affected by: planting density, pigeon pea intercropping, different levels of input use, conservation agriculture, soil management and legume rotations. Overall, the results strongly suggest that, with greater sharing of crop outcomes, the platform could provide actionable early indicators of crop status, and support the concept that the platform may be used for real-time management recommendations.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: X. Yin, X. Liu, J. Chen, D.M. Kramer, Joint Multi-Leaf Segmentation, Alignment, and Tracking for Fluorescence Plant Videos, IEEE Trans Pattern Anal Mach Intell 40 (2018) 1411-1423.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: C.G. Oakley, L. Savage, S. Lotz, G.R. Larson, M.F. Thomashow, D.M. Kramer, D.W. Schemske, Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana, J Exp Bot 69 (2018) 699-709
• Type: Journal Articles Status: Published Year Published: 2018 Citation: R. Fristedt, C. Hu, N. Wheatley, L.M. Roy, R.M. Wachter, L. Savage, J. Harbinson, D.M. Kramer, S.S. Merchant, T. Yeates, R. Croce, RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana, Plant J 94 (2018) 146-156.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Z.Y. Du, B.F. Lucker, K. Zienkiewicz, T.E. Miller, A. Zienkiewicz, B.B. Sears, D.M. Kramer, C. Benning, Galactoglycerolipid Lipase PGD1 Is Involved in Thylakoid Membrane Remodeling in Response to Adverse Environmental Conditions in Chlamydomonas, Plant Cell 30 (2018) 447-465.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: X. Yin, X. Liu, J. Chen, M.K. D, Joint Multi-Leaf Segmentation, Alignment, and Tracking from Fluorescence Plant Videos, IEEE Trans Pattern Anal Mach Intell (2017).
• Type: Journal Articles Status: Published Year Published: 2017 Citation: S. Tietz, C.C. Hall, J.A. Cruz, D.M. Kramer, NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem II associated antenna complexes, Plant Cell and Environment 40 (2017) 1243-1255
• Type: Journal Articles Status: Published Year Published: 2017 Citation: D.D. Strand, N. Fisher, D.M. Kramer, The Higher Plant Plastid Complex I (NDH) is a Thermodynamically Reversible Proton Pump that increases ATP production by Cyclic Electron Flow Around Photosystem I, Journal of Biological Chemistry 292 (2017) 11850-11860
• Type: Journal Articles Status: Published Year Published: 2017 Citation: A. Morales, X. Yin, J. Harbinsonb, S.M. Driever, J. Molenaar, D.M. Kramer, P.C. Struik, In silico analysis of the metabolic regulation of the photosynthetic electron transport chain in C3 plant species, Plant physiology 176 (2017) 1247-1261
• Type: Journal Articles Status: Published Year Published: 2017 Citation: B. Lucker, E. Schwarz, S. Kuhlgert, E. Ostendorf, D.M. Kramer, Spectroanalysis in native gels (SING): rapid spectral analysis of pigmented thylakoid membrane complexes separated by CN-PAGE, Plant Journal 92 (2017) 744756.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: K.L. Liao, R.D. Jones, P. McCarter, M. Tunc-Ozdemir, J.A. Draper, T.C. Elston, D. Kramer, A.M. Jones, A shadow detector for photosynthesis efficiency, J Theor Biol 414 (2017) 231-244
• Type: Journal Articles Status: Published Year Published: 2017 Citation: K. Kohzuma, J.E. Froehlich, G.A. Davis, J.A. Temple, D. Minhas, A. Dhingra, J.A. Cruz, D.M. Kramer, The Role of LightDark Regulation of the Chloroplast ATP Synthase, Front Plant Sci 8 (2017) 1248.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: S. Dutta, J.A. Cruz, S.M. Imran, J. Chen, D.M. Kramer, K.W. Osteryoung, Variations in chloroplast movement and chlorophyll fluorescence among chloroplast division mutants under light stress, J Exp Bot 68 (2017) 3541-3555
• Type: Journal Articles Status: Published Year Published: 2017 Citation: G.A. Davis, A.W. Rutherford, D.M. Kramer, Hacking the thylakoid proton motive force (pmf) for improved photosynthesis: Possibilities and pitfalls., Philosophical Transactions of the Royal Society B 372 (2017) 20160381.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Y. Yang, L. Xu, Z. Feng, J. Cruz, L. Savage, D. Kramer, J. Chen, PhenoCurve: Capturing dynamic phenotype-environment relationships using phenomics data, Bioinformatics doi: 10.1093/bioinformatics/btw673. (2016)
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, A.K. Livingston, M. Satoh-Cruz, T. Koepke, H.M. Enlow, N. Fisher, J.E. Froehlich, J.A. Cruz, D. Minhas, K.K. Hixson, K. Kohzuma, M. Lipton, A. Dhingra, D.M. Kramer, Defects in the Expression of Chloroplast Proteins Leads to H2O2 Accumulation and Activation of Cyclic Electron Flow around Photosystem I, Front Plant Sci 7 (2016) 2073.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, N. Fisher, D.M. Kramer, Distinct Energetics and Regulatory Functions of the Two Major Cyclic Electron Flow Pathways in Chloroplasts, in: H. Kirchhoff (Ed.), Chloroplasts: Current Research and Future Trends, vol. 978-1-910190- 47-0, Horizon Press, 2016
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, N. Fisher, G.A. Davis, D.M. Kramer, Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids, Biochim Biophys Acta 1857 (2016) 1-6
• Type: Journal Articles Status: Published Year Published: 2016 Citation: R.M. Sharpe, T. Koepke, A. Harper, J. Grimes, M. Galli, M. Satoh-Cruz, A. Kalyanaraman, K. Evans, D. Kramer, A. Dhingra, CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites, PloS one 11 (2016).
• Type: Journal Articles Status: Published Year Published: 2016 Citation: S. Kuhlgert, G. Austic, R. Zegarac, I. Osei-Bonsu, D. Hoh, M.I. Chilvers, M.G. Roth, K. Bi, D. TerAvest, W. Prabode, D.M. Kramer, MultispeQ Beta  A tool for large-scale plant phenotyping connected to the open PhotosynQ network, Royal Society Open Science 3 (2016) 160592
• Type: Journal Articles Status: Published Year Published: 2016 Citation: N. Fisher, M.K. Bowman, D.M. Kramer, Electron transfer reactions at the Qo site of the cytochrome bc1 complex: the good, the bad, and the ugly, in: T. Kallas, W.A. Cramer (Eds.), Cytochromes and Cytochromes Complexes, vol. 41, 2016, pp. 419-434.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: G.A. Davis, A. Kanazawa, M.A. Sch�ttler, K. Kohzuma, J.E. Froehlich, A.W. Rutherford, M. Satoh-Cruz, D. Minhas, S. Tietz, A. Dhingra, D.M. Kramer, Limitations to photosynthesis by proton motive force-induced photosystem II photodamage eLife eLife 2016;5:e16921 (2016).
• Type: Journal Articles Status: Published Year Published: 2016 Citation: .A. Cruz, L.J. Savage, R. Zegarac, C.C. Hall, M. Satoh-Cruz, G.A. Davis, W.K. Kovac, J. Chen, D.M. Kramer, Dynamic environmental photosynthetic imaging reveals emergent phenotypes, Cell Syst 2 (2016) 365-377
• Type: Journal Articles Status: Published Year Published: 2018 Citation: L.R. Carrillo, M. Satoh-Cruz, A. Kanazawa, J.E. Froehlich, J.A. Cruz, L.J. Savage, D.M. Kramer, Rapid exchange of ATP by the chloroplast envelope: Implications for the energy budget of photosynthesis, In preparation 87 (2018) 654-663.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: M.L. Campos, Y. Yoshida, I.T. Major, D. de Oliveira Ferreira, S.M. Weraduwage, J.E. Froehlich, B.F. Johnson, D.M. Kramer, G. Jander, T.D. Sharkey, G.A. Howe, Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs, Nature communications 7 (2016) 12570
• Type: Journal Articles Status: Published Year Published: 2015 Citation: H. Scharr, M. Minervini, A. French, C. Klukas, D.M. Kramer, X. Liu, I. Luengo, J.-M. Pape, G. Polder, D. Vukadinovic, X. Yin, S. Tsaftaris (2015) Leaf segmentation in plant phenotyping: a collation study. Machine Vision and Applications DOI 10.1007/s00138-015-0737-3.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: M. Agostoni, B.F. Lucker, M. Smith, A. Kanazawa, G.J. Blanchard, D.M. Kramer, B.L. Montgomery, Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon Algal Research 15 (2016) 110-119
• Type: Journal Articles Status: Published Year Published: 2016 Citation: B. Abramson, B. Kachel, D. Kramer, D. Ducat, Increased photochemical efficiency in cyanobacteria via an engineered sucrose sink, Plant and Cell Physiology 57 (2016) 2451-2460
• Type: Journal Articles Status: Published Year Published: 2015 Citation: M.T. Juergens, R. Deshpande, B.F. Lucker, J.J. Park, H. Wang, M. Gargouri, F.O. Holguin, B. Disbrow, T. Schaub, J.N. Skepper, D.M. Kramer, D.R. Gang, L.M. Hicks, Y. Shachar-Hill (2015) The Regulation of Photosynthetic Structure and Function During Nitrogen Deprivation in Chlamydomonas reinhardtii. Plant physiology 167, 558-573.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: D.D. Strand, A.K. Livingston, M. Satoh-Cruz, J.E. Froehlich, V.G. Maurino, D.M. Kramer (2015) Activation of cyclic electron flow by hydrogen peroxide in vivo. Proc Natl Acad Sci U S A 112, 5539-5544.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: O. Tsabari, R. Nevo, S. Meir, L.R. Carrillo, D.M. Kramer, Z. Reich (2015) Differential effects of ambient or diminished CO2 and O2 levels on thylakoid membrane structure in light-stressed plants. Plant Journal 81, 884-894.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: L. Xu, J.A. Cruz, L. Savage, D.M. Kramer, J. Chen (2015) Plant photosynthesis phenomics data quality control. Bioinformatics 31, 1796-1804.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Tamburic, B., Guruprasad, S., Radford, D. T., Szabo, M., Lilley, R. M., Larkum, A. W., Franklin, J. B., Kramer, D. M., Blackburn, S. I., Raven, J. A., Schliep, M., and Ralph, P. J. (2014) The effect of Diel temperature and light cycles on the growth of nannochloropsis oculata in a photobioreactor matrix, PLoS One 9, e86047.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Im, Y. J., Smith, C. M., Phillippy, B. Q., Strand, D., Kramer, D. M., Grunden, A. M., and Boss, W. F. (2014) Increasing phosphatidylinositol (4,5)-bisphosphate biosynthesis affects basal signaling and chloroplast metabolism in Arabidopsis thaliana, Plants 3, 27-57.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Fisher, N., and Kramer, D. M. (2014) Non-photochemical reduction of thylakoid photosynthetic redox carriers in vitro: Relevance to cyclic electron flow around photosystem I?, Biochim Biophys Acta 1837, 1944-1954.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Attaran, E., Major, I. T., Cruz, J. A., Rosa, B. A., Koo, A. J., Chen, J., Kramer, D. M., He, S. Y., and Howe, G. A. (2014) Temporal Dynamics of Growth and Photosynthesis Suppression in Response to Jasmonate Signaling, Plant Physiol 165, 1302-1314.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Armbruster, U., Carrillo, L. R., Venema, K., Pavlovic, L., Schmidtmann, E., Kornfeld, A., Jahns, P., Berry, J. A., Kramer, D. M., and Jonikas, M. C. (2014) Ion antiport accelerates photosynthetic acclimation in fluctuating light environments, Nature communications 5, 5439.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Sun, W., Ubierna, N., Ma, J. Y., Walker, B. J., Kramer, D. M., and Cousins, A. B. (2014) The coordination of C4 photosynthesis and the CO2-concentrating mechanism in maize and Miscanthus x giganteus in response to transient changes in light quality, Plant Physiol 164, 1283-1292.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Strand, D. D., and Kramer, D. M. (2014) Control of Non-Photochemical Exciton Quenching by the Proton Circuit of Photosynthesis, In Non-Photochemical Quenching and Energy Dissipation in Plants, Algae and Cyanobacteria (DemmigAdams, B., Garab, G., Adams III, W., and Govindjee, Eds.), pp 387408, Springer, The Netherlands.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Lucker, B. F., Hall, C., Zegarac, R., and Kramer, D. M. (2014) The Environmental Photobioreactor (ePBR): An Algal culturing platform for simulating dynamic natural environments, Algal Research DOI: 10.1016/j.algal.2013.12.007.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Kunz, H. H., Gierth, M., Herdean, A., Satoh-Cruz, M., Kramer, D. M., Spetea, C., and Schroeder, J. I. (2014) Plastidial transporters KEA1, -2, and -3 are essential for chloroplast osmoregulation, integrity, and pH regulation in Arabidopsis, Proc Natl Acad Sci U S A 111, 7480-7485.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Kanazawa, A., Blanchard, G. J., Szabo, M., Ralph, P. J., and Kramer, D. M. (2014) The site of regulation of light capture in Symbiodinium: does the peridinin-chlorophyll a-protein detach to regulate light capture?, Biochim Biophys Acta 1837, 1227-1234.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Hall, C., Norman, W., Kovac, W. K., Kramer, D. M., Savage, L., and Cruz, J. (2014) DEPItrol : Control software for theDynamic Environmental Phenotype Imager.
• Type: Other Status: Published Year Published: 2014 Citation: Chen, J., Tessmer, O. L., Cruz, J., and Kramer, D. M. (2014) Visual Phenomics: A software package for high throughput analysis of plant photosynthesis and growth data analysis.
• Type: Other Status: Published Year Published: 2014 Citation: Macaluso, S., and Chen, J. (2014) PhenoMath: A software package for deep analysis of high througput photosynthesis data.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Plant scientists, local and global communities of farmers, researchers, extension agents, global modeling and big data efforts, and entrepreneurs Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has trained graduate students(Donghee Hoh, Isaac Ossei-Bonsu, Chris Hall L. Ruby Carrillo and Geoffrey A. Davis), post-doctoral fellows (Dan TerAvest, Sebastian Kuhlgert, Ben Lucker) and many undergraduate students. The PhotosynQ web site is also a major educational platform, with over 3000 users, and is cited in over 82 publications. How have the results been disseminated to communities of interest?Publications (see Products), presenations at meetings, workshops and our web site (www.photosynQ.org). What do you plan to do during the next reporting period to accomplish the goals?Each of the accomplishments has led to new goals. We will focus in the next year on 1) determining the role of the proton motive force on the responses of photosynthesis to environmental fluctuations; 2) developing advanced methods to identify genetic and mechanistic bases of the regulaiton of photosynthesis using natural variation panels and PhotosynQ-related analytical tools; 3) assessing the roles of lipids and other cellular components in the responses of photosynthesis to temperatures stress; and 4) establishing PhotosynQ as a major international open science hub.

Impacts
What was accomplished under these goals? New photosynthetic parameters,We developed and demonstrated (Tietz et al., 2017) a new method of measuring and imaging a key photosynthetic parameter (nonphotochemical quenching or NPQ). The new method overcomes certain limitations of the standard approach, allowing more rapid measurement and minimizing the impact certain artifacts. It also enables development of high throughput plant phenotyping approaches in both the lab and the field measurements, including high throughput and high resolution imaging of NPQ. In collaboration with the Osteryoung group at MSU, we developed methods for measuring and imaging chloroplast movements and accounting for their impact on photosynthesis (Dutta et al., 2017). A major, unrecognized, limitation to photosynthesis and strategies for improvement.There is considerable interest in improving plant productivity by altering the dynamic responses of photosynthesis in tune with natural conditions. This is exemplified by the 'energy-dependent' form of non-photochemical quenching (qE), the formation and decay of which can be considerably slower than natural light fluctuations, limiting photochemical yield. We recently reported (Davis et al., 2016) that rapidly fluctuating light can produce field recombination- induced photodamage (FRIP), where large spikes in electric field across the thylakoid membrane (delta.psi) induce photosystem II recombination reactions that produce damaging singlet oxygen. Using a series of computational simulations as described in our publication (Davis et al., 2017), we explored the possibility of 'hacking' pmf partitioning as a target for improving photosynthesis. Under a range of illumination conditions, increasing the rate of counter-ion fluxes across the thylakoid membrane should lead to more rapid dissipation of delta.psi and formation of delta.pH. The results suggest that the partitioning of pmf into delta.psi and delta.pH are critical for responding to changes in the Calvin-Benson Cycle, illustrating the importance of integrating various levels of complexity. The central role of the chloroplast ATP synthase in regulating the light and dark reactions of photosynthesis.To optimize photosynthetic energy capture, while avoiding self-destruction, the light and dark reactions of photosynthesis must be finely co-regulated. Kanazawa et al. (Kanazawa et al., 2017) showed that the chloroplast ATP synthase, the enzyme that utilized thylakoid proton motive force (pmf) to drive the synthesis of ATP, plays a central role in the coordination of these processes. Thecfqmutant of Arabidopsis, lacks the ability to downregulate the ATP synthase, resulting in uncontrolled fluxes of electrons to photosystem I, resulting in severe photodamage. These results support a critical role for ATP synthase regulation in maintaining photosynthetic control of electron transfer to prevent photodamage. A new regulatory component of the ATP synthase.ATP synthase is a major energy transducing enzyme in plants and an essential component of photosynthesis, acting as a key regulator in response to light and electron flow. We showed (Carrillo et al., 2016) that the NADPH thioredoxin reductase C (NTRC) is involved in redox regulation of the chloroplast ATP synthase specifically at low light, whereas the canonical thioredoxin-based system functions at higher light. Our results point to multiple roles for NTRC, maintaining photosynthesis under low light via its regulation of the ATP synthase, as well as playing a key role in regulation of photosynthesis under high and fluctuating light. The Energy Budget of PhotosynthesisStrand et al. (Strand et al., 2017) describes the first ever demonstration that the chloroplast NDH complex is a thermodynamically reversible proton pump enables highly efficient ATP production by cyclic electron flow (CEF), and thus catalyzes very efficient ATP production by NDH-related cyclic electron flow (Strand et al., 2016). Fisher et al. (Fisher et al., 2016) describes the "final frontiers" of cytochromebc1andb6fresearch, in particular recent discoveries in the mechanism of the Qosite "bifurcated" electron transfer that powers the translocation of protons across the energetic membrane. Strand et al. (Strand et al., 2016) presents our recent results demonstrating that the ferredoxin-quinone reductase (FQR) pathway for CEF is regulated by a redox (thiol) switch. This work may also explain some of the differences in the reported properties of the FQR pathway. Morales et al (Morales et al., 2017) describes recent advances in understanding the NDH complex and the thylakoid proton motive force (pmf) into a simulation of photosynthetic energy balance for C3 plants. Evidence that higher plant chloroplasts can rapidly exchange ATP, ADP+ Pi with the cytoplasm: Implications for the dynamic energy budget of photosynthesis.Early work suggested that exchange of ATP and ADP between the chloroplast and cytoplasm were slow, and thus the compartments likely have functionally independent adenylate pools, at least over the time scale of fluctuations in light intensity, thus requiring a self-contained photosynthetic regulatory system. However, our work showed that isolated, intact chloroplasts could apparently export ATP and follow up work showed that this activity is catalyzed by the chloroplast NTT transporters, and that it likely represents a mechanism for balancing ATP/NADPH over short time scales during fluctuating environmental conditions. MultispeQ Versions 1.0 and 2.0:In previous reports, I described out accomplishments of our PhotosynQ and MultispeQ phenotyping platforms (Kuhlgert et al. 2016). Recently, we developed, manufactured, tested and deployed the first mass produced versions 1 and 2 of MultispeQ, guided by feedback from our collaborators, including many local researchers in Malawi who have been supported by a variety of grants from USAID, McKnight Foundation etc. Version 2 is more independently produced by PhotosynQ, thus represents the culmination of one of our major goals: to produce a complete, independent and self-sustaining community resource for research. PhotosynQ Open Science Platform.We have continued development of the PhotosynQ platform to improve the collection, analyses and visualization of data more statistically powerful and more user friendly. Analyzing results from a large number of projects showed that most research teams were not capable ofcomplex statistical analyses. We thusadded tools to:1) make accessible, integrated multivariate analyses and machine learning; 2) guide users for robust data collection; 3) automate field identification of plant genotypes and experimental conditions; 4) connect statistical packages to PhotosynQ; and 5) automated Quantitative Trait Loci (QTL)analyses using PhotosynQ. We have demonstrated the utility of these toolswith our partners in Zambia, Uganda, Ghana, Nigeria and Malawi, showing successful application of the platform for identifying drought- and heat related QTLs in common bean and cowpeas.We also hosted these two researchers for a 2-week in-depth workshop at MSU to provide training on the analysis and interpretation of complex data and publish their results. Both projects showed solid, statistically significant results that are likely to be publishable in upper-tier journals. Currently there are 500 version1.0 units and more than 400 V2.0 units functioning in the world, more than 3000 users, 3600 projects and more than 982,000 experimental data sets. Key research questions being asked include assessing how crop productivity is affected by: planting density, pigeon pea intercropping, different levels of input use, conservation agriculture, soil management and legume rotations. Overall, the results strongly suggest that, with greater sharing of crop outcomes, the platform could provide actionable early indicators of crop status, and support the concept that the platform may be used for real-time management recommendations.

Publications

• Type: Journal Articles Status: Published Year Published: 12018 Citation: X. Yin, X. Liu, J. Chen, D.M. Kramer, Joint Multi-Leaf Segmentation, Alignment, and Tracking for Fluorescence Plant Videos, IEEE Trans Pattern Anal Mach Intell 40 (2018) 1411-1423.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: C.G. Oakley, L. Savage, S. Lotz, G.R. Larson, M.F. Thomashow, D.M. Kramer, D.W. Schemske, Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana, J Exp Bot 69 (2018) 699-709.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: R. Fristedt, C. Hu, N. Wheatley, L.M. Roy, R.M. Wachter, L. Savage, J. Harbinson, D.M. Kramer, S.S. Merchant, T. Yeates, R. Croce, RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana, Plant J 94 (2018) 146-156.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Z.Y. Du, B.F. Lucker, K. Zienkiewicz, T.E. Miller, A. Zienkiewicz, B.B. Sears, D.M. Kramer, C. Benning, Galactoglycerolipid Lipase PGD1 Is Involved in Thylakoid Membrane Remodeling in Response to Adverse Environmental Conditions in Chlamydomonas, Plant Cell 30 (2018) 447-465.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: X. Yin, X. Liu, J. Chen, M.K. D, Joint Multi-Leaf Segmentation, Alignment, and Tracking from Fluorescence Plant Videos, IEEE Trans Pattern Anal Mach Intell (2017).
• Type: Journal Articles Status: Published Year Published: 2017 Citation: C.J. Unkefer, R.T. Sayre, J.K. Magnuson, D.B. Anderson, I. Baxter, I.K. Blaby, J.K. Brown, M. Carleton, R.A. Cattolico, T. Dale, Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts, Algal Research 22 (2017) 187-215.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: S. Tietz, C.C. Hall, J.A. Cruz, D.M. Kramer, NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem II associated antenna complexes, Plant Cell and Environment 40 (2017) 1243-1255
• Type: Journal Articles Status: Published Year Published: 2017 Citation: D.D. Strand, N. Fisher, D.M. Kramer, The Higher Plant Plastid Complex I (NDH) is a Thermodynamically Reversible Proton Pump that increases ATP production by Cyclic Electron Flow Around Photosystem I, Journal of Biological Chemistry 292 (2017) 11850-11860
• Type: Journal Articles Status: Published Year Published: 2017 Citation: A. Morales, X. Yin, J. Harbinsonb, S.M. Driever, J. Molenaar, D.M. Kramer, P.C. Struik, In silico analysis of the metabolic regulation of the photosynthetic electron transport chain in C3 plant species, Plant physiology 176 (2017) 1247-1261
• Type: Journal Articles Status: Published Year Published: 2017 Citation: B. Lucker, E. Schwarz, S. Kuhlgert, E. Ostendorf, D.M. Kramer, Spectroanalysis in native gels (SING): rapid spectral analysis of pigmented thylakoid membrane complexes separated by CN-PAGE, Plant Journal 92 (2017) 744756.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: K.L. Liao, R.D. Jones, P. McCarter, M. Tunc-Ozdemir, J.A. Draper, T.C. Elston, D. Kramer, A.M. Jones, A shadow detector for photosynthesis efficiency, J Theor Biol 414 (2017) 231-244
• Type: Journal Articles Status: Published Year Published: 2017 Citation: K. Kohzuma, J.E. Froehlich, G.A. Davis, J.A. Temple, D. Minhas, A. Dhingra, J.A. Cruz, D.M. Kramer, The Role of Light-Dark Regulation of the Chloroplast ATP Synthase, Front Plant Sci 8 (2017) 1248.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: A. Kanazawa, E. Ostendorf, K. Kohzuma, D. Hoh, D.D. Strand, M. Sato-Cruz, L. Savage, J.A. Cruz, J.E. Froehlich, D.M. Kramer, Chloroplast ATP synthase modulation of the thylakoid proton motive force: Implications for photosystem I and photosystem II photoprotection Frontiers in Plant Physiology https://doi.org/10.3389/fpls.2017.00719 (2017)
• Type: Journal Articles Status: Published Year Published: 2017 Citation: S. Dutta, J.A. Cruz, S.M. Imran, J. Chen, D.M. Kramer, K.W. Osteryoung, Variations in chloroplast movement and chlorophyll fluorescence among chloroplast division mutants under light stress, J Exp Bot 68 (2017) 3541-3555.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: G.A. Davis, A.W. Rutherford, D.M. Kramer, Hacking the thylakoid proton motive force (pmf) for improved photosynthesis: Possibilities and pitfalls., Philosophical Transactions of the Royal Society B 372 (2017) 20160381.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Y. Yang, L. Xu, Z. Feng, J. Cruz, L. Savage, D. Kramer, J. Chen, PhenoCurve: Capturing dynamic phenotype-environment relationships using phenomics data, Bioinformatics doi: 10.1093/bioinformatics/btw673. (2016)
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, A.K. Livingston, M. Satoh-Cruz, T. Koepke, H.M. Enlow, N. Fisher, J.E. Froehlich, J.A. Cruz, D. Minhas, K.K. Hixson, K. Kohzuma, M. Lipton, A. Dhingra, D.M. Kramer, Defects in the Expression of Chloroplast Proteins Leads to H2O2 Accumulation and Activation of Cyclic Electron Flow around Photosystem I, Front Plant Sci 7 (2016) 2073.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, N. Fisher, D.M. Kramer, Distinct Energetics and Regulatory Functions of the Two Major Cyclic Electron Flow Pathways in Chloroplasts, in: H. Kirchhoff (Ed.), Chloroplasts: Current Research and Future Trends, vol. 978-1-910190-47-0, Horizon Press, 2016
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, N. Fisher, G.A. Davis, D.M. Kramer, Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids, Biochim Biophys Acta 1857 (2016) 1-6
• Type: Journal Articles Status: Published Year Published: 2016 Citation: R.M. Sharpe, T. Koepke, A. Harper, J. Grimes, M. Galli, M. Satoh-Cruz, A. Kalyanaraman, K. Evans, D. Kramer, A. Dhingra, CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites, PloS one 11 (2016).
• Type: Journal Articles Status: Published Year Published: 2016 Citation: S. Kuhlgert, G. Austic, R. Zegarac, I. Osei-Bonsu, D. Hoh, M.I. Chilvers, M.G. Roth, K. Bi, D. TerAvest, W. Prabode, D.M. Kramer, MultispeQ Beta  A tool for large-scale plant phenotyping connected to the open PhotosynQ network, Royal Society Open Science 3 (2016) 160592
• Type: Journal Articles Status: Published Year Published: 2016 Citation: N. Fisher, M.K. Bowman, D.M. Kramer, Electron transfer reactions at the Qo site of the cytochrome bc1 complex: the good, the bad, and the ugly, in: T. Kallas, W.A. Cramer (Eds.), Cytochromes and Cytochromes Complexes, vol. 41, 2016, pp. 419-434.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: G.A. Davis, A. Kanazawa, M.A. Sch�ttler, K. Kohzuma, J.E. Froehlich, A.W. Rutherford, M. Satoh-Cruz, D. Minhas, S. Tietz, A. Dhingra, D.M. Kramer, Limitations to photosynthesis by proton motive force-induced photosystem II photodamage eLife eLife 2016;5:e16921 (2016).
• Type: Journal Articles Status: Published Year Published: 2016 Citation: .A. Cruz, L.J. Savage, R. Zegarac, C.C. Hall, M. Satoh-Cruz, G.A. Davis, W.K. Kovac, J. Chen, D.M. Kramer, Dynamic environmental photosynthetic imaging reveals emergent phenotypes, Cell Syst 2 (2016) 365-377
• Type: Journal Articles Status: Published Year Published: 2016 Citation: L.R. Carrillo, M. Satoh-Cruz, A. Kanazawa, J.E. Froehlich, J.A. Cruz, L.J. Savage, D.M. Kramer, Rapid exchange of ATP by the chloroplast envelope: Implications for the energy budget of photosynthesis, In preparation 87 (2018) 654-663.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: L.R. Carrillo, J.E. Froehlich, J.A. Cruz, L.J. Savage, D.M. Kramer, Multi-level regulation of the chloroplast ATP synthase: The chloroplast NADPH thioredoxin reductase C (NTRC) is required for redox modulation specifically under low irradiance, Plant J 87 (2016) 654-663
• Type: Journal Articles Status: Published Year Published: 2016 Citation: M.L. Campos, Y. Yoshida, I.T. Major, D. de Oliveira Ferreira, S.M. Weraduwage, J.E. Froehlich, B.F. Johnson, D.M. Kramer, G. Jander, T.D. Sharkey, G.A. Howe, Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs, Nature communications 7 (2016) 12570
• Type: Journal Articles Status: Published Year Published: 2016 Citation: M. Agostoni, B.F. Lucker, M. Smith, A. Kanazawa, G.J. Blanchard, D.M. Kramer, B.L. Montgomery, Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon Algal Research 15 (2016) 110-119
• Type: Journal Articles Status: Published Year Published: 2016 Citation: B. Abramson, B. Kachel, D. Kramer, D. Ducat, Increased photochemical efficiency in cyanobacteria via an engineered sucrose sink, Plant and Cell Physiology 57 (2016) 2451-2460

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Plant scientists, local and global communities of farmers, researchers, extension agents, global modeling and big data efforts, entrepreneurs and international development programs Changes/Problems:We have constantly reassessed our research and development goals based on new knowledge. For our basic science goals, two new discoveries (the Dψ effects on photosystem II and the identification of the probably mechanism for regulating cyclic electron flow through the chloroplast NDH complex) have led us to refocus our efforts on certain processes. Also, the very exciting data from QTL analyses is leading us to explore new processes that may regulate certain photosynthetic responses. For our more outreach-oriented goals, experiences from the previous 3 years of PhotosynQ deployment has shown the effectiveness of on-the-ground training and technical support. To make these same tools available to a wider audience, at lower costs, we conducted 2-day workshops in MSU, Burkina Faso and Columbia, to provide hands-on training to representatives from a range of projects. In addition, based on the needs expressed by plant breeders, we have started development of an integrated system that automatically analyzes PhotosynQ data to produce high quality Quantitative Trait Loci (QTL) maps, making this sophisticated approach much easier to access. What opportunities for training and professional development has the project provided?Classroom Instruction at MSU. While only 10% of my appointment is for teaching, I participate in both classroom and oneon-one graduate education. I teach in the graduate-level Plant Biochemistry course (BMB864), in which I cover the basics of photosynthesis. To prepare advanced students graduate students whose research involves photosynthesis and photosynthetic measurements, I developed a 3-credit interactive special topics course (BMB 960-Photosynthesis), which debuted in 2015, and directly addresses fundamental and current thinking in all areas of photosynthesis. A part of the course uses the PhotosynQ platform to enable students to make their own measurements, the interpretations of which are then discussed as a group and presented in a public poster session. The feedback on this course has been very favorable and I am pleased that the majority of the students who took the class are using the concepts, methods and tools directly in their ongoing research. Interdisciplinary training and catalyzed interactions. My lab is heavily involved in undergraduate and graduate students and post-doctoral teaching through hands-on research and development. The opportunity afforded by MSU and the Hannah funds has allowed us to bring together both from a wide range of disciplines and programs, including Biochemistry and Molecular Biology, Chemistry, Computer Science and Engineering, Crops and Soil Sciences, Electrical and Engineering Sciences, Forestry, Genetics and Cell Biology Horticulture, International Programs and Plant Biology. Having all these disciplines interact in the same space while working on common problems has truly facilitated communication, interactive learning and exchanges of ideas. In the past 5 years, my lab has mentored and supported 15 graduate students, 12 postdocs, 3 research assistant professors, 12 international visitors, and more than 40 undergraduates. (All undergraduates in the lab participate at in research and/or development; no one is simply a "dishwasher"). Outreach impact on education. My lab and the CAAPP are providing innovative educational tools to the MSU and international communities: 1) CAAPP has held a series of workshops on plant phenotyping that have been attended by participants across campus. We have also help PhotosynQ workshops at MSU, Columbia, Burkina Faso and Zambia; 2) The PhotosynQ platform is particularly well suited for educational applications, potentially to teach both specific concepts and the scientific method. I use the platform in my Photosynthesis class (see above), but also distribute the devices freely to graduate students at many MSU labs as a research training tool. Several other formal classes currently use the platform at MSU (in Biological Sciences Program, College of Natural Science, Horticulture, and at KBS) as well as in other countries (Ukraine, Zambia, Ghana, The Netherlands). How have the results been disseminated to communities of interest?Publications (as above) Web sites, in particular PhotosynQ: www.photosynq.org CAAPP: https://prl.natsci.msu.edu/research/center-for-advanced-algal-and-plant-phenotyping-caapp/ Presentations (selected): "PhotosynQ.org: Community-driven plant phenotyping for understanding plant responses to climate change", MSU Jan., 2016 "The Limits of Photosynthesis and Bridging the Gaps between Lab and the World" ENCAPP European Networks Conference on Algal and Plant Photosynthesis, Malta "Disruptive Technologies for High-Resolution, High-Throughput Environmental Phenotyping: Bringing the Lab to the World and the World to the Lab" Plant Improvement Technologies Congress" North Carolina, March 2016 "The Limits of Photosynthesis:What we can learn when we bridging the gaps between the lab and the world?"Colorado State University, April, 2016 "Disruptive Technologies for High-Resolution, High-Throughput Environmental Phenotyping: Bringing the Lab to the World and the World to the Lab" USAID GCFSI Retreat, April, 2016 "High-Throughput Environmental Phenotyping: Bringing the Lab to the World and the World to the Lab" Benson Hill Biosystems, May, 2016 "The Gamut of Photosynthesis and Bridging the Gaps between Lab and the World PhotosynQ" International Congress on Photosynthesis Research, Maastricht, The Netherlands "The Limits of Photosynthesis and Bridging the Gaps between Lab and the World PhotosynQ" Essex Plant Phenotyping Congress, July, 2016 "Proton motive force-induced photosystem II photodamage: A fundamental limitation to Photosynthesis imposed by the interaction of pmf and electron transfer reactions" Photosynthetic Electron Transfer Meeting, Arnham, July, 2016 "What can we learn from phenotyping the gaps between the lab and the world" Plant and Animal Genome Conference, Jan. 2017, San Diego, CA "The Gamut and Gambit of Photosynthesis: What can we learn from phenotyping the gaps between the lab and the world", John Lawrence Seminar Series, Lawrence Berkeley National Laboratory, Feb, 2017 "What can we learn from phenotyping the gaps between the lab and the world" Feb., 2017, Purdue University, Indiana "The Molecular Machinery of Photosynthesis in its Working Environment: What can we learn from phenotyping the gaps between the lab and the world", March, 2017 Japanese Society of Plant Biology, Kagoshima, Japan "Probing the thylakoid proton motive force in vivo", March, 2017 Workshop on The Chloroplast pmf, Kagoshima, Japan What do you plan to do during the next reporting period to accomplish the goals?? Basic scientificquestions: One major discovery during our past year was that photosynthesis can be severely limited by rapid buildup of the thylakoids electric field (Dψ). A major focus of our work in the current year will be on understanding the processes that control the Dψ component of photosynthesis, and how these affect photosynthetic productivity. We are also using new methodology and the deep data set obtained using PhotosynQ and DEPI to determine which photosynthetic parameters are most predictive of ultimate yield and what genetic loci control them. PhotosynQ and MultispeQ: Currently, we are working to extend the capabilities of these platforms along the following aims: 1) Develop and implement a seamless pipeline for data analyses. Lack of computer power and internet bandwidth is slowing progress on QTL analyses. We will address this issue by directly integrating open source QTL packages in the PhotosynQ platform. 2) Equip both MSU researchers and overseas partners with stomatal conductance modules and use them to identify genes and processes that control water use efficiency. HyperspeQ: The next steps will be to integrate the various measurements into one card and to optimize the methodology for preparing and assaying soil samples. We will then test the assays on a range of soil types and validate results against established methodology to establish an integrated system that makes measurements of key soil properties at a cost of a fraction of a cent per assay. We will then integrate these tools into our workflow, e.g. to assess the impact of soil properties on photosynthesis.

Impacts
What was accomplished under these goals? Our accomplishments fall roughly into three categories: 1) The development of enabling technologies that allow us to measure specific plant processes or traits; 2) the use of these tools for understanding how photosynthesis works, and how to improve it; and 3) bringing these tools and knowledge to the world. These activities are completely integrated and depend each other. In the past year, we have greatly expanded the utility of these tools, resulting in a series of publications on new tools (Cruz et al, 2016; Dutta et al, 2017; Kuhlgert et al, 2016; Sharpe et al, 2016; Tietz et al, 2017; Yang et al, 2016), but also one new discoveries made with them, including processes such the critical responses of photosynthesis to rapid environmental changes (Davis et al, 2016; Davis et al, 2017; Kanazawa et al, 2017; Liao et al, 2017; Morales et al, 2017; Yang et al, 2016), the roles of chloroplast movements in protecting photosynthesis (Dutta et al, 2017), adaptation of photosynthesis to low temperatures (Oakley et al, 2017), how photosynthesis maintains the proper energy budget (Carrillo et al, 2016; Davis et al, 2017; Fisher et al, 2016; Kanazawa et al, 2017; Strand et al, 2016a; Strand et al, 2016b), the interaction of photosynthesis with plant defense (Campos et al, 2016) and the role of peroxisomal proteins in maintaining photosynthesis (Xu et al, 2017). In the following, I cover selected accomplishments in more detail. A major, but previously unrecognized, limitation to photosynthesis and strategies for improvement. As described in three recent papers from our lab (Morales et al, 2017) (Davis et al, 2016), we reported (2) that rapidly fluctuating light can produce very large electric field (Dψ) across the thylakoid membrane, and that these spikes in Dψ can induce so-called recombination reactions in photosystem II, leading to the production of highly reactive and toxic singlet oxygen. We also showed that this process is a major limitation to photosynthesis. In a second paper, we presented a series of computational simulations (Morales et al, 2017), which explored the possibility of 'hacking' pmf partitioning as a target for improving photosynthesis. The work shows that ion fluxes may be a viable target for plant breeding or engineering. In the third paper (4), we extended the simulations to include primary metabolic pathways, suggesting that FRIP is critical for responding to changes in the Calvin-Benson Cycle. The central roles of the chloroplast ATP synthase in regulating the light and dark reactions of photosynthesis.To optimize photosynthetic energy capture, while avoiding self-destruction, the light and dark reactions of photosynthesis must be finely co-regulated. We published work (Kanazawa et al, 2017) showing that the chloroplast ATP synthase, the enzyme that utilized thylakoid proton motive force (pmf) to drive the synthesis of ATP, and often limits overall photosynthesis, plays a central role in the coordination of these processes. Briefly, we showed that thecfqmutant of Arabidopsis, which cannot downregulate ATP synthase, suffers from strong, irreversible damage to photosystem I, especially under fluctuating light. This work is an important in that it not only established a central regulatory mechanisms, but clearly illustrates why simplistic approached to improving photosynthesis will likely fail. We next showed (Carrillo et al, 2016) that the NADPH thioredoxin reductase C (NTRC) is involved in redox regulation of the chloroplast ATP synthase specifically at low light, whereas the canonical thioredoxin-based system functions at higher light. Our results point to multiple roles for NTRC, maintaining photosynthesis under low light via its regulation of the ATP synthase, as well as playing a key role in regulation of photosynthesis under high and fluctuating light. PhotosynQ.PhotosynQ consists of a cloud-based network that connects farmers, extension agents, researchers and managers with expertise, data and analytics, and a set of sophisticated, inexpensive and easy-to-use hand-held sensors that measure key environmental and plant performance parameters. Data from these sensors are transmitted wirelessly and seamlessly to PhotosynQ for analysis allowing scientists, plant breeders and even entrepreneurs to collaborate in new ways to make useful, field-based measurements of phenotypes and metadata in the field, aggregate these results, and apply sophisticated analytical tools. Currently, the platform supports more than 2300 users in 28 countries in more than 2000 separate projects. Thus far, of over 640,000 experimental data sets have been collected, not only bringing new research infrastructure to enable cutting edge plant research and breeding approaches, but also giving us an unprecedented look at how plants behave in the real world. MultispeQ:In the previous few years, we developed and deployed the beta version of the MultispeQ plant phenotyping platform. In this period, we published the first paper on the platform and its results (Kuhlgert et al, 2016). Over the past year, we developed, manufactured, tested and deployed the first mass produced version of MultispeQ (Ver. 1.0). Each step in the development was guided by feedback from our collaborators, both at MSU and over the world. The resulting instrument is considerably more sensitive, more robust, easier to use and makes new measurements that meet the specific needs of our collaborators. We produced a full batch of 500 units, all of which are in use by us, collaborators, and independent researchers around the world. Towards a Seamless Phenotype to Genotype Platform.In the previous year, we established the basis of phenotyping technologies and advanced genetics and genomics approaches to identify quantitative trait loci (QTLs) that condition more efficient and robust photosynthesis and productivity in cowpea and common beans. At the same time, we tested the ability of the PhotosynQ platform to enable researchers and farmers to conduct plant phenotyping experiments, analyze data and share results, and thus allow improvements in breeding and management on local to global scales. Using these tools, our partners in several countries, particularly in Zambia, Uganda and USA, have successfully collected large quantities of high-quality, field-based phenotypic data. Analyses of the initial data sets show that they produce high quality QTL maps and that the specific loci vary not only with treatment but also location suggesting the possibility of region- and management-specific plant improvement. HyperspeQ and Qcards.In addition to the MultispeQ instrument, we are in advanced stages of development of new, PhotosynQ-compatible instrument called HyperspeQ that makes "hyperspectral" measurements that are increasingly used to assess crop status. drought or nitrogen stress in plants, soil properties, fruit ripening etc. We also established a collaboration to develop rapid, sensitive and inexpensive measurements of soil composition. Reading these cards with HyperspeQ allows users to make highly sensitive measurements of multiple parameters on the same sample. As an initial proof of principle, we have successfully developed card-based assays for soil aluminum and potassium (K), and are developing ones for phosphorus (P, as phosphate) and soil C. NPQ(T): a fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem II associated antenna complexes.This work is published in (Tietz et al, 2017). We develop a new method to measure the key photoprotective processes of photosynthesis that are much more rapid (seconds rather than hours) and can be applied used to image NPQ, allowing for new types of high throughput anf field phenotyping.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Sharpe, R. M., Koepke, T., Harper, A., Grimes, J., Galli, M., Satoh-Cruz, M., Kalyanaraman, A., Evans, K., Kramer, D., and Dhingra, A. (2016) CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites, PloS one 11.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Strand, D. D., Fisher, N., Davis, G. A., and Kramer, D. M. (2016) Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids, Biochim Biophys Acta 1857, 1-6.
• Type: Book Chapters Status: Published Year Published: 2016 Citation: Strand, D. D., Fisher, N., and Kramer, D. M. (2016) Distinct Energetics and Regulatory Functions of the Two Major Cyclic Electron Flow Pathways in Chloroplasts, in Chloroplasts: Current Research and Future Trends (Kirchhoff, H., Ed.), Horizon Press.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Yang, Y., Xu, L., Feng, Z., Cruz, J., Savage, L., Kramer, D., and Chen, J. (2016) PhenoCurve: Capturing Dynamic Phenotype-Environment Relationships using Phenomics Data, Bioinformatics doi: 10.1093/bioinformatics/btw673.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Davis, G. A., Rutherford, A. W., and Kramer, D. M. (2017) Hacking the Thylakoid Proton Motive Force (pmf) for improved Photosynthesis: Possibilities and Pitfalls., Philosophical Transactions of the Royal Society B 372, 20160381.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Kanazawa, A., Ostendorf, E., Kohzuma, K., Hoh, D., Strand, D. D., Sato-Cruz, M., Savage, L., Cruz, J. A., Froehlich, J. E., and Kramer, D. M. (2017) Chloroplast ATP synthase modulation of the thylakoid proton motive force: Implications for photosystem i and photosystem ii photoprotection Frontiers in Plant Physiology https://doi.org/10.3389/fpls.2017.00719.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Strand, D. D., Fisher, N., and Kramer, D. M. (2017) The Higher Plant Plastid Complex I (NDH) is a Thermodynamically Reversible Proton Pump that increases ATP production by Cyclic Electron Flow Around Photosystem I, Journal of Biological Chemistry 292, 11850-11860.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Tietz, S., Hall, C. C., Cruz, J. A., and Kramer, D. M. (2017) NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem II associated antenna complexes, Plant Cell and Environment 40, 1243-1255.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Davis, G. A., Kanazawa, A., Sch�ttler, M. A., Kohzuma, K., Froehlich, J. E., Rutherford, A. W., Satoh-Cruz, M., Minhas, D., Tietz, S., Dhingra, A., and Kramer, D. M. (2016) Limitations to photosynthesis by proton motive force-Induced photosystem II photodamage eLife eLife 2016;5:e16921.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Dutta, S., Cruz, J. A., Imran, S. M., Chen, J., Kramer, D. M., and Osteryoung, K. W. (2017) Variations in chloroplast movement and chlorophyll fluorescence among chloroplast division mutants under light stress, J Exp Bot 68, 3541-3555.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Morales, A., Yin, X., Harbinsonb, J., Driever, S. M., Molenaar, J., Kramer, D. M., and Struik, P. C. (2017) An in silico analysis of the metabolic regulation of the photosynthetic electron transport chain in C3 plant species, Plant physiology DOI:10.1104/pp.17.00779.

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Plant scientists, local and global communities of farmers, researchers, extension agents, global modeling and big data efforts, entrepreneurs and international development programs. Changes/Problems:The only changes I wish to emphasize is the large expansion of the projects to new areas and applications. What opportunities for training and professional development has the project provided?Classroom Instruction at MSU. While only 10% of my appointment is for teaching, I participate in both classroom and one-on-one graduate education. I teach in the graduate-level Plant Biochemistry course (BMB864), in which I cover the basics of photosynthesis. To prepare advanced students graduate students whose research involves photosynthesis and photosynthetic measurements, I developed a 3-credit interactive special topics course (BMB 960-Photosynthesis), which debuted in 2015, and directly addresses fundamental and current thinking in all areas of photosynthesis. A part of the course uses the PhotosynQ platform to enable students to make their own measurements, the interpretations of which are then discussed as a group and presented in a public poster session. The feedback on this course has been very favorable and I am pleased that the majority of the students who took the class are using the concepts, methods and tools directly in their on-going research. Interdisciplinary training and catalyzed interactions. My lab is heavily involved in undergraduate and graduate students and post-doctoral teaching through hands-on research and development. The opportunity afforded by MSU and the Hannah funds has allowed us to bring together both from a wide range of disciplines and programs, including Biochemistry and Molecular Biology, Chemistry, Computer Science and Engineering, Crops and Soil Sciences, Electrical and Engineering Sciences, Forestry, Genetics and Cell Biology Horticulture, International Programs and Plant Biology. Having all these disciplines interact in the same space while working on common problems has truly facilitated communication, interactive learning and exchanges of ideas. In the past 5 years, my lab has mentored and supported 15 graduate students, 12 post-docs, 3 research assistant professors, 12 international visitors, and more than 40 undergraduates. (All undergraduates in the lab participate at in research and/or development; no one is simply a "dishwasher"). Outreach impact on education. My lab and the CAAPP are providing innovative educational tools to the MSU and international communities: 1) CAAPP has held a series of workshops on plant phenotyping that have been attended by participants across campus; 2) The PhotosynQ platform is particularly well suited for educational applications, potentially to teach both specific concepts and the scientific method. I use the platform in my Photosynthesis class (see above), but also distribute the devices freely to graduate students at many MSU labs as a research training tool. Several other formal classes currently use the platform at MSU (in Biological Sciences Program, College of Natural Science, Horticulture, and at KBS) as well as in other countries (Ukraine, Zambia, Ghana, The Netherlands). Specific outcomes: 1) CAAPP has held a series of workshops on plant phenotyping that have been attended by participants across campus; 2) We held a well attended and well-received PhotosynQ workshop https://prl.natsci.msu.edu/news-and-events/events/past-events/photosynq-workshop/ to train MSU community in the capabilities of the platform. https://blog.photosynq.org/2016/05/12/photosynq-workshop-details-videos/ https://prl.natsci.msu.edu/news-and-events/news/photosynq-first-workshop-a-success/ 3) Established the PhotosynQ Education Project.The PhotosynQ platform is particularly well suited for educational applications, potentially to teach both specific concepts and the scientific method. I use the platform in my Photosynthesis class (see above), but also distribute the devices freely to graduate students at many MSU labs as a research training tool. Several other formal classes currently use the platform at MSU (in Biological Sciences Program, College of Natural Science, Horticulture, and at KBS) as well as in other countries (Ukraine, Zambia, Ghana, The Netherlands). 3) Participated in numerous educational demonstrations including MSU Science Festival. How have the results been disseminated to communities of interest?Publications (as above) Web sites, in particular PhotosynQ: www.photosynq.org CAAPP: https://prl.natsci.msu.edu/research/center-for-advanced-algal-and-plant-phenotyping-caapp/ Presentations: "Dynamic Phenotyping: From Complexity to Elegance" MSU Biomolecular Sciences Retreat Keynote Faculty Talk "PhotosynQ and Emergent Photosynthetic Phenotypes" Western Photosynthesis Conference, Jan., 2015, Asilomar, CA "PhotosynQ" LiCor Corp., May, 2015 "PhotosynQ and AquaspeQ" Algal Biomass, Bioenergy and Biofuels Conference, San Diego, CA, June, 2015 "MSU Center for Advanced Algal and Plant Phenoptyping", Pacific Northwest National Lab, March, 2015 "Is Photosynthesis Enabled or Limited by Complexity?" BioSolar Cells Symposium, Wageningen University, The Netherlands. "Life, Death, electrons and the PMF" Photosynthesis Gordon Research Conference, June, 2015, Bentley University "Plant Phenotyping Tools that You Can Use in your Research Right Now." MSU Plant Genomics Research Experience for Undergraduates Summer Series, May 28, 2015 "Innovation, Exploration and New Directions in Science" MSU Study Abroad Program, Invited presentation to students traveling to China, May 2015 "The Tightrope of Photosynthesis" Colin Wraight Memorial Lecture, University of Illinois, Urbana, Illinois, Sept., 2015 "Electrons, Protons and the Tightrope of Photosynthesis" Yamada Symposium, Nara, Japan, Colin Wraight Memorial Lecture, University of Illinois, Urbana, Illinois, Sept., 2015 "PhotosynQ and CoralpeQ" , National Institute of Basic Biology, Okazaki, Japan, Sept., 2015 "Robust Photosynthesis in Dynamic Environments: PRL 50th Anniversary", Michigan State University, Oct., 2015 "The Dynamic Energy Budget of Photosynthesis" U.S. Department of Energy Photosynthetic Systems PI Retreat, Oct., 2015 "PhotosynQ.org: Community-driven plant phenotyping for understanding plant responses to climate change", Jan., 2016 "The Limits of Photosynthesis and Bridging the Gaps between Lab and the World" ENCAPP European Networks Conference on Algal and Plant Photosynthesis, Malta "Disruptive Technologies for High-Resolution, High-Throughput Environmental Phenotyping: Bringing the Lab to the World and the World to the Lab" Plant Improvement Technologies Congress" North Carolina, March 2016 "The Limits of Photosynthesis: What we can learn when we bridging the gaps between the lab and the world?" Colorado State University, April, 2016 "Disruptive Technologies for High-Resolution, High-Throughput Environmental Phenotyping: Bringing the Lab to the World and the World to the Lab" USAID GCFSI Retreat, April, 2016 "High-Throughput Environmental Phenotyping: Bringing the Lab to the World and the World to the Lab" Benson Hill Biosystems, May, 2016 "The Gamut of Photosynthesis and Bridging the Gaps between Lab and the World PhotosynQ" International Congress on Photosynthesis Research, Maastricht, The Netherlands "The Limits of Photosynthesis and Bridging the Gaps between Lab and the World PhotosynQ" Essex Plant Phenotyping Congress, July, 2016 "Proton motive force-induced photosystem II photodamage: A fundamental limitation to Photosynthesis imposed by the interaction of pmf and electron transfer reactions" Photosynthetic Electron Transfer Meeting, Arnham, July, 2016 What do you plan to do during the next reporting period to accomplish the goals?1) A major focus is on releasing the new, fullversion of the PhotosynQ MultispeQ; 2) Develop the necessary methods for local uise and validation of the platforms; 3) Develop deep learning algorithms for gaining predictive knowledge from our measurements; 4) Assess the use of the technologies for plant breeding and management.

Impacts
What was accomplished under these goals? 1) Fundamental mechanisms of photosynthesis. Our basic research programs on the mechanisms and regulation of Photosynthesis led to important discoveries in several areas key to understanding how photosynthesis responds to environmental fluctuations, including: mechanisms by which photosynthesis regulates its energy budget by activating a molecular proton pump that stores energy in ATP [1-3]; The elusive reactive intermediate that determines the reaction mechanism of the Q-cycle, a process that accounts for a large fraction of the ATP in our ecosystem, with implications for how enzymes deal with reactive catalytic intermediates [2]; Tmportant clues about how the chloroplast ATP synthase co-regulates the light and dark reactions of photosynthesis to optimize the balance between efficiency of photochemistry and the avoidance of photodamage [4]; The importance of the bulk of chloroplast-targeted genes in responding to fluctuating environmental conditions [5]; A new "Achilles heel" of photosynthesis that appears to contribute to photodamage and loss of crop yield under field conditions and on which we propose several new lines of research that connect basic to applied research on improving the efficiency and robustness of photosynthesis [6]; and the coupling of photosynthesis to growth and defense [7]. 2) Expansion of a Photosynthetic Phenomics Center at MSU. We established the MSU Center for Advanced Algal and Plant Phenotyping (CAAPP) to develop and apply transformative phenotyping technologies to enable us to directly address the next big challenges in plant biology, to establish MSU as an international innovation center and "international point of destination" for phenotyping analysis. In its first three years, the Center has established key instrumentation platforms and associated analytical software and approaches that start to bridge the gaps in our knowledge from genes to phenotype and from the lab to the fields. As of Sept, 2016, more than 30 MSU faculty and researchers, from 11 departments and programs have used CAAPP technologies and facilities including 14 different MSU AgBioResearch groups focusing on agricultural-relevant projects. CAAPP facilities have been used in an estimated 50 or more publications (both within and external to PRL), and its capabilities, direct involvement and preliminary data have contributed to more than 20 external grant proposals from MSU. From 2012-2015 over 14 grants were funded, totaling more than $46M, roughly $24M of that went to MSU. In the past year 10 additional grants were obtained by projects using the CAAPP facilities (totaling more than $4.0M) with an three additional proposals pending or in preparation including a major Bioenergy Resource Center . In addition CAAPP serves as a core facility for renewal of the PRL. 3) Development and worldwide dissemination of new instrumentation and techniques. One of the big, "stretch goals" of the proposed work was to bring the tools we develop "to the world" to 1) enable researchers around the work to perform sophisticated scientific experiments; 2) use this data to gain new insights into the basic mechanisms of photosynthesis and its responses to the environment; and 3) use this data to improve agriculture, especially in the developing world. We developed the PhotosynQ platform (www.photosynq.org) to specifically address these issues, by bringing sophisticated phenotyping tools and analytics to farmers, researchers, extension agents and entrepreneurs, with the aim of enabling locally appropriate agricultural intelligence solutions. Using the PhotosynQ platform and tools, these communities will generate actionable data that can guide the management and breeding of plants to improve the productivity and sustainability of agriculture in their region. At the same time, the PhotosynQ platform enables the aggregation of regional data sets across the globe (on plant phenotypes, environmental parameters, outcomes), to produce global-level analytics capable of solving both global and local level problems. The PhotosynQ platform includes a sophisticated plant sensor, called the MultispeQ, that makes a series of useful plant and environmental measurements, yet is inexpensive, easy to use, wirelessly connected, expandable and reprogrammable and can be massively deployed anywhere in the world. In the first year of deployment, we have obtained approximately $1M in external funding, deployed 300 MultispeQ devices, engaged more than 980 members, supporting over 600 projects in 25 different countries, resulting in over 350,000 experimental points. From a pure scientific point of view, the results from our platforms have given us novel insights and basic understanding of photosynthetic responses to environmental changes, which we are pursuing in research proposed for the PRL renewal and other grants, as well as new crop status indicators, which form the bases of proposals to McKnight and Gates Foundations, ARPA-E etc. [1] D.D. Strand, N. Fisher, G.A. Davis, D.M. Kramer (2016) Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids. Biochim Biophys Acta 1857, 1-6. [2] N. Fisher, M.K. Bowman, D.M. Kramer, Electron transfer reactions at the Qo site of the cytochrome bc1 complex: the good, the bad, and the ugly, in: T. Kallas, W.A. Cramer (Eds.), Cytochromes and Cytochromes Complexes, vol. 41, 2016, pp. 419-434. [3] D.D. Strand, A.K. Livingston, M. Satoh-Cruz, J.E. Froehlich, V.G. Maurino, D.M. Kramer (2015) Activation of cyclic electron flow by hydrogen peroxide in vivo. Proc Natl Acad Sci U S A 112, 5539-5544. [4] L.R. Carrillo, J.E. Froehlich, J.A. Cruz, L. Savage., D.M. Kramer (2016) Multi-level regulation of the chloroplast ATP synthase: The chloroplast NADPH thioredoxin reductase C (NTRC) is required for redox modulation specifically under low irradiance. Plant Journal In Press online: 10.1111/tpj.13226. [5] J.A. Cruz, L.J. Savage, R. Zegarac, C.C. Hall, M. Satoh-Cruz, G.A. Davis, W.K. Kovac, J. Chen, D.M. Kramer (2016) Dynamic Environmental Photosynthetic Imaging Reveals Emergent Phenotypes. Cell Syst 2, 365-377. [6] G.A. Davis, A. Kanazawa, M.A. Schöttler, K. Kohzuma, J.E. Froehlich, A.W. Rutherford, M. Satoh-Cruz, D. Minhas, S. Tietz, A. Dhingra, D.M. Kramer (2016) Limitations to Photosynthesis by Proton Motive Force-Induced Photosystem II Photodamage eLife revisions. [7] M.L. Campos, Y. Yoshida, I.T. Major, D.d.O. Ferreira, S.M. Weraduwage, J.E. Froehlich, B.F. Johnson, D.M. Kramer, G.J.D. Sharkey, G.A. Howe (2016) Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs. Nature communications 7, 12570.

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: J.A. Cruz, X. Yin, X. Liu, S.M. Imran, D.D. Morris, D.M. Kramer, J. Chen (2015) Multi-modality Imagery Database for Plant Phenotyping. Machine Vision and Applications 6, 1-15.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: S. Dutta, J. Cruz, Y. Jiao, J. Chen, D.M. Kramer, K.W. Osteryoung (2015) Non-invasive, whole-plant imaging of chloroplast movements and chlorophyll fluorescence reveals photosynthetic phenotypes independent of chloroplast photorelocation defects in chloroplast division mutants. Plant Journal 84, 428-442.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Q. Gao, E. Ostendorf, J.A. Cruz, R. Jin, D.M. Kramer, J. Chen (2015) Inter-functional analysis of high-throughput phenotype data by nonparametric clustering and its application to photosynthesis. Bioinformatics 32, 67-76.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: M.T. Juergens, R. Deshpande, B.F. Lucker, J.J. Park, H. Wang, M. Gargouri, F.O. Holguin, B. Disbrow, T. Schaub, J.N. Skepper, D.M. Kramer, D.R. Gang, L.M. Hicks, Y. Shachar-Hill (2015) The Regulation of Photosynthetic Structure and Function During Nitrogen Deprivation in Chlamydomonas reinhardtii. Plant physiology 167, 558-573.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: H. Scharr, M. Minervini, A. French, C. Klukas, D.M. Kramer, X. Liu, I. Luengo, J.-M. Pape, G. Polder, D. Vukadinovic, X. Yin, S. Tsaftaris (2015) Leaf segmentation in plant phenotyping: a collation study. Machine Vision and Applications DOI 10.1007/s00138-015-0737-3.
• Type: Book Chapters Status: Awaiting Publication Year Published: 2016 Citation: D.D. Strand, N. Fisher, D.M. Kramer, Cyclic electron flow in chloroplasts, in: H. Kirchhoff (Ed.), Chloroplasts: Current Research and Applications, vol. In Press, Horizon Press, 2016.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: D.D. Strand, A.K. Livingston, M. Satoh-Cruz, J.E. Froehlich, V.G. Maurino, D.M. Kramer (2015) Activation of cyclic electron flow by hydrogen peroxide in vivo. Proc Natl Acad Sci U S A 112, 5539-5544.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: O. Tsabari, R. Nevo, S. Meir, L.R. Carrillo, D.M. Kramer, Z. Reich (2015) Differential effects of ambient or diminished CO2 and O2 levels on thylakoid membrane structure in light-stressed plants. Plant Journal 81, 884-894.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: L. Xu, J.A. Cruz, L. Savage, D.M. Kramer, J. Chen (2015) Plant photosynthesis phenomics data quality control. Bioinformatics 31, 1796-1804.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: M. Agostoni, B.F. Lucker, M. Smith, A. Kanazawa, G.J. Blanchard, D.M. Kramer, B.L. Montgomery (2016) Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon Algal Research 15, 110-119.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: L.R. Carrillo, J.E. Froehlich, J.A. Cruz, L. Savage., D.M. Kramer (2016) Multi-level regulation of the chloroplast ATP synthase: The chloroplast NADPH thioredoxin reductase C (NTRC) is required for redox modulation specifically under low irradiance. Plant Journal In Press online: 10.1111/tpj.13226.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: J.A. Cruz, L.J. Savage, R. Zegarac, C.C. Hall, M. Satoh-Cruz, G.A. Davis, W.K. Kovac, J. Chen, D.M. Kramer (2016) Dynamic Environmental Photosynthetic Imaging Reveals Emergent Phenotypes. Cell Syst 2, 365-377.
• Type: Book Chapters Status: Published Year Published: 2016 Citation: N. Fisher, M.K. Bowman, D.M. Kramer, Electron transfer reactions at the Qo site of the cytochrome bc1 complex: the good, the bad, and the ugly, in: T. Kallas, W.A. Cramer (Eds.), Cytochromes and Cytochromes Complexes, vol. 41, 2016, pp. 419-434.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: R.M. Sharpe, T. Koepke, A. Harper, J. Grimes, M. Galli, M. Satoh-Cruz, A. Kalyanaraman, K. Evans, D. Kramer, A. Dhingra (2016) CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. PloS one 11.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: D.D. Strand, N. Fisher, G.A. Davis, D.M. Kramer (2016) Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids. Biochim Biophys Acta 1857, 1-6.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: C.J. Unkefer, R.T. Sayre, J.K. Magnuson, D.B. Anderson, I. Baxter, I.K. Blaby, J.K. Brown, M. Carleton, R.A. Cattolico, T. Dale (2016) Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts. Algal Research.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: D. Kramer, PhotosynQ: Community-driven plant phenotyping for understanding plant responses to climate change, Plant and Animal Genome XXIV Conference, Plant and Animal Genome, 2016.
• Type: Book Chapters Status: Published Year Published: 2016 Citation: N. Fisher, M.K. Bowman, D.M. Kramer, Electron Transfer Reactions at the Qo Site of the Cytochrome bc 1 Complex: The Good, the Bad, and the Ugly, Cytochrome Complexes: Evolution, Structures, Energy Transduction, and Signaling, Springer Netherlands, 2016, pp. 419-434.
• Type: Journal Articles Status: Submitted Year Published: 2016 Citation: S. Kuhlgert, G. Austic, R. Zegarac, I. Osei-Bonsu, D. Hoh, M.I. Chilvers, M.G. Roth, K. Bi, D. TerAvest, W. Prabode, D.M. Kramer (2016) MultispeQ Beta  A tool for large-scale plant phenotyping connected to the open PhotosynQ network. Royal Society Open Science submitted.

Progress 12/01/14 to 09/30/15

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Developed on-line modules to educate users (e.g. https://prezi.com/xvuilvtihvmy/photosynq-msu-global-presentation/) Education Impact of CAAPP work The PhotosynQ platform is highly suited to education, particularly about plant biology, agriculture, photosynthesis, instrumentation, data analysis and statistics. We have produced a series of tutorials that are available on the photosyn.org site. PhotosynQ has is being used in two MSU courses Biological Sciences (BS171) Caroline Knoblock, Instructor Photosynthesis (BMB960-001) David M. Kramer, Instructor At MSU, a large number of graduate and undergrad students have received training using CAAPP facilities or technologies How have the results been disseminated to communities of interest?Engagement with MSU and external research groups More than 18 MSU faculty and researchers, from 9 departments and programs have used CAAPP technologies and facilities in the 2103-2104 period (Table 1). This demonstrates a high level of interest in the technology and science coming out of CAAPP. Indeed, a total of 13 external institutions have become involved in CAAPP research, with particularly strong interest in developing large-scale collaborative grant proposals based on CAAPP enabling technologies. In addition, the PhotosynQ project has gained partners in External Grant Support Generated by CAAPP Technology and Interactions CAAPP has participated in or written letters of support for 25 externally funded grant proposals at MSU, resulting in 11 funded proposals, including the (high priority) renewal of the PRL and an addition 5 pending proposals (Table 2). Table 2. Grants to MSU supported by CAAPP technology Lead Agency Title Grant No. Dates Amount Thomashow (MSU, PRL) U.S. Department of Energy Photosynthetic Energy Capture, Conversion and Storage: From Fundamental Mechanisms to Modular Engineering (PRL funding) DE-FG02-91ER20021 09/01/2014 - 08/31/2017 $12,000,000 Kramer (MSU, BMB/PRL) U.S. Department of Energy The Energy Budget of Steady-state Photosynthesis DE-FG02-04ERl5559 6/2013-5/2016 $640,000 Rob Last (MSU, BMB) and Yan Lu (Western Michigan University) NSF Identifying and Understanding Connections between Photosynthesis and Amino Acid Metabolism MCB1244088 3/1/2013-2/29/16 $589,384 Katherine Osteryoung (MSU, Plant Biology) U.S. Department of Energy Control of Chloroplast Morphology in Plants: Mechanisms and Physiological Significance DE-FG02-06ER15808 08/01/2013-07/31/2016 $540,000 Jan Jaworski (P.I., Danforth Center and D. Kramer (co-PI, MSU, BMB/PRL) U.S. Department of Energy-ARPA-E Center for Advanced Camelina Oil (CECO) 21018-MI 01/01/2012 - 12/31/2015 $9,300,000 ($860,000 to MSU) Jan Jaworski (P.I., Danforth Center and D. Kramer (co-PI, MSU) U.S. Department of Energy-ARPA-E Extension of Center for Advanced Camelina Oil (CECO) 21018-MI-2 01/01/2015 - 12/31/2016 $3,300,000 ($400,000 to MSU) D. Kramer (BMB/PRL) McKnight Foundation "MultispeQ: A Deployable Sensor for the PhotosynQ Network to Enable Critical Plant, Soil and Seed Measurements for African Breeders and Extension Agents" 13-618 09/01/14 - 8/30/16 $300,000 Eric Crawford (MSU), Sub-award P.I.: D. Kramer (MSU, BMB/PRL) U.S. Agency for International Development Global Center for Food Safety Innovations: MultispeQ: A Deployable Sensor for the PhotosynQ Network to Enable Critical Plant and Soil Measurements for Breeders in East Africa AID-OAA-A-13-00006 4/01/14 - 03/31/15 $7,600,000 (Award to CAAPP-related work, $100,000) Irvin Widders (MSU, Horticulture, Legume Innovation Lab), Sub-award P.I.: D. Kramer (MSU, BMB/PRL) U.S. Agency for International Development Improving Photosynthesis in Grain Legumes 08/2015-07/2018 $500,000 Lammers, Peter (P.I., Los Alamos National Lab), D. Kramer (MSU, BMB/PRL, sub-contract P.I.) U.S. Department of Energy Realization of Algae Potential (REAP) DE-EE0006316 01/10/15 - 01/09/16 $3,300,000 ($120,000 to MSU) D. Kramer (MSU/PRL) ExxonMobil Chemical Corporation MSU-EMRE Collaboration Finalizing Contract 01/15/15 - 12/31/16 $1,000,000 D. Kramer (MSU, BMB/PRL), B. Basso (MSU, Geological Sciences), Shinhan Shiu (MSU, Plant Biology) U.S. Department of Energy-ARPA-E PIPER: Platform of Integrated Phenotyping for Energy Research Pending 2015-2020 $10M (requested) Christoph Benning (BMB, MSU) US National Science Foundation Integration of Metabolic Cues and Life Cycle Decisions in Chlamydomonas Pending 07/01/2015-06/30/2018 $773,000 (requested) Thomas Sharkey (MSU, BMB) U.S. Department of Energy The Calvin-Benson Cycle Glucose 6-Phosphate Shunt Pending 9/1/2015-8/30/2018 $719,531 (requested) Jin Chen (MSU, PRL) National Science Foundation A New Framework to Analyze Plant Energy-related Phenomics Data Pending 1/1/15-12/31/17 $641,000 (requested) Oliver Tessmer, Jin Chen and D. Kramer (MSU, BMB/PRL) MSU Translational Research and Commercialization (MTRAC) OLIVER (Observe, Link, Integrate, Validate, Explore and Reveal): A Platform for Visualization and Mining of High-Resolution, High-Throughput Phenomics and Genomics Data Pending 6/1/2015-5/30/2016 $100,000 (requested) What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Deployment of CAAPP technology Established a leadership team (Dr. Jeffrey Cruz, Ms. Linda Savage and Mr. Greg Austic) to oversee the development, testing, outreach, education of CAAPP facilities. Produced an array of 13 DEPI units, which are all used to full capacity; Assembled 10 ePBR units, used to full capacity; Build over 60 PhotosynQ MultispeQ instruments that are deployed in many labs at MSU and across the world; Developed a Laboratory Information Management System (LIMS) to track, record and report results; Dissemination of CAAPP technology DEPI. All DEPI units are being used at full capacity. DEPI has been used to screen (for the MSU community) over 35,480 plants, including more than 2,200 Arabidopsis lines as well as several lines each of soybeans, common beans, Brachypodium, Cucumber, Tobacco and Camelina) for environmental phenotypes. ePBR technologies. There are currently 5 external ePBR users. In addition, the ePBR technology has been successfully commercialized through a MSU-supported start-up, Phenometrics (www.phenometricsinc.com). Currently, the ePBR is the world's most used photobioreactor with well over 300 units in operation. PhotosynQ. The PhotosynQ platform currently has 108 members involved in projects from Malawi to Michigan (Table 3). The PhotosynQ platform has been used to generate more than 17,000 photosynthesis measurements, proving that the device is relatively easy to use and widely applicable. We have demonstrated that PhotosynQ can be used effectively even in developing countries (Malawi, Zambia, India, Mexico).

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: Xu, L., Cruz, J. A., Savage, L., Kramer, D. M., and Chen, J. (2015) Plant photosynthesis phenomics data quality control, Bioinformatics 31, 1796-1804.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Tsabari, O., Nevo, R., Meir, S., Carrillo, L. R., Kramer, D. M., and Reich, Z. (2015) Differential effects of ambient or diminished CO2 and O2 levels on thylakoid membrane structure in light-stressed plants, Plant Journal 81, 884-894.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Strand, D. D., Livingston, A. K., Maurino, V. G., and Kramer, D. M. (2015) Activation of Cyclic Electron Flow by Hydrogen Peroxide in vivo, Proc Natl Acad Sci U S A doi: 10.1073/pnas.1418223112.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Strand, D. D., Fisher, N., and Kramer, D. M. (2015) Cyclic electron flow in chloroplasts, In Chloroplasts: Current Research and Applications (Kirchhoff, H., Ed.), Horizon Press.
• Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Strand, D. D., Fisher, N., and Kramer, D. M. (2015) The Higher Plant Plastid Complex I (NDH) is a Reversible Proton Pump that increases ATP production by Cyclic Electron Flow Around Photosystem I, Nature communications submitted.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Strand, D. D., Fisher, N., Davis, G. A., and Kramer, D. M. (2015) Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids, Biochim Biophys Acta doi: 10.1016/j.bbabio.2015.07.012.
• Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Kohzuma, K., Froehlich, J. E., Temple, J. A., Minhas, D., Cruz, J. A., Kanazawa, A., and Kramer, D. M. (2017) The role of light-dark regulation of the chloroplast ATP synthase, Plant Journal In Revisions.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Juergens, M. T., Deshpande, R., Lucker, B. F., Park, J. J., Wang, H., Gargouri, M., Holguin, F. O., Disbrow, B., Schaub, T., Skepper, J. N., Kramer, D. M., Gang, D. R., Hicks, L. M., and Shachar-Hill, Y. (2015) The Regulation of Photosynthetic Structure and Function During Nitrogen Deprivation in Chlamydomonas reinhardtii, Plant Physiol.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Gao, Q., Ostendorf, E., Cruz, J. A., Jin, R., Kramer, D. M., and Chen, J. (2015) Inter-functional analysis of high-throughput phenotype data by nonparametric clustering and its application to photosynthesis, Bioinformatics In Press.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Dutta, S., Cruz, J., Jiao, Y., Chen, J., Kramer, D. M., and Osteryoung, K. W. (2015) Non-invasive, whole-plant imaging of chloroplast movements and chlorophyll fluorescence reveals photosynthetic phenotypes independent of chloroplast photorelocation defects in chloroplast division mutants , Plant Journal doi: 10.1111/tpj.13009.
• Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Davis, G. A., Kanazawa, A., Shoettler, M. A., Kohzuma, K., Froehlich, J. E., Satoh-Cruz, M., Minhas, D., Dhingra, A., and Kramer, D. M. (2015) The photosynthetic proton motive force regulates photoinhibition of photosystem II, Science submitted.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Cruz, J. A., Yin, X., Liu, X., Imran, S. M., Morris, D. D., Kramer, D. M., and Chen, J. (2015) Multi-modality Imagery Database for Plant Phenotyping, Machine Vision and Applications In Press.
• Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Cruz, J., Savage, L., Zegarac, R., Kovac, W. K., Hall, C. C., Chen, J., and Kramer, D. M. (2015) Dynamic Environmental Photosynthetic Imaging (DEPI): Continuous monitoring of genetic variations in photosynthetic response under dynamic growth environments, Nature Biotechnology Submitted.
• Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Agostoni, M., Lucker, B. F., Smith, M., Kanazawa, A., Blanchard, G. J., Kramer, D. M., and Montgomery, B. L. (2015) Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon Plant Cell and Environment Submitted.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Yin, X., Liu, X., Chen, J., and Kramer, D. M. (2014) Multi-leaf alignment from fluorescence plant images, In IEEE Conference on Applications of Computer Vision (WACV14), Steamboat Springs, CO
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Yin, X., Liu, X., Chen, J., and D.M., K. (2014) Multi-leaf tracking from fluorescence plant videos In IEEE International Conference on Image Processing (ICIP14), Paris, France.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Walker, B. J., Strand, D. D., Kramer, D. M., and Cousins, A. B. (2014) The response of cyclic electron flow around photosystem I to changes in photorespiration and nitrate assimilation, Plant Physiol 165, 453-462.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Tamburic, B., Guruprasad, S., Radford, D. T., Szabo, M., Lilley, R. M., Larkum, A. W., Franklin, J. B., Kramer, D. M., Blackburn, S. I., Raven, J. A., Schliep, M., and Ralph, P. J. (2014) The effect of Diel temperature and light cycles on the growth of nannochloropsis oculata in a photobioreactor matrix, PLoS One 9, e86047.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Sun, W., Ubierna, N., Ma, J. Y., Walker, B. J., Kramer, D. M., and Cousins, A. B. (2014) The coordination of C4 photosynthesis and the CO2-concentrating mechanism in maize and Miscanthus x giganteus in response to transient changes in light quality, Plant Physiol 164, 1283-1292.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Strand, D. D., and Kramer, D. M. (2014) Control of Non-Photochemical Exciton Quenching by the Proton Circuit of Photosynthesis, In Non-Photochemical Quenching and Energy Dissipation in Plants, Algae and Cyanobacteria (Demmig-Adams, B., Garab, G., Adams III, W., and Govindjee, Eds.), pp 387408, Springer, The Netherlands.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Lucker, B. F., Hall, C., Zegarac, R., and Kramer, D. M. (2014) The Environmental Photobioreactor (ePBR): An Algal culturing platform for simulating dynamic natural environments, Algal Research DOI: 10.1016/j.algal.2013.12.007.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Kunz, H. H., Gierth, M., Herdean, A., Satoh-Cruz, M., Kramer, D. M., Spetea, C., and Schroeder, J. I. (2014) Plastidial transporters KEA1, -2, and -3 are essential for chloroplast osmoregulation, integrity, and pH regulation in Arabidopsis, Proc Natl Acad Sci U S A 111, 7480-7485.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Kanazawa, A., Blanchard, G. J., Szabo, M., Ralph, P. J., and Kramer, D. M. (2014) The site of regulation of light capture in Symbiodinium: does the peridinin-chlorophyll a-protein detach to regulate light capture?, Biochim Biophys Acta 1837, 1227-1234.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Im, Y. J., Smith, C. M., Phillippy, B. Q., Strand, D., Kramer, D. M., Grunden, A. M., and Boss, W. F. (2014) Increasing phosphatidylinositol (4,5)-bisphosphate biosynthesis affects basal signaling and chloroplast metabolism in Arabidopsis thaliana, Plants 3, 27-57.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Fisher, N., and Kramer, D. M. (2014) Non-photochemical reduction of thylakoid photosynthetic redox carriers in vitro: Relevance to cyclic electron flow around photosystem I?, Biochim Biophys Acta 1837, 1944-1954.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Attaran, E., Major, I. T., Cruz, J. A., Rosa, B. A., Koo, A. J., Chen, J., Kramer, D. M., He, S. Y., and Howe, G. A. (2014) Temporal Dynamics of Growth and Photosynthesis Suppression in Response to Jasmonate Signaling, Plant Physiol 165, 1302-1314.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Armbruster, U., Carrillo, L. R., Venema, K., Pavlovic, L., Schmidtmann, E., Kornfeld, A., Jahns, P., Berry, J. A., Kramer, D. M., and Jonikas, M. C. (2014) Ion antiport accelerates photosynthetic acclimation in fluctuating light environments, Nature communications 5, 5439.
• Type: Other Status: Published Year Published: 2014 Citation: Hall, C., Norman, W., Kovac, W. K., Kramer, D. M., Savage, L., and Cruz, J. (2014) DEPItrol : Control software for theDynamic Environmental Phenotype Imager.
• Type: Other Status: Published Year Published: 2014 Citation: Chen, J., Tessmer, O. L., Cruz, J., and Kramer, D. M. (2014) Visual Phenomics: A software package for high throughput analysis of plant photosynthesis and growth data analysis.
• Type: Other Status: Published Year Published: 2014 Citation: Macaluso, S., and Chen, J. (2014) PhenoMath: A software package for deep analysis of high througput photosynthesis data.