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Background, Interest, and Capabilities | |
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| Donald Danforth Plant Science Center | James Umen | Member and Principal Investigator |
Non-Profit
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Bioenergy
| Our group has a project in developing synthetic algal and plant chromosomes based on CENH3 tethering technology. We also are involved in testing delivery methods for large DNA fragments into cells which is a significant hurdle for synthetic chromosome applications. We can partner with groups that have multigene traits they want to engineer into bioenergy crops. |
| MO |
| University of Washington | Jennifer Nemhauser | Professor |
Academic
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Bioenergy
| Background: Synthetic and developmental biologist
Capabilities: Integrase-based synthetic circuits, e.g., doi: 10.1101/2024.12.16.628800, 10.1038/s41467-024-53716-1, 10.1038/s41467-023-37607-5 Synthetic repression, e.g., 10.1083/jcb.202404103, 10.1073/pnas.2206986119, 10.7554/eLife.66739, 10.1104/pp.19.01475, 10.7554/eLife.34702 Plants: Arabidopsis, maize protoplasts, Brassica rapa, Benthi Microbes: Yeast |
| WA |
| UCLA | Steve Jacobsen | Professor and HHMI Investigator |
Academic
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Other Energy Technologies
| Our lab has recently developed methods in which tiny CRISPR systems can be encoded in plant viruses to achieve transgene free and tissue culture free germ line editing. https://www.biorxiv.org/content/10.1101/2024.07.17.603964v1. We would like to apply these technologies to bioenergy crops. Our lab has expertise in plant genetics, epigenetics, genomics, viral engineering, and the discovery and improvement of new CRISPR systems. |
| CA |
| Colorado State University | Devin O'Connor | Assistant Professor |
Academic
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Bioenergy
| After 5 years in industry I recently left the gene-editing company Pairwise to start a new academic lab at Colorado State. At Pairwise, as the Associate Director of Row Crops, I led the 5-year trait gene-editing collaboration with Bayer Crop Science, arguably one of the largest plant gene editing pipelines ever. We used new editing tools to develop 25 novel plant trait phenotypes across several row crop species, primarily corn and soy. My team focused on gene target identification and allele design while also managing edits through the pipeline to seed delivery. I'm an inventor on 15 pending and 1 granted patents resulting from this work.
My domain expertise surrounds plant development, genetics, cell biology, and gene edit deployment. My new lab will focus on gene-edit allele design and delivery. We will use both Arabidopsis and Brachypodium as model systems to test edits for eventual crop deployment, especially yield component improvement controlled by developmental mechanisms. We will also utilize advanced confocal microscopy and tissue culture to study plant tissue formation, including plant regeneration. Combined, this experience makes me an ideal collaborator for developing novel gene editing tools, targets, and delivery mechanisms. |
| CO |
| University of Maryland | Gen Li | Assistant Research Professor |
Academic
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Bioenergy
| Background: Dr. Li has extensive research experience in the genetic engineering of bioenergy crops by using state-of-the-art genome editing tools. He also developed some highly efficient genome editing systems in both monocot and dicot plants. He also developed high-quality wood with less energy consumption and waster production by poplar genetic engineering.
Interest: Plant whole-genome engineering for high biomass and highly efficient energy production in bioenergy plants, such as poplar and eucalyptus.
Capabilities: Genome-wide CRISPR screening; advanced plant transformation, cell culture and tissue culture system; applying the most advanced genome editing systems; various DNA delivery systems applicable to different plant types; wood structure, and chemical characterization. |
| MD |
| North Carolina State University | Dr. Amy Grunden | Distinguished Professor/Assistant Director, NCARS |
Academic
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Other Energy Technologies
| Focused on the study of microorganisms called extremophiles, which are capable of thriving in diverse extreme environmental conditions such as high or low temperatures, high salinity, acidic or alkaline environments. The goals of the extremophile research conducted in my laboratory are first to understand the adaptive mechanisms extremophiles use to survive in harsh environmental conditions and second to exploit these adaptations for biotechnological applications. Research projects currently underway involve using selected extremophile enzymes and synthetic biology approaches to (1) decontaminate toxic organophosphorus-based nerve agents found in some pesticides and chemical warfare agents, (2) generate transgenic plants with increased tolerance to harsh environmental conditions for the purpose of developing plants that can survive in marginal environments, and (3) use extremophile genes to optimize fatty acid production in microalgae for biofuel production and (4) develop a synthetic carbon fixation cycle using archaeal and bacterial enzymes to augment the Calvin-Benson cycle in plant systems. Research in my laboratory has been funded by DOD, DOE, NASA, NCBC, NSF, and the USDA. |
| NC |
| Draper Laboratory | Cassandra Canez | Senior Scientist |
Non-Profit
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Other Energy Technologies
| Draper is a multidisciplinary not-for-profit organization pioneering unique technologies to enable and deliver first-of-a-kind solution s through deep expertise and innovation. Developed and delivered novel capabilities with successful results on the IARPA Finding Engineering-Linked Indicators (FELIX) and DARPA Detect It with Gene Editing Technologies (DIGET). Expertise in synthetic biology, microbial engineering, and protein engineering. |
| MA |
| Karadeniz Technical University | Halbay Turumtay | Assoc. Prof. |
Academic
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Bioenergy
| Background: Plant molecular biochemist, 15y+ working in plant cell wall biology, worked for better conversion of biomass for biofuels and biomaterials in academia and government supported national laboratory.
Capabilities; cell wall polysaccharide composition and lignin compositional analysis (mass spectrometry, pyrolysis), plant tissue culture, gene editing and genetic engineering of plants, Experience in working with model systems (arabidopsis) and dedicated biomass crops (sorghum and poplar). ; metabolic engineering; metabolomics and transcriptomics analysis; synthetic biology
1- Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway Emine Akyuz Turumtay, Halbay Turumtay and et al. 2024
2-Engineered reduction of S-adenosylmethionine alters lignin in sorghum Yang Tian, Yu Gao, Halbay Turumtay, and et al. 2024
3-Defined synthetic microbial communities colonize and benefit field-grown sorghum . Citlali Fonseca-García, Dean Pettinga, Andrew Wilson, Joshua R Elmore, Ryan McClure, Jackie Atim, Julie Pedraza, Robert Hutmacher, Halbay Turumtay and et al. 2024 |
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| University of California Berkeley | Markita Landry | Associate Professor |
Academic
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Other Energy Technologies
| The Landry Lab at UC Berkeley develops non-viral and non-biolistic methods for delivering central dogma cargoes DNA, RNA, and proteins to plants for genetic and post-transcriptional manipulation of non-model plants.
The Landry Lab published on a nanoparticle-based method for the delivery of plasmid DNA to mature plant tissues [1] in a manner that avoids transgene integration into the plant host genome [2]. Separately, the Landry Lab also developed several nanoparticle-based methods for RNA delivery in mature plant tissues, first with DNA origami and DNA nanostructures which enabled transient post-transcriptional gene silencing [3] but also, importantly, enabled the first known direct measurement of the size exclusion limit of the plant cell wall to be ~20 nm [4]. Our lab also achieved siRNA delivery with carbon nanotubes and showed, with single-molecule microscopy, the mechanism by which siRNA is protected against endonuclease degradation when loaded onto nanocarriers [5]. Our lab also developed gold nanoparticles for RNA delivery into plants, achieving over 99% efficiency in siRNA-based gene silencing. Most recently, my lab has also discovered a class of plant-derived cell penetrating peptides (CPPs) that enable the delivery of proteins into plants [6], including transcription factors and recombinases, with the potential to extend this technology to the delivery of genome editing nucleases. These tools could be particularly useful for the delivery of DNA, RNA, and protein for rapid bioenergy crop engineering.
1. Demirer, G.S., et al., Carbon nanotube-mediated DNA delivery without transgene integration in intact plants. Nature Protocols, 2019. 14(10): p. 2954-2971. 2. Demirer, G.S., et al., High Aspect Ratio Nanomaterials Enable Delivery of Functional Genetic Material Without Transgenic DNA Integration in Mature Plants. In Vitro Cellular & Developmental Biology-Animal, 2019. 55: p. S3-S4. 3. Zhang, H., et al., Engineering DNA nanostructures for siRNA delivery in plants. Nature Protocols, 2020. 15(9): p. 3064-3087. 4. Zhang, H., et al., DNA nanostructures coordinate gene silencing in mature plants. PNAS, 2019. 116(15): p. 7543-7548. 5. Demirer, G.S., et al., Carbon nanocarriers deliver siRNA to intact plant cells for efficient gene knockdown. Science Advances, 2020. 6(26). 6. Wang, J.W., et al., Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants. Commun Biol, 2023. 6(1) |
| CA |
| Texas A&M University | Amit Dhingra | Professor and Department Head |
Academic
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Bioenergy
| Background: Extensive experience in genetic engineering of several recalcitrant crops - both dicot and monocots. Perform both nuclear and chloroplast genetic engineering. Interest: 1. Enhancing carbon capture in higher plants to increase oil production (previously funded by PETRO), 2. Understanding the photosynthetic efficiency ceiling and feedback inhibition mechanisms, 3. Combining genetic and gene expression approaches to identify genetic determinants of plant traits Capabilities: Gene editing, Agrobacterium and gene gun mediated transformation, vector construction |
| TX |
| University of Adelaide | Jenny Mortimer | Professor |
Academic
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Bioenergy
| Plant biochemist, glycobiologists and synthetic biologist. 15y+ working in cell wall biology, biomass characterisation and engineering biomass for biofuels and biomaterials in academic and government labs.
Working in model systems and dedicated biomass crops. Particularly interested in application of synthetic biology to understand cell wall architecture, synthesis and deconstruction, as well as designing polysaccharide structure for novel material science applications e.g. packaging.
Director or Plant Systems Biology since 2014 at the US Dept of Energy funded Joint BioEnergy Institute (JBEI; team formerly based at Berkeley Lab, now split between Berkeley and Adelaide).
Biomass Conversion Theme Lead of Australian Research Council (ARC) Research Hub starting 2025 "Engineering Plants to Replace Fossil Carbon".
Co-lead of newly funded Plant SynBio Australia biofoundry node hosted at University of Adelaide, starting 2025.
Investigator on ARC Training Hub in "Future Crops Development" and ARC Centre of Excellence in "Plants for Space".
Expertise includes cell wall polysaccharide and lignin compositional and structural analysis (HPAEC, PACE, mass spectrometry, pyrolysis, as well as multi-dimensional solid state NMR analysis of intact walls); growth of plants in 13CO2 environments; plant tissue culture, gene editing and genetic engineering of plants, including Arabidopsis, rice, and sorghum; metabolic engineering; producing new to nature polysaccharides in planta. |
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| National Renewable Energy Laboratory | Steve Decker | Scientist VI - Group Manager Biosciences Center |
Federally Funded Research and Development Center (FFRDC)
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Bioenergy
| Building or testing genetically engineered bioenergy crops (testing the biomass for conversion traits or compositional analysis)
Cellulase engineering and synergy for biomass conversion
Lab automation and high-throughput screening
Fungal molecular biology and fermentation
Non-dilute acid pretreatment technologies
Cellulose nanocrystal applications
Protein biochemistry (enzyme assays and kinetics; protein engineering; protein expression and purification, including fungal/yeast/bacterial; fungal transformation; enzyme synergy/optimization for hydrolysis of biomass; cellulase biochemistry; and protein production through fermentation up to 100L scale)
Biomass conversion (functional understanding of multiple biomass pretreatment strategies, including acid/alkaline/neutral; detailed knowledge of biomass-hydrolyzing enzyme function and interaction with biomass feedstocks; and experience with numerous feedstock types) |
| CO |
| Ondukuz Mayis University | Karam Mostafa | Dr |
Academic
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Bioenergy
| With a recently completed Ph.D. in Plant Biotechnology from OMU, Turkey, I am excited to contribute to cutting-edge research in plant molecular genetics. During my doctoral studies, I was a principal researcher in a project funded by TUBITAK. The project aims to develop root-knot nematode-resistant tomato plants using the CRISPR-dCas9 system. My research objective was to understand the regulatory mechanism of root exudates (especially fatty acids) against plant parasitic nematodes. Accordingly, my research focused on increasing the expression of multiple endogenous genes (FATA, FATB1, FATB2, and FATB3) responsible for synthesizing fatty acid and its derivatives in the roots of the tomato plant by using traditional over-expression and CRISPR-ACT3.0 technology under root-specific promoters. Overall, my field of work seems to be focused on molecular biology, genetic engineering, and plant breeding, with a specific interest in using CRISPR technology for crop improvement. I completed my master’s degree in 2017 in the plant Physiology department, faculty of Agriculture, Cairo University, where I immersed deeply into the fascinating world of tissue culture. During my master’s program, I aimed to investigate the effects of different plant growth regulators on the growth and morphogenesis of date palms via direct organogenesis. My master’s degree has taught me the skills to work with tissue culture techniques for various plant species. While this position may seem to align with my primary expertise as a molecular biologist, my background includes extensive experience in molecular biology techniques. Furthermore, I participated in two transcriptomic studies on common beans and strawberries, which involved clarification of the heat stress factor on the growth and development of these plants. These projects provided me with much information, knowledge, and expertise in NGS data analysis. Moreover, I am keenly interested in expanding my understanding of cell biology, which would enrich my proficiency in molecular biology and biochemistry. This has increased my interest in learning more about this cutting-edge technology. I view this position as an invaluable opportunity, akin to a lifeline, that would greatly enhance my understanding and capabilities in this field. I could learn about new CRISPR-based gene editing techniques or gain hands-on experience with the latest laboratory equipment and software. |
| Samsun |
| UC Davis | Juan Debernardi | Manager Plant Transformation Facility |
Academic
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Bioenergy
| Project Scientist and Manager of the Plant Transformation Facility at UC Davis. I graduated from the National University of Rosario (UNR), Argentina with a degree in Biotechnology, and later with a PhD in Biological Sciences, with a background on plant developmental and molecular biologist. I did a postdoc in the laboratory of Prof. Dubcovsky at UC Davis, California, where I led a group focused on understanding the genetic networks that control wheat plant architecture and flowering time, and their effect on yield. At Dubcovsky lab, I developed a novel transformation method involving GRF and GIF genes that has significantly increased the efficiency of wheat transformation and expanded the range of cultivars that can be transformed. At Plant Transformation Facility, I coordinate plant transformation services, and lead projects focused on developing technologies that improve gene editing and crop transformation. We have extended GRF-GIF technology to other crops, and we have also developed a protoplast-based platform for gene editing in grape varieties. The Facility staff has extensive experience in plant transformation, gene editing and plant cell biology techniques for a wide range of crop plants. |
| CA |
| National Renewable Energy Laboratory | Roman Brunecky | Researcher IV - Biological Science |
Federally Funded Research and Development Center (FFRDC)
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Bioenergy
| Roman has background in plant protein expression for reducing recalcitrance, testing, and assaying plants and proteins, as well as plant cell wall imaging. |
| CO |
| Tennessee State University | Ali Taheri | Associate Professor |
Academic
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Bioenergy
| Dr. Ali Taheri is a research scientist with extensive expertise in molecular genetics, plant biotechnology, and crop improvement. His lab focuses on leveraging advanced genetic tools and methodologies to address critical challenges in agriculture, with an emphasis on functional genomics, germplasm enhancement, and genome editing technologies.
Dr. Taheri’s research incorporates cutting-edge techniques such as CRISPR-Cas9 genome editing, which enables precise modification of targeted genes for functional analysis and crop improvement. His lab has made significant strides in optimizing DNA delivery mechanisms, including the use of various Agrobacterium strains, particle bombardment (Gene Gun), and innovative approaches such as nanoparticles. These tools are employed to overcome challenges posed by large plasmid sizes containing multiple coding regions (e.g., selectable markers, reporter genes, and expression promoters), which typically limit transformation efficiency. The lab’s resource pool includes an array of Agrobacterium strains, custom vectors, and a Gene Gun to enhance transformation success rates across diverse plant species.
A major area of focus in Dr. Taheri’s lab is plant genetic improvement. His team is conducting a large-scale screening of the USDA soybean germplasm collection to identify allelic variations linked to root system architecture and nodulation traits, key factors in optimizing nitrogen fixation and crop productivity. By combining phenotypic analysis with molecular techniques, Dr. Taheri aims to develop resilient soybean cultivars capable of thriving in both optimal and stress environments. He is hoping to expand such knowledge and technology in energy crops.
Dr. Taheri’s lab is uniquely equipped with advanced tools and expertise to pioneer innovative DNA delivery systems and explore the genetic underpinnings of crop traits. His research interests align with the overarching goal of addressing global food security challenges through sustainable agricultural practices and advanced crop improvement strategies. |
| TN |
| University of Wisconsin-Madison and Wisconsin Crop Innovation Center | Shawn Kaeppler | Professor and Director |
Academic
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Bioenergy
| The Wisconsin Crop Innovation is a public fee-for-service and research facility dedicated to transformation and gene-editing in elite varieties of important crop species and some model species. The facility has 28,000 square feet of dedicated greenhouse space and a number of unique high-capacity growth rooms to support large-scale projects. We have licensed and developed methods to increase automation and efficiency of transformation in multiple species. Sorghum is a bioenergy species for which we have advanced protocols with >100% transformation efficiency documented across a range of diverse cultivar. We also have experience with other priority bioenergy species and possible new priority species such as hemp. We are open to partnering to immediately deliver large numbers of plants using existing protocols, to serve as an evaluation partner to implement new protocols in a high-throughput setting, and to develop new protocols. For species such as sorghum, the bottlenecks we find in the process are not the transformation step, but supporting parameters including hypothesis generation and construct design, cost- and speed-efficient edit detection and genotyping, and supporting trialing of plants as most public researchers are not prepared to grow and evaluate large numbers of materials, especially in the field.
In addition to our scientific capacity, we also have completed supporting activities including recently being the first public-sector facility to complete the Excellence Through Stewardship process. We are interested to be a partner in ensuring and supporting proper use of biotech materials from research to commercialization. |
| WI |
| Caltech | Gozde Demirer | Assistant Professor |
Academic
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Bioenergy
| The overarching aim of the Demirer lab is to improve both the plant and planet health using sustainable approaches under three main thrusts in the lab.
In one thrust, we focus on improving plant genetic engineering and transformation processes through the development of novel carbon- and protein-based nanomaterials for biomolecule delivery. Here, by using these nanomaterials, we aim to effectively deliver DNA, RNA, and protein cargoes for transient and stable plant genetic engineering. We also work on delivering antimicrobial peptides and priming agents for crop protection in field conditions using protein-based nanoparticles. To date, we have been working with mostly model species but have recently started to work with tomato, Medicago, switchgrass, and wheat.
In another thrust, we work on improving the CRISPR genetic engineering toolkit in plants, focusing on targeted gene insertion using CRISPR-associated transposases and retroelements, and developing plant cell-type-specific and inducible synthetic biology circuits.
In our third thrust, we study complex plant-microbe-nutrient interactions in the rhizosphere and use this knowledge to enrich plant microbiota with beneficial bacteria through plant root exudate engineering. We also engineer the rhizobacteria themselves to endow plants with improved stress resilience, such as under drought and nutrient-starvation conditions. Lastly, we develop sentinel plants for detecting bioavailable nutrient levels in soil and nitrous oxide greenhouse gas emissions from agricultural fields. |
| CA |
| University of California, Riverside | Sean Cutler | Professor of Plant Cell Biology |
Academic
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Bioenergy
| Plant synthetic biology; plant abiotic stress tolerance; plant chemical biology. |
| CA |
| National Research Council Canada | Pankaj Bhowmik | Senior Research Officer |
Federal Government
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Other Energy Technologies
| Accomplished research scientist with 20+ years of experience leading and managing complex, multi-disciplinary research projects, consistently exceeding expectations in high-pressure environments. Expertise encompasses plant biotechnology, gene editing, commercialization, and a deep commitment to fostering collaborations with Indigenous communities to integrate traditional ecological knowledge into scientific research, advancing reconciliation initiatives. Proven ability to secure significant external funding, build impactful partnerships, and create a culture of research excellence. AREAS OF EXPERTISE • Leading Research and Innovation Strategy: Extensive experience in developing and implementing research strategies, overseeing all aspects of project management from concept to completion, including budget management and reporting. Successfully secured over $8 million in funding from various sources (Genome Canada, SRI, NSERC, ADF, PIC, IRAP industry collaborations). Proficient in all aspects of research grant proposals. Deep understanding of compliance requirements, CFIA confined research field trials and research ethics. • Nurturing People, Culture and Partnerships: Established effective relationships with internal and external clients, collaborators, and stakeholders. Successfully built and mentored multi-organizational research teams, including graduate students, postdoctoral fellows, and technical staff. Experience in providing guidance, feedback, and input to enhance research capabilities and business outcomes. • Enhancing Public Accessibility of Research and Innovation: Extensive experience in presenting research findings at national and international conferences (18+ invited talks), publishing in peer-reviewed journals (36+ publications), and participating in outreach activities. Actively engaged in knowledge transfer and technology commercialization efforts.
KEY ACCOMPLISHMENT • Developed a crop-agnostic CRISPR-based gene editing platform for accelerated crop improvement. • Developed formulations and operational processes for micropropagation in a mobile lab unit for multi-crop production in Yukon. • Developed AI algorithms for digital sensors mediated environmental control and monitoring systems. • Established three multi-organizational research initiatives through successful engagement with industry partners.
https://nrc.canada.ca/en/research-development/products-services/technical-advisory-services/advanced-plant-biotechnology-s |
| Saskatchewan |
| USDA-ARS | Roger Thilmony | Lead Scientist |
Federal Government
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Bioenergy
| Dr. Thilmony’s group performs crop biotechnology research in a wide range of species including bioenergy species like lowland switchgrass (Panicum virgatum), the model annual and perennial grasses Brachypodium distachyon and B. sylvaticum and numerous crops. We have experience in plant tissue culture, Agrobacterium-based transformation, the use of morphogenic regulators to enhance shoot regeneration and the molecular and phenotypic characterization of transgenic plants. Recently we developed the GAANTRY gene stacking technology which enables the generation of large gene stacks (>40kb) and their efficient and high-fidelity introduction into transgenic plants. We also have experience utilizing CRISPR-based gene editing in various crops and have developed novel expression control elements (promoters, terminators, insulators) that can be used to precisely express transgenes. |
| CA |
| Stanford University | Jennifer Brophy | Assistant Professor |
Academic
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Bioenergy
| Synthetic biology in bioenergy grasses (synthetic genetic circuits, gene expression control, etc.) Synthetic microbiomes Non-model bacterial engineering Conjugation as a method of DNA delivery |
| CA |
| University of Missouri; Danforth Center | Bing Yang | Professor |
Academic
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Bioenergy
| Sorghum transformation (Agrobacterium or particle bombardment based DNA, RNP delivery), improving transformation efficiency with aid of developmental regulator genes in sorghum; sorghum genome editing (CRISPRS-Cas9, CRISPR-Ca12a, Prime Editing); Transformation and genome editing capacities in my research lab and MU Plant Transformation Facility; Engineering biotic and abiotic stress tolerance in sorghum in collaborating with different groups. |
| MO |
| Donald Danforth Plant Science Center | Keith Slotkin | Principal Investigator |
Academic
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Other Energy Technologies
| The Slotkin lab has expertise in plant epigenetics, small RNAs, chromatin, genomics, transgene silencing and above all else, Transposable Elements.
Our interests are using these expertise to improve plant genomes, through new technologies for transgene performance, gene editing and genome engineering. We are highly interested in using our expertise to program the large-scale structural variations that can be found in plant genomes, and which are the basis of natural variation that traditional crop breeding is based upon.
Our capabilities include genome engineering in plant genomes (including soybean) that are based upon using transposable elements to perform targeted insertion, gene replacement and gene duplication. We have a pipeline in the lab to develop new technology in Arabidopsis, translate to soybean, and then after soybean further translate into other crops. |
| MO |
| Iowa State University | Shui-zhang Fei | Professor |
Academic
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Bioenergy
| Dr. Fei's research specialty is in molecular genetics of perennial grasses including switchgrass, miscanthus and other temperate C4 tall grasses. He has extensive experience in plant regeneration, genetic transformation and breeding & genetics of perennial grasses. His group successfully established a CRISPR/Cas-based gene editing in lowland switchgrass and created novel genotypes with enhanced tillering capacity. In addition, his group successfully transformed upland switchgrass ecotypes, which are known to be recalcitrant to genetic transformation by the use of morphogenic regulator genes. |
| IA |
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