CABBI Outreach

CABBI scientists will showcase their research and their knowledge by staying involved with events and projects on campus and in local communities. The Center is excited to be involved with educational partnerships, public presentations, and student mentoring. A sampling of outreach initiatives:

New in 2021! Research Program for Undergraduates!

Join us at RISE, a summer internship program providing bioenergy research opportunities for undergraduates from groups currently underrepresented in STEM!

The application deadline is April 23; the program will run 10 weeks (June 1-Aug. 6, 2021). Students interested in gaining experience in plant biology, agronomy, synthetic biology, genetics, environmental sciences, chemical engineering, and civil engineering are welcome to apply for this program, which includes a $4,800 stipend!

Download the RISE flier >>>

Click here to apply!! >>>

More details

Eligibility: U.S. citizen or permanent resident enrolled in degree-granting college/university with at least one semester of course work remaining before obtaining bachelor’s degree.

Program Dates: June 1-Aug. 6, 2021

Application Deadline: April 23, 3021

Stipend: $4,800

Housing Allowance: $2,000

About RISE: This is a 10-week summer research opportunity targeting underrepresented students interested in bioenergy research. Students seeking experience in plant biology, agronomy, synthetic biology, genetics, environmental sciences, chemical engineering, and civil engineering are welcome to apply! Project descriptions in the toggle below.

The Plan: Students will be paired with a CABBI mentor, conduct research, attend career development seminars, learn about the graduate school application practice, and practice STEM communication by presenting research at a summer symposium. Some projects are designed to be done virtually; others have in-person aspects that will be carried out following COVID safety guidelines.

Questions: Contact Elizabeth Murphy, eamurphy@illinois.edu

RISE Project Descriptions

Download a pdf of all project descriptions >>>

 

Project: Plant/microbe/soil interactions

Mentor: Chuck HydeFaculty member: Wendy Yang  

Location: University of Illinois Urbana-Champaign

Virtual or in-person? In-person if permitted

This project centers on the interactions between plants, microbes, and the soil surrounding them, specifically how annual (sorghum) and perennial (miscanthus) grasses change the soil around them. The student will help collect, process, and characterize soil and root samples from field sites around central Illinois to understand nutrient cycling and greenhouse gases.

 

Project: Analyzing emissions data from crop production

Mentor: Dalton StewartFaculty member: Jeremy Guest

Location: University of Illinois Urbana-Champaign

Virtual or in-person? Virtual (computer and internet connection required)

This project focuses on quantifying field-level emissions of crop production using real-time data collected with remote sensors. The student will help collect data on emissions standards (the allowable amount of air pollutants) and organize and coordinate these standards to combine with emissions data for environmental impact determination. Time permitting, the student will also assist with writing code to convert emissions data to environmental impacts according to the information provided by the standards.

 

Project: Analyzing farmers’ willingness to adopt perennial energy crops

Mentor: Pan YangFaculty member: Ximing Cai

Location: University of Illinois Urbana-Champaign

Virtual or in-person? Virtual (computer and internet connection required)

This project focuses on analyzing farmer’s survey data about their willingness to adopt perennial grasses. We will analyze survey data using advanced data analytic tools to identify the roles of various socio-economic factors in affecting farmers’ crop adoption decisions. The student will be taught data analytic tools such as regression and basic machine learning algorithms.

 

Project: Biorefinery simulation for citramalate production

Mentor: Emma BraceFaculty member: Jeremy Guest

Location: University of Illinois  Urbana-Champaign

Virtual or in-person? Virtual (computer and internet connection required)

Citramalate is a high-value bioproduct that can be made via the conversion of glucose by engineered E. coli bacteria. This project includes tasks related to design and simulation of a biorefinery to evaluate how a process to make citramalate could work (design), how much it would cost (techno-economic analysis), and what kind of environmental impacts it might have (life cycle assessment). The student will learn how to review scientific literature, code using object-oriented programming (Python), and contribute to some portion of the overall project (potentially a specific unit operation of interest in the biorefinery design, or a portion of the life cycle assessment).

 

Project: Applying machine learning to synthetic biology

Mentor: Michael VolkFaculty member: Huimin Zhao

Location: University of Illinois Urbana-Champaign

Virtual or in-person? Virtual (computer and internet connection required)

In this project, an existing machine learning tool, Automated Recommendation Tool (ART), will be used to make predictions for synthetic biology by applying it to CABBI datasets or data from scientific papers. In synthetic biology, organisms are engineered to have new useful purposes. The student will be introduced to basic concepts in metabolic engineering and data science and taught some of the basic tools from both disciplines. Part of the research experience will focus on identifying datasets where the ART method gives meaningful results. If time permits, we can begin looking into how to improve the machine learning method to make better predictions.

 

Project: Creating biorefinery process design software tools

Mentor: Sarang BhagwatFaculty member: Jeremy Guest

Location: University of Illinois Urbana-Champaign

Virtual or in-person? Virtual (computer and internet connection required)

The overall project goal is to create a software tool to assist in the process design of biorefineries, and then to integrate the tool with BioSTEAM (the Biorefinery Simulation and Techno-Economic Assessment Modules). The mentor will introduce the mentee to BioSTEAM and the biorefineries developed using it and guide them through literature related to biorefinery design and separations. The mentee will summarize the data flow needed between the proposed process synthesis tool and BioSTEAM and aid in the parallel development (in Python) of the process synthesis algorithm. The mentee will also help collect data from previously implemented biorefineries to generate a development dataset as well as a validation dataset (for qualitative and quantitative comparisons between design decisions that were used in those biorefineries and those recommended by the process synthesis algorithm). Although there are no firm prerequisites, the mentee will be well placed for these tasks with an ongoing bachelor-level degree in a chemical engineering/technology major and prior participation in at least one project (academic or industrial) that involved some form of chemical engineering design.

 

Project: Connecting Sustainability models

Mentor: Yalin LiFaculty member: Jeremy Guest

Location: University of Illinois Urbana-Champaign

Virtual or in-person? Virtual (computer and internet connection required)

This project will lay the groundwork to connect BioSTEAM (the Biorefinery Simulation and Techno-Economic Assessment Modules) with biogeochemical and economic models (e.g., FUN-CORPSE, DayCent, BEPAM) to include the impacts of feedstock when evaluating the sustainability of biofuels and bioproducts. The mentor will introduce BioSTEAM to the student and guide them through literature related to the models on feedstock impacts. The student will summarize the required inputs, outputs, and fundamental methodologies of CABBI’s existing models related to feedstock impacts (in-field and potentially logistic systems) and propose a path for integrating BioSTEAM with these models. There are no prerequisites for the mentee, but basic knowledge of life cycle assessment (LCA) will be helpful.

 

Project: Biological nitrification inhibition

Mentor: Sierra RaglinFaculty member: Angela Kent

Location: University of Illinois Urbana-Champaign

Virtual or in-person? In-person preferred if permitted but can arrange virtual

Sustainable agriculture strives to maximize productivity without depleting soil fertility and plant-microbe interactions play vital roles in achieving this goal. One of these beneficial interactions is biological nitrification inhibition (BNI). In order to investigate how beneficial traits like BNI capacity are lost through the domestication and crop breeding process, we will use sorghum as a model crop species to grow in greenhouse conditions. We will then sample rhizosphere soils and conduct potential nitrification assays in our lab. Students will gain experience in experimental design, greenhouse experiments, soil microbiology, laboratory analyses, and data collection and analysis.

 

Project: Investigating polyhydroxy alkenoates with synthetic biology

Mentor: William CordellFaculty member: Brian Pfleger

Location: University of Wisconsin at Madison

Virtual or in-person? In-person preferred if permitted but can arrange virtual

Polyhydroxy alkenoates (PHAs) are polymer subunits produced from microbes that have potential applications in biodegradable plastics. PHA copolymers, made of two different PHA subunits, have unique biocompatible, biodegradable, and flexible properties making them suitable for more advanced applications like medical device components. Our research direction is twofold, optimizing the production and quantification of PHA monomers and designing novel PHA production pathways for production of PHA copolymers in E. coli from a single carbon source. The student project will begin with the planning of the desired PHA copolymer pathway. Virtually the student will research the needed genes and prepare a file for gene synthesis. If in-person research is allowed, the student will clone the genes into a plasmid expression vector for production cultures. The primary virtual component for the student in this process will be to design a code for easy analysis of the PHA products.

 

Project: Nitrogen cycling in miscanthus

Mentor: Di LiangFaculty member: Angela Kent

Location: University of Illinois Urbana-Champaign

Virtual or in-person? In-person preferred if permitted but can arrange virtual

Bradyrhizobium is a diverse bacterial genus harboring versatile biogeochemical functions related to nitrogen and carbon cycling such as N2 fixation, photosynthesis, nitrification, and denitrification. The overall goal of this project is to understand the role of Bradyrhizobium in N cycling and sustainability of miscanthus cropping systems. We will extract endophytic and soil DNA from parts of the plant, rhizosphere and bulk soils of miscanthus. We will then characterize Bradyrhizobium community composition by targeting the nifH gene using Illumina MiSeq for sequencing. To isolate Bradyrhizobium, endophytes and soil bacteria cell extracts will be plated and the isolates will be confirmed on 16S rRNA gene sequencing using Sanger sequencing. Students will gain experience in experimental design, microbiology, laboratory analyses, and data collection and analysis.

Annual Programs at the University of Illinois Urbana-Champaign

Bioenergy Research Center scientists participate in a breakout session at the February 2020 AI and Machine Learning Workshop in Washington, D.C. Photo by Elizabeth Murphy

2020 AI Machine Learning BRC Workshop

On Feb. 26-27, CABBI facilitated an inter-BRC workshop on Artificial Intelligence (AI) and Machine Learning (ML) for Biosystems Design at the Washington Hilton Hotel in Washington, D.C. Fifty researchers from CABBI, the Great Lakes Bioenergy Research Center (GLBRC), the Joint BioEnergy Institute (JBEI), and the Center for Bioenergy Innovation (CBI) gathered for a day and a half program centered on:

  • applications of artificial intelligence in systems biology and biosystems design;

  • integration of experimental design, automation, and modeling; and

  • determining appropriateness of different modeling strategies (AI, ML, biophysical modeling) to address different types of problems relevant to the BRCs.

The researchers shared presentations and posters on the current state of research on these topics and discussed how the BRCs can collaboratively harness AI and ML to achieve research goals. A white paper is forthcoming.

2019 Events Sponsored by CABBI

2019 BRC Modeling Workshop

On May 2-3, CABBI hosted Bioenergy Research Center scientists for a modeling workshop at the University Club in downtown Chicago. Dozens of researchers from CABBI, the Great Lakes Bioenergy Research Center (GLBRC), the Joint BioEnergy Institute (JBEI), and the Center for Bioenergy Innovation (CBI) worked together on improving understanding for modeling methods. They also explored how to:

  • project potential feedstock yields,
  • understand greenhouse gas flux dynamics in relation to land use change,
  • analyze the implications of alternative feedstocks on water quality,
  • quantify marginal land for energy crops,
  • conduct technoeconomic and life-cycle analyses of biofuel and bioproduct supply chains, and
  • integrate biophysical and economic information to examine potential land uses.

The researchers further identified opportunities to collaborate on data underlying the computational analyses, and they discussed the potential to develop user-friendly platforms to share models and data.  

 

Switchgrass V Conference: Dedicated Energy Crops and Native Grasses for the Emerging Bioeconomy

CABBI Co-PI D.K. Lee and his U.S. Department of Energy-funded team hosted the fifth annual international conference on July 22-25, 2019, in Champaign, Ill.

Participants discussed state-of-the-art research into switchgrass and other dedicated energy crops grown for forage, conservation, and bioenergy feedstock production.

Switchgrass V included keynote speakers; sessions on genomics and genetic improvement, microbiomes and ecosystem services, agronomy and sustainable production, and postharvest processing and economics; as well as a student poster competition. Participants visited Illinois’ 320-acre Energy Farm, a model of production for large feedstock grasses.

Visit the conference webpage >>>

 

At CABBI Partner Institutions

A Sampling of 2021 Outreach Events at CABBI Partners

At the University of Nebraska at Lincoln 

  • CABBI researchers and staff from Nebraska will participate in the UNL Women in Science Day in April 2021 with hands-on laboratory activities for female high school students from across Nebraska to promote interest in STEM education and careers. CABBI also participated in the event in 2018 and 2019; the 2020 event was postponed by the COVID-19 pandemic.

A Sampling of 2019 Outreach Events at CABBI Partners

At West Virginia University

  • In May 2019, Eddie Brzostek (photo, above) and his lab members hosted a group of fifth-graders from Eastwood Elementary School to the WVU research site.

At the University of Nebraska at Lincoln 

  • Nebraska scientists highlighted CABBI research on May 18. 2019, at its Fascination of Plants Day (larger photo, right) in the Maxwell Arboretum on the UNL East Campus.
  • CABBI researchers and staff from Nebraska participated in the UNL Women in Science Day in March 2019 (smaller photo, right) with hands-on laboratory activities for women high school students from across Nebraska to promote interest in STEM education and careers. CABBI also participated in the event in April 2018.

A Sampling of 2018 Outreach Events at CABBI Partners

At Brookhaven National Laboratory

  • BNL is participating in the U.S. Department of Energy’s Science Undergraduate Laboratory Internships (SULI) program. In 2018, an internship went to Stony Brook University’s Brian Samuelson, a Biology major. Samuelson’s description of his work: “My work at Brookhaven National Laboratory focuses on understanding how oil is synthesized and stored in plant vegetative tissues such as leaves and stems. We use Arabidopsis thaliana and tobacco as model systems to help identify enzymes and metabolic regulators involved in oil metabolism in leaves. In the lab, I help with Arabidopsis seed planting on agar plates and seedling transfer from plates to soil. I use adult plants for DNA extraction, oil quantification by thin layer chromatography, protein analysis by Western blotting, and SDS-PAGE for protein expression. I also help with agrobacterium-mediated plant transformation to test some candidate genes for their ability to alter oil production in leaves. This work is exciting to me because increasing oil accumulation in vegetative tissues has potential to expand biofuel production from renewable resources, therefore reduce our dependence on depleting petroleum fuels.”

 

At West Virginia University

  • Members of the Eddie Brzostek Lab helped judge a local school science fair in May 2018 that focused on how light, nutrients, and talking to plants impacted growth. Later in the day, the team participated in a family Science, Technology, Engineering and Mathematics (STEM) fair, which included activities to introduce students and families to the science of climate change, and how soil respiration shifted as a function of air and soil temperature as well as carbon content. The team also walked families through a poster showing how bioenergy grasses might help mitigate future environmental change and provide energy security.
  • A field site event in West Virginia in June 2018 (photo, right) was attended by 100 elementary school students, who learned about carbon and nitrogen cycling in ecosystems — and how healthy ecosystems store carbon, provide clean water, and promote biodiversity. The students measured photosynthesis, soil respiration, invertebrate diversity, nutrient levels, and root biomass.

 

At HudsonAlpha Institute for Biotechnology

  • A researcher at HudsonAlpha discussed CABBI work in 2018 with high school educators enrolled in Genetic Technologies for All Classrooms (GTAC): Advanced Concepts, and spoke at a workshop to more than 100 high school life science educators about “genomics in the field.”

 

At the University of Nebraska at Lincoln 

  • The university developed a curriculum and hosted a two-day high school teachers’ workshop on plant oils in 2018.

 

At the USDA Agricultural Research Service

  • CABBI scientists participated in the 2018 Engineering Day in Peoria, Ill., with a biopolymers theme that was attended by approximately 1,800 people.

 

At Iowa State University

  • CABBI scientists participated in 2018 outreach activities directly to the farming community through extension programs in Iowa.