Research Projects and Mentors

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1. Animal Science: Evaluating heart rate variability for identifying and mitigating poor welfare outcomes in group-housed sows
  • Christopher Byrd, Assistant Professor, NDSU Animal Sciences
  • Project Collaborators: Rex Sun, PhD; Assistant Professor, NDSU Agricultural and Biological Engineering
  • 6 weeks
  • 1 student

Abstract
Many pig producers have adopted a style of animal housing that allows them to place several sows (female pigs) together in a single pen during their gestation period. While these pens are beneficial for a number of reasons (e.g. freedom of behavioral expression, social interaction, etc.), mixing of unfamiliar sows initially leads to aggressive interactions in order to establish a social hierarchy within the pen. Additionally, maintenance of that social hierarchy may lead to higher stress and poor welfare outcomes of lower-ranking sows if their position in the hierarchy affects their ability to obtain needed resources, such as feed.

The student selected for this project will work as part of a research team on a larger project focusing on the use of precision technologies for identifying social hierarchies within sow group housing. Specifically, the student’s portion of the study will evaluate the use of heart rate variability (HRV; a non-invasive proxy measure of autonomic nervous system activity) as a method for determining stress within the pen and identifying sows that may be at risk of poor welfare outcomes due to their position in the group’s social hierarchy. With the assistance of others on the research team, the student will be exposed to real-world swine industry challenges and gain several key experiences in swine handling, behavioral collection, HRV analysis, and the experimental research process.


2. Biological Sciences: Assessing blood parasites in Red-winged blackbird nestlings: can its presence influence nestling growth?
  • Timothy Greives, associate professor, biological sciences
  • 8 weeks
  • 1 student

Abstract
Parasite infection is one factor that may influence the development and survival of young offspring in wild bird populations. The prevalence of parasite infection in young may impact traits related with survival, including growth and development. Infection at a young age can have short- and long-term consequences. For example, previous research found negative survival was reduced in young birds infected with blood-parasites. The objectives of this study are (1) to determinate the prevalence of blood parasites in nestlings, and (2) to assess the effect of parasite infection in the nestling growth. We hypothesize that nestlings infected with blood parasites will grow more slowly than non-infected nestlings. The student will work as part of the Red-winged blackbird team to find and monitoring nests during their breeding season in wetlands near Alice, ND. Morphological measurements (mass and tarsus length), and blood samples will be taken from nestlings on day 6 of the nestling period. Blood samples will be stored in ice until transported to the laboratory, and then frozen at -80 °C. Blood parasite infection will be assessed using PCR designed to amplify DNA segments associated with target blood parasites (Plasmodium spp.,Haemoproteus spp., and Leucocytozoon spp.) followed by gel electrophoresis. Parasite infection status of the nestling will be related with morphological measurements (mass and tarsus length). The findings from this study will contribute to the knowledge about the influence of the parasitism in the traits that could impact survival in wild bird populations.

Expected Outcomes from the REU research experiences
Undergraduate participant will gain hand-on experience in the research process both in the field and laboratory settings. The participant will acquire/enhance skills in writing, data analysis and communicating scientific results. In addition, the participant will learn new field methods and laboratory techniques, such as handling of wild birds, blood sampling, DNA extraction and PCR. Another valuable experience for the participant will be the opportunity to work in a collaborative research group. The participant will be interacting with other graduate student researchers that will be supporting the participant and initiating networking relationship in the scientific community.

Anticipated role of undergraduate researcher
The undergraduate researcher will be participating in the process of reviewing scientific literature, learn and follow protocols for field and laboratory methods, assisting with data collection in the field, conducting laboratory assay for detection of blood parasite infections, preparing a final report. All team members will participate in the aspects of the field research, but the undergraduate researcher will be primarily responsible for the laboratory work and analysis of the parasite data.


3. Biological Sciences: Investigating perivascular cell phenotype changing under the influence of cancer cells
  • Jiha Kim, assistant professor, biological sciences
  • 8 weeks
  • 2 students

Our research is focused on understanding the influence of malignant tumor cells on the tumor microenvironment (TME). Among the various components of the TME, tumor blood vessels orchestrate many tumor-specific features and aggressiveness. Tumor growth depends on a coordinated angiogenic response and vascular remodeling to meet the nutrient and oxygen demands posed by exponential growth. On the other hand, tumor vessels also serve as the main route for therapeutic drugs and immune cell trafficking, making it a double-edged sword for disease progression and targeting approaches.

Pericyte, perivascular cell, is a fundamental component of blood vessels responsible for enveloping the vessels' surface and providing structural support. While all pericytes share its core structure and function, it exhibits specific morphology, and molecular characteristics depend on their location and the status of specific tissue they reside in. Our recent studies showed the great heterogeneity of tumor-associated pericyte phenotype, and cancer cells can manipulate the pericyte phenotype via secreted extracellular vesicles, including exosomes. We are aiming to understand the mechanism of how exosomes influence the molecular changes of pericytes and develop potential ways to change the pericyte phenotype that can be utilized to answer several different biological questions.

Undergraduate researchers will participate in characterizing pericyte phenotype upon exosome treatment using quantitative real-time PCR and western blotting. Also, students will learn about pericyte culture and manipulation techniques. Undergraduate students will interact with graduate students and research scientists to learn routine experimental practices and obtain, organize, analyze, and interpret the data. Students will also learn how to present the research purpose, data, and future goals through regular lab meetings and one-on-one meetings with a mentor.

We anticipate two undergraduate students to work on this project. The project will explore different cancer cells, including pancreatic cancer, breast cancer, and brain cancer. Therefore each student will be working on different cancer cell lines to generate exosomes and apply them to the pericytes.


4. Biomedical Engineering: Synthesis and characterization of nanoclay based scaffolds for bone tissue regeneration
  • Dinesh R. Katti, professor,civil and environmental engineering
  • 6 weeks
  • 1 student

Abstract
The field of tissue engineering involves regenerating human tissue by seeding patient’s cells on a porous cylinder or other shapes made with materials that allow cells to grow and make the intended tissue. Our research group has prepared tissue engineering scaffolds for bone tissue regeneration using nanoclays made with clays treated with an unnatural amino acid, Aminovaleric acid. The proposed REU research investigates making nanoclays with three new unnatural aminoacids and preparing tissue engineering scaffolds with these new nanoclays. The scaffold structure will be evaluated using micro-CT imaging, and mechanical properties will be found using a load frame. A commercial cell line of human adult stem cells will be seeded on the scaffolds. The cell proliferation and tissue regeneration will be studied using microscopy and various assays and gene and protein expressions. The scaffolds' bone tissue regeneration efficacy made with the three new nanoclays will be compared to the bone regeneration efficacy of the currently used scaffolds prepared with nanoclays made with Aminovaleric acid. This research will identify new nanoclays made with different aminoacids that could be more efficient in regenerating bone tissue.

The REU researcher will be paired with an experienced doctoral student who will train the student in various laboratory methods, safety processes and supervise the student daily. The faculty researcher (Dr. Dinesh Katti) will meet with the student twice a week, mentor the student, provide research guidance, assess the student’s research, and guide scholarly output preparation such as paper and or presentation. The student will also participate in regular weekly group meetings and regularly present her/his work at the meetings.


5. Chemistry and Biochemistry: Enzymatic Catalysis in Modification of Monomers to Improve their Stability During Polymerization
  • Mukund P. Sibi, University Distinguished Professor, chemistry and biochemistry
  • 6 weeks
  • 1 student

Abstract
Enzymes are nature’s catalysts. They are used extensively in a variety of industries to carry out organic reactions. Enzymes are also useful in the academic laboratory. Our group is interested in developing new methods for the synthesis of novel monomers derived from biomass. This will enable us to replace fossil fuel derived monomers with those from renewable resources. Some of the monomers from biomass decompose during polymerization. To circumvent this problem, the REU student will investigate enzymatic modification of monomers to improve their stability during polymerization. The goal for the project is to prepare dimers and small oligomers from furan containing monomers using mild reaction conditions(Scheme 1). The REU student will learn hands on techniques to perform organic reactions, isolation, purification, and characterization of the products. The student will become acquainted with different spectroscopic techniques used in structural characterization of organic compounds. The REU student will work closely with a graduate student and learn to work in a team setting. The project is well suited for training the REU student in a variety of soft skills.


6. Chemistry and Biochemistry: Gene Editing using CRISPR-Cas9 to Study Gene Function
  • Stuart J. Haring, associate professor, chemistry and biochemistry
  • 6 weeks
  • 1 student

Abstract
The field of biotechnology is rapidly expanding, but at its core is the ability to genetically modify and manipulate biological organisms and systems to provide for advances in agriculture, engineering, and medicine that are dependent on these organisms and the products they generate. One particular and essential technology driving advances in biotechnology is the ability to change the DNA sequence (genetic information) within a living cell, with the goals of: (1) understanding the importance/function of that particular DNA sequence and (2) manipulating that DNA sequence in a way that is ultimately beneficial to achieving a solution to a biological problem. Examples of biotechnology range from the generation forest-resistant crops resulting in yield increases and quality, to the ability to treat human disease through personalized medicine and potential gene therapies. To get to this point of commercial use, however, one needs to learn and implement basic techniques and technologies that make these research discoveries and developments possible. The project for this REU involves the student learning about and gaining experience in genetic modification of DNA sequences using CRISPR-Cas9 in a simple organism, the budding yeast Saccharomyces cerevisiae​. It also involves techniques and strategies for verifying proper genetic modification and for studying the effect(s) of a genetic modification. This research process in a simple organism is not unlike that which would occur if this process were being performed in the R&D (research and development) department of a biotechnology company. Furthermore, CRISPR-Cas9 works exactly the same, whether it be in a bacterial cell, a yeast cell, a plant cell, or a human cell, making the implementation of this technology and principles learned by the student regarding this technology directly applicable to any biological organism. The goal is for the student to learn the process by which genetic engineering is performed in the laboratory setting.

Expected Outcomes
A student participating in this project will gain first-hand knowledge of genetic modification in organisms using CRISPR-Cas9 (a genetic engineering technology for which pioneering researchers were awarded the2020 Nobel Prize). The student will also gain knowledge in techniques that are commonly used to in gene manipulation, including: polymerase chain reaction (PCR), transformation of DNA into cells, DNA isolation/purification from cells, restriction fragment length polymorphism (RFLP) analysis for geno typing, and experimental procedures to study cell function. Integrated into this project will be daily one-on-one meetings with the student, practice in the scientific method (hypothesis-driven research), practice in proper documentation of research, and weekly lab meetings with practice in communicating research findings.

Number of Students
This project can accommodate 1 or 2 students, as prescribed by the REU program.

Student 1 would be working on the generation of novel mutations in DNA damage response genes and the genotyping analysis (confirmation) of these mutations.

Student 2 would be utilizing already generated gene mutants to test mutated cells' ability to perform DNA repair and proper checkpoint function.

NOTE: Because the goal would be for each student to gain both ​gene editing​ and ​experimental (phenotypic)analysis experience, at three weeks in, each student would foray into the other's part of the project, providing each with the opportunity to not only learn additional techniques, but also to share and discuss their experiences in a setting where both have a vested interest.


7. Civil and Environmental Engineering: Blood flow dynamics in human heart and brain
  • Trung Bao Le, assistant professor, civil and environmental engineering
  • 6 weeks
  • up to 2 students

Abstract
The Complex Fluids Laboratory is looking for two undergraduate researchers to work on the investigation of blood flows in human body. The project involves the use of medical images from patients to reconstruct organ anatomies. The students are expected to learn basic concepts in medical imaging modalities such as Magnetic Resonance Imaging, Computed Tomography, and micro-Computed Tomography. The students will be trained to use professional software (Slicer3D, Seg3D, Osirix) to decode the medical images and translate them into digital models of human heart and brain. Under the guidance of the mentor, the undergraduate researchers will have opportunities to perform simulation of blood flow dynamics in the obtained models.

Expected outcomes
The undergraduate researchers are expected to master the knowledge and skills to work with the state-of-the-art medical images. The students will be able to understand basic human anatomies, segmentation procedures, denosing, and reconstructing 3D anatomical model. At the end of the training, students will be able to develop their own models, which will be ready for 3D printing.

Assignments
One student is expected to work on the heart model, the other will work on the brain model.


8. Civil and Environmental Engineering: Identification of a plant-based compound to inhibit breast cancer progression at bone metastasis
  • Kalpana S. Katti, distinguished professor, civil and environmental engineering; affiliate faculty, biomedical engineering; affiliate faculty, materials & nanotechnology
  • Kalidas Shetty, professor, plant sciences; associate vice president for international partnerships and collaborations
  • 6 weeks
  • 1 student

Abstract
The PI's group has developed an innovative in vitrotestbed to mimic breast cancer metastasis at the bone site. Thein vitrotestbed is based on tissue engineering, where breast cancer cells are seeded on regenerating human bone(bone mimetic scaffolds) to duplicate the cancer tumors in patients accurately. The testbed allows for screening new drug candidates to stem breast cancer growthat the bone site. In the proposed REU project, the student will work on an ongoing research projectfrom the Agricultural Products Utilization Commission (co-PI Dr. Kalidas Shetty, Plant Sciences).The student will evaluate the potential of one plant-based compound from the Oregano plant to inhibit the growth of breast cancer cells at the bone metastasis site and evaluate the compound's effecton bone healthin the in vitromodel.The student will seed twocommercial linesof breast cancer cellson bone mimetic scaffolds, followed by introducing predetermined compound concentrations. Next, overtime ( 5, 10, 20 days),cell proliferationwill be evaluated using imaging and assays,and gene and protein expressionstudieswill be conducted.Experiments will also be conducted to evaluate the compound's effecton bone cells' growthand bone regeneration ability via imaging, assays,and gene and protein expression monitoring.These results will be compared with the results from other studies with other compounds and an anti-cancer drug. The REU student will be guided by a doctoral student working on the project, highly experienced in the experimental, analytical,and statistical methods necessary for the project. Dr. Kalpana Katti, the faculty advisor,will meet with the student twice a week to plan and access the research activitiesand provide mentoring. The student will also interact with other students working in her group and participate in the weekly group meetings. TheREU study's outcomeis to evaluate the ability of the plant-based compound to reduce the growth of breast cancer at thebone metastasis site and a publicationbased on research results.


9. Civil and Environmental Engineering: Smart “PIG” (robotics)for Detecting Internal Damage and Environment Inside Pipes
  • Ying Huang, associate professor, civil engineering
  • 6 weeks
  • 1 student

Abstract
Pipes transport water to each household, wastewater generated in each household to the wastewater treatment plant, and also more than 80% of the oil/gas and chemicals in United States and around the world. The health condition of a pipe is very important to the safety transportation of these important matters related to our daily life. To maintain the pipe in a good condition, smart PIGs are commonly used, which is one of the most high-tech inventions of pipe industry. The “smart PIGs” are used for pipe cleaning and dewatering, and more importantly for pipe health condition inspection. In this project, the students will develop a small smart “PIG” for inspecting pipe damages and corrosive environments inside a pipe. There are various technologies applied on a smart PIG, such as acoustic sensors, ultrasonic sensors, and camera. In this project, we will focus on the development and optimization of camera sensors on the smart “PIG”. The numbers of LED lights needed for the camera to detect correct images inside pipe, the locations of the camera, the types of camera to be used, the run speed of the robot, the size of the robot, the video image quality, and the color detection quality, will all be investigated for real-sized steel pipes. The outcome of this project will provide the REU student a complete understanding of pipeline industry, the importance of pipeline for our nation, challenges in the pipeline industry for maintenance and inspection, and a comprehensive training for the use of automated tools for pipe safety inspection, especially the internal conditions of the pipes.

Roles of students
The REU student will get trained to design robotics for pipe safety inspection. He/she will be paired with Ph. D. student and work with the faculty mentor to design and analyze the data from the pipeline robot.


10. Civil and Environmental Engineering / Electrical and Computer Engineering: Effects of Nano-Sheet Orientation and Morphology on the Thermo-mechanical Behaviors of Polymer Nanocompositesfor Engineered Tissue Scaffold
  • Wenjie Xia, assistant professor, civil and environmental engineering
  • Dali Sun, assistant professor, electrical and computer engineering
  • 6 weeks
  • 1 student

Project abstract
Polymers reinforced with nanoscalethin sheets (e.g., graphene, clay) are promising candidates for advanced nanocomposite materials with excellent thermal, mechanical properties for engineered tissue scaffold in biomedical applications. Distinct from an ideal flat sheet, nanoscopic sheets in polymers tend to exhibit more “disordered” and “crumpled” configurations and corresponding smaller sizes as observed in experiments due to the thermal energy, external stress and interactions with polymer matrices. Such crumpling and random orientations of the sheets can lead to many intriguing properties distinct from a flat one, and thus it is expected that they have a huge impact on the performance of the overall nanocomposite. However, there is currently a lack of understanding of how nanoscale sheet orientation and morphology influence the thermomechanical properties of the nanocomposites. Understanding the structures and dynamics of sheets in the polymer matrix is crucial to develop an extension of structure-property relationships to predict the physical performance of nanocomposites. To overcome this critical issue, it is proposed to perform molecular dynamics (MD) simulations to study the sheet-polymer nanocomposites. To simulate such complex systems, we will employ coarse-grained modeling approach to overcoming spatiotemporal limitations of the molecular models. By employing the CG models, we will systematically explore the structural properties of nanosheets in the polymer matrix, such as the radius of gyration, hydrodynamic radius and relative orientations between the sheets. We will then perform shear and tensile tests of the overall system to understand how the structures of sheets influence the modulus and mechanical strength of the nanocomposite.

Expected outcomes for the REU student from the proposed project

  • Understanding the basic physical properties of polymers, nanosheet, and nanocomposites.
  • Understanding the basics of molecular dynamics (MD) simulation and coarse-grained modeling techniques.
  • Being able to perform MD simulations using high-performance computing (HPC) systems.
  • Developing skills of coding, analysis and calculations.
  • Use of visualization software to visualize molecular simulations.
  • Presenting results in forms of posters, presentations and papers in scientific journals.

11. Civil and Environmental Engineering / Soil Science: Mapping Slope Failures in North Dakota
  • Beena Ajmera, P.E., assistant professor, civil and environmental engineering
  • Aaron Lee M. Daigh, assistant professor, soil science
  • 6 weeks
  • up to 2 students

Abstract
Billions of dollars and hundreds of lives are lost throughout the world due to landslides alone. In North Dakota, over 24,000 slope failures have been mapped. One of the major triggers of landslides is rainfall and the infiltration of water into the slopes due to snowmelt and irrigation activities. As part of this study, rainfall and snowfall conditions prior to the occurrence of the mapped slope failures will be determined. These results will combined with other conditioning factors such as the slope inclination, type of slope materials, land use and land cover, etc. to determine the impact of rainfall and snowmelt in triggering landslides observed across the state. It is anticipated the findings from this study will allow the development of landslide hazard maps to determine vulnerable zones. Such maps will allow local and regional government agencies to proper plan and allocate resources to prevent and mitigate the potential disastrous from future landslides.

Role of REU Students
Up to two undergraduate students from the Summer 2021 REU cohort can be engaged in this research project. The students will work on different aspects of the proposed research project. In particular, one student will focus on impact of rainfall in conditioning and/or triggering the observed landslides across the state. He/she will gather relevant rainfall data including durations and intensities of the rainfall events in addition to data associated with conditioning factors within the slope materials, such as the existing moisture and ground water levels. The second student will focus on the impact of snowfall on the observe slope failures. As part of his/her focus, he/she will collect data related to the snow accumulations, snow melt and runoff, and the frost depth at the locations of the landslides. Independently, the students will combine statistical analyses with basic slope stability theories to establish the influence of rainfall or snowfall on triggering the slope failures. It is anticipated that by the end of the summer, the students will be able to present their results. Students will be invited following the summer session to participate in co-authoring the results for journal and/or conference papers.


12. Computer Science: Analysis of Gene Expression Cancer RNA-Seq Data Set using Machine Learning and Evolutionary Computation Methods
  • Simone Ludwig, professor and interim chair, computer science
  • 6 weeks
  • up to 2 students

Overview and Background
Gene expression is a process by which the information that is encoded in a gene is used to control the structure of a protein molecule. The cell reads this sequence of the gene in groups of three bases. Each group of these three bases (codon) corresponds to one of twenty different amino acids that are used to build the protein. A particular gene expression cancer RNA-Seq data set will be investigated in this study. The data set consists of 20,531features and 801 instances, and thus is considered a large data set. Different machine learning algorithms and evolutionary computation methods will be applied to generate different learning models. These machine learning methods are standard datamining algorithms and can be used from open-source libraries. Different evaluation measures will be employed in order to compare the different machine learning and evolutionary computation methods.

Project Objectives
Different machine learning and evolutionary computation methods will be applied to the gene expression data set and the generated machine learning models will be evaluated based on accuracy, efficacy, and speed. The REU student(s) will be introduced to the data mining / machine learning area by learning and applying the different algorithms. Furthermore, a deeper understanding of gene expression data will also be gained.

Project Plan
REU student(s) will be exposed to the different machine learning algorithms available when addressing the research objectives. The first step will be to get familiar with Python programming, followed by the datamining methodology. As part of the data mining framework different machine learning algorithms and evolutionary computation methods will be discussed and used in this research study followed by an evaluation in order to compare the different methods.

Student Outcomes
Students will learn Python programming since the machine learning algorithms are provided as Tensorflow/Keras libraries. Furthermore, the students will learn the machine learning life-cycle of data pre-processing, model generation, training and testing, and evaluation. In addition, the students will get exposed to GUI (Graphical User Interface) programming and design as well.

One or two students could be working on this project; twos tudents could work together, which would allow more machine learning techniques to be applied to the data set.


13. Computer Science and Civil Engineering: Authentication in Cross-Device Interaction
  • Jun Kong, professor, computer science
  • Ying Huang, associate professor, civil engineering
  • 6 weeks
  • 1 student

Though electronic communication is developing rapidly, face-to-face meetings are still important, particularly in collaborative applications. With a large screen, tabletop computers are especially suited to co-located group work. However, it is challenging to avoid interference during simultaneous interaction in a multi-user environment. For example, each tabletop is only equipped with one speaker, which inevitably causes interference if multiple users are playing multimedia contents simultaneously. In addition, the availability of only one single virtual keyboard prevents multiple users from engaging with data entry at the same time.

Cross-device interaction can address the above challenging issues by providing smooth and seamless information sharing among a tabletop and multiple mobile devices. Specifically speaking, a large display serves as a public space while each user takes a mobile device as a personal space. According to a user’s action, a unique personal interface is generated on an associated mobile device with appropriate input and output modalities. The above interaction style seamlessly integrates a large public display with a personal mobile device, which facilitates information sharing without sacrificing privacy.

Since cross-device interaction involves multiple users, authentication is an essential requirement to protect sensitive information and user privacy. However, traditional passwords are not suitable in cross-device interaction since multiple users may sit close to each other and a password can be compromised due to shoulder surfing. This project will investigate biometrics-based authentication. Biometrics indicate body measurements and calculations related to human characteristics. Since each human has a unique biometric pattern, analyzing biometric features can correctly authenticate the identity of a user without compromising usability. Especially, this project will apply machine learning techniques to analyze pressure features to enhance the security of authentication.


14. Electrical and Computer Engineering: MXene nanomaterial-based enzymatic biofuel cell 
  • Qifeng Zhang, assistant professor, electrical and computer engineering
  • 8 weeks
  • up to 2 students

Abstract
This project is to explore the use of MXene (M = a transition metal, X = C or N) materials for enzymatic biofuel cell. MXene materials are of a layered nanostructure (Figure 1) first discovered in 2011. They possess a very high specific surface area, a good electric conductivity and abundant surface hydroxyl groups that result in a highly hydrophilic surface. These features make the materials a good fit for effective catch of enzymes and transfer of charges, and the materials are therefore believed to be a promising candidate for building enzymatic biofuel cell with much improved capability in generating electricity. Specific activities of this project include (1) fabricating MXene materials and electrodes, (2) characterizing the materials and electrodes in terms of morphology and composition, (3) assembling an enzymatic biofuel cell that uses the MXene electrodes, (4) measuring the electricity (i.e., the current density) generated by the biofuel cell, and (5) optimizing the electrodes towards improving the power of the biofuel cell. The goals of the research are to (1) develop a novel nanomaterial-based enzymatic biofuel cell with a high energy density and high power density, and (2) make students gain fundamental understanding about how nanostructured materials can benefit the performance of electric or electrochemical devices like the enzymatic biofuel cell. The expected outcomes are (i) students being satisfied with the knowledge and skills that they learn through participating in the research, (ii) students demonstrating the ability in analyzing experimental data, writing a paper-like report, and presenting their research findings professionally, and (iii) a prototype of enzymatic biofuel cell with a certain power output ideally adding new knowledge to the field of biofuel cells.

Students: 2

Expectation
A chemistry, biochemistry or materials science background.

Focuses
Student A - Material synthesis; electrode fabrication and characterization.
Student B - The assembly, measurement and optimization of the biofuel cell.


15. Industrial and Manufacturing Engineering/Biomedical Engineering: IoT devicefor the monitoring and diagnosis of Obstructive Sleep Apnea in Cancer Patients under Treatment
  • Trung (Tim) Le, assistant professor, industrial and manufacturing engineering and biomedical engineering
  • 6 weeks
  • up to 2 students

Cancer patients with comorbidities have suboptimal treatment outcomes and lower survival rates because of the negative effects caused by comorbid conditions. Previous work reported that the mortality rate of prostate cancer patients with more than two comorbidities is 40% higher within 5 years of diagnosis; breast-cancer patients with more than two comorbid conditions have a 4-fold higher rate of mortality compared to patients without comorbid conditions. One of the underdiagnosed and undertreated cancer comorbidities that needs greater recognition is sleep-disordered breathing, especially obstructive sleep apnea (OSA).The use of opioid medication in cancer curative-intent therapy induces respiratory depression at night. Other causes, including sedatives, narcotics, radiotherapy, and chemotherapy, increase the risk of hypoventilation and OSA. The most common consequences of untreated OSA are frequent episodes of hypoxia, irregular arousals, and fragmented sleep. It has been shown that fragmented sleep and intermittent hypoxemia in OSA can initiate malignant transformation, hasten tumor proliferation, increase metastasis invasion, and increase patient mortality. Hence, cancer patients during radiotherapy should be monitored for symptoms or progression of OSA. However, barriers to OSA monitoring during cancer treatment include the burdensome nature of the sleep lab’s polysomnography, a lack of communication between health care providers and cancer patients about sleep, the inefficiency of methods to monitor sleep during cancer therapy, and a lack of tools and guidelines for clinicians to evaluate sleep disorders in cancer patients.

The PI propose a smart IoT solution for the monitoring and diagnosis of OSA onset and progression before, during, and after radiotherapy cancer treatment. Two undergraduate students will be working on the project. The first student will work on quantifying the biomarker for the diagnosis of OSA progression in the cancer patient and the second student will work on developing smart IoT platform.

The proposed work provides a manageable diagnostic solution for mitigating negative OSA consequences in cancer patients undergoing radiotherapy. In the long term, the system can be used as an assistive at-home OSA monitoring and forecasting system that can dynamically update oncologists with predictive diagnostic sleep information of cancer patients undergoing treatment.


16. Mechanical Engineering: Grow Your Own Home!
  • Faculty Mentor: Ali Amiri, assistant professor of practice, mechanical engineering
  • Collaborative Mentor: Chad Ulven, professor, mechanical engineering
  • 6 weeks
  • 2 students

Project Abstract
Hemp fiber (extracted from hemp plant) is one of the most widely used natural fibers. It is mainly used in composition with a binding material (resin) to form a composite material. This composite is referred to as a “bio-composite” because it uses a bio-based material as a constituent. Bio-composites have a wide range of use such as sports equipment, automotive, aerospace, and construction/structural applications. One critical application of hemp is hempcrete (also a composite)that is made with concrete, lime and hemp and has shown promising properties as an effective building material. By absorbing/releasing moisture, hempcrete regulates the humidity inside buildings while offering desirable thermal and acoustic insulation, and mold proof properties invaluable for areas with high moisture. In addition, hempcrete has a great potential for thermal control and improvement of thermal properties of a structure. Figure 1 shows an example of non-load-bearing wall using hempcrete.

The goal of this research project is to study and investigate improving thermal properties of hempcrete by incorporating Phase Changing Materials (PCM) in the mixture. PCMs are micro capsules that have paraffin waxcore and are wrapped (encapsulated) in a polymer shell. These materials can change phase by absorbing and storing heat or release heat and therefore improve the thermal properties of the buildings. In this study, two types of PCMs will be compounded and mixed with hempcrete and thermal and mechanical properties of the ensuing material will be studied and investigated.

Expected Student Outcomes

  • Learn about bio-composites, their properties and applications
  • Learn about mechanical and thermal testing as well as materials characterization techniques
  • Investigate and study optimized process for hempcrete and incorporation of PCMs
  • Study thermophysical properties of hempcrete-PCM as a carbon-negative, bio-based building material

No prior knowledge of composites, materials or heat transfer is required.


17. Mechanical Engineering: Mechanical Testing of One-dimensional Biological Fibers at the nanometer scale
  • Xinnan Wang, associate professor, mechanical engineering
  • 6 weeks
  • up to 2 students

Have you have a time helping your dad or mom drag a cut tree branch from back yard to the front? Don’t you feel sometimes the branches are so heavy? Naturally you get surprised looking at a big tree with many thick branches. Not only they can manage to stand in the soil without “complaint”, but also can wave wildly in a strong wind. Why are they so strong?

Also if you want to tell if a material is brittle (like a chalk) or ductile (a gum), you may try to use your hand to pull it to get a feel. How will you “pull” it if the material is too small to see for your eyes, and too small to touch for your hands?

Hi, my name is Xinnan Wang, a faculty at department of Mechanical Engineering at NDSU. I would like to give students opportunities during the 6-week summer time in my lab to know and learn how to do the mechanical testing on one-dimensional (1D) biological fibers at the nanoscale.

The student, after the 6-week learning, should:

  1. Have a clear understanding of the importance of mechanical properties of bulk materials.
  2. Specify the current popular mechanical testing techniques for testing bulk materials at our department at NDSU.
  3. Know the importance of mechanical properties of micro/nanometer sized materials.
  4. Specify the current popular mechanical testing techniques for testing 1D to 3D materials at my lab.
  5. Grasp the basic theory of my nanotool: Atomic Force Microscopy in my lab.
  6. Gain the hands-on experience and research on 1D biological fibers/fibrils.
  7. Form an idea of of writing a research paper and presentation/poster.

For this 6-week research, students have access for my lab, and lab computer, internet. Students are faculty are expected to meet every week day to summarize what we have learned and what the plan is. According to the ability and progress of the students, the goal may be adjusted accordingly.

Either one or two students is fine with me.

I welcome you to work with me for 6 weeks of fun quality time. From discussion and learning, you will have a glimpse of how research of this type is done and how fun it is to discover the beauty of the governing laws that hide under the barks of the trees.


18. Microbiological Sciences: Agricultural Microbiomes of North Dakota - linking microbial communities to soil health and crop production
  • Samiran Banerjee, assistant professor, microbiological sciences
  • John McEvoy, professor, microbiological sciences
  • Abbey Wick, associate professor, school of natural resource sciences
  • 8 weeks
  • 2 students

Soil microbial communities are important in North Dakota cropping systems because they contribute to soil health properties and nutrient availability. You can think of this as a highly functioning soil that is working for the farmer to improve timeliness of planting and soil nutrients available to crops (microbially-driven nutrient cycling) amongst many other services. While North Dakota leads the nation in wheat production, our knowledge about the contributions of microbial properties, especially when wheat is in rotation, is limited. For example, we do not know the diversity and functions of microbial communities or if certain microbial groups are particularly beneficial for wheat production. In Summer 2020, we conducted an extensive field survey and collected over 1800 plant and soil samples from just over 200 wheat fields from 50 out of 53 counties of North Dakota. From all sites, we also collected samples from the rhizosphere, or the soil just outside the roots where the plant-microbe interactions take place. We collected both root and soil samples across three stages of wheat growth: seedling, heading and ripening. We also measured plant biomass and yield data from all of the wheat fields. Moreover, we sent out a questionnaire to the collaborating growers and we are currently obtaining management information for all of the fields. To our knowledge, this is the most comprehensive project of this nature in the world, and it will substantially improve our understanding of the importance of microbial community function related to wheat production.

Student 1 will explore the contribution of microbial communities to soil health. The student will perform DNA extraction, DNA quantification using Nanodrop, gel electrophoresis, PCR and quantitative PCR. Training will be provided for all analyses and regular meetings will ensure timely progress of the project.

Student 2 will assess the link between microbial diversity and wheat yield. The student will be performing PCR and preparing samples for next generation sequencing. Thus, the student will have the opportunity to learn the latest molecular approaches. Training will be provided for all analyses and regular meetings will ensure timely progress of the project.


19. Microbiological Sciences: Engineering the microbiome of plants and humans
  • Barney Geddes, assistant professor, microbiological sciences
  • Glenn Dorsam, associate professor, microbiological sciences
  • 8 weeks
  • 2 students

For decades, microbiology has been performed with a few model strains that were easily isolated and amenable to manipulating in the lab using genetics and molecular biology. With the advent of next-generation sequencing we’ve learned about the incredible diversity of life present in our microbiota, the world around us, and even in the food we eat. The plant microbiome offers a new frontier for improving crop productivity, while the potential of the human microbiome could transform human health in the centuries to come. 

In this project, students will engage in pioneering work to develop new biotechnology to engineer the microbiomes of plants (using the model crop alfalfa) and humans (using a diabetic mouse model). Students will evaluate molecular tools for their ability to manipulate the microbiota by engineering stable gene expression from plasmids, repressing gene expression with CRISPR interference, and performing forward genetics with transposon mutagenesis. Once tools are developed we plan to engineer the microbiome to manipulate glucose metabolism in a diabetic mouse model, and alter plant hormone levels to improve biomass production. 

Two students will work as a team to apply a hypothesis-driven proof-of-concept set of experiments aimed at manipulating the microbiome of the plant and mouse. This novel biotechnology research effort will provide the REU students to engage in an intradisciplinary, team effort between two laboratories with research expertise in plant (Professor Geddes) and mouse (Professor Dorsam) models link by their respective microbiota.  In the short term, these technologies will improve our abilities to study the microbiomes of plants and humans, and in the long term this biotechnology could even be used to endow microbiomes with new properties beneficial to plant and human health.


20. Pharmaceutical Sciences: Biotechnological intervention to augment the regeneration potential of the kidney
  • Sijo Mathew, assistant professor, pharmaceutical sciences
  • 6 weeks
  • up to 2 students

Abstract
The regeneration potential of kidney tubular epithelial cells is critical for recovery from any form of kidney injury. This project is testing the hypothesis that adhesion receptors influence the abundance of the kidney stem cell population. These maladaptive repair processes leading to the early onset of chronic diseases and loss of organ function. The processes involved are termed fibrosis, mainly mediated by cell proteins, adhesion receptors. Our recent studies proved that these receptor proteins decreased during aging. This is one of the reasons for making the aged individual more susceptible to the worst outcome after injury. The proposed project will investigate how these adhesion receptors influence stem cell populations in kidneys using molecular, cellular, and in vivo models. It is expected that the deletion of the adhesion receptor integrin β1 decrease the stem cell population in the kidney cortex. This change in the stem cell population is mainly mediated by complex formation with another protein named Cd98 in the kidney. Both these proteins present together in the cells.

Role of students
Student 1: The major role is to investigate the importance of integrin β1 in the kidney stem cell population. We have animal models for this investigation. Candidates will confirm the kidney-specific deletion of integrin β1 using PCR. After confirming the genetic background, the undergraduate student investigates the influence on stem cell population using qRTPCR, WB, and immunofluorescence. Integrin β1 will be deleted from human kidney epithelial cells using shRNA to evaluate the effect on cell functions.

Student 2: The proposed project for this student is to investigate the role of Cd98 in integrin-mediated cell functions and kidney stem cell population. We have animal models of kidney-specific deletion of Cd98hc using a similar card system that is used for integrin β1. Candidates will confirm the kidney-specific deletion of Cd98 using PCR. After confirming the genetic background, the undergraduate student will investigate the stem cell population using qRTPCR, WB, and immunofluorescence. Cd98hc will be deleted from human kidney epithelial cells using shRNA to evaluate the effect on cell functions.

Both the students will compare and contrast the results with their counterparts. This analysis will determine the mechanisms of stem cell regulation. They also get an opportunity to investigate the complex formation between these proteins. The influence on cell biological functions also will be investigated.


21. Pharmaceutical Sciences:  Biotechnological production and characterization of full-size anti-RAGE IgG antibodies and fluorescent labeled anti-mouse nanobodies
  • Estelle Leclerc, associate professor, pharmaceutical sciences
  • Stefan Vetter, assistant professor, pharmaceutical sciences
  • 6 weeks
  • up to 2 students

This REU research project is designed for two students who will work collaboratively using biotechnology to produce and to characterize recombinant immune proteins in mammalian and bacterial recombinant expression systems. The students will produce a full-size IgG anti-RAGE antibody in mammalian cells and will express two anti-mouse specific nanobodies in E.coli bacterial cells (weeks 1 and 2) . The proteins will be purified using several chromatographic techniques and fully characterized using biophysical and immunological techniques (weeks 3 and 4).

The anti-RAGE antibody will be used to suppress RAGE signaling in melanoma cancer cells and to study the potential of RAGE inhibition to improve chemotherapy of cancer. The purified nanobodies will be used after fluorescent labeling as secondary detection agents in multiplex immunofluorescence microscopic imaging of cancer tissue sections (weeks 5 and 6).

Both projects are stand-alone independent projects that are ready to go as soon as the REU students arrives. Necessary reagents for immune protein expression are available in the lab and proof of concept studies have been performed by undergraduate and graduate students from the laboratory in the fall of 2020, some studies are currently ongoing.

The Leclerc/Vetter laboratory is performing research on the RAGE receptor (Receptor for Advanced Glycation End products), that is involved in many cancers. Our lab has developed antibodies against RAGE that can block the deleterious effects of the receptor in tumors. Because these antibodies are not commercially available, we produce them in our lab. We also develop novel antibodies (e.g. nanobodies) with improved properties.The students will learn many aspects of pharmaceutical biotechnology, which is also a topic that Dr. Vetter teaches in the PharmD program of the School of Pharmacy. The hand-on experience of recombinant protein expression, purification, analytical characterization and application of the products in biomedical experiments will provide students a look into the preclinical biomedical research activities in an academic laboratory. This will hopefully encourage students to choose a graduate education in a biotechnology and/or life science related discipline.


22. Pharmaceutical Sciences: Genotyping Assay for in vivolung mechanics study
  • Sathish Venkatachalem, associate professor, pharmaceutical sciences
  • 6 weeks
  • 1 student

Abstract
The prime research focus of our laboratory is to study human lung diseases such as asthma, chronic obstructive pulmonary disease and pulmonary hypertension. The incidence and severity of asthma suggest a sex-skewed occurrence of asthma amongst men and women with increased asthma prevalence observed in women as compared to men. Furthermore, women may be biologically more susceptible to cigarette smoke exposure than men, when it comes to incidence of and complications from smoking-related airway diseases. Taken together, these observations point towards sex steroids playing a crucial role in asthma. Since, puberty is an important parameter in the incidence and severity of asthma (boys>girls, men<women), our current research project hypothesizes that Kisspeptins signaling could be protective in asthma by affecting the airway remodeling. In this context, our laboratory investigation focuses on sex-steroid signaling using specialized models of genetically modified mice. The structural and functional activity of the lungs are primarily controlled by the airway smooth muscle cell. Our in vitro studies have evaluated the effect of sex steroid receptor activation on primary human airway smooth cell function. Therefore, our current studies involve using global ERα/ERβ and KISS1R KO mouse models. Our studies using tissue-specific knockout animals will substantially enhance our understanding of how and why sex steroids influence the asthmatic airway. The littermates obtained from the breeding pairs of the aforementioned knockout animals will be assessed for study inclusion by performing our in-laboratory optimized genotyping assay to confirm successful KO of the respective sex steroid receptor.

Role of Undergraduate Researcher
The student candidate will perform and/or assist the following lab duties:

  • Collecting/labeling the samples for DNA extraction
  • Performing DNA extraction from the collected tissue samples
  • Running an agarose gel electrophoresis for DNA
  • Analyzing the gel and interpreting results from the genotyping
  • Assisting to Perform lung mechanics studies
  • Pathological interpretation

The undergraduate researcher will be tagged to a lab mentor for the initial 2 weeks before independently performing the above mentioned tasks.


23. Pharmaceutical Sciences: Pharmacological Activation of Mas Receptor for the Treatment of Inflammatory Stress in Diabetes
  • Yagna PR Jarajapu, associate professor, pharmaceutical sciences
  • 6 weeks
  • up to 2 students

Abstract of Research project for student-trainee(s)
Prevalence of diabetes is exponentially growing worldwide. According to CDC, just over one in ten Americans have diabetes and one in three have pre-diabetes. Long-term diabetes increases risk for cardiovascular disease, which appears to be the leading cause of morbidity and mortality in diabetic adults. Our lab is interested in identifying and characterizing novel pharmacological agents for the treatment of diabetic vascular complications. We have recently shown that treatment with an endogenous peptide, angiotensin-(1-7) (Ang-(1-7)), restores vascular health in mouse models of type 1 and type 2 diabetes. We have shown evidence for the cellular and molecular actions of Ang-(1-7) via Mas receptor in bone marrow-derived stem/progenitor cells and vascular endothelium that collectively produce vasoprotective functions in diabetic vasculature. We are currently extending these studies to characterize diabetes-induced pro-inflammatory pathways in the stem/progenitor cells and in the vasculature. Specifically, we are characterizing the effect of Ang-(1-7)on molecular mechanisms of diabetes-associated myelopoietic bias and the role of S100 proteins.

Our lab utilizes several in vitro and in vivo experimental methods and strategies to accomplish hypothesis-driven research objectives. Here are a few examples: In situ evaluation of myelopoietic functions of mouse or human stem/progenitor cells and flow cytometric evaluation of monocyte-macrophages. In vitro functional and biochemical assays such as migration, proliferation, western blotting and ELISAs.In vivo studies that involve developing and maintaining mouse models of type 1 and type 2 diabetes, chronic or acute treatments, glucose tolerance tests, vascular injury and blood flow measurements.

Mentoring plan
Student-trainee(s) will have an opportunity to choose from a variety of techniques and tools that are routinely used in our lab for hands-on experience. Trainee(s)will be required to work towards answering a specific research question tha twill be discussed and decided in the first week of research experience. While hands-on technical training will be provided by a graduate student or a post-doc in the group, trainees will interact with the faculty mentor for technical and conceptual discussions regularly. Trainee(s)will participate in the weekly lab meetings where weekly progress of research work is discussed. Trainee(s)is/are expected to read relevant literature and expected to present one original research publication of his/her interest to the group during the training period. Importantly, trainee(s) is/are expected to submit a research report that details the research experience at the end.


24. Soil Science: Crop Residue Characteristics Influencing Their Decomposition
  • Larry Cihacek, professor, soil science
  • 6 weeks
  • 1 student

Abstract
Conservation tillage has become widely adopted across North Dakota with many benefits to soil health. In the North Dakota, there is a short growing season with variable precipitation conditions from year to year which can lead to delayed mineralization of crop residues in fields under long-term conversation tillage. With this, gaining a better understanding of crop residue decomposition in a frigid environment is important as mineralization of crop residue recycles nutrients back to the soil for plant use. One of the nutrients of interest is nitrogen cycling from the crop residue decomposing. We would like to better understand the physical and chemical structure of the residues being studied (corn, spring wheat, soybean, radish) as it relates to their breakdown. We will use electron microscopy (EM) and near-infrared reflectance (NIR) technologies in this study.

The student will be involved in preparation of residue samples for EM and NIR analysis, basic chemical characterization analysis, reagent preparation and some field sample collection related to a larger overall study. The student will gain knowledge on basic lab principles and practices, sample preparation for lab analysis, and selected chemical analyses. A post-doctoral research associate will assist the PI in mentoring the student. The student will also be involved in the overall project to provide them an understanding of how their research fits into the bigger picture of research.

Student expectations

  • Eager to learn
  • Hold responsibility for the task that is given
  • Work ethically in the lab
  • Patience and attention to detail
  • Take safety training and practice safety first
  • Possess an interest in natural resources, plant sciences, soil science, chemistry, and/or environmental science
  • Demonstrates an understanding of general laboratory processes (some course work involving lab work)
25. Soil Science: Effects of Acid Soils on Crop Root Development
  • Larry Cihacek, professor, soil science
  • 6 weeks
  • 1 student

Acid soil has become a topic of interest for farmers in North Dakota as a result of long-term fertilizer use. The last known work on soil pH in this region was in the early 1990s and since then there has been a lot of advancement in understanding the soil, yet a lack of research to track soil pH changes. Soil pH is positively related to soil productivity and nutrient availability to plants. We will examine the effects of increased soluble Al3+ effects (toxicity) on the development, morphology and growth of plant roots in crops grown on acid soils. We plan to evaluate the effects of increased Al3+ effects on plant roots and the associated soil mineralogy using electron microscopy (EM) and X-ray diffraction (XRD) technology.

The student will be involved with the preparation of soil samples for X-ray diffraction (XRD)analysis, plant materials for EM analysis, preparation of lab reagents for chemical characterization of study materials, as well as r chemical characterization of acid soils. The student will gain knowledge on soil and plant sample preparation techniques for analysis, interpretation of EM and XRD data and field sampling techniques for sample collection. Some travel may be required to collect samples. A post-doctoral research associate will assist the PI in mentoring the student. The student will also be involved in the overall project to provide them an understanding of how their research fits into the bigger picture of research.

Student expectations

  • Eager to learn
  • Hold responsibility for the task that is given
  • Work ethically in the lab
  • Patience and attention to detail
  • Take safety training and practice safety first
  • Possess an interest in natural resources, plant sciences, soil science, chemistry, and/or environmental science
  • Demonstrates an understanding of general laboratory processes (some previous course work involving lab experience)

26. Biological Sciences: Detecting the Hidden: Using High Throughput Sequencing and Metabarcoding to Characterize the Fungi that Live in Coffee and Its Relatives
  • Laura Aldrich-Wolfe, assistant professor, biological sciences
  • 6 weeks
  • 1 student

Fungi play key roles in ecosystems, as agents of disease and decomposers, and also as beneficial mutualists. Molecular identification using high throughput sequencing allows us to detect the many hidden fungal species that live in plants, helping them or harming them. Coffee, Coffea arabica L., is an important crop of the montane tropics worldwide. We will be examining the leaves of coffee in plantations and closely related plants in the tropical forest understory to determine whether the way in which farmers grow coffee, in sun or in shade, changes the beneficial and harmful fungi that colonize plant species in the coffee family. Coffee farming, by changing the abundances of different fungi, may indirectly alter the fungal communities and the success of coffee relatives in adjacent forests. The undergraduate student involved in this project will learn how to isolate and quantify DNA from plant material, prepare samples for high throughput sequencing, and use online bioinformatics tools to characterize fungal communities from the DNA sequences that code for their ribosomes. The student will test hypotheses they develop in collaboration with their advisor and prepare a poster for public presentation of their findings.


27. Electrical and Computer Engineering: Emerging Memory Circuit and System Analysis
  • Sumitha George, assistant professor, electrical and computer engineering
  • 8 weeks
  • up to 2 students

This project will explore the design of memories with post CMOS devices and emerging memory technologies.  This specifically includes circuit level proposition and evaluation of a small memory array and of Content Address Memory (CAM) with emerging technologies.  CAMs are typically used in caches for searching contents of an array in a single operation and network routers.  Application performance will be evaluated with these newly designed circuits such as pattern matching. The simulations will be carried out using HPSICE or Cadence environment. The second part of the project requires quantitative evaluation of the memory and cache systems. The memory and system need modifications to accommodate newly designed memory.  This requires exploring the existing functional simulators and writing a new simulator to emulate the proposed changes in the systems for benchmarking.

Student Expectation
Electrical or Computer Engineering background.

Focuses
Student A – Circuits, VLSI ; Expectation : Digital circuits
Student B – Programming in C++/Python : Expectation (preferred): Basic Knowledge in Linux commands and Programming;  basic computer architecture


This REU program is supported by NIH Award # 2 P20 GM103442-19A1/Subaward UND0025451.

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