2024 Graduate Student Symposium
About the Event
The 17th Annual Graduate Student Symposium will be held September 19th, 2024 from 1:00 pm to 5:00 pm PST.
The Graduate Student Symposium (GSS) bridges the gap between industry and academia. The event is a daylong seminar held as a means for students to share their research with colleagues, faculty, and representatives from industry. It also serves as a forum in which students can practice their presentation skills to a highly interdisciplinary audience and gain valuable feedback from people both in and outside of academia. The event includes an industry keynote speaker, panel discussion, as well as student talks and posters to showcase the latest research in biotechnology, energy, materials engineering, and data science
For the past seventeen years, the GSS has become a vital forum for both graduate students and industry representatives. With over 100 graduate students, faculty, and industry participants this event provides a chance to learn about the innovative research conducted at the University of Washington, meet future research leaders, and help improve the quality of graduate education in the Chemical Engineering department.
This year, GSS was modified to a reduced event consisting of only student oral and poster presentations. This was decided due to a lack of designated GSS organizers.
Format and Schedule
The event will be held in person this year. All activities are listed in Pacific Daylight Time (PDT).
Location: NanoES Building – Room 181, 3946 W Stevens Way NE, Seattle, WA 98105
Agenda
- 12:30 – Lunch and Social
- 1:00 – Opening Remarks
- 1:15 – Student Presentation Session
- 2:45 – Student Poster Session
- 4:15 – Closing Remarks
- 4:30 – Open Social
Congrats to our 2024 Oral and Poster Presentation Winners!
Oral Presentation Winners:
Cyrus Haas
Zach Wylie
Yifeng Cai
Poster Presentation Winners:
Abishek Sankaranarayanan
Nicholas Kaplan
Emily Du
Oral Presentations
Yifeng Cai, Baneyx Lab
Dynamic Reconfiguration of ELP-functionalized Gold Nanoparticles for Precision Delivery of Molecular Cargos
Thermoresponsive elastin-like peptides (ELPs) have been extensively investigated in biotechnology and medicine, but little attention has been paid to the process by which coacervation causes ELP-decorated nanoparticles to aggregate. Using pre-synthesized 20 nm and 60 nm gold nanoparticles (AuNPs) functionalized with a cysteine-terminated 96-repeat of the VPGVG sequence (V96-Cys), we show that the size of the clusters that reversibly form above the ELP transition temperature can be finely controlled in the 250 to 930 nm range by specifying the concentration of free V96-Cys in solution and using AuNPs of different sizes. We exploit this fine control over size to homogeneously load precise amounts of the dye Nile Red and the antibiotic Tetracycline into clusters of different hydrodynamic diameters and deliver cargos near-quantitatively by deconstructing the aggregates below the ELP transition temperature. Beyond establishing a key role for free ELPs in the agglomeration of ELP-functionalized particles, our results provide a path for the thermally controlled delivery of precise quantities of molecular cargo. This capability might prove useful in combination photothermal therapies and theranostic applications, and to trigger spatially and temporally uniform responses from biological, electronic, or optical systems.
Cyrus Haas, DeForest and King Labs
Computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks
Zach Wylie, Pozzo Lab
Synthesis and Self-Assembly of Ultrasmall Antimony Sulfide Nanoparticles
Antimony (III) sulfide nanostructures have the potential to be an extremely important material in thermoelectric, photovoltaic, and electrochemical energy systems. For electrochemical applications, the amorphous phase is the most useful as the increased defect concentration assists ion mobility. The relatively high thermodynamic stability of the bulk orthorhombic phase, however, requires that highly reactive precursors, which are often injected at high temperatures, be used to synthesize amorphous Sb2S3. These methods are often unscalable and unsustainable. We demonstrate a facile, room temperature, synthetic procedure to synthesize ultrasmall and weakly crystalline Sb2S3 nanoparticles which have the added ability to self-assemble into hexagonally close packed rods. We characterize these particles using small angle X-ray scattering and demonstrate that the assembly is directable by the choice and concentration of ligand and solvent, introducing a facet specific capping mechanism novel to this material. These seeds are also shown to match the battery performance of the current best Sb2S3 sodium and lithium-ion batteries.
Poster Presentations
Nicholas Kaplan, Marchand Lab
High-Accuracy Nanopore Sequencing of 6-Letter DNA for Synthetic Biology Applications
Expanding the genetic alphabet from 4-letters (ATGC) to 6-letters (ATGCXY) has been a goal of synthetic biology for decades. Several sets of synthetic nucleotides that base pair orthogonally to A:T/G:C pairs have been developed and have been shown to be tolerated (to various extents) by biology. These synthetic nucleotides, known as unnatural base pairing xeno-nucleic acids (ubp XNAs), are being explored for various applications, with genetic code expansion as a conspicuous example. Although implementing ubp XNAs into synthetic biology could be transformative, challenges in reading (sequencing) and amplification (PCR) of sequences containing these XNAs have limited their impact. In this poster, we present machine learning models for high-accuracy XNA sequencing (>98%) on commercially available nanopore sequencing devices. We apply these robust single-molecule sequencing methods to study the replication fidelity of XNAs in vitro, generating quantitative results that elucidate replication dynamics during PCR. Together, these methods allow us to screen various PCR conditions to optimize the replication of 6-letter (ATGCBS) DNA. By modernizing the synthetic biology toolkit available for XNAs, we look to improve access and application of XNAs to therapeutic, synthetic biology, and chemical biology research.
Marchand Research Lab
Hinako Kawabe
Xenobiology lab: Expanding nucleic acid technology with xenonucleic acids
Nucleic acids are the building blocks of life as we know it. With just four bases, DNA encodes for the 20 standard amino acids and performs complex biochemistry. Xenonucleic acids (XNAs) are nucleic acid analogues that expand the biochemical space we have access to. While multiple XNAs have been previously developed, the Marchand Lab works with XNAs that are structurally similar to the standard bases; our goal is robust incorporation of these XNAs into synthetic biology. This poster will outline the tools we must develop to utilize XNAs in synthetic biology, including sequencing methods and engineered organisms. We also highlight some future applications and additional directions in XNA work, including enzymatic synthesis of XNAs and genetic code expansion.
Jenekhe Research Lab
Stanley Cho, Anna Stewart
Organic Electronics Materials Chemistry and Device Engineering
Bergsman Research Lab
Jane Keth, Joelle Scott
Carothers Research Lab
Amanda Robert, Yejun Kim
Engineering bacterial CRISPRa/i transcriptional programs
To advance metabolic engineering in both model and non-model organisms, precise control of gene expression and fine-tuning of its components are essential. We have developed CRISPR-Cas transcriptional programs in Escherichia coli and Pseudomonas putida, enabling controlled biosynthesis through various metabolic pathways. Now, we aim to transfer these CRISPR-Cas systems into purple non-sulfur bacteria, a class of non-model microbes, to leverage their photosynthetic potential. However, progress is hindered by the lack of synthetic biology tools specific to these organisms. To address this, we have characterized key gene regulatory elements—such as promoters, ribosome binding sites (RBSs), and origins of replication—as well as methods for heterologous DNA integration. With these tools, we can precisely control the expression of both endogenous and heterologous proteins across diverse microbial hosts. These advancements pave the way for enhanced production and utilization of biomolecules, optimizing metabolic flux within target pathways. Our toolkit holds broader potential for developing genome-wide transcriptional and translational programs, as well as applications in signal transduction mechanisms.
Abishek Sankaranarayanan, Mittal Lab
Automated, Standardized and Open-source End-to-end Pipeline for Spatial Analysis in Cancer using Multiplexed Immunofluorescence Imaging
Maddie Soltani, Rorrer Lab
Sustainable Catalysis
Baneyx Research Group
Yifeng Cai
Protein-Based Hybrid and Hierarchical Nanomaterials
Ryan Brady, DeForest Lab
Grayscale Image-Guided 3D Photocustomization of Biomaterials
Ruby Jin, Nance Lab
Evaluating therapeutic potentials of neuroprotectants in neonatal ferret preterm brain injury model
Background: No targeted neuroprotective intervention is currently in use for improving the neurodevelopmental outcomes of extremely preterm infants born before 28 weeks’ gestation. The ferret brain is structurally similar to the human brain, providing a platform to explore the underlying biochemical and cellular responses preterm brain injury and two promising neurotherapeutics – azithromycin (Az) and erythropoietin (Epo). Objective: To examine microglial and transcriptomic signatures of combined Az and Epo neuroprotection in a postnatal day (P)14 extremely preterm-equivalent ferret ex vivo brain slice model of oxygen glucose deprivation (OGD). Methods/Approach: 300μm whole-hemisphere live ferret brain slices were obtained at P14. After 72h culturing in vitro, slices were subjected to 2h of OGD followed by treatment with Epo (3 IU/mL), Az (15uM), or Az+Epo for 24h. Cell death was determined using confocal microscopy of DAPI-stained pyknotic nuclei counts. Microglial morphology was assessed using a machine learning pipeline. Digital transcriptomics were analyzed using a ferret-specific NanoString nCounter panel of 255 genes. Results: Cell death was significantly reduced by Az+Epo, more so than either drug individually. In regions where Az and Az+Epo did not have neuroprotective effects, the presence of ameboid microglial morphology was increasingly observed compared to OGD alone. Augmentation of inflammatory macrophage responses, and reversal of oxidative stress and apoptotic cellular responses were related to Az+Epo neuroprotection with emergent transcriptomic signatures that were synergistically regulated. Conclusions: In the extremely preterm-equivalent ferret brain, Az+Epo provide synergistic neuroprotection via mitigation of cell death pathways, morphological microglial changes, and transcriptomic responses, that are not seen with either drug individually. These pathways warrant further investigation as targets for neuroprotection in the extremely preterm brain.
Z Lab Research
Ayça Ersoy
Brendan Butler, Nance Lab
A rotenone organotypic whole hemisphere slice model of mitochondrial abnormalities in the neonatal brain
Mitochondrial abnormalities underscore a variety of neurologic injuries and diseases and are well-studied in adult populations. Clinical studies identify critical roles of mitochondria in a wide range of developmental brain injuries, but models that capture mitochondrial abnormalities in systems representative of the neonatal brain environment are lacking. Here, we develop an organotypic whole-hemisphere (OWH) brain slice model of mitochondrial dysfunction in the neonatal brain. We extended the utility of complex I inhibitor rotenone (ROT), canonically used in models of adult neurodegenerative diseases, to inflict mitochondrial damage in OWH slices from term-equivalent rats. We quantified whole-slice health over 6 days of exposure for a range of doses represented in ROT literature and identified a suitable exposure level for OWH slices to inflict injury without compromising viability. At the selected exposure level, we confirmed exposure- and time-dependent mitochondrial responses using MitoTracker imaging in live OWH slices and RT-qPCR screening. We leveraged the regional structures present in OWH slices to quantify cell density and % damage in the cortex and midbrain regions for all cells as well as microglia and mature neuron populations, and observed cell-type dependent susceptibilities to ROT exposure as a function of region and exposure level. Live-video epifluorescence microscopy of extracellularly diffusing nanoparticle probes also captured changes in extracellular microstructure and local viscosity as a function of region, culture time, and number of exposures.
Emily Du, Nance Lab
Nicotinamide-Loaded Peptoid Nanotubes for Energy Regeneration to Drive DNA Repair in Neonatal Brain Injury
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Huat Chiang (Pozzo Lab)
Ms. Jade Hudson