Epigenetic modifications regulate chromatin structure and function, playing important roles in altering DNA transcription levels and subsequently cell fate decisions. Various next-generation sequencing (NGS) methods have been developed to detect these epigenetic changes in the genome, such as chromatin immunoprecipitation followed by sequencing (ChIP-seq). Even though ChIP-seq is extensively used to analyze DNA and histone modification levels, this method is limited to one histone marker at a time and requires significant amount of input cells, which masks the profiles of cell-to-cell variation and the complex interaction between the epigenome and gene expression. To overcome these limitations in current next-generation sequencing methods, we have been developing a multiplexed assay that could detect multiple epigenetic modifications in single cells. So far, I have developed a NGS data analysis pipeline to identify potential gene candidates that are highly differentially modified by histone markers. In the future, we hope to use these gene candidates as templates to design DNA-fluorescent in situ hybridization (DNA-FISH) probes and perform Expansion Microscopy and DNA-FISH with these probes to link histone modifications to specific gene loci at high resolution. After the assay is fully developed and validated, we plan to utilize the assay to take the epigenetic profiles of hematopoietic stem cells and study cell fate decisions in hematopoiesis.

Traumatic spinal cord injuries may lead to devastating loss of neurological function and there are currently no effective clinical methods to regenerate damaged nerve tissues. Besides, the inflammatory response can cause secondary injuries and inhibit regeneration. Novel treatments like cell therapy and localized drug delivery have shown greater efficacy when delivered by hydrogel scaffolds. However, effective scaffolds that can both culture neuronal cells and deliver therapeutic drugs are rare. Therefore, there is a need for an effective treatment of spinal cord injury that can locally deliver therapies with anti inflammatory properties to the spinal cord, as well as provide a support material for neural stem cell therapy. Here, we report a hydrogel composed of peptides that can self-assemble into a hydrogel in physiological conditions. The self-assembling peptide is conjugated to a polymer that enables drug loading and bioactive properties. Self-assembling peptides and a drug loading polymer were synthesized and characterized, loaded with bivalirudin, a model anti-inflammatory peptide drug, and assembled into a hydrogel formulation. The hydrogel was used to encapsulate neural stem cells to assay its efficacy as a support material. The gel was also assayed for its ability to release the anti-inflammatory drug when exposed to enzymes upregulated during inflammation. We anticipate seeing effective ligation of the polymer with the self-assembling peptide, successful hydrogel formulation, and neural stem cell viability when encapsulated in the hydrogel. A successful self-assembling formulation will ultimately work to provide effective cell therapy and anti-inflammatory drug delivery to the spinal cord, with potential for broader drug loading applications in the future.

Organic electronics have generated wide interest and excitement because they are relatively inexpensive to produce and are created from abundant resources, unlike their inorganic counterparts. Many organic materials also possess the unique potential of being stretchable in electronic applications including solar cells, OLEDs, and transistors. These materials can be made into wearable electronic devices and have the potential to power other advanced technology. Organic electronics are often made using semiconducting polymers. However, these polymers are semi-crystalline and brittle in solid state. To enhance their stretchability, our approach is to incorporate stretchable rubber into the semiconducting material by chemically linking the two polymers to combine their properties. This research investigates the crosslinking the well-known semiconducting polymer P3HT, poly(3-hexylthiophene), with polybutadiene (PB), a common rubber, to create a stretchable semiconducting material. To make crosslinking possible, we synthesize P3HT that includes a functional bromine to produce P3HBrT, poly(3-(6-bromohexyl)thiophene). Once the P3HBrT is synthesized, it can then be crosslinked with PB at different ratios to optimize for conductivity and stretchability. The crosslinked P3HBrT/PB can then be made into a thin film transistor and characterized for the desired properties. Ultimately, future research in this area will lead to a new generation of electronic devices with improved material properties.

Periodontal disease (PDL) results from a serious infection in the gingival tissue (gum) that can eventually lead to tooth loss and jawbone damage. The disease is common with more than 3 million cases in the US per annum. Bacteria build up in plaque lead to gingivitis and periodontitis under improper oral hygiene. If left untreated, the supporting tissues of the teeth e.g., cementum and periodontal ligaments will be lost, therefore making the teeth and supporting tissues vulnerable to bacterial attack, leading to serious infections and, even, to death. Current approaches in regenerating periodontal ligaments include the use of bioactive molecules and barrier membranes for guided tissue regeneration using human stem cells. Although the utilization of such materials enhances the cell proliferation and differentiation to a degree, the absence of cementum-like tissue prevents the complete regeneration of periodontal ligaments on the tooth surface. The aim of this project is to develop a biomimetic strategy to restore cementum tissue and regenerate the periodontal ligaments using human periodontal ligament (hPDL) cells in vitro. Using peptide-guided remineralization, we created a new cementum-like mineral layer on exposed dentin. The hPDL cells are then cultured and seeded on the novel cemento-mimetic layer and induced to differentiate. The proliferation and differentiation of the hPDL cells are monitored in detail using 3-(4,5-Dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) and alkaline phosphatase (ALP) assays, respectively. Our results show that the newly formed cemento-mimetic mineral layer facilitates the hPDL growth and differentiation. The method described herein offers a unique biomimetic solution to regenerate periodontal ligaments and thereby ultimately prevent tooth loss and eliminate periodontal disease. This work is supported by WA-State Life Sciences Discovery Funds, UW-School of Dentistry Spencer Funds, and Amazon-UW/CoMotion Catalyst Program.

UW Solar is an interdisciplinary student-led organization committed to developing solar infrastructure projects at the University of Washington. Solar arrays on campus not only produces clean renewable energy, but also helps the UW meet its carbon neutrality goals of its Climate Action Plan while providing a sustainable return on investment. UW Solar is working with UW Sustainability to maximize solar capacity on campus in support of the first UW Sustainability Plan to achieve the goals of the UW Climate Action Plan. Therefore, UW Solar is proposing a multi-phase plan for solar development at UW Seattle which aims to maximize solar capacity while providing a positive return on investment for Capital projects. UW Solar assessed all buildings on campus, and has identified the top 30 projects to be developed over the next 30 years to meet the UW’s 2050 Carbon Neutrality Goals. UW Solar’s scope of work for the Campus Plan includes the evaluation of all buildings on campus for potential solar installations and ranking them based on a suite of criteria that takes into consideration the following: energy generated, financial value of energy generated, cost of installation, return on investment, identifying funding options, working with campus stakeholders to develop the solar plan and timeline, assisting with schematic design, selection of contractor, oversight of installations, monitoring of energy generated for research and education. The total solar capacity for the Seattle campus could reach 8,000,000 kWh/year, with an annual energy value savings of $600,000. UW Solar will continue evaluating buildings on campus and working with all stakeholders to decide the priority of solar installations over the next 30 years.

As demand for accurate evaluation of chemicals and their potential to cause effects on humans increases, we have designed in vitro methods to facilitate such assessments. However, models of in vitro cell cultures are limited in their approach typically using a monoculture of limited cell types. Using a 3 dimensional organotypic approach to culture multiple cell types more reflective of a functioning organ can provide a framework for evaluating systematic interactions minimizing the need for in vivo assessment. We utilized a novel organotypic, in vitro model of testicular development that mirrors the development shown by in vivo studies. Our baseline study isolated testes that were harvested from C57BL/6 male mice on post-natal day 9. Testicular co-cultures were maintained for up to 16 days in 24 well plates with data collections occurring at days in vitro (DIV) 3, 7, and 16. Plates were stained with antibodies providing markers that correspond to morphological features of specific cell type markers. Five different primary antibodies were used as markers to visualize the change in cell populations. Markers for Sertoli cells corresponded to Vimentin, Leydig cells with 3b-HSD, Germ cells to DAZL and c-kit, and proliferation with PCNA. For each well, we used an immunofluorescence dual staining technique with Scanning Laser Image Cytometery (iCys) to observe the percentage of cell types and to determine change in phenotypic distribution of the cell population. From our preliminary observations, we were able to observe changes in Sertoli cells, Leydig cells and Germ cells throughout testicular development. Future studies would further develop and confirm the population and morphological changes observed with the testicular cell cultures. With a baseline model created, this in vitro model can be used to test the lethality of chemicals without the need of in vivo alternatives.

Diet, lifestyle, and environment can influence an individual’s behavior and brain function through epigenetic mechanisms. The Lattemann lab is investigating the effect that one factor, high fat diets, has on epigenetic regulation in hippocampus a key area for learning, memory and cognition. Previously, the lab determined that rats fed high fat diets exhibited increased sucrose motivation, and this behavioral effect was later linked to stearic and palmitic fatty acids explicitly. It was also shown that high fat, high sugar diets are associated with impaired place memory in rats. Most recently, the lab has analyzed hippocampal chromatin from rats fed high stearic and palmitic acid diets and is in the process of determining the effect of these diets on histone modifications. Histones regulate gene expression by binding to DNA: modifications to these histones influence how readily the DNA is transcribed, and how the gene expressed. These modifications are being screened for using Western blot analysis. In addition to screening for modifications in histones, the Lattemann lab also directly analyzed DNA for the expression of target genes. This screening procedure included measuring expression of candidate histone-target genes using PCR, and ChIP-Seq (Chromatin Immunoprecipitation and unbiased gene screening) assays. By locating histone modifications and quantitating the expression of hippocampal candidate genes, the lab has provided an epigenetic explanation for the behavioral effect of the diets, and a possible molecular mechanism by which the diets can induce this effect.

T cells of the immune system protect humans from most threats because they can recognize and eliminate foreign targets, as well as protect from reinfections. However, the persistence of an infection in the body leads to chronic stimulation of T cells, causing them to lose their effector function and enter a state known as “exhaustion”. Exhausted T cells are defined by increased expression of inhibitory receptors, loss of immune cell regulation, and most importantly, loss of cytotoxicity and effector function. Studies have shown that the transcription factors, T-bet and Eomes, play crucial roles in regulating T cell differentiation, with T-bet being highly associated with effector T cell differentiation. T-bet expression is dampened in exhausted T cells, and therefore, I hypothesize that controlled induction of T-bet expression can reverse the exhausted phenotype in antigen-experienced T cells. I constructed a T-bet overexpression vector containing T-bet cDNA fused to a fluorescent protein and destabilizing domain. The destabilizing domain, or degron, facilitates degradation of the constitutively expressed T-bet transgene in the absence of the ligand, Shield-1, which when added at varying concentrations allows for a range of protein stability. This method of overexpression confers faster control kinetics compared to commonly used transcriptional approaches, such as inducible promoters. I have characterized the range of the T-bet transgene in Jurkat cells by titrating Shield-1 to provide a working range of 5-60% overexpression of T-bet compared to endogenous levels. Validating these parameters in primary T cells will allow me to apply this T-bet overexpression vector in a mouse model of T cell exhaustion. This tool has significant implications for improving immunotherapy strategies, such as TIL and CAR-T therapies, where exhaustion of the therapeutic T cells has led to reduced efficacy of the treatment.

Despite the significant increase in the efficiency of perovskite-based solar cells, their instability remains a problem. Using zinc oxide (ZnO) as an electron transport layer in a solar cell easily degrades the perovskite layer because of ZnO’s basic nature. To try to prevent or slow down this degradation process, a silane layer was placed between the ZnO and the perovskite. Once glass substrates were spin-coated with diluted ZnO, they were immersed in diluted (3 chloropropyl)trimethoxysilane or (3-aminopropyl)trimethoxysilane and spin-coated with a perovskite solution and toluene. It was observed that the substrates that were immersed in silane layer degraded slower and with less intensity than the substrates that were not immersed. Based on these findings, it is imperative to conduct more research about the interaction between the silane and the compounds in the perovskite to determine ways to make photovoltaic cells more stable and functional.

First-generation college students (FGs; students whose parents have not completed college) often experience more difficulties transitioning into college compared to continuing-generation college students (CGs; students with at least one parent who has completed college). We hypothesize that some of these difficulties stem from the different cultural roles and expectations among interdependent FG families compared to independent CG families. In two studies, we examined cultural models of family (i.e., patterns of ideas and practices implicit in the family context) among FGs and CGs. In Study 1, we documented the prevailing ideas and concepts that FGs and CGs (N=518) associated with family by coding open-ended free-association responses. Both FGs and CGs associated the idea of family with affection, support, immediate family members and personal development. Although not statistically significantly different, FGs tended to associate family more with biological lineage, negative emotions, extended family members, and interdependence. In Study 2, we used a close-ended design to further investigate the patterns that emerged in Study 1. For instance, we anticipated that while both FGs and CGs would associate the family with support, FGs would be more likely to think more of emotional support while CGs would be more likely to think of instrumental support (e.g., financial assistance, career advice). Socioeconomic status is largely invisible and often overlooked in the college setting. By understanding more about FGs’ conceptions of families and their relationships to college, we hope to find ways to help FGs balance their roles as family members and college students and thus ease their transition to college. 

Palatal shelf elevation is an essential morphogenetic process during closure of the secondary palate. It has been proposed that palatal shelf elevation results from an intrinsic elevating force while also relying on extrinsic factors associated with development of other orofacial structures, such as the lower jaw and tongue. While in vitro palate culture is commonly utilized to study palate shelf elevation, it requires removal of the tongue or mandible prior to culture, which prevents any determination of the role of extrinsic factors in regulating palatal shelf elevation. Therefore, the aim of our project was to improve upon palate culture methods to better mimic in vivo conditions of palate development for studying the mechanism of palatal shelf elevation. We modified culture conditions to maintain the integrity of the oral cavity by leaving the tongue and mandible in place and cultured these mouse palate explants in suspension in dynamic conditions. Using this technique, the palatal shelves successfully elevated after 24-48 hour culture and displayed morphology like that of in vivo elevation, suggesting that our method improves upon previous culture techniques for investigation of the roles of both intrinsic and extrinsic factors during secondary palate development.

Primary sclerosing cholangitis (PSC) is a rare liver disease associated with inflammatory bowel disease (IBD) that causes strictures of the biliary tree and could result in the need for liver transplantation. One disease mechanism is upregulation of the mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) protein and subsequent increased lymphocyte migration to the biliary epithelium. The purpose of this research project is to compare the levels of enzymes (especially alkaline phosphatase, ALP) that represent surrogate markers of liver inflammation in PSC patients before and after infusion of vedolizumab (VDZ), a drug to treat IBD that interferes with this lymphocyte migration. We conducted a retrospective observational study to collect information on PSC patients from their electronic medical records and enter it into Excel. Information collected before and after VDZ infusion included: demographics, medical and social history, laboratory blood tests, information from first clinical encounters, and histology and radiology reports (e.g. ERCP, CT, MRI, endoscopies). Subsequently, we wrote a script in R to import the dataset, visualize the enzyme levels before and after VDZ infusion, and perform statistical inference using a matched-pairs t-test to determine if there was a significant difference in mean ALP levels in PSC patients before and after VDZ infusion. We obtained the following results (n = 13, α = 0.05): mean ALP difference = 10.67 U/L, t = 0.23, df = 12, p = 0.82, 95% CI = (-88.41, 109.76). Since our p-value was greater than 0.05 (and our confidence interval contained the value 0), we failed to reject our null hypothesis and could not conclude that there was a significant difference in mean ALP levels before and after VDZ infusion. Thus, more information is needed to determine if VDZ may have a beneficial effect on liver function.

Raven is a research prototype surgical robot that helps a surgeon perform surgery remotely. The purpose of my project is to develop a program to keep the surgical camera automatically focusing on the current surgical location. I wrote a GUI (graphical user interface) to perform object tracking and eye detection through the programing language Python with the OpenCV library. I created a ROS (robot operating system) node to program Raven. I expect the result will make Raven a more convenient tool for performing surgery remotely in the future.

Current diagnostic techniques for bacterial infections are time-consuming, and lead to over prescription of wide spectrum antibiotics. Surface plasmon resonance (SPR)-based biosensors can be used to reduce these diagnostic times, but often suffer from diffusion-limited mass transport. Dielectrophoresis (DEP), the movement of dielectrically polarized particles due to application of electrical inhomogeneous fields, can be used to overcome these mass transfer limitations in SPR devices. Current DEP-enhanced SPR devices separate particles with different dielectric properties by generating an electric field gradient and inducing positive DEP (p-DEP) force and negative DEP (n-DEP) force simultaneously. Depending on the dielectric properties of the particles, the particles are collected either in negative DEP at the center of electrodes or in the positive DEP at the edges. My research focuses on fabricating DEP-enhanced SPR biosensors for rapid detection and separation of pathogenic bacteria. Interdigitated electrodes are chosen to reduce detection limits and increase sensitivity. The structures of electrodes are fabricated by soft lithography techniques. To optimize the performance of DEP, electrode patterns with various gap widths are tested. Ultimately, the DEP-enhanced SPR sensors developed in my research could serve as a powerful diagnostic platform for rapid and sensitive detection of pathogenic bacteria by reducing the time of diagnosis and minimizing morbidity and mortality from infectious diseases.

The ultimate goal of robotics is to be able to interact with robots as one would with another person; hand in hand with this goal lies the ability for robots to understand natural language and carry out tasks in practical environments. Let us take for example, if a human were to command a robot to “pick up a can of coke inside a cardboard box on a table”. The robot should be able to extract relational information such as a can of coke is inside a cardboard box and a cardboard box is on a table. If “coke” is unknown, the robot should be able to ask clarifying questions to ascertain the qualitative aspects that define it. So, robots should be able to reason in the presence of uncertainties during object manipulation in the real world. We use a Fuzzy Markov Logic Network (Fuzzy-MLN) to learn and predict object classifications given input from multiple sensory modalities. Inputs from vision (RBG-D), haptics, and audio are used along with a prior knowledge base to identify objects in the robot’s environment and annotate various attributes which are added to the MLN. Audio input is processed for natural language which can provide information to contextualize the robot’s environment or give instructions to/answer queries from the robot in order to learn new relations, update Fuzzy-MLN weights, and improve annotator accuracy.

Dental hypersensitivity (DH) is a common oral health condition in the U.S. affecting the majority of the adult population. It is caused by the exposure of dentin due to the demineralization of the protective cementum or enamel that covers the tooth surface. When the dentinal tubules are exposed, nerve fibers in the pulp or predentin are stimulated by the displacement of the fluid and report pain. The stimulus that triggers the onset of pain can be of thermal, chemical or mechanical origin. There is still no effective agent to completely resolve the patient’s discomfort with DH. Over-the-counter products are commonly advised in the management of DH while toothpastes containing strontium, oxalate or potassium salts, or fluoride are recommended with limited efficacy to reduce the sensitivity from DH. Restorative materials using composite, glass ionomer or amalgam are adapted to treat the affected area with limited success. The goal of this project has been to develop a biomimetic treatment by restoring cementum tissue using a peptide-guided remineralization approach, thereby occluding the exposed tubules with a newly formed mechanically and thermally stable mineral layer. The College of Engineering working closely with School of Dentistry-UW involves mimicking the hypersensitivity condition by removing enamel/cementum of extracted human teeth to expose underlying dentin. The samples are then treated with peptide-guided remineralization resulting in 10+ micrometer thick new layer over the damaged dentin. Our results exhibit a highly effective way to occlude the exposed dentinal tubules by a newly formed mineral layer which penetrates into the dentin tubules. The method described herein offers a unique biomimetic treatment protocol for dental hypersensitivity, which will be developed as a platform technology for effective in-clinic and over-the-counter hypersensitivity treatments. The work is supported by WA-State Life Sciences Discovery Funds, UW-School of Dentistry Spencer Funds, and Amazon-UW/CoMotion Catalyst Program.

Phytoliths are microscopic silica bodies that form in many plants. Being resistant to organic decomposition, they can be used to track plant evolution and past vegetation changes. Although they were traditionally considered as non-functional cellular by-products, recent studies suggest that phytoliths may have photonic, structural, nutritional and defensive benefits in plant growth and survival. Grasses, which are large terrestrial producers of biogenic silica, are the suitable model system for studying the adaptive significance of silica accumulation in plants. Identification of phytoliths within the plants (for studying function) and inside the sediments (for studying evolution of vegetation) have so far been limited to optical microscopy-based methods where fluorescent dyes are commonly used to increase contrast between silica bodies and plant tissue. Due to their non-specific nature, however, fluorescent dyes often accumulate in different parts of the cells and silicified tissues, causing false positives and leading to incomplete staining and difficulties to construct 3D structures. With exquisite molecular recognition and assembly properties, solid-binding peptide tags (dubbed GEPIs) are surface functionalization moieties that can be chimerized with fluorescent and utilized as material-specific probes to selectively label variety of inorganic materials at surfaces and within interfaces. Our goal is to develop peptide-based phytolith-specific fluorescent probes to identify and delineate phytolith shapes with high precision and in situ. Using phytoliths-specific peptides probes, designed and chimerized with fluorescent molecules, our goal is to incubate different grass species, and visualize them using laser-confocal microscopy. We hypothesize that the novel molecular construct enable specific detection of phytoliths in situ. The method we are developing will offer a unique solution for fast and accurate identification and 3D organization of inorganic nano- and micro-structures in tissues from living plants and in paleontological samples.

At the terminus of every robotic arm is an end-effector. These are the hand-like devices that directly interact with the environment. Collecting data from the vantage point of an end-effector is highly desirable, though difficult to accomplish in practice. Wired data transmission solutions which use internal cables suffer from signal degradation due to proximity to power conduits. Moreover, the solutions which use external cables are subject to tangling and often impose limits on the robot’s kinematics. Finally, existing wireless data transmission solutions are rarely used due to the low transmission rate, high latency time and unstable connection. This research focuses on developing a general approach to stream visual (RGBD) and haptic (force) data wirelessly to other devices. The resulting system should consist of an architecture which interfaces with a suite of end-effector sensors and handles signal compression, transmission, and decompression efficiently. Additionally, this project involves a hardware design portion which aims to neatly package and mount this infrastructure at the robot end-effector while satisfying power and kinematic constraints for the robot. This research chose the Intel Joule, an embedded Linux board, as the infrastructure to handle wireless transmission. The embedded board uses a low-level Python networking package, which forms the connection to transmit data to other devices on the same network. This project implements packages to encode, transmit and decode the data stream with Python. The receiving device decodes the compressed data and makes the data available to other devices on the same network. This project allows sensors and the main computer of the robot wireless connected and future robot would operate movement more freely.