As more technology that utilizes personal electronic devices (PEDs) are being integrated in classrooms, the possibility of cell phone distraction is a real concern amongst many educators. Because of this, we became interested in cell phone use patterns in highly interactive biology classrooms at UW, and what factors influence their use. To answer this, we investigated the impact of in-class polling using PEDs or using clickers (older, standalone devices). We compared cell phone use in two different quarters (same course, same instructor) that either used PEDs or clickers for in-class polling. We also compared the cell phone use in the beginning of quarter vs. the end. In addition, we looked at whether classroom seat location correlates with cell phone use. To assess cell phone use, we directly observed active learning introductory biology lectures. Three to four researchers observed each seat in a designated section of the lecture hall and noted if a cell phone was visible (used as a proxy for use), three to five times during a class session. We used logistic regression and model selection to find a best fit model to determine if polling technology type, seat location or time of quarter (beg. vs end.) can predict cell phone visibility. To our surprise, the results indicated that neither Poll Everywhere nor time of quarter increased the already low cell phone visibility. However, our results also indicated that students that are sitting away from professor (back of classrooms) are more likely to use their cell phone than their peers regardless of polling technology. Taken together, we suggest instructors with highly interactive classrooms should not worry about integrating newer polling technologies. Further, instructors may look into having more TAs or peer facilitators roam around the classroom, especially in the case of large lecture halls to avoid cell phone misuse.

Childhood asthma accounts for 571,000 ER visits, 136,000 hospitalizations, and $10 billion in healthcare costs annually in the United States. Fewer than 50% of children with asthma are adherent to their treatment regimen, leading to worse health outcomes. The purpose of this study is to develop and test the usability and acceptability of the symptom monitoring and response module of the Child Asthma Management Program (CHAMP), a new web-based, tailored asthma shared management health application for 7 to 11-year-old children with persistent asthma and their parents. A user-friendly and visually engaging module was developed with content focused on asthma symptom identification, monitoring, and response. Using a human-centered design framework, dyads of children and parents were recruited to participate in two rounds of design and usability sessions with prototypes of the module. Additionally, dyads completed the Asthma Responsibility Questionnaire, CHAMP acceptability questionnaire, and a semi-structured interview following the sessions. Thematic analysis using an investigator-developed coding frame was used to code all interview data using ATLAS.ti software and quantitative data from the acceptability survey was transferred to SPSS 24 for analysis. Results from both design and usability sessions will inform final revisions to the module. The final version of this module will guide dyads in improving their asthma shared management. This module meets a considerable need for effective asthma management interventions and represents a step towards better tools for improved chronic disease management for pediatric patients.

In developed economies, medium sized firms make up roughly half of all economic growth and employment. Among poor economies however, these firms are virtually absent, as is financing for the creation of them, despite the rise of innovative microfinance institutions. This phenomenon is termed the “missing middle”. My paper sought to understand how firms of this size were established in the developed world, by juxtaposing the financial ecosystem of Industrial Revolution era Scotland to those of developing countries today. I choose Scotland because of its’ rapid development during the 18th and 19th centuries, despite relative poverty and lack of infrastructure compared to contemporary western European countries. I studied primary sources such as accounting documents, and letters between firm owners and managers to develop a picture of the business strategies and financial products used by these firms. These historical strategies were compared to those employed by modern microfinance institutions such as Grameen, based on their published financial statements. Similarities abounded: schemes where individuals pool their savings to create loanable capital, easy loan terms, co-signing, and other practices. The differences however, are stark. Scottish banks lent small and medium sized debts, and rarely had more than a few hundred, local accounts. Modern microfinance institutions service millions of tiny borrowers. Additionally, Scottish banks were universally general-partnerships, a form mostly extinct today. I conclude by suggesting that these differences were key in allowing Scottish banks to finance the Industrial Revolution in Scotland, and that they could assist in financing the “missing middle” in the developing world today.

Joubert syndrome (JS) is a neurodevelopmental disorder characterized by developmental delay and a specific hindbrain malformation resulting in the “molar tooth sign” (MTS) as seen on MRI. Individuals with JS have variable intellectual disabilities, polydactyly, retinal dystrophy and cystic kidney disease. JS is classified as a ciliopathy—disorders with overlapping phenotypes affecting 1/1000 live births combined. Currently, 36 genes when mutated cause JS, and all their encoded products localize in and around the primary cilium—a cellular organelle important for signaling and human development. We recently identified the newest JS-associated gene ARMC9 and its function, like the molecular mechanism(s) underlying JS, is unknown. Our preliminary data suggest that ARMC9 is required for cilium stability by promoting post-translational modifications (PTM) of ciliary microtubules. In stably ciliated, fixed (non-living) cells, ARMC9 localizes to the ciliary base, but to understand ARMC9’s role in cilium stability, we must determine ARMC9 localization during ciliogenesis (ciliary growth). We hypothesize that ARMC9 redistributes to the ciliary tip to promote tubulin PTMs during ciliogenesis. To test this hypothesis, I am using GFP and BFP (green and blue fluorescent protein) tags to visualize ARMC9 and primary cilia respectively. I created 5HT₆-BFP, a DNA vector encoding a BFP-tagged serotonin receptor fragment called 5HT₆ which naturally localizes to cilia. Currently, I am optimizing the transfection of 5HT₆-BFP and ARMC9-GFP into control cells for live imaging. As suggested by our data, I expect to see ARMC9 at the ciliary tip during growth, then redistribution to the base once the organelle is built. Determining where ARMC9 localizes during ciliogenesis will give us additional insight into its mechanism of action and role in JS. Ultimately, this work will allow us to identify therapeutic targets to mitigate the progressive features of JS and improve the quality of life of affected individuals.

Active student reasoning during peer discussion reinforces students’ conceptual understanding of lecture material and provides students with the opportunity to practice articulating the logical explanations required for exam questions. The quality of student reasoning during in-class discussion, and hence their usefulness in improving exam performance, may be affected by the questions instructors choose to ask. To determine which question properties prompt higher reasoning quality, we recorded and transcribed instructor questions asked and eight volunteer student group discussions to those questions over seven days in an active learning introductory biology classroom. We coded the in-class discussions for reasoning quality. We characterized questions in four ways: 1) Bloom’s taxonomy level (i.e., higher or lower order cognition questions), 2) question format (i.e., clicker question using peer instruction, think-pair-share, in-class Canvas questions where students must upload a picture of their work to Canvas), 3) number of dimensions of science learning using the 3-D Learning Assessment Protocol, and 4) if the question included a general model of physiology. Our results indicate that, in general, higher Bloom level questions encourage higher quality of reasoning. However, clicker questions using peer instruction prompt higher reasoning quality regardless of Bloom level. Additionally, the highest level of reasoning quality was seen during in-class Canvas questions. Both questions types that are incentivized by course credit (i.e., clicker and in-class Canvas) prompted higher reasoning quality than non-credited questions (i.e., Think-pair-share). We suggest that instructors should incorporate credited and higher Bloom level questions to increase the amount of high level reasoning during student discussions in their classrooms.

Adaptive learning technologies are regarded as an innovative approach to personalize student learning in large college classrooms where interaction with instructors is limited. Such software allows students to learn at their own pace, and to concentrate their efforts on topics which need improvement. However, studies on adaptive learning systems across disciplines have yielded mixed results as to whether they have an impact on improving course mastery. Our research focused on testing how use of adaptive learning reading quizzes in the final quarter of an introductory biology series impacted student exam performance. Students (n=576) enrolled in this course were distributed across 25 lab sections. Students were randomly assigned by lab section to either static or adaptive learning pre-lecture reading quizzes. Both types of quizzes were provided to students through Macmillan’s LaunchPad portal, and points were awarded on a completion/ no completion basis. We used multiple linear regression with model selection to compare student performance between the two treatments, controlling for student characteristics (e.g., GPA, gender). When student performance on in-class reading quizzes and course exams was compared, no statistically significant differences were found between treatments. Similarly, through the administration of three surveys throughout the quarter, we were able to measure students’ attitudes toward different course components. Our findings show that there was no statistically significant difference as a result of adaptive learning reading quizzes on how prepared students felt for class, how much they enjoyed the course, how much they valued reading quizzes, or if they preferred the reading quiz format in this course to those in previous courses. Our findings suggest that given the additional financial cost of adaptive learning technologies to students, instructors should first verify that adaptive learning significantly impacts mastery of course material prior to fully integrating it into their course structure.

Plants recycle resources from dying organs to feed the development of new ones. For example, chloroplast degradation in senescing leaves is a major source of nitrogen for seeds. Darkness or shade can induce leaf senescence and chloroplast degradation, but if light returns soon enough, new chloroplasts are made and the leaf remains photosynthetically active. Phytochrome B (PHYB) is a protein that serves a key role in resource allocation throughout the plant. phyB null mutants of the model crop species Brassica rapa (Br) exhibit low chloroplast count, poor seed production, and a reduced increased growth response to high CO2, as compared to wild type. We will investigate the underlying cause of these phenotypes by comparing the transcriptomic response of chloroplast-biogenesis and nitrogen-assimilation-related genes in wild-type and BrphyB null mutants before and during dark-induced senescence, as well as after recovery. Establishing a deeper understanding of the scope of PHYB's role in resource recycling will help us isolate appropriate targets for engineering more drought-resistant and nutrient efficient crops.

Auxin is a hormone that is crucial for plant growth and development. Auxin promotes the activity of auxin responsive transcription factors (ARFs) that induce transcription of target genes. Though, we know a lot about auxin response in the model plant Arabidopsis, very little is known about ARF behavior in maize. It has been previously shown that auxin and ARFs mediate many diverse developmental responses in Arabidopsis and maize. We hypothesize this diversity of response may be caused by different ARFs binding to different promoters, allowing different genes to be activated. The goal of the project is to examine the activity of maize ARFs on different promoter structures. We tested if maize ARFs show similar rules of ARF-promoter interactions as Arabidopsis ARFs. By comparing Arabidopsis and maize ARF activity, we are be able to understand how the two species have evolved over time, and if ARF function and auxin response are conserved in the two species. Working on maize is also important because it such an essential food crop for people and animals and can help us resolve issues such as food shortage. To investigate how ARFs regulate the activation of genes, we used a synthetic yeast system to quantify transcriptional activation. We engineered yeast to express both a maize ARF and a synthetic auxin-responsive promoter regulating transcription of a fluorescent reporter. We quantified fluorescence, a readout of ARF activation of the promoter, by flow cytometry. We systematically tested how activation is impacted by the sequence, orientation, and number of cis-elements within a promoter sequence, and how these effects differ among different ARFs.

TOPLESS (TPL) is a transcriptional co-repressor protein that plays a central role in the regulation of plant growth and development. In the model plant Arabidopsis thaliana, TPL acts in essential hormone response pathways, including that of auxin, a small signaling molecule. TPL acts in the auxin response pathway by binding another co-repressor from the Aux/IAA family (henceforth referred to as IAAs). In the presence of auxin, IAAs are degraded, relieving TPL repression and allowing for transcription of auxin responsive genes. Despite its central role, the molecular mechanism by which TPL confers repression is not well understood. Recent structural analyses indicate that TPL has interfaces for both homodimerization and homotetramerization. Synthetic assays have shown that TPL truncations in which the tetramerization interface has been deleted have a significant decrease in repressive function. To determine the repressive mechanisms of TPL, we created a structure-function map. We have created full-length TPL variants with point mutations at the dimerization and tetramerization interfaces, as well as serial domain deletions. We tested the repressive function of these variants in a yeast synthetic assay in which TPL represses expression of a fluorescent protein. Repressive function was then quantified from fluorescent reporter output with stronger repression corresponding to decreased fluorescence. We then validated the results of our synthetic assays in planta by expressing TPL-IAA14 variants that negatively regulate lateral root development. The repressive strength of each TPL variant will be quantified by measuring the number of lateral roots, with fewer lateral roots corresponding to increased TPL repressive strength. TPL homologs exist in many species. Defects in TPL homologues have been implicated in the causes of many cancers and developmental diseases, therefore a better understanding of the functional mechanisms of TPL will have broad implications across organisms, including humans.

This project considers how we might address barriers to coalition building across difference using interdisciplinary knowledge from social psychology, neuroscience, human centered design, and critical race theory. The first question this project asks is: how might we translate strategies from social psychology that are known to increase the self-other overlap into engaging, immersive virtual experiences (IVE) for coalition building? The concept of the self-other overlap relates to coalition building because of the breadth of research indicating empathy as a self-centric process wherein people are much more likely to feel empathy for people they see as like themselves. This project focuses on IVEs because of their unique ability to create interactive, low stakes environments in which participants can embody experiences outside of their own and play with abstract ideas, such as the social constructs of race, sex, and gender. Given these qualities, the project seeks to specifically explore how IVEs might facilitate compassion, and thus coalition building across identity differences, such as race, gender, and nationality. This project differentiates compassion as empathy with action and views compassion as a potentially proactive approach to social equity. Because of the complex ethics involved in this endeavor, this project must also ask: how might we use human centered, participatory design and critical race theory to ethically design these experiences while motivating and supporting audiences to engage? In this way, this project proposes to use a range of design tool fidelities to discover and design for barriers to coalition building, and thus forge a bottom-up pathway from the people being represented to their IVE representations. The products of this project include a literature review and a suggested protocol for the ethical production of IVEs designed to facilitate coalition building across difference using human centered, participatory design, and critical race theory.

Active learning has often been described as the key to increase retention rates among undergraduate STEM majors because students are engaged in meaningful learning. Common activities associated with active learning include completing worksheets in groups, clicker questions, or discussion questions followed by reporting out by random call during class. Random call differs from cold call as the instructor allows discussion time where students can work together to formulate an answer prior to random call. However, previous research has demonstrated that implementing active learning principles may increase student anxiety. Specifically, answering questions in class, either by volunteering or random call, may cause the highest level of anxiety for students. We have conducted a study investigating how student demographics impact the likelihood of students responding to random call. Our study was conducted in an Introductory Biology course with 576 students, in a lecture-hall style classroom. The instructor utilized random call, then recorded which students either gave a response or passed the question when called upon. A binary logistic regression was performed to create a best fit model in which student demographics could predict which students were more likely to answer or pass. Students who are the first in their family to go to college (1st generation students) were 57% less likely to respond to random call questions compared to other students, even when controlling for incoming GPA. This result indicates that students with diverse demographics participate differently in some active learning activities and further investigations are necessary to determine if this has an impact on their learning. To bridge this “responding” gap between 1st generation and Non-1st generation students, instructors should implement additional techniques such as group random call as opposed to individual random call to increase student comfort during random call, thereby increasing the likelihood of students responding regardless of student demographics.

Understanding the principles that underlie physiological problems can help students succeed in the mastery of a wide range of physiology topics. Understanding the principle of flux, which governs pressure gradients, can greatly improve a student’s ability to solve problems related to bulk flow and pressure in a variety of physiological systems. In general terms, the principle of flux describes the rate of movement of a substance from one compartment to another. It is defined as the magnitude of the driving force (gradient) divided by resistance. We examined how students in an introductory physiology class think about flux in the context of a pressure gradient within the cardiovascular system. We began by incrementally refining a variety of gradient-related questions through successive rounds of think-aloud interviews with individual student volunteers. Using these responses, we generated a cardiovascular pressure gradient question that elicited a wide variation of student answers. We collected responses from 200 introductory physiology students both before and after relevant course content to be sure our question captured both novice and advanced reasoning. We examined the responses and constructed a rubric to categorize student responses into a hierarchy of response sophistication and completeness. Generally, level 1 represents the most novice responses, while level 5 represents the most advanced. In our rubric, level 1 answers relied on vague reasoning relating to homeostasis, equilibrium, or intuition. Responses categorized at levels 2 and 3 showed an understanding of the components that contribute to pressure without successfully identifying how they connect to changing pressures. Lastly, answers at levels 4 and 5 showed an understanding of these components as well as the ability to successfully relate them to changes in pressure. Identifying patterns in student responses to a pressure gradient problem can give instructors a starting point from which they can target common misconceptions to ensure conceptual mastery in their classrooms.

Prior research shows adolescents’ negative pain memories predict greater subsequent postsurgical pain. However, understanding of the content of memories and whether memories change over time is limited. We applied emotional stress theory, which proposes that negatively perceived events are recalled with more central (relevant) than peripheral (irrelevant) details, to examine how post-surgical pain memories change in adolescents and their parents. We hypothesized that 1) central memories would contain more negative emotion than peripheral memories, 2) ratio of peripheral to central memories would increase over time as memories become less negative, and 3) parent and adolescent memories would be associated at each time-point. Nineteen adolescents (12-18 years;63% female) who underwent major surgery and their parents were asked individually at 2-months and 12-months after surgery to recall “everything you remember” about being in the hospital and the initial weeks at home following surgery. Linguistic Inquiry and Word Count software was used to identify negative emotion words and N-Vivo software was used to code central and peripheral memories. Central memories included specific (“going through the doorway was…sheer pain”) and general (“kinda got better”) memories of post-surgical recovery. Peripheral memories ranged from inside (“clowns…visited me”) to outside details (“dad split his finger open”). As expected, central memories contained more negative emotion words than peripheral memories (p’s<.05). Use of negative words and ratio of peripheral to central memories were stable over time for parents and adolescents. In regression analyses, controlling for adolescent age, parent peripheral to central memory ratio was significantly associated with the adolescent peripheral to central memory ratio at 12-months (β=.57;p=.02), but not 2-months (β=.04;p=.88) after surgery. Findings suggest that memories are stable after two months. Associations within parent-child dyads were stronger at later follow-up. Future studies should assess earlier memories to increase knowledge of temporal association between memories and subsequent pain experiences.

Pregnant women often get their bellies touched without their permission by people ranging from family members, to coworkers, to strangers. While usually well-intentioned, people who touch pregnant bellies are unaware that their actions may be unwanted and invasive. Previous works, such as Asta Roseway’s Printing Dress, have shown that wearable computing can bring attention to social issues by provoking discourse. Those works lead us to our wearable design that highlights the issue of personal space for pregnant women. We implemented a maternity shirt that reacts to inappropriate touches upon contact in various ways, such as displaying messages, vibrating, and setting off an alarm. We plan to deploy this shirt on experimental participants and gather qualitative data in addition to the quantitative data collected through the shirt about when and where touches occur. Moreover, findings from the experiment will provide insight into pregnant women’s experiences, and how to design wearables that benefit to pregnant women. Our future goal is to have the shirt deter the toucher as they approach the belly. Through this interactive design piece we hope to raise awareness and provoke conversation around themes of consent, inappropriate touching, and women's bodies.

The first-year population, with students transitioning from high school to college, is full of novel experiences. These experiences, be they academic, social, etc., influence the well-being of the student. The purpose of the study is to understand the first-year experience in a data-driven manner to create a cornerstone for institutional change. Although replicating a previously piloted study at Carnegie Mellon University in Spring 2017, this study extends focus to investigating stressful life events of first-years. Over the 2018 Winter and Spring quarters, a participant sample size of around 200 UW first-year undergraduate students (around 50% pre-/engineers) contribute data to the study. Data consists of both active and passive collection methods: participants actively respond to Qualtrics surveys, with questions investigating stressors, and passively via our phone software and FitBits. The two quarters of this study will yield tangible data that can be analyzed to advance the science of behavioral health and trauma. This data is unique in providing a picture of student behavioral changes after stressful experiences. Additionally, this advancement in science can become a basis for institutional change for student wellness. As the first-year population is only a slice of the overall student experience, we hope to expand this study further by encompassing the graduate student experience and the full four-year college experience in addition to a larger sample size.

HRI is a serious health risk for agricultural workers that can result from prolonged exposure and overexertion in hot temperatures. The four different types of HRI in increasing severity are heat rash, heat cramps, heat exhaustion, and heat stroke. These conditions are preventable using simple approaches such as proper hydration and limiting one's time in the sun. To better equip agricultural supervisors and safety trainers responsible for conveying heat safety to their workers, I collaborated with members of University of Washington’s Pacific Northwest Agricultural Safety & Health (PNASH) Center to develop a modular flipbook that will serve as training material, covering the following topics: symptoms, risks, and treatments, clothing, hydration, and other preventative measures; as well as where and how to cool off in the home and community. I helped advance this project by taking the lead on the production of the flipbook content under the direction of the Research Scientist. I collated images, researched instructional designs, and developed prototypes of the flipbook, as well as edited the written instructions for facilitators. The educational activities in the book consists of an interactive portion, guiding questions for the facilitator to pose to the group, role-play scenarios, take-home points to reinforce the educational messages, and 3-dimensional educational charts. Modules also contain a “Knowledge Evaluation” section with questions for the facilitator to ask participants both before and after the activities to gauge their change in knowledge and to ensure the material has been understood. As a final product, the flipbook will be a portable and convenient resource for safety trainers to use in the field. My goal is to ultimately make this flipbook accessible to the general public, as it is not only a great safety resource for agricultural workers, but also for their families and surrounding community.

Within the United States, plea bargaining has become the dominant method of case resolution. The Bureau of Justice estimates that 95% of all cases processed are resolved with a plea. This study seeks to examine the factors that motivate defense attorneys in their plea recommendations. The primary factors that this study was interested in include likelihood of conviction at trial, defendant’s preference over whether they would like to proceed to trial, and length of sentence if convicted. One-hundred and fifty defense attorneys were contacted through listings on the Washington State Bar Association's website, and subjects were mailed both a survey and one of eight randomized scenarios containing a potential case manipulated upon primary variable lines in a 2x2x2 fashion. These scenarios scored responses under a 5-point Likert scale (‘extremely unlikely’ to ‘extremely likely'). Responses were analyzed in a MANOVA. Surveys were analyzed along a 5-point Likert scale ('extremely unimportant' to 'extremely important') which analyzed results through an ANOVA. Results indicate that the length of potential sentence was not significant on an attorney’s recommendation to enter a plea (p=.43); however, strength of evidence (p= <.001) and defendant’s preference (p=<.001) both significantly impacted this recommendation. However, implicit and explicit analyses of factors indicated no significant differences in plea considerations based on defense attorney subtypes. Strengths of the study include the maintaining of participant’s anonymity to protect against social desirability bias, random selection and overt and covert measurement of factors. Our hypotheses lines were drawn in consideration that the 'meet-'em-and-plead-'em' model of case resolutions may have resulted in plea factor habituation. However, despite considerable limitations, assigned counsel continue to evaluate relevant factors and seek to provide the best defense possible.

Changing developmental patterns is an essential strategy for plants to survive environmental stressors, and the hormone auxin coordinates much of plant development. In the auxin signaling pathway, Aux/IAAs are co-repressors that block expression of auxin target genes. When auxin is present, Aux/IAAs are ubiquinated by an E3 ligase and then degraded via the proteasome. This results in an increase of auxin response gene expression. Past research in the Nemhauser lab found that a dominant mutant in the Aux/IAA known as IAA28 alters the placement of lateral organs around the stem (a process called phyllotaxy). IAA28 loss-of-function mutants show no phenotype, so we hypothesized that another gene or genes could be acting in a redundant manner. IAA28 is closely related to two other Aux/IAAs called IAA18 and IAA26. Using CRISPR/Cas9 technology, I am making triple mutants that lack function of IAA18, IAA26, and IAA28. Once I have these mutants, I will measure phyllotaxy and other developmental phenotypes to look for differences when compared to wild-type plants.

Mobile and worn sensors have been increasingly used in order to gather data in long term behavioral studies, especially as the cost has decreased for such sensors. These kinds of studies provide increased information that can be used in order to understand behaviors and to elicit changes in them. Such studies have been conducted at CMU, MIT, and Dartmouth. UW is conducting a similar study that uses mobile phone sensors via a custom app, surveys via Qualtrics, and FitBit sensors in order to collect relevant behavioral data that may be related to academic performance in college. Because such studies rely on participants following the protocol and actively participating in the study, it is important to create and modify tools that allow for analysis of participant compliance, such as the rate of survey completion and amount of sensor data. These tools allow researchers to keep track of participants and work on collecting more high quality data for later analysis. There is little information about the design of compliance tools for similar studies. In this work, the focus is on modifying an existing dashboard from a similar study at CMU. Development will be focused on adding additional functionality based on the needs of the research staff. In particular, work will begin by developing filtering functionality for non-compliant participants and creating useful views for researchers in terms of contacting participants around possible broken sensors or missing survey data. Usability of the tool will be analyzed for future improvement. The hope is that this tool can be used to gather better quality data in this UW study and can shape future dashboards for similar experiments that gather behavioral information.

Soil contamination occurs when human-made chemicals seep into the ground. It can have negative effects on human and animal health, pollute groundwater, and reduce crop yields. Chlorinated ethenes are toxic chemicals used in degreasing and dry cleaning, and their improper disposal can result in contamination. Before remediation to remove the contaminant happens, the affected site must be assessed. Magnetic susceptibility is a measurement of a substance’s ability to be magnetized when put in a magnetic field. Magnetite, a common mineral with the formula Fe₃O₄, is strongly magnetic and has a high average susceptibility. Indeed, magnetite can dominate the magnetic properties of Earth materials such that magnetic susceptibility can be used as a proxy for magnetite abundance. Soil contaminated with chlorinated ethenes has several biotic and abiotic degradation pathways. One abiotic pathway is through magnetite, which is known to affect the detoxification of this pollutant. Choosing the best pathway is aided by the software tool BioPIC. In this study, soil was analyzed using a protocol developed for frequency-dependent discrete specimen magnetic susceptibility measurements to determine magnetite content, and thus to estimate ethene degradation rates. Frequency-dependent measurements allow for estimating magnetite particle size, which influences reactivity. We also explore other magnetic properties to more conclusively determine magnetite concentration. A further avenue for research in the future would be to discern the source of magnetite in the soil, whether it is transported by water or air, precipitated from chemical solutions, or synthesized by certain bacteria. Abiotic degradation of ethenes is just one parameter to consider in an overall remediation strategy. Options for remediation include removing and disposing of the affected soil, containing the soil in place, aerating the soil, and using microorganisms to digest the pollutant.

Joubert syndrome (JS) is a rare recessive genetic disorder characterized by hindbrain malformations appearing as the “molar tooth sign” on axial brain imaging. Causal genetic variants for JS need to fulfill three criteria: They need to be 1) rare, 2) deleterious, and 3) present in both alleles in the patient. Patients in our cohort are sequenced for rare predicted-deleterious variants (RDVs) to identify variants that satisfy the first two criteria. To determine whether the segregation pattern of the variants satisfies the third criterion, we sequence both parents, each of whom should carry only one of the variants. My research uses Next-Generation Sequencing to determine the segregation pattern for families in whom RDVs have already been identified. Specifically, I performed targeted-sequencing of putative causal variants in the parents using molecular inversion probes, and then I used the sequencing data to determine the segregation pattern. In most families, one RDV will be present in each parent, indicating that they affect both alleles in the child, because these variants are robust candidates that have passed the filters for being rare and deleterious. If both RDVs are present in one parent, then they have to be on the same allele and cannot be the cause of JS in the family. In these families, we will have to consider other variants or perform additional sequencing to identify the causal variants. Ultimately, the goal of my research is to elucidate the genetic basis of JS to improve prognostic and risk recurrence information, provide diagnostic, carrier and prenatal testing, and delineate the biological mechanisms of JS that will be the targets of future precision therapies.

Global climate change and population growth pose a significant risk to global food security. Estimates suggest that animal products alone, such as animal feed, must increase by 60-70% by 2050 to keep up with population growth. Crop species are needed to feed people directly and to feed livestock. How crop species respond to predicted climate change compounds the complexity of this challenge. Phytochrome B (phyB) is a photoreceptor that affects the plant’s ability to respond to changing resource availability. Plants with a reduced phyB function make less seeds, whether measured in the model plant, Arabidopsis thaliana, or in the crop, Brassica rapa. The reason for this seed yield phenotype is unknown. Characterizing reproductive structures in Brassica rapa from before fertilization through the production of viable seeds to identify the role phyB plays in seed production will give insight in this process. Doing this may ultimately lead to the identification of potential targets for engineering higher yielding oil seed varieties.