Tag: Biology

Misfolded but not Malicious: Prion Proteins in Budding Yeast

Presenter: Mikala Capage − Biology

Faculty Mentor(s): David Garcia

(In-Person) Poster Presentation

Prion proteins, although frequently associated with neurodegenerative diseases, are not universally harmful to cells. Instead, prions may serve as a beneficial epigenetic mechanism, allowing cells
to alter their phenotype to adapt to adverse environmental conditions. Prions form when a protein adopts alternate folding conformation. The Garcia Lab aims to identify beneficial prions using the budding yeast, Saccharomyces cerevisiae. We are particularly interested in prion conformations of RNA modifying enzymes (RMEs), because these proteins can affect the expression of many genes simultaneously. After screening hundreds of yeast strains, the Garcia Lab has identified six strains of yeast—associated with the RMEs Abd1, Cet1, Ppm2, Pus4, Pus6 and Trm5—that exhibit resistance to harmful chemicals . Extensive tests are needed to confirm that the resistance to stress is caused by a prion conformation of an RNA modifying enzyme. Here, data describing the meiotic inheritance, protein dependance, and cytoplasmic inheritance are presented. Taken together, these results are key in attributing the previously identified growth states to a prion conformation of each of the six RNA modifying enzymes . The Garcia lab will continue to investigate these putative prions in future experiments to determine the mechanism for resistance. This research represents an important contribution to our understanding of prions as a protein-based epigenetic mechanism and their effects on key cell processes.

Observation of Corneal Guttae by Plasma-FIB Microscope

Presenter: Mayurika Bhaskar − Biochemistry, Biology

Faculty Mentor(s): Hiro Uehara

(In-Person) Poster Presentation 

Fuchs Endothelial Corneal Dystrophy (FECD) is an inherited disease that leads to blindness. FECD is characterized with the thickening of the Descement’s membrane, corneal endothelial cell loss, and the formation of guttae (deposition of the extracellular matrix). Once corneal endothelial cells are lost, the cornea cannot maintain its transparency. Since these cells do not proliferate in vivo, the current treatment is through a cornea transplant, but this comes with risks such as infection and tissue rejection.

The purpose of my research is to observe the structure of guttae in FECD mice corneas to better understand its condition.

In this study, normal and FECD mouse corneas were compared. After euthanizing the mice, the eyeballs were harvested, and corneas were removed. Then they were stained with osmium tetroxide, fixed with epoxy resin, and microtomed. Finally, the sample was mounted on a 45-degree tilt and cut with a 45 nanoampere oxygen beam at a slice size of 50 nm by a Plasma-FIB microscope to obtain ~700 images. Some issues included the bending of the cornea once harvested and the time it took to image a sample.

We successfully 2D imaged the normal and FECD mouse corneas. The normal mouse corneal endothelium is smooth and thick, but FECD mouse cornea showed signs of bumps and thinness. I’m currently developing these images into 3D models to better analyze them. Overall, I hope that my work will provide information about guttae developed from FECD for future research.

Pupillary Dilation Response to Changes in Sound Stimuli

Presenter: Temerity Bauer − Biology

Faculty Mentor(s): Santiago Jaramillo

(In-Person) Oral Panel—Stimuli and Response, Poster Presentation

To understand the world around us, the auditory system of our brains discriminates between different sounds to interpret our surroundings. Normally, simple sounds (like pure tones) are used to study the neural mechanisms for processing sounds by training animals. Training animals to discriminate between sounds is an arduous endeavor. Further, using simple sounds limits our understanding of how the brain interprets sounds of the complexity that is experienced every day. To address these problems, we developed a methodology to study sound discrimination in naive mice without training the animals by using pupillometry.

Changes in pupil size is one of the many responses to stimuli an animal can have. A study performed by Montes-Lourido et al. found pupil diameter changes correlate with an increase in motivation, effort and arousal in the brain in subjects (Montes-Lourido et al., 2021). Previous studies found changes in pupil sizes to sounds like pure tones and animal calls (Montes-Lourido et al., 2021). We hypothesized pupil responses would occur when the animal is presented with complex sounds that are found in nature. To study natural complex sounds, we first had to establish if pupillary dilation responses occurred to changes in simpler sounds like chords. We found that the pupils exhibited a pupillary dilation response to changes in frequency. Through this project, we determined pupillary dilation responses can be used as a method to study frequency discrimination in mice.

Effects of essential amino acid supplementation on muscle structure before and after eccentric exercise

Presenter: Ryan Angeloni − Biology

Faculty Mentor(s): Hans C. Dreyer

(In-Person) Poster Presentation 

We have recently shown in older adults that daily ingestion of essential amino acids (EAAs) for seven consecutive days can increase muscle stem cells (satellite cells). We want to see if we can measure a similar increase in satellite cells in younger adults. Satellite cells are important for muscle maintenance and repair. One way to stimulate muscle repair is to perform eccentric-type contractions (muscle lengthens and is damaged under tension). As such, we gave subjects EAA or placebo 3x/ day for 7 days before and after a single bout of damaging exercise to test the following hypotheses compared to placebo: 1) EAAs for 7 days will increase satellite cell numbers, 2) cause more satellite cells to be activated/proliferate 24 hours after damaging exercise, and 3) lead to more robust repair (less damage) 7 days after damaging exercise (14 days after EAAs began). Tissue samples from eight subjects have been processed. Additional subjects are in various stages of recruitment/consenting. Immunohistochemical methods will be used to measure muscle satellite cell and myonuclei numbers associated with type I, IIa and IIx fibers, satellite cell distance to nearest capillaries, and muscle fiber denervation and immune cell responses. Our overarching objective is to devise ways to boost resilience of muscle tissues in active and inactive young and older adults.

Quantitative Mapping of Male Traits Affecting Female Longevity and Fecundity in C. Remanei

Presenter: Emily Ebel, Biology

Poster: A-8

Mentor: Patrick Phillips, Biology

Differing reproductive interests between the sexes can manifest in surprising ways, including a conflict, or tradeoff, between female reproductive effort and longevity. In some species, including the soil-dwelling nematode Caenorhabditis remanei, the act of mating has been demonstrated to reduce female lifespan by up to 50%. Interestingly, males from different genetic backgrounds affect female longevity—and fecundity— to varying degrees. To understand the genetic basis of these differences, and why they may have evolved, I am cataloguing the effects of males from 30 unique C. remanei strains on female lifespan and reproductive output. When this phenotypic data is combined with Restriction site Associated DNA (RAD) marker data from each line, I will be able to generate a Quantitative Trait Loci (QTL) map to approximate a genomic region that may be responsible for the male effects. Gaining this insight into the “battle of the sexes” in C. remanei will elucidate how sexual conflict, as an evolutionary force, can shape the morphology and behavior of many animals.

Genomic News From an Old Fish: Understanding Gene Regulation by Sequencing the Genome of a Living Fossil, the Spotted Gar (Lepisosteus oculatus)

Presenter: Margo Werner, Biology

Poster: D-3

Mentor: Ingo Braasch, John Postlethwait Biology

Cis-regulatory elements (CREs) are important regions of the genome that modulate the expression of nearby genes. However, their role in the evolution of genes is not yet well understood. To examine the function and evolution of CREs in fish, we study the spotted gar (Lepisosteus oculatus). The gar is a ‘living fossil’ that diverged from teleost fishes just before a teleost-specific whole genome duplication. Comparing the genome sequence of gar to teleosts allows us to investigate the appearance of CREs in relation to this genome duplication. We screen a genomic library of the gar in order to find regions of the genome containing developmentally relevant genes and their CREs. These genomic regions are then sequenced using next generation sequencing techniques. The results will potentially help us to understand the evolution of gene regulation in fish.accurate indicators of ancient local species distribution.

Chromatin Regulation During Fin Regeneration in Zebrafish

Presenter: Matthew Garish, Biology

Poster: B-1

Mentor: Kyrn Stankunas, Institute of Molecular Biology

Vertebrate organisms such as the Zebrafish have developed molecular processes to regenerate their fins after amputation by epigenetic cell reprogramming. An insight into the molecular processes could prove clinically useful in addressing such problems as tissue repair. The transcript of KDM6B.1, a histone demethylase (me3K27H3), has already been established in caudal fin regeneration in zebrafish via in situ hybridization. I hypothesize that KDM6B.1 plays a crucial role in zebrafish fin regeneration. I propose to spatially and temporally establish expression patterns of KDM6B.1 during fin regeneration. To address this question, I have purified a KDM6B.1 antigen and antibodies against the antigen. I performed techniques to surgically remove a portion of the Zebrafish’s fin. I have characterized the antibody using such in vitro methods as affinity purification and immunocytochemistry (ICC) analysis. After characterizing the antibody, I performed studies on the zebrafish such as immunohistological analysis during fin regeneration. The results concluded higher expression of KDM6B.1 specifically in regenerating tissue. I believe that understanding the results of a histone demethylase during fin regeneration has given insight to the ability of a cell to reprogram itself in response to injury which will give insight to tissue repair.

Effects of a Natural Environment on Caenorhabditis elegans

Presenter: Anna Crist, Biology

Poster: A-4

Mentor: Patrick Phillips, Biology

The nematode Caenorhabditis elegans is an important model organism in the field of biology and yet little is known about how it lives in its natural environment. In order to study C. elegans in a more naturalistic setting, we created artificial soil microcosms. Populations of C. elegans were estimated over time by taking small periodic samples. We were able to maintain large, stable populations for over one month, or twelve generations. This methodology could be a useful tool in many areas of C. elegans biology. We are investigating the effects that this naturalistic environment has on a known aging mutant, daf-2. The effect of this mutation, although well characterized in a laboratory setting to have an extension in lifespan, is unknown in a natural environment. Artificial soil microcosms will aid future C. elegans studies in determining the effects of a natural setting on lab-characterized traits.

Scaling Up: Expanding Community Health Worker Programs for Refugees and Internally Displaced Persons in the Bururi Province, Burundi, East Africa

Presenter: Alex Goodell, Biology

Poster: B-2

Mentor: Janis Weeks, Biology

Burundi, a small and often-forgotten country in East Africa, lies directly south of Rwanda. Though poorly covered in the media, Burundi suffered a similar conflict as its northern border, with ethnic-driven violence plaguing the nation for 13 years. When the conflict officially ended in 2006, Burundi was ranked as the poorest country in the world. Its health statistics are equally low. According to the WHO, one in five children die before their fifth birthday, half of those driven by malaria. Only 200 doctors serve the population of 8 million and most of the poor have no access to healthcare. In some areas, days of walking are required to reach the closest physician. Additionally, hundreds of thousands became refugees or internally displaced persons during the conflict and have little access to resources. In this setting, the use of “Community Health Workers” (CHWs) is appropriate. Village Health Works, a small clinic in the rural Bururi province, has implemented a small CHW program similar to Partners in Health. Over a six-month period in 2009 and 2010, data was collected on 10000 patients regarding their medical status, location, and demographic information at VHW. Additionally, GPS data was collected on the location of the CHWs. This presentation looks at the history of CHW programs worldwide and analyzes the health metrics of the area surrounding VHW. It then makes a series of suggestions on how VHW could better serve its patients with CHWs, specifically focusing on refugees and internally displaced persons.

Differences in Acute Stress Response between Lab Adapted and Non-Lab Adapted Caenorhabditis remanei

Presenter: Catherine Ituarte, Biology

Poster: B-5

Mentor: Bill Cresko, Biology

Organisms can adapt to the environments they inhabit in amazing ways, but sometimes adaptation to one environment can lead to a decrease in fitness in another environment. One example of this phenomenon is the potential difference in an organism’s ability to respond to stress depending on if the organism is kept in laboratory conditions or in its natural environment. I used the small nematode worm, Caenorhabditis remanei, to address the interplay between lab adaptation and stress response. I hypothesized
that populations that have adapted to laboratory conditions would be less stress resistant than non-lab adapted populations. Six populations of C.remanei were maintained under standard laboratory conditions for four months while six populations did not have prolonged exposure to laboratory conditions. These populations were then assayed for their resistance to acute heat and oxidative stress. The populations that were in the lab for four months had a lower average percent survival after an acute stress event than the populations that were not, supporting my hypothesis. These results suggest that evolving under laboratory conditions compromises an organism’s ability to respond to environmental stress, highlighting the importance of considering adaptation to laboratory conditions when designing experiments. My experiments form the basis for studying the complex relationship between an organism and its environment in this model organism, opening the possibility of identifying the genetic basis of this laboratory adaptation.