Biological Sciences

Student Research Symposium Abstracts

Spring 2018


BIOL 152, Principles of Ecological, Evolutionary, and Organismal Biology
Christopher Ivey,

BIOL 152, Adrienne Edwards,

Fruit Count on Gallium acarine as a result of plant height v. soil temperature
Jillian Douglass, Alexander Vina, Maia Taylor, Diana Mosqueda,,,
Fruits are costly to plants because fruits usually don’t photosynthesize. There may be limits to the number of fruits a plant can make at a particular time. In this experiment, we studied the number of fruits produced on the whorls of Galium aparine (sticky weeds). We compared soil temperature to plant height on nine plants from three locations on the CSUC campus along Big Chico Creek, and found no difference in growth rates. Using the three locations as replicates, we then counted the number of fruits at six whorls starting from the base on 12 plants from each location (N=36 plants). At each whorl fruit number ranged from 0-10. The average number of fruits per whorl did not differ significantly from the null expectation of 4.1 fruits at every whorl. There appears to be a limit on average fruit number that is less than the number of flowers produced at every whorl. The resource allocation to fruits appears equal across all whorls. It appears likely that because these fruits photosynthesize, the number of fruits on one whorl does not affect the number of fruits on adjacent whorls.

Anthracnose Resistance in California Sycamores and London Plane Trees
Josh Roter, John Nyznyk, Dean Gorans,,
Anthracnose (Colletotrichum spp.) is a fungal disease that infects a variety of plants where symptoms include, leaf spotting, blotches, distortions, defoliation, and blight. Two trees that are affected by anthracnose are the California sycamore (Platanusracemosa) and the London plane tree (Platanus acerifolia). The London plane tree was widely used instead of the California sycamore in part because it was thought to be more resistant to the fungal disease. We hypothesized the London plane tree would have lower percent damage from Anthracnose compared to the California sycamore. To test this, data were collected haphazardly along Big Chico Creek from CSUC campus to the Yahi trail in Bidwell Park and compared using a chi squared test. There was a significant difference in the likelihood of being damaged by the disease between the two trees. The California sycamore had, on average, 30% higher damage than the London plane tree. Our results support the common belief that London plane trees are more resistant to Anthracnose than the California sycamore.

How to BEE Attractive 
Melissa Madrigal, John Vang, Matthew Rubalcava,,
The significance of this project is to improve bee pollination efficiency and possibly modify plants in response to the bee’s attraction towards certain flower characteristics. The treatment of flower petals and stamens could be applied in agricultural settings. Our null hypothesis is that bees will go towards the stamen instead of the petals, while our alternate hypothesis is the bees will most likely go towards the petals instead of the stamens. Group members observed the Rhaphiolepis indica for bee visitations ten minutes at a time for two different treatments. One treatment included the removal of all stamen from a cluster of 7-10 flowers, the other treatment involved the removal of all petals from a cluster of flowers, and one cluster was left as a control. A t-test was done and the alternate hypothesis was accepted since the bees gravitated towards flowers with petals and without stamens, more than those without petals. This means that placing plants with an abundance of flower petals in agricultural areas could promote more bee activity in the surrounding areas.  

College Squirrels
Miranda Truhe, Kiara Onuoha, Kevin Flores,,
The experimental hypothesis for this experiment was that Eastern grey squirrels would prefer apples over nuts in their nutritional diet. We used the cafeteria method for this experiment by setting out three trays of food with apples and two kinds of nuts (hazelnuts and almonds). By the end of our experiment, squirrels preferred apples over nuts. The overall significance of this experiment was to give us a better understanding of the squirrels eating habits to learn more about its behavior and way of living in the Chico community.

BIOL 152, Badri Ghimire,

Effective Soil Additives on Bean Growth
Allen Benavidez, Mark Sanchez, Troy Agers, ,
There are varieties of soil additives but there is not a definite fertilizer for the promotion of growth for bean plants. In our experiment, we tested the amount of bean plant growth with fertilizer and Worms with fruit. We collected soil from Big Chico Creek and filled three individual cups adding fertilizer to one, apple and worms to another, and maintaining one control group. Plant lengths were measured every week for three weeks since they were planted. Our results were that our control group grew at a faster rate than our other two groups. We concluded that our experiment does not support that soil additives are detrimental to soil growth due external influences such as centipedes, fertilizer ingredients and fruit acidity. (Control final length: 4” Fertilizer final length: 2” Worms with apple final length 0”) Our worms with apple plant soil contained a small amount of centipede larvae which affected the worm population. Apples could have taken part in preventing the bean to grow when worms are absent from the decomposing process.

Effects of temperature increase on rate of respiration in three different species of fish
Allissa Burns, Edith Deras, Jamie Arteaga,,
Temperature is a factor that influences aquatic life.  We tested how water temperature affects the respiration rate in three different species of fish: Guppy, Cichlid, and Platy. We predicted that the respiration rate in all species of fish will increase when temperature increased. We established a control group with three fish, one of each species, with an automated heater keeping a temperature of 23°C.  We established an experimental group with three of the same species as well, but with a controlled heater that increases the temperature by 2°C weekly.  The starting temperature for the experiment group was 23°C and ended at 31°C by week number five.  The two groups were separated by a glass barrier.  We monitored and counted each fish’s breaths for one minute to calculate the respiration rate. A t-test was conducted.  The p-value for the Guppy was 0.022. The Cichlid had a p-value of 0.0204. The Guppy and Cichlid have p-values which are significant. The p-value for the Platy species was greater than 0.078 meaning it’s insignificant. The results supported that increase in the temperature of water is significant in the respiration rate of the Guppy and Cichlid species, but not the Platy species.  

Picky Bettas
Brittany Sanders, Michael Siva, Brian Stabenfeldt,,
Betta fish are a common pet that people own throughout the world, and their health is affected by many factors, particularly their diet. However, most people are unaware of which type of food is most preferred by a betta fish; the exact problem we set out to address. We hypothesized that the betta fish will display a preference towards the more nutritionally dense food source. First, we established three treatment groups, each consisting of a betta fish inside a standard fish tank. We then identified four common food sources betta fish eat; standard fish flakes, blood worms, freeze-dried brine shrimp, and steamed peas, and determined the varying nutritional values of these food sources. Then, upon feeding, we recorded the amount eaten of each food source, and conducted this test three times a week for three weeks, collecting a total of 27 data entries. We found the betta fish don't have a significant preference for any particular food source (p>0.05). In conclusion, our results showed betta fish don’t have food preferences

Endemic Life of Hordeum jubatum 'Foxtail Barley" in response to proximity of water source
Toua m.k. Yang, Carl Conserve, and Evan Cardinaux,, 
Endemic life growth is greatly depending on the habitat that it is a part of, and the resources that are available to any given species. The species in question was the foxtail barley and how the subsurface growth would respond to a general vicinity to the main water source in the area. We hypothesized that the roots of the foxtail barley would increase in length as the distance from the water source increases. We examined two sites, one near the water and one further away in totality of thirty samples using a shovel and sieve to remove any remaining aggregates of dirt from the plant’s roots so that they could be measured and recorded. Results showed a trend in the root length opposite of what was originally hypothesized. Plants closer to the water had an average root length of 14.61 centimeter, while plants further from the water source averaged a root length of about 11.18 centimeter. It was found that the root length of foxtail barley was not increasing as distance from the water was increased and the specified species was more mature along the edge of the river. 

Stomatal Differences Based on Sunlight in Eudicot Plants
Connor O'Leary, Ian Schneider,
Previous studies have revealed that plant phenotypic plasticity can be altered by the sunlight. We examine how sunlight exposure might alter stomatal density distribution in plant leaves. We examined the leaves found in varying sunlit environments from 3 different plants. We used Orange (Citrus sinesis sp), Mock Orange (Philadelphus californicus), and Fava Beans (Vivia faba). Each leaf sample was examined under a microscope, and we counted the stomata. Data analysis from T-TEST shows that each of the three cases were significant. We found P-values,0.003, 0.006, and P<0.0001 from plants orange, mock orange and fava beans respectively. There is in fact a higher stomatal density in leaves that are exposed to higher amounts sunlight. This shows that stomatal density is highly affected by sunlight.

Effect of Soil pH on Plant Growth
Derrick Deak, Shannon Smith,
We hypothesized that plants grown at the “natural” pH of 6.5 would have the highest ratio of healthy plants and that the highly acidic and basic watered plants would show differing signs of nutrient deficiency and an overall stunt in growth. For trials, we established five testing groups and measured their initial height and health and over a three week period we watered each group daily with water in their desired range (1-4 pH, 5-6 pH, 6.5 pH, 7-8 pH, 8-12 pH). Our results indicated significant a stunt in growth and health to all but the control group (6.5 pH), as evidenced by slight discoloration in the veins and the tips of the leaves. This means we can safely surmise that plants grown outside of the optimal pH range do not prosper and may not survive to the next generation as compared to those grown within the range. This is of great significance because with that knowledge one can take steps to create optimal conditions for crops and thus maximize yields.

Habitat Preference of Western Gray Squirrels
Destiny Del Papa, Kerry Schnitter,
Western Grey Squirrel (Sciurus griseus) is native to California. They rely on trees for travel and habitats to build their nests. We hypothesized that the average number of S. griseus would be lower in more urban areas due to the increased human population. In the field, squirrel population and their behavior was recorded in two different locations, one more densely populated than the other, for four weeks. Even though we could not find a significant difference between sites (P= 0.390), we found that the mean number of squirrels in the rural area was about 22% higher than the mean number of squirrels in the urban area. This difference in means may be due to the increased number of trees found in the rural area. In conclusion, we found that S. griseus do not show a habitat preference.

Feeding Behaviors Among Squirrels
Yesica Nava, Ariana Guerrero, Danielle Donovan,,
When dealing with mimicry, species can begin to learn the difference between palatable and non-palatable options. The motive behind our experiment was to evaluate the feeding behavior among our western grey squirrels (Sciuridae). For the experiment, we used cranberries (twenty palatable), peanuts (twenty palatable and non-palatable), and almonds (twenty palatable and non-palatable). We coated the peanuts with onion powder, and as for the almonds we lightly saturated them in lemon juice. Due to inconsistent weather, our data ended up being skewed from our null hypothesis. The squirrels did not end up learning the difference between the palatable and non-palatable options. In conclusion, we found that the western grey squirrel did not learn to distinguish between the palatable and non-palatable options. For example, the squirrels did not eat the palatable cranberries, but they did eat a majority of the peanuts every day of our data collection. They ate about eighty percent or more of the non-palatable peanuts for every data entry.

Pollinator Flower Color Preference
David Veach , Vivian Gallegos ,
Pollinators such as bees, butterflies, and beetles are essential to the functioning of terrestrial ecosystems. Color is one of the main floral traits used by pollinators to locate flowers. For this experiment, a total of 167 flowers were examined to see if certain pollinator groups prefer flowers of specific colors. Data was recorded from two loci, North Table Mountain Ecological Reserve and on the Chico State campus. Data was recorded when the weather conditions were bright and sunny, and when pollinators were expected to be most abundant. Flower colors and pollinator groups were categorized so that their values could be compared. Flowers were observed at random to look for pollinators in action and their quantity was recorded. After conducting a Chi-Squared test, the results displayed no significance in the selection of flowers by certain pollinators (8.6x10-14 < 0.05). In conclusion, it was found that there was no significant preference of flower colors by any of our pollinators.

Water stress levels on radish growth
Joy Cooper, Tanner Kranig, Cristian Brady,,
Plants grow at different rates according to their environmental stressors.  We hypothesized that fast growing radish plants watered with distilled, carbonated, and regular water would have different growth rates. Each plant was given one capful of water and measured everyday. Our results showed that the radishes watered with distilled grew the fastest, carbonated water grew second fastest, and regular water resulted in the slowest growth rate (we graphed the measurements and the slope of the distilled water was .6204 where carbonated had a slope of .6069 and regular water only had a slope of .5848). In conclusion, our plants that were given distilled and carbonated water grew the fastest and as we predicted regular water was the slowest growing of the three.

Insect Population Density
Jesus Garcia, Angel Zavalza,
As tiny as they may be, insects play a huge role in soil richness. Whether it’s ants and beetles creating canals for water storage or earthworms working as decomposers to nourish the soil, it is all a community effort. In this experiment, insect density and diversity is measured depending on the rock size (circumference). According to the data collected, nearly 50% of insects observed resided under larger rocks with an average circumference of 44.6 inches. In closing, an insects positive role in soil richness should be taken into account; thus, preserved to live in larger rocks. 

Carrying Capacity of Garlic Chive Seeds
Jakob Gardner, Seth Wise,
In natural forests, where plant life could be overlapping each other. We hypothesized that the population of the plants in the soil increases the rate of the plant growth will be reduced. We planted five different pots with garlic chive seeds that had different populations in each of them. The first pot had 2 seeds, second 5, third 10, fourth 20, and the fifth pot had 50 seeds. Plants in the higher population groups from (40 to 100%) sprouted sooner (on day 2) while the lower density plants from (4 to 20%) sprouted later (day 3). After the initial sprouting, the plants had relatively similar growth patterns until day 7 where the higher density plants started to fall off. We concluded that the carrying capacity of our environment was around 10 plants and was supported by the results (Pot #1 reached maximum height of 130mm, #2 134mm, #3 142mm, #4 124mm, #5 104mm) of the experiment.

The rate of moss regrowth based on its location
Krystian Bonis , Marcus Rehrman ,
There are many different species of moss (Bryophyta) which grow in different places and even on different objects. We identified patches such as Medusa moss, which grows on the rocks along the Big Chico Creek, Carpet moss, which resides on the ground roughly ten feet from the creek, and Bryopsida moss on the branch of an Oak tree. The purpose of this project was to slightly trim an area within the moss patch and see how well it regrew, based on where the patch was located and how well it had access to nutrients and water for optimal growth. We hypothesized that the moss on the rock would grow the fastest due to its water resource, the moss on the ground would follow because of the nutrients in soil, and the moss on the branch would trail because it is attached to the thick bark. At the start, measurements were taken from each patch, and then within all the patches a small area was cut down to around the same length. The results showed that the moss patch which regrew the strongest was the Medusa moss, which nearly regrew to its original average size, the Carpet moss saw very little yet noticeable growth, but the Bryopsida moss saw no regrowth in length whatsoever (rock patch had around 17.8% more regrowth). In conclusion, the rainfall that occurred in Chico during the trial rose the creek waters and held the rock underwater, giving the moss patch an advantage for optimal regrowth.

Examining Batesian Mimicry in the Viceroy Butterfly (Viceroy Limenitis archippus)
Cara Tamcke, Kevin Johnson, Hunter DeHerrera,,
In nature, organisms are forced to inhabit a form of defenses against predators, mimicry for example, has been studied for over a century in various organisms. In this study, we examine experiments that have studied the survivorship of the Viceroy Limenitisarchippus through their use of mimicry. We hypothesized that the Viceroy Limenitis archippus used Batesian mimicry to resemble the Monarch Danaus plexippus. However, it was later discovered this relationship is far more complex and the Viceroy Limenitisarchippus actually exhibits Mullerian mimicry. In a experiment performed in Florida, it was found that 40% of Viceroy Limenitisarchippus that were ingested by birds, were fully eaten. The experiments supporting this form of mimicry is implemented through a series of “taste tests”. It can be concluded that the Viceroy Limenitis archippus mimics the appearance of the Monarch Danausplexippus as a form of defense, and is later found to not have a difference in palatability.

The Effect of Human Frequency and Habituation in Squirrels
Leslie Garcia, Madison Gutierrez ,
Are mimics less likely to be eaten by predators depending on which type of mimicry they exhibit? In this experiment, we wanted to examine the effectiveness of Mullerian mimicry. Our null hypothesis being that the type of mimicry doesn’t have an effect on survivorship of the mealworms, and the alternate hypothesis being that it does impact survivorship. We set out two different trays in two different locations, one showing Batesian mimicry and the other Mullerian. After leaving them out for two weeks and checking on them each day, we found that the rates of survivorship were slightly higher in the mealworms from the Mullerian tray. The average rate of removal from the Batesian tray was around 2.8. From the Mullerian tray the average rate of removal was 1.9. In the end, our hypothesis was supported by the data and results we yielded - Mullerian mimicry is more effective at keeping prey alive than Batesian mimicry.

Survivorship of Batesian vs. Mullerian Mimicry
Miguel Castro, Ginger Shaffer,
Are mimics less likely to be eaten by predators depending on which type of mimicry they exhibit? In this experiment, we wanted to examine the effectiveness of Mullerian mimicry. Our null hypothesis being that the type of mimicry doesn’t have an effect on survivorship of the mealworms, and the alternate hypothesis being that it does impact survivorship. We set out two different trays in two different locations, one showing Batesian mimicry and the other Mullerian. After leaving them out for two weeks and checking on them each day, we found that the rates of survivorship were slightly higher in the mealworms from the Mullerian tray. The average rate of removal from the Batesian tray was around 2.8. From the Mullerian tray the average rate of removal was 1.9. In the end, our hypothesis was supported by the data and results we yielded - Mullerian mimicry is more effective at keeping prey alive than Batesian mimicry.

Birds Observed In Different Urban Locations Throughout Chico
Matt Konopka, Katie Mata,
Urbanization influences bird diversity in Chico by affecting the species of birds and frequency of bird activity. We hypothesized that there would be more birds in less urbanized locations such as the creek on campus. We expected to see a distinct change in the species of birds found at the different locations. There was some cross over of the same species being observed at the sites, the outlier was the Pigeon and Humming Bird. The Pigeon has grown accustomed to living on buildings and spending their days in the busy city but on the other hand the Humming Bird prefers the less noisy atmosphere that is found near the creek. There were four locations with varied levels of urbanizations from parks and creeks to the Downtown Plaza. We observed birds for 30 minutes three times a day with a replication at each site. After analyzing the data, the results showed that there were more birds active in the morning, with an average of 27 birds near the creek but the afternoon had more bird activity Downtown, with an average of 32 birds. We also observed difference in the number of species at each location. All the locations are relatively close together and there are distinct changes between the frequency of the birds and the different species that we observed. The time where peak bird activity happens is dependent on the type of environment of the habitat.

Ideal germination and growth
Pastor Magana, Brooke
Environmental stress such as water availability can affect a plant by stunting it’s growth. We explored whether over watering or under watering would affect the germination and growth rate of radish seeds. Determining the amount of water each individual radish seed requires would help farmers to grow plants more efficiently by demonstrating the appropriate amount of water needed. Using six seeds for six trials, each seed was isolated and was given a water ranging from a eighth cup of water to two in a half cups of water twice daily. The seeds were all placed on a table by the window allowing for equal sunlight and other environmental factors. During our experiment, we conducted an Annova test and concluded since our p-value was (.42) there is no significant difference between germination and growth rate within varying amounts of water.

Correlation Between Proximity to Big Chico Creek and Bird Density
Ryan Rosenbaum, Mary Cate Hoeft, Joe Fucigna,,
Our experiment sought to determine whether or not bird density in Chico is affected by proximity to the Big Chico Creek. We hypothesized that a greater density of birds would be observed near the creek as opposed to one mile away in the University Village. Data was collected during a fifteen minute interval every day for one week near the creek and in the University Village. No tools were required to conduct our experiment. Our calculated P-value (8.54812E-05) indicates a significant difference between the densities of birds near the creek and at the University Village. In conclusion, preferential bird habitat was found to be affected by proximity to the Big Chico Creek.

Comparing Invasive Ivy Coverage on Trees of Lower Park
Sofia Lepore, Jake Kincaid,
The Hedera algeriensis (Algerian Ivy) is an invasive species prevalent in Bidwell Park. It displaces native plants, which can alter an ecosystem within the Big Chico Creek Watershed and disrupt it beyond the individual plant.  We hypothesized that we would see higher percent cover of H. algeriensis on and around trees near the creek. For field trials 15 random plots (15x15 m2) were generated throughout Lower Bidwell Park. While there we observed the factors of creek proximity, tree count, and percentage of trees with H. algeriensis on them. We compared the percentage of H. algeriensis coverage in relation to creek proximity, with our t-test resulting in a mean value of 67% coverage on trees near the creek, and 70% coverage on trees further from the creek. We found a p-value of .389, therefore we could not support that percent cover due to creek proximity is significantly different within Lower Park.

Does Temperature Effect the Activity of Squirrel Populations
Victoria Dennis, Skylar Tomasetti, Nitzairian Ramirez,,
Living on a campus with an abundant population of squirrels have allowed us to inquire if there is a difference in activity of squirrels at different temperatures. We conducted this experiment by going to different locations with high populations on campus, outside Holt hall, behind Colusa hall, and in front of the physical science building, when temperatures were a low of 50 degrees and a high of 82 degrees, we were able to monitor the squirrels’ activity. Our hypothesis was squirrels are less active in the cold weather due to them wanting to stay warm and conserve energy. When the weather is warm they will be more inclined to roam, mate and look for food sources to store for when it is colder. The type of data that will be collected will be discrete and nominal. By observing when the squirrels come out, how long they are out and what they are doing; for example, eating, gathering, playing or mating a conclusion can be drawn on their behavior. During the experiment the we will be evaluating independent frequencies and comparing means between the warm and cold weather and use an ANOVA comparisons. The results show that there is a significant difference between the temperature and the time of day in squirrel activity.  The P-value for the warm weather is 0.386 and for A.M. is 0.139.  Our conclusion for the experiment is that our hypothesis is correct as based on our evidence, squirrels are more active in higher temperatures. 

Stomatal Density Variation Between Distances of Water Source
Victoria Trejo, Vanessa Mendoza, Samantha Romero,,
Stomata are essential for plant survival as they exchange CO2 and O2. We examined the differences in stomatal density in the leaves of Blue Elderberry (Sambucus nigra L. ssp. cerulea) growing closer and away from the Big Chico Creek, inside Chico State University. We hypothesized that leaves further away from the creek would have a higher stomatal density than the leaves closer to the creek. Thirty leaves were collected from each plant and counted stomata under microscope (400X). We found a significant difference between the two different locations (P-value 0.00000143). In conclusion, the stomatal density is greater in the plants further away from the creek than the plants in close proximity to the creek.

BIOL 152, Drew Gilberti,

Earthworm Soil Preference 
Amber Lydia, Semranjit Kaur, Aisha Shaikh,,
Earthworms belong in soil, but the real question is what type of soil are they most attracted to. We hypothesized that red worm preference for soil type is influenced by proximity of water sources. To test our hypothesis, 25 worms were placed on a plate in the center of 3 away from water and 3 near water sources. This was done to give each sample of soil an equal advantage of exposure to the round works. The result was that that the worms hated the soil samples near a water source and jumped over to the soil samples that were not collected near a water source. The statistical value was 7.78331E-05, which was statistically significant. Worms showed a preference for soil not found near a water source and this did support our hypothesis. 

Comparing Latex Production in Native and Non-Native Plants
Jessica Poundstone, Ceres Phillips, Scarlett Echeverria,,
Plants have developed multiple mechanisms to defend themselves from herbivores. Latex, a thick, creamy white, milky emulsion plant defense, coagulates when exposed to air and hardens around insect mandibles. Latex only occurs in about 10% of angiosperm species. We hypothesized that nativity has an effect on how much latex is produced. With 2uL micro capillaries we measured latex produced by species from the milkweed, dogbane and Euphorb families. Our results showed that non-native species tend to produce more latex when compared to native species.

Leaf Density Indicates Location of the Meristem 
Jesse Garcia, Aaron Ragsdale, Kyrstin Brown, Kenneth Touhey,,, 
Cabbage proliferates through means of asexual reproduction which is induced by the shoot apical meristem. However, inquiries remain unresolved in regard to where the meristem is located on a Napa Cabbage, Brassica rapa Pekinensis. The purpose of this study was to identify the location of the meristem on Napa Cabbage by relying on visual indication of asexual regeneration. We hypothesized that leaf density is an indicator of the meristem location which is responsible for asexual reproduction. To test our hypothesis, we examined four cabbages, stripped the leaves, segmented them into three portions of stem and situated them into suitable environments for daily observation. We found a significant relationship (p<0.05) between meristem location and leaf density suggesting that new leaf growth is an indicator of meristem position. Therefore, our results support our hypothesis, which present consistent data of meristem location. These results inspire possible implications related to ecological concerns; dependable knowledge of meristem location can motivate utilization of segmenting the meristem to maintain cabbage yield and reduce waste.

Algae growth
Kasity Watkins, April Amajoyi, Amanda Ramirez , ,
The oxygen we breathe in everyday is made by a process called photosynthesis. Here in the Chico Creek there is a large amount of algae that grows on various rocks in the creek which also contributes to producing oxygen. With this process in mind, we hypothesized that the amount of sunlight that a plant receives will determine its growth and we decided to test this by measuring the surface areas of rocks covered in algae that were both in the sunny and shaded areas of the creek. We predicted that the growth would be more abundant in plants that are in the sun rather than those in the shade. To test our hypothesis, we quantified algae growth across 60 rocks by finding the average surface area of them in both areas of the creek. We found that there was no significant (P= 0.2001) relationship between the algae growth of rocks in the sun and in the shade, which did not support our hypothesis. However, we did find that there was a 28% increase in algae that was growing in sunny areas.   

Habitat Preference of Two Species of Squirrels in the Chico Area
Milla Konings, Ross Schaefer, David Salgado,,
This experiment was conducted to study the invasive Eastern Gray Squirrel, and how well it competes with the native Western Gray Squirrel in 3 different habitat types, including riparian, urban, and oak woodland habitats. These habitats were surveyed to discern which environment had the highest proportion of introduced squirrels, with the hypothesis being that this likely due to habitat preference.  A count was made at a variety of locations that represent the squirrels habitat, tallying squirrels of the regular all gray variety, or the reddish-tailed Eastern variety.  This experiment supported our hypothesis, which is that Eastern Gray Squirrels have strong habitat preference to Oak Woodland habitats over Riparian or Urban, suggesting that there is more food, shelter, and other resources in that habitat. The fewest Eastern Squirrels were observed in urban habitats, which came as a surprise given that the Squirrels were introduced by humans.  There were almost 40% more Eastern Gray Squirrels, in proportion to Western, present in oak woodland habitats than in urban or riparian areas had an intermediate amount.  In the future, if Eastern Gray Squirrels begin to push out our native populations, data suggests that conservation efforts should start in oak woodlands, as the highest concentration of the potentially harmful introduced squirrels exist in these areas.

Is Squirrel Activity Affected by Human Presence?"
Sarybell Castro, Julia Huskisson,
Humans have a tendency to influence ecosystems they inhabit. The purpose of this experiment is to see if the growing population of college students will affect the squirrel population. We hypothesized that if there was more human activity, there would be less squirrel activity. We predict that humans will have a negative influence on squirrels due to squirrels feeling anxious We tested our hypothesis by comparing the number of squirrels in an area to the number of humans in that area at the same time (also including any other variables such as dogs). After going for several days to a variety of places, we collected our data and performed a T-test. The average squirrel count was 2.6 squirrels and 23 people. Our data did support our hypothesis that...If there are more humans in one area of Chico, and we see very little squirrel activity, it is probably due to the fact that humans make squirrels nervous. But, that is not to say there aren’t other factors involved, such as other animals near them, the weather patterns, and sources of water. 

BIOL 152, Rachel Schleiger,

Moss Density
Briana Flores, Sara Deleon, Wai hnin Phyu,,
Because aspect is the compass direction in which a slope faces, it has an effect on the temperature and how much moisture is available. Certain plants are highly dependent on aspect for abiotic environments necessary for survival and reproduction. This study investigated how bryophyte (moss) patterns changed based on different aspects. Sunlit environments lack the moisture and shade that moss thrive in. Specifically moss cover was estimated with 0.1m2 quadrats in North and South facing aspects adjacent to a riparian environment. The results indicated a significant difference in moss growth by at least 25% on the north facing side of the Big Chico Creek and no moss growth on the south facing side. Thus, our results support that plant growth patterns are relied upon certain ecological circumstances. These patterns offer insight on an environments climate and available nutrients.

Batesian mimicry on Chico bird population.
Isaac Adelman, Sophia Schmerling, Tanner Wahl,,
Mimicry is the resemblance of one organism to another. This research attempts to demonstrate how mimicry effects consumption of bird seeds in birds. By finding the correlation between color, type of bird seed, and consumption, we would be able to prove that mimicry does affect consumption. This project attempts to determine if birds are affected by the color of the food they are consuming. We wanted to apply what we have been learning to a small-scale experiment; we set up different colors and types of bird seeds to see what color of seeds the birds prefer. Despite our predictions, the birds were drawn to the sunflower seeds much more than the bird traditional bird feed, regardless of the color. Now that we have determined that it is the type of food and not necessarily the color of food; We can conclude that we need less variability when testing for mimicry, as well as a more controlled environment, for more conclusive results. In ecology, it is essential to understand the effects of mimicry on trophic interactions between species.

Effect of fire on Petrorhagia dubia in Big Chico Creek Ecological Reserve
Jeremy Scheffler, Richard Prentice, Sophia Bennett, Kiley Quevedo,,, 
This study investigates how fire affects the growth and spread of the invasive flower species, Petrorhagia dubia, in an upland oak environment in BCCER. After a fire, the presence of Petrorhagia dubia will increase in burned areas, particularly those with an open canopy. To collect data, we took parallel transects, one in a burned affected area and the other in an unburned area. Based off the data collected, the unburned area saw far fewer flowers than the burned (p-value= 0.9997). The unburned areas have less invasive flowers present because the natural vegetation was not affected by the fire, so it is more difficult for the invasive flowers to colonize that space. In the burned area, newly open soil allowed for less competition with native plant species and easier colonization for invasive plant species, such as Petrorhagia dubia. Confirming our hypothesis; we concluded that the burned area was more susceptible to these invasive flower species.

Species richness as a Function of Solar Radiation 
Scott Stokes, Carlo Jimenez, Jacqueline Mendiola garcia
Solar radiation, is an absolute necessity for any plants development and health. This study explored how variation in solar radiation affect species richness. It was hypothesized that areas with intermediate solar radiation would have the highest species richness because this area would receive enough sunlight to photosynthesize properly while not being thermally stressed by high levels of radiation. Solar radiation readings were made in three different areas, on clear days with little to no atmosphere obstructions, at five different times of the day order get average radiation readings. Richness was assessed in a 1yd2 quadrant was placed randomly fifteen times for all three areas. An ANOVA indicated there was a significant difference between areas richness (p-value = 3.38E-8). Post-hoc t-tests indicated that intermediate solar radiation had the most species (p-value = 0.0001998, p-value = 3.731E-7). It is believed that the intermediate radiation sight had the most species because it received plenty of incoming radiation, was close to the river and had signs of intermediate disturbance. Area one was close to the river and had signs of disturbance but lacked sufficient solar radiation. While area two was also close to the river and got plenty of solar radiation but lacked signs of disturbance. Understanding these types of patterns can contribute to specific areas of biology, such as conversation biology.

Yellow Flowers in Upper Bidwell Park; The North Rim Trail vs. The South Rim Trail
Tonya Boskovich, David Gleason, Megan Bleiler, ZoeyZanotti,,,
For this study, we compared the plant pattern changes of Ranunculacae canus on the North Rim Trail and South Rim Trail based on abiotic differences in the habitat and the amount of foot traffic they each receive. Ranunculacae canus, Sacramento Valley Buttercup, has been observed at many different aspects in Chico, CA, USA. Ranunculacae canus abundance would vary in abundance depending on the terrain and location. To test this, 1m2 quadrats were used to record the abundance of flowers in two different aspects. A T-test indicated no difference in the abundance of Ranunculaceae canus (p-value = 0.079) at the two separate locations. Because of the high p-value, our data shows no significant difference in mean populations of Ranunculaceae canus on the North Rim Trail versus the South Rim trail. Visually it appeared that there were different abundances of Ranunculaceae canuson the North Rim than the South Rim, however the data didn’t support this assumption. This means that our hypothesis couldn’t be accepted and was therefore rejected. This is important to understand on a broad scale for two reasons.  The first being the implications of human activity on natural habitats; and the following has implications that despite seeing a plant population in different abundances in two separate locations, it doesn’t indicate the data will support it if a statistical analysis is performed on the plant population.


BIOL 350 Fundamentals of Ecology
Colleen Hatfield,

BIOL 350, Adrienne Edwards,

Species' Cover in Three Chaparral Land Treatments
Andre Colunga, Greg Barry, Jared Decker,,
Fire is not as devastating to an environment as is believed. Fire can lead to healthy new growth in a chaparral environment and remove dense old growth, increasing biodiversity. We hypothesized that species relative cover will vary depending on whether burned, unburned, or in a fire break. Our predictions stated that species cover would be lowest on fire break plots compared to burned and unburned plots. Working in Big Chico Creek Ecological Reserve in Chico, CA, we recorded the percent cover of plant species in 2m2 plots in and around an area that burned in September 2017. Unburned areas had the highest percent cover, as predicted. Our results accurately reflected our prediction because in areas where there has been no fire the cover is, in some cases, greater than 100% because of canopy height differences. In the burned areas, the percent cover was lower but had the most resprouts and herbaceous plants. The fire break areas had the least amount of percent cover of plants, most of it consisting of coarse woody debris and bare ground with some grasses. Percent cover varies in the three different treatments, but each has its own dominant cover: burned is dominated by resprouts, unburned by scrub oak and fire break by coarse woody debris but no plants. It is apparent that regeneration in fire breaks deviates from natural vegetation regeneration.

Comparison of Habitat of Desmocerus californicus dimorphus
Al Wallace, Autumn May,
Desmocerus californicus dimorphus also known as the Valley Elderberry Longhorn Beetle (VELB) is listed as threatened at the federal level. One of the limitations of the VELB is that it is confined to an extremely specific haitat: the elderberry bush (Sambucus nigra ssp. caerulea). This beetle needs branches on the elderberry bush to be within a certain circumference. The VELB ovaposits eggs into branches. The larvae live and develop in the branch cambium and then burrow out to emerge as adults. Unfortunately, recent brush clearing inadvertently pruned away some of the VELB habitat along the Big Chico Creek that runs through campus. This study compared VELB habitat on campus along Big Chico Creek versus habitat at Pine Creek unit of the Sacramento River Wildlife Refuge. Ten trees were sampled at each location and the number of habitable and inhabitable branches per tree were counted. It was found that there is a significant difference with an average of 73 habitable branches at Pine Creek versus 6 habitable branches on campus. With a significance level of .05, a p-value of .009 was obtained. After conducting the ANOVA test, it was found that we were able to reject the null hypothesis and state that there is a significant difference between the two sites. This suggests that pruning around the creek on campus produced significant damage to the VELB habitat. This study suggests that there should be an increase in caution around this habitat to preserve the Valley Elderberry Longhorn Beetle.

A Survey of Potential Habitat Loss for Valley Longhorn Elderberry Beetles at CSU-Chico
Ian Schneider, Colin Kroeker, Selena Hennessey,,
The Valley elderberry longhorn beetle (Desmocerus californicus dimorphus), or VELB, is a particular species of wood-boring beetle that is endemic to the central valley of California, and is only found in association with the host plant, blue elderberry (Sambucusnigra spp. caerulea ). Our goal for this project was to determine the amount of viable habitat within the Chico State campus and predict the average amount of potential habitat lost during an unintentional removal of blue elderberry. We measured the base diameter of cut and uncut elderberry trunks that supported the preferred stem diameter. After measuring the trunks and counting the ‘ideal’ stems that were present on cut and uncut plants, we used a standard regression to determine the relationship between trunk size and potential suitable VELB habitat. There was a significant but weak positive association (R2 = 0.29) between the trunk diameter and the number branches that facilitate suitable VELB habitat. We estimated that approximately 11.5 branches were lost (minimum of 6 to a maximum of 25). With a larger sample size, we predict we would be able to use this method to determine the environmental take after an unintentional VELB habitat loss event. 

Density of Invasive Himalayan Blackberries In Bidwell Park as a Function of Water 
Kira Price, Angie Persell, Michaela Fahlen, Jake Kincaid ,,, Angie P.
The Rubus armeniacus (Himalayan blackberry) is an invasive species prevalent in Bidwell Park. As an invasive plant it displaces native riparian species. By taking over native plants, invasive species can alter an ecosystem in negative ways. We hypothesized that we would see higher densities of invasive R. armeniacus in riparian zones with more water permanence because R.armeniacus does not originate from a Mediterranean climate and does not thrive in extended drought conditions. We measured throughout upper and lower Bidwell park, where blackberries occurred, with the factors of creek proximity, shade level, and percentage of blackberries present along each of the 23 transects.  We estimated patch size by calculating an ellipse area from our transect data. The average patch size of Lower Park was 252.1m² and Upper Park was 268.2 m². There was no significant difference in patch size due to water permanence.  While R. armeniacus patch sizes may be impacted by other factors, we cannot determine that water permanence between Upper and Lower park is significantly different.

Competition within the seed pod of the Western redbud, Cercis occidentalis
Maria Avelar, Marvin Barrios,
Competition operates at multiple levels between organisms, and competitive interactions are even more interesting when observed in a self-contained system. We focused our research on the effects of competition for nutrients among the seeds of western redbud, Cercis occidentalis. Since seeds are resource sinks in need of sucrose, we predicted that the seeds closer to the basal region of the pod (near the stem) would outcompete its neighboring seeds simply due to its proximity to the source of nutrients, the stem. We conducted our experiment on CSU Chico State’s campus. A total of ten western redbud trees were sampled, 250 seed pods were collected, and 1,035 seeds were analyzed. We counted the seeds based on their location within the pod, as basal, medial or apical and specified further whether the seeds were viable or inviable. Although we had initially predicted the seeds in the basal region would have a higher probability of allocating most of the nutrients due to a proximity effect, there was a significantly higher percentage of inviable basal seeds, 5.12% than inviable apical seeds, 3.48%. Overall, there were 2.36 times more viable seeds in the middle and in the apical region than in the basal region. In conclusion, it is clear there is an unequal allocation of nutrients among the seeds of Cercis occidentalis. The seed’s proximity to the stem did not account for the number of viable and inviable seeds, instead genetics may be responsible for the pod’s phenotypic traits. 

Does Seed Position in Seed Pods of Cercis occidentalis Affect Predation by Gibbobruchus mimus?
Mohammad Mukhtar, Emily Barber, Aracelie Agraz,,
When multiple seeds are contained within a fruit, seed arrangement and position can influence allocation of nutrients and predation risk. We studied these ideas by analyzing seed position and predation on seed pods of Cercis occidentalis (Western Redbud). To test our hypothesis, a total of 50 seed pods from each of 8 trees found on the CSU Chico campus were sampled (n = 400). Each seed pod was divided into 3 sections: basal, medial, and apical with respect to the peduncle. The number of seeds in each section along with the presence or absence of predation by Gibbobruchus mimus (Seed Weevil) was recorded. The analysis of gathered data, via chi-square test, showed a significant difference in the number of seeds in each position as well as a significant difference in the site preference for predation. The data analysis suggests that there is a correlation between seed location within a seed pod and the site of predation. As the number of seeds within a certain position increases, so does the likelihood of predation in that position. 

The Effects of Intraspecific vs Interspecific Competition on R. satvia species
Ceres Phillips, AJ Samra, and Oscar Kalfsbeek,,
Competition drives many interactions in ecology, determining which members of a population, or specific species, will survive. The two most common forms of competition seen in nature are interspecific competition, where members of different species compete, or intraspecific competition, which involves members of the same species. We hypothesized that, when it comes to R. sativa, or radish, intraspecific competition will be more detrimental to the seedling growth than interspecific competition. We created five treatments in order to test our hypothesis, with two groups measuring low and high intraspecific competition, respectively, two groups measuring low and high interspecific competition, respectively, and a control group. We utilized Beta vulgaris (beet) for the interspecific treatments, weighed the initial biomass for the seeds that would undergo a specific treatment, and performed the experiment over a span of four weeks. We then weighed our seedlings for each treatment, and we found a significant difference in radish biomass, when grown with other radishes, was far less than the biomass of radish seeds grown with beets. These results significantly support our hypothesis that intraspecific competition between radish seeds was stronger than interspecific competition. 

Pollinators Prefer the Middle-Aged Flowers in an Inflorescence of Vicia villosa
Shelby Bomke, Diana Ledford, Alexandra Wynter,,
Pollinators, such as bees, butterflies, and beetles, provide crucial pollination services to the ecosystem. In recent years, pollinator population densities have declined threatening seed production in many animal-pollinated species, like hairy vetch (Vicia villosa). It is critical to understand the way pollinators behave and utilize resources while pollinating. There is a balance between reward and cost of obtaining reward for the pollinator; with decreasing reward per flower, pollinators have to expend more energy. We tested the hypothesis that pollinators prefer the middle-aged flowers in an inflorescence compared to the older or younger flowers of the hairy vetch. We predicted that the pollinators would prefer the middle-aged flowers in the inflorescence because of a higher nectar reward and lower energetic cost. We conducted eleven, ten minute observations in Upper Bidwell Park and Little Chico Creek footlands in Chico, California. We observed meter squared plots of hairy vetch. We then recorded the number of pollinators that landed on old, middle-aged, and young flowers. We observed that pollinators visited the middle-aged flowers significantly more than both the older and younger flowers. The rewards of the middle-aged flowers outweigh the energetic costs to the pollinators because of a higher nectar reward.

Analysis of earthworm populations in soils.
Terrence Carter, Giovani Gutierrez, Aisha Sheikh, Brittany Simpson,,,
 The occurrence of European earthworms (Lumbricus cf. terrestris) is directly related to human disturbance. We examined whether the population density of earthworms was directly related to whether it was in a fertilized grass covered area versus leaf litter covered area. Our leaf litter covered test location had a large understory of California Blackberry (Rubus ursinus) and an overstory of Sycamore (Platanus spp.).  We treated nine- 0.6 m sq plots within each treatment location: fertilized grass cover and leaf litter cover areas.  An aqueous solution of water and tea tree oil was applied to each plot and the number of earthworms that erupted from the surface was counted. This was then replicated two other times which resulted in 18 data points. Earthworm density was 74% higher in our Sycamore leaf litter covered location compared to our fertilized grass covered location (p <0.05). Abundance of earthworms is affected by the amount of organic matter available, and conventional lawns. have reduced organic matter available to earthworms. 

Influence of Urbanization on Water Quality
Cole Gleaton, Thomas McNairn, Francisco Preciado, Will Baker,,,
Urbanization has been known to affect the quality of water. We hypothesized that there would be poorer water quality in Big Chico Creek (BCC), a stream running through a more urbanized area, compared to Butte Creek (BC), a stream running through a less urbanized area. Also, we hypothesized that water quality would degrade more downstream within both creeks. In this study, we considered downstream to be more urbanized. To quantify water quality, we measured levels of Dissolved Oxygen Content (DOC), pH, Nitrates (NO3), and Phosphates (PO4) at three locations on each creek. Multiple ANOVA tests were run to compare the response variables between each location. Overall, our results indicated BCC had poorer water quality compared to BC. BCC was significantly more acidic and had lower DOC compared to BC, although DOC values for BCC were not significantly different. In addition, BCC had higher levels of both Nitrates and Phosphates, but levels were not significantly different along both creeks. Moving downstream within both creeks, the pH became significantly more acidic and DOC also degraded. However, the DOC measurements moving downstream for BCC were not significantly different. Within both creeks, higher levels of NO3 and PO4 were found moving downstream, although there was not a significant difference throughout each creek. Therefore, urbanization has a negative effect on water quality by significantly lowering pH within BCC and BC.

BIOL 350, Tag Engstrom,

The Color of Nectar Impacts Hummingbird Foraging
Alana Taylor, Joseph Garcia,
Hummingbirds are known for being attracted to brightly colored flowers. It is known that there is an evolutionary relationship between plants and their pollinators because plants have adapted to not only be visually appealing, but to allow easy access. The purpose of this experiment was to determine whether or not hummingbirds have a color preference of nectar. We tested whether hummingbirds were attracted to colored nectar from the warmer end of the colored spectrum (red and yellow) versus the cooler end (purple and blue). In order to conduct this experiment, we filled five identical, clear, hummingbird feeders with store bought nectar. We then used food dye to color the nectar red, yellow, blue, and purple. Our control was the clear store-bought nectar. We then hung the five feeders at the Camellia Garden on the CSU Chico campus and observed the amount of nectar consumed from each feeder. Each feeder was hung 10 inches from the tree branch and was later removed and brought back the following observation time. We had a total of four two-hour observation days. We then measured how much nectar of each feeder was consumed. We conducted an ANOVA test to determine whether there was a relationship between color of nectar and amount consumed. Based on our analysis, we can conclude that red colored nectar was preferred more than the other color options. Our results support the ecological principle that red colored flowers attract hummingbirds. 

Lichen communities on rocks support the theory of island biogeography
Connor Bouch, Carlos Estrada, Hannah Guiles,, 
The theory of island biogeography is one of the major ecological principles explaining patterns of isolated communities. One of the predictions indicates that a larger isolated habitat, or island, will have greater species diversity when compared to smaller isolated habitats. We set out to investigate this theory by gathering data on species diversity within lichen communities on isolated rocks found in the Big Chico Creek Ecological Reserve. When rocks on which lichen can grow are separated by unsuitable habitat, they behave as separate island habitats to the lichen. We separated rocks into two categories based on diameter, large rocks (>3ft) and small rocks (<3ft). Data on species diversity was collected by counting the different lichen species present on each island. We identified lichens as different species based on color. Larger habitat islands had a higher mean in species diversity (p-value < 0.05). The results support the general principles of the theory of island biogeography, showing a greater species diversity being present on larger islands. The results from this experiment could be used to help predict the relative species diversity between similar biomes. 

Bloom Density of Vinca major (Big Leaf Periwinkle), an Invasive Riparian Plant Species Increases Under Low Canopy Coverage.
Roberta Overman and Charles Wheeler,
 Plant species display a wide range of tolerances of light and shade. Some are extremely shade-tolerant and others are very light dependent. While some plants grow well in shaded areas their reproductive structures can be light dependent. We observed flower density of the Vinca major (bigleaf periwinkle) in different canopy covers. Vinca major thrives in full sun as opposed to the closely related species, Vinca minor, which is best suited for shaded areas. We hypothesize that the more canopy cover for the selected areas the less bloom density will be. In our experiment, we tested this by taking flower counts from one square meter quadrants of Vinca major in low canopy cover, partially canopy cover and high canopy cover. The results show bloom density was higher in low canopy cover and lower under high canopy cover. These results support our hypothesis that Vinca major is a sun adapted species.

Soil Properties of Flower Patches in Upper Bidwell Park
Kristen Morris, Shyanne Rizzo,
Physical and chemical properties of soil can be a factor in determining what plant life is supported in an ecosystem. Varying soil properties within an area can also influence the heterogeneity of flora on a relatively small scale. After observation of Upper Bidwell Park in early April, we noticed there are defined patches of flowers spread throughout the grassland. We wanted to understand what causes flowers to grow in these distinct patches, rather than evenly throughout the landscape. We hypothesized that there were differences in soil properties within the patches than adjacent areas with just grass. We collected soil samples within three flower patches and right outside these flower patches. We tested a variety of different soil properties, including electric conductivity, pH, total dissolved solids, soil moisture and soil water holding capacity. Soil moisture was observed qualitatively on a scale of wet to dry at time of sampling. Overall, we found that soil moisture seemed to be the determining factor in varying presence of flower patches in comparison to the other soil properties we tested. This suggests that heterogeneity of this area is due to mosaic of moisture and water flow, rather than differing chemical properties within the soil. This study helps to better understand how micro-climates influence biodiversity in this area.

The Rate of Degradation and Analysis of the Nutrient Cycle in Chaparral Communities That Have Experienced Recent Fire
Lauren Howey, Erica Aldanese,
The Big Chico Creek Ecological Reserve (BCCER) was subject to a wildfire that burned roughly 60 acres in September 2017. Fires can be a healthy and necessary aspect of our ecosystem, when plant matter burns the ashes are returned into soil as nutrients. Therefore, our question was to see if there is a difference in the nutrient cycle of soil that has experienced a recent fire compared to soil that has not experienced a recent fire. We hypothesized that recent fires will increase the amount of nutrients to soil, so a natural process like decomposition will occur at a faster rate than in an area that has not experienced a recent fire. To keep our data consistent, we used 15 potatoes that were cut in half, each half going to either fire or non-fire chaparral. Within the BCCER, 15 half potatoes were placed in 3 rows of 5 in an area that has not experienced a recent fire, this will be the controlled experiment testing of the nutrient cycle. The second set of 15 half potatoes was placed with identical arrangement in an area that has experienced recent fire. First, each potato was weighed and then, was reweighed within their chaparral every 5 days for a total of 15 days. Using a 95% confidence interval, we obtained a p-value of 0.02 (.02 < .05), therefore we can conclude there is significant difference in the nutrient cycle within both chaparrals with the recent fire chaparral having a faster degradation rate.  

Germination of Yellow Lupine (Lupinus luteus) Seeds Continues after Exposure to Cold Conditions
Ryan Dearborn, Josh Sandige, Ryan Rowe, Austin Miller,,, 
Seed germination depends on a variety of factors, one of the most important being temperature. During the winter, cold periods can be interrupted by days or even weeks of warmth uncharacteristic to the season, potentially triggering the seed’s germination. This premature germination can lead to large scale die offs of certain plants, including grasses and flowers. Our experiment evaluated the extent to which a Yellow Lupine (Lupinus luteus) seed can withstand a warm period before germinating prematurely, to determine the severity of these warm periods and how they effect flowering plants. Our experiment consisted of 100 seeds placed between wet paper towels in a freezer, in which we would keep the seeds cold, thus preventing germination, and then expose to warmth for a set amount of time. After this period of warmth, the seeds were brought back into the cold, and germination was evaluated on a percent scale of partial to full germination. Our hypothesis was that it would take 7 days for the seeds to germinate in a warm period, half of the projected germination rate since the seed had time to soak up water between the towels for several days before hand. The seeds germinated within 4-5 days, even in the treatments that were only exposed to 2-3 days of warmth.  This indicates that Lupine and similar flowers can germinate succeeding a warm period that is only a fraction of the average germination time.  This makes them more susceptible to premature germination than may have been previously thought.

Observing the Effects of Acid Rain on Seedling Germination
Sastina Thammavongsa
Germination of seeds is relied on by farmers throughout the world. The effects of acid rain can change their entire livelihood. Varying pH levels have different effects on seeds and will help to determine if the crop will be viable. The effects of pH on tomato seeds were observed closely at 4 different pH levels. To observe the effects of acid rain, the 4 experimental pH’s were 2, 4, 5, and 7. The number of days for germination varied between the different pH levels. The number of germinating seeds was greatly reduced when the pH was extremely low and may give insight to the future of agriculture and vegetation around the world. 

Variation in seasonal temperature and precipitation does not affect growth of Arctostaphylos manzanita in 2016 and 2017
Whitney Branham, KC Sicheneder, Alan Mata,,
Plant communities within Mediterranean environments experience significant variability in climate. As a result, organisms must be well adapted to extremes such as long, hot summers with very little moisture as well as very cold and wet winters. We studied the Common Manzanita, Arctostaphylos manzanita, in the Manzanita Grove at Big Chico Ecological Reserve (BCCER). Branch measurements were taken from 160 different branches for both 2016 and 2017 by analyzing stem lengths. Temperature and amount of precipitation were collected from the US Climate Data website for Chico for each month in the growing season from January-May for both 2016 and 2017 and the average was taken for each year. T-tests were utilized to determine if significant variation in temperature and precipitation affect growth. Overall, variation in temperature and precipitation didn’t affect average growth in 2016 and 2017. Thus, other environmental factors such as aspect within the hillside, nutrient availability, or access to sunlight could be playing a more significant role in determining growth rates.

BIOL 409 Molecular Biology
Kristopher Blee,

BIOL 409, Juan Araujo-Sarinana,

Investigation of the gene AT2G33420 expressed in Arabidopsis thaliana
Manpreet Mann, Amandeep Dhillon, Theodore Lee , , 
Arabidopsis thaliana is a very popular organism in plant biology due to its genome sequence that has helped researchers discover a variety of gene functions. In Arabidopsis thaliana, 73 genes coding for class III peroxidase proteins have been identified. To determine the function of the peroxidase gene AT2G33420, the location of the expressed protein has to be determined. It is hypothesized that the protein is expressed in the root tissues of the plant Arabidopsis thaliana. An experiment was conducted by first tagging the gene with yellow fluorescent protein (YFP) using the Tri-Template PCR. Then the tagged gene was cloned and subcloned into plant transformation vectors. Then the Isolate binary vector subclones were transformed with Agrobacteriumtumefaciens and pipetted onto Arabidopsis thaliana flowers. The seeds from the Arabidopsis plant that were coated with agro, were then harvested, plated and allowed to germinate to develop roots. Microscopes were used to see the fluorescence in the lateral root caps of the germinated seeds. From the fluorescence light intensity obtained, it can conclude that the protein coded by the gene AT2G33420 is located in the roots.

Exploring Arabidopsis thaliana peroxidase gene expression using fluorescence
Alexis Carual, Maci Meyers,
While 73 genes exist in Arabidopsis thaliana, the class III peroxidase multigene family is not very well known. Because so many isoforms exist within one family, it is difficult to know what each gene is responsible for in plant development.  With the use of bioinformatics, we were able to narrow down a gene of interest, AT2G33420, which expressed mRNA abundance in root tips during early development of Arabidopsis thaliana, to be localized outside of the cell and in vesicular pathways. To test this, a YFP fluorescent tag was inserted into the gene sequence and transformed into Agrobacterium. The Agrobacteria was then taken and introduced to Arabidopsis thaliana through its flowers and left to grow. Seeds were collected from these plants and plated to allow roots to develop. Fluorescence was observed in the root tips through microscopy. Based on the data collected, there is indication of fluorescence in the root elongation zone of Arabidopsis thaliana, with the tagged protein of interest being expressed in the cell wall. Knowledge of where the peroxidase protein AT2G33420 is located can help narrow down what this gene contributes to the early stages of plant development.

Plant Cell Location of Peroxidase Protein, Gene AT2G33420, in Arabidopsis thaliana based on signal peptide and C-terminus Amino Acid Sequence.
Derrald Buis, Jessica Miccio ,
Lignin, an important structural component in plant vascular tissue, is found in high concentration in plant cell walls. In the paper industry, high lignin concentration is associated with weakening paper quality. Removing lignin requires a substantial amount of time and energy. Enzymes, peroxidase (POX) and laccase, are believed to produce lignin. The focus of the study is to determine the protein location of POX gene AT2G33420 within the plant cell of Arabidopsis thaliana.  Based on the von Heijne signal peptide and the C-terminal amino acid sequence, protein location is hypothesized to be in the plant cell wall. The POX gene was tagged with Yellow Fluorescent Protein (YFP) using PCR, sub cloned into a plasmid vector, and then transformed into Agrobacteriumtumefaciens. A. tumefaciens was inserted into A. thaliana through floral inoculation. Using fluorescent microscopy, protein location of POX gene AT2G33420 tagged with YFP, was confirmed to be in the plant cell wall of root tips. Determining POX protein location provides evidence that POX may play a role in lignification of the plant cell wall. The significance of finding the location of POX protein could help in the future by repressing POX expression in plants to see if there is a decrease in lignin production. 

Locating Potential Lignin Affecters in Arabidopsis thaliana
Gian Gomez, Alex Gonzalez,
Lignin is a polymer deposited in the cell walls of many plants, significantly affecting their rigidity. Genes targeting their proteins toward the cell wall are typically responsible for lignin formation. Through analysis of a gene’s amino acid (AA) sequence one can determine where in the cell it will target its proteins. An AA-sequence containing a non-hydrophobic C-terminus is predicted to direct its coded proteins to the cell wall or outside of the cell. By tagging peroxidase gene At2G33420 – a gene highly expressed in the root tips of Arabidopsis thaliana – with Yellow Fluorescent Protein (YFP), one can determine the cellular location of this gene’s activity. Polymerase chain reaction was utilized to construct a reporter gene containing YFP, which intensifies the amount of fluorescent light observed through microscopy. The gene construct underwent subsequent processes of cloning and sub-cloning into plasmid and plant transformation vectors. Escherichia coli was used as a host to grow and amplify the construct. This construct was then transformed into a bacterium capable of introducing the reporter gene by floral inoculation of A. thaliana. The resultant seeds contained the constructed reporter gene with YFP and their root tips were analyzed by inverted microscopy. The fluorescence in and around the cell walls of the experimental specimens was of a higher intensity than the fluorescence observed in the root tips of control seeds. The increased fluorescence indicates gene At2G33420, now containing the YFP construct, directs its proteins toward the cell wall and may affect the formation of lignin in A. thaliana.

Arabidopsis thaliana Peroxidase Gene AT4G33420 Expression and Protein Subcellular Location Investigation
Jennifer Morales Mazariegos, Emily Poitan Mendez,
Arabidopsis thaliana is a model organism, containing 73 class III secretory peroxidases, many of which serve multifunctional purposes through the plant’s physiology. Of the seventy-three, peroxidase gene AT4G33420 was used in an investigation of protein targeting. Hypotheses of the location of the gene’s expressed protein, which is dependent on the amino acid sequence and cleavage sites was made using Bioinformatics. It was hypothesized that protein expressed by AT4G33420 gene would be located in the elongation zone of the Arabidopsis root tip, more specifically, subcellular localization of the protein would be in cell walls. In order to preserve the native promoter sequencing, a procedure was developed that introduced a YFP gene tag into a selected site within our target gene. The YFP gene would be used to assess protein location using fluorescence microscopy. Results displayed significant fluorescence in the cell walls of the experimental plant tissue which supports what was hypothesized that the protein will be secreted to the cell wall. This research can be used for future work in the investigation of lignin formation in plants.

Peroxidase (AT2G33420) Location in Arabidopsis thailana
Kimberly Macias, Stephanie Barajas ,
Peroxidase proteins are involved in the lignification of cells in the xylem root tip. We used bioinformatics to choose gene AT2G33420 which codes for a peroxidase protein that it is highly expressed in the root tip.  We hypothesize the peroxidase protein will fuse to the plasma membrane and will be targeted into the cell wall. Our research was conducted by first isolating Arabidopsisthaliana DNA and used PCR to insert the Yellow Fluorescent Protein into the coding sequence of AT2G33420. We followed this by recombining peroxidase AT2G33420 and cloning it into a plasmid. We proceeded with the transformation of Agrobacterium and inoculated Arabidopsis thaliana flowers to harvest the seeds. We visualized the protein using microscopy and were able to see the gene being localized at the cell wall.

A Transgenic Investigation into the Peroxidase Gene AT2G33420 in Arabidopsis thaliana
Payton Hurley, Sukhwinder Sarai,
Peroxidases within the Arabidopsis plants serve many functions which include plant defense and are thought to be involved in the polymerization of lignin. Being able to track where these peroxidase proteins end up, allows for determination of their function. When investigating genes with the Arabidopsis plant our research was narrowed down to the gene AT2G33420. Using bioinformatics a hypothesis was made that this protein would be targeted in the cell wall, if the gene was successfully expressed. The gene was tagged with YFP using PCR then cloned into Agrobacterium tumefaciens. Inoculation of Arabidopsis flowers with the Agrobacterium plasmid cells led to the production of transgenic seeds, which then germinated. These seeds were then used in fluorescence microscopy to visualize the root tips under both bright field and YFP filters. Within our images, we were able to see the fluorescence of the YFP within the root tip and along the cell wall.

BIOL 409, Mandeep Grewal,

The Protein Coded by the Gene AT4G33420 of Arabidopsis thaliana is Targeted to the Cell Wall 
Daisy Avila, Miriam Ibarra, Korina Sigala,,
Class III peroxidase genes are involved in lignin formation. There are 73 class III peroxidase genes found in Arabidopsis thaliana. Predicting the location of a gene, allows for the determining of its subcellular mechanical function. If the protein that the gene, AT4G33420, encodes for follows the von Heijne rule, it does not contain a KDEL signal and whose last three amino acids are not all hydrophobic then it will be secreted to the outside of the cell. Using bioinformatics, a gene of interest was selected, and primers were designed in order to tag our gene with the yellow fluorescence protein (YFP), mRNA analysis via genevestigator suggested that protein encoded for by the gene AT4G33420 is in high accumulation in the steel area. The reporter construct was cloned in to pDONR, and subcloned into pMN20GW which lead to the transformation of agrobacterium. Agrobacterium was then used to transform Arabidopsis thaliana. From the fluorescence microscopy images, in the transformed A. thaliana roots there was evidence of fluorescence throughout the root however, greater intensity is noted at the cell wall area of the stele cells. This could be an indication of the presence of peroxidase AT4G33420. From the collected data, it is indicated that the hypothesis is supported. In the future, the KDEL signal can be introduced to the retention site which could potentially lead to determining the destination of the expressed protein.

The Key to Softer Toilet Paper: Finding the “Roll” of the Class III Peroxidase Coded for by Gene AT4G33420 within Cell Walls of Arabidopsis thaliana
Brad Underwood, Simone Burdick, Dara Stroup,,
Lignin is a complex organic polymer deposited in the cell walls of many plants, making them rigid and woody.  The 73 class III secretory peroxidases in the Arabidopsis thaliana plant species are known to play a role in lignin formation and plant detoxification. We chose the peroxidase coding gene AT4G33420 using the online sources PSORT and Genevestigator. We hypothesized that the protein will be located in the cell walls of the plant’s root tip due to the high abundance of mRNA in the steele. The absence of a KDEL motif at the C-terminus, the hydrophilicity of the last three amino acids and the presence of a signal peptide at the N-terminus means that the protein will be secreted through the biosecretory pathway to the cell wall, and therefore may play a role in lignin formation.  We tagged the gene AT4G33420 with YFP, inserted the reporter construct into Arabidopsis thaliana gametes and analyzed the seedlings using fluorescence microscopy.  We observed fluorescence within the cell walls of the transformed seedling’s root tips, suggesting that the peroxidase AT4G33420 may play a role in lignin formation.  To test this hypothesis further, we could knock down expression of the genes for future plant generations, to see if lignin formation subsides.  Finding the genes that code for lignin formation enzymes, and knocking down expression of those genes in future plant generations could simplify the steps of the paper making processes and could also create a new, more efficient plant food source for livestock.

Class III Secretory Peroxidase AT4G33420 Presence in the Cell Wall and Stele of Transgenic Arabidopsis thaliana Plants
Gavin Monges, Whitney Branham, Jackie Sanchez,,
Molecular biology seeks to understand functions of enzymes. Among the most abundant of these enzymes are peroxidases. Genes that code for peroxidase enzymes encompasses a multigene family coding for 73 peroxidases. In Arabidopsis thaliana, peroxidase plays roles in cell wall modification, yet specific functions of individual enzymes remain unclear. This experiment attempts to elucidate the role of peroxidase 47, a class III secretory peroxidase present in Arabidopsis thaliana predominantly expressed early in development. Specifically, the design answers the question where expression will occur for a gene that codes for a peroxidase in both the cell and anatomically in the plant. Using Genevestigator to view mRNA accumulation of peroxidase III gene, we selected a gene for a protein likely expressed in early growth of the stele of Arabidopsis thaliana. Bioinformatics data determined that the protein will be excreted to the cell wall due to a signal peptide sequence, absence of KDEL sequence, and hydrophilic nature of the c-terminal amino acids that direct secretion down biosecretory pathway. The hypothesis is two-fold, peroxidase III protein will be expressed in the stele of Arabidopsis thaliana and the protein will be excreted to the cell wall. This hypothesis was tested by transforming Agrobacterium tumefaciens bacterium with a peroxidase gene fragment tagged with YFP sequence. Floral inoculation of Arabidopsis thaliana produced transgenic seeds for visualization of the tagged secreted protein via fluorescence microscopy. This experiment provides support for the mechanism of peroxidase 47 as the tagged protein was observed in the stele of the root tip.

Class lll Secretory Peroxidase AT2G22420 are Targeted to the Cell Wall and Support Lignification of the Arabidopsis thaliana
Hadja Stringfellow, Taryn Mullen,
Class lll secretory peroxidases are a family of plant-specific oxidoreductase that are widely thought to support the lignification in plant cell walls. Arabidopsis thaliana contains seventy-three class lll secretory peroxidase genes, all of which having various activity levels and functions throughout the plant. In our research, peroxidase gene 17, AT2G22420, was used to gain more information on protein targeting. Bioinformatic tools were used to create hypotheses of the location of this gene's expressed protein. We were able to hypothesize that when the peroxidase gene is expressed, the targeted protein would be found in the xylem of root, and more specifically, the sub-cellular localization would be in the vacuole. Using PSORT, we were able to determine that the native N-terminus was conserved in order to preserve signal peptide sequencing that targets insertion of the protein to the ER. In addition to this, the hydrophobic C-terminus segment was conserved and lacked KDEL sequencing which resulted in protein targeting to the cell wall. To test our hypothesis, we tagged the peroxidase gene with YFP sequence which will be able to visualize with fluorescence microscopy. Arabidopsis was then transformed using agrobacterium and after observing the whole plant, fluorescence was observed supporting our hypothesis that our protein was targeted to the cell wall. We can use these results of the sub-cellular location to further investigate the functions of our peroxidase lll gene not limited to detoxification, lignification, defense against pathogens, catabolism, and root elongation within the plant.

Subcellular Location of Class III Secretory Peroxidase AT2G22420 Expressed in the Cell Wall through the Transformation of Arabidopsis thaliana
Jessica Malanco Ayala , Judith Barajas, Monica Furubotten,, 
Class III peroxidases are secretory peroxidase enzymes found in plant cells that are responsible for catalyzing lignin formation. Lignin assists in providing structure and pathogenic defense in plants. The aim of this experiment was to identify the subcellular location in which the peroxidase AT2G22420 of Arabidopsis thaliana would be expressed. We used Genevestigator to identify where mRNA was most abundant, and chose a gene with a high rate of transcription. AT2G22420 was investigated through  PSORT a bioinformatic tool which revealed that it had no KDEL and the three terminal amino acids were hydrophilic, indicating it would leave the endoplasmic reticulum, travel through the golgi and exit through exocytosis to its final location in the cell wall. Our hypothesis was tested by tagging a coding sequence and tracing it through fluorescent microscopy in a transformed Arabidopsisplant. This was done by cloning the selected gene, tagging it with YFP, and transforming the amplified fragment into the plant through the plant pathogen Agrobacterium. Microscopy techniques were utilized in order to visualize subcellular gene expression within the cell wall. After analyzing a sample from Arabidopsis root tips through microscopy, it was found that the protein was expressed in the cell wall, which supported our hypothesis. After knowing the plant specific location of the protein, further experiments could be performed to test the function of this peroxidase in the cell wall. 

Peroxidase 17 (AT2G22420) of Arabidopsis thaliana localized in the cell wall
Jackelin Villalobos, Rana Yousaf, Austin Testa,,
Class III secretory peroxidases are plant oxidoreductases that support lignification in plants. Arabidopsis thaliana contains 73 different peroxidase enzymes that are all part of the same gene family. The peroxidase chosen was PER17 since it was highly expressed in the root tip. Our question presented was; where is the protein made by PER17 expressed intracellularly? It was predicted that the protein made by PER17 would be expressed in the xylem of the root, specifically in the vacuole. Through PSORT it was discovered that the C-terminus contained amino acids that were mostly hydrophobic and no KDEL meaning that the protein made by the chosen peroxidase enzyme would be targeted to the vacuole. It was also found that the N-terminus helped preserve the signal peptide sequencing, meaning it would be allowed to enter the ER and eventually be secreted. Through several amplification processes, we were able to tag the peroxidase with YFP and clone it into pDONR221. This was also subcloned into pMN20 and used to transform agrobacterium. The Agrobacterium was then used to transform Arabidopsis thaliana flowers in order to obtain transformed seeds. Fluorescence was observed in the cell wall which supported our hypothesis that this protein created by the chosen enzyme would be located in the cell wall. Further research could however be done to investigate the function of this enzyme in more than just lignification of the plant.

Arabidopsis thaliana class III Peroxidase AT2G22420 Is Secreted into the Cell Wall
Kelsey Hanson, Dam Diaz, Allie Moore,, 
Class III peroxidase enzymes constitute a diverse and multigene family with a variety of functions at various locations. There are three classes of peroxidase enzymes, that play significant roles in detoxification or lignification. Arabidopsis thaliana has 73 class IIl secretory peroxidases, with their function dependent on their location within the cell. The purpose of this experiment was to locate a single peroxidase protein inside of a plant cell. To do so, we used bioinformatics to identify mRNA accumulation throughout different areas of the Arabidopsis thaliana plant and chose the peroxidase AT2G22420 sequence. We hypothesized that AT2G22420 would be secreted into the cell wall due to the hydrophilic C-terminus protein and lack of a KDEL sequence. Using the peroxidase sequence and our retained promoter of the Arabidopsis thaliana plant as the independent variable, we had the ability to observe the location of the peroxidase protein which acted as the dependent variable. To test this, amplification of AT2G22420 with designed primers and YFP fragment were used to prepare for insertion into the plant. Sub-cloning with bacterial plasmids and antibiotic resistance positively selected for transformed Arabidopsis thaliana plants. The transformed bacterial plasmid containing the AT2G22420 sequence was used to inoculate the flowers of Arabidopsis thaliana yielding the desired transgenic plant. 

Arabidopsis thaliana Class III Secretory Peroxidase AT4G33420 is Secreted in the Cell Wall 
Kelsey Linden, Oscar Chavez, Justine Rios,,
Peroxidases are found in plant, fungi, bacteria and are members of a superfamily that consist of 3 major classes. Class III secretory peroxidases catalyze the formation of lignin in plants. Our goal was to determine the location of a Class III secretory peroxidase, AT4G33420, in Arabidopsis thaliana. To create genetically modified A. thaliana plants, we used bioinformatic tools such as Genevestigator and PSORT.  PSORT, showed the pathway of which the protein would travel throughout the cell by showing us the gene did not contain the motif KEDEL. Thus, it will not reside in the endoplasmic reticulum and instead will enter the secretory pathway. Since it has hydrophilic amino acid residue in the C-terminus it cannot be retained in the vacuole and instead it will be secreted out to the cell wall. Furthermore, using an mRNA detection tool in Genevestigator it identified the accumulation of mRNA in the elongation zone of the root. Our hypothesis is the protein will be secreted out to the cell wall and found in the elongation zone of the plant. In order to visually analyze our results, a yellow fluorescent protein (YFP) was inserted by designing primers and performing PCR. Analysis of roots were conducted through imaging of our Arabidopsis thaliana plant, where fluorescence was present in the elongation zone of the root. For future investigation we could manipulate this gene to overexpress it or knock it out to determine the phenotypic deviation from the wild type.

AT4G33420 Transformation of Arabidopsis by Floral Inoculation with A. tumefaciens in the Root Tip
Marvin Barrios Rodas, Eric Madrigal,
Class III secretory peroxidase genes are plant-specific oxidoreductase that have been known to show involvement in several physiological processes in Arabidopsis thaliana. PER 3 was chosen, using bioinformatics, in this experiment since it was greatly expressed in the root tip of the plant. This lead to the question; where is the protein that is made by PER 3 expressed inside the cells? With the help of PSORT, we were able to predict that the protein is expressed around the cell wall since it lacks the ER retention sequence KDEL and contains hydrophilic terminal amino acids. To prove this, we conducted PCR on primers we produced in lab and inserted a Yellow Fluorescence Protein (YFP) which tags our protein to be able to detect under a fluorescence microscope. Cloning of various plasmids such as pDONR and PMN20GW were completed to result in the production of Agrobacterium cells. The Agrobacterium cells contain the plasmid that was constructed molecularly and were then inoculated onto Arabidopsis thaliana leaves, using drip the method, to infect the plants’ chromosomes with the selected gene. After the inoculation, our protein was fluorescing in the cell wall and on top of the root tips of the plants.

Arabidopsis thaliana Class III Secretory Peroxidase AT4G21960 Expression and Localization
Nida Ejaz, Mikala Herr, and Madison Brandt,,
Peroxidases are enzymes that can be found in plants, animals, and bacteria and can be viewed as members of a large family consisting of 3 major classes. Class III comprises the secretory plant peroxidases, which are responsible for catalyzing lignin formation in plants; lignin is a hydrophobic polymer that lines cells such as xylem, and is important in providing structural support and pathogen defense in plants. In Arabidiopsis thaliana, there are 73 peroxidase genes. Genevestigator was used to select AT4G21960 (PER 42) peroxidase gene and determine its sub-cellular location in the cell. We hypothesize that the protein coded by peroxidase PER 42 is expressed in the cell wall of cells based on the signal peptide sequence such as the absence of KDEL sequence and hydrophilic amino acids on the C-terminus. To test this hypothesis, primers were designed to amplify the gene via PCR. Following PCR, homologous recombination was used to insert Peroxidase 42 DNA into the T-DNA region of the plasmid vector pBlee containing YFP gene and 3x FLAG.  The modified plasmid vector pBlee was then used to transform Agrobacteria and then infiltrate transformed Agrobacteria onto Nicotiana benthamiana leaves. Fluorescence microscopy was used to visualize N. benthamiana leaves to determine the location of fluorescent protein. Results showed significant fluorescence in the cytoplasm of the experimental plant tissue, in contrary to our prediction. For further research, we could attempt to transform the Peroxidase gene 42 into another plasmid and insert that into another plant species to see where the protein fluoresces. 

Gene AT4G33420 Located in the Apoplast of Roots in Arabidopsis thaliana
Oscar Kalfsbeek, Sang Pham, and Tracy Rojas,,
Plant class III peroxidase enzymes support lignin formation because they are plant specific oxidoreductase. The reaction occurs when the mono lignin strips off an electron from the peroxidase, and the electron that is stripped off could form a covalent bond. Thus, leading to lignin polymerization to occur in the cell wall. Peroxidase protein is hypothesized to be in the apoplast because peroxidase helps in the formation of lignin which is abundant in the apoplast. In Arabidopsis thaliana there is 73 peroxidases, and we chose the peroxidase gene AT4G33420 which we hypothesized would be secreted into the apoplast. We came to this conclusion based on the data provided by Genevestigator and PSORT. Genevestigator allowed us to select a peroxidase where mRNA was abundant in the roots, and we used PSORT to identify a potential subcellular location. PSORT gave us a signal cleavage peptide, no KDEL, and the last three amino acids. Therefore, the peroxidase protein would be located in the apoplast. To visually analyze our experimental results, we inserted a yellow fluorescent protein (YFP) sequence by designing primers and performing PCR on the gene AT4G33420. Then we performed a tri-template PCR to anneal the gene fragments. Analysis of the apoplast of roots was conducted by taking fluorescence pictures of Arabidopsis thaliana roots. The fluorescence was present in the cell wall; therefore, our hypothesis is supported. In the future, we could tag the gene to determine the retention time of the (ER).

Arabidopsis thaliana Class III Peroxidase AT2G22420 is located in the Cell Walls of Elongation Zone Cells
Victoria Coia, Austin Van Alstyne,
Peroxidase genes are known to take part in plant development including cell wall maintenance and detoxification. There is difficulty in determining the individual function of each peroxidase in Arabidopsis thaliana as previous studies have only looked into the function of in vitro development. The purpose of this research was to determine the location of peroxidase AT2G22420 in Arabidopsis and how it relates to its function in the plant. We hypothesize that peroxidase AT2G22420 will be found most abundantly in the elongation zone of the root tip using an mRNA accumulation heat-map from Genevestigator. We also hypothesized that the peroxidase AT2G22420 will be found in vacuoles determined by PSORT which showed us the cleavage site amino acids, terminal amino acids, and lack of KDEL. We conducted this research by tagging AT2G22420 with yellow fluorescent protein (YFP) and then transforming the Arabidopsis gametes using Agrobacterium. Using fluorescence microscopy, we were able to identify the tagged protein in the elongation zone of the root tip and the cell walls within the root. AT2G22420 was where we predicted it to be in the plant root, however we did not expect it to be found in the cell walls. Based on the location of the protein, the expected function of peroxidase AT2G22420 is in lignin formation associated with cell wall maintenance.

Location of Peroxidase AT2G22420 within the cell walls of Arabidopsis thaliana
Zach Scott, Dominic Valeriote, Kyle Colombi,,
The Peroxidase gene family (PER) has a wide variety of functions in all land plants and specifically within Arabidopsis thaliana including pathogen defense, lignification, and detoxification. Due to the many functions in this large peroxidase family, it is difficult to assign a specific role to each Class III peroxidase. Using GENEVESTIGATOR, the peroxidase gene AT2G22420 was chosen and hypothesized to be targeted to the root tip of the plant. Using PSORT, the subcellular location was hypothesized to be located within the cell wall because AT2G22420 lacks the ER retention sequence KDEL and contains hydrophilic terminal amino acids. To test this hypothesis, the gene was tagged with yellow fluorescent protein sequence (YFP) using Tri-Template PCR. The fluorescently tagged gene was then cloned into the pDONR221 plasmid and finally sub cloned into a second plasmid, pMN20GW. pMN20GW was used to transform Agrobacterium tumefaciens, which was then pipetted onto Arabidopsis thaliana flowers for the transformation of the developing single cell egg / embryo to create transgenic seeds. These seeds were then harvested, plated, and allowed to germinate. Using fluorescence microscopy thus far, our hypothesis seems to be supported by the cell specific location of the peroxidase being located within the cell wall of the germinated seeds. Further implications of these results could include areas involving the production of lignin such as lessening cost of the creation of lignin based products such as paper.

BIOL 412 Bacterial Physiology
Emily Fleming,

In silico analysis of Leptothrix cholodnii Lcho_0478 Localization and Function
Ashley Case
Located in freshwater microbial iron seeps, Leptrothrix cholondii SP-6 is a heterotrophic, sheath-forming betaproteobacterium that oxidizes both iron and magnesium. The mechanism by which these sheathes are formed is under research as well as the proteins that participate in its formation. In this study, we examine the function of the protein Lcho_0478 and find that it codes for a transporter activator protein, indicating it could participate in sheath formation. To do this study we utilized a variety of bioinformatics resources. 

Lost and Found Lcho_1854 in Leptotrix cholodnii
Ashley Hernandez 
Leptothrix cholodnii SP-6 belongs to the betaproteobacterium family, characterized by their ability to generate tubular sheath deposited with oxidized manganese or iron. Most Leptothrix spp are located in oligotrophic iron-rich water environments. Many studies have illustrated the composition of the sheath including manganese and iron metals and bacterial exopolymers. It’s clear that bacterial secretion plays a vital role in the sheath formation yet the mechanisms involved in the sheath development is unclear. In this study, we aim to determine whether the gene Lcho_231 is associated with the sheath formation for L. cholodnii. We believe that the putative gene with the locus tag, Lcho_2341 is related to bacterial sheath formation for L. cholodnii. We show that Leptothrix cholodnii SP-6 gene with a locus tag Lcho_2341 codes for a glycosyl transferase enzyme. Our data suggests that glycosyl transferase, a gene product of Lcho_2341 is involved in the biosynthesis of teichoic acid, an important putative pathway for cell envelope formation for Gram positive bacteria, even though L. cholodnii is a Gram Negative. 

Characterization of Lcho_2341 for Leptothrix cholodnii SP-6
Grace Prator 
Leptothrix cholodnii SP-6 belongs to the betaproteobacterium family, characterized by their ability to generate tubular sheath deposited with oxidized manganese or iron. Most Leptothrix spp are located in oligotrophic iron-rich water environments. Many studies have illustrated the composition of the sheath including manganese and iron metals and bacterial exopolymers. It’s clear that bacterial secretion plays a vital role in the sheath formation yet the mechanisms involved in the sheath development is unclear. In this study, we aim to determine whether the gene Lcho_231 is associated with the sheath formation for L. cholodnii. We believe that the putative gene with the locus tag, Lcho_2341 is related to bacterial sheath formation for L. cholodnii. We show that Leptothrix cholodnii SP-6 gene with a locus tag Lcho_2341 codes for a glycosyl transferase enzyme. Our data suggests that glycosyl transferase, a gene product of Lcho_2341 is involved in the biosynthesis of teichoic acid, an important putative pathway for cell envelope formation for Gram positive bacteria, even though L. cholodnii is a Gram Negative. 

Understanding the Roadblocks of Leptothrix cholodnii
John Machado, Kerrick Swangler
Leptothrix cholodnii is an Iron oxidizing bacterium that actively creates sheaths around the cells and lives within them. In the microbial genetics class (BIOL 472) a sheath and motility mutant was generated, however the genes affected by the transposon mutagenesis used in BIOL 472 were not fully understood. We expand upon one protein sequence that was found in L. choldnii’sgenome: Lcho_0658. The protein Lcho_0658 is a member of LC7/ Roadblock domain which is primarily responsible for the regulation of flagellar movement. The sequence interactions between the LC7 domain, which 0658 is a part of, and other neighboring proteins within the membrane of L. cholodnii provide evidence that supports flagellar regulation. One of the strongest relationships that LC7 has is to Phosphate/ Phosphonate ABC transporter periplasmic protein. This relationship establishes that this protein works in tandem with phosphate transporter systems which cooperate and in turn regulate the movement of flagellar systems. The LC7 protein domain is also similar to that of dynein; a protein in eukaryotes that responsible for regulating motor components of a cell. In both flagellar movement and cilia movement, this protein can be seen in the membrane regulating the movements independent of each other. In terms of L. cholodnii, the related protein 0658 is responsible for movement in the extracellular environment while also being responsible for movement within the sheaths formed by the bacteria.

Leptothrix cholodnii SP-6: Type II Secretion System of the Gene Lcho_0549
Lyndsey K. Corral
Leptothrix cholodnii is a sheathed, metal oxidizing bacteria that can generate a sheath or tube of iron and then grow inside of a tube. Leptothrix cholodnii has its genome sequenced and can be used to look at the putative pathways that are involved in the cell envelope formation in bacteria. By using bioinformatics, the gene locus tag of Lcho_0549 was investigated by using different online databases to reveal information such as alignments, phylogenetic trees, and the network and relationship to other genes. The gene of interest for this experiment, Lcho_0549, was found to be a type II secretion system (T2SS) by using these online databases. One way this was discovered was by looking at the genes protein families (pfam). This revealed the T2SS and also showed how the T2SS is closely related to the systems that assemble type IV pili on the cells surface. T2SS are known to be very complex and consist of many different proteins. By using the online database Uniprot, an image of gene Lcho_0549 was made by showing protein-protein interaction. This protein-protein interacting showed how there are 11 nodes which are the proteins, and 33 edges which are the interactions between the nodes, displaying the complexity of T2SS. The Uniprot database also revealed functional enrichments of the network of proteins. This showed that the KEGG pathway being a bacterial secretion system (pathway ID 03070) and concurred with earlier results of pfam of a T2SS. This shows how protein secretion systems are a way that Leptothrix cholodnii is able move proteins across its membrane. 

The study of type IV pilin secretin protein in Leptothrix cholodnii
Mercedes Angara
The protein, locus tag Lcho_3403, is involved in cell sheath formation. Bioinformatics are used to analyze the location and putative function of the protein. The location and putative function of the type IV pilus protein might be involved with sheath formation in Leptothrix cholodnii.

Unsheathing the function of type IV pilus in Leptothrix cholodnii
Melissa French
Leptothrix cholodnii SP-6 are known to produce an organic microtubule sheath in which it is the site of metal oxidation that leads to mineralization of the sheath. The production of this sheath does not appear to be essential for the survival of the organism. A sheathless variant of SP-6 was generated from another lab by multiple passes in a liquid rich media and it has been seen that sheath production does not revert which indicates that sheath production is more than likely chromosomal. With the knowledge of sheath production being chromosomal, bioinformatics can be used to help identify a chromosomal gene that plays a role in sheath production. To identify the function of Lcho_2870, bioinformatics was used to identify where the gene was located in the L. cholodnii genome, what the nucleotide sequence is and the amino acid sequence. With the amino acid sequence, the function of the gene was determined to be a type IV pilus biogenesis/stability protein PilW. With the use of bioinformatics, a network of the associated genes was created to understand what the functional partners around the gene Lcho_2870 do and how they are associated with the function of the gene. The functional partners that are associated with Lcho_2870 have various pilus functions, two of the functions are various assembly proteins and secretion. With the knowledge on what the function of the gene Lcho_2870 is, this can help further understand if the type IV pilus biogenesis/stability protein PilW plays a role in sheath production in SP-6.

Rhomboid Protease in Leptothrix cholodnii SP-6 involvement in Sheath Formation
Miriam Ibarra
Leptothrix cholodnii are a part of a group of sheath forming bacteria which are largely found in swamps, iron seeps and springs that are iron and manganese rich environments. L. cholodnii contain rhomboid proteases that are serine proteases that catalyze the hydrolysis of peptide bonds. It is hypothesized that rhomboid protease in sheath forming bacteria are involved in sheath formation. Many of the proteins associated with rhomboid protease in L. cholodnii appear to be involved in the formation or folding of proteins. A neighbor-joining tree was design and it appeared bacteria were clustering together depending on their ability to form sheaths or not. Gene neighbors for rhomboid protease in sheath forming bacteria appeared to share more similarities to one another than compared to those of non-sheath forming bacteria. This may suggest a different evolutionary history for rhomboid proteases in sheath forming versus non-sheath forming bacteria. To determine if rhomboid proteases do in fact differ in function between these two groups the associated proteins to these proteases in sheath forming and non-sheath forming bacteria need to be explored.

Localization and Characterization of Lcho_4331 Protein in Leptothrix cholodnii
Max Lorey
Leptothrix is a genus of Gram-negative bacteria in the class Betaproteobacteria, whose energy metabolism is strictly aerobic. Leptothrix cholodnii SP-6 is the only species with the ability to possess sheath formation under laboratory conditions. Sheath’s form from filaments grown from swarmer cells produced by Lepthothrix bacteria. The purpose of the experiment is to determine the structure and function Lcho_4331 protein and if its function is involved in sheath formation. A series of bioinformatic tests were run with the nucleotide sequence of Lcho_4331 protein and the results concluded that Lcho_4331 is a methyl-accepting protein (MCP). MCP’s are sensor proteins located in the membrane and their general function is the transport of specific substances across the membrane. MCPs allow bacteria to detect concentrations of molecules in the extracellular matrix so that the bacteria may move or tumble towards the source. According to RCSB the signal transduction regulates the activity of associated kinases, altering the behavior of the flagellar motor and hence cell motility. Signaling is in turn modulated by selective methylation and demethylation of specific glutamate and glutamine residues in an adaptation subdomain. This experiment has shown that Lcho_4331 has no known functional relationship with sheath formation in Leptothrix cholodnii SP-6.

Role of Leptothrix cholodnii SP-6 Lcho_0670 gene
Rocio Clara
Leptothrix cholodnii is an aerobic, sheath forming, filamentous bacteria, species that oxidize Mn2+ and Fe2+ and are usually found in oligotrophic, slowly running, iron- and manganese-rich water (1). L. cholodnii SP-6 generate a sheath or tube of iron and grow inside the tube as a means of movement. In Fall 2018 semester, the Microbial Genetics class at CSU Chico isolated sheath and motility mutants of L. cholodnii SP-6, however were unable to determine the genes were targeted and mutated. Our purpose was to follow up with the isolated mutants in order to determine the involvement of the altered genes in cell envelope structure and motility.  The BIOL 472 class identified the targeted genes in the L. cholodnii SP-6 mutants and our class individually analyzed their role via bioinformatics. The Lcho_0670 gene, which is the gene I was assigned, codes for an integral membrane protein, MviN, putative peptidoglycan lipid II flippase. This protein is essential in the peptidoglycan synthesis pathway as it is responsible for transporting the lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane. After a series of complex steps, these precursors ultimately polymerize into mature peptidoglycan thus composing the cell wall.

Iron Shells of Leptothrix cholodnii
Sarah Brown
Leptothrix cholodnii SP-6, be found in aquatic environments that is rich in iron and manganese. It is known as a sheath forming bacteria, with filamentous attachments. The bacteria form thick mats by oxidation of either iron or manganese. These mats can cause clogged pipes, especially when they are thriving in waste water treatment plants. This is a unique trait for sheathed bacteria. In order to find out more about Leptothrix cholodnii SP-6, bioinformatics was done on the protein LCHO_0476. L cholodnii’s protein LCHO_0476 is, 4-hydroxy-tetrahydrodipiocolate reductase, which is known for a catalyzing step in the lysine biosynthesis. Picolinate is a natural chelator. A chelator bonds other ions and molecules to metal ions. We hypothesize that picolinate could play a role in the adherence of iron molecules to the cell’s sheath. To further test this protein within the genome of L. cholodnii, metabolic pathway analysis is suggested. We can do this by radio labeling metabolites to figure out where in the cell 4-hydroxy-tetrahydrodipiocolate reductase is located. We would also suggest fractionation of the protein. 

Beneath the sheath: Lcho_0550's role in Leptothrix cholodnii SP-6 sheath formation 
Sophia Phillips
Leptothrix cholodnii SP-6 is a sheathed metal-oxidizing bacteria commonly found in swamps, springs, and other iron and manganese rich environments. Previous studies have suggested a relationship between cellular excretion and sheath production. Determining the genes responsible for sheath production in Leptothrix cholodnii could be vital in developing a sheath production model. Lcho_0550 is a gene isolated from a sheath and motility mutant Leptothrix cholodnii strain obtained by the Chico State Bacterial genetics class. I hypothesize Lcho_0550 is involved in Leptothrix cholodnii sheath formation. To test this hypothesis, I used a series of bioinformatics tools to determine Lcho_0550's location, relationship to other proteins, and ultimately, it's involvement in Leptothrix cholodnii SP-6 sheath formation. IMG determined Lcho_0550 is a Type IV_A pilus. Type IV_A pilus are powered by ATPase PilB and are essential for the formation of type II secretory pathways in gram negative bacteria. Type II secretion systems assemble type IV pilus, which are located in posterior and anterior of cell, and provide motility to the cell through a series of contractions known as twitching.  Previous studies have linked motility and sheath production, suggesting motility is caused by the extrusion of sheath. Based on its involvement in cellular motility, I conclude that Lcho_0550 could be involved in Leptothrix cholodnii SP-6 sheath formation. To determine Lcho_0550's role in sheath formation I would delete the Lcho0550 gene and examine the phenotype.

Localization and Characterization of Lcho_2909 Protein in Leptothrix cholodnii
Xochith Herrera
Leptothrix cholodnii, a bacterium from the genus Leptothrix, is well known for its ability to oxidize metals such as Fe(II) and Mg(II) that is used in the formation of sheath formation and consequently releases energy. Locus tag Lcho_2909 is a protein found in Leptothrix species. The structure, function, localization, and role of Lcho_2909 in sheath formation is not well known. Further examination of these characteristics was done using Uniport, PSORTb, Joint Genome Institute (JDI), and NCBI. Results from a PSORTb examination suggested that the location was in transmembrane, with a low probability, therefore speculative.

Analysis of Leptothrix cholodnii Lcho_3646 Function and Location
Nancy Martinez
The Leptothrix cholodnii SP-6 species are associated with causing bulky biofilm and pipe clogging in wastewater treatments due to the formation of sheaths, which allows an attachment solid surface. The sheath matrix is known to be a hybrid of bacterial polymers, aquatic metals, and minerals. Because the sheath is extracellular, bacterial secretion is essential for sheath formation. Unfortunately, the mechanisms involved in sheath formation and synthesis are still unknown. In this study, I determined that Lcho_3646 indirectly participates in the sheath formation in Leptothrix species. To test this hypothesis, I used bioinformatics to determine peptide positions, tranmembrane helicies, and multiple sequence alignments using the ncbi, psort, phobius databases, for example. Lcho_3646 appears to be a small multidrug resistance transporter. These transporters catalyze multidrug efflux driven through the ATP synthase complex, suggesting that they are indirectly involved with sheath formation.

BIOL 434 Ornithology
Jay Bogiatto,

Habitat Utilization and Selection by Birds within a Foothill Woodland Ecotone, with notes on Avian and Vegetation Diversity
AJ Samra, Nikkie Werner, Katherine Tucker, and Brad Underwood,,,
We conducted an investigation of habitat utilization by birds within a low elevation, foothill woodland ecotone located in Upper Bidwell Park, Chico, Butte County, California.  Data were collected between April 13 and May 4, 2018, along 10 parallel 100 meter (m) transects, each 10 m apart, within our 1 ha study site.  The objectives of our study were (1) to generate plant species and foliage height profiles for our study site, (2) to calculate Shannon Diversity values (H’) for avian species, plant species, and foliage heights, and (3) to determine whether birds are randomly or selectively using those plant species and vegetation foliage height intervals present within our study area; our null hypothesis states that there are no differences in the proportion of plant species and foliage height intervals available within our study area and the utilization of these habitat components by birds. The most common avian species at our site include Acorn Woodpeckers, European Starlings, California Quail and Yellow-Rumped Warblers. Our results will be presented on our poster.

BIOL 476 General Virology
Troy Cline,

Isolation and characterization of bacteriophage from raw sewage
Maria Mercedes Angara, Madison Brandt, Dan Carlson, Ashley Case, Ashley Dearden, Nida Ejaz, Melissa French, Stephanie Keck, Caitlin Keene, Jessica Lopez, Nely Lopez, Glenda Macco, Jaya Nolan, Victoria Ramirez, Jesse Slaton, An Tolley, Dominic Valeriote, Brandon Van Curler-Clements
Bacteriophages are viruses that infect bacterial cells. They are among the most numerous and diverse forms of life. Bacteriophages have an impact on the biology of other microorganisms and thus have a significant effect on the environments around them. The goal of these experiments was to determine the characteristics of bacteriophage present in a sample of filter-sterilized raw sewage. Using six different bacterial hosts, we were able to isolate six different bacteriophages. We measured the host range of each phage and found that the phages had varying degrees of host-specificity, a feature that is common to most viruses. Additionally, we determined the heat stability of each phage and whether or not the phage contained a lipid envelope. While there were some similar characteristics between the phages that were isolated, a great amount of diversity was still observed, underscoring the extensive variety within the phage community.

Investigation of the structural and biochemical characteristics of bacteriophage isolated from sewage
Daisy Avila, Sarahy Barcenas-Silva, Jacob Bomagat, Laura Bowker, Casey Combs, Kelsey Dani, Megan Erickson, Ashley Hernandez, Andrew Kang, John Machado, Brandon Maddox, Sandra Martell, Nancy Martinez, Claudia Menchaca, Kaleigh O'Brien, Sophia Phillips, Grace Prator, Jennifer Salazar, Makenna Soudan, Rana Yousaf
Bacteriophages are viruses that are capable of infecting and replicating within bacterial cells and are abundant and diverse in nature. By studying bacteriophage, researchers have been able to better understand bacterial genetics, the evolution of microorganisms, and a vast range of applications such as antibacterial phage therapy. As a class, several different phages were isolated from filter-sterilized sewage collected from the Chico Water Pollution Control Plant. Several structural and phenotypic traits of the phages were characterized. After selection and isolation, each lab group was responsible for determining the concentration of phage in a lysate, the host range for each phage, the relative abilities of the bacteriophage to attach to a bacterium that serves as a host for productive replication and a non-productive host, and the temperature stability of the phage. These compiled results highlight and reflect on the diversity and principle concepts of virology. 

BIOL 482 Bioinformatics (for Biologists)

BIOL 482, Gordon Wolfe,

Investigation of transit peptides in Emiliania. huxleyi acyl lipid biosynthesis proteins
Donald Beck
After multiple rounds of endosymbiosis, many plastidial genes in eukaryotic phytoplankton have relocated to the nucleus. For the plastid proteins to localize to the plastid from the nucleus a signal peptide and transit peptide are required. The signal peptide allows entry of the protein into the secretion pathway. Enough is known about signal peptide sequences that programs have been developed to infer the signal peptide cleavage site based on amino acid sequence. Far less is known about the cleavage site between the transit peptide, responsible for targeting proteins to plastids after they enter the secretion pathway, and the functional or mature portion of the peptide. The goal of this work to discover patterns at the TP-MP cleavage site which can be used to create a program capable of searching for these cleavage sites and infer the destination of the mature protein. This study was done using protein data from Emiliania huxleyi (Ehux), a species of coccolithophore (haptophytes) abundant in oceans around the world. This work only examines those proteins involved in acyl lipid biosynthesis. BLASTp was used to compare Ehux sequences to close relatives and cyanobacterium Leptolyngbya to determine the conserved portion of the protein which is likely to be the mature peptide. Signalp 3.0 was used to find the signal peptide cleavage site. Sequences were aligned by hand. Weblogo was used to generate a logo of amino acid consensus in the sequence flanking hypothetical TP-MP cleavage sites.  Twelve of the thirteen examined proteins were determined to contain transit proteins.

Investigation of Biosynthesis, signaling, and transporter Peptide Proteins in Emiliania. huxleyi
Jessica Malanco Ayala, Kirstie Steiner,
Plastids are double-membrane organelles found in photosynthetic eukaryotes. Plastid proteins must be transferred from the nucleus across several membranes to get to their target location. Organisms that have developed through secondary endosymbiosis contain bipartitite targeting sequences upstream from the mature peptide. The N-terminal signal peptide (SP) transports the peptide through the endoplasmic reticulum to a secretion pathway, where it is then guided to its target location in the plastid by the transit peptide (TP). Both pre-peptides are removed by peptidases. Our goal was to deduce the TP pattern for the haptophyte Emiliania huxleyi.  We used BLASTp to find orthologous proteins in haptophytes and the cyanobacteria Leptolygbya. We narrowed these to include only those with reasonable signal and transmit peptide sequences (determined with SignalP 3.0 HMM to predict SP; SP+TP should be ~20-45 amino acids). We analyzed peptides involved in general biosynthesis, signaling, and transporters which were likely or potentially plastidial as determined by BLASTp searches. These proteins were color-coded by their side chain properties to visualize patterns. We then determined the mature peptide sequence for each organism by comparing peptide sequence to Leptolygbya. We will present our TP-mature peptide cleavage patterns compared with those known for diatoms (Huesgen et al. 2013).  
Citation: Huesgen PF et al. (2013) PLoS ONE 8(9): e74483. 

Plastidial Protein Targeting in the Marine Haptophyte Emiliania huxleyi
Jamison Sydnor
The marine unicellular haptophyte Emiliania huxleyi is one of the most abundant organisms on the planet. Its evolutionary history suggests multiple endosymbiosis events including the consumption and subsequent conversion of an ancestral photosynthetic eukaryote into a plastid. In this process, many of the genes encoding plastidial proteins shifted from a plastidial to nuclear origin. For proteins to reach their final plastid destination, a signal peptide (SP) is necessary to enter the secretory pathway, followed by a transit peptide (TP) to enter the plastid. In this study, I analyzed plastidial protein synthesis peptides in E. huxleyi. Initially SP cleavage sites were identified using SignalP 3.0. Using BLASTP, mature peptides were found by aligning multiple haptophyte sequences with mature peptides found in the cyanobacteria Leptolyngbya, lacking a SP and TP. Finally, transit peptides were deduced with manual alignment. I will present my results and also compare my findings to those inferred from diatoms, a functionally similar unicellular eukaryote. The purpose of this study is to find patterns in transit peptides with a plastid target to better understand the metabolism of this highly successful organism. 

Investigation of transit peptides in Emiliania huxleyi Translational and Nucleic Acids biosynthesis proteins
Oscar Chavez, Sandra Martell,
Organisms arising from a secondary endosymbiosis acquired plastids from a photosynthetic eukaryote, whos genes subsequently moved to the nucleus. These proteins are translated in the cytoplasm and transported across four membranes by a bi-partite targeting sequence which include a signal peptide (SP) and a transit peptide (TP).TP are known in diatoms however in an important hyptophyte, Emiliania huxleyi (EHUX), they are unknown. Therefore, our goal was to identify a TP motif of EHUX and compare them to those known for diatoms.In order to determine the TP cleavage sites, BLAST sequences against proteins that are responsible for DNA replication and translation were performed. BLASTp orthologs of diatoms were used to determine conserved regions between these sets of organisms. Protein sequences were color coded by amino acids residues composition for interpreting purposes and SignalP 3.0 HMM were used to predict the cleavage site of the SP. The cyanobacterium Leptolyngbya was used to determine the mature peptide (MP) start. This was used to align our sequences manually and determine a visual pattern that is present in the TP and MP cleavage site. Weblogo was then used to determine any conserved region between the TP and MP.

BIOL 482, David Keller,

Data mining the pancreas
Elizabeth Bianchini, Cody Rice,
PDX1 and NeuroD1 are transcription factors required for proper pancreas function and development. The goal of this project was to determine whether or not their co-regulated genes are also critical in insulin production and pancreas development/function. Using multiple bioinformatics tools, we compared datasets from PDX1 and NeuroD1 and genes associated with them. NeuroD1 vs. PDX1 appear to cluster within 750bp of each other and most reads also seem to cluster within 500bp of the 5’ promoter ends. Further analysis demonstrates that PDX1/NeuroD1 overlap with microRNA-4281, a non-coding region on chromosome 5 in humans. This microRNA appears to be involved in neural cell precursors. Additionally, there are multiple genes from the PDX1/NeuroD1 dataset that overlap with other datasets generated by researchers studying the effects of pregnancy on insulin production in islets and pancreatic development in neonates. In relationship to the effect of pregnancy on insulin production, the PDX1/NeuroD1 dataset has 575 overlapping genes with functions such as: structural development, process regulation, and protein binding. 

Analysis of potential NeuroD1 and PDX1 gene targets
Rebecca Belmonte, Ryan Nielsen,
The transcriptome of a cell is the set of genes that are actually expressed in that given cell. These genes are carefully regulated to control the development of different cell and organ types. Beta cells of the pancreas do not properly function in diabetes, causing a decrease in the amount of insulin secreted. Understanding how beta cells are regulated can help us to understand how to better treat diabetes. We decided to investigate which genes are potentially being co-regulated by Pdx1 and NeuroD1, hypothesizing that these co-regulated genes are crucial for proper pancreatic function. Pdx1 and NeuroD1 both bind to the insulin promoter, suggesting that these two proteins regulate multiple genes involved in pancreatic functionality. By identifying these regions we can identify ‘signal integration centers’. We found which genes were bound by both Pdx1 and NeuroD1 near a transcriptional start site. These genes were then compared to experimental data showing altered gene expression in response to inhibition of CDK2, a gene which regulates the secretory function in beta cells. We found a list of 306 genes which had its expression levels tested in response to CDK2 inhibition and interacted with both Pdx1 and NeuroD1 near a transcriptional start site. Interestingly, some of the genes that were down-regulated in response to decreased levels of CDK2 play a role in protein secretion, endocytosis, and membrane integrity. This supports the idea that CDK2 is crucial for insulin secretion and suggests that these genes may be important for insulin trafficking.

Genes Involved in Pancreatic β-Cell Biology are Targeted by PDX1 & NEUROD1 Proteins
Usman Rehman
PDX1 and NEUROD1 are transcription factors essential for pancreatic development. Previous experiments identified target genes bound by PDX1 and NEUROD1 proteins. We hypothesize that genes bound by both PDX1 and NEUROD1 proteins are critical for pancreatic β-cell function and development. We predict that PDX1 and NEUROD1 binding sites cluster as the base pair window increases. PDX1 and NEUROD1 binding data was analyzed in R Studio to determine read clustering. The UCSC Genome Browser, Biomart Ensembl, DAVID, ReviGO, and KEGG provided information on genes that PDX1 and NEUROD1 act upon; it was discovered that PDX1 and NEUROD1 reads cluster within 750 base pairs of each other and within 400-600 base pairs of the promoter. The UCSC Genome Browser converted mouse chromosomal data to human chromosomal data and noncoding genes associated with PDX1 and NEUROD1 were obtained. One dataset was selected from the NCBI GEO analyzer and the fold change for experimental and control treatments was calculated. ID’s from the two datasets were aligned and DAVID, ReviGO, and KEGG provided pathway maps for GLUT2, a target of both PDX1 and NEUROD1. Biological processes, cellular components, and molecular functions maps revealed that coding and non-coding genes associated with PDX1 and NEUROD1 are involved in pancreatic β-cell biology. Over-expression and knockdown of PDX1 and NEUROD1 would provide biological confirmation of in silico data. In silico, in vitro, and in vivo experiments will provide further understanding of a link between PDX1, NEUROD1, and pancreatic β-cell biology. 

Effects of PDX1 and NeuroD1 genes on diabetes 
To investigate the significance of Pdx1 and NeuroD1 genes and how they relate to diabetes. We used bioinformatics to gain new information on novel genes that are responsible for insulin production and pancreas development. We used this data to help us find new genes to focus our research on in hopes of discovering more about diabetes. We could discover important roles of Pdx1 and NeuroD1. We also considered SNP mutations that could be deleterious which could help us target important genes for further research. Which we can then hopefully target with new kinds of drugs in the future to help treat diabetes.

BIOL 484, Field Ecology
Amanda I Banet,

Spring Water Quality and Macroinvertebrate Diversity at the Big Chico Creek Ecological Reserve (BCCER)
Brandon Ertis, Leslie Esquivel, Lindsey Xayachack,,
Protecting the integrity of freshwater sources and preventing decreases in biodiversity is a nationwide concern as water is a basic necessity all organisms require for survival. Responsible management cannot be accomplished without understanding current conditions and how they may change over time. This study characterizes water quality and macroinvertebrate populations on the Big Chico Creek Ecological Reserve (BCCER). We analyzed temperature, salinity, pH, dissolved oxygen (DO), turbidity, nitrate, and phosphate at Big Chico Creek and three springs (Headquarters Spring, Horse Trough, and Saline Spring). Results were compared to prior data to evaluate if water quality is changing over time. We also collected macroinvertebrates, identified them to taxonomic order, and compared results between springs. Preliminary results suggest that water quality is not changing over time, though macroinvertebrate diversity and richness do vary from site to site. Of all the study sites, Saline Spring appeared to have the highest macroinvertebrate diversity and richness.  The results of this study can inform future research, and has the potential to influence management practices at BCCER as they relate to these freshwater springs and the biological communities that they support.

Assessment of the Riverine Wetland at Big Chico Creek Ecological Reserve
Lynsey G. Ryan T. Forrest M.
Riverine wetland systems are comprised of the river and its active flood plain, and are intended to include any adjacent riparian areas contributing to bank stabilization and organic material inputs. These systems connect not only watersheds, but also flora and fauna of terrestrial, freshwater, and marine habitats. California has lost a large amount of its wetland habitats and continues to do so, due to development, pollution, and the effects of climate change. This study uses the California Rapid Assessment Method (CRAM) to determine the quality of Big Chico Creek Ecological Reserve (BCCER) riverine system. We used the CRAM protocol to evaluate the physical and biotic structure, buffer, and hydrology of an 115 meter long assessment area downstream of Henning Hole at BCCER. Preliminary results suggest that the riverine system at BCCER is a fully-functioning riverine wetland system. This study allows for comparisons of the integrity of riverine wetlands throughout the state of California using this rapid assessment. It may also be used as a time series to reliably compare BCCER rapid assessments throughout time. 

Lobation of Blue Oaks (Quercus douglasii) along Big Chico Creek Canyon
He-Lo Ramirez, Trevor Garrison, Micheal Klemm,,
Blue Oaks (Quercus douglasii), have highly variable leaf morphology ranging from the absence of lobation to moderate lobation. Previous studies on closely related deciduous oak species have found that abiotic factors in the soil, including water availability and nutrient content, can significantly affect leaf morphometrics such as degree of lobation. This study looked at two study sites of Blue Oaks within the Big Chico Creek Canyon on two extreme soil types, the Tuscan Formation (Hogspring) and Chico Formation (BCCER), Hogspring and BCCER, are located approximately five miles from one another, and found at similar elevations. At each site, five leaves were collected per quadrant, per tree. We used ImageJ analysis software to measure degree of lobation (perimeter:area) of each leaf. Our hypothesis is that soil type, and abiotic factors associated with each soil type, cause differences in leaf morphology with all other variables equal. Preliminary results show a significant effect (p<0.05) of study site, tree quadrant, and aspect for lobedness. However, this significant effect was driven by only 5 leaves from a single quadrant of a single tree. More data needs to be collected to confirm this result.

How does mountain lion (Puma concolor) urine affect the presence of conspecific and heterospecific individuals observed with camera traps?
Sonia Alvarado-Ray, Mariby Cruz, Kelly Scott, Trevor Moore,,,
Puma concolor, commonly known as the mountain lion, is an elusive mammal, making it difficult to determine their abundance and life history. Camera traps are commonly used to gather more information about them and many other species. Because it can still be difficult to capture predators on camera, some research teams have tried using bait to attract them. The goal of this project is to determine if using mountain lion urine to bait camera traps will attract more predators, specifically mountain lions. Because most felines display territorial behavior, we predict that baited traps will have significantly higher mountain lion encounter rates. Previous work has suggested that 2-phenylethylamine, a chemical present in the urine of many predators including mountain lions, can deter small prey species. Because of this, we hypothesize that prey species will be less abundant at baited sites. Preliminary results show a higher occurrence of both heterospecific and conspecific species at the baited sites. More data is being collected to control for camera location. The results of this study will provide useful information for the design of future camera trap studies.

Distributions of native Emys marmorata and invasive Trachemys scripta elegans across local regions of Big Chico Creek
Annie Enos, Laura Lampe, Arians Maestas, Jack Selzer
Competition from invasive species can detrimentally affect native populations, particularly when two species have similar habitat preferences. The red-eared slider (Trachemys scripta elegans) is invasive on seven continents, and previous work has shown these turtles negatively influence European pond turtle populations. However, few studies have evaluated the interactions between the red-eared slider and the western pond turtle (Emys marmorata), a California native. The goal of this study was to examine the relative numbers of these species in Big Chico Creek across a gradient of elevation and urbanization. We surveyed areas known or expected to support turtles in the Big Chico Creek Ecological Reserve (BCCER), Upper Bidwell Park, and Lower Bidwell Park. We recorded the presence of the native western pond turtle at all three locations. There were no red-eared sliders observed in BCCER or in Upper Bidwell Park, but two individuals were recorded in Lower Bidwell Park - an area which may be more prone to human introductions of the species. Understanding the distribution of native and invasive populations is important for management purposes. This survey may be repeated in the future to provide a more comprehensive representation of the two species in Big Chico Creek, and is a means of monitoring any potential encroachment of red-eared sliders upstream.


BIOL 613, Population Ecology Christopher Ivey

Gall clustering does not increase resistance to parasitoids for the galling wasp Disholcaspis eldoradensis
Drew Gilberti
Parasites often have large impacts on host population densities.  Difficulty arises in understanding the impact of parasites when considering insect behavior. The galling wasp Disholcaspis eldoradensis is attacked by parasitoids that cause mortality in larvae.  In addition, the wasp gall secretes a nectar-like substance that attracts ants which deter would-be parasitoids. Galls occur in both clusters and solitary patterns, which may influence ant abundance. Galls occurring in clusters may enjoy reduced parasitism if ant recruitment increases in response to locally available nectar, but galls in clusters may also form more attractive targets for parasitoids. This study aimed to test the hypothesis that gall aggregation reduces successful parasitoid attacks. Because gall clusters are expected to secrete more nectar than solitary galls, and thereby recruit ants more successfully, I predicted that gall clusters will also have lower rates of parasitism. To test this hypothesis, galls were collected and sorted by cluster size.  A total of 114 galls were collected, 56 of which were parasitized.  Number of galls in a cluster was not correlated rates of successful parasitoid attacks, which is in contrast to similar studies. The timing of collection may have influenced the results as my study. I collected in April, near the beginning of the asexual generation, whereas other studies collected in October, near the end of the asexual generation.

150 years of herbarium records demonstrate species-dependent shifts to earlier flowering time
Laura Lampe
As the global climate undergoes significant and rapid changes, all organisms will be affected, directly or indirectly. The ability of organisms to respond, for example via shifts in phenology or distributions, may be significant to the persistence of any organism. It is therefore important to identify the shifts that are occurring and their direction and magnitude. Herbarium and museum collections provide historical records of species phenology and distributions, which can give insight into climate-related shifts when compared to modern records. I examined 150 years of herbarium records of Clarkia unguiculata, Gilia tricolor, and Lupinusalbifrons to determine correlations between flowering times, year of collection, elevation, and latitude. In C. unguiculata, flowering time is 24 days earlier most recently than in the earliest collections, which is consistent with previous research. Similar trends were not observed in G. tricolor or L. albifrons, which suggests that California natives may have varied responses to changes in climate over time. Identifying these responses provides the type of insight necessary to predict and prepare for continuing shifts.

Stomatal density and water mass of Quercus douglasii (Blue Oak) not correlated with tree size 
Anna Burns
Water availability is an important environmental factor influencing stomatal density. Water vapor lost through stomata accounts for more than 90 percent of total water transpired by a plant. Oaks, unlike some other trees, can produce relatively deep taproots. This may improve access to ground water. Because plants in wetter environments generally have higher densities of stomata, larger Quercus douglasii trees were predicted to have progressively higher stomatal densities and percent foliar water mass compared to smaller trees. Height, foliar water mass, and stomatal density measurements were obtained for 12 Q. douglasii trees representing a size gradient from 0.4 to 10.7 m in height. Linear regression was used to test whether the density of stomata in leaves was explained by both tree size and percent water mass in leaves. Stomatal density was not associated with tree height (P = 0.25), nor was percent water mass in leaf tissue correlated with tree height (P = 0.19). Increases in tree size did not appear to affect access to water nor to induce variation in stomatal density and foliar water mass.

Distribution of manzanita leaf gall aphids (Tamalia coweni) on whiteleaf manzanita (Arctostaphylos viscida) 
Stephanie Parker
The spatial dispersion of a species is important when considering the distribution of that species within the available habitat. Two mechanisms of dispersal include random dispersion driven by environmental influences (e.g. wind, physical barriers), and direct dispersion driven by resource availability. The distribution of a species provides insight into the population and use of available habitat. Tamalia coweni, a galling-aphid, induces galls on new leaf growth on manzanita species. For this study, I examined the distribution of 2017 T. coweni galls and the available new growth leaves from that year using 45 sampled plots over 9 individual plants (Arctostaphylos viscida). The gall distribution did not significantly differ from a Poisson distribution, suggesting a random distribution of galls across these plots. In contrast, a different test, Morisita’s index of dispersion, suggested the dispersion pattern of the galls was aggregated. The proportion of habitat use (number of galls) to habitat available (number of leaves) was low. Because gall induction is limited by growth of new leaf tissue, a direct dispersion of T. coweni foundresses is inferred, driven by habitat availability. 

Flower age and nectar production: significant differences found in young and old flowers of Rosmarinus officinalis.
Trevor Garrison
Pollinators rely on nectar as a reward for visiting flowering plants. In turn, flowering plants rely on pollinators for their own reproductive success. The dynamics of nectar production in flowers can influence the behavior of pollinators, which can impact plant reproductive success. Pollinators respond to changes in available nectar, and flower phenology may contribute to nectar dynamics. Flowers from a Rosmarinus officinalis plant were bagged and their 24-hour nectar production and sucrose percentage were measured at 1 day and 6 days following opening. Significant differences were found for the mean nectar volume secreted by young and old flowers (mean young: 0.22µL, SD: 0.1, mean old: 0.16µL, SD: 0.05), but no significant differences were found when comparing the mean sucrose percentage of nectar secreted (mean young: 44%, SD: 15, mean old: 40%, SD: 8.8). This study suggests that older rosemary flowers secrete less nectar. This could lead to changes in pollinator foraging behavior, by influencing them to visit more plants, increasing pollen dispersal


Pallid Bat Seasonal Activity in Northern California
Cameron Divoky, Trevor Moore, Colleen Hatfield, Shahroukh Mistry,
Faculty Mentors: Colleen Hatfield and Shahroukh Mistry,,
Antrozous pallidus is a Species of Special Concern in California and a State Vulnerable species. Previous studies of A. pallidus have focused mainly on behavior and roosting patterns, with limited information available on long-term seasonal activity. This study examines patterns of seasonal activity in A. pallidus at three sites in northern California, ranging from the Central Valley to the Cascades. Activity was documented daily for 3 years using acoustic data loggers at the Eagle Lake Field Station, Big Chico Creek Ecological Reserve and the CSU Chico University Farm. Bat species identity was established using SonoBat software. Antrozouspallidus showed the greatest seasonal activity in the summer (June-July) with minimal activity during the winter months (November-February). This pattern was most noticeable at BCCER. This indicates seasonal migratory activity by pallid bats and a preference for oak woodland habitat with adjoining rock outcrops, over valley agricultural landscapes.

Activity Patterns of the Western Red Bat, Lasiurus blossevillii, in Northern California
Trevor A. Moore, Cameron Divoky, Colleen Hatfield, Shahroukh Mistry,
Faculty Mentors: Colleen Hatfield and Shahroukh Mistry,,
Lasiurus blossevillii is a tree-roosting bat found throughout the western United States. It is present year-round in the Central Valley, however, the seasonal migratory patterns in the state are not well understood. The aim of this study is to examine the seasonal activity patterns of L. blossevillii in Northern California. Using acoustic recordings, we examined the activity patterns at three different habitat types: an agricultural area in the valley, canyon and ridge oak woodland, and a pine-juniper forest. Species were identified using SonoBat software. Lasiurus blossevilli had the highest levels of activity during June and July across all sites, with the pine-juniper forest showing the greatest activity. The lower elevation sites retained low levels of activity throughout the winter suggesting temperatures warm enough for occasional foraging. The site in the valley showed a late-year increase in activity during October and November, possibly indicative of migratory activity.

Leaf trait variation in a Quercus lobata common garden experiment is not explained by climatic conditions of maternal seed source
He-Lo Ramirez, Victoria L. Sork, Jessica W. Wright, Christopher Ivey
Faculty Mentor: Christopher Ivey,
Oak leaves are remarkably variable. Previous studies found that leaf morphology of some oak species covaries with climate, which may reflect local adaptation or plastic responses to climate. We tested the hypothesis that variation in leaf dissection and specific leaf area in Quercus lobata was genetically based. The study was conducted in a provenance test involving 672 maternal families collected from 97 locations throughout the range of the species. We subsampled leaves from 54 trees grown from 27 maternal families (9 locations) representing extremes and median of multivariate climate phenospace, used digital image analysis to measure shape, and weighed leaves to calculate specific leaf area. If variation in traits reflects adaptation to climate, we predicted that leaves sampled from trees originating from contrasting climates would contrast significantly in traits measured, even when grown in this common garden. Instead, we found no significant differences in leaf traits among the climate categories sampled, suggesting that the variation is largely shaped by local environmental conditions

Leptothrix cholodnii, how do your tubes grow? 
Sandra Martell, Emily Fleming
Faculty Mentor: Emily Fleming,
Leptothrix cholodnii SP-6 is an aquatic bacterium that is known for its production of extracellular sheaths. These extracellular sheaths are the site of metal oxidation. Due to product of these insoluble solids, these organisms are nuisance organisms because they influence biocorrosion, and cause biofouling of water distribution pipelines. Its influence on biofouling makes it important to understand and know the genes responsible for sheath production. Leptothrix cholodnii SP-6 is being used as a model for sheath production because it retains the ability to produce sheaths when grown in the laboratory. The goal of this study is to determine genes responsible for sheath production. To determine which genes are responsible one needs to have a robust assay to assess sheath production. Quick screen assays are needed to characterize the phenotypes of natural variants with and without sheath. The four ways I will characterize sheath production will be by quantifying movement with motility assays, visualizing the sheath using Scanning Electron Microscopy, quantifying sheath using stains, and observing sheath production in capillary tubes. In preliminary experiments, I observed that: 1) That motility and sheath production are mutually exclusive. This needs to be further confirmed with pure cultures of sheathless mutants. 2) Initial trials using stains did not bound to organism know to contain a sheath. Future efforts are focused on staining the metal bound oxides that typically adhere to the sheath. Despite these challenges, I will continue to establish protocols for screening and quantifying sheath production as this will help classify future sheath mutants.

Isolation of Sulfur Oxidizing Acidothiobacillus
John Machado, Serban Sarbu, Emily Fleming
Faculty Mentors: Emily Fleming and Serban Sarbu,
Caves and cave systems have been points of interest in the scientific community for decades due to their isolation from the outside world. This provides opportunities to explore and document possible live forms that live there. With each cave a new environment allows new and unexplored organisms to thrive there without human interaction. Within most caves and cave systems there is typically an entrance that is easily accessed, however the environment of the inside of the cave may prove to be more dangerous than entering it. Sulfur Cave in Romania, which experiences gas runoff from a dormant volcano that lies deep beneath the cave floor provides an atmosphere consisting of a small percentage of H2S and 96% CO2 which is much greater than the normal CO2 conditions we experience (0.04%). Since the cave is rich in CO2, the cave consists of an extremely acidic environment. Along the walls of this cave where the volcanic gasses meet with our atmosphere there exists a gaseous interface where sulfur oxidizing microorganisms are present. Research has been conducted on the cave and those similar to Sulfur cave, however the microbes that are present at this interface have yet to be grown in a lab setting. Microorganisms that are able to survive in harsh environments like volcanic caves present unique opportunities of exploration and research into the lifestyles of these microorganisms which can provide a bigger picture of how they are able to grow, potentially in extraterrestrial environments such as Mars. Over the past semester I set out to isolate and grow one of the dominant species of bacteria that are present in Sulfur Cave.

FeRB <-> MeHg
Sophia Phillips, Teal Myers, Gordon Wolfe, Emily Fleming,
Faculty Mentor: Emily Fleming,
Methylmercury is highly toxic and biomagnifies in aquatic biota, making it a critical environmental concern. Iron reducing bacteria (FeRB) and sulfate reducing bacteria (SRB) methylate mercury in freshwater ecological systems. However, previous studies have demonstrated that SRB are responsible for only ~50% of mercury methylation in Fe-rich, Hg-contaminated marshes, and the complete set of bacteria responsible for methylation has not been identified.  In this study, we determined total mercury and total iron across a transect in Walker Marsh on the CA coast. We characterized the microbial community using 16S rRNA sequencing, and also estimated the numbers of known mercury-methylating taxa by PCR amplification of the hgcA/B gene. Our observations suggest sediment iron levels are correlated with higher mercury. Sulfate- and iron-reducing proteobacteria were both highly abundant in the community, and hgcA/B-containing bacterial genera were dominated by β-proteobacterial sulfate and iron reducers, with only low abundance of Firmicutes. We propose that mercury methylation is shared between both groups in these environments.

Characterization of Bacterial Degradation of Polyhydroxybutyrate
Emily Egusa, My Lo Thao, Daniel Edwards, Tara Burns, Larry Kirk, Larry Hanne
Faculty Mentor: Larry Hanne,
Polyhydroxybutyrate (PHB) is a biodegradable bioplastic that can be used to replace conventional, petroleum-based plastics. PHB can be both synthesized and degraded by bacteria. This research project has focused on the isolation, identification, and characterization of bacteria that can degrade PHB. Eight PHB degrading bacteria were isolated from the environment and polyhydroxybutyrate depolymerase activity was determined on PHB-nutrient agar plates. One isolate, Acidovorax wautersii, was chosen for further investigation based on its high levels of depolymerase activity. Results in liquid culture indicated that the enzyme is inducible and highest activity occurs between 4-8 hours following PHB exposure at 36˙C. SDS-PAGE comparison of concentrated supernatant from PHB induced cultures showed a band at approximately 60 kDa, not present in the uninduced samples. The primary breakdown product of PHB was determined to be the monomeric unit, 3-hydroxybutyrate (3HB), by HPLC analysis.

Development of axenic Aiptasia: a vital tool for Cnidarian-Bacteria symbiosis research
Dearden Ashley, Sydnor Jamison, Cawa Tran,
Faculty Mentor: Cawa Tran,
Coral bleaching caused by rising sea temperatures continues to threaten coral reef health. Mass bleaching events across the globe have provided a preview of the loss that will ensue if corals are unable to adapt to their changing environment. It has been hypothesized that corals may be able to acclimate to the thermal stress of global warming by altering their composition of symbiotic bacteria. The sea anemone Aiptasia has been used as a model for coral reef research, and analysis of its microbial communities may provide valuable insights into cnidarian host-microbe interactions. Investigation into the physiological benefits that symbiotic bacteria may confer on their cnidarian hosts is limited by the lack of proper experimental methods. This work aimed to produce a method for the exploration of the role of bacteria in cnidarian health by developing axenic Aiptasia. Through the use of antibiotic treatments and various sterilization procedures, we have made progress towards the establishment of axenic Aiptasia. Presence of bacteria was tested using 16S rRNA gene sequencing. Future studies will involve careful testing of bacterial effects by re-infecting axenic anemones with known bacterial strains. These functional studies, made possible by the development of axenic Aiptasia, will focus on identifying bacterial species that contribute to host thermotolerance. This work will advance knowledge that is urgently needed to preserve Earth’s corals and the diverse ecosystems they support.

Light in the Marine Environment and its Effect on Cnidarians and Their Algal Symbionts
Gavin Monges, John Machado, Sophia Phillips, Cawa Tran,,
Faculty Mentor: Cawa Tran,
The health of coral reefs worldwide is threatened by a combination of natural and anthropogenic stresses. Many of these stresses have resulted in mass deaths observed in coral reefs in events commonly referred to as coral bleaching. Under normal environmental conditions, the algae exist in a mutually beneficial relationship with their hosts, providing them with energy derived from their photosynthetic processes. Thus, light plays an important role in growth and development of these organisms. Sea anemones are organisms that also rely on light to grow and reproduce. Aiptasia is a symbiotic sea anemone used as a model for coral symbiosis studies, as it is easy to rear in lab and can be grown symbiotically (with algal symbionts) and aposymbiotically (without algal symbionts). These anemones are known to exhibit behavioral responses as a result of light exposure, such as phototaxis (bodily movement towards light) and phototropism (orientation and growth towards light). We hypothesize that anemones with algal symbionts will exhibit a stronger phototactic and phototropic response than those without algal symbionts. To test this hypothesis, we exposed both symbiotic and aposymbiotic anemones to light.  Because the algae have a range of photoreceptors (phytochromes, cryptochromes, and phototropins), we examined the anemones’ responses to varying wavelengths of light (blue, red, and white light). Overall, the greatest phototactic response was observed in symbiotic anemones exposed to the blue wavelength of light.  The goal of this study is to understand how simple, yet critical marine organisms detect light to best benefit themselves and their symbionts. 

Investigation of Expression of the cMed2b Gene in Medaka, Oryzias latipes, with the Idiopathic Scoliosis Phenotype
Karsten McDonell, Kristen Gorman
Faculty Mentor: Kristen Gorman,
Idiopathic scoliosis (IS) is a prevalent deformity with no known cause. It is defined by abnormal spinal curvatures that occur after birth and during pediatric growth. For this reason, IS has been considered a post-natal syndrome. The goal of my project is to investigate the expression of an IS candidate gene (cMed2b) during development. I hypothesize that there will be different expression in curved versus normal embryos. My work uses a strain of the Japanese Rice Fish, Oryzias latipes, with non-induced genetic scoliosis as a model. Gene expression will be measured at various time points during development by RT-PCR, in order to identify differential expression. Results of this experiment will contribute to an understanding of a genetically complex disease, as well as provide a foundation for future work.

Detection of Scoliosis gene, cMed2, during embryonic development
Sandra I Arellano, Kristen Gorman
Faculty Mentor: Kristen Gorman,
Idiopathic scoliosis (IS) is an abnormal spinal curvature. The cause of IS has been unknown for thousands of years, but we are making progress in discovering the disease’s biology. Historically, IS was considered exclusive to humans because it is not observed in quadrupedal animals. However, the fish model Oryzias latipes has a lineage with heritable scoliosis that is similar to IS. Human studies have not identified IS causative genes. Prior genomic work in the O. latipes model has identified several candidate genes. One of these, cMed2, is not expressed in curved fish after hatching. The goal of my project is to assay cMed2 during development. I hypothesize that there will a lack of expression during development. Total RNA will be extracted from pools of curved and normal embryos, and then converted to cDNA. Using primers designed for the cMed2 transcript, I will then amplify parts of the gene. Amplicons will be run on electrophoresis gels. A band is anticipated if the gene is expressed. Results will help with understanding the molecular pathways associated with the etiology for IS. This may lead to improvements in healthcare for how efficiently IS is treated.

The Role of cMed3 in Scoliosis Formation
Victoria Coia, Kristen Gorman
Faculty Mentor: Kristen Gorman,
Human idiopathic scoliosis (IS) is a genetic disorder characterized by an abnormal curvature of the spine. Between 0.5 - 10% of children around the world have IS. Because curve onset occurs after birth, the deformity is not considered congenital. Although it is known to be genetic, the biological basis of IS remains unknown.  The goal of my research is to evaluate the expression of an IS candidate gene during embryogenesis. For my research I use the Medaka fish as a genetic animal model, and an inbred lineage having phenotypic similarities to IS. I will be evaluating the expression of my candidate gene (cMed3) at various developmental stages in two groups: curved and normal embryos. I hypothesize that there will be stages that show different gene expression in curved fish. If so, my results will demonstrate that IS has a congenital defect. The ultimate goal is to discover the biological basis for IS. This can contribute to improved screening methods for early detection of scoliosis. 

Investigating the Effects of CRISPR/Cas9 genome editing in human cells
Grace Y. Prator, David Keller
Faculty Mentor: David Keller,
The CRISPR/Cas9 genome editing system has recently emerged as a novel approach in biomedical research pertaining to applications in gene therapy. Coupled with a customizable guide RNA, Cas9 endonuclease can be engineered to induce a double strand breaks in a targeted gene sequence, activating endogenous DNA repair mechanisms. In this study, we aim to address whether utilizing Cas9 nuclease co-expressed with a gRNA can edit the gene for green fluorescent protein (GFP) expressed in human embryonic kidney (HEK) 293 cells. Lipofectamine CRISPRMAX was used to deliver Cas9 protein and gRNA complexes into a GFP+ stable cell line of HEK 293 cells. Fluorescent microscopy was used to visualize significant changes in GFP fluorescence while Image J was used for quantification of the images. Here, we demonstrate that by transfecting Cas9 and gRNA into a GFP+ stable cell line resulted in two-fold reduction of GFP fluorescence. Because there was a significant decrease in GFP fluorescence, this suggests that we successfully edited the GFP gene in HEK 293 cells.

Generation of Fluorescent Zebrafish Kidney Cell Lines
Dara Stroup, Katerina Arca, David Stachura,
Faculty Mentor: David Stachura,
Blood is important for the health, support, and survival of vertebrate organisms and it needs to be constantly replenished.  The production and regulation of blood cells is necessary for proper vertebrate functions such as the ability to carry oxygen to tissues and the ability to fight off pathogens. Any problems in this process can have severe consequences, such as anemia, neutropenia, or leukemia.  Zebrafish (Danio rerio), a small common aquarium fish species, are an excellent model system for studying numerous developmental and molecular processes that are conserved across vertebrate species, including blood formation and regulation.  We previously generated cells from the zebrafish kidney (the site of blood formation in fish)  that support blood cell growth and differentiation outside of the fish’s body, allowing an in-depth understanding of signals needed for these processes.  To add to the toolkit available to study blood development we generated kidney cell lines from fluorescent fish known as GloFish that have fluorescent blue kidney cells. The advantage GloFish have over other zebrafish is that we can use their exceptionally vibrant and distinct colors to track cells and their secreted intracellular components under a microscope and with flow cytometry. These fluorescent blue kidney stroma cells will help us visualize blood cell activity in an unprecedented manner, allowing more in-depth studies of the molecular processes involved in their generation and regulation.                

Stem Cells- it’s What’s for Dinner
Katerina Arca, Dara Stroup, David Stachura,
Faculty Mentor: David Stachura,
With more than 7 billion people on the planet, our increasing dependence on the ocean to provide us with food sources to support growing populations requires that we develop alternative seafood sources before we completely collapse the ocean ecosystems.  Cellular agriculture is the production of agricultural products from cell cultures; this technique could establish a clean, nutritious, and sustainable source of fish for human consumption without negative ecological effects. We are utilizing zebrafish (Danio rerio) as a model organism for studying the mechanism behind directed differentiation of embryonic blastomeres to generate mature skeletal muscle, fat, and cartilage, important components of fish tissue for human consumption.  By altering cell isolation techniques, extracellular matrix growth conditions, and media components, we have established cell lines that survive for weeks in culture and can be stimulated to differentiate towards muscle tissue.  Our long-term goal is to fine-tune the number and amount of exogenous factors added to the cultures so that we can use zebrafish as a model system to discover cell-supportive factors required to generate sustainable sources of threatened species such as bluefin tuna, yellowfin tuna, albacore, and various species of salmon.  

kal1b Plays a Role in Thrombocyte Production 
Matthew Boice, Peter Kure, David Stachura,
Faculty Mentor: David Stachura,
HSCs emerge in developing zebrafish from the wall of the dorsal aorta and migrate to caudal hematopoietic tissue (CHT) for expansion. Three cell lines were created from zebrafish tissues which support HSPC proliferation; zebrafish kidney stroma (ZKS), Zebrafish embryonic stromal trunk (ZEST) cells and Caudal hematopoietic embryonic stromal tissue (CHEST) cells. Prior studies conducted by Stachura labs have shown 447 overexpressed transcripts are shared among these hematopoietic supportive cell lines.  Of these 447 transcripts, the one hundred highest expressing genes were analyzed and marked for further study. kal1b was chosen for further investigation. 
In these investigations, morpholinos (MOs) are used to target the gene of interest (kal1b) and reduce its expression. MOs are injected into a developing embryo in its first hours, and the development of the embryo is monitored. Survival rates of the embryos are measured, and the gene’s role in hematopoiesis is determined.


Impact of increased incubation temperature and thermal stress on the aerobic scope and thermal tolerance of juvenile rainbow trout (Oncorhynchus mykiss)
Nicholas M. Balfour, Carlos A. Estrada, Rebecca A. Pilakowski, Dylan K. Stompe, Amanda I Banet,,,
Faculty Mentor: Amanda I Banet, 
Recent research has investigated the impact of higher temperatures on sockeye salmon (Oncorhynchus nerka) and found that increased incubation temperatures resulted in lower thermal tolerance later in life by decreasing critical thermal maximum (CTmax). The oxygen and capacity limited thermal tolerance hypothesis (OCLTT) proposed by Portner provides one possible explanation. This hypothesis suggests that the thermal tolerance of aquatic ectotherms is limited by insufficient oxygen delivery to cells. We hypothesize that fish exposed to high temperatures early in development will exhibit reduced aerobic performance later in life, as compared to fish incubated at lower temperatures. We also hypothesize that this difference will be magnified when fish are swimming in high temperature waters. To test this, we reared rainbow trout eggs in three temperature treatments: 50F, 55F and 60F. After hatch, CTmax and aerobic performance of fish were measured across a range of swimming temperatures.

Habitat-specific Diet Analysis of Sacramento Pikeminnow (Ptychocheilus grandis) and Striped Bass (Morone saxatilis) in the Sacramento River
Dylan Stompe, Nick Balfour, Stacey Alexander, Mandy Banet,,
Faculty Mentor: Amanda I Banet, 
California native fish populations have experienced decline in recent years. One possible cause of decline is predation, which may be exacerbated by the presence of non-native predators, predator size class effects, the presence of man-made structures, and hatchery rearing effects. In an effort to quantify predation and identify associated factors, we examined the diets of non-native striped bass and native Sacramento pikeminnow within the lower Sacramento River. Sampling was conducted twice weekly during 2017 via hook-and-line sampling along a 22-mile section of the Sacramento River, in Butte County, California in addition to haphazard fyke trap sampling in Sacramento, California. Striped bass and Sacramento pikeminnow stomach contents were recovered via gastric lavage and are to be examined with the aid of qPCR to determine habitat, size, season and species specific diets. Quantification and analysis of predator diets with the use of Pinka’s Index of Relative Importance and non-parametric statistical methods will afford insight into the effects of predation on vulnerable Sacramento River native fish populations.

Understanding sweet bottom-up and top-down trophic cascades- Disholcaspis eldoradensis
Drew Gilberti, Christopher Ivey
Faculty Mentor: Christopher Ivey,
Trophic interactions may provide insight into understanding the distribution and abundance of organisms. Predators and producers influence other trophic levels through unexpected and complex interactions. The wasp Disholcaspis eldoradensis induces galls on valley oak trees, which are distinctive for their secretion of nectar. The nectar attracts ants which reduce parasitism of wasp larvae within the galls. I propose to test the hypothesis that parasitoid attack on galling wasps is directly influenced by both lower and higher trophic levels. A factorial experiment has been designed that will systematically test every trophic level within the system.  Host trees, ants, and nectar will be stimulated or impaired in order to measure the direct or indirect impact on the distribution and abundance on wasps.

The Impacts of Gall Size and Shape on Housekeeping Behavior of the Gall-inducing Aphid, Tamalia coweni
Stephanie Parker, Don Miller
Faculty Mentor: Don Miller,
There are multiple traits we use to define sociality in insects. Often, we associate colonial insects such as bees, ants and termites, with eusociality. When we expand sociality to include defensive and housekeeping behavior, we can analyze the varying levels of sociality in insects such as galling aphids. After inducing a gall on a leaf, the founding female aphid will raise multiple generations of offspring that live and feed inside the gall. In some species of galling aphids, specialized soldier castes defend the colony and remove waste from the gall, a housekeeping behavior. Analyzing housekeeping behavior alone suggests that some aphids we consider nonsocial exhibit many of the same behaviors as social galling aphids. Tamalia coweni induces galls on manzanita species and does not have a recorded soldier caste. Unlike other galls, T. coweni galls do not have an opening that waste may be actively pushed out of, instead we are seeing housekeeping behavior in the form of arranging the exoskeletons in clustered lines at the corners of the gall. This arrangement occurs in galls on one species of manzanita, Arctostaphylos viscida, and not on another, A. manzanita. This study seeks to quantify the arrangement of cast exoskeletons, as well as the differences of gall size and shape between the two species of manzanita that may be driving this difference in behavior. This rudimentary housekeeping behavior would indicate an independent evolutionary origin of more complex sociality in T. coweni

Landing rate of the walnut twig beetle, Pityophthorus juglandis, on two western North American walnut species, Juglans californica and J. major
Irene Lona, Don Miller
Faculty Mentor: Don Miller,
The walnut twig beetle (WTB), Pityophthorus juglandis, vectors a phytopathogenic fungus, Geosmithia morbida, which causes Thousand Cankers Disease (TCD) in walnut trees, Juglans. We are investigating the susceptibility of two walnut species native to the western USA (Juglans californica and J. major) by comparing the WTB flight and landing responses to small diameter branch sections. Twenty unbaited branch sections (10 each of J. californica and J. major) were presented in a completely randomized design to a population of WTB at Wolfskill Experimental Orchards (Winters, California) and the Agricultural Teaching and Research Center (ATRC) in Chico, California. Stickem-coated acetate sheets were placed around the branch sections and exchanged weekly. Three assays were completed in Wolfskill (Assays 1-3), and one assay was completed in ATRC (Assay 4). Landing rates on these traps were compared between J. californica and J. major. An additional assay (Assay 5) was completed at the Wolfskill site to measure responses to J. californica and to a cardboard tube (negative control). A statistical analysis that pooled results from Assays 1-3 showed a preference by WTB for J. californica. Assay 4 and 5 however showed no preference to either host perhaps due to the low population of WTB during the assays. The observed preference of the WTB in this study indicates that host preference may be determine by long-range olfactory cues. 

Migration Patterns of Flammulated Owls Using Light-Level Geolocators
Shannon Rich, Colleen Hatfield
Faculty Mentor: Colleen Hatfield,
Flammulated owls (Psiloscops flammeolus) are small nocturnal owls that are thought to migrate long distances every year from summer breeding grounds in the Western United States to winter habitat in Mexico. They are cryptic and elusive cavity nesters and little is known about their migratory patterns or their winter habitat. They have been named a Species of Concern by the U.S Fish and Wildlife Service because of potential habitat destruction. The goal of this research was to track the movements of these owls during their migratory season and over the winter using light-level geolocators. The geolocator records ambient light levels that correspond to sunrise and sunset times to determine specific bird locations. During 2012-2013, 60 geolocators were attached to male and female Flammulated owls in breeding sites in Washington, Colorado, Utah, and California. In 2013-2014, 16 of these geolocators were recovered from birds in California, Utah, and Colorado. The migratory routes of these birds were analyzed using GIS and further analysis was performed to determine kernel density estimates and habitat characteristics of their winter home ranges in Mexico. This geolocator analysis along with additional research on habitat preferences of Flammulated owls in California is the first step in assessing the current status of this species with the goal of a broader western U.S. effort in the future.

Influenza viruses differentially alter macrophage polarization in a strain dependent manner 
Donald Beck, Armando Sotozuniga, Troy Cline,
Faculty Mentor: Troy Cline,
H5N1 influenza viruses cause human infections with a high mortality rate. The mechanism of enhanced disease severity is not understood. Macrophages play a critical role in protection against influenza viruses yet have been implicated in enhanced disease severity following H5N1 infection. H5N1 influenza viruses are unique in their ability to replicate in macrophages, a feature that maps to the viral hemagglutinin (HA) gene. We hypothesize that H5N1 influenza viruses cause severe disease by altering macrophage functions. Macrophages have been classified as classically-activated (M1) or alternatively-activated (M2) as defined by the cytokines that drive macrophage activation and the gene expression profile of the polarized macrophage. M1 macrophages are pro-inflammatory, while M2 macrophages are involved in tissue repair. We investigated the impact of influenza virus infection on macrophage polarization by infecting macrophages with the H1N1 virus CA/09 (unable to replicate in macrophages) or with CA/09 expressing an H5 HA gene (CA/09+H5 HA; replicates in macrophages). Cells infected with CA/09 expressed both iNOS and MMR (markers of an M1 and M2 polarization, respectively), suggestive of a balanced M1/M2 response important for recovery from infection. Infection with CA/09+H5 HA induced expression of MMR only, indicating a polarization toward the M2 phenotype. Further, macrophages infected with the CA/09+H5 HA were not responsive to an M1-polarizing stimulus (IFN-γ) while remaining responsive to the M2 stimulus, IL-4. These results suggest that influenza viruses modify macrophage functions in a strain-dependent manner correlating with replication of the virus in macrophages.

Isolation and characterization of avian influenza viruses in Northern California 
Elizabeth Bianchini, Analucia Barragan Trejo, Raymond Bogiatto, Robin Donatello, Magdalena Plancarte, Walter Boyce, Troy Cline
Faculty Mentor: Troy Cline,
Recent human infections with influenza viruses of avian origin highlight the need for continued surveillance of avian influenza viruses (AIV) in waterfowl. In 2014, highly pathogenic avian influenza (HPAI) H5N8 first detected in South Korea entered North America through the Pacific Flyway, a major migratory route for waterfowl, and caused outbreaks in poultry in the United States. California’s Sacramento Valley is an important wintering site for waterfowl from which avian influenza viruses may be isolated. To better understand the risk posed by avian influenza viruses circulating in California, we collected cloacal swabs from 2,066 hunter-killed ducks across three hunting seasons at different locations in the Sacramento Valley. Sixteen waterfowl species were represented in our sampling. The presence of influenza viruses in cloacal swabs was determined by PCR for the matrix gene. The overall prevalence rate was 10.5% with diverse HA and NA subtypes represented. We observed a significantly higher positive rate in 2015-2016 (19.9%), a phenomenon that may be related to overcrowding on wetlands due to drought conditions. Northern shovelers had a statistically higher carriage rate (21.3%) relative to other species. Of particular interest, we detected HPAI H5 influenza viruses by PCR but were unable to retrieve an egg isolate. Three H7N3 isolates were obtained and, given recent human infections with H7 viruses, were characterized with respect to in vitro replication kinetics in mammalian tissue culture. All three H7 viruses were capable of replication in mammalian cell culture at levels similar to a human H1N1 virus.

Mutation mapping to demystify sheath production in Leptothrix cholodnii SP-6
Kirstie Steiner, Malory Brown, Sandra Martell, Betsey Tamietti, Emily Fleming
Faculty Mentor: Emily Fleming,
Metal-oxidizing bacteria like Leptothrix-Sphaerotilus generate complex surface structures to avoid becoming entombed within an iron or manganese crust and to remain suspended in the water column. These bacteria possess cellular machinery to generate a highly ordered organo-metallic fibrillar microtubule sheath and have been generating these structures for hundreds of millions, if not billions of years. While the sheath structure is well known to be composed of long polysaccharide fibrils bonded by amino acids, the microtubule sheath assembly machinery and regulation of sheath production is unknown. Determination of sheath-related genes has been complicated due to a lack of a tractable genetic system in these metal-oxidizing bacteria. We developed a genetic system, obtained several sheath mutants using transposon mutagenesis, and identified the genes that were disrupted. Of these mutants, many either overproduced or did not produce sheaths. The genes associated with these mutants are connected to motility, suggesting a link between sheath production and motility. To confirm a specific gene’s involvement in the observed mutant phenotypes, we will reconstruct the mutant from wild-type using targeted gene deletion. Lastly, we obtained natural sheathed and sheathless variants and will sequence their DNA and use bioinformatics to identify more potential genes involved in sheath production. 

Does the Bacterial Community Associated with the Sea Anemone Aiptasia Change in Response to Thermal Stress?
Jamison Sydnor, Ashley Dearden, Cawa Tran
Faculty Mentor: Cawa Tran,
The sea anemone Aiptasia is a model organism for studying the symbiotic relationship between corals and photosynthetic dinoflagellates belonging to the genus Symbiodinium. With climate change driving ocean temperatures to rapidly increase, thermal stress is implicated as the primary culprit disrupting the cnidarian-dinoflagellate symbiosis. As dinoflagellates vacate their host in response to thermal stress, the symbiosis collapses, causing bleaching to occur. In the worst cases, large-scale bleaching events wipe out the framework for entire ecosystems. To address this increasingly dire issue, research has recently adopted a new approach to understanding these processes by shifting focus to the bacteria associated with Aiptasia. We hypothesized that the bacterial community associated with Aiptasia changes in response to thermal stress.  In order to examine the bacterial communities, symbiotic and aposymbiotic (lacking algae) anemones were subjected to both control (27°C) and thermal-stress (34°C) temperatures to emulate their natural environment and bleaching threshold respectively. Metagenomics analysis was then performed. Community composition determined from metagenomics output was compared to live cultures prepared from the same samples. Results from this experiment provide insight into both the biological function and taxonomic annotation of associated bacteria, allowing us to discern which species confer a potential benefit to the host under heat-stressed conditions.

ccl44 plays a key role in hematopoietic stem and progenitor cell proliferation
Payton Laurie, David Stachura
Faculty Mentor: David Stachura,
Blood development is a complex and highly regulated system where hematopoietic stem and progenitor cells (HSPCs) differentiate into the numerous types of cells that make up the hematopoietic system. Understanding the genetic and molecular pathways involved in this process is an important step to treating many diseases associated with the blood system. Due to the conservation of this system and many of its genes across vertebrate species we turn to zebrafish (Danio rerio) as a model organism. Three cell lines from sites of hematopoiesis were isolated, which expanded HSPCs when they were plated on these stromal cells. With the use of RNA sequencing we compared transcript expression of these three stromal cell lines and generated a list of 447 genes that we believe are important regulatory factors in the hematopoietic system. A highly expressed transcript from these cells was chemokine (C-C motif) ligand 44 or ccl44. In order to test its effect on hematopoiesis we performed knockdown experiments using morpholinos (MOs). Transgenic zebrafish lines with fluorescently labelled myeloid, erythroid, and lymphoid cells were injected with ccl44 MO and a decrease in those cell lineages was observed with the help of flow cytometry, fluorescence microscopy, and quantitative RTPCR. Further characterization of ccl44 could have clinical importance for HSPC expansion and treatment of diseases like anemias and leukemias.

son is necessary for proper blood maturation
Rebecca Belmonte, Erin Ahn, David Stachura
Faculty Mentor: David Stachura,
Zebrafish (Danio rerio) is an excellent model organism for studying embryonic vertebrate development due to its conserved genome with humans, external development, and ease of observation under the microscope. Previously, we showed that mutations in the mRNA splicing co-factor gene SON cause spinal and brain malformations in human and zebrafish. We performed these studies by knocking down the expression of the zebrafish homolog of SON in zebrafish at the single-cell developmental stage with specific morpholinos (MOs). In addition to the brain and spinal malformations, we also observed abnormal blood cell levels with SON knockdown. Decreased levels of SON resulted in impaired blood flow and changes to the amount of red blood cells, thrombocytes, and myeloid cells. As we continue to investigate SON and its effect on blood development, we will be able to establish how over- and under-expression of this gene negatively impacts human health.

Analysis of novel inhibitors of the GRB2 SH2 domain that decrease proliferation in chronic myeloid leukemia
Tina Hanson, Stephanie Aguiar, Kallie Griffin, Skylar Tomasetti, Sofia Rodriguez, Carolynn Arpin, David Stachura,,,,
Faculty Mentor: David Stachura,
Chronic myeloid leukemia (CML) is a disease affecting the normal growth of myeloid cells in the blood and bone marrow caused by a chromosomal translocation linking the breakpoint cluster region (BCR) gene to the Abelson murine leukemia viral oncogene-1 (ABL1). Once transcribed, this fusion protein, known as BCR-ABL, causes an over-proliferation of myeloid cells. Downstream of BCR-ABL is growth receptor bound protein-2 (GRB2), an intracellular adapter protein involved in cellular growth and differentiation. BCR-ABL binds with the SRC homology-2 (SH2) domain of GRB2 accelerating leukemic transformation. We created four novel SH2 antagonists (NHD2-15B, NHD2-92, NHD2-107, and NHD2-114) and tested their effects on the growth of K562 cells, a BCR-ABL+ immortalized myelogenous leukemia cell line, and found significant growth reduction after 48 hrs. To verify the mechanism of action, an enzyme-linked immunosorbent assay (ELISA), to determine if the drugs outcompeted GRB2’s natural ligand, a biacore surface plasmon resonance assay, to determine Kd, and a cellulose nitrate filter assay, to determine site specificity, were performed. Each antagonist was then tested on developing zebrafish to ascertain the toxicity of these molecules. These assays indicated that our SH2 antagonists do, in fact, antagonize GRB2 and kill CML cells, bringing us closer to determining a key mechanism in CML oncogenesis and developing targeted therapies for this disease.