undergraduate research

Tomatillo fruits and calyces don’t grow together

Anonymous — Mon, 03 Jan 2022 05:55:40 +0000

Tomatillo fruits and calyces don’t grow together Anonymous (not verified) Sun, 01/02/2022 - 22:55

Fruit and calyx development in the sharpleaf groundcherry, by Erica Au

Project Background

Pollination happens when either an organism or abiotic factor aids in the transport of pollen to the stigma of a plant. In order to reach the ovary to fertilize the ovules (eggs), the pollen grows down the style (Fig. 1). This is where the factor of compatibility of the pollen to the plant comes into play. Only compatible pollen can reach the ovules and fertilize them to grow into seeds. A self-compatible plant can create seeds (and fruits) using its own pollen while self-incompatible plants cannot. Self-incompatibility ensures genetic diversity because these plants only take in foreign pollen, which is advantageous for obtaining beneficial traits that could increase the fitness of offspring. Conversely, self-compatibility is useful for farming because SC plants will always have its own pollen to use to reproduce and make fruits to harvest.

This fall I studied the sharpleaf-groundcherry, Physalis acutifolia, a plant that can either be self-compatible (SC) or self-incompatible (SI). It is a member of the tomatillo genus and yields small round fruits that are enclosed by a papery, lantern-like calyx that grows after fertilization, as the fruits mature (Fig. 2). Examining the compatibility of pollen in P. acutifolia can give researchers, agriculturists, and horticulturists more insight on breeding and the evolution of P. acutifolia in dynamic climates within the Southwest region of the United States, as well as in agricultural settings. Additionally, it may also create predictions on how other species within genus Physalis may perform when being self-compatible or self-incompatible . Examining the fruit size yield of the edible members of the genus can be key to cultivating them efficiently. For example, by knowing how compatible the plant is with itself can allow agriculturists to devise an appropriate procedure on farming the largest fruit and knowing if either SC or SI individuals are best for farming.

Project Overview

My interest in botany and plant evolution led me to join the Smith lab with Chelsea Pretz as my mentor. I started assisting Chelsea on her project on the evolution of self-compatibility of P. acutifolia in 2021 under the interest of plant morphology and controlled greenhouse crosses. When I joined the Smith lab not only did it cater to my interests in plant biology, but also provide the ideal environment to obtain skills that are useful for a future working with plants. Additionally, working in a professional lab setting can help me become familiar with a lab work environment.

Throughout the semester, I was able to work in a greenhouse and lab setting. In the greenhouse, I learned to properly collect and organize data on fruits, flowers, and calyx. While in the laboratory, I got to observe and assist in the process of extracting and weighing styles. Later in the semester, I learned to extract seeds and take images of individual calyx and fruits. I then used the ImageJ program on these images to measure calyx length and width, as well as calculate fruit area size.

My independent project within the lab will act as preliminary data in looking into differences between calyx area and fruit area size among plants grown from different crossing treatments (SC self, SC/SI, SI self, SI/SC, note: SI self are seeds from SI individuals that had become SC within their lifetime). I was interested in seeing if there was a relationship between cross type and the size of calyx and fruit it yields. Using the data I collected from ImageJ, I selected 3 individuals of each treatment and took 3 measurements from each of these individuals to graph. To get a rough estimate of calyx size, I used the product of calyx length and width. I used a standard box plot and violin plot in Rstudio to visualize my data. The variations of boxplots I used were appropriate visualizations for what I wanted to examine because they display the quantiles and outliers of areas. This can allow me to see a general range of the area measurements in each treatment and see how much these ranges differ between the treatments.

The average calyx areas among the different treatments are relatively consistent, ranging from 3-4.5 cm² with some outliers in the SC self and SI/SC treatments. The p-value of 0.406 indicates that there is little or no significant difference between the treatment mean areas.

Across the treatments, there is high variation of the concentration of measurements and the fruit area means. Fruit area of the SI self treatment has the highest values around 1.5-2 cm², while SC self, SC/SI and SI/SC had varying spreads around 1-1.75 cm². The p-value of 0.00752 indicates that at least one of the treatments means significantly varies from the other treatment groups, which in this case, is the SI treatment.

Interpretation and Final Thoughts

From the results of graphing calyx and fruit sizes of the different treatments, there seems to be little difference between calyx sizes but some significance between fruit sizes. This shows how even though the calyx sizes are relatively consistent, the fruit inside could vary significantly, which is interesting since calyx and fruit grow simultaneously. The SI self treatment has the highest range of fruit area size, which could suggest that there is better performance of creating larger fruit by transitioning from SI to SC. This may also suggest that there could be inbreeding depression with the SC treatments because their fruit area ranges are lower than the SI treatment. Inbreeding depression happens when individuals of close genetic relation mate, and as a result, their offspring have reduced fitness. Smaller fruits decrease fitness because less seeds are produced compared to a large fruit. Although, because this is preliminary data, conclusions may change with larger sample size.

My independent research experience allowed me to contribute to data collection and get to do some data management and analysis on my own. My project challenged me to use skills and knowledge that I’ve learned in previous courses and apply them effectively to my data and analysis. For example, using Rstudio to plot my data and determine what kind of graphs would provide the best visualization of what I want to examine.

When collecting fruits and extracting seeds, I’ve noticed an interesting disparity between the SI and SC plants and the diversity of seed size and color. Some fruits yielded thin and pale seeds, while some were more round and of light or darker brown color. The thin, paler seeds look unviable and underdeveloped compared to the seeds with more pigment and rounder shape. This would be an interesting future project to consider studying because these contrasting seed types may be connected to their viability and can provide further insight on SC and SI individuals.

Undergraduate researcher Erica describes her fall research project in which she found the inflated calyces of Physalis fruits can hide fruit size differences

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Stories from fossil seeds

Anonymous — Thu, 06 May 2021 04:03:55 +0000

Stories from fossil seeds Anonymous (not verified) Wed, 05/05/2021 - 22:03

Reflections on a semester of undergraduate research in paleobotany by Abel Campos

Plants in the fossil record

Life has existed on Earth for a really, really long time. So long that It has become extremely difficult for us to determine just how old different groups of organisms actually are. One of the only viable options for us as scientists to figure out the age of different organisms is by studying the fossils they have left behind. Unfortunately, fossil evidence is not always readily available to researchers. Now, you may be thinking to yourself, “There seems to be plenty of evidence, look at all the dinosaur fossils that have been found!”. And while it is true that an incredible body of knowledge has been accumulated around the dinosaurs, other very interesting and important groups of organisms, due to a variety of different factors, have been studied significantly less than dinosaurs. One of these understudied groups is plants.

Plants are one of the oldest and most widespread groups of organisms on Earth, yet compared to dinosaurs, we have learned very little about the plants of the past from their fossil records. This is partly due to the fact that plant parts, like leaves and stems, don’t fossilize as well as bones, giving scientists less of a chance to find good plant fossils. However, this does not mean that there are no plant fossils at all, and another reason that little has been inferred about plants from their fossil record is that scientists have not paid the plant fossil record sufficient attention. The fact that plants maybe aren’t as exciting as things like dinosaurs, as well as the fact that plant fossils are less common, have deterred scientists from really studying the plant fossil record. The Fossils, Fruits and Seeds project is an attempt to direct the eyes of the scientific community towards the plant fossil record, and show that overlooking these fossils is not a viable option if we want to know the details of how life evolved on Earth.

My Experience Contributing to the Project

I joined the lab and started contributing to the Fossils, Fruits and Seeds project, under the mentorship of Rocio Deanna in January of 2021. It was the first time I had ever worked in a professional research environment, so the first month was dedicated to learning about the current state of research on the tomato family (Solanaceae) by reading about the most important findings from the last 20 years and discussing them with my mentor. Over the course of those discussions, it started to become clear that one of the foremost gaps in understanding was the timeline during which major groups in the tomato family evolved.

After becoming oriented with the current state of the field, I started learning techniques for data collection. One of the goals of the project is to review the tomato family’s fossil record and create a database of fossil fruit and seed characteristics. So, I was introduced to the twelve traits that would help indicate to us whether these seeds were members of the tomato family or not. I was then taught how to digitally check each fossil seed specimen for those traits. I spent the remaining three months working my way through the seed specimens that had not yet been analyzed (like the ones below) and checking each of them for the twelve traits we had decided on, and recording the absence or presence of those traits in our database. By determining whether these fossil seeds displayed traits indicative of the tomato family, we can start to get an idea of how long those kinds of traits have been present on earth, and when they started to appear. It also gives us the chance to appreciate just how morphologically diverse seeds can be, even within the same family.

On the right, a fossil seed described as Physalis pliocenica (within the tomatillo genus) and on the left, a seed from an extant species of angel's trumpet, Datura inoxia. The fossil seed has an attached structure on the bottom right that could be a food reward body for dispersers (an elaiosome). Elaisomes are only found in Datura, so the fossil might belong in Datura instead of Physalis. Photos by Rocío Deanna.

Next Steps for the Project

Now that the data collection of fossil seed traits is beginning to wrap up, we will be moving into fruit trait data collection in the summer. Since the currently known fruit fossils from the tomato family are older than the seed fossils, the compilation of a database of fossil fruit traits is a crucial step towards advancing our understanding of how and when the family’s most iconic traits started to evolve. A compilation of fossil fruit traits in conjunction with the data we have collected on fossil seeds will allow us to begin narrowing down the age of the tomato family. As more and more studies like this one are carried out, each pursuing the evolutionary history of specific group of plants, we as a scientific community will be able to build a more comprehensive picture of how flowering plants evolved on Earth.

Undergraduate researcher Abel Campos shares his experiences conducting paleobotanical research on Solanaceae seeds.

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Remote CUUB interns from Arizona to North Carolina

Anonymous — Tue, 11 Aug 2020 03:53:49 +0000

Remote CUUB interns from Arizona to North Carolina Anonymous (not verified) Mon, 08/10/2020 - 21:53

The pandemic has brought many changes this year. We originally planned to host summer interns in person, but instead organized remote internships. While we wish we could have met in person, one unforeseen benefit of doing internships remotely was the potential for students to pursue projects relevant to their communities and regions. This summer, we had the pleasure of working with three undergraduates who participated in the CU Upward Bound (CUUB) program as high school students. Each was paired with a graduate student mentor and carried out independent research while making an educational video inspired by their experience. Amy and Luke worked together to oversee this mentorship program. Here's what each of them did:

Chantelle Yazzie, mentored by Chelsea, is a student at Utah Valley University and member of the Navajo Nation. She designed a project around a native plant of cultural importance in her community,Thelesperma megapotamicum (Navajo Tea). This plant is used medicinally and also as a dye. She gathered samples from populations near her reservation and compared their dyeing properties and flavonoid pigment content. She is continuing this research with the aim to publish it in the future. You can hear about her work in this video she produced.

Mikayah Oxendine, who recently transferred from Robeson Community College to UNC Chapel Hill, spend the summer working with Sukuan on bioinformatics and carnivorous plants. Since she is majoring in information science, she learned the basics of Python. She also took advantage of her location in North Carolina to study local carnivorous plants, which are abundant nearby! Mikayah and Sukuan made this fun educational video about carnivorous plants, where they live, and the conservation issues they face.

Chandra Jacobs, an undergraduate at the University of North Carolina Pembroke, worked with Jesse, to build a phylogeny of medicinal plants from plastid sequences on Genbank. Chandra's interests are in medicine and after graduating this December, she will be applying for nursing school. She and Jesse created this educational video to explain phylogenetics concepts and introduce some of the applications of phylogenetics in medicine, like tracing viral outbreaks (hello, COVID!).

We mentored three summer undergraduate interns, all alums of the CUUB program for Native students. Read more to find out about their work and outreach videos!

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