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Plants have mass, they matter!

Project by group gehsbeardsleyfall2018

Info

Explore We are experimenting to discover how different wavelengths of light impact wildtype plants and mutated plants. We’re using the mutation of Phytochrome B at gene number AT2G18790. This mutation causes de-etiolation, which results in the plant being unable to perform shade avoidance.
Research Question How do the wildtype and mutant of Phytochrome B differ in hypocotyl length and leaf area depending on the light source: close red, far red and white?
Predictions If we place the mutation of Phytochrome B seeds; (with a mutation at the gene AT2G18790) in far red light and close red light, the hypocotyls will be shorter, leaf area larger in comparison to the wild type. If placed in white light, the mutated seeds will be similar in comparison to the wild...
Experimental Design We have three different set ups. We have a far red light, a white light with red film, and a white light. The red lights are used to simulate shade and the white being light. In each of the three groups we have two different planting chambers. Each setup consists of two planting chambers:...
Conclusion Our experiment tested the effects different wavelengths of light have on the growth of Landsberg Erecta and mutation phy-5 in Phytochrome B. In Far Red Light: both the mutant and wild type were unable to grow as expected, and died. In Near Red Light phy-5 does not etiolate whereas Landsberg...
About this Project

Updates

Get to know your team’s scientist mentor, who will encourage and guide you through the scientific process of discovery. The more you share your ideas and research info, the more your mentor can help. You may also hear from a scientist mentor liaison who will be helping all the teams in your class.
PlantingScience Staff
said
Farewell and Best Wishes
As this research project is now in the final stages of wrapping-up, we wish to thank everyone who participated in this inquiry; the students, mentors, teachers and others behind the scenes. We appreciate all of your efforts and contributions to this online learning community.

Scientific exploration is a process of discovery that can be fun! There are many unanswered questions about plants just waiting for new scientists to consider, investigate, and share.

We will be archiving groups and projects on December 17, after which time new posts will not be able to be added. Please come back and visit the PlantingScience Project Gallery anytime to view this project in the future. You can search the Gallery by key word, team name, topic, or school name.

Good bye for now.
Warm regards,
The PlantingScience team
PlantingScience Staff
has been updated by administrator
PlantingScience Staff
has been updated by administrator
Emmie
updated the project info
PlantingScience Staff
uploaded FINAL Research Planting Science Poster.pdf in project files
Emmie
uploaded FINAL Research Planting Science Poster.gslides in project files
PlantingScience Staff
said
Looks like you are in the final stages of your projects.
It’s great to see that teams from your school are wrapping up and posting conclusions. Enjoy the final stages of your project, and feel free to post any final comments or questions you have for your mentors.
Chris J. Meyer
said

Hi Ammarah, Salmah & Emmie,

It’s great to see that you had some interesting results from your experiments! I hope your class presentation was also a success. You all conducted great work and had plenty of thoughtful questions on the topic; these are some of the keys to success in scientific research.

From this experience, I hope you consider higher learning and careers in the plant sciences. Many colleges and universities offer such programs, plus there is a large and engaged community of plant scientists and teachers online as a part of professional societies such as the American Society of Plant Biologists (https://aspb.org/) and the Botanical Society of America (https://www.botany.org/).

Good luck at school and with all your future pursuits!

Ammarah
said

Dear Chris J.Meyer, thank so much for all the help that you have provided throughout our experiment. Your guidance really aided us and for that we are so grateful. 

Sincerely, Ammarah

Salmah
said

Hi Chris, 

We'd like to thank you for guiding us through our project. Your feedback really helped us learn as much as we could about our work and will help us even more later on. Thank you, and good luck with any future research!

Emmie
said

Hi Chris, we wanted to say personally thank you much for helping us. You were very helpful with opinions on what’s best for us. I personally appreciate how much advisory you gave us. I know you are very busy and so it means a lot that you took time to help us, thank you so much. 

Emmie
updated the project info
Salmah
said

Hi,

Today is our last day of measuring the plants. We are currently finding the area measurements of a cauline leaf from each plant. We’re using a program called Image J to find the leaf area.

Emmie
said

Hello, 

thank you for the advice. Our teacher said she has a program that calculates leaf area... so we are thinking to use that. We will measure each rosette and find an average, we will use that to create a bar graph. 

Chris J. Meyer
said

Thanks for sending along the labelled photo of some of your plants.

First, there are two types of leaves in Arabidopsis: 1) “rosette leaves” located at the base of the plant, and 2) “cauline leaves” located further up the stem. I see that the focus of your measurements will be rosette leaves, which is good. (That said, you may also want to measure the area of cauline leaf blades…)

Your blue labels denote the widest diameter of the whole rosette. Such a measurement includes the lengths of rosette leaf blades and petioles. It is a good idea to measure this so that you can then calculate total rosette area. There is advanced software that helps scientists calculate this properly, but feel free to assume the general shape of the whole rosette and use an appropriate area equation (for example, area of a circle = pi * radius2). Calculate rosette area for each white light wildtype plant (how many plants?), and then calculate the average ± standard deviation. Repeat these same calculations for all other groups of plants (white light mutants, red light wildtypes, red light mutants). All this data would look great together on a bar graph!

Your red labels specifically denote the length of rosette leaf blades, but you may also want to measure the width of these blades. Then you can then calculate rosette leaf blade area using an equation such as for an ellipse = pi * length radius * width radius. Calculate leaf blade area for each healthy and mature leaf on each white light wildtype plant (how many leaves and how many plants?), and then calculate the average ± standard deviation. Repeat these same calculations for all other groups of plants (white light mutants, red light wildtypes, red light mutants). All this data would look great together on a bar graph! In addition, you may want to measure petiole lengths as they appear shorter in mutant plants compared to wildtype.

Emmie
updated the project info
Emmie
uploaded DE446785-C930-4878-85D0-EEA02E5A4161.jpeg in project files
Emmie
said

Hello! 

Thank you for your opinion. We are thinking about just focusing on leaves and stem length.. with the idea of leaf area, we have a question. In what way would you recommend measuring the leaves. The total leaf area (blue) of the entire plant or individual plants (red)? I attached pictures to show the two idea of measuring I’m describing. 

Chris J. Meyer
said

Hi team,

Good to hear that you are getting interesting results. Plus, it is a valuable experience for you having to discard the “red light plants”. Although scientists have good intentions when starting a new experiment, they also need to prepare for the possibility of unusual or unexpected outcomes and then adapt appropriately without getting overly frustrated. Perseverance, optimism, and thoughtful tweaks to experiments are often needed.

While quantifying chlorophyll in leaves is an important measure of plant health, you may be able to omit this analysis if it will be too time consuming or labor intensive. That said, you should at least photograph and qualitatively observe the green color of the leaves, and then describe similarities or differences in your results. You may want to suggest to your teacher to purchase a hand-held chlorophyll meter for future classes. Here is the one I’m thinking of: www.atleaf.com

Emmie
said

Also... do you think it would be okay if we didn’t do chlorophyll. We were thinking about just sticking to leaf area and stem length because they correspond with each other. There doesn’t seem to be much of a difference in chlorophyll.. or enough to do a whole section about.

Emmie
updated the project info
Emmie
said

Hi Chris, 

today is October 30 and we are on day 18 of our experiment. Our red light plants have dies so we were told to dispose of them. Our red film plants are working perfectly! The wildtype is tall and has small leaves, whereas the mutant is short and wide with many thick leaves. In white light, our wildtype is growing very tall! Our mutant is pretty tall as well. Everything is on point. We will probably measure the leaf area in less than a week!

Salmah
said

Hi Chris,

Today is day 13 of our experiment. We took measurements of all our plants and realized that our plants in red light have stopped growing. We won’t be measuring them from now on. The white light wildtype and mutant plants have grown at similar rates. We also noticed how for the white light with red film, the WT has a longer stem and less leaves, but the mutation has a shorter stem and many leaves. We’ll keep collecting data for the next few weeks!

Emmie
updated the project info
Emmie
updated the project info
Emmie
updated the project info
Emmie
updated the project info
Emmie
updated the project info
Emmie
uploaded Far red light comparison.jpeg and 5 more files in project files
Emmie
uploaded White light red film comparison.jpeg in project files
Emmie
uploaded White light red film comparison.jpeg in project files
Emmie
uploaded Copy of Research Report .pdf in project files
Emmie
said

Okay! Thank you so much! 

Ammarah
said

Hey! We need some clarification about the Phytochrome B. We originally said that the mutant will promote etiolation and have a longer hypocotyl and petiole length along with lower chlorophyll abundance. However our teacher said that it was the opposite. The regular type promotes etiolation while the mutant phy-B will have a shorter hypocotyl and petiole length along with a higher chlorophyll abundance. What do you say? Thanks in advance!

    Chris J. Meyer
    said

    Hello,
    For clarification about the Phytochrome B mutant, see the TAIR website that I linked for you previously:
    https://www.arabidopsis.org/servlets/TairObject?type=gene&id=34960
    On that site, look to the “Description” where the following two sentences are important:
    “Red/far-red photoreceptor involved in the regulation of de-etiolation.”
    “Overexpression results in etiolation under far-red light.”
    The second sentence is interesting, because it implies that if the mutation results in an “over expression” of the gene, then the seedlings will be etiolated in far red light. However, I’m assuming that your mutation does the opposite; that is, the gene is “not expressed”. Hence, we would expect seedlings not to be etiolated under far red light.
    Also, remember that etiolation is a normal developmental trait for wild type plants grown in the dark. So we expect the Landsberg wild types grown in the dark to have longer hypocotyls and less chlorophyll than wild types grown in white light conditions.

    Your experimental setup looks great. Looking forward to seeing the results!

Ammarah
said

Hey! We need some clarification about the Phytochrome B. We originally said that the mutant will promote etiolation and have a longer hypocotyl and petiole length along with lower chlorophyll abundance. However our teacher said that it was the opposite. The regular type promotes etiolation while the mutant phy-B will have a shorter hypocotyl and petiole length along with a higher chlorophyll abundance. What do you say? Thanks in advance!

Ammarah
said

Hey! We need some clarification about the Phytochrome B. We originally said that the mutant will promote etiolation and have a longer hypocotyl and petiole length along with lower chlorophyll abundance. However our teacher said that it was the opposite. The regular type promotes etiolation while the mutant phy-B will have a shorter hypocotyl and petiole length along with a higher chlorophyll abundance. What do you say? Thanks in advance!

Emmie
uploaded 2148DAE2-3A9E-4119-802A-D0A96B73FCB9.jpeg and 9 more files in project files
Emmie
said

Thank you for the help. We attached pictures of our setup!

Chris J. Meyer
said

Hi, thanks for uploading your proposal. Here are a few things to consider and revise as you begin your experiments.

  • Be sure to clearly distinguish between germination rate, hypocotyl lengths and petiole lengths; you can collect data for each of these three parameters. Plus, you may want to calculate leaf area near the end of your experiment (or just before processing for measuring chlorophyll abundance). To do this, measure leaf length and width, and then plug those values into an area equation that best resembles the leaf shape (ellipse = π x length radius x width radius; circle = π x radius2).
  • When you are germinating seeds and then growing seedlings in tubes, what will the tubes contain? Soil, agar, water, something else?
  • When stating your hypotheses, be specific about what you are comparing. For example: “We hypothesize that in far red light, Arabidopsis plants with a Phytochrome B mutation will have longer hypocotyls and a lower concentration of leaf chlorophyll compared to wild-type plants. When plants are grown in white light, we expect the Phytochrome B mutant and wildtype to have similar hypocotyl lengths and leaf chlorophyll concentrations.”
  • Interestingly, in etiolated plants that lack chloroplasts, there is another type of plastid called “etioplasts”. Etioplasts contain membrane lattice structures called prolamellar bodies. In wildtype plants, if an etioplast is exposed to light, the prolamellar bodies can develop into thylakoids, leading to the formation of a typical chloroplast. (Do you think this will happen in your Phytochrome B mutants?) I have attached three figures to help you visualize etioplasts and chloroplasts.
Chris J. Meyer
uploaded Chloroplast - transmission electron micrograph.jpg and 2 more files in project files
Emmie
said

I just submitted our current research proposal! 

Emmie
uploaded Copy of Research Report .gdoc in project files
Chris J. Meyer
said

Thanks for the info and questions regarding the leaf chlorophyll concentrations. Keep in mind that the plants will probably need to be at least 35 days old before you can harvest leaves for chlorophyll analysis. Also, if using a spectrophotometer, you will need to first grind the leaves in a small plastic tube with a solvent (such as acetone – also known as nail polish remover!). Then the resulting green liquid (chlorophyll solution) can be quantified with the spectrophotometer; this is a great way to measure chlorophyll concentrations.

A green colour scale is a neat idea, however I do not use such scales. (If you ask an artist or graphic designer, they may be able to help.) Instead I recommend simply taking photos of representative leaves from both genotypes and all light treatments. Have all the leaves side-by-side when photographing, then qualitatively describe the green colour differences. Combining qualitative observations (photos) with quantitative data (chlorophyll concentrations presented on a graph) is an excellent way to report your findings in a presentation or report. See the attached PDF file – particularly the Figures – for good examples of how scientists display leaf photos and chlorophyll data together.

Looking forward to hearing more exciting ideas!

Chris J. Meyer
uploaded Ling etal 11 Phytosyn Res - SPAD equation w Erratum.pdf in project files
Emmie
said

Also, our plan is to have a color scale to compare the leave colors to. It will be a spectrum of green... do you have anything that can help us with that?

Emmie
said

Hi, 

We were planning on having a control... so one of each type in just white light. Then have one of each is the 800 red light. As well as, one of each type in a white bulb with a red film. We will test out as many of the seeds as we are provided. We have a scientific proposal we have been writing up as a team... we will submit that as soon as possible. Thank you for all the help. 

Chris J. Meyer
said

Hello,

If you have time and space, I recommend trying both red light sources (the 800 nm far red source and a white light bulb covered with a red film). But if you can only try one of these, then the red film is probably best so that you can test the red wavelengths in the visible spectrum. Also, don’t forget that experimental controls are essential – complete darkness and white light. Without these controls, you can’t properly examine and describe how your red light treatments affect plant growth and development. (In fact, controls are always required when conducting any scientific experiment.)

Next, when designing experiments, it is important to think about “replicates”. How many seeds will you test for germination rate for each light treatment? The more seeds and plants you can grow and examine, the better/more rigorous your results will be; meaning your results are legitimate and typical, and not caused by chance. Also, I’m assuming you are germinating the seeds on a piece of wet paper in a petri dish. How many plates do you plan on using? If possible, I recommend at least three plates per genotype (meaning wildtype and mutant) for each light treatment, and of course many seeds (minimum of 10?) in each plate.

Lastly, could you briefly describe for me how you plan to measure chlorophyll abundance.

Keep up the good work!

Emmie
said

Thank you!   Overall we have been trying to figure out the setup of our experiment now. We read that our mutation respond to close red lightly ranging from 780-622. The light we are provided is an 800. Would it be worth trying the 800 or should we try a different technique such as possibly a red film over the light? We also edited our purpose a bit:   We will search for how the mutation of red-light photoreceptors in Landsberg Erecta as shown in Phytochrome B, impacts the rate of germination and chlorophyll abundance. Thank you again. 

Chris J. Meyer
uploaded 01 chlorophyll absorption spectra.jpg in project files
Chris J. Meyer
said

To get you started with some background research on phytochrome B, try the following two websites:

https://www.ncbi.nlm.nih.gov/gene/816394

https://www.arabidopsis.org/servlets/TairObject?type=gene&id=34960

Both of these websites are used by professional scientists to access peer-reviewed information and data about Arabidopsis. Importantly, on the “arabidopsis.org” site, as you scroll down the page, you will see a short description of your mutation, photos of what different mutant plants typically look like along with links to published research articles.

Admittedly, there is way too much expert-level information on both of these websites for your project. But you should be able to pick out a few things that will be valuable for you. Plus, it is good to familiarize yourselves with the types of information that scientists use on a daily basis.

Next, you may need to revise your statements about “close red light” and “far white light”. Often in plant science research, people are interested in the effects of “far red light” on plant growth and development. Please look up information about far red light. Also, don’t forget that white light is actually a collection of all the coloured wavelengths in the visible light spectrum (recall what happens to white light when it moves through a prism). I’ve attached a figure from a textbook that I use with my students that shows all the colours in the visible light spectrum, along with the wavelengths where chlorophyll pigments absorb and consequently where photosynthesis is most active. I hope this figure will help you understand and describe part of what is happening in your mutant and wildtype plants.

If you have any questions, please ask :)

 

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