nutrient stress project 3

Project by group gehsbeardsleyfall2019

Info

Explore While the effects of a deficiency in zinc on the Arabidopsis thaliana have been tested thoroughly, the impact of an increased amount of zinc in this plant has not been explored as substantially. Over the course of our research however, the impacts of this were determined to consist of the...
Research Question To what extent does an increased amount of zinc impact the germination, chlorosis, condition of the leaves (color, strength, length, etc), and height of the wild type (Arabidopsis thaliana) and its mutants nca1-1 and zip-2?
Predictions Controlled Group Colombian Wild Type is expected to grow relatively normally. Germination is expected to be relatively normal (at least 20 out of the 30). The colors of the plant and of the leaves are anticipated to be standard. The overall conditions of the plant are believed to be healthy and...
Experimental Design Independent variable: The amount of zinc (toxic levels) available to the wild type nca1-1 and zip-2 Controls: Amount of water Temperature Light Air quality Same containers Amount of test subjects Other than the experimental amounts of zinc, same amount of micronutrients in the soil ...
Conclusion In all, the research conducted in this experiment indicates that the Colombian Wild Type and zip2 mutant were deeply impacted by zinc toxicity, however the nca1-1 mutant did not depict a significant difference through the use of stem height and biomass. Colombian Wild Type The results of the...

Updates

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PlantingScience Staff
has been updated by administrator
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.

After the end of the session, we will be updating the platform and archiving groups and projects, after which time new updates/posts will not be able to be added to projects or groups. Please come back and visit the PlantingScience Project Gallery anytime to view this project in the future. You can search the Gallery by keyword, team name, topic, or school name.

Good bye for now.
Warm regards,
The PlantingScience team
Julie Fowler
said

Hi all!

I just wanted to pop in as the liaison and say that I was very impressed with your final poster! The layout and organization rivals a lot of what I see in posters made in undergrad and beyond and I am proud to see you all really seem ready to pursue science in the future if you would like to!

Good luck and have a great rest of your semester!

Julie

    Marina Borges Osorio
    said

    Hi team,

    I totally agree with Julie. Your work is comparable to university-level science research, so I hope you are proud! I also hope this is just a start and you can dive deep into your scientific endeavours in the future.

    Have an awesome festive season! :D

ella
said

Dear Marina,

Thank you so much for your comments on our poster! We will be sure to include them in our final project. Thank you so much for also giving us some more clarity on why the nca1-1 mutant performed as it did! Concerning your comments on our nca1-1 there was slight difference on our graphs but it was very difficult to tell. On the height graph the control had an average height of 4.94 cm by the end of the experiment and the added zinc had an average height of 5.12 cm. The biomass for the nca1-1 was even more difficult to identify a difference as the control had an average mass of 0.04186 g and the increased zinc had 0.04184 g. We be,eve this data shows a small impact from the zinc but not enough to be noteworthy. Have a good day!

Best Wishes,

the Zinc Team

    Marina Borges Osorio
    said

    Hi team ,my pleasure!

    Well, usually we don't consider such small differences as you reported for nca1-1, so you better say there's no effect of zinc in this mutant until you prove otherwise (after doing many repeats of this experiment and actually seeing if you obtain different results).

    Best luck in your poster presentation tomorrow! And I like your new team name :)

     

Marina Borges Osorio
said

Hi Ella, Teresa and Kuba,

First of all, thank you so much for your kind words and acknowledgements! I must say you should be proud of having this project accomplished, despite the setbacks.

Although this was my first time with Planting Science, I can tell you for sure this project was in a higher level of research (comparable to postgraduate work) and hence more difficult to perform than the other projects I've mentored. So congrats for having it done and analysed! 

It's been a pleasure mentoring your team, especially since this topic was very close to my PhD research in Arabidopsis nutrient sensors. So very happy to see you making in through. I hope you could learn some more about the life cycle and the needs of plants, as well as on how to use the scientific method to conduct an investigation, the importance of multiple repetitions for each variable in question, and how setbacks and experimental issues are normal in the life of scientists.

Regarding your poster, I think it looks super comprehensive and you have a nice mix of text, pictures and graphs. I think you have a good set of new hypothesis and conclusions on the effects observed for the WT plants and zip2 mutants. I do have a couple of questions about things that you may want to check further, in case there's still time for some editing:

1. When you mention experimental 'errors' that might have led to inaccurate results, it's probably nicer to say 'setback' or 'issues' rather than errors. Every scientist has to deal with these setbacks, especially during the first time an experiment is performed. The important thing is that you learn from your attempts about the factors affecting your experiment, for example, fungus contamination and air humidity, drought and sample variability, so that you can improve your experiment the next time you perform it.  :)

2. Regarding the shoot biomass of nca1-1 control x nca1-1 treatment. Was there a difference after all or not? For what I see on your graph there's no difference at all. However, you mentioned in the text and in your conclusion that the control plants did weigh more...

3. Still on nca1-1. I believe you did not see such a strong stress response to Zn treatment, as you were expecting, due to two factors: firstly because, according to Li et al (2015), the stress sensitivity of nca1-1 is evident at high pH (8 or above), and the Zn sulfate solution you used as treatment is acidic, hence the expected effect was hindered. Plus, as I've mentioned in other posts, the nca1-1 mutant line does not have the NCA1 gene functional, and also according to Li et al (2015) the Zinc ion binding property requires NCA1. If the gene is not functioning, then it makes sense that these plants are unable to bind to zinc when required. So that might explain the higher tolerance to Zn toxicity you observed. :)

I think that's it! I hope you enjoy presenting your work and exchanging your Planting Science experiences with your classmates. Have a nice Thanksgiving break too!

All the best,

Marina

 

kuba ps745174
said

Hello Marina,

Thank you so much for all the help you have provided with our project. As finalize details on our poster, I would like to thank you for all advice you provided on our experiment and about the mutants as it benefitted us greatly to have someone who knew more about our topic help and guide us through it!

ella
uploaded PPTX-Genigraphics-Poster-Template-24x48.pdf in project files
ella
said

This message is from Teresa as her technology is malfunctioning:

Hello Marina!

I want to say thank you so much on behalf of all of us for helping us with our experiment. We’re almost done with our poster and can’t wait for you to see what we’ve done. Once again, thank you for your knowledge and advice throughout the project, it was a huge help. 
 

-Teresa 

ella
said

Dear Marina,

 

As our research comes to a close, we would like to especially thank you for the work you have done for our group. Through the trials and frustrations, you have continued to lead us on the right path. Thank you for your continuous encouragement and advice when we were lost. Thank you also for your patience with us throughout the experiment. We are very appreciative of the time that you put into our research as well as your assistance in writing and testing. The work that has been completed could not have been done without you by any means and we hope that our final product is worthy of the effort you put into our project. We also hope that this experience has been a good one, and that you may continue to develop your research as well as be an advisory to other aspiring researchers such as ourselves. We wish you the best of luck in your work and cannot thank you enough for your help with ours!

 

Best wishes, 

El

ella
changed the project settings
ella
updated the project info
Marina Borges Osorio
said

Hi Ella, Teresa and Kuba!

Yes, please let me know if there's any support or feedback I can give you to help you with the presentation of your results. I'll be glad to help. Otherwise, I'm looking forward to seeing how your poster turns out soon...

 

Also, once you make your final conclusions, please fill them in at the Project Info section above, so that future groups have access to your full project.

All the best,

Marina

Julie Fowler
said

Hi all!

How is the finishing up of your experiment going? Do you have any questions about poster-making?

Julie (Liaison)

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.
Marina Borges Osorio
said

Hi Ella, Kuba and Teresa,

Good work with keeping an intensive scientific record of the facts on your journal and taking lots of pictures! 

It's a shame you've had some setbacks with fungal infestation and the drought effect that followed as an attempt from trying to make the plant growth environment less humid. This is normal though, sometimes we have to perform pilot experiments to check whether our available growth room, chamber or box are ideal for plants. As usual, we learn from observation and then repeat the experiment including the optimized growth conditions.

Regarding the drought, in particular, this is clearly due to extra transpiration by plants from not having the boxes covered. So great effort in noticing this and acting fast to adding extra water, saving the plants that you could! I suggest you discard the really dry ones and do not include them in your final measurements since this will not be an accurate representation of each genotype.

Regarding the flowering observed in multiple plants, this usually means that the plant is reaching maturity and heading toward the end of its life (Arabidopsis plants die out once the new seeds are formed and matured). So it will eventually happen in normal growth conditions, and this will depend on how many hours of daylight have the plants been exposed to every day. This is called the photoperiod.

Could you please let me know the photoperiod in your experiment? The shorter it is (~10 hours), the longer it will take for plants to flower, and vice versa, longer photoperiods (~12 to 16h) lead to faster flowering. However, you're right that in more stressful conditions, plants may eventually flower early in order to ensure the next generation (seeds) will be produced before the stress is too strong. 

I think your experiment must be due to finish by now, since your plants are already quite big. So time to ensure you organize your data well and make graphs, bar plots and panels with photos to show what are your inferences and conclusions. Usually we give priority to showing results that you can measure (quantitative data) as well as photos, so I hold my suggestion to weigh your shoots on the very last day, and make plots with shoot diameter as well as the height that you've been showing already. And the day when each genotype started to flower could be nice too. 

I hope that's helpful for now! Anything, just ask. 

All the best,

Marina

kuba ps745174
said

Dear Marina,

We uploaded a few files to update you on how our plants our doing. If any problems occur with viewing our documents like the last time then just let us know.

kuba ps745174
updated Pictures.pdf and 2 more files in project files
ella
said

Dear Marina,

We are distraught to hear you could not see the pictures we posted. We will post some more today and have a bigger collection of photos by Sunday so you may see the progress of our plants throughout the week. 
 

Best wishes,

Teresa, Kuba, and El

    Marina Borges Osorio
    said

    Hi Ella, 

    Oh maybe there's a confusion. I hadn't seen your pictures on October 25 but after you've uploaded the file again I could see them on October 28. So all good, I hope you can have a look at my suggestions posted below (on October 28). 

     

    I'm looking forward to seeing some updated photos and data from this week! 

    All the best, 

    Marina

ella
said

Dear Marina,

It’s great to hear from you! Thanks again for your support through this experiment!

As for your comments;

  1. Yes we have noticed differences between the Wildtype control and the Wildtype treatment. We have noticed a difference in the soil, as the soil is noticeably more dried up than the control. We hypothesize that this is because the plant is taking up more nutrients to combat the extra zinc. We have also noticed differences in the coloration of the leaves and the condition of said leaves. As for the coloration, there are visible patches of yellow. This was also expected as our research emphasized this as significant symptoms of zinc toxicity. The condition of the leaves has also been impacted as the treatment plants showed some weakness and were frail. This was also expected due to zinc toxicity. What was unexpected from these experiments however, was the short time between starting the treatment and the signs of these symptoms.

  2. While the adding of extra plants would be extremely helpful to our experiment, it is not possible for us to add them at this point. This is due to the lack of time we have for the experiment as well as the resources we have been provided with. So I am sorry to report that adding more seedlings will not be possible. However you brought up some good points in height and growth variability and we will be sure to include this diversity in our next measurements. 

  3. The biggest concern when measuring our mutants is the variability based on its genetics. In other words, it is difficult to distinguish the growth of these plants as being caused by zinc toxicity or by its genetics (because it is a mutant). In this variability however, we have not noticed many differences other than the mutants that are controlled seem to grow a bit better than the ones receiving the treatment. 

  4. Our last day of measurement is scheduled to be on November 8th. From now on we will take your picture suggestions into account, but here are the ones we have today just to give you a quick idea of how everything is going. Those can be found in the updated pictures file we have attached.

 

Thank you so much!

-Ella, Teresa, and Kuba

      

 

    Marina Borges Osorio
    said

    Hi guys, 

    Happy to hear your experiment is progressing and that you're putting some thought on the possible reasons behind your observations. Great work!

     

    I believe you might have forgotten to attach the updated Pictures file, as I can only find the old one. Looking forward to see how you're plants are doing this week!

    Cheers,

    Marina

    Marina Borges Osorio
    said

    Hi everyone,

    Glad to see your progress! It looks like you’re really diligent around your plants! Plant physiology experiments require strong attention to details. Through intense observation, you end up developing an awareness of what healthy plants look like and what are the multiple factors affecting plant health and leading to stress. It also good to see that you’re keeping record of your data, through journals and pictures, and even starting to transform this data into charts!

    Here’s my feedback for now:

    1. Fungus infestation: I’m sorry to hear about it, this is a common issue that we have to deal with when growing plants in soil. I absolutely agree that you need to remove the lids covering your containers! I apologize I didn’t notice that there were lids on your proposal scheme, otherwise I would’ve warned you earlier. Usually we cover trays during seed germination (sometimes with a plastic wrap) so that there’s plenty of moisture for the germination process. However, when lids are kept for too long they create a highly humid environment, increasing the chance of fungus infestations. One question, did you see this infestation throughout your experiment or only affecting some genotypes (Columbia, nca1-1 or zip-2)? This will be relevant for interpreting your results later on.

    2. Zn treatment and effects: I can’t really see the leaf discoloration at this stage, but maybe it’s just because you’re seeing it live and close up. If it is in fact due to Zn toxicity, symptoms should be aggravated as the experiment progresses, so let’s keep an eye. Make sure you take lots of photos!

    3. Data recording and presentation: it’s great that you’re taking lots of measurements on a regular basis. This will help you create plots that contain several time points. It would be nice to include them in your plant height chart you have now. It would also be good to include your sample deviation values (error bars), assuming that you have created the charts from average height (including multiple plant measurements per genotype/treatment). Is that right?

    Also, it would be nice to see the charts of shoot diameter, since you’ve been recording this measurement throughout. At this stage of little seedlings, this information is very important to compare growth, since we can also clearly see it from the pictures you’re taking.

    I still hold my suggestion to cut off and weigh whole shoots as a final measurement at the end of your experiment.

    4. zip2 mutant variability: you’re absolutely right that the variability seen in germination and development of this mutant line is due to it’s genetics. In fact, it is likely due to the involvement of ZIP2 gene in epigenetic regulation of plant development, such as gene silencing. I’ve had similar experience before, it seems like it’s not easy to try to obtain even mutants for these types of epigenetic genes, some plants show clear growth defects and some plants don’t. But let’s see if despite these difficulties you are able to assess the effect of Zn treatment.

    Hope that's helpful. Best luck!

    Marina

kuba ps745174
said

Dear Marina,

We just sent out a few files just to update you on how we are doing. There’s a journal with a few annotations with what has been going on with our project. Additionally there is a data chart and a few pictures on how our plants are growing. 

kuba ps745174
uploaded Data charts.pdf, Scientific Journal.pdf. Updated Pictures.pdf in project files
Marina Borges Osorio
said

Hi Ella, Teresa and Kuba,

Thank for uploading the figure legends. It looks like your experiment is up and running! 

1. I assume you have already started your zinc treatment on the pots marked with Z, is that so? I can already see clear differences in plant growth between the treatment and control, at least in the Columbia WT. Do you see the same? Is it as you expected or contrary to your expectations?

2. Regarding the Arabidopsis mutants, I see more variability in growth aside from less growth. I suppose that's normal since these seeds struggle more to develop, so don't be scared! That's why I suggested you to add as many seeds as you can of a single genotype in each treatment. These are called replicates and in the end, you can try to average the effect that you see overall (and perhaps even exclude the seedlings that don't follow the overall pattern, but only if you have a decent amount of seedlings left).

3. Still on the mutants, do you see any effects on the Zn treatment versus the control? Is it what you expected or not? Just to be clear: it's totally normal that sometimes we don't see any effect or the effect observed is different from our expectations. I'd be happy to hear your thoughts...

4. Until when are you planning to carry on your experiment? Have you already decided what you'll do in terms of data collection until the end of the experiment? I suppose pictures are great because you can monitor growth. One suggestion is to set a camera stand that is always kept at the same height to ensure you can actually measure growth. Including a ruler on the outer side of each tray when taking photos is also a good idea for this aspect. Another suggestion is to weigh the shoots of your seedlings of each batch of plants at the end of your experiment. Weighing roots in soil is too messy so don't bother! Let me know if you need more help on that.

Best luck for the coming week of treatment! Any questions, just shoot! :)

Cheers,

Marina

 

ella
updated Pictures.pdf in project files
Marina Borges Osorio
uploaded Proposal organizer_suggestions_Marina_new.docx in project files
Marina Borges Osorio
said

Hi Ella, Teresa and Kuba,

You're welcome, I'm super glad to help you! I'll upload your proposal as a word file with my comments to ensure you guys can check them out.

I noticed you have also uploaded pictures of your experiment now, how exciting! Could you perhaps add legends or a description to each picture so I can understand which genotype (Columbia WT, nca1 or zip-2) and Zinc treatment is on each tray?

All the best,

Marina

PS.: You're welcome to call me by my first name if you wish :)