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

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

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

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

 

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!

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 

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

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

Hi all!

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

Julie (Liaison)

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.

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

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.

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

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

      

 

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. 

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

 

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 :)

Dr. Osorio, 

We also wanted to let you know that we can not access the comments that you made, but can only see that there was a comment.

We’ll be in touch,

Teresa, Ella and Kuba 

Dear Dr. Osorio, 

Thank you so much for the detailed advice on our project! We really appreciate your in depth research on our topic and continual determination to help us achieve our goals. We are updating our proposal now to fix the problems that you’ve discovered. Hope you have a great rest of your day! 
 

Teresa, Ella and Kuba

Dear Dr. Osorio, 

Thank you so much for the detailed advice on our project! We really appreciate your in depth research on our topic and continual determination to help us achieve our goals. We are updating our proposal now to fix the problems that you’ve discovered. Hope you have a great rest of your day! 
 

Teresa, Ella and Kuba

Hi Marina,

To answer your question on why we are doing an increased zinc amount in our experiment, it is because we do not have the resources to conduct an experiment with decreased zinc. It is much easier in our situation to produce a solution to increase the zinc levels than decrease them. However, there is not as much research containing the results of increased zinc on the Arabidopsis thaliana, and we think the experiment could be very interesting in respects to finding new information on zinc toxicity.

 

As for creating the solution, we are planning on creating a solution made of zinc sulfate and giving to the plant in place of water. We are working with our chemistry honors teacher here in order to create an adequate solution that will show the symptoms of zinc toxicity without killing the plant. This will have no effect on maintaining the other nutrients in the plant as we are only adding excess zinc.

 

The importance of the zip-2 mutant in our experiment is related to its possession of a deficient gene in cellular transport, greatly lessening the amount of passive/active vesicular transport through the plasma membrane, and thus it may not accomplish transporting all the extra zinc in the soil. We hope that this will give us some interesting results. We also noticed that there was not much research containing the results of zinc increases with this plant and we believe it could provide some new evidence on how zinc impacts this plant in general. 

As of now, we will try and compile a better explanation of what we know about zip-2 and share it with you asap.

Thank you so much,

Teresa, Ella, and Kuba

Hi Maria, we shared a document of our proposal and how we will go about our experiment.

Hi team!

In order to maintain student privacy, please DO NOT post links to Google documents. Please upload Word documents or PDFs to the "Files" tab to the left.

Thank you!

Hi everyone,

Thanks for sharing your updated project with me. I think you're doing good progress, you seem to have a pretty thorough experimental setup! I just have one question on this aspect: how will you increase the amount of zinc in your treatment while maintaining the other nutrients at an adequate level?

I am concerned about one thing though, which is why I asked for the exact codes of your Arabidopsis genes of interest and their mutants. I am having a hard time understanding what's the connection of the zip-2 mutant with zinc metabolism. For what I can see on the TAIR browser (locus AT1G69440, the gene affected in zip-2 is ARGONAUTE 7 (AGO7 / ZIPPY).  While this is indeed a very important gene for plants, as reflected by the strong defects displayed by the mutant (precocious maturity), there doesn't seem to be any evidence (from scientific literature) of its direct involvement in metal uptake or processing in plant cells and tissues.

I believe there could have been some confusion with Zinc-Regulated Transporter, Iron-Regulated Transporter (ZRT-IRT)-like proteins (ZIP) transporters, which in fact transport zinc. Was that the case? If you can, I suggest you try to choose mutants for one of these transporters instead. Or else for Zn-transporting MTP proteins (MTP1, AT2G46800 or MTP3, AT3G58810). Then you could perhaps have a clearer observation of different effects (on your control and treatment condition) of plants that are unable to metabolize zinc properly. Would it still be possible? 

I've uploaded in the Files Tab a review on zinc homeostasis in plants, that is, the mechanisms that plants use to maintain adequate levels of zinc and other metals in their cells and tissues. I hope it helps a bit.

I apologize if I got it all wrong, but if you can please let me know your reasoning for using the AGO7 gene (zip-2 mutant) in your zinc experiment that would be helpful too :)

 

Link removed

Hi Marina , we are sharing a document of our current proposal and how we will go about our experiment 

Hello Kuba,

Unfortunately, I do not have access to your proposal file. Could you perhaps upload it on the Planting Science File Tab on the left? Or else allow my email access?

Cheers,

Hi guys,

I could finally have a look at your project info properly. Your project choice looks really exciting! At the moment it also looks a bit complex, so I'd like to ask you some background info that will help us be on the same page on the whys and hows of your research, and get your ideas across more clearly. 

Regarding your Arabidopsis lines:

1. Yes, the Columbia WT is definitely a must on any Arabidopsis experiment, since it allows you to see what to expect in terms of normal plant growth, that is, in a plant that has no defects in functioning. So great choice! 

2. I did a bit of reading on the NCA1 gene since I had no idea about it before. I think your description looks ok; however, it would be nice to state where you got the info from. For example, we often use the TAIR database (https://www.arabidopsis.org) to search for Arabidopsis genes and mutant lines. Did you do that? If so, it is often useful to include the At locus code so it is clear for everyone which gene you're talking about. For NCA1, I understand the code is AT3G54360. 

3. Now, I understand you're using a NCA1 mutant line, called nca1-1. I know it might sound a bit tedious, but it’s a good idea to always write down the mutant names in italic lowercase, so there is no confusion between the gene (NCA1) and the mutant plant where this gene is not functional (nca1-1). I believe the info for this mutant line is found here: https://www.arabidopsis.org/servlets/TairObject?type=polyallele&id=502824091

4. Regarding ZIP-2, I wonder if you could indicate the At locus for this one too, since I’m having a hard time identifying this gene: Arabidopsis has a whole family of ZIP transporters, so indicating the locus number is important to have things nice and clear. As for the mutant line where this gene is not functional, it would also be nice to check and write down the exact naming and code on TAIR database, as with the nca1-1 example.

5. I would like to know a bit more about your reasoning on the response of mutants to higher zinc levels. I would assume if your genes of choice encode for chaperones/transporters, not having them functional (in the mutant lines) would result in lower zinc accumulation, rather than toxicity. Happy to hear your comments on that :)

Well I suppose that’s already a lot for a start, I think you guys have an exciting project ahead and I hope my feedback is useful. Once we have these questions sorted, we can move on to exploring the experimental setup.

Best wishes,

Marina

Hi guys, your project on zinc mutants sounds exciting! 

I noticed you were unable to insert your full description on project info due to limited character space on each dot point (predictions, experimental design etc). I wonder if there's a way to shorten it, or perhaps sending me a word file with a thorough description?

Cheers,