Superphotosynthesizer: Cat Island Baldcypress

Today May 18, 2015 is ‘Fascination of Plants Day,’ an initiative organized by the European Plant Science Organisation with other events organized by the American Society of Plant Biology. On this blog, there’s no shortage of reasons why plants are fascinating, but to most they are still just the scenery. Take some time today to consider all that these primary producers do for you. Here are just a few things plants do for us- food, forestry products, paper, pharmaceuticals, energy, and beauty.

Of course, I am partial to the oxygen that they provide for us. In that spirit, today’s post will feature another superphotosynthesizer: the Cat Island Baldcypress located on the Cat Island National Wildlife Refuge in West Feliciana Parish, LA. This tree is the national champion of its species and also noted as the largest tree of any species east of the Sierra Nevada range.

It is located at the end of an easy walking trail (0.75 mile round-trip), but it only accessible for part of the year. Access to portions of the Cat Island NWR is prevented by levels of the Mississippi River since at least a couple of low bridges must be traversed to get you from the main road to the trailhead. If the river stage at Baton Rouge is greater than 20 feet, which is usually between February and June, there is no vehicle access to the trail. I was able to make a trip there in early February just before the river restricted access. It’s not quite clear whether the base of the tree itself is submerged at any point during the spring flooding because there is a really nice decking just before the tree at the end of the trail. As of today, the river stage at Baton Rouge is 27.8 feet, so it may still be another month before access is regained.

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The tree is impressive. At 96 feet it is taller than all the other trees around, but it’s certainly not the tallest tree east of the Sierra Nevada. However, its girth is undeniably impressive. It has the characteristic buttressed-base of all baldcypress trees, which measures 17 feet in diameter and 56 feet in circumference.  It has knees as tall as me. Well, for those of you who know me in real life maybe that’s not so impressive, but for a random root outgrowth that is still significant.

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This brings me to one of the real secrets of the swamp- cypress knees. These strange growths at the base of cypress trees have been puzzling botanists and plant biologists for centuries since Francois Andre Michaux wrote in 1819, “No cause can be assigned for their existence.” Many people have had theories as to how they contribute to cypress biology- increased aeration capability for growing in inundated swamps, methane (swamp gas) emission conduits, vegetative reproduction, mechanical support, nutrient acquisition, and carbohydrate storage. None of these hypotheses have really held up to analysis and the biological function* of these root outgrowths are still fascinating plant biologists today.

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This is just one local fascinating plant example. Check out the links below for more information about Fascination of Plants Day or follow #FOPD on social media.

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Johnna

*These expendable appendages are painted and carved for folk art projects. They are also fairly proficient at disemboweling lawnmowers of homeowners with cypress trees in their yards and capsizing careless motorboat operators in the swamps. Perhaps this is a plant defense mechanism ahead of its time.

References and Links:

http://www.plantday.org/

http://fascinationofplantsday.org/home.htm

http://blog.aspb.org/fascination-of-plants-day/about-fascination-of-plants-day/

http://blog.aspb.org/fascination-of-plants-day/

http://www.fws.gov/refuges/profiles/index.cfm?id=43697

http://www.fws.gov/refuge/Cat_Island/visit/plan_your_visit.html

http://www.monumentaltrees.com/en/trees/baldcypress/deep_south/

http://www.na.fs.fed.us/pubs/silvics_manual/Volume_1/taxodium/distichum.htm

http://en.wikipedia.org/wiki/Cypress_knee

http://www.venerabletrees.org/good-knees-said-baldcypress/

http://arnoldia.arboretum.harvard.edu/pdf/articles/2000-60-4-cypress-knees-an-enduring-enigma.pdf

Becoming Real

I’ve been in my new teaching position for an academic year now. It has been quite the transition from my research position as a postdoc. Because of the designed transient nature of research training as a graduate student and a postdoc, I’ve often joked about not being ‘Real’ for quite some time. The elusive career path of many PhDs seems to be filled with the same question as the Velveteen Rabbit in the tale by Margery Williams.

“What is REAL?” asked the Rabbit one day.

There has been much discussion about what this means for a career in science these days. It used to only mean one thing- a tenure-track position at a research university. However, more often that path is less traveled, only the fantasy of whispered voices among labs of senior members who were fortunate (?) enough to be raptured away to the ranks of assistant professors. The majority of us are still working out what it means to be real in terms of career and still live with ourselves as human beings. I am still on that path, but the way seems to be clearing.

THERE was once a velveteen rabbit, and in the beginning he was really splendid.

I love research and working with my hands in the lab. I’m very good technically at performing biochemical experiments. I like developing new experiments to answer questions stemming from previous results. I even like meticulously assembling publications from my results; there are not many details I miss in the instructions for authors. I can graciously respond to reviewers’ comments. While I do fewer of these things today, all of these things are still true for me. Despite years of tedious experimental drudgery and the inevitable walls you encounter during research, I still say that I enjoy it, but the systematic practice of research wears down even the tenacious. Eventually, you realize you are not new and splendid any more, but you are not yet real.

“Real isn’t how you are made,” said the Skin Horse. “It’s a thing that happens to you. When a child loves you for a long, long time, not just to play with, but REALLY loves you, then you become Real.”

The Skin Horse has some good advice for PhDs. It isn’t how we are made. There isn’t a single formula that we should all be following. This is terribly disappointing for someone like me that so enjoys checking items off of to-do lists. If only I could accomplish all these tasks and then I would be real. However, it doesn’t just happen to you either. You have to be an active participant. At some point, you must make a decision and take some risks. Real involves risk. For me, it was leaving a research career for something my training had only minimally prepared me for- teaching.

“Does it hurt?” asked the Rabbit.

“Sometimes,” said the Skin Horse, for he was always truthful. “When you are Real you don’t mind being hurt.”

Risk means you could get hurt. Of course, I run a tight ship around the lab (even more so in the teaching lab) so there was little chance of actual physical pain in my transition to teaching. Nevertheless, there was a steep learning curve for figuring out time management in a teaching position. The feedback from my students has been rewarding so that weakens the memories of late-night grading sessions and last-minute-laboratory-troubleshooting.

“Does it happen all at once, like being wound up,” he asked, “or bit by bit?”

“It doesn’t happen all at once,” said the Skin Horse. “You become.”

“It takes a long time. That’s why it doesn’t happen often to people who break easily, or have sharp edges, or who have to be carefully kept. Generally, by the time you are Real, most of your hair has been loved off, and your eyes drop out and you get loose in the joints and very shabby. But these things don’t matter at all, because once you are Real you can’t be ugly, except to people who don’t understand.”

I’ve only been in my current position for an academic year now. The jury is still out on real, but I am becoming. No matter the career choice (teaching, tenure-track, private, start-up, other altac) if you have a PhD, you are not someone that must be carefully kept. If you are happy in the career choice that has made you real, then you can never be ugly, ‘except to people who don’t understand.’

And so time went on, and the little Rabbit was very happy–so happy that he never noticed how his beautiful velveteen fur was getting shabbier and shabbier, and his tail becoming unsewn, and all the pink rubbed off his nose where the Boy had kissed him.

I have been surprisingly happy in my instructor position, but I am quite certain the teaching has given me a new wrinkle or two. I furrow my eyebrows together much more in my new position puzzling over the interpretations of instructions by my students than I ever did interpreting the results of new research. I also have an eye-twitch at the thought of grading some assignments. Thankfully, my blonde hair has resisted any grays up to this point, but I may not be able to stave them off for many more semesters. I really haven’t noticed these changes too much, and I’m sure I will lose a few more whiskers along the way.

“He doesn’t smell right!” he exclaimed. “He isn’t a rabbit at all! He isn’t real!”

“I am Real!” said the little Rabbit. “I am Real! The Boy said so!” And he nearly began to cry.

The students call me ‘Dr. Roose’ and even sometimes ‘Professor.’ Remembering to answer to these titles was the strangest part of the transition into my new role. In my head, imposter syndrome raised doubts. “A real instructor would have already made that presentation. A real teacher would have worded that question more clearly. A real professor would have graded those exams by now.” I just took it day by day, but sometimes I still felt like the rabbit yelling into the wind. “I am real! I have a laser pointer and a remote slide-changer. I wrote a syllabus! I use Moodle!” I’m sure I’m not the only PhD on a career path with delusions of insufficiency. The truth is, we are simultaneously none of us real and all of us real. You just get up every day and become as best you can and that’s real enough for today.

“Wasn’t I Real before?” asked the little Rabbit.

“You were Real to the Boy,” the Fairy said, “because he loved you. Now you shall be Real to every one.”

No, my tears this year did not conjure a nursery magic fairy to restore my wrinkles. Teaching has not suddenly become easy and perfect. As much as I thought I was real getting through two semesters, I have more improvements that I would like to try for the future. Given the budget climate for higher education in my state, I (like the Velveteen Rabbit) am just glad to have escaped being burned with the garbage pile. However, the Department did make me real to everyone in one way- my very own legitimate name plate for my office door. Becoming real indeed.

Door

He was a Real Rabbit at last, at home with the other rabbits.

Links

http://digital.library.upenn.edu/women/williams/rabbit/rabbit.html

What scientists do… in summer!

johnnaroose:

This has never been more true for me than now. Academic year 2014 – 2015: It’s all over but the grading!

Originally posted on New Under The Sun Blog:

Frozen

Let’s start the Frozen series with some summer fun for everyone. Here’s what Olaf (a snowman) thought about summer…

Have you ever wondered what scientists do in summer?

I’ve always loved the idea of summer… Really, I’m guessing you don’t have much experience with breaks, do you?

Nope, but I like to close my eyes and imagine all the potential productivity when summer does come.

There’s no classes… except that new course you wanted to develop for fall

There’s no students… except the half a dozen HHMI undergrads in the lab

No committees… except that one search that’s planning to beat the competition

PI’s will have time to work in the lab… except they don’t remember how to use the equipment.

A flask in my hand,

A burner flaming under ring-stand,

Squinting, yes, that could be a band,

So many experiments to do in summer!

The joy of preliminary data,

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Biochemistry Casino: Glycolysis Black Jack

“Money won is twice as sweet as money earned.” The Color of Money

Teaching has kept me busy since my last post. The days leading up to midterms, the grading and the office visits by concerned students in the aftermath have been too full for blog writing. In my biochemistry lecture course, the students and I are making our way through the core metabolic pathways, and I’m trying to come up with creative ways of getting the main ideas across.

 First stop: Glycolysis Blackjack

Glycolysis is a universal metabolic pathway for all organisms that consume glucose. (Yes, that includes plants. They just happen to make their own glucose from sunlight and CO2 instead of eating other organisms.) As far as energy-yielding pathways go, it’s not that complex. Glucose molecules are converted to pyruvate yielding a net of 2 ATP molecules. However, the names of the enzymes and the metabolic intermediates all start to sound the same and it’s easy to get lost in the details. Here’s an analogy to keep the overall picture in mind.

ATP is often referred to as the biochemical cash of the cell. The simplest game to win some ATP is at the glycolysis black jack table.

First, you have to pay to play. Invest an ATP to get your cards.

ATP

Congratulations! Glucose-6-Phosphate is just like being dealt a pair of aces.

Aces

If you’re dealt this hand at any casino biochemistry or otherwise, your next move is to split those cards into two hands. (You’ve either got 2 or 12 and the chances of you beating the dealer are much better if you know you are starting with an ace.) As in any casino, you have to pay to split; so you invest another ATP. In glycolysis, you’re splitting a 6 carbon sugar into 2 3-carbon molecules (glyceraldehyde 3-phosphate).

ATP

splitaces

In this contrived situation at the biochemistry casino, betting is limited to your investment. However, when you get your second card for both of your hands, you get jacks. Black jack on both hands. You win! Your winnings on one hand mean you break-even on your investment. Your winnings on the other hand mean you net back your initial investment (2 ATP). In glycolysis, the two molecules of glyceraldehyde 3-phosphate can each be used to yield 2 ATP molecules, giving a net of 2 ATP from glucose.

winnings

Sure, it’s not the drama of winning at slots, roulette or the lottery. But at this casino, you always get these cards. If you can ante in the first ATP molecule, you’ll get a pair of aces. If you can ante in the second ATP, you can split them and get jacks and double your investment. Every. Time. Sure, betting is limited, but if you’re guaranteed to win, you would sit at that table all day and all night. And you do. Eventually, you take those winnings and those cards to another table with higher stakes, but that will be a separate analogy. Other organisms make a perfectly good living at this table alone using glycolysis coupled with fermentation.

Of course, there isn’t a money casino in the world that works this way. The house always wins. But you should really split those aces when you get them. That’s still good advice.

Here’s a link to the BiochemistryBlackJack Powerpoint slide with animation if you’re interested in using the analogy.

Johnna

A special thanks to my husband SuperChef for patiently explaining the finer details of blackjack to me to make this analogy work.

Figures and Figure Legends

This is part of a series of tutorials I’m putting together for my students.

So, you have collected some interesting data from your experiments. Since no one but you will be reading your lab notebook (but hopefully people could if they wanted to), you need to present that data in figures so the rest of the world can know what you did and decipher your results.

Deciding what data gets to be a manuscript figure

The purpose of your manuscript is to show evidence for a new conclusion and the data presented in your figures should tell this story. Remember, the order of your figures for your manuscript may not necessarily (and probably won’t be) the order in which you collected the data. So, once you have all of your figures assembled, print them out one per page and work on defining the best order of presentation to make the case for your new conclusion. Now is a good time to evaluate whether there are any potential weaknesses regarding support for your conclusions, either in the data you already have or data you may still need to collect. You want to present the strongest possible case before your manuscript is submitted for review, but everything is a cost-benefit analysis and you’re always against the clock.

At this point you may also notice that some of the data presented in figures may be tangential, not quite fit with the rest or break up the flow of the story you are trying to tell. Authors can decide to cull certain figures (Sorry, data you have to remain in the lab notebook) or move them to ‘Supplementary Figures.’ Many journals allow for the inclusion of Supplementary Material- extra figures, longer versions of methods, large tables of data or files that would never be appropriate for print format. These Supplementary Materials exist as electronic files only linked to your final accepted manuscript as it appears as a journal article. Each journal has a different policy for what is acceptable for Supplementary Material. Some are more inclusive- the more data the merrier, drag everything out of all authors’ lab notebooks. Others are very limiting- essential data and files in appropriate for print only and anything else must be incorporated into the main body of the manuscript or cut out completely.

Preparing figures starts with high-quality data.

Images should be of sufficient resolution. Any adjustments of brightness and contrast must be made to the entire image; adjusting selective portions is unethical data manipulation and scientific fraud. Cropping is OK, but again beware of excessive image manipulations. They are usually an indicator that you need to repeat the experiment to obtain the necessary data.

Experimental data should be free of technical errors or other artifacts. The results should come from experiments as described in the methods section. Consistency in following experimental protocols (and including all of those details in your notebook) should be standard lab practices. Controls must be performed for each experiment so that the results can be properly interpreted. As you evaluate the figures you have made from your data, check again to see if all necessary controls have been included. When in doubt, don’t skimp on this- repeat the experiment with the proper controls. Your co-authors and reviewers will likely eventually tell you the same thing.

Your data should also be repeated enough times to be statistically relevant. Note that this does not mean you repeat an experiment enough times until you get the data you want. This ‘cherry-picking’ is another unethical manipulation of data. Unfortunately, this type of fraud is the most difficult to catch by the peer-review system. Reviewers have no way of knowing that you have a hundred other experimental trials with contradictory data in your lab notebook. Scientists must have the integrity to accurately present their results and have legitimate justifications for excluding some data (altered variables, confounding variables, improper controls etc). It is not always possible to show all repetitions of an experiment and in some cases (like gels) it is not even feasible to average the results. Showing ‘representative data’ (a single instance of the most common result) is perfectly acceptable, but it should be just that- representative of your average results.

Don’t pursue perfect data at the expense of integrity. The rising standards of scientific work and competition for rewards based on that work create an enormous amount of pressure to compromise your integrity for the sake of publication. RESIST! Research fraud undermines our entire enterprise. Biological systems are inherently complex and imperfect- we should not expect results to be simple and pristine.  Control for what you can when you can, but do not otherwise force data to yield a certain result.

Putting together figure files

Usually your data will consist of images or graphs. These electronic files must be edited to include the raw data as well as appropriate labels. The simplest way of doing this is to drop the images into a PowerPoint slide to assemble all the necessary parts. Text boxes can be used to add labels. Lines and arrows can be added to draw attention to certain features. All labels and features of your figures should be properly aligned using the automatic tools for doing so. More complex figures consist of multiple parts that are designated by letters (Ex: Figure 1A and Figure 1B), and these letters can be added as text boxes. Journals tend to have preferences for the exact labeling details (fonts, sizes etc) and the instructions to authors will have this information. Make sure you read this information carefully and apply it consistently across all figures. Don’t use Arial capital letters to label the parts of Figure 1, Calibri Roman numerals for Figure 3 and lower case Times New Roman on Figure 5. You’re not in cloud cuckoo land. Editors, reviewers and other scientists appreciate consistency.

Remember that in the final manuscript format, the sizes of all labels and images will be considerably reduced. Make sure that your figure as submitted in manuscript form is sufficiently large so that it is still interpretable at a much smaller size. Any lines on graphs should be of sufficient thickness so as not to disappear or lose their pattern upon reduction. Note that it is generally easier to number samples like gel lanes, mulitpart images, etc than to write out the full sample description in the figure. Save the full sample names and descriptions for the figure legend.

When available, move up in the food chain to a program like Adobe Photoshop or Illustrator or Corel Draw to put together figure images. These programs have a steeper learning curve, but offer more sophisticated options for putting the figure file together and saving it as a high resolution image. For many journals, your figures must be submitted as image files (usually .tiff) or as PDF pages. Most journals use the manuscript submission phase as their quality control phase, meaning the files you submit for review must be of sufficient quality for the manuscript proof. Speaking of higher quality software, programs like OriginLab and Kaleidagraph are much better at generating image quality graphs than Microsoft Excel.

Color vs. Black/White or Grayscale Figures

Journals will typically charge you more to print color figures over black and white or grayscale images. (Oh, so yeah, if you didn’t get the memo, the authors typically pay publication charges to cover the printing and/or access for the published work. But then again, if you’ve gotten this far, you’ve realized you’re not in science for the money.) When possible use black and white or grayscale figures. If graphs become too complicated in monotone, try breaking up the number of samples shown on the same axis. Of course, you shouldn’t completely eschew color. Use it when it is most appropriate to distinguish samples. For example, it’s not that big of a deal to show a Coomassie-stained gel in black and white, but pictures of Arabidopsis showing wild-type and mutant plants with varying degrees of pigmentation should definitely be in color. Finally, as part of the ‘use color judiciously rule’, stick with the basic colors (8 crayola box, not the 196) so that there are no incompatibilities or unexpected shifts in tone when transferring files or changing file-types. Also keep in mind that there is ~10% prevalence of red-green colorblindness, so avoid using these colors together to differentiate between key samples. (Hey, after #TheDress this week, maybe you should just avoid color altogether.)

The figure heading, title and legend

Each figure should have a heading as defined by the journal (Ex: ‘Figure 1.’ ‘Fig. 1’ or ‘Figure 1:’). Each figure should also have a title, the formatting of which may be explicitly defined by the journal. It may be required to be in the form of a complete sentence or just a concise phrase; it may be required to be in bold or italics to distinguish it from the legend. The legend should tell the reader what they are looking at. It is not necessary to include lengthy procedural details, but it is useful to mention the name of the experiment and any details about treatment or sample preparation useful for interpreting the data in the figure. It should define all parts shown. Every sample or label on the figure must be defined in the legend.

Other random and lesser commandments

  1. Thou shalt be consistent across all figures.
  2. Thou shalt not use yellow for graph lines.
  3. Thou shalt include error bars.
  4. Thou shalt have elements sized appropriately relative to one another.

Include your figure and figure legend tips and lesser commandments below.

Johnna