The Instructor Chronicles: Semester 1, Part 2

We last left Superhero PhD and her troop of Superhero TAs in a morass of educational glitches

The semester had not gotten off to a smooth start. Surely this trend would change, but there was no data indicating otherwise. Then, there was a glimmer of hope. The powers that be in the department had pity on our hero’s plight and found a way to pay for a new ice machine in her teaching lab. Without hesitation, she calls the refrigeration company and orders a replacement. It is installed as the molecular biology segment of the semester is ending. Now that the traditional biochemistry experiments are set to begin, the students can be properly trained to be Fast. And. Cold. “Now, if only the hefty charge on the university-issued procurement card will clear without holding me personally liable,” thinks Superhero PhD.*

It was a great victory, but not a sign that the fortune was changing for our heroes. Meanwhile, back at the lair, a problem was waiting in Superhero PhD’s mailbox. Superhero PhD rarely checks her mailbox as it is never filled with anything of great importance, only local store ads and unwanted credit card offers. This week an official envelope is there summoning Superhero PhD to jury duty the week of midterms and that changing of the guard from Superhero TAs #1 and #2 to Superhero TAs #3 and #4. “Noooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo!” she yells shaking her fist at the sky frightening Junior PhD. Canis familiaris even howls along with her gut-wrenching cry. She composes herself as she remembers, “It’s a government agency. There’s always fine print. A way out.” She is in luck. She is within 24 hours of the deadline to fax over a postponement request to the clerk. She quickly pens the numerous specific reasons why the 19th Judicial District would have to wait until the semester break to conscript Superhero PhD into service. She calls a few hours after it has been faxed away. Success! The Clerk of Court has heard Superhero PhD’s pleas and had mercy. Her service is postponed until the semester break.

Superhero TA #4 was diligently preparing the experiments he would lead for the first time this semester, and something was terribly wrong. The first enzyme inhibition lab exercise is not matching the data in the TA Manual. There’s no inhibition. Superhero PhD invokes her first rule of biochemical troubleshooting, “Make everything fresh and repeat.” Superhero TA #4 also follows this rule with no success, and it is time to invoke the next rule, “Order new reagents, make everything fresh and repeat.” “It’s still not working.” reports Superhero TA #4. “Now it’s time to put out the ‘PhD Signal’.” Superhero PhD states. E-mails are sent to Retired Instructor and Recently-Graduated-Former-Superhero-TA detailing the problem and our futile attempts at troubleshooting. What critical step was being overlooked? Was this merely another revolt of the Teaching Lab to its new master? Over the next week, everyone tried their hand at the troublesome inhibition with no luck. A remarkably detailed e-mail outlining the experiment’s execution from Recently-Graduated-Former-Superhero-TA arrived in Superhero PhD’s inbox, but it did not illuminate any significant differences in our attempts. Late one afternoon, Superhero PhD enters the Teaching Lab only to find Retired Instructor herself performing the vexing inhibition assays. Alas, she is also unsuccessful. Inhibition could not be observed by anyone, with any reagents, nor any enzyme, nay even preparations previously showing inhibition. It is a defeat, but the lab must go on.

After midterms, the students realize that they should come to see Superhero PhD in her office. There she answers the lingering questions they had but did not ask during class. She illustrates biochemical concepts on the newly-hung white board. She calculates ways for them to improve their letter grades with the remaining graded activities. They seem to be calmed. Yet, Superhero PhD soon learns that the vast majority of students are poor project managers, relying on short bursts of intense cramming rather than steady attention to the course and its assignments. Much of their misery is of their own making. Superhero PhD also occasionally sends out e-mails with important information. It is clear that some of the students do not read them; they are unprepared for scheduling changes, oblivious to related content for exams and unaware of upcoming important dates. Superhero PhD is beginning to think that Moodle mail uses some unfortunate translation tool after she hits the ‘send’ button that rewords her carefully crafted e-mails into “Blah, blah, blah, important date, blah, blah, blah, exam info…” but she has no time to take this up with IT services.

On report due dates, Superhero PhD sighs, “Less than an hour before the listed deadline and still half of the students have yet to click the submit button, and five submitted in the last five minutes.” She muses this is not so different from real science and grant deadlines. A briefly evil thoughts cross her mind as to how to change the course to better prepare her students for a career in professional science. Of the reports submitted 10% would be sent back with no grade at all because of formatting issues, 80% would be reviewed favorably but still not receive a passing grade because of the few available to go around, and the final 10% would be both favorably graded and receive A’s. In the lab, exercises would be graded as follows: the first group to finish collecting data for the day and write it up in their notebook would receive an A (the equivalent of publishing findings first in a decent journal), second place would receive a C (because good 2nd place research could probably be dumped into some lower tier journal) and everyone else will fail. Of course, some of the later finishing groups could decide to hold onto their work, opting to file for a patent thereby subverting the advancement of the work of the 1st and 2nd place finishing groups in the future. These patent-holders would then get a guaranteed A for the course. Then Superhero PhD remembers, it’s only an undergraduate course, “They can figure out how science really works after they graduate.” Plus, this alternative system would surely negatively affect instructor evaluations at the end of the semester.

Troubles continue to plague the experiments entrusted to Superhero TAs #3 and #4. At the conclusion of the protein purification exercises, the students subject their purified enzyme to dialysis so that it will be in the most appropriate buffer for the subsequent enzymatic activity assays. This experiment takes a significant amount of time, so care must be taken to be cold. Unfortunately, the deli-cooler cold box in the lab used for this purpose died the day before Superhero PhD assumer her new role as Instructor because of course it did. Other departmental cold rooms were available, but these were less conveniently located and the buffer contained a foul-smelling reagent that would preferably be contained in a smaller space. Superhero TA #4 offers the cold box in his lab. Unbeknownst to him, the required stir plate had recently started malfunctioning such that when the necessary stirring function was initiated, so was the heating element. By the time the Superhero TAs retrieved the students’ precious enzyme samples, the solution was boiling. The first rule of biochemistry had been violated in horrific fashion. Superhero PhD and the Superhero TAs could only stare in shock at the dialysis bags containing the students’ boiled protein, looking like scrambled eggs and utterly ruined for future activity experiments. Superhero TA #3 offers, “There’s still a ton of enzyme from our previous preps and the other half of their precipitated sample for a different experiment. We could just divide that up among the groups for them to have.” “Let’s do it. They’ll never know and we won’t speak of this again,” says Superhero PhD. The lab goes on with the students none the wiser that an equipment glitch had ruined weeks-worth of their efforts. Superhero PhD also muses that this could be another opportunity for re-structuring the teaching lab to be more like real life science. When the experiment fails, go back to the beginning and repeat all of your work.

In a separate exercise, the students use a mutant enzyme to compare to the wild-type version they have meticulously purified and analyzed. This enzyme is prepared by the Superhero TAs and generally lasts for a few years before activity drops below a useful value. When Superhero TA #4 checks the activity of the purified mutant enzyme available in the freezer, it is insufficient because of course it is and by now this semester is just snake bit. Superhero PhD locates what should be the corresponding mutant DNA, but it is not useable. Attempts to locate other freezer stocks of the critical bacterial strain fail. Once again, Superhero PhD calls upon Retired Instructor, who has superior abilities at deciphering the glyphs on tubes in the bowels of the -80 freezer. A tube is found and Superhero PhD quickly determines it will express the necessary mutant protein. Superhero TA #4 isolates the enzyme and verifies that it behaves as expected. As Superhero PhD receives this news, the Hallelujah Chorus rings in the background and a bright light appears ahead- it is the light at the end of the semester. Everyone just might survive and manage to learn some biochemistry along the way.

Meanwhile in the laboratory, the students have finally entered the home stretch of their experiments- the doldrums of enzyme kinetics. It’s a greater than two week stint of exercises in which their hands must perform the same tedious assays with various reagents to understand the details of how their enzyme works. Even with the help of numerous others, Superhero TA #4 is unable to troubleshoot the problematic inhibition experiment. Superhero PhD decides to cut that experiment short and rely on data found within the Holy TA Manual for the students to analyze. It is within this series of experiments many students are reconsidering their choice of major.

The repetitious lull of kinetics assays on the spectrophotometer dulls their senses. They are less vigilant about manually recording their data in their notebooks. Inevitably, the unthinkable happens. After more than two hours of data collection, one group asks to be checked out to leave. “Do you have your data for the day? Make sure everyone in your group gets a copy of the Excel file you were working on.” says Superhero PhD. “Yes Ma’am.” they reply, but as they try to add the attachment, the file is nowhere to be found and the spectrophotometer files are woefully incomplete. They begin to panic, but Superhero PhD says, “That sucks if the computer ate your file, but you can re-enter your data from your notebook.” She is met with only blank stares and a rising sense of panic. “You did record all of your data by hand in the notebook you are keeping for the course? At least one of you did, right?” she asks. More uncomfortable silence. “Not one of the three of you wrote down any numbers today?” she asks rhetorically. “I will see if IT Services can possibly recover your file, but it appears that it has been improperly saved and no longer exists. Fortunately for you, this is the inhibition experiment for which we will be providing you with data, so you can use that. You’ve just wasted two hours of your life. If you continue to pursue a career is science, I doubt it will be your last. This is an important lesson in data management that you have learned in class instead of real life.” As it turns out, IT Services could not recover their data. There may be computer forensic scientists at the FBI that may have been able to recover the students’ file, but these methods are not routinely available to public universities. This instance has forced Dr. PhD to append the Rules of Biochemistry to include #6: Thou shalt manually record thy data. Always.

As the semester winds down, Superhero PhD can begin to think about the next semester. Some experiments will be adjusted. Also, Superhero TA #3 will transition full time into Dr. Postdoc, and at least on new TA, preferably with powers of chromatographic separation will be needed. Tenured PI’s Graduate Student is willing to take on the role, but Tenured PI is not in agreement with this decision. Graduate Student’s research is at a critical point and she won a student award that will allow her to give up her double life as a TA. Fortunately, Superhero TA #2 is able to recruit another graduate student from his lab to join the team. Superhero TA #1 will also be available for one more semester. It looks as if the team will be ready for the next semester. That is, of course, if Superhero TA #2’s visa renewal goes smoothly between semesters and he is able to travel back to the university as intended the day before classes start. “Only if my luck changes significantly,” thinks Superhero PhD. She does not underestimate the bureaucracy involved in coordinating paperwork between two sovereign nations over the holiday season. So, she writes a polite but persuasive letter addressed to the Visa Officer requesting expeditious resolution of this matter.

The battle of Semester 1 is over. All students, Superhero TAs and Superhero PhD have survived… barely. “Take that Chaos and Ignorance,” muses Superhero PhD as she indulges in the fine chocolate cookies stashed in her office.** More biochemistry majors have been indoctrinated in the practice of good laboratory techniques. The mysteries of the pKa, molecular biology and Michaelis-Menten enzyme kinetics have been unraveled for a new generation. Off they will go to Medical School, Graduate School and The Job Market empowered with this new biochemical knowledge. Superhero PhD has taught them the most important thing about biochemical research,

“It is tedious and awful both at the bench and digging through primary literature, but if you’re paying attention and you persevere, you can synthesize prior knowledge and new results into a better future.”

Stay tuned next time for new and exciting adventures in the Instructor Chronicles: A New Hope Springs. Will the new Superhero TA exhibit chromatographic supremacy? Will they ever get that one inhibition experiment to work again? Will they find a replacement for that debacle of a gel filtration lab? Will Superhero TA #1 get his visa renewal in time to return for the Spring semester? What new obstacles await our team? But before any of these questions can be answered, stay tuned for Superhero PhD: Call of Civic Duty as she serves her mandatory jury duty.

Johnna

*It did.

**A 2nd place prize for her ugly Christmas sweater-wear at the Departmental Holiday Party.

The Instructor Chronicles: Semester 1, Part 1

We last left Superhero PhD leaving the funeral of her research career for a new adventure in biochemistry laboratory instruction…

The course she was entrusted with has a really great structure- starting from cloning a gene to expressing a protein to enzymology and protein crystallization. There was just precious little time between Superhero PhD’s start date and the first day of class. She just really needed an electronic version of the manual to get it churned out for the students or instead of alcohol dehydrogenase, biochemistry majors would be working on Photosystem II* (Dr. PhD’s forte). Fortunately, Retired Instructor was willing to be incredibly helpful, she had just been out of town visiting grandchildren. There was no time for significant edits, but it was much better than the other nightmarish scenarios that flashed through Superhero PhD’s brain.

With the lab manual in hand, Superhero PhD felt confident in her prospects for successfully completing the semester’s lab exercises. There was only one thing standing in her way, the thing that stands in the way on anyone that’s ever walked into a new lab- finding out where the hell everything is. The room was lined with benches containing identical equipment, tons of cabinets filled with God knows what, and freezers and refrigerators possessing an uncalled-for amount of previous years’ samples.** If only X-ray vision were one of Superhero PhD’s superpowers! Alas, she had to rely on the lesser power she did possess- painstakingly opening each cabinet and drawer, taking an inventory and labeling the contents on lab tape.

Of course, Superhero PhD was not alone in this new quest. The class came with 4 Superhero TAs with tons of experience running the lab exercises. Thankfully, they knew the location of everything Superhero PhD couldn’t find. However, there was one major concern held among all the TAs. The great secret to their power resided in a trilogy of binders they reverently called the ‘TA Manuals.’*** These holy books were nowhere to be found since the teaching lab had been vacated by Retired Instructor. “By the power invested in me by the search committee, I swear I shall deliver these holy texts to you by the start of class.” promised Superhero PhD. So she embarked on a crusade to acquire the TA manuals. It turned out that another e-mail to Retired Instructor specifically requesting them and coordinating delivery of the precious relics between Retired Instructor’s visits to her grandchildren was all that was required. With that, the Superhero TAs set about prepping for the semester’s labs.

The first day of class started with a strange omen. As Superhero PhD was driving on campus to her usual parking spot, she nearly hit two cyclists that thought it was appropriate to blow through a 4 way stop as if they were not vehicles. It was a sign of other obstacles to come. All seemed to be well with the TAs until Dr. PhD’s second day on the job when Superhero TA #3 mentioned he was trying to graduate and had, in fact, found a local postdoc job starting immediately. Superhero PhD isn’t one to begrudge anyone with a PhD finding gainful employment, but on the inside she felt like this. On the outside, her panic was probably only a brief eye-twitch. The next day, while she was still thinking of the lies she would have to tell to recruit another TA on such short notice, a miracle of miracles happened. Since Superhero TA #3 had not yet defended, he still qualified to be a TA and his new employer was willing to accommodate his schedule such that he could be both a Superhero TA and a Dr. Postdoc simultaneously. At this news, Superhero PhD smiled and began breathing again. “Now, we are really ready for the semester,” she thought naively.

As part of her new role in the Department, Dr. PhD actually got her own office. The space was glorious by postdoc standards- 4 walls, a small window with a view of the stadium, and a door. Even when she first laid eyes on it, filled as it was with file cabinets that seemed to be holding up the walls, flood damage along the exterior wall, and ductwork to who knows where in the corner. Her eyes welled up with tears and not solely due to the decades’ worth of dust that had accumulated. Nothing comes without a price of some kind and this room came with a whole other to-do list to manage: painting, sheet-rocking, cleaning, a computer, a printer, a phone, a phone number, a key, transferring all those file cabinets to surplus property. Each job meant a separate person handling it.

The office was not move-in ready on the first day of class, but it didn’t take too long before 90% of things were in place. Surplus furniture was moved into the hallway. A better desk chair was inherited from the Departmental Office. The whiteboard was not re-hung, but Superhero PhD owns a drill and a Home Depot card, so no big deal. Someone else a Facility Services even fixed the interior side of the door knob (Superhero PhD had some concerns that she would accidentally become trapped inside when it fell off). Surely at any moment, her new students would come pouring in for office hours seeking biochemical laboratory guidance. Alas, the only person to visit her office in the first month was Tenured PI.

As the semester began, chaos ensued. Superhero PhD received a minor in Chaos Management at the Evening Academy of My Family Circus, so most of the instances about to be described in no way affected the learning environment for the students, but nevertheless took years off of Superhero PhD’s life.

Critical reagents needed to be ordered for the lab, reagents with a hefty price tag for special expedited handling. In one case, the shipping company failed to deliver the package on time and in another, the reagent was backordered indefinitely. Superhero PhD managed to get a refund of the shipping charges for the late package and Superhero TA #3 suggested doing away with the backordered reagent entirely for the other experiment.

The teaching lab uses an ancient glass still to produce the dH2O necessary for experiments. It is a finicky contraption whose secrets were relayed to Superhero PhD by Retired Instructor. The plumbing connections are not to be trusted. Sure enough, the first day Superhero PhD started it running, the tubing for the cooling water jacket source blew off as she dropped off her laptop in her office. It was a mess, but luckily no damage was done to any equipment or labs on lower floors. Dr. PhD did not even enlist the help of janitorial staff.

On the first lab exercise doing molecular biology work, Superhero TA #1 opened the ice machine to find it empty. This ice machine that had worked perfectly for all prep work until then was now broken. Again, if only Superhero PhD had more traditional superpowers like Elsa’s freezing powers she and Superhero TA #1 and #2 would not have had to cart ice from the common equipment room for every class thereafter. Perhaps it was just a maintenance error light. Superhero PhD’s power of randomly pressing buttons failed to resurrect the ice machine. The refrigeration serviceman was contracted to revive the ice machine. It was not in need of routine maintenance. It needed a completely new motor and a new unit was the most cost effective way of doing that.

Another experiment was giving us more trouble than it should have. The second transformation by electroporation to generate the expression cell line was not working. After re-making reagents and new competent cells, it turned out to be the electroporator. Luckily again, the lab had another fully functional back-up instrument.

Now that Superhero PhD’s schedule was more inflexible due to class schedules, all manner of personal emergencies seemed to occur. In her spare time, Dr. PhD’s life involves a lot of child-, pet-, and elder-care. And honestly, for someone who’s not-that-kind-of-doctor, she still ends up dealing with more bodily fluids than one can imagine. Nevertheless, quick texting allowed her to communicate with other caregivers and coordinate emergency room situations from the classroom. If only the superpower of being in two places at once was something Superhero PhD possessed, she’d have tenure a Nobel Prize by now. Since she does not possess this power, she is just ecstatic to have made it through so far without having to pay per minute overage charges for Junior PhD’s after care.

At some point Superhero PhD decided that her office was in fact stable enough without half a dozen file cabinets crammed in it. There was no way she wanted another piece of furniture in it and it was time to rid the hallway of the extras. The proper forms had to be filled out detailing the property inventory numbers for each. One perk of Superhero PhD’s new position is a handful of undergraduate minions to help with support tasks. With the forms filled out and sent away to the appropriate university office, the months-long wait for retrieval began. Upon inspection of the copies of the forms, Superhero PhD notices that her undergraduate minion was a little overzealous in listing items- not all of the furniture in the hallway was her surplus. Neighboring lab had a nice lunch table and other cabinet in the hallway for their convenience. Superhero PhD was their neighbor for less than a month and she’s already giving away their property. “I’ll just have to be on the lookout for Facility Services again.” she thinks. The next day there is a crash outside her office, the sound of metal being unceremoniously moved about. “They’re here already?!?” she thinks. She walks into the hallway to explain the mistake on the paperwork. Speaking quickly to the man in the hallway, he appears to listen briefly before signing that he is deaf. Finally, a situation appears for which Superhero PhD can summon one of her lesser-used powers- a basic understanding and use of ASL. She manages to point to the paper and the misidentified furniture and sign, “Wrong. Must Stay. Thank You.” It worked! “Now that the hallway is clear, my students will surely come to my office hours,” she thinks to herself.

Just when Superhero PhD thinks all office-related work has been completed, other workmen from Facility Services show up to replace a 6 ft stretch of plastic baseboard along the back wall where sheet rock had been replaced. Every little bit helps. While they are there, they notice that no one has re-hung Superhero PhD’s white board. They just so happen to have the appropriate clips and bolts in the truck and hang it up for her. “This will really come in handy when I have to explain biochemistry to my students during office hours,” thinks Superhero PhD.

In some ways, research labs can be like the Mafia- they never really let you leave The Family. Superhero PhD still attends the lab meetings of Tenured PI to keep tabs on the research projects she left behind, offer insightful experimental suggestions and tell others in the lab where to find things. One week both Tenured PI and Lab Manager will be absent and Superhero PhD is called upon to preside over lab meeting. Experiments are reported without much incident. Superhero PhD and the Research Team retire back to the lab. Just as she is leaving, Superhero PhD hears the one sound that strikes fear into every researcher- the piercing cry of the high temperature alarm of the -80 F freezer. Graduate Student says, “By the way, this alarm was going off before lab meeting, but it doesn’t seem to be getting better after being shut for another hour.” Superhero PhD can sense the precious biochemical samples thawing and decades of freezer stocks becoming perilously warm. There’s no way Tenured PI or Lab Manager will be around to handle this. Superhero PhD and the Research Team**** spring into action securing additional freezer space in other departmental labs’ freezers. All samples are safely stored in time. Scientific crisis averted.

Stay tuned for the next installment of Superhero PhD’s inaugural semester in the Instructor Chronicles. How can she be Fast. And. Cold. without a functional ice machine? What will become of Tenured PI’s freezer? Will students ever come to her office hours? Is anybody really learning anything about biochemistry? What new slings and arrows of outrageous fortune await Superhero PhD and her TAs for the remainder of the semester? All of these questions will be answered in the next episode of the Instructor Chronicles.

Johnna

*Working with a large membrane protein complex whose substrates are water and light definitely qualifies as the deep end of the biochemistry techniques pool, so it’s probably not the best place to start.

**They took Rule #2 to the extreme, even for molecular biology samples and cultures that could never hope to be resurrected.

***The TAs were awesome apart from the TA Manual, but it contains all manner of useful information for managing the course that makes their lives a lot easier.

****Collectively, the new name for the group is the Chlorophyll-a Team. Homage to @AmeliaRWright who came up with that gem for #ScienceAMovieTitle. When I have spare time, I’ll write a spin-off with this title.

A Green Deal for Black Friday

It’s Black Friday. The blog may have been dark for the last couple of weeks while I’ve been busy with my day job, but today I have a special deal for all my readers. I’ve been writing about the holiday plants we use in our celebrations for the past year and now you can have all of those posts to yourself in convenient downloadable PDF format*. All this plant science for the low, low price of absolutely free! How’s that for a green Black Friday Deal?

Here is the link to download:

Holiday Plants: An Autotrophic Almanac

 

Johnna

*Sorry, the Youtube video links don’t work any more, but the rest of the links are still hot.

Binding P’s and Q’s, Minding T’s and I’s

When it comes to nailing down the location of P and Q in plant Photosystem II, you have to be careful how you cross your t’s and dot your i’s.

A longstanding question in the area of Photosystem II research involves the complement of proteins on the lumenal side of the enzyme in plants vs. cyanobacteria. This region of the complex serves to split water into molecular oxygen- a seemingly conserved reaction in all oxygenic photosynthetic organisms. However, it has long been known that the extrinsic proteins associated with the lumenal face of the complex differ significantly between plants and cyanobacteria.

Differences in the lumenal extrinsic proteins, plants vs. cyanobacteria

Differences in the lumenal extrinsic proteins, plants vs. cyanobacteria

Studies from various disciplines in recent years (structural, mutants, proteomic) have layered on more questions. Biochemical work on plants indicates there are three extrinsic proteins- PsbO, PsbP and PsbQ. Biochemical analysis and structural studies of cyanobacteria have shown that their PSII complexes contain PsbO, PsbU and PsbV. Other proteomic analysis and mutant studies have shown that cyanobacteria also contain homologues of PsbP and PsbQ (aka CyanoP and CyanoQ, respectively). Sure, this accumulation of data sounds like alphabet soup to those outside of our field, but it also leaves photosynthesis researchers wondering how appropriate it is to use structural information from cyanobacteria to infer anything about PSII structure in plants.

For all the knowledge we’ve gained, we’ve been comparing green apples to blue-green oranges. New research from the Bricker lab has used chemical crosslinking and mass spectrometry to gain more information on the organization of extrinsic proteins in plant PSII- directly from plant material. I’ve written about these techniques before in another paper addressing a similar problem from the cyanobacterial extrinsic protein vantage point. In a publication available electronically this week, Mummadisetti et al provide new information on the arrangement of the PsbP and PsbQ proteins in higher plant PSII. This work goes beyond what either of the individual protein crystal structures (not in the context of the PSII complex) could tell us. Distance constraints from the crosslinking data were used to guide modeling studies to fill in gaps in the solution structure of PsbP as well as identify interaction sites with PSII membrane components and another extrinsic protein, PsbQ. Altogether this gives us a more complete picture of an important enzyme.

In addition to the satisfaction that comes with publishing this great work in a top journal, the authors have also been featured in a research highlight by the university. Since I like to take things a step further on this blog, this post will feature the behind the scenes story of how this project came to be a publication worthy of a press release- especially with regard to how the story is told with imagery.

As is typical of any press release, an image is used to capture the essence of the research. In the featured image, we see Manju Mummadisetti without lab coat and gloves, holding her PSII membranes proudly aloft the pristine ice bucket next to a carefully positioned bag of spinach leaves that have yet to meet their demise in the Waring blender. I get it. In photosynthesis research labs we always have a tube or bubbling flask of something green-ish that easily fits the stereotype non-scientists have of what scientists must do all day long. Every. Day.

Credit: Louisiana State University

Credit: Louisiana State University

Long time readers of this blog will realize that in this image Manju is breaking the first rule of biochemistry. Fast. And. Cold. No self-respecting biochemist would gaze longingly at their biochemical sample that wasn’t on ice or in the cold room. Moreover, photosynthesis researchers opt for darkness or dim light for their preparations in order to keep activity low and avoid damage. I can say unequivocally that Manju knows and obeys all of the rules of biochemistry. This sample was only for practice or for show. A more true picture would look like this.

What real research looks like

What real research looks like

Notice the lab coat and gloves. Samples are kept in the ice bucket. For all you know, there’s nothing in there at all green or otherwise.*

Manju spent considerably more time gazing at data on her computer screen than she ever did her green samples. In the picture below, she is analyzing mass spec data and evaluating the validity of calls made by the software. p > 0.005 need not apply for her results, but anything better is painstakingly recorded on a brown paper towel.

005

But really, Manju’s research is more appropriately captured in other images like this one.

It's harder than you think

It’s harder than you think

It may not make for click bait, but carefully filling out FedEx shipping forms is an essential part of her research. After Manju prepares her samples, they must be shipped overnight on dry ice (Fast. And. Cold.) to collaborators in Cincinnati for the mass spectroscopy analysis. These shipments are carefully planned so that someone is available to receive them and perform the analysis. This isn’t always easy over the summer when it is necessary to coordinate the travel schedules of half a dozen researchers in two different labs.

On one such occasion, forms and labels were not filled out appropriately. Not because Manju forgot to dot and i or cross a t, but because she did. Packages with dry ice require a special hazard label that must include all address information for both the sender and recipient in a very small area. We never knew how critical it was to avoid crossing that dotted line of the diamond.**

Notice how the last 'ti' in Manju's name infringes into the label

Notice how the last ‘ti’ in Manju’s name crosses over the dotted line and into the hazard label. Such a distraction could interfere with proper handling of this hazardous substance.

IMG_0038 (2)

Really FedEx? Her name is 20 characters long! Plus, the all caps just makes it seem like they’re yelling. It’s that serious.

A diligent FedEx employee at the Baton Rouge office rejected the shipment and sent it back to the lab at LSU the next day. I know rules are rules, but really this is on the verge of Gas Station Manager Syndrome. The samples were fine and promptly placed back in the freezer. A flurry of NSFW text messages about the situation were exchanged among people still on vacation. A new shipment date was coordinated and new forms were completed. It went away without a hitch and was promptly turned into data.

A new lesson was learned that day- Thou shalt not write within the dotted line of the hazard label. It’s an extension of a long-standing research rule- Obey arbitrary formatting and paperwork requests from people that control what you need.

 

Johnna

*Full disclosure- there was NO sample in that ice bucket. No one in the lab had any membranes prepped that day and real biochemists don’t pull good samples out of the freezer for a photo op.

**It’s like crossing the streams in Ghostbusters apparently. It would be bad.

References and Links:

http://www.pnas.org/content/early/2014/10/24/1415165111.short

http://www.lsu.edu/ur/ocur/lsunews/MediaCenter/News/2014/10/item73226.html

Plant Skulls

snapgdragon seed pod skull dragons skullIf you didn’t know this was a plant science blog, you might think these were macbre trophies of some ancient tribe. This isn’t so much an appropriate plant costume for Halloween as it is an interesting confluence of floral anatomy and human propensity for recognizing facial forms.

Snapdragons or Antirrhinum sp. are a colorful staple of summer gardens. We’re more used to seeing them look like this image with tall inflorescences boasting clusters of ruffled flowers in a variety of color schemes.

Antirrhinum majus Credit: Michael Apel via Wikimedia Commons

What’s responsible for this spooky transition from delicate flowers to haunting faces? It all comes down to the snapdragon’s flower structure and its bilateral symmetry. The skulls are really the seed pods of the plant after the flowers have been pollinated and the petals have withered away. Dissecting the flowers in their prime shows the ovary at the base of the bloom. The pollen-containing stamens and the style emerge from the orifices in the ovary. These structures leave behind gaping holes that look like a mouth and eye sockets.

Snapdragon flower anatomy

Snapdragon flower anatomy

The striking resemblance of these seed pods to human skulls has led to their association with supernatural powers. They were purported to help women stay young and beautiful as well as protect humans of all ages from witchcraft and evil spirits. I don’t have any scientific evidence of that, but if you’re looking for new ideas for botanical Halloween decorations that go beyond cucurbits and mums, dried snapdragon stems with seed pods make a wicked wreath.

Johnna

Links and References:

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

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

http://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?kempercode=a561

http://www.kuriositas.com/2013/07/the-dragons-skull-macabre-appearance-of.html

http://www.waitwow.com/snapdragons-make-cute-flowers-die-turn-skulls/

http://gardenofeaden.blogspot.com/2014/02/the-dragons-skull-seed-pod.html

http://weirdworldwonders.com/the-dragons-skull-snapdragon-seed-pods/

https://s10.lite.msu.edu/res/msu/botonl/b_online/library/snapdragon/flower.html

http://www.flowersplans.com/snapdragon-flower-dry/

http://www.gardenguides.com/126335-history-snapdragons.html

Flying Duck Orchid

Caleana major off the Elvina Track, Ku-ring-gai Chase National Park, Australia Credit: Peter Woodard via Wikipedia

Today’s featured floral form is Caleana major, an orchid from Australia. It looks like a duck. It flies like a duck when the wind blows, but it’s just a flower. Why would an orchid develop such an elaborate costume? The answer is again pollination.

While this may look like yet another case of autotroph posing as heterotroph, it’s not the one you think. Caleana major’s flowers are designed to attract male sawflies. When the flies enter the larger ‘body’ portion of the flower, the ‘neck and head’ portion of the flower snaps closed behind them. For about a minute or so, the sawflies buzz around in a slight frenzy and become coated in pollen. This ensures that flower pollinates itself and any pollen remaining on the fly travels with it to the next flower.

Closed Flying Duck Orchid Credit: Peter Woodard via Wikipedia

The secret to this strategy is the sensitive ‘neck’ strap of the flower. This portion can sense when a fly has landed within the bottom part of the flower and trigger a response to have the ‘head’ snap closed. This trigger must also be reversed on a relatively short timescale to release the captive fly. He just needs enough time to be coated in pollen but none the worse for wear (unlike other carnivorous plants that intend on killing their insect victims with triggered mechanical responses).

This is an painting of Caleana major by Ferdinand Bauer, based on a drawing by him of material collected at Sydney in September 1803. It first appeared as Plate 8 in Stephan Endlicher’s 1838 Iconographia. It was scanned from Plate 13 of Mabberley, D. J. (1984) Jupiter Botanicus. via Wikipedia

There must be some interesting biochemistry underneath that response, not to mention the developmental gymnastics that must occur to make flowers that look like flying ducks. I’m not sure scientists will figure out these tricks because Caleana major cannot be cultivated outside its native environment. Because of its novel form and potential popularity with orchid enthusiasts, experienced growers have tried to grow it under greenhouse conditions, but with little success. It is speculated that a symbiosis with another microorganism in the soil of its native habitat is necessary for growth.

 

Johnna

References and Links:

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

http://www.odditycentral.com/pics/what-the-quack-australias-amazing-flying-duck-orchid.html

http://gardenofeaden.blogspot.com/2013/11/the-flying-duck-orchid.html

http://www.friendsoflanecovenationalpark.org.au/Flowering/Flowers/Caleana_major.htm

http://nossa.org.au/tag/caleana-major/

http://plantnet.rbgsyd.nsw.gov.au/cgi-bin/NSWfl.pl?page=nswfl&lvl=sp&name=Caleana~major

http://books.google.com/books?id=kUGL1TAaEtEC&pg=PA203&lpg=PA203&dq=Caleana+Major+pollination&source=bl&ots=bV-qtKkB8T&sig=-RSeg-ieBXJS428M6HdXHMuOOCY&hl=en&sa=X&ei=IehIVOWJBIi2yQT24IC4Cg&ved=0CF0Q6AEwDQ#v=onepage&q=Caleana%20Major%20pollination&f=false

http://books.google.com/books?id=SYvGAQAAQBAJ&pg=PA36&lpg=PA36&dq=Caleana+Major+pollination&source=bl&ots=fz35wIjm6P&sig=C-XAlmqySg2u2zznI5KzYcaCSa8&hl=en&sa=X&ei=U-hIVPi6N5epyASv_IHACA&ved=0CCYQ6AEwAjgK#v=onepage&q=Caleana%20Major%20pollination&f=false

 

Aliens

Some floral forms make you wonder if they know something we don’t. Take Calceolaria uniflora for example.

When photographed at just the right angle, these slipper-shaped blooms look like the face of an alien wearing beats headphones and holding an empty white tray as a peace offering. Calceolaria is native to the southernmost portion of South America in Tierra del Fuego whose rocky alpine terrain could also be confused with an inhospitable planet in another solar system.

Cacleolaria uniflora Credit: Butterfly voyages serge Ouachée via Wikimedia

If it isn’t an orange alien, what exactly are we looking at? The stalk-like eyes are the stamens, which contain the pollen-producing anthers at the end. The petals of the flower are asymmetrical such that there is a large lower lip and a much smaller upper portion. The green sepals are even larger than the upper part of the petals giving the illusion of halo or headset. The lower lip of the slipper contains a prominent folded appendage in white, a striking contrast from the other features.

Calceolaria uniflora colony Credit: Thomas Mathis via Wikimedia

The purpose for this elaborate costume isn’t mimicry, it’s attraction. But they are phoning home for E.T., they’re setting the table for birds. Birds are a part of many plants’ reproductive strategies and it’s usually in the form of oil and nectar producing floral structures that entice hummingbirds and other small birds over for a drink. Even other Calceolaria species produce nectar for their bee pollinators, but not C. uniflora. In this case, the white tray and larger lower lip of the flower are edible. Birds eat the tray and slipper portion of the flower while the upper portion dusts the top of their heads with pollen. As the birds move from flower to flower, pollen is transferred as well.

Calceolaria uniflora with missing trays Credit: Javier Martin via Wikimedia

There are many other examples of plants using edible portions of themselves in their reproductive strategy. Seed dispersal by the animals that eat them is the whole point of fruit. However, the case of C. uniflora, where the plant offers up part of itself as a meal before seed production seems out-of-this-world risky to me.

 

Johnna

References and Links:

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

http://www.seedsofeaden.com/ornamental-plants-k7/the-happy-alien-plant-calceolaria-uniflora-b76.html

http://www.strangewonderfulthings.com/257.htm

http://encyclopaedia.alpinegardensociety.net/plants/Calceolaria/uniflora

http://www.botanicalgarden.ubc.ca/potd/2011/09/calceolaria-uniflora.php

http://www.efn.uncor.edu/departamentos/divbioeco/otras/bioflor/pdf/Sersic%20&%20Cocucci%201996.pdf