(if you’re here for the first time look at the excerpts 1-7 in earlier posts)
Maddie sat across the wide desk from the gray haired man and looked around Dr. Gates’ office, trying to familiarize herself with it. The walls were lined with tall shelves filled with boxes of reprints of published papers. She knew he had co-authored hundreds of them over a thirty year span. She had asked to meet with Dr. Gates because she didn’t know what to do next. Time was ticking, they were well into the semester, and despite endless hours spent working on the harvest, she wasn’t clear what her research priorities were supposed to be. She kept hoping he would clarify things but he never seemed to have time. After waiting a whole week for an appointment, Dr. Gates had managed to squeeze her in at eight o’clock on Friday morning, before his nine o’clock lecture.
He arrived fifteen minutes late, and then proceeded to make a phone call to the departmental secretary, with some lengthy instructions on a manuscript to be finalized. Maddie just knew they were going to run out of time, before she could get what she had come for.
She shifted her feet under the seat, and then crossed her ankles to keep them still. She looked through her field book for the umpteenth time and then realized it was unnecessary, she knew everything in there.
“What was on your mind then, Maddie?” Dr. Gates asked.
She tried to discipline herself to speak coherently and concisely. Without “feelings.” Although she had been at UW several months she did not feel she knew this man at all. He didn’t have a very demonstrative personality.
“Well, Dr. Gates, I was hoping we could outline my research project further.” She still used the formal address because he had not yet given her permission to address him by his first name. She wondered how some of the other graduate students did it, was the liberty just taken or was it given?
“At this point how many diseases do you have data on, Maddie?” he asked.
“I tried to screen for eight, but I really think I have good data for only five. In the case of white mold[i] and powdery mildew[ii] there was no real infection in the field this summer so it was hard to rate the different lines.” She leafed through the fieldbook as she spoke, but it was awkward to show him anything across the wide desk.
“And in the case of Ascochyta[iii] I didn’t really know what I was looking for. So, that was a bust.” She was slightly embarrassed at the admission.
“But you think you have good enough data on the others?”
“Yes, I think so.”
“What diseases did you end up with then?”
“Very well. I would say that phase of the work was completed well. Now we must proceed to the next step. As I told you Maddie, when you first arrived, we are interested in correlating the seed proteins of these newly discovered wild lines[vii] with the high levels of resistance to certain diseases.”
“Yes, Dr. Gates, I remember our earlier discussions.” She hadn’t been asleep altogether. “What I’ve been wondering about though, is this: aren’t most of the diseases we’re looking at manifested in the leaf stage?”
“Why then, are we looking at proteins in the seed? Wouldn’t… it be more logical to look for a resistance compound in the leaves?”
“Ah. I’m glad to see you’ve been thinking. In looking for a correlation here, we are not trying to identify the compound that confers resistance.”
“We’re not?” She scrunched her forehead.
“No. We are simply looking for a clue that will indicate which lines have that resistance. We call that a marker[viii].”
Maddie frowned. Goodness, she knew what a marker was. “But why don’t we grind up the leaves instead of the seeds?” she asked.
“Because we can scrape just enough powder off the seed to assay without damaging the embryo. We make an extract of that, run it through electrophoresis[ix], which separates out the proteins based on their size…”
“Yes, I know, the electrical charge of a protein is proportional to its molecular weight.” She wished he would speed up.
“Correct. Now, the fact that we have not damaged the embryo means that we can go on to plant that seed, once we know it has the desired marker, and grow it into a plant that we can cross.”
“Okay, so you don’t have to wait to test something in the field, you can just assay it in the lab.”
“Yes, you’re beginning to see the possibilities.”
“Uh-hum. Now I really have a lot of questions.”
“Go ahead.” He looked at his watch.
Some of her questions she could voice, others she couldn’t. She knew he wasn’t inviting any confidences, only the facts. She couldn’t ask him, for instance, “How do you balance everything you’re supposed to do?” or “How do you survive your first semester of your Ph.D.?”
The light from the window behind his head was glaring, giving her the beginnings of a headache, but she focused on the task at hand. She knew her time was running out.
“Is our next step to try and transfer this resistance from the wild to cultivated bean lines?”
“So…if I cross a wild line and a cultivated one, then I would use this screening technique to identify those seeds with the right protein band, and that should also give us the resistance?”
“If!” He raised his index finger in a sign of caution and then repeated, “if it was a good marker there would be a high correlation.”
“So then we can breed for resistance without having identified the compound responsible.” That was a light bulb.
“Exactly. It’s done all the time.”
“What if we want to identify the compound?”
“Well, if you want to pursue that you can, perhaps with assistance from a lab in the Biochemistry department, but first we have to make sure that the transfer is stable.”
“What do you mean?”
“If we transfer the protein band but the resistance doesn’t come along with it, then there’s no use trying to use this screening method to breed resistant lines.”
“Oh! Okay, I see,” she nodded.
“Now, since we only want to transfer those genes for disease resistance and not bring a whole lot of other garbage with them, you have to keep crossing back to the cultivated line.”
Maddie looked up from her hurried note taking. “Backcrossing[x],” she said.
“Yes, I estimate four or five backcrosses[xi] would be needed to eliminate most of the undesirable wild line genes.”
“But I can only get in two generations between now and next summer, even if I grow them continuously in the greenhouse,” she said.
“That’s true Maddie, but you can screen them in the field again next summer, select the best ones and then continue on during the next year, if it’s still necessary.”
By selection she would greatly increase her chances of getting only desirable traits.
“You can select for the best yielding lines and get rid of the late maturity problems that usually come with using wild material,” he continued.
Maddie was nodding her head. “Then it seems my first priority is to learn how to do the electrophoresis,” she said, tentatively.
“Yes,” he agreed. “It’s easy. One of the other students can show you how.”
Maddie doubted it would be as easy as he promised. “And…and after I screen the lines, I should plant them out in the greenhouse?”
“That’s right. Edgar will give you a bench.”
Maddie left Dr. Gates’ office with a full-blown headache. She was wondering how she would be able to get everything done that needed to be done, and in a timely fashion. She stopped by Alex Vieira’s desk. She might as well get started.
“Alex, I have a favor to ask.”
“Sure, what can I help you with,” he replied, in his Brazilian accented English.
“You’ve been running some electrophoresis gels, right? Can you show me how the procedure is done?”
“Yeah, I can show you. I am going to run some tonight, you can watch me, okay?”
She didn’t let on that tonight was not the best time. After all, beggars couldn’t be choosers. If he was willing to show her how to run the procedure she would have to jump at it. But it meant that after the lab run she would probably have to pull an all-nighter to get the assignment for Plant Genetics done in time for tomorrow’s class.
She met Alex in the lab at seven p.m. Apparently, he always went home to married student housing to have dinner. “If I don’t go – I don’t see my kids,” he said, with a smile. “So, dinner time is, how you say, sagrada, sacred!”
“Sure. I admire that, that you take time out. It must be pretty hard to be a graduate student with a family.” Like many such foreign students, however, Alex was graced with a wife who saw to all the details of their children’s lives. Maddie had met the vivacious Maria Elena and liked her a lot.
“Did you read the manuals I gave to you?” Alex asked.
Maddie nodded. She had pored over them for the last two hours. “Yeah, I took notes. I’m lucky to have someone to walk me through the process, it seems really involved.”
“Well, what we do here is old fashioned way,” Alex said.
“What do you mean?”
“Well, I think they developed some new techniques, but we still have old glass plates, we have to make everything from, how you say—scratch.” Alex said.
Maddie made a mental note that there was an easier way to do this.
The process of making the agar gels was an extremely tricky one. She had botched her own attempt and from then on had let Alex take over and had simply watched. She felt guilty for the delay she had caused him. Around twelve o’clock they finished loading the protein extracts, and Maddie was wondering how much longer the rest of the process would take. It seemed interminable. To her extreme relief, Alex said they could run the gel overnight and come back in the morning to continue the procedure.
After thanking Alex she went back to the office to stare at the computer screen and try to write up her paper for Plant Genetics. She was now asking herself how she could have left it to the eleventh hour. It wasn’t like her. But then, she had tried to advance the readings and make an outline, doing a little at a time, fitting it in between other commitments. But it had gotten away from her. The semester had swiftly gathered momentum and now seemed to be spinning out of control. Now she was wondering how she was going to do it. She was wondering how everybody else did it. Nobody complained, everybody seemed to be handling it, except her.
Watch it, Maddie. She shook her head to clear away the demoralizing thoughts. It was late. Her perceptions were distorted by exhaustion. Her back was aching, her shoulder muscles stinging. She got up to see about making herself a cup of coffee at the counter. She wasn’t generally a coffee drinker but she knew she couldn’t get through this particular night without some.
[i] White mold – a disease of beans.
[ii] Powdery mildew – a disease of beans.
[iii] Aschochyta – a disease of beans.
[iv] Anthracnose – a disease of beans.
[v] Bean Pod lesion – a fictitious disease of beans.
[vi] Rusty Leaf spot – a fictitious disease of beans.
[vii] Wild lines – Lines of beans which have not been domesticated. They are usually collected in different regions of the world and have many undesirable traits such as tiny seeds and low yield.
[viii] Marker – a measurable trait.
[ix] Electrophoresis – a technique by which proteins are separated and identified.
[x] Backcrossing – a cross between the offspring of a cross (the F1) and one of the original parents.
I’LL POST SOME MORE OF “THE HARVEST OF REASON” TOMORROW. IF YOU CAN’T WAIT THAT LONG TO FIND OUT WHAT IS GOING TO HAPPEN YOU CAN GO TO THE “BUY IT HERE” TAB ABOVE.
I’m really interested in your comments.
DISCUSSION QUESTION 8 What seems to be Maddie Hawkins’ Achilles heel?