Lagging

I don't feel much incentive to post lately. I've been caught up doing lab work and dealing with unusual personal turmoil. Besides, this blog hasn't been shaping the way I wanted it to. And for my work, phytochromes have momentarily slipped into the background while one research mentor is away and the other hasn't had time to set up our LED arrays for a trial run of the experiment. I keep seeing and thinking about phytochromes everywhere anyway. The plants in our first row of greenhouse mesocosms are tall and pale and developmentally trailing behind the rest due to lower light exposure (or is it over-watering?). My houseplants are pale and starved because I keep closing the shades to decrease energy consumption (and Apollo-dog "pruning" off their new leaves doesn't help either). Everywhere outside I see plants reaching for sun. I still don't have a map of how they do it.

Instead I spend my time pretending I understand what I'm doing as I learn to extract RNA from plants I heat shocked. Why is it so difficult for me to apply classroom concepts I learned in college to practical experience? I feel like I have a wall in my brain. I am constantly aware of how little I know and how badly I piece together the little I do. It doesn't help that I am so burdened lately that I have resorted to writing bad poetry while I wait for the samples on the centrifuge to spin down. I am turning into someone I do not recognize.

Image middle right: Arthurium nemesis (the redoubtable Apollo), photographed by Arabidopsisgirl

Light Ratios

Today's topic is all about light: the spectrum, the wavelengths, and what happens when light hits leaves. Most of the following info is paraphrased from Keara A. Franklin's Tansley Review on Shade Avoidance (New Phytologist 2008).

Most basic science textbooks have a bit about the light spectrum, with a picture that looks something like this:

Red light is right next to infrared (heat). Wavelength is measured from the crest (highest point of each wave) across the trough (lowest point after the peak) to the next crest and for visible light is expressed in nanometers (nm). A nanometer is a billionth of a meter. The visible spectrum of light ranges approximately 400-700 nm. Red light falls at the 625-740 nm end of that. For plant study purposes, red light is considered 660-670 nm and far-red light is 725-735 nm.

Plants don't absorb all wavelengths of visible light equally. That's why they appear green to us humans--they reflect off green spectrum light while preferentially absorbing reds and blues. A shaded plant will receive much less of these desirable wavelengths because their opportunistic neighbor will get to them first. Thus, plants have phytochromes to detect the relative difference in amounts of red and far-red light. Interestingly, plants have another way of knowing the difference between shading by a neighboring plant and the shade of, say, a building. They can also detect higher levels of the hormone ethylene around a plant. In any case, if a cell on a plant leaf gets hit with lots of far-red light and just a little red light, the phytochromes within it change their form. And that's how it all begins.

Image above: the light spectrum, from the World Wide Web

First Post

It seems trite to quote Shakespeare on anything now, but my blog title fits my intentions for this journal-of-sorts: to explore why I love flowers and plants and genes and ecology and biology--all things green and growing and photosynthesizing. I've been reveling in nature for as long as I can remember, but I've studied biology for just five years and the going gets rough. I feel a stronger sense of duty to my work now that I am at a facility where the data I collect ultimately may be used to solve practical problems beyond the realm of pure science. But I want greater clarity so I can contribute more to all the projects I work on. Lately my focus has been taking disturbingly long vacations leaving me dilly-dallying in front of the computer, exasperated at the reams of papers I've been digging through. I'm trying to piece together the molecular pathways that allow plants to detect and respond to shade. That means not just hours of reading, but hours of looking up definitions of words I hazily recall from undergrad and hours of decoding stats, graphs, and the possible implications of mutant phenotypes.

I expect this blog will stray to the "dull" side for a while as I grapple with molecular biology terms and the necessary problem of drawing a picture of a process no one really understands yet. Writing distills concrete statements from the amorphous blur floating through my mind when I read other people's writing. Maybe a few light-hearted posts will emerge later on when I understand more about what I am supposed to do. In the meantime, I will describe this thing called the phytochrome and its relation to the shade avoidance response:

Everyone thinks of plants as stationary entities, kind of like rocks, but plants do move--by growing. If a seed germinates in a shady spot, the plant can move away from the shade by growing tall and spindly. That's fine...we've all seen pale, gangly, unhappy looking plants starved for sun, but how does a plant "know" that it's in the shade and tell itself to grow skinny and tall? By detecting and responding to the quality of the light that shines on it. Plants have several photoreceptors, or types of proteins that sense light: phototropins, chryptochromes, and phytochromes. The first two respond to blue light and have to do with germination, elongation, direction of growth, and photoperiodism (the act of following the sun, like sunflowers); the phytochrome responds to red and far-red light and tells the plant to grow tall to escape from the shade. Phytochromes detect the light with a light-sensing pigment and respond to the red:far red ratio by switching the shape of their protein (zing!). This shape change affects a whole cascade of other molecules throughout the cell. Genes are switched on and off, other types of proteins are produced, hormones (plants have hormones too) are activated, and the plant grows tall, its leaves reorient upwards, chlorophyll content decreases (causing it to look pale), growth is concentrated in the main shoot (gangly and tall), it flowers sooner, and the plant produces less biomass (leaves, shoots, and other organs). If the plant gets lucky and hits a sunny spot, the phytochrome switches its shape back and all those morphological changes reverse in the new growth--the plant greens up, grows bushier, and waits a bit longer to have babies.

It's mildly impressive stuff when you think about it. Who'd have thought up a shape-shifting protein? But for me all this information is simply maddeningly inadequate both in scope and detail. How does the phytochrome change its shape? What other molecules does it interact with? Which genes are switched on and off, and by whom? How do hormones come into play? And how and in what order do all the different molecules and genes work together? I'm combing the literature trying to figure out what a hundred different scientists know about these processes. So far I am coming up with a cacophony of maybes and indirect evidence from studies of mutant lines. What I need to do is draw a picture (a pathway map) showing the step-by-step interactions of the different molecules and genes. There is so much information out there. I have barely scraped the surface of this subject and haven't even touched the unknown steps and murky conclusions about shade avoidance and phytochromes that are troubling me and slowing the map-drawing process. The review paper I am supposed to use to try to construct a basic map is one of the most confusing ones I've ever attempted to read.