Okay, so what the heck are “omics”?

In the National Academy of Science’s genetically engineered crop study report released a few days ago, they proposed a new regulatory framework for analyzing the safety of any crop variety that relies on a technology called “omics”? So what in the world is an omic and how is it useful?

There are many different types of “omics”. It all started with GENomics which involves figuring out and comparing the GENES between organisms. This has allowed scientists to identify different genetic “markers” associated with diseases and other traits. However, genomics are only part of the story. Just because a gene is present doesn’t mean it is active.

Active genes are used as a template to TRANSCRIBE molecular messengers called RNA. Analyses of the levels of RNA within an organism in a given tissue or in response to a certain stimulus are known as TRANSCRIPTomics, but it doesn’t stop there.

RNA transcripts serve as instructions that enable cells to build PROTEINS. Proteins are the real workhorses of the cell, and are largely responsible for an organism’s traits. Comparisons of the protein landscape in an organism are accomplished by PROTEomics.

But what about all the other cool stuff floating around in cells? Hormones, pigments, vitamins, ethanol? These molecules are assembled within cells and are called METABOLITES (and plants have way way way more of them than people: nicotine, caffeine, capsaicin…..). And guess what? Where there’s a molecule there’s an “omics”, so now we’ve got METABOLomics.

So omics includes the study of the genes, RNA, proteins, and metabolites in an organism (there are even more, but I won’t go there). Sound complicated? It gets worse. When scientists gather data for omics studies, they get it in pieces.

So you know the human genome project? It’s not like somebody scanned a human blood sample and printed out the entire genome. To put it into perspective, if the human genome was unravelled and blown up to the diameter of a strand of hair, that hair would be 30 miles long and form a wad the size of a volleyball.

The genome had to be sequences piece by piece (not particularly systematically) and then those pieces had to be reassembled. To put it into perspective, Dr. Keith Bradnom uses the following analogy: Take 100 identical jigsaw sets, mix all the pieces together, throw away 10% of the pieces, randomly mix in the contents of an unrelated puzzle, throw away the cover of the box, and assemble!

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Some scientists on twitter even called this analogy an over-simplification! As you can imagine, this takes not only a lot of brain power, but also a lot of computing power. Then once you finally get it assembled….

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So that’s why the National Academy of Sciences said that we need to further develop these technologies. The idea is that we could compare the “omics” between new crop varieties and existing varieties and analyze any significant differences for potential safety concerns. As you can see, this is no small project, and that’s why they call it “big data”.

If you are a non-scientist, I hope you found this explanation helpful. If you are a scientist, particularly a computational scientist, please let me know in the comments if I’ve made any mistakes or am missing important details.

It’s the plants. They’re learning. They…remember

 

Sorry Mark Wahlberg, this is not a prequel to the 2008 sci-fi thriller “The Happening,” but maybe M. Night Shyamalan was onto something. Could plants learn that large groups of people are threatening, then kill them with an aerosol neurotoxin? Probably not. But they do learn, remember, forget, and even make decisions in some capacity.

If you’ve ever touched a mimosa pudica, the so-called sensitive plant, you know that plants can freak out. They sense a disturbance and react, possibly to protect themselves from hungry insects. Could they learn to tell the difference between threatening and non-threatening stimuli?

To find out, Dr. Monica Gangliano, associate professor in the school of animal sciences at the University of Western Australia, stimulated mimosa plants repeatedly with water droplets. After several showers, the plants stopped responding. Remarkably, months later, the same plants still didn’t recoil from a water droplet. The plants seemingly learned the water was not a threat, and remembered, even in the absence of stimuli.

These results are striking, but discoveries of learning and memory in plants are not new. Plants are exposed to a variety of stresses. Some are enduring like the cold of winter. Others are transient like heat stress in the late afternoon. Responding to stress requires energy, and often stalls growth. Thus it is beneficial for plants to remember and respond quickly to some stresses while learning to ignore others.

Plants have several strategies for recording memories and passing them on to future generations. In response to stress, plants can reorganize their DNA to activate or inactivate certain genes in a semi-permanent and heritable way. Plants can also store molecules of RNA, which act like molecular messages to enable a rapid response to future threats. A recent discovery by Dr. Susan Lindquist’s group at Massachusetts Institute of Technology suggests that plants may also store and transmit memories using proteins called prions

Prions are best known as the causal agent for mad cow disease (scrapies in sheep and Creutxfeldt-Jakob Disease in humans), but they are also associated with long-term memory storage in animals. Prions are able to adopt unique folding patterns. These patterns can be inherited and transmitted to neighboring proteins like a molecular switch that causes cascading and permanent changes.

Lindquist’s group used computational methods to look for genes in plants that resembled those encoding prion proteins in yeast. They then expressed the functional domain of what appeared to be a plant prion in yeast. The plant domain was able to functionally replace an analogous domain in a yeast prion protein. This strongly suggests that plants have prions or prion-like proteins.

Does this mean plants have brains, or plant neurobiology is the next big field of study? Doubtful. What some have called plant neurobiology is remarkably similar to what has always been recognized as stress response. To say that plants are making decisions probably gives them a bit too much credit. Decision-making is a more-or-less voluntary response. Plant reflexes might be a more appropriate term to describe the changes that occur in a plant in response to stress.

Nonetheless, similarities between plants and animals should not be ignored. Gangliano and Lindquist’s studies demonstrate the value of breaking down organism barriers in science. In the current structure, plant scientists go to plant science meetings, veterinary/livestock researchers go to animal meetings, and everyone else goes to meetings focused primarily on human health. Plants, humans, and other animals coexist in an interdependent web, so should our approaches to studying them.

Sources

S Chakrabortee, C Kayatekin, GA Newby, ML Mendillo, A Lancaster, S Lindquist. Luminidependens (LD) is an Arabidopsis protein with prion behavior..Proc Natl Acad Sci U S A , (2016).

PA Crisp, D Ganguly, SR Eichten, JO Borevitz, BJ Pogson. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics.. Sci Adv 2, e1501340 (2016).

S Berry, C Dean. Environmental perception and epigenetic memory: mechanistic insight through FLC.. Plant J 83, 133-48 (2015).

M Gagliano, M Renton, M Depczynski, S Mancuso. Experience teaches plants to learn faster and forget slower in environments where it matters..Oecologia 175, 63-72 (2014).

The birds and the bees and the flowers? The not-so-secret sex life of plants

It’s springtime, so those of us with allergies might have noticed plants getting all animal planet with our sinuses. Seems most plants are pretty lose with their pollen, but when it comes to procreation, they’re very particular. So how do plants swipe right on a match? (For my married friends, that’s a tinder reference. For my mom, tinder is an app people use to meet people. For my dad, an app is a phone capability)

First base is geography. Plant breeders can take related plants from different regions, play some Barry Manilow, and cross them in a green house yielding new varieties. But under normal conditions, plants have to live and thrive in the same environments to cross.

Second base is timing. To our dismay allergy season is a season not a day. That’s because different plants flower at different times. They respond to environmental cues like day length and temperature and flower at the time that will yield the maximum chance of survival and success for their offspring. The timing differs depending on the plant and the method of seed dispersal/germination. So even in plants, equivalent levels of maturity are necessary for a fruitful relationship.

Third base is anatomy. For some plant species, male and female reproductive parts are found on different plants (sound familiar). I’ll spare you the analogy, but for many species, both genitalia appear on the same plant. In some cases they’re right up next to each other within the same flower. The location of plant privates determines whether plants are more likely to breed with their neighbors or themselves.

Plants are actually pretty content with pollinating themselves, and some almost exclusively self-fertilize. These loners like rice can be a real pain for breeders hoping to cross different varieties. On the other hand, corn man parts, called tassels, stick right out of the top of the plant. Wind blows the pollen from the tassels and it lands on the silky hairs that stick out of the ears of neighboring plants as much as 200 feet away

Home runs require chemistry. Assuming our gentle-pollen and lady-ovule live in the same zip code, are age-appropriate, and are serendipitously brought together (totally not by online dating), there’s still got to be chemistry. And I’m not being cute here, I’m talking about literal chemistry. In order for fertilization to occur, pollen has to produce a straw-like appendage called the pollen tube which delivers the sperm to the egg. Pollen tube growth is guided by chemicals called chemoattractants which are produced by the ovule.

Aw scent of a woman! The molecules that ovules use to lure pollen tubes had been previously identified. Just last month, two studies published in the prestigious journal Nature uncovered the male receptors that recognize their female partners. Why are these breakthroughs important? If we can figure out what prevents different species from crossing, we might be able to create inter-species mixes (like an actual “grapple” or the blue raspberries my brother keeps pushing for).

Happily ever after. So that’s what happens when two plants love each other very much. For a real R-rated experience, check out these absolutely incredible videos of plant and insect mé·nage à trois encounters.

  1. Flowers trick male wasps into thinking they are female wasps. A BBC production.

2. Flower requires bee “vibrations” to release pollen. Also a BBC production.

For scientist readers, here are the less fun but fascinating nature papers:

3 Surprising Facts About Plants: Immunity, Indeterminacy, and Immortality

As an undergraduate, I sat through human biology lectures, shouldered up with ambitious pre-meds at the University of Colorado. When they marched off to anatomy, I wandered into the councilor’s office, wondering what biology careers don’t require memorizing musculature.

I met with professor emeritus and plant biotechnology enthusiast Andrew Staehelin who insisted, “you should get a PhD in Plant Biology at UC Davis”. Thinking to myself “UC where?” I applied for a graduate program in a subject I’d never studied at a University I’d never heard of.

When I got to the University of California in Davis I learned two important things:

  1. “What’s your favorite plant?” is everybody’s favorite ice-breaker question
  2. “I dunno, the kind you eat” is not an appropriate answer

So when a seed company recruiter started my internship interview with “What’s your favorite…” I was relieved that she finished with “…thing about plants?” Now that is a question I can answer. After 4 years studying plant biology, I still don’t have a favorite plant, and my plant taxonomy skills are lacking, but I have learned a whole lot about how plants work from the brilliant faculty and students at UC Davis.

So as an-ex human molecular biologist who’s come over to the plant side, here are my three favorite things about plants:

  1. Immunity: Plants have immune systems too! Plant immune systems are actually somewhat similar to human and animal immune systems. They can even be vaccinated against viruses. For example scientists inserted a bit of DNA from the papaya ring-spot virus into the papaya genome. The resulting disease-resistant plants saved the Hawaiian papaya industry. Studying disease response in plants also contributes to our understanding of human disease pathology. In fact, microorganisms were first found to be a cause of diseases in plants! (Think Irish potato famine)
  2. Indeterminacy: All plant cells are indeterminate or “totipotent”-as in-“totally capable”. This means that every single plant cell acts as a stem cell, which, under the right conditions, can develop into a whole new plant. Check out this picture of a rose flower sprouting a whole new plant from the UC Davis Plant Transformation Facility. Screen Shot 2016-03-23 at 7.15.28 PMTotipotency is what makes “clonal propagation” possible. For example, all bananas are actually clones of one parent banana, the Cavendish. Instead of reproduction by seeds, every new banana plant is grown from the cutting of another. Many other food crops such as apples and strawberries are also clonally propagated.
  3. Immortality: Unlike animal cells, plant cells can essentially live forever. Although whole plants don’t typically live forever due to environmental factors, plant cells are not limited in the number of times they can divide. That’s why trees can grow for thousands of years, and seeds can germinate after tens of thousands of years.

In conclusion, plants are pretty amazing and very underrated. Plants tend to blend into the background of our existence, like buildings or landscapes. This phenomenon is called “plant blindness.” But plants are quite dynamic, and we rely on them for food, oxygen, medicine, fuel, fibers, and more. Further, plant research has significantly contributed to our understanding of human disease. Nonetheless, basic plant science is seriously underfunded and understudied. I hope to counter plant blindness by sharing facts and new discoveries in my “That’s Plantastic” segment. I’m happy to answer (or more likely find an expert to answer) any questions you have about plants in the comments section.