Saturday, April 9, 2016

Blog Update

Sorry for the lack of posts the last 2 weeks, hit a rough patch in real life. Between spring break work load and then child and I both got sick, there was no extra time to work on the blog. I made some goals for 2016 at the beginning of the year.

As a refresher the goals:
  • Read a scientific paper at least every work day, goal by year end 200 papers (#365papers"win" with 200)
  • Write more for the blog, one post a week (#50posts)
  • Shout out the little things that make me happy in Mommyhood (#PositiveParentMoment) 
  • 500 words a week in my PhD dissertation
  • Read 2 fun/non-sci books a month
  • Detailed edit of my NaNoWriMo 2015 by this upcoming NaNo  

Now the update...

What a hopeful person I was for this year! At this about 1/4 mark through 2016 I have
  • read 23 papers into #365papers before I got distracted and then fell behind and then forgot completely. 
  • written 12 blogposts(13 counting this one!) for #50posts (only 2 weeks off not terrible!)
  • #PositiveParentMoment has completely died off and I really need to refocus on that as it does help keep things with Boo in perspective
  • I have written 0, yes that's right, 0 words towards my PhD diss.. this needs to change STAT
  • I've read 3 fun books all year, short of the goal of 6
  • I did finish draft 1 of NaNo2015 and have started editing so I'll consider that goal on target
There we have it, out of 6 goals that I gave myself for 2016, I have sorta kept up with 2 of them.  Never to late to try again though! Here's to July 1 where hopefully I will have 100 papers in my #365papers Excel sheet, 26 #50posts, many thousands of words in PhD dissertation, and 12 fun books read!

We'll be back to science next week! 

Friday, March 18, 2016

Species Spotlight: Clover

As Saint Patrick's Day was yesterday, I thought we'd take a look at one of the popular symbols: the four-leafed clover. Botanically, clovers are any species within the Trifolium genus. They are in the Fabaceae family, as are soybeans! Over 300 species have been described within the Trifolium genus. There are clover species found practically worldwide. They make a very good cover crop and the most common honey is made from clover flowers which bees enjoy. Below is the common white clover (Trifolium repens).

The name trifolium literally means 3 leaves in Latin, and most clovers do indeed have only 3 leaves. But some clovers end up with 4 leaves. And these are the ones celebrated to give the finder good luck. Why are they so hard to find? To understand that we have to take a look at their genetics.. the blueprint that makes up life.

The genome, the entirety of the blueprints that makes up the organism, is pretty unique in this case. White clover has an allotetraploid genome, it has 1 copy of 2 different genomes! Each one of those genomes are diploid (2), this it has 4 gene copies! How does this happen? Well, in this case it is suspected that Trifolium occidentale and T. pallescens crossed. The resulting offspring kept both genomes to become T. repens. Because of this it has been difficult to map the genome and tease apart which genes control which traits.

Thankfully, there have been a few studies that have shed some light on this subject. It turns out that the progenitor of the Trifolium genus had 5 leaflets and the number of leaflets has decreased over evolutionary time to become 3 leaflets. But the 3+ leaflet is still a genetic possibility.  At least one multifoliate gene has been discovered. This gene is a recessive gene that is not only inherited (about 1 out of every 10,000) but can be activated by environmental conditions. Four leaf clovers like it hot, studies have shown there are more 4 leaf clovers in the summer than winter, and more in the greenhouse than outside during winter.

As Saint Patrick's Day occurs in March, this is not the ideal time to be searching for that "lucky" four leaf clover. Come back in June, when the days are warmer, to increase your odds!


Ford and Claydon Inheritance of multifoliate leaves in white clover. Agronomy Society of New Zealand Special Publication No 11. 167-170
Griffiths et al 2013. An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago. BMC Genomics 14:388
Gustine and Huff 1998. Genetic variation within among White Clover populations from Managed Permanent Patures of Northeastern USA. Crop Science 39:524-530
Tashiro et al 2010 Leaf Trait Coloration in White Clover and Molecular Mapping of the Red Midrib and Leaflet Number Traits.  Crop Science 50:1260-1268

Saturday, March 12, 2016

Species Spotlight: Crocus (with a little bonus Best Biochemist)

We are barreling towards spring here in the Northern Hemisphere. One of the early signs of spring are crocus flowers. The Crocus genus contains about 100 species. The flowers are cone shaped and live for about 3-4 days while they produce a massive amount of pollen. It's estimated that 1 flower can produce 1.9 milligrams (that's almost 7 ounces) of pollen!
Crocus from grandparents yard - personal image
Crocus often start to bloom in late winter/early spring. They can break through the snow. The flowers are, on average, 3 degrees Celsius higher than surrounding ambient temperature. The bowl shape of the flowers helps keep the heat in the interior floral area. Because they flower early, produce a lot of pollen, and generate heat in the flowers they are crucial for bee survival.

If you have any saffron in your house, you have a container of Crocus sativus stamen (flower male sex organs). Saffron is the most expensive spice in the world. It takes 70,000 hand-picked flowers stripped of their stamens to make 0.45 kilogram (about 1 pound). The scent, flavor, and color of saffron comes from unique carotenoids that are produced only by C. sativus. Technically, these compounds are apocarotenoids as they are shorter chains of carbon cut from zeaxanthin (which is also important in the xanthophyll cycle). The 3 apocarotenoids produced in the stamens of C. sativus are crocin, responsible for the red color, picrocrocin, providing the bitter taste, and safranal resulting in the characteristic aroma.

Researchers have been trying to elucidate the pathway used to produce saffron in the hopes of being able to synthesize it. Recently, the enzyme responsible for the initial step in this process was discovered to be a member of the carotenoid cleavage dioxygenase enzyme family.  All CCD are rigid 7-bladed propeller shaped with a central iron active site surrounded by 4 histidine residues which facilitate oxygen induced cleavage (cuts) of double bonds in carotenoids. CCD2 is the first enzyme to be described that is unique to saffron synthesis. CCD2 cuts zeaxanthin at the 7,8 double bond on both ends of zeaxanthin. Each bond is cut individually in a two step process to produce crocetin dialdehyde which is further processed to produce crocin, picrocrocin, and safranal.

It's amazing how one little flower can be so important and potent!


Frusciante, et al (2014) Novel carotenoid cleavage dioxygenase catalyzes the first dedicated steps in saffron crocin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America 111 (33):12246-12251. doi:10.1073/pnas.1404629111 

McKee and Richards 1998 Effect of flower structure and flower colour on intrafloral warming and pollen germination and pollen-tube growth in winter flowering Crocus L. (Iridaceae) Botanical Journal of the Linnean Society 128: 369-384

Weryszko-Chmielewska and Chwil, 2011. Structure of the Floral Parts of Crocus vernus (L.) Hill Acta Agrobotanica 64(4):35-46
Whitney and Chittka 2007 Warm flowers, happy pollinators Biologist 54(3) 154-160.

Friday, March 4, 2016

In the News: Soybean Cold Stress!

In the Midwest US it is not uncommon to have a frost or snow event in early spring. My Mom's gardening practice is wait until after Mother's Day to be sure a cold snap won't kill her plants. Soybean are sensitive to cold, especially in the young seedling stage.  But why is this? And is there anything that can be done about it? Last week an important paper came out that shines some light on this subject.

Impact of cold on soybean seedlings (Pers. Photo)

The article looked at the CBF cold responsive pathway, which is known to play a very important role in cold acclimation and tolerance in other plants. This multi-step pathway is well documented in cold tolerant species, especially the labrat plant Arabidopsis. In this pathway, CBF (also called DREB, as it is in this paper) is the main transcription factor. A transcription factor is the cell's version of a foreman, going into the nucleus and telling the cell what genes need to be activated.

Cold stress in plants, personal illustration
Turns out, soybean also has these same genes. And that CBF turns on when soybean is exposed to cold much in the same way that it does in Arabidopsis. The researchers were able to draw a line in the sand between working and non-working portions of the CBF cold responsive pathway within soybean. Turns out only half the pathway is non-functional, the other half is working just fine! You might wonder how they figured that out, great question!

The first question that they examined was, does soybean have similar genes to Arabidopsis CBF cold pathway? By examining the soybean genome, they were able to compare gene sequences with the Arabidopsis genome to generate a list of potential homologs (genes that are the same between species). This is only good on paper, just because the sequences match does not guarantee the functions match.

But once you narrow an entire genome down to less than a dozen genes, it is easy to examine functional responses. Toss the soybean in the cold, use quantitative PCR to get a measure of the gene expression amount before and during the cold. When the authors did this, they found that the CBF transcripts (mRNA) increased drastically and transiently. This is the same response that is seen in Arabidopsis. From this they concluded that all the steps in the cold response are active in soybean, and the "problem" lies between CBF transcription and cold responsive gene translation.

Perhaps the "problem" is that CBF itself has mutated in soybean and is damaged so that it can no longer interact and activate the cold responsive genes. The researchers set out to test this by taking the soybean CBF and moving them into Arabidopsis. This new genetically modified Arabidopsis will always be expression the soybean CBFs. If soybean CBF works, it should turn on the Arabidopsis cold responsive genes without having to expose the Arabidopsis plants to cold.

Simplified Fig 5 from Yamasaki & Randall 2015, provided by S. Randall
And that is exactly what happened! The downstream cold responsive genes COR47, RD29a, and ADH1 all increased in the transformed Arabidopsis. This told the researchers that the soybean CBF are indeed functional, at least they are capable of activating their target genes when expressed in Arabidopsis.

So what is the "problem" with soybean's cold responsive pathway? We still do not know. But we do know that it is not upstream of CBF transcription. Thus this article allows us to focus in on part of the pathway as the "problem" area. Hopefully these researchers are still examining this and will find the solution!

Yamasaki, Y, and Randall SK, 2015.  Functionality of soybean CBF/DREB1 transcription factors (paywall)

Saturday, February 27, 2016

Best Biochemist: ABA

Growth hormones are critical to plant development, much in the same way they are for animals. Previously, I wrote about ethylene, the ripening hormone. Today, we'll look at abscisic acid (ABA), an important growth and stress hormone.

Biochemically, ABA is a 15 carbon derivative of zeaxanthin, a carotenoid, with the following chemical structure.

public domain
ABA was discovered over 50 years ago in abscising leaves. Abscission is the process by which plants detach leaves or ripened fruit. Thus the name abscisic acid. Though we now know that ABA does not play a role in abscission itself but rather cessation of growth that precedes the actual detachment process. In the 50 years since discovery, ABA has been shown to play a role in a multitude of pathways. These include: seed dormancy, embryo development, germination, cell division, flower induction, stress responses (drought, salt, cold, UV, pathogens), and stomatal closure. Let's start at the beginning of the plant's life cycle and take a look at the roles ABA plays in these processes.

Seeds in the ground remain dormant, in a state of suspended growth. The production of ABA is high during late embryo maturation which drives dormancy. Dormancy must be broken for the seed to germinate. When it is time for the seed to germinate, gibberellic acid and ethylene production results in a cascade that mutes the detection of ABA breaking dormancy. Germination then occurs and the plant grows.

As plants grow they can encounter many abiotic stressors. Personally, I research abiotic stress biology so I find the stress responsive role ABA plays to be one of the most interesting. Plant perception of environmental conditions such as, high salt, low water, cold, and wounding, all involve ABA. These stressors increase ABA levels which in turn activates stress responsive genes. The main function of ABA in all of these stresses seems to be controlling the water level within the plant in a number of ways, including gene activation, increasing water uptake in the roots, and closing the stomata.
Stomata Personal Image
Stomata are pores on the leaf that allow gas exchange, including water vapor. To close the stomata, ABA binds to receptors on the guard cells that control opening and closing of the stomata. These receptors allow the flow of ions such that the guard cells lose water and close the pores. This prevents water from leaving the leaf!

Flowering is an important stage in plant development, resulting in the production of seeds and the next generation of the species. As with all developmental phases, several hormones play important roles. The ratio of each and amount of cross-talk between the various hormone pathways results in the change of developmental stage.  Floral development requires an increase in ABA and decrease in ethylene to the proper ratio.

As the plants age, they will inevitably undergo senescence and die. The biosynthesis of ABA, along with a suite of other hormones, is increased while cytokinin is decreased. ABA works in a positive feedback manner. As ABA levels increase, water and minerals are pushed out of the leaf and into the stem. This results in dehydration of the leaf and further production of ABA. This sets up the leaf for abscission which is controlled by ethylene.

As we can see, ABA is an incredibly important hormone. It plays a role in almost every developmental stage a plant undergoes from germination to senescence. How exactly the plant knows when ABA means flowering, dehydration stress, or senescence is still a mystery. It is probably in part to genetic control, age of the plant, and coordination with other hormone levels. Plant growth and development is just as complicated as it is in animals.

Beaudoin, N., et al., 2000. Interactions between Abscisic Acid and Ethylene Signaling Cascades. The Plant Cell 12:7 1103-1115

Daszkowska-Golec, A., 2013. Open or Close the Gate - Stomata Action Under the Control of Phytohormones in Drought Stress Condition. Frontiers in Plant Science 4 138 doi 10.3389/fpls.2013.00138

Finkelstein, R. 2013. Abscisic Acid Synthesis and Response. Arabidopsis Book. 2013; 11: e0166. Published online 2013 Nov 1. doi:  10.1199/tab.0166

Lee, I., et al, 2011. Age-dependent action of an ABA-inducible receptor kinase, RPK1, as a positive regulator of senescence in Arabidopsis leaves. Plant Cell Physiology 52(4) 651-662

Tuteja, N. Abscisic Acid and Abiotic Stress Signaling. Plant Signaling & Behavior 2(3) 135-138 

Wilmowicz, E., 2008. Ethylene and ABA interactions in the regulation of flower induction in Pharbitis nil. Journal of Plant Physiology 165 (18) 1917-1928