The Well Tempered Helix

Bach's works were technical and strongly annotated giving him control as the composer, but still layered with an energetic and beautiful quality in their complexity. These attributes produced a legacy of musicians dedicated to Bach, observable in the importance of his major work: The Well Tempered Clavier [1]. The first work, prelude No. 1 in C major, has been a beloved piece for both beginners and professionals for almost three hundred years. Listen here to the Tureck recording. A simple structure and steady cadence yield stability yet the changing tones cast a simultaneous instability. Music theorists explain that the evolving harmony of the sixteenth notes transforms the longer tones from a solid state to a high tension state [2]. This simple piece possesses an elegant charge as the discordance proceeds in a measured way known as prepared dissonance. The coexistence of simplicity and complexity pleases us, feeling consistent, grounded but never boring.

This duality is not just for baroque composition, but is instrumental in the function of our DNA.

Sixty years ago, three papers were jointly published in Nature, regarding the structure of deoxy-ribonucleic acid [3,4,5]. The famous X-ray crystallography, ‘Photo 51’ pictured below, was an pivotal piece in our understanding of the helical structure. Franklin was the Bach of DNA; her committed, methodical work was critical for producing these precise images. Note that the diffraction forms a symmetrical X; this tells us the molecule is in the form of a helix with regularly spaced turns and a constant diameter. (More information.)

source: [5]

Wilkins et al. noted, “While the biological properties of deoxypentose nucleic acid suggest a molecular structure containing great complexity, X-ray diffraction studies described here [6] show the basic molecular configuration has great simplicity.” [4]

In the 60 years since the 1953 papers, those four bases held firmly on a sugar backbone have yielded just as many surprises as they have given answers. The bases A T G and C supply a steady and reproducible cadence encoding twenty amino acids. The intricacies of DNA arise when we consider how the expression of our genes is regulated. Each of our cells possesses a code of 3 billion base pairs. How each cell references that code determines its function and fate.

Adding to the gene labyrinth, environmental cues can be imprinted onto our DNA as ‘epigenetic’ factors. In some cases, events of the past alter our genes to the point that stressful life events become heritable in a sense. In my following posts, I will report on some of the most fascinating, developing stories of our complicated and evolving, heritage make-up. From the Dutch famine of 1944 to the number of hours in the day, environmental sources provide our simple DNA with a dynamic charge essential to our complexity, our evolution.

Sources:
[1] Bach, J. S., The Well-Tempered Clavier (Das Wohltemperierte Klavier), BWV 846 (1722)
[2] http://www.lukedahn.net/ColorCodedBach.htm
[3] Watson J.D. and Crick F.H.C., "A Structure for Deoxyribose Nucleic Acid." Nature 171, 737-738 (1953)
[4] Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R.,"Molecular Structure of Deoxypentose Nucleic Acids."
Nature 171, 738-740 (1953)
[5] Franklin R. and Gosling R.G., "Molecular Configuration in Sodium Thymonucleate." Nature 171, 740-741 (1953)
[6] Astbury, W. T., Symp. Soc. Exp. Biol. 1, Nucleic Acid, 66, Camb. Univ. Press, (1947).

A Traveling Substance: Flowering mechanisms from dark to light

   The advent of spring always feels impulsive, arriving overnight in an unconstrained force of petals and leaves. A few days past the first bud, we suddenly exist in our awakened, stunning environment. It has an annual familiarity, but at the same time, it feels so foreign from the elongated grays of winter. There are adequate words to dictate our visual experience, but we often fail in finding the right expression for our emotive response. D.H. Lawrence addressed the feeling in his poetry:

And I, what fountain of fire am I among

This leaping combustion of spring? My spirit is tossed

About like a shadow buffeted in the throng

Of flames, a shadow that's gone astray, and is lost.

-excerpt from ‘The Enkindled Spring’

D.H. Lawrence, Amores (1916)

   To reign in this ‘leaping combustion’ a bit, I investigated a small history of the science behind the flowering season, and what I found was an arduous tale of scientists chasing after the explanation of the opening bud.

   Plant physiology was not a rigorous academic study until Julius von Sachs began his pioneering lab in nineteenth century Germany. By illuminating the leaves of the morning glory, he could induce flowering at the end of a shoot which he enclosed in a light-proof box. In 1865, he hypothesized that a physical substance traveled slowly from the light-exposed leaf to the apex of the stem, triggering the flower cascade. There was still a great mystery as to why plants only flowered at particular times of the year. In 1920, Wightman Garner and Henry Allard expanded our understanding with the concept of photoperiodism, whereby the plant detects the change of seasons as the day-length shifts.

   The Armenian-Russian scientist, Mikhail Chailakhyan, applied von Sachs theory in his plant grafting experiments of the 1930’s. Taking the leaves of plants exposed to a controlled number of hours of light, he could induce flowering by grafting them onto other plants, even those of differing species. He hypothesized that the flower-inducing substance was a universal hormone to be known as ‘florigen’. The term florigen stuck, but the substance was remarkably elusive for the next seventy years. 

   With the advent of molecular biology, the story accelerated in the late twentieth century. Two genes: constans (CO) and flowering locus T (FT) proved to be critical in the night length regulation of flowering. Finally, a Swedish lab published a study that established FT messenger RNA (mRNA) to be the long-distance molecule that traveled from leaf to shoot apex. Their finding was published in Science magazine and called one of the most important scientific discoveries of 2005. Well, it was, until the paper was retracted. 

   As it turned out, the data were flawed and it is actually the FT protein (not the preceding mRNA) that is taking the long trip. Green fluorescent protein was the key molecular tool used to finalize the story. One hundred and forty years after von Sachs proposed his idea, Corbesier and collegues at Max Planck Institute grafted leaves containing an FT-GFP fusion protein to stems without the molecule. They then tracked the fluorescent molecule as it crossed the graft junction and traveled to the apex where flowering ensued.

   Looking back on the life of Julius von Sachs, there were many complexities to his character that make the history of florigen somewhat tragic. His commitment to research had him working by 4 am and then continuing for fifteen hour periods. He later admitted that he paid for each of his published books with ill-health in his later years. In the end, Sachs not only had problems with his physical health but he developed a dark-side that alienated him from his contemporaries. At first a Darwin-enthusiast, he changed his position of support to one of fierce criticism. His assistant, Karl Goebel, wrote, “The latter part of his life found him a lonely man who had estranged many of his friends by bitter and sometimes even unjust criticisms.” Ironically, Sachs himself attributed much of his unhappiness to a lack of sunshine in the winter months:

   “there are no signs of blossoms …I should not complain, liking as I do to take things 

as they come, but unfortunately I cannot live without sunshine and the lack of it 

makes me ill."

Kanzan blossoms at night (Mott, 2013)


Sources:
[1] "Sachs, Julius von." Complete Dictionary of Scientific Biography. 2008. Encyclopedia.com. 20 May. 2013.
[2] Romanov GA Mikhail Khristoforovich Chailakhyan: The fate of the scientist under the sign of florigen. Russian Journal of Plant Physiology 59:443-450.
[3]Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C, Coupland G (2007) FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis. Science 316:1030-1033.
[4] Julius Sachs, by Professor K. Goebel in Flora (1897). Archived here.

Tracking Words and Fire: The vast geography of activity maps

These past two weeks I have been on a ‘data expedition’, sorting through about 3.4 million data points (14 data sets, each containing ~50 neurons, over 1200 time points for four conditions). I admit that I do not have a lot of enthusiasm for my data mining; it has been a slow, painful process. The goal is exciting though – I am seeking emergent characteristics in neurons that recover from an injury, distinguishing them from those that perish. In particular, do certain neural activity patterns promote rapid recovery from brain injury? 

Well, stay tuned…I have a lot of staring at the computer to do. Along the way, I find myself paying attention to ‘activity maps’ in general – and wow, there are some fascinating-odd-big things out there. 

Here is a small curation….

First, we have the 3 billion dollar one: Brain Activity Map (BAM).

Definitely read the short paper linked above for a good explanation of the goals. The project plans for a concerted effort to develop new tools to precisely measure brain activity, starting with simple organisms like C. elegans (a transparent roundworm) and moving up the metazoan ranks to fruit flies and then possibly the smallest mammal, the Etruscan shrew (just a few million neurons…). Currently, the best data we have on brain activity come from calcium imaging (thank you dear jellyfish!). The technology for calcium imaging is pretty fantastic. 

Nature Methods (2013) Doi:10.1038/Nmeth.2434

Here are the latest: from a larval fish brain (Ahrens and Keller, Nature Methods, 2013), but the scientists of the BAM project want to attain higher temporal resolution by measuring voltage changes, which cause the changes in neuronal calcium. There are a number of naysayers who claim the proposal to be a political stunt with poorly defined goals, but I think in the hands of the right scientists, the emergent activity maps will be well worth the funding.

Meanwhile, in the world of the social sciences, the data are abundantly popping out of smartphones with more than adequate temporal details. Social networking data have been making some very odd maps, including one from a ‘hedonometer’ that predicts the happiest and saddest cities in the US by measuring the frequency of ‘happy’ and ‘sad’ words from Twitter data: hedonometrics.

It appears that the abundant use of the word ‘sh*t’ in the tweets of Beaumont, Texas has made it into a ‘sad’ place – happier than Louisiana though, possibly from their abundant use of lol. Meanwhile, the inhabitants of Napa California maintain contentment with beauty, Christmas and of course, the keyword: wine. By the way, guess what one of the happiest words is? Yeah, rainbow. 

Here is a very dynamic social networking map. It is from a smartphone app called foursquare, showing check-ins to restaurants, clubs, etc. in two cities as dawn progresses to twilight. Watch the change in colors indicating the type of activity over time. 

The new social data are quite cool, but I found my absolute favorite activity map in an old film, For All Mankind. This is a beautifully composed documentary on the Apollo missions of 1968-1972. At about 14:32, the astronaut is looking back at the earth as they gain elevation over Africa. Down below, he sees small points of light dotted throughout the dark, open plains. He realizes that they are campfires from nomads resting for the night. Maybe dots on a plane are not as visually alluring as electric movement through a city, but I love that the context is clear and pure, making it the easiest to connect to.

If you don't mind a foreign link, here is the full-length film: http://www.tudou.com/programs/view/8DvtsjYg53g/

Okay, I think I am inspired enough now to return to my maps.

Squeezing the Gap

This past month, our lab picked up the latest version of a 'genetically encoded calcium indicator' known as GCaMP from the GENIE project at Janelia Farm. Below is an example of calcium levels changing inside of neurons. GCaMP utilizes GFP (green fluorescent protein) to fluoresce brightly as calcium concentrations rise and then dims as calcium levels drop (note the movie has been false-colored to improve contrast, and to look cool, of course):

GCaMP movie

After some intense left-brain activity, analyzing these data, I kind of just wanted to take a minute to think about the source of GFP, the crystal jellyfish. Some of the best crystal jellyfish stories are from the accounts of nobel-laureate Osamu Shimomura, who started his quest to understand the bioluminescent glow back in 1961 off the coast of Washington state. Shimomura's advisor, Dr. Frank Johnson, constructed a chopping device, so that they could plow through tens of thousands of these creatures. The unknown glowing substance was then squeezed out, as 'the squeezate', for further purification and analysis. Fifty years later, everything has been solved - the chemical details, genetic code and crystal structure of two molecules essential to the natural process: aequorin and GFP. Over the years, things have been shuffled around to generate brighter greens and better calcium grabbers.

Wait a minute, I just spent my time writing about the details of a tragic end to 50,000 mysterious creatures as they were scooped out of the ocean and slapped down onto the chopping blocks. Oh, my ... I need to make sure that this little organism is alive and well.

Claudia E. Mills at the University of Washington knows these creatures, Aequorea, in great detail and has some answers:

Aequorea facts from Dr. C. E. Mills

I am relieved to find that those fervent scientists of the 1960's were not responsible for a major depletion of our jelly friend. Reading through her facts, you will quickly notice an impassioned rant on the misrepresentation of Aequorea in the popular news media - things being false colored green for the most part. As it turns out, the glowing substance does not permeate the entire jelly, but precisely exists around the edge of his dome, hence the special chopping device that dissected out the rim. My first thoughts are 'well, this scientist is over-reacting - really what's the harm in a little photo-shopping to get the green-glow idea across?' Then I read her statement:

I am increasingly concerned that people studying green fluorescent protein recognize neither the animal from which it derives nor natural fluorescence when they see it. The "cool inner light" (phrase used in opening text of the Science News article, vol. 152, p. 55) of the above-mentioned photo was actually reflected light from the photographer's flash, not fluorescence. This article has inadvertently highlighted the growing gap between the reductionist and the naturalist in science. 

The 'growing gap'. As scientific finding builds upon scientific finding, we do become distanced from the organism itself. Perhaps the best discoveries by Shimomura were made when he was closest to the natural home of the jellyfish. For many months, he had a tough time deciphering the luminescent reaction. He finally developed the correct hypothesis after long hours, close to the sea, quietly thinking...

I often meditated on the problem on a drifting rowing boat under clear summer skies. Friday Harbor in summer at that time was quiet and peaceful, quite different from the present day, when it is saturated with busy pleasure boats and noisy seaplanes. Meditation afloat was safe but if  I fell asleep the boat was carried away by the tide so that I had to row for a long time to get back to the laboratory.

Aequorea has been silently drifting in the ocean for 160,000,000 years. To date, we still do not know exactly for what purpose these jellyfish glow.



Sources:
Mills, C.E. 1999-present. Bioluminescence of Aequorea, a hydromedusa. Electronic internet document available at http://faculty.washington.edu/cemills/Aequorea.html.
Shimomura, O., Journal of Microscopy, Vol. 217, Pt 1 January 2005, pp. 3–15
http://www.cooperlab.wustl.edu/PracticalAdvice/Shimomura2005.pdf

Preamble

                 A Statement of Purpose of Sorts

With the rapid progression of science, a new dominion has emerged, one where man can readily manipulate the beautiful underpinnings of the natural world. When existing in a society where whole organisms can be broken down into parts, molded to our liking and rebuilt, is it inevitable that we become irreverent of the natural world?

As a neuroscientist, I work in a field where we are considerably far from any complete understanding of our muse, the brain. It is possible to be in constant wonder of this organ as we have little knowledge of how the molecular details translate to complex functions. On the other hand, it is very easy as a scientist to become bogged down by the details (neuroscience has a barrage of those details!) to the point that one completely forgets how wondrous the whole thing is. 

So yes, even when practicing something as exciting as brain science, we can easily slide into a distanced state, risking our connection to the bigger picture.

What I have found most helpful, is taking time out each week to read, reflect and bring myself back to the enthusiastic state I had when learning neuroscience for the first time.

A neuron grows extensive branches along the surface of a plastic dish as it searches for neighbors to form connections with. (RE Mott, 2009)

I started this blog for that reflection, and to start a dialogue with others regarding neuroscience, scientific policy, the practice of science, and 'the bigger picture'.

So here it begins ....