Suzannah+Smith

(Complete) Who Needs Legos, When You Can Have DNA Origami? By: Suzannah Smith December 21st, 2012   Post #1, Topic: Genetics (Author's note: a Vimeo video at the bottom of this post may start playing automatically. If it does, simply scroll down and pause it until you are ready to watch it.) Two hundred years ago, no one had any clue what DNA (deoxyribonucleic acid) was, or that it even existed. When it was first discovered by Johann Friedrich Miescher in the late 1800's, it was definitely not given full credit for the huge part it plays in genetics. Even today, when we think we have at least a reasonable understanding of it, there remains so much more to be learned. Still, it is remarkable that humans have gone from ignorance of DNA's presence to being able to play with it, like building blocks, to form hundreds of shapes - which is precisely what many scientists have been doing since 1991. This form of DNA nanotechnology has come to be known as DNA origami.

__ What is DNA Origami? __ Essentially, DNA origami consists of folding strands of DNA to form specific 2D or 3D shapes. Over the past years, it has evolved from a process that took years to something that could be done in an hour. The way these molecular shapes are made has changed greatly though, so to understand more about DNA origami, we must look at it's fairly brief but interesting history.

__ Basic Technique __ Things were set in motion when Ned Seeman first took advantage of the basic structure of DNA (adenine bonds with thymine, cytosine bonds with guanine) to form specific structures. He annealed separate single-stranded DNA strands together to form cubes, tubes, and lattices (see pictures).

However, this process was tedious, and took a very long time (sometimes years) to do. For what he wanted to use this nanotechnology for, it took more effort to make than it was worth. Plus, the shapes formed were absolutely tiny.



__ Scaffold and Staples Technique __ Then Paul Rothemundcame along in 2006 and revamped the process. He simplified it by taking a single-stranded length of free-floating DNA about 7000 nucleotides long (for the long "scaffold" strand, Rothemund used often DNA from a harmless virus), and inserting short DNA stands with specific sequences. Then, one end of a short strand would attach to a certain spot, and the other end would anneal to another spot, thus "stapling" the single stranded DNA, and forcing it to make a loop. After repeating this step with hundreds of "staples" (the double-stranded, sticky-ended DNA), the shape automatically folds into a specific shape. The process is shown in the pictures below.

This video is a short TED talk, presented by Paul Rothemund himself. He talks about DNA origami and how he makes it, and I chose it because it includes good visual explanations so that you can better understand how this process works. For the most relevancy to my topic, please only watch from 4:37-10:00. media type="youtube" key="WhGG__boRxU" height="315" width="560" align="center"

__DNA Brick Block Technique__ The stapling technique was used for many years, and is still popular today, but Bryan Wei (a postdoctoral scholar) recently returned to creating the DNA origami in a way similar to Ned Seeman. He took individual single strands of DNA (about 42 letters long) that fold into rectangular tiles, and mixed it with other complementary DNA tiles to form a much larger rectangle (see diagram below). Since each tile has a specific sequence, it can only attach to specific neighbors, and so it has a predictable, set place in the large rectangle. By using the same tiles every time, scientists can just leave out certain pre-selected tiles to form more complex shapes. As a result, they could make hundreds of shapes from just one set of DNA tiles. Unlike Rothemund's method, which required new DNA strands with new sequences for every time he wanted to make a different shape, Wei and his colleagues had a library to work with, from which they could make practically anything.

Yonggang Ke has further improved this process. Here is a quote from an article in Discovery magazine, by Ed Yong about his new and improved origami: "The latest DNA bricks are a logical extension of [Bryan Wei's] simple tiles, taking the same principles from two dimensions into three. They keep the simplicity of the tiles, and they’re even smaller (32 letters long, rather than 42) so they should assemble with greater precision. As before, the team designs shapes on a program called CanDo that selects which bricks to include, and a robot mixes them together. With the same set of bricks, they produced over a hundred shapes."



__ But... Why? __ At the moment, a lot of scientists are skeptical of DNA origami, because they cannot see very many plausible uses for it. On the contrary, there are many fields in which it might be useful. At the moment though, possible applications for this nanotechnology are still ideas, not realities.

media type="custom" key="21797604" align="left"One foreseeable use for them is to deliver drugs directly to specific cells. A 3D DNA container could be programmed to recognize markers on certain cells, such as cancerous ones, and release their contents on contact. The video on the side explains this process, and I included it because it give a complete overview of nanorobots. These scientists are using Rothemund's method. Another possible application is that DNA origami shapes could serve as a ruler for microscopic items. Since DNA folds into precise and predictable lengths as a result of it's basic structure, you could use it as a standard, compare it to something otherwise impossible to measure, and voila! You have an accurate measurement in nanometers.

Other uses include them binding biomolecules together, supporting artificial organs, carrying electric current, and even controlling elctron transfer sites in cells.

__ Conclusion __ Even if we don't fully understand what these synthesized biomolecules are capable of, it is very probable that they could have a huge (or very tiny, depending on how you look at it) impact on our world. The history of DNA origami is full of remarkable discoveries. Who knows, maybe the next big advancement in this nanotechnology will help us cure cancer!

__Further reading:__ This [|article] explains in more detail what part DNA origami could play in our future, and how important it might prove to be for us. This article  talks about Ke's progress in making DNA origami. [|This article] gives an extensive look into Rothemund's techniques and applications for it. [|This website] is the home page for the computer program CanDo, that many scientists use to predict the final shapes of their DNA origami.

__References:__ (Note: Bryan Wei's and Yonggang Ke's research is very new, so many websites only mention Rothemund). http://blogs.discovermagazine.com/notrocketscience/?p=8022#.UM-7Qbvyfud http://www.nature.com/news/dna-robot-could-kill-cancer-cells-1.10047 http://www.nature.com/news/fast-dna-origami-opens-way-for-nanoscale-machines-1.12038 http://www.nature.com/news/2010/100310/full/464158a.html http://www.guardian.co.uk/nanotechnology-world/dna-origami-gets-into-the-fold-of-drug-delivery http://www.popularmechanics.com/science/health/genetics/how-it-works-dna-origami-7383319 http://www.dna.caltech.edu/~pwkr/ http://www.foresight.org/Conference/MNT05/Papers/Seeman/ http://www.youtube.com/watch?v=WhGGboRxU


 * Interesting fact: The online scientific journal //Nature// that I used for much of my research is the same journal in which Watson and Crick originally published their findings on the double-helix structure of DNA.

(complete) Cooperation and Natural Selection: Paradox or Not? By: Suzannah Smith January 14th, 2013 Post #2, Topic: Evolution

Almost everyone knows at least a little about Charles Darwin's popular method of evolution, natural selection. It is made possible by the fact that different organisms in one species may have a variant that makes them more likely to survive and reproduce than others. As a synonym of "survival of the fittest", it is the very archetypal result of competition in nature. So, how does cooperation fit into that "everyone for their-self" view of evolution? How did humans, a species that has extensively evolved through the process of natural selection, develop an integral sense of cooperation, especially one that is so deeply ingrained into our society? There are many theories to explain it, and there is a lot of controversy among today's scientists concerning the whole subject. A popular theory today is inclusive fitness, which stipulates that fitness includes how many organisms of close kinship it can add to the population by helping and supporting others. It was introduced of course, by Charles Darwin. At first, he was really puzzled by acts of altruism (the practice of selfless concern for the wellbeing of others) in nature, such as worker bees, ants, and termites, which all sacrifice their lives to protect their homes. He though this might be the counterexample that would destroy his natural selection theory (ex: because the worker bees were not reproducing at all, they should be extinct), but eventually he realized that there was an explanation for this phenomena. By sacrificing themselves to protect their close relatives, the worker bees would be enabling the queen bee to reproduce in great numbers. Since close relatives share similar genes, Darwin concluded that natural selection could be applied to families as well as individuals (which is the kinship theory). He also agreed with the group selection theory (that even though the fitness of an individual with altruistic traits may suffer, it will increase the overall fitness of the group) though, which is now widely criticized because of the flaws it has.

Many scientists, such as J. B. S. Haldane, Sewall Wright, and Ronald Fisher, later tried to further prove the inclusive fitness theory, but it was not until William Hamilton published his scientific works in the 1960s that a solid model was put down on paper. Hamilton had come up with a mathematical equation that explained the relationship between how much an organism benefits and how much it suffers as a result of altruism. However, this still only explained how cooperation between family members developed, and not how it happens on a large scale, between organisms that are completely unrelated.

Then Martin Nowak, a biologist and mathematician at Harvard university, came along and rocked the boat, big time. He set aside inclusive fitness as the main mechanism for the development of cooperation, and instead opted for a much simpler view. Going back to the basics of natural selection, he said that altruism came about just because it gives some individuals a greater chance of success and reproduction than others (whether or not he considered the fact that altruists are usually less fit to survive their environment is uncertain). Then, those individuals would pass on their genes more effectively, and the offspring would have a higher tendency toward altruism. Those offspring would band together with other altruists to form communities that would have a much higher overall fitness than non-cooperating individuals. This theory, which lacks the dependance on kinship, can be applied globally and impacts how evolution as a whole would work. Nowak faces great opposition however, as a lot of scientists are very reluctant to let go of inclusive fitness as a pivotal point. Even though it's not certain how cooperation between relatives spread to organisms of no relation to each other, scientist have explained why cooperation might happen in the latter. The 3 Rs account for it: reputation, reciprocation, and retribution. Reputation is how likely someone is to cooperate with an unrelated individual based on what others have said about them (also know as indirect reciprocity). Reciprocation means that an organism will likely do to another organism what that organism did to it in the past. Retribution is an organism's fear that it will be punished (or suffer, lose out) if it does not cooperate.

The video below extensively explains the evolution of cooperation from beginning to end. It gives an orderly view of all the different theories, and shows which ones make the most sense. I chose to show it here because it puts a lot of information together in one place and elaborates further than I did on a lot of topics. (The lecture starts at 9:00, so to skip all the introductions, go there.) media type="youtube" key="CYH0k7Nkons" height="315" width="420" align="center"

Scientists have come a long way in explaining how cooperation evolved. However, it may never be fully explained by genetics and evolution alone. I think that culture and social interactions should be brought into account if we want to see the full picture.

__Further reading:__ This [|article] lays out a sequencial history of the development of inclusive fitness in great detail. This article explains what group selection is, it's flaws, and why it is so controversial. This article is a scientific paper that shows how culture and society affects the evolution of cooperation. This paper was adapted from Robert Axelrod book, "The Evolution of Cooperation", and shows his views on how cooperation evolved.

__References:__ http://discovermagazine.com/2012/dec/29-cooperation#.UOr4VLuFxgp http://www.genetics.org/content/176/3/1375.full http://www.sscnet.ucla.edu/anthro/faculty/boyd/BoydRichersonTransRoySoc09.pdf http://www.cooperationcommons.com/node/346

(complete) The Sleep Cycle  By: Suzannah Smith January 18th, 2013 Post #1, Body Systems (Endocrine) What tells us that we're tired? Does light vs. dark really have anything to do with how well we're able to sleep? Is there times of the day that are more beneficial for sleeping than others? These are all questions that many, many people have wondered about for a very long time. Today, even though scientists do not fully comprehend the extent of how internal and external factors affect the sleep cycle, they do know enough to answer many commonly asked questions. __Parts of the Brain that Control Sleeping Patterns__ The brain is the ultimate controller of the sleep cycle, and it is what determines if you are tired or not, and when you fall asleep or wake up. Neurons in different parts of the brain promote wakefulness, others promote sleep, and they all inhibit the functions each other. More specifically, neurons from parts of the brainstem and hypothalamus are known to send arousal signals (signals that promote wakefulness) to the cerebral cortex. Since the cerebral cortex controls things like memory, awareness, consciousness, thought, and attention, these signals, which are sent via neurotransmitters, keep the body functioning well so we can stay awake. An example of one such area is the tuberomammillary nucleus (TM), located in the posterior part of the hypothalamus (see diagram above). The neurons in this area release the neurotransmitter histamine, which was only recently scientifically connected to symptoms of wakefulness, but is nonetheless very important. Previously thought to simply activate inflammatory response to counteract foreign pathogens, it has been proven that histamine plays an important role in arousal and wakefulness as well. Anti-histamine drugs that combat allergy symptoms are also notorious for inducing sleepiness, as might be expected. Other neurons in the TM release orexin (also called hypocretin), which functions in much the same way as histamine. On the other hand, a part of the hypothalamus that shuts down arousal centres and smooths the transition into sleep is the entrolateral preoptic nucleus (VLPO). Axons from this area forge a direct path to arousal-promoting centers, but instead of stimulating activity here, they inhibit them by releasing neurotransmitters like GABA and galanin.

Another factor is the pituitary gland, which releases melatonin. This neurotransmitter is influenced by the level of lighting in your environment. When it is light out, melatonin production decreases, but when it's dark, melatonin increases drastically, promoting sleepiness. <span style="font-family: Arial,Helvetica,sans-serif;">Mutual inhibition helps maintain homeostasis between the neurons of opposing functions. For example, the areas of the brain that maintain wakefulness by activating the cortex also inhibit VLPO neurons. The opposite is true as well. When VLPO neurons fire rapidly and induce sleep, they inhibit activity in the arousal centers such as the TM.

__<span style="font-family: Arial,Helvetica,sans-serif;">Internal Cycles Affecting the Tendency to Sleep __ <span style="font-family: Arial,Helvetica,sans-serif;">Now that we know how sleep is controlled, we must ask how it is regulated. For example, the vast majority of people will feel very tired if they stay up late in the night, even if they sleep in for a long time the next day. Why is that?

<span style="font-family: Arial,Helvetica,sans-serif;">There are 2 main factors that control sleep propensity (the likelier you are to be tired or fall asleep); the homeostatic sleep drive, and the circadian alerting system. Homeostatic sleep drive is the build up of the need to sleep over extended periods of wakefulness. This means that for every hour that you are awake, parts of your brain (like the VLPO) increasingly promote sleep. It's not completely certain how this works, but a common theory is tha<span style="font-family: Arial,Helvetica,sans-serif;">t adenosine accumulates in the brain throughout the day. Adenosine is a by-product of cells consuming energy through processes like cellular respiration, but it is also an inhibitory neurotransmitter (a transmitter that stops neurons from firing) that promotes sleepiness and suppresses waking up. Studies have shown that adenosine levels increase during wakefulness and decrease while sleeping, further supporting this theory. <span style="font-family: Arial,Helvetica,sans-serif;">However, our sleep propensity does not solely depend on our sleep drive - or else everyone would be falling asleep at random times throughout the day. Each of us has an internal biological clock, which regulates many of the body's daily cycles. One of these cycles is the circadian alertness signal - a signal that, under normal circumstances, repeats every 24 hours. This rhythm promotes the brain be more alert increasingly throughout the day, counteracting the sleep drive. What controls the alertness cycle? The suprachiasmatic nucleus (SCN), or the "master clock". It's located in the hypothalamus, and works by stimulating parts of the brain (like the TM) to release neurotransmitters that stimulate alertness centers in the brain. When signals from the SCN drop off (around 10 PM in a average adult), the sleep drive becomes overwhelming, usually forcing sleep. <span style="font-family: Arial,Helvetica,sans-serif;">The video below further explains and gives examples of the sleep cycle. I chose it because the speaker gives clear, useful examples of the sleep cycle in living organisms. media type="youtube" key="-Z-vyLHi2us" height="315" width="560" align="center" __<span style="font-family: Arial,Helvetica,sans-serif;">Negative Effects of Disrupting The Cycle __ <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Both factors in the sleep cycle must be balanced correctly in order to maintain optimal awareness and periods of deep, relaxing sleep. If either your sleep drive or your internal clock gets messed up, you will mostly liked suffer the consequences (refer to picture below). For example, if you stay up late one night, even if you stay in bed the next morning and sleep for the same amount of time you do regularly, your sleep drive will have accumulated more than normal, and though sleeping for a long time should fix that, it can't. The circadian alertness signal will still kick in early in the next morning, like it normally does. This cycle is also why jet lag, night shifts, and lack of sleep, etc., are so devastating. It's much harder to regain a balanced sleep cycle than it is to disrupt it.

Moral of the story: Get a good sleep, and do it at the same time every day. Further reading: This article completely outlines all you need to know about sleep, including things like nonREM and REM sleep that I didn't mention here. This article indicates how to treat sleep disorders like insomnia and restless leg syndrome (RLS), and what causes them. This article explains the role of the hypothalamus, melatonin, and light sensitivity in regulating the sleep cycle. This article relates the connection between sleep (or the lack of it) and depression. References: http://www.acnp.org/g4/GN401000075/CH075.html http://www.nigms.nih.gov/Education/Factsheet_CircadianRhythms.htm http://publications.nigms.nih.gov/insidelifescience/biological-clocks.html http://healthysleep.med.harvard.edu/healthy/science/how/neurophysiology http://healthysleep.med.harvard.edu/healthy/science/how/internal-clock http://sommeil.univ-lyon1.fr/articles/lin/frenchcorner/sommaire.php http://www.sleepfoundation.org/article/sleep-topics/melatonin-and-sleep