Genetics

About a month ago, Ordo graduated from high school (congratulations!) and he built a MOC to celebrate completing each final exam. Here we see his MOC for his biology class, genetics. The others aren't science-based, but you should still check out the MOCs based on his German literature, English and economics exams.

T4 virus

Recently NewScientist held a LEGO contest. Lisa Strazdina was runner up with her model of enterobacteria phage T4. This virus infects E. coli, injecting DNA into the bacterium and using the bacteria's own enzymes to reproduce itself, killing the bacterium in the process.

What is black and white and red all over?

A recent study that appeared in Nature Communications saying that zebra stripes somehow help them ward off biting flies. Here's a zebra that I'm pretty sure is from the life-size animal displays that Sean Kenney has been building for zoos around the US.

Nobel week!

Okay, in my general blogging malaise recently, I've gotten behind in the most exciting week for science geeks. Better than March Madness, better even than Shark Week, it's Nobel week! Monday (okay, it was a day ago, I missed it), is Physiology or Medicine Day. The 2013 prize was jointly awarded to James E. Rothman, Randy W. Schekman and Thomas C. Südhof. These three scientists have done groundbreaking work in examining how molecules are moved around in the cell. Molecules are wrapped up in membrane bound parcels called vesicles. These three looked at how the transfer of these parcels and their unwrapping to release their contents is regulated in the cell. Essentially they worked out how the cellular post office works (this picture is of an official DUPLO set, btw).

Rosalind Franklin

I'll get back to symmetry tomorrow, but I'll do an aside today, spurred by the Google doodle in honor of what would have been Rosalind Franklin's 93rd birthday. I've peviously noted how important she was in the discovery of the structure of DNA. If she had not sadly passed away at a very young age, she surely should have been considered as part of the 1968 Nobel Prize. Last year Wendy Staples of the Quirky Cookie made a lot of science and women-scientist themed cookies for the launch party of the ScienceGrrl Calendar at the London Science Museum. ScienceGrrl is a British organization to promote science education, particularly to young girls. Anyway, here we see cookies of LEGO versions of Rosalind Franklin and Hedy Lamarr (best known for her movie career, but she also developed a radio frequency hopping technique that formed the basis for much of today's wireless technology). BTW, you really should go see all of the cookies. They're really cool, and I'm sure were perfect for a science themed event.

DNA patent ruling

Here's some DNA. I'm not sure who built this, as this was at a public display and turns up in several people's photo streams. Anyway, you might ask why post this today, as I just posted a model of DNA in my last post. Well, this gives me a chance to write about the ruling from the US Supreme Court in the case of Association for Molecular Pathology v. Myriad Genetics, Inc. As I understand it, Myriad held a series of patents, and some were upheld while others were struck down. To understand this case, we have to start with a description of transcription/translation. DNA resides in the nucleus, and protein synthesis takes place at the ribosome outside the nucleus. In order to get the information from the DNA to the ribosome, a copy is made, the complementary strand of RNA. So, for instance, let's say there is a DNA strand that goes GCGCAAGC. The complementary strand of messenger RNA is CGCGTTCG (C's match with G's, G's match with C's, T's match with A's). But, let's go a little further. About 98% of the human genome is not used for making proteins. When this non-coding DNA (sometimes called 'junk DNA', but it does actually have important regulatory function) comes in the middle of a DNA sequence, it is called an intron. So the unwanted parts are removed. So, for instance, our CGCGTTCG strand could be trimmed down to just CGCGCG, and this mature mRNA would code for the protein Arg-Ala (groups of three RNA bases are called 'codons', and code for different amino acids). Okay, back to Myriad Genetics. They found that a mutation in the code for a particular protein is associated with certain kinds of breast cancer. So, in our example the healthy cell has DNA GCGCAAGC, which leads to mRNA CGCGTTCG, which is modified to mature mRNA CGCGCG, which codes for protein Arg-Ala. Let's say the potentially cancerous cell has DNA CCGCAAGC, which leads to mRNA GGCGTTCG, which is modified to mature mRNA GGCGCG, and this would code for protein Gly-Ala, and let's say this protein is associated with cancer. Myriad came up with a test for the presence of this mutation. Their test involved creating a shortened form of DNA with the introns removed, called complementary DNA. In our example this would be CCGCGC (note it is missing the AA from above). They take mRNA from the patient, and see if it binds to this complementary DNA. If it does, it indicates the presence of a mutation that could lead to cancer. They then took out patents on the process of comparing the mRNA to their complementary DNA, the sequence in the complementary DNA (CCGCGC), and also the sequence in the initial DNA (CGCGCAAGC). What the Supreme Court ruled yesterday is that the third type of patent is invalid, as the sequence of DNA in the living cell (either healthy or cancerous), is a 'product of nature'. That is, Myriad did not invent it, so they cannot patent it. OTOH, the complementary DNA is not naturally existing, and so therefor may be patented. It is also valid to patent a novel method involving this complementary DNA. So it was a mixed ruling, but IMO a correct one. The human genome is still there available for anyone to do research without fear of being sued for patent infringement, but there is still incentive for companies to produce new types of tests that they can protect with patents.

DNA

There are a lot of LEGO renditions of DNA out there, indeed I chose one for the banner of this blog, but most don't really have an accurate structure. This one by SICP_DNA, though, is very good about keeping to the actual structure of DNA. In DNA, the strands on either side are pointing in opposite directions, and the white and gray backbones have the studs pointing in different directions here. Since the backbone sugars are asymmetric, the 'grooves' are different sizes. Another aspect of DNA is that two of the bases, the purines A and G, are larger than the other two, the pyrimidines T and C. The connections here are such that it only works out when A lines up with T or G lines up with C. They also got the sizes right here, so that one complete twist takes ten steps, and the width to height ratio is approximately correct.




Here you see a comparison between the 'real' structure of DNA, and a simplified depiction. BTW, the LEGO version below is from Nathan Sawaya's Building Bricks of Life. I certainly mean no disrespect, as it is a great model. But as Nathan has said elsewhere he's an artist, not a scientist, and he writes that he decided to go with this more artistic approach (as a commissioned piece for the Archon Genomics X Prize) rather than try to do a more accurate version. Someday I'd like to see him go back and do an accurate depiction of DNA. He's a great sculptor and I'm sure it would be quite cool.



BTW, since I've posted two Cuusoo projects in a row, I wanted to say a little about that. I was corresponding with another LEGO blogger the other day about these, and I agree with him that a great number of the things posted there are not actually viable LEGO sets, including this one (sorry, SICP_DNA). So if I blog something, it is not necessarily true that I am supporting it as a Cuusoo project. I just see Cuusoo as another place where LEGO builders post their creations, along with other photo sharing sites.

Petri dish

As anyone who uses Google knows, today they recognized Julius Richard Petri's 161st birthday. A Petri dish, aka a cell culture dish, is a shallow round dish with a raised edge, often used by microbiologists to grow bacteria or other microorganisms (here in LEGO by MorsLEGO). Usually the dish is partially filled with a warm liquid mixture of agar and nutrients. After it cools the agar becomes a semi-solid gelatin that is an appropriate surface for growing the bacteria, which can be studies as they grow.



In a fun twist, artist Darlene Charneco made Podland Petri.

DNA

Continuing with my mini-focus on the models in my new banner, DNA's double helix (here by Andreas) is one of the most widely recognized structures from modern science. This wasn't always true. By the 1940's it was commonly accepted that DNA held the key to genetic information. It was known that DNA was made of four bases - G, C, A, and T - and also sugars and phosphates, but it was not known how these came together. Erwin Gargaff discoverd that each cell had an equal number of G's and C's, and also an equal number of A's and T's. Linus Pauling proposed a structure that involved a triple helix, with the phosphates on the insides. At this time, Rosalind Franklin was doing some ground breaking work on X-ray crystallography, and she determined that the structure involved a double helix, and the phosphates must be on the outside. Watson and Crick put this information together, and they came up with the now famous double helical structure shaped like a twisted ladder, where the outside strands (the blue bricks in this LEGO model) are comprised of repeating sugar-phosphate units, and the rungs of the ladder (the red and yellow here) are pairs made up of either A and T or G and C bases. Their paper describing the structure has one of the best lines ever in science writing: "This structure has novel features which are of considerable biological interest." Indeed, the base-pairing and the double helix are at the heart of explaining how DNA is copied, bringing information to the next generation of cells, and also explaining how DNA is used by the cell to make proteins.



BTW, the elucidation of DNA's structure is a great story of egos and infighting, probably sexism, and accusations of international politics. Franklin didn't get much credit for her discoveries because another scientist, Wilkins (another DNA researcher who eventually shared the Nobel with Watson and Crick) shared her data with Crick without asking her first. After she left Kings College, the research director there refused to let her continue on with her data, so she turned to other subjects, where she made ground-breaking discoveries on tobacco mosaic virus and polio virus. So one of her key papers was not even published until after her death. Another interesting side story is that Linus Pauling reportedly felt he would have come up with the structure first if he hadn't missed a flight due to passport issues, so he didn't see a talk by Franklin where she shared some of her results. The Wikipedia entry disputes the significance of this missed flight, but I first heard the story at a conference in honor of Pauling on the occasion of his 90th birthday, where several of his former students gave talks. BTW, he was there at the start of the conference, but I didn't make it until the afternoon session, so I didn't get to see him.

Electron Transport Chain

ATP is the cell's currency of energy. To make ATP takes energy, though. In order to do this, energy is used either from sunlight in photosynthesis or from chemical reactions in respiration to move electrons across a membrane via an electron transport chain, here illustrated by Medieval Guy. When you move negatively charged electrons across the membrane, though, you create an imbalance of charges. In order to bring charges back into balance, positively charged protons flow from one side of the membrane through the other, and the movement of these is harnessed by ATP synthase to produce more ATP. BTW, I was at UCLA in 1997 when Paul Boyer was awarded the Nobel for his role in the elucidation of the ATPase mechanism. I was also there in 1995 when UCLA won the NCAA basketball championship. On one of these occasions there was a reception hosted by the Department of Chemistry and Biochemistry. On the other occasion there was mini riot in Westwood Village of drunken college students. Can you guess which was which?

Genome sequencing

Your genome is the sequence of nucleic acids found in your DNA. This sequence is the template for your proteins, and basically makes the blueprint that makes you a human and not, say, a tree. Knowing the genomic sequence for an organism has many applications, from basic research to applied medicine. For instance, you could identify some bacteria by its sequence to diagnose a disease, or you could find out if a person has the markers for some inherited disease. A number of companies have developed laboratory instrumentation for genomic sequencing, such as the Life Technologies Ion Torrent Personal Genome Machine. Torsten Seeman built a LEGO rendition for his son.

Microscope

Gilcélio Chagas built this great microscope. Rather than give my own explanation, I'll just quote his:

A microscope (from the Ancient Greek: μικρός, mikrós, "small" and σκοπεῖν, skopeîn, "to look" or "see") is an instrument used to see objects that are too small for the naked eye. The science of investigating small objects using such an instrument is called microscopy. Microscopic means invisible to the eye unless aided by a microscope. There are many types of microscopes, the most common and first to be invented is the optical microscope which uses light to image the sample. Other major types of microscopes are the electron microscope (both the transmission electron microscope and the scanning electron microscope) and the various types of scanning probe microscope. The first microscope to be developed was the optical microscope, although the original inventor is not easy to identify. An early microscope was made in 1590 in Middelburg, Netherlands.Two eyeglass makers are variously given credit: Hans Lippershey (who developed an early telescope) and Zacharias Janssen. Giovanni Faber coined the name microscope for Galileo Galilei's compound microscope in 1625 (Galileo had called it the "occhiolino" or "little eye").

Nobel Prize in Physiology or Medicine

This year's Nobel Prize in Physiology or Medicine was shared by John Gurdon and Shinya Yamanaka. Gurdon's work goes back fifty years to when he first cloned an adult frog by taking DNA from mature cells and transplanting them into frog eggs to produce new tadpoles. The key thing here was that the mature cell held all of the information to code for all of the cells in the body, that is, a liver cell has all of the information to make blood cells or neurons or whatever, and so could become the basis for a complete organism. Yamanaka's work brings this idea forward, and he developed ways to turn back the clock on mature cells, essentially tricking them into reverting to the same state as embryonic cells that can grow into all sorts of new cells (i.e. they are pluripotent). These are called stem cells, and are one of the most promising areas of medical research today. Towel made these LEGO vehicles based on frogs and tadpoles.

Ornithology

Ornithology is the branch of zoology that focuses specifically on birds (Kingdom: Animalia, Phylum: Chordata, Class: Aves). Ornithology is a fun science in that anyone can get involved. I grew up with a field guide to North American birds and a pair of binoculars sitting next to our kitchen window where we could sit and watch the various birds (and squirrels) coming to our bird feeders. You can tell that DeTomaso is a bird lover as well, as he has made a large number of very accurate and lifelike models of different birds. He's done over 20 so far, and keeps on going. He's proposed this as a series of actual LEGO sets, which you can suppor on Cuusoo.

Scarlet Tanager



Robin



Goldfinch



Kingfisher

Polymerase Chain Reaction

DNA replication is the process that your cells use to copy their genetic blueprint. This occurs every time cells divide, so that each new cell has a complete set of instructions. The process involves unzipping the two complementary strands of the parent DNA, and then using free nucleic acids and an enzyme called a DNA polymerase to construct new strands to pair up with each of the parent strands.

Polymerase Chain Reaction, or PCR, is a process to run this replication artificially in a laboratory. This is often used to analyze DNA samples. Typically analysts get only a very small amount of a DNA sample, and by using PCR they can create a large amount of identical DNA to study. This might be used to identify a blood sample or other evidence at a crime scene, in something like paternity testing, or to identify the DNA of a bacteria or virus to diagnose disease. The Abbott m2000(R) is an automated instrument to run PCR testing to identify various disease agents. Dave and John from briXwerX have made a number of m2000 models on commission for Abbot Molecular.

DNA

All living creatures are coded by the same four nucleic acids, just put together in different orders. Hydrogen bonding allows for the bases to pair up into a twisted ladder structure, which is key to replication, transcription and translation. William Keckler shares this mosaic of the familiar DNA double helix. I suspect that this is actually digitally created rather than built of actual LEGO brick.

Zoetrope

I've previously noted how a zoetrope uses a series of still pictures to trick your brain into seeing movement - essentially the same thing that happens in a movie projector. Here is a zoetrope of a galloping horse by Lego Tron. The galloping horse is a particularly appropriate subject (as Lego Tron notes), because it hearkens back to the work of Eadweard Muybridge. Muybridge was a photographer who was interested in seeing how animals move. In a famous experiment, he set up a series of cameras along a racetrack that were triggered to snap photos as a horse galloped past. These pictures could be strung together in an early version of a motion picture, similar to the zoetrope, called a zoopraxiscope. These pictures also proved that at points during the gallop, all four feet were in the air at once. BTW, I first learned about the Muybridge work after Ahmed Zewail won the 1999 Nobel Prize in Chemistry, since he compared his work to Muybridge. Zewail used extremely short (femtosecond) bursts of laser light to "photograph" a reaction in motion, and actually characterize something at (or very near) the transition state. In comparison to the Muybridge work, this is like being able to sit and study the horse with all four feet in the air. Of course you normally can't do that, since the horse would fall to the ground, but you can study the photograph that captures that moment in time. A transition state (which is a point in the reaction path where some bonds from the starting material are breaking and other bonds from the product are being formed) can normally not be observed, since it is so instantaneous, but Zewail gave us a peek behind that curtain.

Smaller frog

I previously blogged Dave Kaleta's great dissected frog. George G made this tribute.

Galapagos Tortoise

The Galapagos tortoise played a role in Darwin's development of the theory of evolution. He realized that the tortoises on different islands had developed differently in response to their environment, writing "animals on separate islands ought to become different if kept long enough apart with slightly differing circumstances. – Now Galapagos Tortoises, Mocking birds, Falkland Fox, Chiloe fox, – Inglish and Irish Hare."
The news reported yesterday that a species of Galapagos tortoise previously thought to be extinct is still alive. Biologists found genetic markers unique to that species in living tortoises that appear to be cross-breeds.
Here Kaptain Kobold depicts Darwin observing a tortoise.

PhD!!

Congratulations to MorsLEGO's wife, who just completed her PhD in Cellular and Molecular Biology. He made her this small scene of her at her microscope in commemoration of her achievement.