Saturday, September 15, 2012

Drawing your portrait using your DNA

"You look just like your mother."

"Easy to pick out a Smith kid."

It's common knowledge that our looks are inherited. But just which genes make the face? Those pieces of the puzzle are now being picked out of the pile. Well, five of them at least. Researchers at Erasmus University Medical Center in Rotterdam conducted a study using head magnetic resonance imaging and portrait photographs to map the face. Then they sifted through each individual's genome to find genes that seemed associated with the facial landmarks. Three of the genes, called PRDM16, PAX3 and TP63, had already been identified in other studies. Two, C5orf50 and COL17A1, were previously unknown.

There are a couple of interesting things here. First, these genes code for other things, not just facial characteristics. PAX3 is a gene that regulates muscle-cell formation, and it also controls the distance between the top of the nose and the right and left eyes.

Second, PAX3 had been identified in a previous study (by Lavinia Paternoster in research that was part of the Avon Longitudinal Study of Parents and Children) that used different methods. This is a classic and strong example of replicating results.

We aren't quite able to have a computer draw a picture of a face using a the DNA from a swab of the cheek. There are hundreds, maybe even thousands of genes which give us the faces we so identify ourselves with. But we are getting closer.

For more details check out the article at NBC science.

Saturday, September 8, 2012

Spring caught up with me! It was gardening time, and extra things at school time, and yet another spring bug that hit our family. If you want to read about my gardening, I'm talking about it at my main blog, which right now is only slightly more active than this one. And then came the need to hunker down and get organized. I'm a mom, wife, writer, active volunteer, and church goer. I also knit and garden. And cook my dinners from scratch. If I'm going to keep hold of this rope, I need to make sure the ends don't fray. So I purposefully set the summer to get things under control. And I was pretty successful at it. More of that is on my other blog too.

But now, it's fall. So here is a cool link.

The Human Genome Is Far More Complex Than Scientists Thought

The Human Genome is Far More Complex than Scientist Thought

We already knew that epigenetics was big, but we didn't know it was this big. Around 80% of what we thought of as "junk DNA" is biochemically active. In this active section, there are 70,000 sites which control whether or not nearby genes are activated and over 400,000 sites which influence the activity of genes. And there are only about 20,000 protein encoding genes. Makes you think, doesn't it? Read the article, and then link through to Not Exactly Rocket Science to learn even more.

Also, that image is totally computer generated. DNA does not look like that under an electron microscope. Even if we could actually see it that close up, it would look much lumpier and wouldn't be that regular it all. It would be bunched up or stretched out, bulged out, and sometimes split apart.

Tuesday, April 3, 2012

DNA: the molecular goddess

WOOPS! It's been a while (sick kids, getting my garden in, taxes, etc.) but not as long as I'd intended. I found I had posted this on my other blog, Over the Dither and Through the Words. Well, here it is now and I'm getting my next post prepared. Enjoy!
In my last post on cell structure, we took a look at cell membranes which are made of a phospholipid bilayer. They protect the cell and cell organelles from the outside environment while letting a few players in and out to do their job. But what is it that membranes protect? Primarily, DNA (short for DeoxyriboNucleic Acid), a molecule that can make copies of itself. How DNA works was the next thing that blew my mind in biology, and pretty much cemented what I wanted to study.
DNA is the ultimate celebrity superstar of molecules. It’s the subject of many a science fiction story, volumes of textbooks and encyclopedias, various t-shirts, jewelry, and a scarf I want to knit someday. Everyone has heard of it, knows what it looks like, and knows that it carries our genes. If DNA is news to you, then you are probably fairly young or you’ve been living under a rock.
So how does this double helix encode our genes? You might think of a gene as that bit of information which gives us our eye color, makes us tall or short, shapes our nose, and gives us ADD (or not). While many of these things can be traced to a single gene, the more accurate definition of a gene is a sequence of DNA which gives instructions to put together a protein.
DNA has an alphabet of four letters, called nucleotides, nucleobases or bases for short. These nucleotides can fit together in two matching pairs called base pairs. The base pairs make up the rungs of the twisted ladder structure of DNA, with the sides being the twinned backbones of the macromolecule. The base pairs connect to each other across the rung, matching molecular shapes in the middle to make a light bond which can be zipped or unzipped. On one side of the ladder is the complementary template, and on the other is the actual code that creates a protein when transcribed.
These four nucleobases of DNA are Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). A pairs up with T, and C pairs up with G. Ever watched the eugenics dystopian movie Gattaca? It's title refers to the bases of DNA.
Three of these bases together make a word, called a codon. This codon represents an amino acid. The twenty amino acids are the building blocks of proteins. There are also codons which say stop and start. This dictionary of codons which can be translated into amino acids, or stop and start is calledthe genetic code. How we got this genetic code is one of those mysteries that we still haven’t solved.
When making a protein, DNA is unzipped by certain enzymes, and a copy of it is made. This copy isn’t DNA, but RNA – a single strand instead of a double strand. Instead of Thymine, RNA uses a base called Uracil which still pairs with Adenine. Once the sequence of RNA is copied from the DNA (beginning at the start codons and ending at the stop codons), it is moved to a part of the cell where the protein can be built. This special sequence of RNA is called messenger RNA, or mRNA.
A DNA molecule being unzipped, transcribed, and it's mRNA template going on to a ribosome as a molecular blueprint for building a protein out of amino acids.

Another form of RNA is transfer RNA, or tRNA. tRNA is connected to an amino acid and has an anti-codon which has the three bases matching the codon for the amino acid. The mRNA goes to a ribosome, which is kind of a molecular reader. There can be up to 10 million ribosomes in a single cell. As the mRNA clicks through the ribosome, tRNAs connect to the proper mRNA codon, and then their amino acids are bound together. In this way, the long protein chain is created.
DNA doesn’t just code for proteins. In fact, only about 1.5% of the human genome represents protein sequences. It also has regulatory sequences, which control what proteins are made and how much and structural sequences for the chromosomes. And there can be a lot of repetitive DNA which doesn’t appear to do anything, though we can’t be positive about that right now. All of these can affect our genes and how they're expressed - in other words, what kind of inborn traits we have. But some of it does appear to be fossils of a type: broken copies of sequences we use or perhaps ones we no longer use. It’s this extra DNA which is another proof that species, including humans, have evolved over time. In the human genome, there are over 3 billion base pairs with approximately 23,000 protein coding genes. We are still exploring what each of those genes do.
So, cell membranes and DNA were the two sirens that pulled me into biology. Before I go any further into the other cool molecules, I think it's a good idea to get the lay of the land. In my next post on cell structure we'll take a brief look at a whole animal cell and get a simple description of each of the cell organelles.

Thursday, March 15, 2012

How cell membranes patch holes

Cell membranes of our muscle cells can get ripped when we exercise. Ack! But don't shy away from the gym or the great outdoors. Of course our cells have a way to repair the tiny holes. It happens all the time. But we haven't been quite sure how things got patched up. In this article, scientists were actually able to observe the repair of cell membranes of living cells in a living organism. To do this, they used a zebrafish embryo, which is tiny and mostly transparent. They tagged proteins with florescent proteins (a cool technique for seeing molecules which I'll blog about someday) which the researchers knew were involved in repair. Then they burned holes in the cell membrane with a laser and watched what happened under a microscope. Holes in a cell membrane with a laser - wow.

This was done by Prof. Uwe Strähle and Dr. Urmas Roostalu from Karlsruhe Institute of Technology (KIT) and Heidelberg University. Read more about what they observed in the article from Science Daily.

Monday, March 12, 2012

How Telomeres Incriminate Cells That Can't Divide

I've been writing a post about DNA, so when I came across an article about telomeres and cell division, I thought cool! Not only does this article have a great explanation of what telomeres are, but it describes the scientific process. Scientists at the Salk's Molecular and Cell Biology Laboratory under Jan Karlseder have been studying these telomeres and their involving in aging and cancer. Reading between the lines, you can just see how these scientists would observe the changes and try to determine what was happening and why, and further how it could help cancer patients.

So what are telomeres? They're the end caps of the long DNA strands that make up your chromosomes. Every time a cell divides, these end caps shrink just a little. When they're gone or too much DNA damage is detected, other proteins are released so the cell shuts down and dies. Cancer cells often reset these telomeres so that they keep on dividing. One of the most famous cases of this are the HeLa cells, from Henrietta Lacks a black woman who died of cervical cancer in the fifties. Her cells are still alive and have been used many, many studies that have resulted in cures for several diseases. I wonder if HeLa cells were used for this study? Unfortunately, her family has been given no compensation, though many biological companies are making lots of money of HeLa cell cultures. But I digress.

Wanna learn something cool? Go read the telomere article at Science Daily. I'll be posting mine on DNA soon.

Wednesday, March 7, 2012

Rudolph Ludwig Carl Virchow: cell theory and bioethics

Today, we take it for granted that we’re made up of cells. But it was only in the mid nineteenth century that scientists really began to understand this. Two obstacles stood in the way of understanding. The first was simple observation: without microscopes, no one could even see cells. The second was the prevalence of a theory, or group of theories called Vitalism. Scientists believed that there was a distinct difference between organic matter and non-organic matter, and part of this difference was a kind of life energy. But that’s a cool dead theory for another post.

Because of the entrenchment of Vitalism, it was still over a hundred years after the first cells were seen through a microscope before anyone really understood that they were the basic building blocks of all life. Several scientists were involved. One of them was an interesting fellow named Rudolph Virchow.

Virchow was a physician and later an anthropologist. He was remarkable not only for his insistence that medicine be based on observation and experimentation, but also for being a revolutionary with strong ethical convictions.

Born in Germany on October 13, 1821, Virchow started out life as the only child of a farmer. Early on he showed a love for the natural sciences. Because of his aptitude he was given a fellowship which paid for him to attend medical school.

Self confident almost to a fault, he regularly challenged his teachers. At one point as a student, he conducted several experiments to disprove the theories of his professors that the causes of phlebitis (inflammation of the vein) were in the fluids rather than the vein walls (the cellular structure).

He received his medical degree from the University of Berlin in 1843. A few years later, he was sent to investigate a typhus outbreak in a poor province of Prussia. Instead coming back with a few medical guidelines, as had been expected, he insisted that the cure for such epidemics was the freedom of the people. The outbreaks weren’t just from poor hygiene, but were caused by the abject poverty and illiteracy which were caused by the economic and political subjugation of the people. Public health required “full and unrestrained” democracy, and everyone should have a constitutional right to health care.
After that, he became a political activist, often campaigning for free democracy and the equal treatment of peoples. And he firmly held fast to that ideal, even turning down noble status which was offered later in life in honor of his scientific achievements.

His political activism got him booted as a faculty member at his medical school. Fortunately, this allowed him to spend more time in the laboratory. It was during this period that he studied cells. The fact that all living things were made of cells had already been established by Matthias Jakob Schleiden and Theodor Schwann. But these scientists still believed that cells might form by crystallizing or some other kind of precipitating process. As well, they faced a great deal of opposition from the vitalists. Once again, going against the norm, Virchow agreed with the observations of Schwann and Schleiden. But instead of a kind of spontaneous generation of cells, Virchow observed cells dividing under the microscope and developed the theory that all cells come from other living cells by cell division. He popularized the saying “Omnis cellula e cellula”. His focus on cells was in pathology on how they lead to disease.

He combined his love of science and medicine with his insistence one the standard of equality for all men his whole life. In his later years he joined the city council in Berlin, working with the government to improve public health. He was one of the first to put forth socioeconomic and political factors as the source for many predispositions for diseases. And when he later became interested in anthropology, what he did was to gather data which disproved the then popular notion that people of Aryan or Nordic descent were superior to others. He proclaimed that medicine was the highest form of human insight and the mother of all sciences.   He died in 1902, after a life which moved medicine forward towards being evidence based and established a foundation for bioethics.

Tuesday, February 28, 2012

Cell membranes: way cooler than the wall of China

Cell membranes are one of the tiny wonders of the world. More than just a barrier, they selectively keep things out or let things in to the cell. They have components which identify the cells they protect, receive signals that change what the cell is doing, and send out signals as well.

But what is more amazing is that they are self assembling. If you have a test tube with the molecules that make up a cell membrane mixed evenly in water, you'll find that they quickly form up into spheres of cell membrane. It's one of those things that is both simple and complex. I still have to admit to being a bit awed by them.

The main ingredients of a cell membrane are phosphoglycerides (more commonly known as phosphlipids). There are several versions, but their main construction is a single phosphate head and two fatty acid tails. The phosphate head likes to be around water and mixes with it regularly. The fatty acids are basically oil, and try to avoid water. When you mix these molecules up randomly in water, they come together in a double layered sheet of molecules with the water loving phosphate heads spread out on the outside and the water avoiding tails bunched up on the inside. Beautiful!

Only small molecules such as water, carbon dioxide, and oxygen can pass through membranes made of just phospholipids. These substances enter or exit the cell by diffusion, which basically means things bumping around each other enough that they get spread out evenly. Laws of probability and all that. But cells may need to ingest large molecules such as sugars and proteins. And they may want to keep a concentration of some substances higher or lower in the cell than its surrounding environment.

For this, there are proteins that imbed themselves all the way through the membrane, called integral proteins. Some of these proteins are just pores that certain molecules can fit through. This is how glucose enters the cell. A cell is constantly breaking down glucose to create energy, so there is usually less glucose in the cell than outside of it (the cell is always breaking down glucose to create energy), so it naturally diffuses into the cell. But because a glucose molecule is so big, it must move through the transport proteins in the membrane. No energy is needed to let these kinds of molecules pass.
But some proteins are pumps that actively move molecules in or out. A good example of this are the mineral salts that plants need. These minerals are in a lower concentration in the soil or water than in the cell. To absorb the minerals, the plant cell must use active pumps to keep a higher concentration.

Other integral proteins receive signals which don't have to enter the cell to affect it. These special signal molecules will change the shape of the protein when they attach to it. On the inside of the cell, this shape change starts a chain reaction which causes the cell to either start producing something, stop producing something, or in the case of muscle cells, to change shape.

Some proteins might be stuck to just the surface or partway through a membrane. These peripheral can act as identifiers. In blood cells, surface proteins determine the blood type.

There is a lot more to cell membranes, far more than can be covered in one post or even a series of posts. They are an essential component of all biological life, as important as DNA. Not only do they protect the cell from the outer environment, they protect the cells organelles and store molecules that they don't want to use yet. They can store things for later use, which would otherwise be quickly metabolized in the cell's cytoplasm.

We are learning from these natural technologies. Scientists have now created artificial membranes, an important step to creating artificial life forms. This could have applications in medicine, building, convenience, and many other things (some of them admittedly scary but that's another post). Other technologies which take their cue from the cell membranes are the liposomes found in our face lotions.  Another possible technology  is protecting buildings. While we'll still face pitfalls and dangers, I firmly believe that learning from nature and protecting it, rather than trying to circumnavigate it will propel us into a better world.