Tag Archives: dna

Algorithmic Self-Assembly

Paul Rothemund, scientist at Cal Tech, provides a interesting look at DNA folding and DNA based algorithmic self-assembly. In the talk he shows the promise ahead for using biological building blocks using DNA origami — to create tiny machines that assemble themselves from a set of instructions.

Algorithmic Self-Assembly of DNA Sierpinski Triangles, PLoS paper.

I posted a few months ago about how you can participate in the protein folding, with the Protein Folding Game.

DNA Passed to Descendants Changed by Your Life

How your behaviour can change your children’s DNA

Until recently that would also have been the opinion of most scientists. Genes, it was thought, were highly resilient. Even if people did wreck their own DNA through bad diet, smoking and getting fat, that damage was unlikely to be passed to future generations.

Now, however, those assumptions are being re-examined. At the heart of this revolution is a simple but controversial idea: that DNA can be modified or imprinted with the experiences of your parents and grandparents.

According to this new science, known as epigenetics, your ancestors’ diet, smoking habits, exposure to pollutants and levels of obesity could be affecting you today. In turn, your lifestyle could affect your children and grandchildren.
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If we drink heavily, take drugs, get fat or wait too long to reproduce, then epigenetics might start tying up some of the wrong genes and loosening the bonds on others. Sometimes those changes will affect sperm and egg cells.

It seems to me this area is still far from having conclusive proof. But it is another great example of scientists seeking to improve our knowledge of how things work.

Speciation of Dendroica Warblers

Speciation for Dendroica Warblers

They developed a mathematical model that attributed patterns of speciation to the way that closely related species divide up their environment. According to this model, when there are few relatives around to compete for resources, such as when an environment is first colonized, species differentiate rapidly.
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This model is robust: even when the authors assumed that their phylogenetic tree contains only 25 percent of all Dendroica species, they found that their Î³ test was still valid, indicating that this genus experienced an explosive bout of adaptive radiation before settling down to a “more normal” rate of speciation.

This mathematical model provides an incisive tool to gain a clearer understanding of the pattern and rate of speciation for groups of closely related species, even in the absence of a fossil record, simply by analyzing their DNA.

Cell Signals Webcast

Very cool animation, by Cold Spring Harbor Laboratory and Interactive Knowledge, of the working of the inner workings of our bodies as they react to a cut. If you want to get right to the science, skip the first minute. Providing these types of educational animations is a great way for educational institutions to take advantage of technology to achieve their mission in ways not possible before.

It is annoying how many of those “educational” institutions don’t provide such educational material online (and even take material offline that was online). Have they become more focused on thinking and operating the way they did in 1970 than promoting science education? It is a shame some “educational” institutions have instead become focused on looking backward. I will try to promote those organizations that are providing online science education.

Curious Platypus Genome is No Surprise

Platypus Genome Found Fittingly Strange by Rick Weiss

a team of scientists has determined the platypus’s entire genetic code. And right down to its DNA, it turns out, the animal continues to strain credulity, bearing genetic modules that are in turn mammalian, reptilian and avian.

There are genes for egg laying — evidence of its reptilian roots. Genes for making milk, which the platypus does in mammalian style despite not having nipples. Genes for making snake venom, which the animal stores in its legs. And there are five times as many sex-determining chromosomes as scientists know what to do with.

“It’s such a wacky organism,” said Richard Wilson, director of the Genome Sequencing Center at Washington University in St. Louis, who with colleague Wesley Warren led the two-year effort, described today in the journal Nature.

Yet in its wackiness, Wilson said, the platypus genome offers an unprecedented glimpse of how evolution made its first stabs at producing mammals. It tells the tale of how early mammals learned to nurse their young; how they matched poisonous snakes at their venomous game; and how they struggled to build a system of fertilization and gestation that would eventually, through relatives that took a different tack, give rise to the first humans.

“As we learn more about things like platypuses,” Wilson said, “we also learn more about ourselves and where we came from and how we work.”

Very cool stuff. Related: Platypus genome explains animal’s peculiar features; holds clues to evolution of mammals – Platypus genome mapping boon for human and livestock researchers – Platypus genetic code unravelled – Weird Creatures – Evolution is Fundamental to Science – Long-Eared Jerboa – Cat Joins Exclusive Genome Club – Your Inner Fish

Bacteria Can Transfer Genes to Other Bacteria

From page 115 of Good Gems, Bad Germs:

Microbiologists of the 1950’s did not appreciate the stunning extent to which bacteria swap genes… In 1959 Japanese hospitals experience outbreaks of multidrug-resistant bacterial dysentery. The shigella bacteria, which caused the outbreaks, were shrugging off four different classes of previously effective antibiotics: sulfonamides, streptomycins, chloramphenicols, and tetracyclines… In fact, the Japanese researches found it quite easy to transfer multidrug resistance from E. coli to shingella and back again simply by mixing resistant and susceptible strains together in a test tube.

DNA Seen Through the Eyes of a Coder

Great paper looking at DNA from the perspective of a computer programmer. DNA seen through the eyes of a coder by Bert Hubert:

The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 – hence the ‘bi’nary), DNA has 4 positions, T, C, G and A. Whereas a digital byte is mostly 8 binary digits, a DNA ‘byte’ (called a ‘codon’) has three digits. Because each digit can have 4 values instead of 2, an DNA codon has 64 possible values, compared to a binary byte which has 256.

A typical example of a DNA codon is ‘GCC’, which encodes the amino acid Alanine. A larger number of these amino acids combined are called a ‘polypeptide’ or ‘protein’, and these are chemically active in making a living being.
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Furthermore, 97% of your DNA is commented out. DNA is linear and read from start to end. The parts that should not be decoded are marked very clearly, much like C comments. The 3% that is used directly form the so called ‘exons’. The comments, that come ‘inbetween’ are called ‘introns’.

Amazing Science: Retroviruses

One of the great things about writing this blog is I find myself more focused on reading about interesting science. Retroviruses are very interesting and frankly amazing. Darwin’s Surprise by Michael Specter, The New Yorker:

A retrovirus stores its genetic information in a single-stranded molecule of RNA, instead of the more common double-stranded DNA. When it infects a cell, the virus deploys a special enzyme, called reverse transcriptase, that enables it to copy itself and then paste its own genes into the new cell’s DNA. It then becomes part of that cell forever; when the cell divides, the virus goes with it. Scientists have long suspected that if a retrovirus happens to infect a human sperm cell or egg, which is rare, and if that embryo survives – which is rarer still – the retrovirus could take its place in the blueprint of our species, passed from mother to child, and from one generation to the next, much like a gene for eye color or asthma.

When the sequence of the human genome was fully mapped, in 2003, researchers also discovered something they had not anticipated: our bodies are littered with the shards of such retroviruses, fragments of the chemical code from which all genetic material is made. It takes less than two per cent of our genome to create all the proteins necessary for us to live. Eight per cent, however, is composed of broken and disabled retroviruses, which, millions of years ago, managed to embed themselves in the DNA of our ancestors. They are called endogenous retroviruses, because once they infect the DNA of a species they become part of that species. One by one, though, after molecular battles that raged for thousands of generations, they have been defeated by evolution. Like dinosaur bones, these viral fragments are fossils. Instead of having been buried in sand, they reside within each of us, carrying a record that goes back millions of years. Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “junk DNA.” Many still manage to generate proteins, but scientists have never found one that functions properly in humans or that could make us sick.

How amazing is that? I mean really think about it: it is incredible. The whole article is great. Related: Old Viruses Resurrected Through DNA – DNA for once species found in another species’ Genes – New Understanding of Human DNA – Retrovirus overview (Tulane) – Cancer-Killing Virus
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One Species’ Genome Discovered Inside Another’s

Video describing genome inside genome Watch video of Professor Werren describing the genome-in-a-genome at the University of Rochester.

More incredible gene research. Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. The research, reported in today’s Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits.

“This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.”

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Evolution In Action

the way they watched the process was to sequence the whole genome of each bacterial isolate. What they found were a total of 35 mutations, which developed sequentially as the treatment continued (and the levels of resistance rose). Here’s natural selection, operating in real time, under the strongest magnifying glass available. And it’s in the service of a potentially serious problem, since resistant bacteria are no joke. (Reading between the lines of the PNAS abstract, for example, it appears that the patient involved in this study may well not have survived).

The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.

Very interesting. He is exactly right that the technology advances continuing at an amazing pace allow for experiments we (at least I) can’t even imagine today to become common in just a few years. And the insights from those experiments will allow us to think of new experiments… Wonderful.