Tag Archives: genes

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.

Our Genome Changes as We Age

Our Genome Changes Over Our Lifetime

For the new study, researchers first collected DNA samples collected in 1991 and again between 2002 and 2006 from 600 participants already enrolled in the AGES Reykjavik Study. The AGES study is renowned for its value to genetics research because of the historic isolation and reduced number of genetic “variables” among Iceland’s population, making certain patterns of genetic information easier to identify.

Among the 600, the research team measured the total amount of DNA methylation in each of 111 samples and compared total methylation from DNA collected in 2002 to 2005 to that person’s DNA collected in 1991.

They discovered that in almost one-third of the subjects, methylation changed over that 11-year span, with some gaining DNA methylation and others losing it.

“The key thing this part of the study told us is that levels changed over time, proof of principle that an individual’s epigenetic profile does change with age,” said M. Daniele Fallin, Ph.D., an associate professor of epidemiology at the Johns Hopkins Bloomberg School of Public Health.

Still a puzzle, though, was why or how, Fallin said, “so we wondered whether the tendency to those changes was also inherited, right along with our DNA sequences. That would explain why certain families are more susceptible to certain diseases.”

Lancelet Genome Provides Answers on Evolution

Lancelet genome shows how genes quadrupled during vertebrate evolution by Robert Sanders

“If you compare the 23 chromosomes of humans with the 19 chromosomes of amphioxus, you find that both genomes can be expressed in terms of 17 ancestral pieces. So, we can say with some confidence that 550 million years ago, the common ancestor of amphioxus and humans had 17 chromosomal elements.”
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Each of those 17 ancestral segments was duplicated twice in the evolution of vertebrates, after which most of the routine “housekeeping” genes lost the extra copies. Those left, totaling a couple thousand genes, found new functions that, Putnam said, make us different from all other creatures.

“These few thousand genes have been retooled to make humans more elaborate than their simpler ancestors. They are involved in setting up the body plan of an animal and differentiating different parts of the animal,” he said. “The hypothesis, pretty strongly supported by this data, is that the multiplication of this particular kind of gene and differentiation into different functions was important in the formation of vertebrates as we know them.”

“The most exciting thing that the amphioxus genome does is provide excellent evidence for the idea that Ono proposed in 1970, that the human genome had undergone two rounds of whole-genome duplication with subsequent losses,”

A great example of the scientific method in action. It often isn’t a matter of developing a theory one day, testing it the next and learning the outcome the next. The process can take decades for complex matters.

How Humans Evolved Allergies

Ancient antibody molecule offers clues to how humans evolved allergies

The chicken molecule, an antibody called IgY, looks remarkably similar to the human antibody IgE. IgE is known to be involved in allergic reactions and humans also have a counterpart antibody called IgG that helps to destroy invading viruses and bacteria. Scientists know that both IgE and IgG were present in mammals around 160 million years ago because the corresponding genes are found in the recently published platypus genome. However, in chickens there is no equivalent to IgG and so IgY performs both functions.

Lead researcher, Dr. Rosy Calvert said: “Although these antibodies all started from a common ancestor, for some reason humans have ended up with two rather specialised antibodies, whereas chickens only have one that has a much more general function.
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Professor Brian Sutton, head of the laboratory where the work was done said: “It might be that there was a nasty bug or parasite around at the time that meant that humans needed a really dramatic immune response and so there was pressure to evolve a tight binding antibody like IgE. The problem is that now we’ve ended up with an antibody that can tend to be a little over enthusiastic and causes us problems with apparently innocuous substances like pollen and peanuts, which can cause life-threatening allergic conditions.”

Shaw Laureates 2008

Image of the Shaw Prize Medal

The Shaw Prize awards $1 million in each of 3 areas: Astronomy; Life Science and Medicine; and Mathematical Sciences. The award was established in 2002 by Run Run Shaw who was born in China and made his money in the movie industry. The prize is administered in Hong Kong and awards those “who have achieved significant breakthrough in academic and scientific research or application and whose work has resulted in a positive and profound impact on mankind.” The 2008 Shaw Laureates have been selected.

Astronomy
Professor Reinhard Genzel, Managing Director of the Max Planck Institute for Extraterrestrial Physics, in recognition of his outstanding contribution in demonstrating that the Milky Way contains a supermassive black hole at its centre.

In 1969, Donald Lynden-Bell and Martin Rees suggested that the Milky Way might contain a supermassive black hole. But evidence for such an object was lacking at the time because the centre of the Milky Way is obscured by interstellar dust, and was detected only as a relatively faint radio source. Reinhard Genzel obtained compelling evidence for this conjecture by developing state-of-the-art astronomical instruments and carrying out a persistent programme of observing our Galactic Centre for many years, which ultimately led to the discovery of a black hole with a mass a few million times that of the Sun, in the centre of the Milky Way.

Supermassive black holes are now recognized to account for the luminous sources seen at the nuclei of galaxies and to play a fundamental role in the formation of galaxies.

Mathematical Sciences
Vladimir Arnold, together with Andrei Kolmogorov and Jurgen Moser, made fundamental contributions to the study of stability in dynamical systems, exemplified by the motion of the planets round the sun. This work laid the foundation for all subsequent developments right up to the present time.

Arnold also produced extremely fruitful ideas, relating classical mechanics to questions of topology. This includes the famous Arnold Conjecture which was only recently solved.

In classical hydrodynamics the basic equations of an ideal fluid were derived by Euler in 1757 and major steps towards understanding them were taken by Helmholtz in 1858, and Kelvin in 1869. The next significant breakthrough was made by Arnold a century later and this has provided the basis for more recent work.

Ludwig Faddeev has made many important contributions to quantum physics. Together with Boris Popov he showed the right way to quantize the famous non-Abelian theory which underlies all contemporary work on sub-atomic physics. This led in particular to the work of ”²t Hooft and Veltman which was recognized by the Nobel Prize for Physics of 1999.
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Mapping the Human Proteome

The human genome is old news. Next stop: the human proteome

Unlike the genome, which remains essentially static between cell types and over time, the proteome is tremendously dynamic, changing constantly in response to cell-cell signalling and environmental stimuli. Thus even though -with some small exceptions – every cell in your body carries the same genome, the proteome can be wildly different between different tissues and can change rapidly over time
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At the very least, large-scale analysis of the human proteome should allow researchers to tentatively place many of our currently anonymous genes into functional pathways. That’s a step forward for personal genomics: knowing that you have a loss-of-function mutation in a gene that may be involved in cholesterol biosynthesis is a lot more useful (in terms of guiding further clinical testing) than simply knowing that you have a mutation in hypothetical gene C11orf68.

The Subtly Different Squid Eye

The subtly different squid eye by PZ Myers:

the inside out organization of the cephalopod eye relative to ours: they have photoreceptors that face towards the light, while we have photoreceptors that are facing away from the light. There are other important differences, though, some of which came out in a recent Nature podcast with Adam Rutherford, which was prompted by a recent publication on the structure of squid rhodopsin.

Superficially, squid eyes resemble ours. Both are simple camera eyes with a lens that projects an image onto a retina, but the major details of these eyes evolved independently – the last common ancestor probably had little more than a patch of light sensitive cells with an opsin-based photopigment. The general properties of this ancient eye can still be seen in modern eyes. They detect light with a simple molecule called retinal that is capable of absorbing a photon, changing its shape from the 11-cis form to the all trans form; basically, it flips from a chain with a kink to a straight chain. Retinal is imbedded in a protein called opsin. When retinal changes shape, it changes the shape of the opsin protein, too, which can then interact with other proteins in the cell membrane.

The next protein in the sequence is called a G protein. G proteins are ubiquitous intermediates for many cellular processes; when a receptor, like opsin, is activated, it activates a G protein, which then activates other proteins, starting a signaling cascade. In the podcast, I compare this to starting an avalanche. Opsin is an agent standing on a hill; when it receives a light signal, it nudges a small boulder (the G protein), which then tumbles down setting a whole series of rocks in motion. The G protein is an intermediate which takes a small change, the initial nudge, and amplifies it into the activation of many other proteins.

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

Amazon Molly Fish are All Female

No sex for all-girl fish species

A fish species, which is all female, has survived for 70,000 years without reproducing sexually, experts believe.
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The species, found in Texas and Mexico, interacts with males of other species to trigger its reproduction process. The offspring are clones of their mother and do not inherit any of the male’s DNA. Typically, when creatures reproduce asexually, harmful changes creep into their genes over many generations.
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One theory is that the fish may occasionally be taking some of the DNA from the males that trigger reproduction, in order to refresh their gene pool.

Dr Laurence Loewe, of the university’s School of Biological Sciences, said: “What we have shown now is that this fish really has something special going on and that some special tricks exist to help this fish survive. “Maybe there is still occasional sex with strangers that keeps the species alive. Future research may give us some answers.”

He added that their findings could also help them understand more about how other creatures operate. “I think one of the interesting things is that we are learning more about how other species might use these tricks as well,” he said. “It might have a more general importance.”

E. Coli Individuality

Expressing Our Individuality, the Way E. Coli Do by Carl Zimmer

A good counterexample is E. coli, a species of bacteria that lives harmlessly in every person’s gut by the billions. A typical E. coli contains about 4,000 genes (we have about 20,000). Feeding on sugar, the microbe grows till it is ready to split in two. It makes two copies of its genome, almost always managing to produce perfect copies of the original. The single microbe splits in two, and each new E. coli receives one of the identical genomes. These two bacteria are, in other words, clones.
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A colony of genetically identical E. coli is, in fact, a mob of individuals. Under identical conditions, they will behave in different ways. They have fingerprints of their own.
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E. coli appears to follow a universal rule. Other microbes exploit noise, as do flies, worms and humans. Some of the light-sensitive cells in our eyes are tuned to green light, and others to red. The choice is a matter of chance. One protein may randomly switch on the green gene or the red gene, but not both.

In our noses, nerve cells can choose among hundreds of different kinds of odor receptors. Each cell picks only one, and evidence suggests that the choice is controlled by the unpredictable bursts of proteins within each neuron. It’s far more economical to let noise make the decision than to make proteins that can control hundreds of individual odor receptor genes.

Identical genes can also behave differently in our cells because some of our DNA is capped by carbon and hydrogen atoms called methyl groups. Methyl groups can control whether genes make proteins or remain silent. In humans (as well as in other organisms like E. coli), methyl groups sometimes fall off of DNA or become attached to new spots. Pure chance may be responsible for changing some methyl groups; nutrients and toxins may change others.