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Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle Age

Posted on October 26, 2011  Comments (2)

Family living conditions in childhood are associated with significant effects in DNA that persist well into middle age, according to new research by Canadian and British scientists.

The team, based at McGill University in Montreal, University of British Columbia in Vancouver and the UCL Institute of Child Health in London looked for gene methylation associated with social and economic factors in early life. They found clear differences in gene methylation between those brought up in families with very high and very low standards of living. More than twice as many methylation differences were associated with the combined effect of the wealth, housing conditions and occupation of parents (that is, early upbringing) than were associated with the current socio-economic circumstances in adulthood. (1252 differences as opposed to 545).

I find Epigenetics to be a very interesting area. My basic understanding as I grew up was that you inherited your genes. But epigenetics explores how your genes change over time. This has been a very active area of research recently. Your DNA remains the same during your life. But the way those genes are expressed changes.

I don’t know of any research supporting the idea I mention in this example, but, to explain the concept in a simple way: you may carry genes in your DNA for processing food in different ways. If you have very limited diet the way your body reacts could be to express genes that specialize in maximizing the acquisition of nutrition from food. And it could be that your body sets these expressions based on your conditions when young; if later, your diet changes you may have set those genes to be expressed in a certain way. Again this is an example to try and explain the concept, not something where I know of research that supports evidence for this example.

The findings by these universities, were unfortunately published in a closed way. Universities should not support the closing of scientific knowledge. Several universities, that support open science, require open publication of scientific research. It is unfortunate some universities continue to support closed science.

The research could provide major evidence as to why the health disadvantages known to be associated with low socio-economic position can remain for life, despite later improvement in living conditions. The study set out to explore the way early life conditions might become ‘biologically-embedded’ and so continue to influence health, for better or worse, throughout life. The scientists decided to look at DNA methylation, a so-called epigenetic modification that is linked to enduring changes in gene activity and hence potential health risks. (Broadly, methylation of a gene at a significant point in the DNA reduces the activity of the gene.)

Related: DNA Passed to Descendants Changed by Your Life – Black Raspberries Alter Hundreds of Genes Slowing Cancer – Breastfeeding Linked to More Intelligent Kids

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I Always Wanted to be Some Sort of Scientist

Posted on October 17, 2011  Comments (0)

A nice simple post by a soon to be Dr. of Genetics and Molecular Biology on what being a scientist is like for her. I like her take, which I think is much more accurate than some of the generalities people use. The main reason people (men or women) become scientists because they want to be scientists.

photo of almost-Dr. Caitlin

Photo the almost-Dr. Caitlin

The truth is science requires you to be social. We share ideas, techniques, and equipment. A good scientist knows her limitations and uses someone else’s expertise when her own is not enough. The modern scientist communicates not only through conferences and journals, but also through blogging and Facebook.
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When a non-scientist (usually my parents or some other close relative) asks me about what I do, they inevitably want to tie it back to how I’m curing a disease and saving the world. I am not curing a disease or saving the world.

I study science because it’s cool. I study basic science — asking questions for the purpose of learning the answer. That doesn’t mean what I do isn’t important. Lots of ground-breaking medical advances have been made just because someone asked a question no one else thought to ask.
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To all you ladies fighting the good fight in other fields, keep at it, because the numbers are going up for women with advanced degrees.

I’ve always wanted to be some sort of scientist. When I was in elementary school I wanted to be a paleontologist because dinosaurs are awesome (and so was “Jurassic Park”). When I was 11, I read the Hot Zone and knew I wanted to be a biologist. Though there were times that I flirted with the Dark Side, i.e., medical school, but mostly only because when my teachers figured out I was good at science they said go to medical school. No one even suggested becoming a scientist.

Great stuff. Good Luck, Caitlin.

Related: Movie Aims to Inspire College Students With Tales of Successful Minority Scientists – Kids on Scientists: Before and After Talking to Real Live Scientists – Women Choosing Other Fields Over Engineering, Math, Physics and Computer Science

Most Genes? A crustacean the size of a grain of rice

Posted on February 8, 2011  Comments (4)

photo of Daphnia, a crustacean

“Daphnia are ubiquitous in freshwater ponds and lakes and are often used to assess the health of ponds. Since the creature is so well studied by ecologists, knowing its genetics should reveal a lot about how genes respond to different environments.

The first scientists to describe Daphnia thought they were a kind of flea because they assumed the red color came from sucking blood as fleas do. It turns out they’re not bloodsuckers – they’re blood makers. Daphnia have genes that make hemoglobin, so when the animal is stressed out, those genes switch on and the animal looks red.

In fact Daphnia have an astonishingly large number of genes. “We count more than 31,000 genes,” says [John] Colbourne. By comparison, the human genome has more like 23,000 genes. If Guinness tracks such things, Daphnia would hold the record for the most genes of any animal studied to date.

“Many of those genes – we estimate around 35 percent of them – are brand new to science,”

Daphnia can grow its own spear and helmet when threatened by an attacker

Related: Our Genome Changes as We Age – Amazing Designs of Life – One Species’ Genome Discovered Inside Another Species – Bdelloid Rotifers Abandoned Sex 100 Million Years Ago

Boa Constrictor Gives Birth to Clones

Posted on November 3, 2010  Comments (0)

Snake gives ‘virgin birth’ to extraordinary babies

A female boa constrictor snake has given birth to two litters of extraordinary offspring. Evidence suggests the mother snake has had multiple virgin births, producing 22 baby snakes that have no father. More than that, the genetic make-up of the baby snakes is unlike any previously recorded among vertebrates, the group which includes almost all animals with a backbone.
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“All offspring are female. The offspring share only half the mother’s genetic make-up,” he told the BBC.
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Humans for example have X or Y sex chromosomes; females have two X chromosomes and males have a combination of an X and a Y chromosome. In place of X and Y, snakes and many other reptiles have Z and W chromosomes.

In all snakes, ZZ produces males and ZW produces females. Bizarrely, all the snakes in these litters were WW. This was further proof that the snakes inherited all their genetic material from their mother, as only females carry the W chromosome.

“Essentially they are half clones of their mother,” says Dr Booth. That is because the baby snakes have inherited two copies of one half of their mother’s chromosomes, including one W chromosome.
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More astonishing though, is that no vertebrate animal in which the females carry the odd sex chromosome (in this case the W chromosome) has ever been recorded naturally producing viable WW offspring via a virgin birth.

“For decades WW has been considered non-viable” says Dr Booth. In such species, all known examples of babies that are the product of parthenogenesis are male, carrying a ZZ chromosomal arrangement.

Related: No sex for all-girl fish species – Virgin Birth for Another Shark Species – Bdelloid Rotifers Abandoned Sex 100 Million Years Ago – World’s Smallest Snake Found in Barbados – Androgenesis

Essentials of Genetics Website Reference

Posted on May 24, 2010  Comments (1)

Scitable is a science library and personal learning tool on genetics developed by Nature. I must admit I am against the closed science stance Nature normally supports. But this is a good effort on their part at actually talking advantage of the internet to openly promote science. I imagine Nature will eventually more and more move toward supporting open science.

The website has a library of over 200 faculty-written, peer-reviewed articles on core concepts in genetics, plus a video-based online primer called Essentials of Genetics, glossaries, spotlights on key issues, and lots more high quality faculty and student resources.

Scitable is a great place to research and learn more about genetics topics such as diseases, evolution, genetics and society.

Related: Gene Duplication and Evolution – DNA Passed to Descendants Changed by Your Life – Anger at Anti-Open Access Press Strategy

Microcosm by Carl Zimmer

Posted on December 26, 2009  Comments (0)

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Related: Bacteriophages: The Most Common Life-Like Form on Earth – Foreign Cells Outnumber Human Cells in Our Bodies – Amazing Designs of Life – Amazing Science: Retroviruses – One Species’ Genome Discovered Inside Another’s

Antigen Shift in Influenza Viruses

Posted on May 4, 2009  Comments (3)

Antigenic shift is the process by which at least two different strains of a virus, (or different viruses), especially influenza, combine to form a new subtype having a mixture of the surface antigens of the two original strains.

Pigs can be infected with human, avian and swine influenza viruses. Because pigs are susceptible to all three they can be a breeding ground for antigenic shift (as in the recent case of H1N1 Flu – Swine Flu) allowing viruses to mix and create a new virus.

Related: Swine Flu: a Quick Overview – One Sneeze, 150 Colds for Commuters – Washing Hands Works Better than Flu Shots (study results) – Learning How Viruses Evade the Immune System – Alligator Blood Provides Strong Resistance to Bacteria and Viruses

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Gene Duplication and Evolution

Posted on February 17, 2009  Comments (1)

Roughly 10 million years ago, a major genetic change occurred in a common ancestor of gorillas, chimpanzees, and humans. Segments of DNA in its genome began to form duplicate copies at a greater rate than in the past, creating an instability that persists in the genome of modern humans and contributes to diseases like autism and schizophrenia. But that gene duplication also may be responsible for a genetic flexibility that has resulted in some uniquely human characteristics.

“Because of the architecture of the human genome, genetic material is constantly being added and deleted in certain regions,” says Howard Hughes Medical Institute investigator and University of Washington geneticist Evan Eichler, who led the project that uncovered the new findings. “These are really like volcanoes in the genome, blowing out pieces of DNA.”

Eichler and his colleagues focused on the genomes of four different species: macaques, orangutans, chimpanzees, and humans. All are descended from a single ancestral species that lived about 25 million years ago. The line leading to macaques broke off first, so that macaques are the most distantly related to humans in evolutionary terms. Orangutans, chimpanzees, and humans share a common ancestor that lived 12-16 million years ago. Chimps and humans are descended from a common ancestral species that lived about 6 million years ago.

By comparing the DNA sequences of the four species, Eichler and his colleagues identified gene duplications in the lineages leading to these species since they shared a common ancestor. They also were able to estimate when a duplication occurred from the number of species sharing that duplication. For example, a duplication observed in orangutan, chimpanzees, and humans but not in macaques must have occurred sometime after 25 million years ago but before the orangutan lineage branched off.

Eichler’s research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period.

Related posts: 8 Percent of the Human Genome is Old Virus Genes – Mutation Rate and Evolution – DNA Passed to Descendants Changed by Your Life
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Extinct Ibex is Resurrected by Cloning

Posted on February 1, 2009  Comments (1)

Extinct ibex is resurrected by cloning

The Pyrenean ibex, a form of wild mountain goat, was officially declared extinct in 2000 when the last-known animal of its kind was found dead in northern Spain. Shortly before its death, scientists preserved skin samples of the goat, a subspecies of the Spanish ibex that live in mountain ranges across the country, in liquid nitrogen.

Using DNA taken from these skin samples, the scientists were able to replace the genetic material in eggs from domestic goats, to clone a female Pyrenean ibex, or bucardo as they are known. It is the first time an extinct animal has been cloned.

Sadly, the newborn ibex kid died shortly after birth due to physical defects in its lungs. Other cloned animals, including sheep, have been born with similar lung defects. But the breakthrough has raised hopes that it will be possible to save endangered and newly extinct species by resurrecting them from frozen tissue.

It has also increased the possibility that it will one day be possible to reproduce long-dead species such as woolly mammoths and even dinosaurs.

Related: tree climbing goats of Morocco – Baby Sand Dollars Clone Themselves When They Sense Danger – Mojave Desert Tortoises

Educating the Biologist of the 21st Century

Posted on December 28, 2008  Comments (0)

An Introductory Science Curriculum for 21st Century Biologists by David Botstein (webcast)

At Princeton’s new Lewis-Sigler Institute, Botstein is spearheading an innovative effort at interdisciplinary undergraduate education. Students will take advantage of state of the art laboratories and computers capable of crunching vast amounts of data generated by actual research. Professors will “provide essential fundamental concepts as required, using the just-in-time-principle” – no more of the “learn this now, it will be good for you later” approach, which Botstein likens to hazing. Botstein says there is “lots of overhead in teaching historical and traditional origins” so his students will learn instead “with ideas and technologies of today.” He wants to create a new basic language that will enable his biology students to make sense of the fundamental issues of other disciplines.

Very good look at future of biology education.

Related: MIT Faculty Study Recommends Significant Undergraduate Education Changes – The Importance of Science Education – Webcast: Engineering Education in the 21st Century – Educating the Engineer of 2020: NAE Report

MicroRNAs Emerged Early in Evolution

Posted on October 2, 2008  Comments (1)

New Research Shows MicroRNAs Emerged Early in Evolution

“MicroRNAs have been available to regulate and shape gene expression as far back as we can go in animal evolution—they might even predate animals,” says Bartel, a leader in the discovery and functional study of microRNAs. “They might have helped to usher in the era of multi-cellular animal life.”

First discovered in 1993, microRNAs are strands of RNA that are 21-24 nucleotides in length. They dampen gene expression by intercepting messenger RNA before it can turn the cellular crank that translates a gene into a protein. Earlier, Bartel’s research team showed that each microRNA can regulate the expression of hundreds of genes.

The ability of microRNAs to silence gene expression likely evolved from a more ancient defense against viruses, bacteria, and other mobile genetic elements that can mutate host DNA.
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The scientists determined that the starlet sea anemone has both microRNAs and piRNAs. In addition, the anemone makes proteins resembling those that interact with these small RNAs in humans. Both types of small RNA were also found in the sponge. The third target of their search, Trichoplax, did not contain any microRNAs, though Bartel suspects they may have existed in ancestral forms and later disappeared.

Related: Scientists discover new class of RNA – RNA related posts – Nobel Prize in Chemistry – 2006

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