Posts about genetics

Essentials of Genetics Website Reference

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 EvolutionDNA Passed to Descendants Changed by Your LifeAnger at Anti-Open Access Press Strategy

Microcosm by Carl Zimmer

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 EarthForeign Cells Outnumber Human Cells in Our BodiesAmazing Designs of LifeAmazing Science: RetrovirusesOne Species’ Genome Discovered Inside Another’s

Antigen Shift in Influenza Viruses

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 OverviewOne Sneeze, 150 Colds for CommutersWashing Hands Works Better than Flu Shots (study results)Learning How Viruses Evade the Immune SystemAlligator Blood Provides Strong Resistance to Bacteria and Viruses

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Gene Duplication and Evolution

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 GenesMutation Rate and EvolutionDNA Passed to Descendants Changed by Your Life
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Extinct Ibex is Resurrected by Cloning

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 MoroccoBaby Sand Dollars Clone Themselves When They Sense DangerMojave Desert Tortoises

Educating the Biologist of the 21st Century

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 ChangesThe Importance of Science EducationWebcast: Engineering Education in the 21st CenturyEducating the Engineer of 2020: NAE Report

MicroRNAs Emerged Early in Evolution

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.

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 RNARNA related postsNobel Prize in Chemistry – 2006

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.

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.

Related: Nova on EpigeneticsEpigenetics: Sins of the fathers, and their fathersEvidence for Transgenerational Transmission of Epigenetic Tumor Susceptibility in Drosophilaposts on DNA

Bananas Going

photo of a baboon eating bananas and holding a kitten

I posted on the threat of extinction for bananas. Dan Koeppel has written an excellent book, Banana: The Fate of the Fruit That Changed the World. He also has a great Banana blog with serious and fun posts:

Urgent threat to Africa’s Bananas:

In Uganda, meanwhile, the disease has become so widespread that yields on banana farms have reached dangerously low levels. Acres and acres of crops have been lost, creating a cascade of economic losses in a trading system that spreads from the tiniest villages to Uganda’s cities, all based on the transport and trade of bananas.

The urgency of this cannot be overstated. Uganda and the nations surrounding it absolutely depend on bananas as a staple foodstuff. Millions rely on bananas for survival. And the spread of BXW into Kenya is yet another indicator that this deadly disease is on the march. As with Panama Disease – the wilting fungus that threatens our banana, the Cavendish – BXW (a bacterial malady) is incurable. The difference between the two is that BXW moves faster and threatens, right now, food supplies in nations with fragile governments.

First, banana diversity. In order to mitigate the spread of disease, the number of kinds of bananas being grown needs to be increased.

Second, genetic engineering: It is time for the general public to recognize that working at the DNA level is not always a corporate trojan horse into destroying local agriculture and contaminating the environment. This isn’t all about Monsanto. While consumers in the suburbs and Whole Foods stores protest against all GMO foods – while barely knowing what GMO is – they bluntly prevent out legitimate public research that might stop hunger. Time learn that everything has nuance, the disease that are killing the bananas: they work in just two modes: off – and on.

The photos is from a fun post: Baboon Prefers Bananas over Kittens. Thank Goodness.

Related: Plumpynut a Food SaviorThe Avocadoposts on foodWheat Rust ResearchArctic Seed Vault

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.

Related: Blocking Bacteria From Passing Genes to Other BacteriaBacteria generous with their genesDisrupting the Replication of Bacteriaarticles on the overuse of anti-bioticsRaised Without Antibiotics

Young Geneticists Making a Difference

Young Geneticists Making a Difference

After an early phase of discouragement, Johannes Krause was able to follow his long interest in genetics and even link it to another passion of his, paleoanthropology. Krause initially chose to study biochemistry at the University of Leipzig. But “I was almost about to quit” at the frustration of learning much more about basic chemistry than biology, he says. However, in the third year of his bachelor’s degree, he took some specialised courses in genetics as an Erasmus student at the University College Cork in Ireland that revived his interest for the field.

Back in Leipzig, a summer internship on comparing gene expression between humans and chimpanzees at the Max Planck Institute for Evolutionary Anthropology sparked Krause’s enthusiasm for good. He stayed on in the lab as a research assistant for 2 years before graduating in 2005. While there, Krause helped develop a biological method to read large pieces of ancient DNA, sequence the complete mitochondrial genome of the mammoth from fossil samples, and place it in the context of evolution. “Johannes has great technical skill and the judgment to distinguish a good project from a blind alley. Like few others he can see the interesting pattern that can hide in sometimes confusing data,” Svante Pääbo, his principal investigator, writes in an e-mail to Science Careers.

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