genome – Page 2 – GOLLYGEE!

03.18.2013

DNA from HeLa cells is sequenced

HeLa cells viewed under a light microscope

Nature magazine reports that a German lab has sequenced the DNA of HeLa cells. Like cells from most tumors, there are multiple copies of many genes. Excerpt:

Previous work showed that HeLa cells, like many tumors, have bizarre, error-filled genomes, with one or more extra copies of many chromosomes. To get a closer look at these alterations, a team led by Lars Steinmetz, a geneticist at the EuropeanMolecular Biology Laboratory in Heidelberg, Germany, sequenced the popular ‘Kyoto’ version of the cell line and compared the sequence with that of a reference human genome. The team’s results are published in G3.

Steinmetz’s team confirmed that HeLa cells contain one extra version of most chromosomes, with up to five copies of some. Many genes were duplicated even more extensively, with four, five or six copies sometimes present, instead of the usual two. Furthermore, large segments of chromosome 11 and several other chromosomes were reshuffled like a deck of cards, drastically altering the arrangement of the genes.

Without the genome sequence of Lacks’ healthy cells or that of her original tumor, it is difficult to trace the origin of these alterations. Steinmetz points out that other cervical tumors have massive rearrangements on chromosome 11, so the changes in the HeLa cell may have contributed to Lacks’ tumor.

HeLa cells have been the subject of many biological studies as they are easy to culture and replicate very fast. The cells were originally isolated from an African American woman named Henrietta Lacks, and have been cultured for over 60 years. There is also a fascinating book about the origin of these cells called The Immortal Life of Henrietta Lacks.

02.06.2013

too many chromosomes

Oxytricha trifallax

This tiny pond creature has 15,600 chromosomes. From Ed Yong:

Within its cell, Oxytricha contains two nuclei, which enclose its DNA. One of these—the micronucleus— contains the complete edition of Oxytricha’s genome, just like the single nucleus within our own cells. That’s the tidy encyclopaedia shelf. But while the material in our nucleus must be constantly decoded and transcribed so that we can live, Oxytricha’s micronucleus is largely inactive. The encyclopaedia’s are barely read.

Instead, it relies on a second structure called the macronucleus. That’s the messy drawer. All of the DNA in the micronucleus is copied thousands of times over, and shunted into the macronucleus. In the process, it is broken up at tens of thousands of places, rearranged, and pruned. What’s left is a collection of thousands of “nanochromosomes” that contain all the information Oxytricha needs to survive. This is the stuff that gets decoded and transcribed, used and reused while the originals gather dust.

Sequencing this almighty mess must have been a devilish task, but Etienne Swart from Princeton University rose to the challenge. Leading a team of US and Swiss scientists, he has sequenced Oxytricha’s complete macronuclear genome. …

The team found around 15,600 of these nanochromosomes. On average, each is around 3,200 DNA ‘letters’ long, and around 80 percent of them contain just a single gene.

dogs, wolves and carbs

Domesticated dog breeds evolved long ago from the wolf. In a study published in Nature, researchers examined differences in the genomes of modern domesticated breeds and wolves and made some interesting discoveries. They expected differences in the nervous systems since the species behave differently. They also found many differences in genes effecting metabolism, especially digestion of carbohydrates. Domesticated breeds digest starches much better than wolves. From Science News:

The new study focuses on genetic differences between 60 dogs representing 14 breeds and 12 wolves from around the world. Those changes, the researchers reasoned, could identify genes that were important in separating dogs from wolves.

The researchers determined the genetic makeup of groups of dogs and compared the results to those from wolves, concentrating on parts of the genetic instruction book that differ between the two species. As they had expected, the researchers uncovered differences in many genes relating to the brain. But the search also revealed lots of genes involved in starch digestion and metabolism, and in the use of fats. Dogs, the team found, have more copies than wolves do of the AMY2B gene, which produces an enzyme that breaks starch into easily digestible sugars.

Other genetic variants seem to contribute to dogs’ increased ability to convert a sugar called maltose to glucose, the sugar that cells prefer to burn for energy. Yet other genetic changes improve dogs’ ability to move glucose into their cells. Combined, the tweaks alter dogs’ metabolism so they can get more energy out of a carbohydrate-rich diet than wolves can, the researchers conclude. The scientists confirmed the effect of the genetic variants by identifying biochemical differences in starch metabolism in blood and tissue samples from dogs and wolves.

GOLLYGEE!

Tag: genome (page 2 of 3)

DNA from HeLa cells is sequenced

too many chromosomes

dogs, wolves and carbs