Thursday, October 15, 2009

Death of End Note

I guess now End Note software will die a natural death!! I am not saying this just because I am not particularly fond of this software, but lately it has fierce competitions from various resources including my NCBI. Before My NCBI came into picture, I was very fond of connotea. Connotea is very easy to link to a browser, all that you will need is to drag and drop it to the menu bar. You can create your own login and password and update all the bibliography you ever wanted. Export the bibliography as you wish.

With My NCBI, it has struck the nail right on the head of End Note. Tutorials are readily available for My NCBI for easy use. Anytime, I would prefer a browser based application than a stand alone application. End note particularly needed endless filling up forms very tedious ways. I had bad experience of interference of end note with MS office 2007. Now I will breath easy writing a manuscript.

Monday, October 05, 2009

This years Nobel Prize in Medicine

This years Nobel prize in Medicine goes jointly to Elizabeth Blackburn, Carol Greider, and Jack Szostak for their work on telomeres. In the 1970s, Blackburn identified repeating segments at the ends of DNA in Tetrahymena while Szostak found that single-stranded DNA was rapidly degraded in yeast. Blackburn and Szostak then collaborated on a project, finding that the Tetrahymena DNA protected the single-stranded DNA from degradation in yeast. In 1984, Blackburn and Greider, her graduate student, discovered telomerase. The Nobel citation lauds these researchers for their contribution to the study of aging, cancer, and other diseases. "The discoveries by Blackburn, Greider and Szostak have added a new dimension to our understanding of the cell, shed light on disease mechanisms, and stimulated the development of potential new therapies," it says.

The mysterious telomere

The chromosomes contain our genome in their DNA molecules. As early as the 1930s, Hermann Muller (Nobel Prize 1946) and Barbara McClintock (Nobel Prize 1983) had observed that the structures at the ends of the chromosomes, the so-called telomeres, seemed to prevent the chromosomes from attaching to each other. They suspected that the telomeres could have a protective role, but how they operate remained an enigma.

When scientists began to understand how genes are copied, in the 1950s, another problem presented itself. When a cell is about to divide, the DNA molecules, which contain the four bases that form the genetic code, are copied, base by base, by DNA polymerase enzymes. However, for one of the two DNA strands, a problem exists in that the very end of the strand cannot be copied. Therefore, the chromosomes should be shortened every time a cell divides – but in fact that is not usually the case (Fig 1).

Both these problems were solved when this year's Nobel Laureates discovered how the telomere functions and found the enzyme that copies it.

Telomere DNA protects the chromosomes

In the early phase of her research career, Elizabeth Blackburn mapped DNA sequences. When studying the chromosomes of Tetrahymena, a unicellular ciliate organism, she identified a DNA sequence that was repeated several times at the ends of the chromosomes. The function of this sequence, CCCCAA, was unclear. At the same time, Jack Szostak had made the observation that a linear DNA molecule, a type of minichromosome, is rapidly degraded when introduced into yeast cells.

Blackburn presented her results at a conference in 1980. They caught Jack Szostak's interest and he and Blackburn decided to perform an experiment that would cross the boundaries between very distant species (Fig 2). From the DNA of Tetrahymena, Blackburn isolated the CCCCAA sequence. Szostak coupled it to the minichromosomes and put them back into yeast cells. The results, which were published in 1982, were striking – the telomere DNA sequence protected the minichromosomes from degradation. As telomere DNA from one organism, Tetrahymena, protected chromosomes in an entirely different one, yeast, this demonstrated the existence of a previously unrecognized fundamental mechanism. Later on, it became evident that telomere DNA with its characteristic sequence is present in most plants and animals, from amoeba to man.

An enzyme that builds telomeres

Carol Greider, then a graduate student, and her supervisor Blackburn started to investigate if the formation of telomere DNA could be due to an unknown enzyme. On Christmas Day, 1984, Greider discovered signs of enzymatic activity in a cell extract. Greider and Blackburn named the enzyme telomerase, purified it, and showed that it consists of RNA as well as protein (Fig 3). The RNA component turned out to contain the CCCCAA sequence. It serves as the template when the telomere is built, while the protein component is required for the construction work, i.e. the enzymatic activity. Telomerase extends telomere DNA, providing a platform that enables DNA polymerases to copy the entire length of the chromosome without missing the very end portion.

Blackburn was also the Daily Scan poll favorite. She led the pack with 43 percent of the vote. She was followed by her co-laureate Szostak who garnered 25 percent of the vote.

Szostak JW, Blackburn EH. Cloning yeast telomeres on linear plasmid vectors. Cell 1982; 29:245-255.
Greider CW, Blackburn EH. Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell 1985; 43:405-13.
Greider CW, Blackburn EH. A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis. Nature 1989; 337:331-7.

Friday, October 02, 2009

Oldest Human ancestor discovered

How old are humans? Until recently I thought Lucy to be our oldest ancestor, that is around 3.9 to 2.9 million years old. A recent finding by a group of scientists reveals our oldest known ancestor "Lucy" is now replaced by "Ardi"(Ardipithecus ramidus) which is older by 1.4 million years than Lucy.This individual, 'Ardi,' was a female who weighed about 50 kilograms and stood about 120 centimetres tall.

In its 2 October 2009 issue, Science presents 11 papers, authored by a diverse international team, describing an early hominid species, Ardipithecus ramidus, and its environment. These 4.4 million year old hominid fossils sit within a critical early part of human evolution, and cast new and sometimes surprising light on the evolution of human limbs and locomotion, the habitats occupied by early hominids, and the nature of our last common ancestor with chimps.

Science is making access to this extraordinary set of materials FREE (non-subscribers require a simple registration). The complete collection, and abridged versions, are available FREE as PDF downloads for AAAS members, or may be purchased as reprints.

The last common ancestor shared by humans and chimpanzees is thought to have lived six or more million years ago. Though Ardipithecus is not itself this last common ancestor, it likely shared many of this ancestor's characteristics. Ardi is closer to humans than chimps. Measuring in at 47 in. (120 cm) tall and 110 lb. (50 kg), Ardi likely walked with a strange gait, lurching side to side, due to lack of an arch in its feet, a feature of later hominids. It had somewhat monkey-like feet, with opposable toes, but its feet were not flexible enough to grab onto vines or tree trunks like many monkeys -- rather they were good enough to provide extra support during quick walks along tree branches -- called palm walking.

Another surprise comes in Ardi's environment. Ardi lived in a lush grassy African woodland, with creatures such as colobus monkeys, baboons, elephants, spiral-horned antelopes, hyenas, shrews, hares, porcupines, bats, peacocks, doves, lovebirds, swifts and owls. Fig trees grew around much of the area, and it is speculated that much of Ardi's diet consisted of these figs.

The surprise about the environment is that it lays to rest the theory that hominids developed upright walking when Africa's woodland-grassland mix changed to grassy savanna. Under this now theory, hominids began standing and walking upright as a way of seeing predators over the tall grasses. The discovery of Ardi -- an earlier upright walker that lived in woodland -- greatly weakens this theory.

Scientists have theorized that Ardi may have formed human-like relationships with pairing between single males and females. Evidence of this is found in the male's teeth, which lack the long canines that gorillas and other non-monogamous apes use to battle for females. Describes Professor Lovejoy, "The male canine tooth is no longer projecting or sharp. It's no longer weaponry."