The genome sequence of woolly mammoth,an extinct species of Elephant is almost complete.This species of Elephant was adapted to live in cold and was found in Tundra region.Scientists from Penn state university have sequenced four billion DNA bases using next-generation DNA-sequencing instruments and a novel approach that reads ancient DNA highly efficiently.Stephan C. Schuster, Penn State professor of biochemistry and molecular biology believes that the genome size of this extinct mammoth might be similar to that of modern day’s African Elephant genome.

The sequencing of nuclear genome of extinct animal was possible using the DNA extracted from hair of two female woolly ,one being around 20,000 year old and other died roughly 60,000 years ago.Researchers suspect out of four billion bases in dataset ,only around 3.3 billion could account for extinct elephant and rest could be contaminants in the form of bacteria and fungi.The answer to this problem and how much of the full woolly-mammoth genome they have sequenced can be known only by comparing with the sequence of African elephant,which currently is being generated by scientists at the Broad Institute of MIT and Harvard.

The sequence data obtained by group of Schuster suggest that mammoths and modern-day elephants separated around six-million years ago, roughly the same time that humans and chimpanzees separated.However ,unlike in the case of Humans and chimps ,which evolved rapidly ,mammoths evolved gradually.The data also reveals that woolly mammoths had low genetic diversity and that might made them susceptible to some disease and climate change ,leading to their extinction.

The scientists can now use this sequence data to understand exact reason of woolly’s extinction from the planet and unique characters ,which enabled them to survive is extreme cold conditions. Researchers hopes that clues from the mammoth genome about why some animals go extinct while others do not will be useful in protecting other species from extinction, such as the Tasmanian devil.

One of the other interesting aspect of this work is that the sequence was completed by a small group of scientists at a relatively low cost and over a short period of time.

How times change. Within the space of less than a decade, the development of high-throughput technologies has transformed the task of sequencing a mammalian genome from the years-long, multimillion-dollar endeavour it was originally, to a project that can be performed by an individual laboratory within a few months–Michael Hofreite ,Max Planck Institute for Evolutionary Anthropology.

Reference:

Sequencing the nuclear genome of the extinct woolly mammoth

Webb Miller, Daniela I. Drautz, Aakrosh Ratan, Barbara Pusey, Ji Qi, Arthur M. Lesk, Lynn P. Tomsho, Michael D. Packard, Fangqing Zhao, Andrei Sher, Alexei Tikhonov, Brian Raney, Nick Patterson, Kerstin Lindblad-Toh, Eric S. Lander, James R. Knight, Gerard P. Irzyk, Karin M. Fredrikson, Timothy T. Harkins, Sharon Sheridan, Tom Pringle & Stephan C. Schuster

doi:10.1038/nature07446

Image Credit:
FlickR / Opacity

Yesterday I stumbled upon a beautiful website ,displaying some breathtaking Drosophila images. Drosophila Image Award Website is supported by Genetics society of America, has initiated an annual award to recognize the importance of images in the field of Drosophila research. By doing this they encourage the continued generation of compelling images that communicate important biological results relevant to Drosophila.Initiated in year 2004 ,the collection of images till 2008 are awesome and must watch.My personal pick from last year collection is the one which stood runner up .The image was from the lab of N. Perrimon and E. C. Lai showing mir-315 can activate wingless signalling in the drosophila wing imaginal disc.On their website they have classic collection comprising of Lewis four wing fly, Gehring’s PAX6 discovery, Mcgginis Homeodoamin discovery and many more excellent stuff.So i encourage you all to just visit this website if you don’t want to miss on some of the magnificent stuff created by the amalgam of nature and man.

Link for the website

One of the most fascinating thing about life is to understand how we grow from a single celled embryo to a functional human being or for that matter to know about development of all the beautiful forms of life around us. All living organisms arise from a single cell and it was always an interesting puzzle to understand How different tissue forms an organ and how these different organs gets perfectly placed in the animal body?Are these things preplanned ? Is it possible to have eyes coming out from our legs? Are the positions of hind limbs and fore limbs pre programmed?

Thanks to excellent work done by some great scientists and their students we have decent enough information about development of an embryo into a multicellular organism. Hox genes play a pivotal role in organization of body plan with help from other important proteins (Signaling molecules, transcription factors etc.)These Hox genes are conserved throughout evolution.

There are not many exclusive books available of these transcription factors ,but slowly with increasing amount of research being done on these proteins and more information available ,lead to an intresting book called “Hox gene Expression”. This book is published by Springer and is divided into 9 chapters encompassing 159 pages. The book starts with an excellent chapter dealing with discovery of homeodomain 25 years ago by Walter Gehring.Other chapters gives the reader a deep insight about role played by Hox proteins in Nervous system and vertebrate limb development.But my favorite chapter is one written by David E.K. Ferrier on Evolution of Hox Gene Clusters.There is also something for chromatin followers also -Laila Kobrossy and Mark Featherstone talks about Chromatin and the Control of Hox Gene Expression.Final two chapters deal with Hox genes normal and abnormal function.

Its a must buy for all researchers and students of biology and medicine.This book can be bought online on springer and Amazon.

This is not all about exclusive books on Hox genes,come April 2009 there will be one more book on HOX GENES by Elsevier.The contents of this book are :

1) Hox Genes in the Nervous System of Vertebrates Author: Krumlauf 2) Evolution of Hox Gene Clusters Author: D Ferrier 3) Hox Genes in Breast Development and Breast Cancer Author: C Hagios 4) Endocrine Regulation of Hox Genes Author: G Daftary 5) Role of Hox Genes in Bladder Cancer 6) Consequences of Hox Gene Duplication in Vertebrates Author: McClintock 7) Hox Genes and Limb Evolution Author: Jimenez

Edited by Olivier Pourquie.

These two books will be a great addition to your home library.

The Australian scincid clade Lerista provides an excellent model for studying limb reduction in squamates (lizards and snakes).These Small lizards are a commonly found in Australian continent and nearly 75 different species are available.

Species of Lerista show a very high variability in limbs -ranging from pentadactyl to complete loss of limbs.Recent work published in BMC Evolutionary Biology Journal (Open access) demonstrate that several species of these Lizards have rapidly evolved an elongate, limbless body form.Mark Hutchinson’s lab lead by Adam Skinner had investigated the pattern and rate of limb reduction and loss in Lerista, employing a comprehensive phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes.

The reason for loss of limbs in these lizards is believed to be thier habitat ,which happens to be sand and they spend most of time swimming through soil;”limbs are not only unnecessary for this, but may actually be a hindrance”.

The results of phylogeny(Which was done to investigate the pattern and rate of limb reduction ) revealed that evolution of a snake-like body form has occurred not only repeatedly but also very rapidly and without any evidence of reversals.

“At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within 3.6 million years”. Compared to similarly dramatic evolutionary changes in other animals, this is blisteringly fast.–Adam Skinner

Citation and Image Credit:

Adam Skinner, Michael S Y Lee and Mark N Hutchinson

Rapid and repeated limb loss in a clade of scincid lizards.

BMC Evolutionary Biology 2008, 8:310doi:10.1186/1471-2148-8-310

Staying with adaptations of organisms to different environments ,but unlike the previous post (which deals with computers and simulations) lets talk about Snails.To understand the role played by proteomic changes during speciation ,Emilio Rolán-Alvarez and colleagues from Spain compared the proteome of two ecotypes (RB and SU) of the marine snail Littorina saxatilis, a case of sympatric incomplete speciation, originated as a byproduct of adaptation to distinct habitats.

RB has the ability to resist stresses of desiccation and temperature while staying at upper shore and SU ecotype lives on the lower shore, typically submerged in water and protected from large changes in temperature.Snails of SU ecotype defies strong physical disturbances due to wave action.Its pretty well known that animals of the same species can have different physical characteristics enabling them to survive in different habitats. But on the contrary very little is known about the biochemical aspects responsible for such adaptations.

Studying the proteome of these two marine snails from different environments (staying only few feet apart on Spanish coast).Mass spectrometry analysis showed major differences in about 12 percent of the proteins in the snail, a subset of proteins that apparently enables the snails to survive in different environmental conditions.Among the proteins identified by mass spectrometry authors found that fructose-bisphosphate aldolase and arginine kinase were up-regulated in the SU ecotype, which indicates an increase in the level of energy available as ATP, in order to withstand its wave-exposed habitat.

Reference:
Mónica Martínez-Fernández, Ana M. Rodríguez-Piñeiro, Eliandre Oliveira,‡María Páez de la Cadena, and Emilio Rolán-Alvarez .
Proteomic Comparison between Two Marine Snail Ecotypes Reveals Details about the Biochemistry of Adaptation.
J. Proteome Res., 7 (11), 4926–4934, 2008. 10.1021/pr700863e

Image Credit: Gwylan / Flickr