Category Archives: Transhuman News

An international team of scientists has sequenced the genome of the chickpea, a critically important crop in many parts of the world, especially for small-farm operators in marginal environments of Asia and sub-Saharan Africa, according to an announcement from researchers at UC Davis, and the International Crops Research Institute for the Semi-Arid Tropics in India.

The researchers published this week in the online version of the journal Nature Biotechnology the reference genome of the chickpea variety known as CDC Frontier and the genome sequence of 90 cultivated and wild chickpea lines from 10 different countries.

"The importance of this new resource for chickpea improvement cannot be overstated," said Douglas Cook, a UCD professor of plant pathology.

"The sequencing of the chickpea provides genetic information that will help plant breeders develop highly productive chickpea varieties that can better tolerate drought and resist disease -- traits that are particularly important in light of the threat of global climate change," he said.

Cook is one of three lead authors on the chickpea genome sequencing project, along with Rajeev Varshney of the International Crops Research Institute for the Semi-Arid Tropics and Professor Jun Wang, director of the Beijing Genomics Institute of China.

The chickpea plant, whose high-protein seed is also referred to as a garbanzo bean, is thought to have originated in the Middle East nearly 7,400 years ago.

India grows,

The announcement of the chickpea genome sequencing is the culmination of years of genome analysis by the International Chickpea Genome Sequencing Consortium, led by the International Crops Research Institute for Semi-Arid Tropics. The consortium includes 49 scientists from 23 organizations in 10 countries.

Funding for the sequencing project was provided by the U.S. National Science Foundation; Saskatchewan Pulse Growers of Canada; Grains Resource Development Corporation of Australia; Indo-German Technology Corporation of Germany and India; National Institute for Agricultural and Food Research and Technology of Spain; U.S. Department of Agriculture; Ministry of Education, Youth and Sports of the Czech Republic; University of Cordoba, Spain; Indian Council of Agricultural Research; BGI of China; and International Crops Research Institute for the Semi-Arid Tropics.

Read more here:
UC Davis helps global team sequence chickpea genome

Novel Microscale Epigenomics Technology developed by GIS makes it possible to study the epigenome of rare cell populations and biopsy samples

Scientists at A*STARs Genome Institute of Singapore (GIS) have successfully developed a method to map the epigenome using 100 times fewer cells than was previously possible. The discovery, published in the journal Developmental Cell, means that it is now possible to study the epigenome of parts of the body with rare cell populations such as germ cells (which differentiate into the egg or sperm), and clinical biopsy samples (to advance the study, diagnosis and prevention of cancer).

This is an extremely important advancement since the proper regulation of the epigenome is essential for normal growth and health, while any abnormality in the regulation could be the cause of diseases such as cancers.

The genome, which refers to the complete set of DNA (deoxyribonucleic acid) in a cell, is identical in every cell of an individuals body. Chemical markers (also known as epigenetic markers) target the genome and influence which genes get turned on or off. It is the turning on or off of the genes that gives rise to the existence of different cells in the body, even though the genomes are identical. The epigenome refers to the record of these chemical changes that occur to the DNA.

Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) is a commonly used method to study the epigenome of cells. In ChIP-Seq, DNA fragments that are associated with specific epigenetic marks are baited out, sequenced and mapped to a reference genome. However, the conventional method typically requires large quantities of cells, which makes it difficult to study rare cell populations of the body or in precious clinical biopsy samples.

This limitation prompted the GIS scientists to miniaturize the ChIP method such that it is now possible to map the epigenome using much fewer cells (1,000 to 100,000 cells). The conventional method required one million to 10 million cells.

The scientists further applied this technology on a small number of mouse germ cells, which are the embryonic precursors of the sperm and egg, and uncovered many interesting epigenomic features that provide insight into the biology of the germ cells.

GIS Executive Director Prof Ng Huck Hui said, Epigenomics is an exciting frontier for human biology research. While the sequence of human genome tells us the code for life, it doesnt tell us how this code is utilized. The mystique of the epigenome lies in the multiple forms it takes and the remarkable information that it harbours. At the Genome Institute of Singapore, we are investing efforts to develop new microscale technologies to analyse the epigenomes of human cells and tissues.

"The new ChIP-seq protocol allows us to map the epigenomes of very small populations of cells that are not accessible by conventional methods, said GIS Principal Investigator Dr Shyam Prabhakar. It's akin to having a more powerful microscope that provides a more fine-grained view of critical biological processes. We are very excited about using this new technique to peer into the inner workings of tiny groups of cells that have a massive impact on human health. For example, tumours in cancer patients are known to be heterogeneous at the fine scale - some sub-regions are relatively benign, while others are lethal. The new protocol will help us characterize this fine-scale variation, and hopefully lead to more precise treatments for cancer and a host of other diseases."

Read more here:
:: 11, Feb 2013 :: A*STAR’S GENOME INSTITUTE OF SINGAPORE DEVELOPS ADVANCED METHOD TO STUDY EPIGENOME OF CELLS ...