Genome Institute of Singapore’s (GIS) Associate Director of Genomic Technologies, Dr Yijun RUAN, led a continuing study on the human genome spatial/structural configuration, revealing how genes interact/communicate and influence each other, even when they are located far away from each other. This discovery is crucial in understanding how human genes work together, and will re-write textbooks on how transcription regulation and coordination takes place in human cells.

The discovery was published in Cell, on 19 January 2012. The GIS is a research institute under the umbrella of the Agency for Science, Technology and Research (A*STAR).

Using a genomic technology invented by Dr Ruan and his team, called ChIA-PET, the Singapore-led international group, which is part of the ENCODE (ENCyclopedia Of DNA Elements) consortium, uncovered some of the fundamental mechanisms that regulate the gene expression in human cells.

“Scientists have always tried to understand how the large number of genes in an organism is regulated and coordinated to carry out the genetic programs encoded in the genome for cellular functions in our cells. It had been viewed that genes in higher organisms were individually expressed, while multiple related genes in low organisms like bacteria were arranged linearly together as operon [1] and transcribed in single unit,” Dr Ruan explained. “The new findings in this study revealed that although genes in human genomes are located far away from each other, related genes are in fact organised through long-range chromatin interactions and higher-order chromosomal conformations. This suggests a topological basis akin to the bacteria operon system for coordinated transcription regulation. This topological mechanism for transcription regulation and coordination also provides insights to understand genetic elements that are involved in human diseases.”

GIS’ executive director Prof Huck Hui NG said: “This is an important study that sheds light on the complex regulation of gene expression. Yijun’s team continues to use the novel method of Chromatin Interaction Analysis with Paired-End-Tag sequencing to probe the higher order interactions of chromatin to discover new regulatory interactions between genes.”

“This publication describes ground-breaking work by Dr Yijun Ruan and his team at Genome Institute o Singapore,” added Dr Edward Rubin, Director of the Joint Genome Institute in US. “They address the fundamental question of how communication occurs between genes and their on and off switches in the human genome. Using a long range DNA mapping technology called ChIA-PET, the study reveals in three dimensional space that genes separated linearly by enormous distances in the human genome can come to lie next to each other in the cell when it is time for them to become active. I expect this study to move rapidly from primary scientific literature to textbooks describing for future students the operating principles of the human genome. The ChIA-PET technology, that is the telescope used in this exploration of the human genome, is an innovative and powerful molecular technology invented by Dr Ruan and his collaborators.”

The ENCODE is an ongoing project which was awarded to Dr Ruan’s team by the National Human Genome Research Institute (NHGRI), an institute belonging to the National Institutes of Health (NIH, USA). The project was set up in 2003 with the aim of discovering all functional elements in the human genome to gain a deeper understanding of human biology and develop new strategies for preventing and treating diseases. So far Dr Ruan’s team has received over US$2 million towards this project.

The technique builds on previous research in which microbubbles were used to improve the way algae is cultivated.
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Research involving scientists at The University of Nottingham has taken us a step closer to breeding hardier crops that can better adapt to different environmental conditions and fight off attack from parasites.
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Clues into the evolutionary diversification of brassicas have emerged from the draft Chinese cabbage genome sequence. Brassica crops include many agriculturally important vegetables, such as Chinese cabbage, pak choi, turnip, broccoli, cabbage and cauliflower, as well as various oilseed crops.
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Researchers from the Biotechnology and Biological Sciences Research Council (BBSRC) Sustainable Bioenergy Centre (BSBEC) have discovered a family of genes that could help us breed grasses with improved properties for diet and bioenergy.
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A team of scientists from Bio Architecture Lab (BAL), has developed breakthrough technology that expands the feedstocks for advanced biofuels and renewable chemicals production to include seaweed (macroalgae). The team engineered a microbe to extract the all the major sugars in seaweed and convert them into renewable fuels and chemicals, thus making seaweed a cost-effective, renewable source of biomass.
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Source: Wikipedia

(PhysOrg.com) — Scientists have cracked the genetic code and predicted some high priority drug targets for the blood parasite Schistosoma haematobium, which is linked to bladder cancer and HIV/ AIDS and causes the insidious urogenital disease schistosomiasis haematobia in more than 112 million people in Africa.
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Discovery reveals new possibility for gene silencing in bacteria and other organisms

Athens, Ga. – The knowledge that bacteria possess adaptable immune systems that protect them from individual viruses and other foreign invaders is relatively new to science, and researchers across the globe are working to learn how these systems function and to apply that knowledge in industry and medicine.

Now, a team of University of Georgia researchers has discovered how to harness this bacterial immune system to selectively target and silence genes. The finding, published today in the early online edition of the journalMolecular Cell, reveals a powerful new tool that has far-reaching implications for biotechnology and biomedical research.

“Scientists study bacteria and other microorganisms to understand essential life processes as well as to improve their use in the safe production of foods, biofuels and pharmaceuticals, and to fight those that cause disease,” said Michael Terns, a professor in the departments of biochemistry and molecular biology, and genetics in the UGA Franklin College of Arts and Sciences. “And now we have a new way to engineer bacteria to decrease or even eliminate the expression of the genes of our choosing.”

The bacterial immune system consists of two components. The first is an RNA (a molecule that, like DNA, contains genetic information) that acts as a homing signal to target a virus or another cellular invader. The second component is a complex of proteins that cleaves the invader’s genetic material. In a 2009 paper published in the journal Cell, Terns, co-principal investigator Becky Terns and their colleagues were the first to describe how this pathway, known as the Cmr branch of the CRISPR-Cas immune system, works.

In their latest study, the researchers further their understanding of the system and use that in-depth knowledge to essentially hijack the bacterial immune system to direct its homing system to a target of their choosing. Using customized CRISPR RNAs with a modified homing signal, the scientists were able to destroy the message for a protein that is responsible for resistance to the most commonly prescribed family of antibiotics, the beta-lactam antibiotics (that includes, for example, amoxicillin).

Becky Terns, co-leader of the UGA team, explained, “In this study we identified the key features of the RNAs that the system normally uses, and then showed that using this information we can program the system with engineered ‘homing’ RNAs to destroy new targets. New targets would go beyond viruses and other invaders to include essentially any gene present in the organism being studied. And because we have defined the components of this system, it is possible that we can introduce it into organisms that do not already possess it to further expand the potential industrial and biomedical applications.”

She pointed out that most known CRISPR-Cas systems target and cleave DNA. The system that the UGA team studies is the only known example of a CRISPR-Cas system that targets RNA, the molecule that functions as an intermediary between DNA and the proteins that carry out various functions within cells. “Cleaving its own DNA would kill an organism. Silencing specific RNAs allows more sophisticated applications,” Terns said.

Researchers could systematically shut down the function of individual genes, for example, to discern the role they play in essential cellular processes. Gene expression could be modified in bacteria that are used to break down plant materials for biofuels or that produce medications, such as insulin, to improve quality and production.

“This detailed biochemical study of a new branch of the CRISPR-Cas defense system—one that targets RNA molecules—has shed light on a powerful weapon in the bacterial arsenal against invading viruses and mobile elements,” said Michael Bender, who oversees RNA processing and function grants at the National Institutes of Health’s National Institute of General Medical Sciences. “In addition, by defining the key components of the system, Drs. Terns and their colleagues have set the stage for the development of a new tool for targeting specific RNA molecules in diverse cell types, potentially providing biomedical researchers with a valuable new way to analyze gene functions.”

Michael Terns added, “The possibility of exploiting the CRISPR-Cas system in biotechnology has been discussed since its discovery, and this work begins to realize some of that enormous potential.”

The Bio-resources Innovations Network for Eastern Africa Development (Bio-Innovate) Program is a newly established multidisciplinary competitive funding mechanism, for biosciences and product oriented innovation activities in Eastern Africa, through the bioresources innovation fund, supporting applications for regional, multi-disciplinary innovation projects in Burundi, Ethiopia, Kenya, Rwanda, Tanzania and Uganda.The Bio-Innovate niche is characterized by a focus on the applications of bio-resource innovations, to support sustainable growth and transformation of the agricultural and environmental sub-sectors, from primary production to value addition, while enhancing adaptability to climatic change and strengthening innovation policy.

Building on previous investments and regional initiatives, the Program is focusing on delivering new products through bioscience innovation systems involving multiple actors, including scientists, private sector, Non Governmental Organizations (NGO’s) and other development actors. A central objective of the Bio-Innovate Program is to build functional innovation consortia able to take bioscience Research for Development (R4D) and innovations to the market.

The Bio-Innovate Program is being implemented under four Thematic Areas and through nine regional, multi-disciplinary innovation and policy projects selected through the Program’s Competitive Grant Scheme (CGS). These innovation and policy project consortia are comprised of a range of value chain actors critical to span the process from science to production and markets. Involvement of market actors and other practitioners in the innovation project consortia is crucial in order to ensure that products, knowledge and new technologies emanating from the Bio-Innovate Program reach the market and specified end users.

In its first three-year phase call for proposals on “Adapting to Climate Change in Agriculture and the Environment in Eastern Africa”, the Bio-Innovate Program is supporting five innovation projects working to improve the productivity of sorghum, millet, cassava, sweet potato, potato and bean farmers; to help smallholder farmers adapt to climate change (thematic area 1); to improve the processing of wastes in the production of sisal and coffee; and to better treat waste water generated in leather processing and slaughterhouse operations (thematic area 2).

In the second call for proposals on “Innovation Incubation and Promotion of Targeted Value Chains and Bio-resources Innovation Policy and Sustainability Analysis in Eastern Africa”, The Bio-Innovate Program is supporting four innovation incubation and policy projects. The Bio-Innovate projects from the second call will help build agricultural and environmental innovation incubation and targeted value chains in the region and a supportive policy environment for bioresources innovations.

We are pleased to report that the Bio-Innovate Program Secretariat has successfully set-up and implemented the Program’s Competitive Grant Scheme. Two round calls for concept notes followed by full proposals development, review, selection and approval for funding have been made for all the four thematic areas of the Program. Nine regional, interdisciplinary innovation and policy projects were selected and approved for funding with a total fund of SEK 69.8M (USD 9.3M) over three years period through the Program’s competitive bidding process involving more than 50 implementing institutions and 100 innovation and policy consortium teams from universities, national, regional and international research organizations, national councils for Science and Technology, private sectors/ industries and development organizations from within Bio-Innovate participating countries and outside the region.

For more details contact Bio-Innovate Secretariat:

Dr. Seyoum Leta
Bio-Innovate Program Manager,
International Livestock Research Institute
P.O. Box 30709, Nairobi, Kenya
Email: s.leta@cgiar.org
Direct line: +254 (0)20 422 3216
Fax: +254 (0)20 422 3001
Website: www.bioinnovate-africa.org
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