SynBioFromLeukipposInstitute

"5 March 2012 Latest issue of IDT’s Decoded newsletter explains the fundamentals of artificial gene construction

CORALVILLE, IA: Integrated DNA Technologies (IDT), the world leader in oligonucleotide synthesis, provides a unique insight into the fundamentals of isothermal synthetic gene assembly in this quarter’s edition of the company’s Decoded newsletter. The technique, which was pioneered in 2009 by Daniel Gibson and colleagues at The J. Craig Venter Institute in Maryland, USA, allows several overlapping DNA fragments to be combined in a single reaction. In this way, large synthetic DNA molecules many hundreds of kilobases long can be generated using a minimal number of enzymatic steps. This limits potential errors due to repeated handling of samples and reagents, while simplifying the process by avoiding the need for multiple experimental setups. The article in the latest issue of Decoded outlines the theory behind isothermal assembly, and provides advice for designing and creating synthetic gene constructs using the method..."

We live in a biological world completely surrounded by rich communities of micro-organisms, but often in a cultural world that emphasizes total antisepsis. The bacteria on our skin and in our gut are crucial to keeping us healthy, but microbes often remain invisible until something goes wrong. Intitiatives such as the Human Microbiome Project, the Belly Button Biodiversity project, the Bioweathermap, and the Microbiology of the Built Environment Network seek to sequence the super-genome around us, to catalog the bacteria of our bodies and our environment.

Bacterially.org has related and parallel aims to these cataloging projects. We seek to isolate, classify, and characterize microbes from the human skin, to better understand the ecosystem of the human body, to explore the connections between our bodies and our food, and to create microbial communities with new properties. Through exploration of the human microbiome and its connection to our lives we aim to promote acceptance of the microbial world and to explore new avenues for design.

This project is a continuation of work done with Synthetic Aesthetics, a collaboration between synthetic biologist Christina Agapakis and smell researcher Sissel Tolaas. We are fascinated by how microbes work together with one another and with the human body to produce chemicals and odors, and we explore these ecosystems as artists and as scientists, dissecting and analyzing as well as synthesizing and re-creating.

"We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 bp long, derived from unique nonrepetitive sequence, and are enriched in the 5' untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the “Thousand Genomes” project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a new DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci."

Biotechnological, genomics and systems-synthetic biology revolution: redesigning genetic code for a pragmatic systems medicine.

"Synthetic biology needs more oversight, and the government needs to put in place regulations specific for this field. That is the bottom line for 111 environmental, watchdog, and other organizations that released a report today with specific recommendations for managing new biological techniques for building and remaking organisms for research and commercial uses ranging from medicines to biofuels.

Calling synthetic biology "an extreme form of genetic engineering," the report said that current practices for regulating and assessing biotechnology were inadequate. The group, which includes the watchdog organizations ETC Group and Friends of the Earth, wants to ban the use of synthetic biology to manipulate the human genome or the genomes of microbes in and on the human body. Full disclosure of the nature of the synthetic organisms and of safety testing should be required to ensure the safety of workers and the environment. Until these regulations are in place, the group wants a moratorium on the release and commercial use of synthetic organisms and their products....."

"Genetically encoded sensors are powerful tools for imaging intracellular metabolites and signaling molecules. However, developing sensors is challenging because they require proteins that undergo conformational changes upon binding the desired target molecule. We describe an approach for generating fluorescent sensors based on Spinach, an RNA sequence that binds and activates the fluorescence of a small-molecule fluorophore. We show that these sensors can detect a variety of different small molecules in vitro and in living cells. These RNAs constitute a versatile approach for fluorescence imaging of small molecules and have the potential to detect essentially any cellular biomolecule."

An interactive tool to help you decide what is right or wrong, and why.