Other Publications

Review – CEP – Unlocking access to DNA in chromatin

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Unlocking access to DNA in chromatin
Barrett C and Haynes KA (2018) Chemical Engineering Progress. https://www.aiche.org/resources/publications/cep/2018/september/unlocking-access-dna-chromatin

Since the early 1970’s when scientists first began using bacterial enzymes to cut purified “naked” DNA, scientists have further developed bacterial enzyme-based systems to target and edit specific DNA sequences in eukaryotic hosts, including human cells. However, DNA within eukaryotic cells is not always fully exposed. Instead, it is packed into DNA/protein complexes that form a structure called chromatin. This review highlights new technologies that have enabled scientists to better understand and manipulate the chromosomal structures that impede or enhance access to the underlying DNA.


Review – NAR – Molecular structures guide the engineering of chromatin

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Molecular structures guide the engineering of chromatin
Tekel SJ and Haynes KA (2017) Nucleic Acids Res. https://doi.org/10.1093/nar/gkx531

Specialized proteins within the nuclei of human and other eukaryotic cells wrap DNA into a structure called chromatin. For decades, scientists have used biochemistry, genetics, and comparative evolutionary biology to understand the specific interactions and processes that guide the highly-regulated packaging of DNA into chromatin, as well as chromatin features that act to switch gene expression on and off. Basic research has enabled chromatin engineering by rational design for building new tools to further understand chromatin, and for applications such as molecular interventions of cellular disease states. This review highlights key discoveries in chromatin research and engineering efforts that have been supported by this knowledge.

Text Book – CRC Press – Synthetic Biology Handbook

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Eukaryotae Synthetica: Synthetic Biology in Yeast, Microalgae, and Mammalian Cells
Schofield D, Templar A, Borg Y, Daer R, Haynes K, Nesbeth D. (2016) Synthetic Biology Handbook. 145-182

A new educational resource for the growing field of synthetic biology, the “Synthetic Biology Handbook,” has just been released. The chapter on mammalian synthetic biology was co-authored by Dr. Karmella Haynes, SBHSE PhD student Rene Daer, lead editor Darren Nesbeth, and co-authors Desmond Schofield, Alexander Templar, and Yanika Borg.

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Commentary – Nature – Synthetic biology: Building genetic containment

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Synthetic biology: Building genetic containment
Haynes KA (2016) Nat Chem Biol. 12:55-56.

Dr. Karmella Haynes’ News & Views article discussing Chan et al.’s recent work on genetic containment of genetically modified organisms has been published in Nature Chemical Biology, part of the Nature Publishing Group. Read the rest of this entry »

Editorial – Frontiers in Bioengineering – Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities

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Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities
Ceroni F, Carbonell P, François J-M and Haynes KA (2015) Front. Bioeng. Biotechnol. 3:120. PMID: 26347864

This editorial was written for a special topic issue in the journal Frontiers in Bioengineering and Biotechnology. Featured articles included the latest progress in synthetic biology with. Research papers focused on rational design within the context of a complex, natural cell or system. In spite of (or because of) biological complexity, bioengineering has produced some concrete biotechnological applications. The cover art was created by Dr. Karmella Haynes.

Review – Frontiers in Bioengineering – Can the natural diversity of quorum-sensing advance synthetic biology?

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Can the natural diversity of quorum-sensing advance synthetic biology?
Davis RM, Muller RY and Haynes KA (2015) Front. Bioeng. Biotechnol. 3:30. PMID: 25806368.

Quorum sensing takes place when small molecules generated by one bacterium diffuse over to a neighbor and control that neighbor’s genes. With 100 morphologically and genetically distinct species of eubacteria that use quorum sensing to control gene expression, why does the bioengineering community only use about 4 variants to control cell communication? This review explains quorum sensing systems, their use in engineering, the problem of crosstalk between parallel QS systems, and how natural QS diversity might be used to address this problem.

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Review – Frontiers in Bioengineering – Preparing synthetic biology for the world

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Preparing synthetic biology for the world
Moe-Behrens GHG, Davis R, Haynes KA (2013) Front. Microbio. 4: 1-10. PMID: 23355834

Synthetic biology aims to develop self-replicating systems that are durable enough to operate reliably in complex environments such as the human gut, polluted soil, and other areas in which disease or toxins need to be remediated. Although helpful, this robustness in “open environments” (outside of the research lab) has raised concerns about lack of control of genetically engineered cells. In this review we discuss early development and advances (from the 1980’s to the present) in built-in, genetically encoded safety switches.