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Oscillator

Tag archives for papers

Symbiosis is everywhere. From the Greek for “living with,” symbiosis is simply a close association between two different species in nature. These relationships can be mutualistic, parasitic, or somewhere in between. Bacterial symbionts live inside bodies, like the bacteria that help us and other animals digest our food, and they live inside cells, like the…

Making Cellular Memories

Cells permanently change their behavior in response to temporary changes to the environment, a kind of biological memory that controls processes as important and complex as how stem cells differentiate into specific tissues or how the immune system “remembers” dangerous pathogens. At its simplest, cellular memory is achieved with a positive feedback loop–once activated by…

Making blind mice see

Evolution connects all living things on earth, from the arsenic tolerant bacteria in the news this week to the human scientists and bloggers chatting about it. Eyes are intricately complex structures made up of many many cells, but even single-celled microbes can sense and respond to light through the function of proteins that share evolutionary…

Holding on to cells with DNA

Mammalian cells need something to hold on to before they can stick to each other and form tissues. The plastic dishes that cells grow on in the lab need to be first coated with special chemicals that grab the cells and convince them to stick. Once the first batch of cells is down they start…

Engineering Hybrid Silks

There was some big news yesterday in transgenic silk from Notre Dame and the University of Wyoming, where scientists have genetically engineered silkworms to produce silk that is a mixture of spider silk and the regular silkworm stuff. Silkworms produce the strong and versatile silk that is used to make clothes, but spiders produce silk…

So I was browsing the internet for info on G-protein coupled receptors and ended up finding some interesting facts about sperm. It turns out sperm don’t just swim blindly, hoping to randomly bump into eggs. Instead, like bacteria, sperm can sense their chemical environment and adjust their swimming accordingly. Sperm have a sense of smell.…

My two great thesis project loves are hydrogen and symbiosis, and as such, the recent news of a multicellular organism that lives in a completely oxygen free environment and gets its energy from hydrogenosomes instead of mitochondria is totally fascinating. Hydrogenosomes are organelles that are evolutionarily related to mitochondria. Mitochondria generate energy for the cell…

Xenobiology

An interesting paper in BioEssays last month looks at the potential future of xenobiology, totally orthologous biological systems made out of synthetic nucleotide and amino acid bases, new cells that use XNA instead of DNA. The author, Markus Schmidt, argues that while the design of such systems current poses a difficult technological challenge to researchers…

Agapakis et. al.

My paper, “Insulation of a synthetic hydrogen metabolism circuit in bacteria” just came out in the Journal of Biological Engineering! And it’s open access! We designed a metabolic circuit in bacteria that produces hydrogen (a potentially useful fuel) from natural precursors in the cell. The proteins in our synthetic pathway work to make hydrogen by…