research blogging

Oscillator

Tag archives for research blogging

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…

Great Balls of Evolution

One organism’s trash is another organism’s treasure. Our cellular wastes, carbon dioxide and water, nourish plants, which with added energy from sunlight produce the oxygen and sugars that we need to survive. At microscopic scales, these cycles of waste and food can get much more complicated, with many species of microbes working together to survive…

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…

Emergent Cooperation

My good friend and labmate just published an awesome paper: “Emergent cooperation in microbial metabolism.” His experiment started with 46 strains of E. coli that had mutations in their metabolic pathways that prevented them from being able to grow without supplementing the media with extra metabolites. Alone they died, but grown together in the same…

Wireless Cellular Communication

Cells are constantly jibber jabbering, sending messages to each other to coordinate behavior, both within a population of single-celled organisms or between cells of an individual multicellular organism. Most of these signals are chemicals that float around in the liquid that surrounds the cells but there recently has been an increased appreciation for cells’ sense…

Carboxysomes in a row

Carboxysomes are small compartments inside photosynthetic bacteria where the machinery for capturing carbon dioxide is concentrated. You can see carboxysomes and their characteristic virus-like shape when you look at slices of these bacteria under an electron microscope: Until recently, no one had looked at carboxysomes under the microscope in cells that were still alive. My…

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…

Expanding the Genetic Code

Almost every living thing shares an identical genetic code, with three nucleic acids in an RNA sequence coding for a single amino acid in the translated protein sequence. While there are 64 three-letter RNA sequences, there are only 20 amino acids and degeneracy in the code allows some amino acids to be coded by multiple…

My labmate Bruno’s newest paper, “A synthetic circuit for selectively arresting daughter cells to create aging populations” came out today in the journal Nucleic Acids Research (and it’s open access!). Using a cleverly designed genetic circuit that activates cell growth arrest in newly divided cells only in the presence of a drug, Bruno was able…