Make sure your cell cycles are regulated, kids.
Let me just say that I am a very, very lucky researcher this summer. My lab was in a perfect position to offer me a project that allows me to learn a LOT, work on my own, and still contribute to their research. In addition, I get to work with three undergrads from VIP, and I get to take advantage of everything they are learning as well. My project is fairly simple to understand, if long. 
A basic depiction of the four phases of the cell cycle in eukaryotes.
So this is the cell cycle. Everything has to be very regulated and ordered. That makes sense - if you don't finish replicating your DNA before you start dividing, you get aneuploidy, polyploidy, and messed up chromosomes in general. Therefore, it is very important to understand what regulates the function and correct oscillation of the cell cycle. The established theory is that the majority of periodically transcribed processes - that is, genes and the like that are activated at particular points in the cell cycle, then turned off, then turned on again at the proper time when the cycle restarts - are regulated by complexes between proteins called cyclins and cyclin-dependent kinases, or cyclin-CDK complexes.
The important point to begin with: it is thought that oscillation, or a cell's internal clock, is regulated by cyclin-CDKs. But is it?
Long story short, about ten years ago Dr. Haase performed some experiments using budding yeast that had S-phase and M-phase cyclins deleted from their genomes, cyclins essential for cell cycle progression. The absence of these cyclins prevents the cell from moving past G1 phase. Theoretically, this would cause the cell to arrest at the G1/S border - the cell would be large from its growth phase and budded as if ready to begin DNA replication, but would not have any further cell-cycle activity.
But G1 events cycled as they would in normal wild-type cells, even though S-phase and mitosis did not occur. It was as if parts of the cell involved in periodic events didn't know that a change had occurred in cyclin activity. This indicates the presence of an oscillator that functions independently of cyclin-CDKs. These conclusions were published in the paper "Evidence that a free-running oscillator drives G1 events in the budding yeast cell cycle" (Haase and Reed).
After years of work to understand what this free-running oscillator could be, my lab decided to investigate what would happen to periodic transcription throughout the cell cycle, not just in G1. In experiments with S-phase and mitotic, or M-phase, cyclins deleted, over 70% of the phase specific genes continued to be expressed periodically. These results were published a paper in Nature entitled "Global control of cell-cycle transcription by coupled CDK and network oscillators" (Orlando et al). In short, throughout the cell cycle, oscillation continued even in the absence of cyclin-CDK complexes thought to be essential to cell cycle progression.
So, if it's not cyclin-CDKs, then what does control the oscillation in the cell cycle? The proposed mechanism is a network of transcription factors, that functions either in conjunction with or independently of cyclins to regulate cell cycle transcription.
Cells with different cyclins deleted to prevent certain functions - by counting the buds, we can understand roughly where they are in the cell cycle at any given time.
So, currently, the Haase Lab is trying to describe and characterize this proposed network - what transcription factors are invovled and which ones are the most important. This question is being attacked from two sides - in the lab, we are running experiments with yeast cell lines that have different transcription factors deleted. By letting them grow and taking samples along the way - a "time course" - we can analyze what effect different deletions, and combinations of deletions, have on the period of the cell cycle. Then, the math/stats members of the team use this data to put together a model of the network, and in turn help us determine which tf's are the most important for us to be analyzing.
My job (finally!) is to run experiments with one of these lines, yeast cells with the YHP1 gene deleted. It's not as easy as it sounds - there is a lot of troubleshooting invovled. My cells in particular seem to have trouble with cytokinesis as they progress through the cell cycle - it's difficult to analyze them if you can't tell how many cells you have! But the problem is potentially with one of the reagents I have been using - I will finish another experiment tomorrow that will help us to be more certain. I may also be working with some different methods to sychronize the cells in preparation for time courses. In the end, the work requires a lot of sterile technique, a thorough lab notebook, and my favorite - counting cells.
Hah. Counting cells. If only you guys knew the torture I went through to help my lab help you keep your very important cell cycles in check :)
