Experiment
shake, rattle, and shoot...
04/19/08 09:29 PM Filed in: Science
hello from Chicago,
I am currently at APS (advanced photon source) shooting crystals with the brightest xray source in the US, except that their currently is a problem with the hutch and we can't open the shutter. This explains why I am updating my blog at 2am Saturday morning. The trip has been pretty good so far...save the wandering goniometer and this little vacuum pressure problem. The best part of the trip, however, has to be the fact that I experienced my first earthquake!
I awoke at around 4:30am by the sensation someone was shaking me, but upon opening my eyes noticed that Chris was still asleep and I was still shaking. This utterly confused me since I am not used to moving back and forth on the x, y plane. Being extremely groggy, I decided that I must be dreaming and immediately went back to bed, thinking that this couldn't have just occurred. As soon as I woke up the next morning I thought of the shaking, which meant that I probably wasn't dreaming because I normally don't remember my dreams. I opened my computer and saw on CNN that indeed, there was a 4.5 richer earthquake with an epicenter around 350 miles away.
I am currently at APS (advanced photon source) shooting crystals with the brightest xray source in the US, except that their currently is a problem with the hutch and we can't open the shutter. This explains why I am updating my blog at 2am Saturday morning. The trip has been pretty good so far...save the wandering goniometer and this little vacuum pressure problem. The best part of the trip, however, has to be the fact that I experienced my first earthquake!
I awoke at around 4:30am by the sensation someone was shaking me, but upon opening my eyes noticed that Chris was still asleep and I was still shaking. This utterly confused me since I am not used to moving back and forth on the x, y plane. Being extremely groggy, I decided that I must be dreaming and immediately went back to bed, thinking that this couldn't have just occurred. As soon as I woke up the next morning I thought of the shaking, which meant that I probably wasn't dreaming because I normally don't remember my dreams. I opened my computer and saw on CNN that indeed, there was a 4.5 richer earthquake with an epicenter around 350 miles away.
watching DNA die
09/18/07 09:16 PM Filed in: Science
viruses are some of the most difficult foreign bodies that your immune system has to deal with; think aids and ebola. since viruses use the host's own cells to replicate the body has a hard time destroying the virus the same way that it destroys a bacteria or other foreign invader.
for these reasons the study of viruses is an important part of science and there has been an amazing breakthrough in the field.
Dr Robert Henderson's group from the University of Cambridge has produced amazing footage of a protective enzyme unraveling the DNA of a virus trying to infect a bacterial host!
the group used a Scanning Atomic Force Microscope to look at the enzyme/dna interaction at the nanoscale level.
the video shows a bacterial type III restriction enzyme binding to the dna and cleaving it before it has time to infect the bacteria and it could be a model for how many other organisms use enzymes to cleave viral dna.
the work has implications beyond the use of novel microscopy since it gives clues on where the enzyme binds to the dna and can be used to look at other dna binding molecules.
read the full paper here.
for these reasons the study of viruses is an important part of science and there has been an amazing breakthrough in the field.
Dr Robert Henderson's group from the University of Cambridge has produced amazing footage of a protective enzyme unraveling the DNA of a virus trying to infect a bacterial host!
the group used a Scanning Atomic Force Microscope to look at the enzyme/dna interaction at the nanoscale level.
Dr Robert Henderson, who led the Cambridge research, explains: “This is the first time that such a process has been seen in real time. To be able see these nano-mechanisms as they are really happening is incredibly exciting. We can actually see the enzyme ‘threading’ through a loop in the virus’s DNA in order to lock on to and break it, a process known as DNA cleavage."
“The microscope and new techniques give us a clear view of the molecular interactions between proteins and DNA that we could only previously interpret indirectly. The indirect methods require scientists to make assumptions to interpret their data, and video footage like this can help to provide a more direct understanding of what is really happening."
the video shows a bacterial type III restriction enzyme binding to the dna and cleaving it before it has time to infect the bacteria and it could be a model for how many other organisms use enzymes to cleave viral dna.
the work has implications beyond the use of novel microscopy since it gives clues on where the enzyme binds to the dna and can be used to look at other dna binding molecules.
read the full paper here.
so small and yet so big
06/28/07 09:03 PM Filed in: Science
as a biochemist, i often think about the structure of the proteins i work with, thus i have been thinking a lot about KcsA. KcsA is a potassium ion channel and i am currently doing experiments to figure out how it physically moves potassium through the membrane.
KcsA is an extremely well studied protein and this is kind of a learn what electro physiology is all about project for me, to teach me the ways of single channel recording and such. even still i have been thinking about how it works...
the one aspect of a channel that really blows my mind is how small it is and how small the ions are that pass through it. potassium ions are what, 2.2ish angstroms. that is extremely small. it is 220 picometers, 220X10^-12, or 0.00000000022 meters. in other words...they are small.
but the problem i and some people have is what is a picometer? how small is 10^-12 and now big is 10^12? i found these videos one serious one that looks at sizes of things via distance, and one which is a simpson's spoof of the first...maybe it will shed some light on relative sizes, distances, and masses for you as it did me.
KcsA is an extremely well studied protein and this is kind of a learn what electro physiology is all about project for me, to teach me the ways of single channel recording and such. even still i have been thinking about how it works...
the one aspect of a channel that really blows my mind is how small it is and how small the ions are that pass through it. potassium ions are what, 2.2ish angstroms. that is extremely small. it is 220 picometers, 220X10^-12, or 0.00000000022 meters. in other words...they are small.
but the problem i and some people have is what is a picometer? how small is 10^-12 and now big is 10^12? i found these videos one serious one that looks at sizes of things via distance, and one which is a simpson's spoof of the first...maybe it will shed some light on relative sizes, distances, and masses for you as it did me.