Wednesday, July 27, 2011

Week 3

Week 3 is over which means this RET is halfway over. Jessica and I have completed the skeleton of the mouse cage as well as the side panels. Our next step is to figure out the best way to attach the sensors that will be used to gather data about the mouse behavior. This is a tedious task because the side panel boards are not as easy to cut, because even though the supplier claimed the board could be cut with scissors (which it can), it's impossible to make a straight line cut and is hard on the hand.

This week we have also been working on creating a video, which neither of us have ever done before. Jessica and I each have to make our own video, but we have decided to collaborate for each video because we came up with both of the ideas together. The video I am heading up is about the construction of our mouse cage, aka "Mouse Behavior Box" as the researcher calls it. Jessica is taking charge of the video interviewing our PI, postdoc and possibly some random people we find on the street about what research is. We are curious as to what the general population believes regarding what researchers do. Our videos are still a work in progress but will hopefully be up by the end of Week 4.

Delaying getting our video done is going to add a little bit of stress because we have a lesson plan due next Friday, July 29th, as well.I keep changing my mind on what I want to do. This week's Friday pedagogy talk was on project based learning, or PBL, and was the best pedagogy workshop during this RET to date. The already made PBL's shown to us were very well thought out and seem easy to implement. The pre-made PBL's are available at  I am debating about making a PBL for my lesson because the science content taught in the pre-made PBL's focus primarily on environmental science issues and drawing certain physics ideas out of it would be a stretch.

It's hard to believe I am halfway through already. I imagine with all that is left to do that the coming 3 weeks will fly by even faster than the first! I am somewhat sad that we have so little time left because I am really enjoying working with out postdoc and trying to help him with his research.

Saturday, July 16, 2011

Week 2

Hypothesis we are testing:
My lab group is currently following the design process rather than the scientific method. Jessica and I are in the process of designing and building a better (and cheaper) mouse cage for the lab researchers to conduct experiments in. The current mouse cages they can purchase are very expensive and do not suit the needs of the research team. Jessica and I have talked with the research team to find the pros and cons of the current model and have discussed multiple ways of constructing a cage will meet the needs of the research without becoming a confounding variable in their experimentation.

Controls of the experiment:
Since our research team is in the process of duplicating a research study completed by a  previous group at a different university, it is important that we use identical procedures to make sure the data we collect is truly comparable to the previously done experiment. Some of the controls include using the same type of mice, the same type of reward/punishment, and the time for each trial. The term punishment is a bit misleading because they don't truly punish the mice. The mice are trained to think they did something wrong if a certain light goes on or a certain sound is heard (depending on the trial). If a mouse pokes the wrong sensor to get the reward, then the sound is played or a light turns on to tell the mouse he needs to try again.

Measure our results:
The success of our cage depends on the research team being able to collect reliable data. Our data will be collected using a MatLab program that will be written by one of the researchers.

Reliability of our data:
The reliability of our data may be limited due to certain unknown specifications of the original experiment. One    difficulty is trying to make sure the hole that the mouse sticks his nose into "nose poke" is both the right size and the correct height for the mouse to easily access. We tried to match the height of the existing nose poke hole with cage panels that existed on the original cage but we will be doing further testing to see if this is the best height for the mouse to actually poke into and trigger the sensor to gather data.

Wednesday, July 6, 2011

Week 1

Process of assimilation:
The assimilation process has been somewhat difficult because the initial amount of information is exorbitant. However, most everyone in the lab has been very helpful and friendly. I greatly appreciate having the two orientation days to become accustomed to the parts of the BU campus in which we will be working. My only complaint would be that we didn't get to meet our PI until our 3rd day because she was unavailable and, at first, difficult to track down. Overall it has been a fairly smooth process transitioning in to the laboratory setting. My brain is still spinning around all the possibilities of research within photonics and what our PI specificially researches, optogenetics.

Environment & Equipment:
The overall environment is fairly friendly. Everyone in our lab seems to get along well with each and works together with a certain goal in mind. My lab partner and I are currently working with a postdoctoral researcher that is trying to duplicate a published study that involves training mice to perform certain tasks. They have had some difficulty duplicating the study due to design limitations of their current cages for the mouse experiments. Jessica and I have decided to help design a new cage based on specifications given by the postdoc. We have been in a rush to figure our measurements of this new cage, develop a material list so that we can get materials ordered and constructed within our 6 week time frame.

Jessica Leach and I are working under Dr. Xua Han in her biomedical engineering lab studying neurophysics. Her lab is occupied by a number of undergraduate, graduate, and post-doc students that work together to research an up and coming branch of biophysics known as optogenetics. We are helping a postdoc named Jiamin with  his research.

Essence of Research:Dr. Han's lab focuses on an up and coming branch of science dubbed optogenetics. The explanations given to us for what exactly they research sounds like something out of a science fiction book. Dr. Han directed us to her website which has links to her various research articles as well as to a TED talk that would help us form a foundation of  understanding for her research.

The TED talk gave a basic understanding of what optogenetics is and many reasons as to how this new field of science can benefit humanity.

My narrow understanding of optogenetics is that they want to use light to trigger certain brain cells to be turned on or off. The ability to activate certain brain cells and see how they respond when given a certain stimulus will help us better map and understand the many functions within the brain. Down the road, information obtained through the study of optogenetics could be used to treat brain disorders such as depression, and Parkinson's disease. If we could target the brain cells that are either overactive or underactive  and causing a brain disorder, then through optogenetics, we could use optical fibers implanted in the brain to act as a sort of pacemaker for these malfunctioning cells. 

The initial challenged we faced was trying to figure out what we are doing. My lab partner and I did not meet our PI until Tuesday afternoon so we felt a little behind in understanding our project. After meeting with her we soon realized that she did not have a set project in mind for us to help with. Instead, she gave us a general overview of her lab and gave us the opportunity to choose our own direction of research. I do appreciate the open-endedness but it was a little overwhelming at first knowing we had to find where our knowledge and skills could best be used.

For me, one of the hardest parts has been getting the graduate researchers to understand that we are not just "dumb teachers." In asking questions, some gave too basic of an answer. For example, I asked one researcher what he was working on and he replied "neurophysics" and walked away. At the time I didn't press further because I was frustrated and felt any response I made would be rude. Over the next few days I did press further and have been able to share that I have a stronger background in biomedical physics than they thought which in turn has lengthened the responses and descriptions the researchers provide. Overall, Dr. Han has been very helpful and welcoming of us in her lab and the undergraduate students have seemed a little more receptive of us being there. Everyone now seems receptive to working with us and I anticipate the coming weeks will go smoothly.