Week 6 - Ben

This week I realized how soon the summer immersion term will be over! It is surprising how little time there is left. As such I have been trying to make slides and take as many images as I can. Unfortunately this week I ran into trouble because the microscope I have been using was broken. I frantically searched for another microscope to use and set up several meetings, but right before my first training, the microscope got fixed! It is interesting how connected all the different hospitals are for use of cores like imaging facilities. In my search for other microscopes, I was able to contact and get potential use of facilities at Weill Cornell (I have been in the HSS research building). Using various connections, I was also able to make contact with imaging centers at Rockefeller and Memorial Sloan Kettering. It seems that the ability to work with various researchers and use various facilities is a major strength of the concentrated academic and medical campuses here. However, in spite of the willingness of people to collaborate, the bureaucratic hurdles are considerable. Each institution uses a different system for registering, tracking, and approving access where each system requires a series of convoluted steps that are largely unclear to new (and even experienced) users. Doubtless this is an inevitability when each institution is independent, but perhaps it would be worthwhile to make efforts to ease collaboration. 

E. coli embedded in a synovial tissue sample and labeled with fluorescent oligonucleotide probes (stain is Alexa 488).

I had an interesting meeting with a researcher in the histopathology core discussing the issues involved with immuno-histochemistry. Since I am trying to develop an analogous technique, it was incredibly informative to be taught by someone with extensive experience in various staining methods. She mentioned that paraffin embedding leftover is often the cause of most sample autofluorescence, which was new for me! Cryostat sectioning seems to be a better option, but requires extensive expertise and is quite costly. It also seems that antibodies must be specifically designed to be robust to alterations caused by fixation techniques. This makes me wonder what sort of alterations are happening in the ribosomal RNA due to formalin cross-linking. The lab I've been working in has recently started using a fixative that preserves DNA and RNA much better than formalin and I am interested in comparing hybridization results between the two methods. 

This week I also got a closer look at the inner workings of the histopathology core. The machines used for fixation, dehydration, clearing, and embedding are very efficient and produce reliable results. Although the system is efficient, there is potential for contamination with (dead) microbes that may force me to use my own fixation-embedding technique. Furthermore, the issue of communication between the doctor taking a human sample, the person carrying it to lab, the person who fixes it, and the person who analyzes is incredibly difficult and convoluted. Even being on hand to ask questions, the confusion involved is considerable. This makes collaboration between campuses intimidating to say the least, but it will be very helpful for me to have been here this summer to establish the face to face relationships that will allow such collaboration to be successful.