Commuting in to New York
everyday has really started to take a toll on me. Every morning I wake up at
6:20 to make a 6:55 train which brings me into Newark at 8. From there I have
to take another 30 to 40 minute long path train to get to Greenwich Village. So
in essence I have a two hour long commute once walking is factored in. The
first week I didn’t mind it that much, the hustle and bustle of Newark and New
York was almost fun, now it has become more and more boring. Still, being in
New York, the hectic city shows you something new every day and being in the
city is a very worthwhile experience in and of itself. I am also one of the
first ones to get to the lab every morning. I would be very glad to come in
later; only problem is that after the 6:55 train there isn’t another one until
9:15, which I did take one time and by the time I got to New York I was the last
one into the lab, which was not fun.
Right now we are just about wrapping up my mini-project
on the different types of buffers. We were able to correctly predict several
things from our hypothesis but there were other areas that were not correct. For
example, the Sodium Borate buffer is able to withstand much higher voltages
without heating up, however, when SB was ran parallel to TAE buffer there was
no increase in the speed of band migration across the gel. Also, in general,
the bands of most of the ladders and samples we tested came back more
pronounced and sharper in the Sodium Borate buffer. As for Lithium borate, the
first test proved that the solution heats up very fast under high voltage and
therefore is not going to satisfy our lab’s demand for quick and accurate gel
electrophoresis. We also tried staining the gels using SYBR gold, a ‘cousin’ of
SYBR safe used in biotech, through washing it onto and over the gel after being
run, and loading it into the solutions on each well before it was run. The
better approach was by far loading it into each solution first, and then
loading that solution into the wells. From this method, we were able to reduce
background staining while providing sharper clearer bands to read overall. I
might actually be presenting this to the lab at our next lab meeting, wish me
luck.
(Print out of the Gel results: Left LB buffer, Right TAE buffer)
I am also in the beginning stages for my real summer
project. We are working on a new technique called DASH or Depletion of Abundant
Sequences through Hybridization. It is very good for sequencing the RNA of
specific strains of flu as well as for characterizing the other types of
microorganisms (specifically in the respiratory and digestive tracts) during periods
of influenza infection and periods without it. For example, if our lab wants to
determine what species of bacteria live in a healthy human respiratory system,
DASH is very helpful. We know that we can determine the organism by looking at
the variable regions in the DNA gene that codes for ribosomal rRNA. We can do
this because that gene is conserved throughout basically all organisms, and
most of that DNA (16S gene in prokaryotes) is the same across all organisms
except for small regions called variable regions, which functionally do not do
a whole lot. We can use DASH (through usage of restriction enzymes and/or
CRISPR/Cas9) to eliminate all the DNA that is constant, leaving just the
variable regions. We then amplify the variable regions using PCR and sequence
them. We can then compare them across databases and determine what species of
bacteria were present. In short, DASH specifically is very good at making sure
we are not amplifying the wrong regions of DNA/RNA and allow us to more accurately
isolate the genetic material we want.
(Basic Diagram of DASH)
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