Well, we leave tomorrow so this will be my last post!  Tonight, we will be attending a “Beer Festival” and will have our last shot at genuine Japanese food and spirits.  It will be located on the NIRS campus and will be with NIRS staff.  We’ve been looking forward to this and it is perfect timing considering the fact that we leave tomorrow.

I want to thank everyone here at NIRS for being so helpful and nice.  Especially, Dr.s Kato, Okayasu, and Fujimori.  Thank you for hosting us, taking us sight seeing, introducing us to new foods, and teaching us the art of radiobiology (cell culture & survival curves)!  It has been a wonderful and unique experience that I am extremely appreciative of.  I have fallen in love with Japanese culture and hope that I will return to this beautiful country.




Bad Danny

Holy guacamole! Where did the time go!? Sorry about the skipped post everyone, but I’m finally at house 1 of 3 of the places I will be until the fall. I’m very thankful my friend Justine let me crash at her place for a week! Well now back to business!

So we got our DCPS sequenced and unfortunately it doesn’t seem there is a fit. We haven’t had the time to look at the sequence of XRN1, but that one’s pretty stubborn so I don’t have my hopes up for that. We ran a protein gel on our purification of DCP1 and LSM1 and there is a possibility something is there, but the band is really faint so we are going to have to find a way to concentrate it more.

And today I had a lab presentation which went pretty well. I think.  I made these little cartoons and made some of the lab laugh pretty hard because one of my cartoons looked,well let’s just say I shouldn’t have added yellow in a certain place I did and it made it look like Danny the DNA was relieving himself! oops. Hahahaha. I said a couple of wrong things, but eh, I tried my best and there were only a few sly remarks.  Also, I brought caprisun and cookies (always a classic) which turned out to be a hit (score).

Well I am off to go finish organizing/unpacking! I hope everyone’s week is nice and I’ll post again Thursday!

Becca T

Radiation Station

Hey all!

So, this is our last week here.  Which means i’ll probably post once more (if that) after this one.  I figured I’d post some good pictures of the equipment and facilities that we’ve gotten to see here.  I can’t tell you how many radiation warning signs-which are very similar to ones in the US- are posted everywhere.  As is Japanese custom, we take off our shoes and step into slippers when entering a person’s home.  Well, for certain rooms and areas at NIRS, we do the same thing.  Notice, the fashionable yellow slippers that we get to wear when in the HIMAC research center (see picture).  I inquired about how they choose which rooms to change shoes and which rooms you don’t and I’ve determined that it’s relatively random.  Almost all of the culturing and lab rooms require that you change slippers…sometimes entire floors or even buildings require it.  However, most offices don’t require that you take your shoes off but some do.  My thoughts on this topic initially would not go away but when I could come up with no answer, I eventually settled for the fact that it’s just random.

Anyway, enough about shoes.  The pictures below show our visit to the HIMAC treatment & research facilities (separate areas) and a few other random pictures of NIRS.

Check ya lata!


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The search continues…

This is Erin reporting the latest on the search the elusive temperature sensitive phenotype.

  I knew it was too good to last. I had a sneaking suspicions my project was being too cooperative. I know this sounds cynical but I usually never go this long without weird or no results.

I have finally hit the point in my project where trial and error has become my only option.

When the mutation combinations were electroporated into B. thailandensis, plated, and patched for screening, neither combination yielded Ts phenotype.

The revertant plasmid and Ts control were transformed back into E. coli patched out and will be isolated for sequencing early next week. However, there is some funny business going on with the Ts phenotype.

Also, six plasmids were sent for sequencing that were mutated with multi-site mutagenesis with the last point mutation to be tested. Two out of six are positive for a D to G mutation at site 145 in the rep gene. This is exciting for me because I have not been able to isolate a plasmid with this single point mutation yet. This point mutation will also be screened for Ts in B. thailandensis early next week.

 I wish I had more to post but for the time being I will just have to keep plugging along and see what the next new development is.

 Thanks for reading and as always, enjoy.

1,2,3,4 ….ichi, ne, san, chi!

Count, count, count.  I’ve been helping Fujimori Sensei by doing the monotonous and inevitable job that follows cell culture….counting of colonies.  I had a nifty little pen that beeps and counts for you every time you mark a colony but then it dried up.  😦  Which, by the way, I don’t understand since it is sooooo humid here!  Oh well.

Last week I got to help Dr. Allen run an experiment where we irradiated multiple cell lines at different doses with the HIMAC (Heavy Ion Medical Accelerator) and then performed a gratuitous amount of cell culturing till 3AM.  Oi vay. Since then, the cells have been allowed to grow (or not grow) in the incubator.  Some of the dishes already had colonies today so I washed and stained those dishes and will be counting those next week.  To refresh your memory (and mine), most of these projects that I am helping with are all concerned with DNA damage & repair after exposure to radiation (i.e. X-ray or Heavy Ion).

well. that’s it for today!  keepin’ it short!  🙂


I’d like to begin by saying thanks to several readers for their
thought-provoking questions/comments….I’ve been in-and-out of the lab for
the past few weeks so I apologize for the long delay between posts, so
thanks also to everyone for bearing with me. In my last post I provided
a little info about basic puma and bobcat ecology and how it pertains to the
NSF project on which I’m working. We are particularly interested in disease
transmission dynamics between domestic and wild felid populations across
multiple landscapes. These populations are known to be susceptible to
numerous viral, bacterial, and protozoal pathogens. These animals can also
be reservoirs for several zoonotic agents, which we discussed in the
comments section of my last post. (*Side note: From here on I will focus
primarily on the viral agents that are capable of causing disease in felines
only. I certainly hope all the bacteriologists and parasitologists out there
continue reading though*.*)

Our lab investigates two notable feline retroviruses, feline
immunodeficiency virus (FIV) and feline leukemia virus (FeLV). FIV is the
feline analogue to HIV, demonstrating affinity for similar cell types as
well as displaying comparable clinical symptoms and outcomes. Infection in
domestic cats can cause immunosuppression ultimately resulting in death.
However, many animals remain asymptomatic carriers for the duration of their
lives. The fitness impacts on wild felines have yet to be fully understoood,
but seroprevalence rates across our study areas are found to be quite high.
A major objective of our project is to determine the impacts of this disease
on the health and behavior of large carnivore populations facing varying
environmental stressors.

Continue reading

Hurry Up and Wait

Well hey there again! Alan and I have been working on DCPS and XRN1 still. We ran a gel to see which colonies we picked had our fragments in the bacteria’s plasmid and I think the gel turned out good, but we will send them for sequencing soon I hope!
Tomorrow we are going to work on running a protein gel to see if our purification of the LSM1 and DCP1 proteins worked so that I can have more to present at our lab meeting next week. I was able to get a protein gel on these in June and Alan started the purification but never ran the gel. So hopefully that works!

Next week me and the other undergrad (Amber) are going to present our results and whatnot to our lab at our lab meeting, so I’ve been trying to work on getting pictures and more results for my presentation.

Unfortunately not a ton of exciting stuff has been happening recently, as Alan always says “Microbiology is a lot of hurry up and wait”. We have to hurry on mixing and pipetting, but then we have to wait for the machines to run. That’s why for the waiting, I keep my handy Sudoku book nearby…score. Most of the time, we try to start or finish other things while we wait, but if we start too much at once, we could overwhelm ourselves when we have to finish it all.

Also, I’ve begun packing and moving, so if I get so caught up with that, that I forget about posting Thursday, I apologize ahead of time. But I will do my best! Hasta luego y buenos noches mi amigos!

Becca T