Digging trenches in Jordan!

Hey everyone! Currently I'm in Jordan and have been for the last week and a half, though this is one of the few times I have internet, since I am in Amman for the day. The team this year consists of Oxford Professors Dr. Aaron Stutz and Dr. Liv Nilsson-Stutz, former Oxford student Brittany Mayo, Emory PhD student Joshua Robinson, Dr. Jamie Clark, Anna Trainer (former student of Dr. Aaron Stutz), and myself.

This year in Jordan we are doing test excavations ... which have quickly turned into an ACTUAL excavation. The site we were here to determine whether or not it was actually a paleolithic site, is definitely a site, though what time period we are unsure of, all of the artifacts, which there are TONS of, are very ambiguous, since we are still only a few centimeters under the surface. At the moment, it appears that there are also ruins of a wall structure or a pavement near the surface, we are trying to see how to excavate the feature effectively.

Days start at 4 in the morning, when we wake up so that we can get to the site no later than 5:30 am, since we need to start work early because by noon it is too hot to continue working, since we are working on the East Bank of the Jordan Valley. Working in our cave on the East Bank allows us to see the West Bank from where we are working. Each day some of the team members get text messages on their phone saying "Welcome to Palestine!" the reception isn't that accurate here in the valley haha... Though one day it was a little hairy in the morning, we heard explosions coming from the West Bank an looked over and saw the smoke. Along with a few gunshots and aircraft, we decided that wasn't the best thing to be hearing in the morning coming from the West Bank... but we learned from our dig house's caretaker that it was just the Israelis doing training exercises on their side of the Valley which they do occasionally, and none of the locals seemed worried. It did make for a very interesting morning though! Nothing like a bit of excitement to add to your adventure!

We also took a trip to the ancient Roman city of Jerash and saw the ruins there and the Temple of Artemis, though it was weird because all the writing on the ruins was in ancient Greek and not Latin, which according to Brittnay who is majoring in classics, is extremely strange considering the Romans are usually known for using Latin and writing over everything in Latin.

So as you can tell, a LOT is going on right now! I've posted some pictures below but I will leave the update at this considering I'm exhausted from all the physical work and waking up at 4 in the morning daily! Though I'm having an amazing time once again this year, and even have gotten to see some of the other archaeologists I met last year and chat with them about their projects this weekend, so it was somewhat like a mini reunion for me! I hope you all are having a great summer as well!!

Pictures Below:

Dr. Stutz setting up the grid and grad student Josh
Roman Ampitheater 2 at Jerash
Me in the Temple of Artemis
The Temple of Artmeis
City of Jerash
At work with smoke on the West Bank in the background
Working on the terrace of the cave
Working on the terrace more

Exciting Adventures on the Research Front

Well, it comes a time in every one's research when you get extremely frustrated and you wonder if anything will ever work or are you at a dead end. Let me say that I have felt that way about my research this summer for the past couple of weeks.

First off, the sequencer in our lab, the primary machine I need to verify many mutations for my research, was not working at all. No peaks were coming up and I feared that I would not have any data at the end of the program except for some gel electrophoresis images. While these photos are nice, they cannot conclude if the one-base pair mutation is there or not. Then this week, Lynn, the research assistant in my lab who has taught me so much figured out what was wrong with the machine: the cable was on "test" rather than "run." That's all! We just had to change the cable hook-up and viola! it's working now! Now, I'm quite excited that I shall have data!

Also, for the past couple of weeks, I have been testing primers to find the optimal conditions for them. For the first 15 out of 16 primers, everything was great: I got the conditions down right away. But this one primer just would not work. I must have prepared about 5 PCRs and ran the gel just as many times. But to avail. I would either have no bands (which is quite distressing for a student who always had clear bands in her gels from her labs in general Biology and genetics) or I would have multiple bands. Finally, I gave up on that primer, designed a new one for the same locus of DNA I wanted and the new primer came in today. So, I'm in the process of preparing it.

Then, on Tuesday, I decided to do a PCR of about 10 samples for various genes. I was so afraid that I would mess up again and there would be no bands on any of the samples. BUT every sample produced a band! And the band lengths were just right. I was so excited that I started dancing in front of the imaging machine. Thankfully, no one walked into the room while I was doing this, because then they would have thought that I was insane.

So, I've been feeling a little better about my research. I'm finally getting data. My mentor returned from a trip to Europe and brought me back cookies! And told me to keep up the good work (I had been emailing him daily about my distressing primer situation and the later fantastic gel along with the dancing. I also think that the research assistant was filling him in about how I was helping around the lab). He's off to a convention for the Endocrine Society and I'll see him in about a week. He also wants me to present at his lab meeting when he gets back. And these lab meetings are not just him and the research assistant that helps me, it's everyone who works in the lab, along with collaborators from other labs and Ob/Gyns from the hospital because they help out with the clinical aspect of his research. (My mentor is an Ob/Gyn, but also has a lab to investigate specific puberty disorders)

Well, time to get back to research. I'm sorry if this is boring for all the non-science people out there! But I cannot imagine working outside of the science/medicine world!

Peace and love,
Lizzy-

Hello all! I am now in northern Minnesota taking my molecular genetics class to get ready for summer research. I work in the lab from 8AM to 6PM isolating plasmids and RNA, doing tissue cultures, running PCR, gel electrophoesis, basically cool stuff if you are a science nerd :) I am having so much fun meeting other people who share my interests and learning and practicing skills that will be very valuable in my future as a researcher this summer, next year back at Oxford, and beyond undergrad. I am kind of thankful for the weekend because it has been a VERY full week. I am excited to start my project a week from Saturday.

While my research will take place in the Twin Cities, I am taking the class 4 hours north at Lake Itasca, which leads into the headwaters of the Mississippi River. I have been kayaking and hiking, roasting marshmallows, and am planning a long bike ride for this weekend. It has been a wonderful experience so far, and I can't wait for the rest of the summer!

If you are interested, I have some more specifics about my summer research. I will be studying a very involved biochemical pathway that activates transmembrane proteins called integrins that are found in T-lymphocytes. These integrins, when activated, direct the T-cell to antigens and promote cell adhesion. The pathway that activates the integrins is really complicated with many steps, enzymes, proteins, and reactions. I don't know which piece of the puzzle I will be focusing on directly, but I assume I will be studying some sort of gene expression in this pathway. That means real time PCR and isolating mRNA!!!! It's rather complicated, and I was rather unsuccessful at doing those things this week. However, it was my first try, and I am excited to learn and get better and better!!!

Ok no more science stuff for now!! BYE BYE
Susanna

From Oxford to Oxford

It’s almost been a month since the end of my first year of college. My first year of college was filled to the brim with various things that made my experience so enjoyable. Looking back, it seems crazy that I managed to do so much in such a short period of time.

Summer has been relaxing so far. I’ve done various sorts of activities in order to keep myself busy. It is great to finally have some time to read for leisure. I’m currently tackling The Brother’s Karamazov by Fyodor Dostoevsky. Not only have I been able to read, I’ve also been able to do some writing and even draw. The rest of my time is spent playing basketball, running, or watching sports. I run three times a week on Monday, Wednesday, and Friday. I've managed to cover about five miles a day in recent weeks.

June 29. That is the day I’m leaving the US for the UK. In less than two months I will have gone from one Oxford to the other. Oxford University is one of the oldest universities in the world. It would be an understatement to say that I’m extremely excited about this trip. This will be my first venture into Europe and I expect I will learn plenty during my stay in the UK. I am taking two classes: British Anti-Slavery and Chuchill and Modern Britain.

Stay tuned for more on Jeffrey’s Summer Adventures!

Summer Plans!

Hey Y'all

Guess what!?! I'm taking two trips at the end of the month through two different scholarships that I got when I was a freshman. I'll give a more detailed post, with pictures, after I come back.

Here are some hints about my two destinations:

1. I am very familiar with the first city that I'm visiting -- you could call it my second home
2. I've only been to the second city once, in the 8th grade
3. Both cities have long and rich histories
4. Both cities are capitals. . .  one of a state the other of a country

Can you figure out where I'm going???

'Til Next Time,
imani :)

Researching!

Hi again!

So, I have a few minutes while waiting for a gel electrophoresis and an ethanol precipitation to write this post.

Like I said in a prior post, I am researching at Medical College of Georgia in Augusta! It's been really awesome so far. Last week, I had to give a powerpoint presentation to our lab group about my project that I researching this summer. It was very nerve-wrecking, but my mentor told me a did good job, so that made it worth it!

For my first part of my research, I am verifying a series of mutations found in patients with IHH/KS. So, I've been looking at a lot of chromatograms, identifying the single base mutations and designing primers so that I can repeat PCR and sequencing to make sure that these mutations are really there! I finally got a hughe shipment of primers this week! I've been working with them, making sure I have the proper controls with a series of controls we have in the lab.

The second part of my project has to do with NELF knockdown. A knockdown is when you, in effect, "knockdown" the representation of that gene, as though it was not there. You can knockdown genes with miRNA. My mentor is working on the knockdown. After we get a confirmed knockdown of NELF, I shall be observing the effects of downstream genes. This is to see if NELF is a transcription factor that hinders or aides the transcription of certain genes.

Well, my ethanol precipitation is almost done. I should get back to it and start the sequencing reaction!

Peace and love,
Lizzy

Orientation's Great!

Orientation planning has already begun and our orientation leaders (PALS) are so excited to meet you all! Please visit the orientation website for details about the orientation schedule and more!

Make sure you have checked out our Deposited Student Handbook online for all the forms and more information you will need before you arrive on campus in August!