Monday
Jul082013

Exciting Things Happening In the Hooker Lab!

Greetings! This post is aimed at giving everyone who visits this group website a more behind the scenes view on what takes place on a day-to-day basis in the Hooker lab. There is a great diversity in this lab, so every day there is something new and exciting going on. Here is a preview as to what some of our group members will be doing this week:

Misha: Running Western blots on rat brain tissue from animals treated 
with novel radioprobes; Analyzing immunohistochemical data from rat 
brain tissue, and reconstructing PET images collected for a clinical study 
investigating chronic pain.

Nicole -  I am currently finishing a response to the IRB based on elements from an exciting Autism kick-off meeting on Monday as well as working on a review, while attenuation maps for an MR/PET study are running in the background. I also spent some time trouble-shooting the lab computer.

Marjorie: "The matlab week!"
I'm currently processing PET-MR data using a mix of tools from FSL, 
FreeSurfer, SPM and my own matlab codes. I'm proud of my first 
FreeSurfer-derived ROI to process our dynamic PET images!

Al Schroeder;
1. rat brain protein analysis (Does our new inhibitor predictably 
suppress enzyme activity?)
2. human brain PET imaging analysis (Using small regions of interest, 
can we gain insight into how an anesthetic drug works?)
3. switching desks (Can I swing my arms around freely and NOT hit 
anyone?)
4. contributing to the blog (Will posting increase my street cred?)

Stephanie Lie - Building and performing parametric map analysis of the group's past non-human primate fMRI studies of the brain utilizing a variety of pharmacological challenges. 

William Taylor- improving yield and purfication methods for the Palladum-catalyzed Suzuki cross coupling reaction.

These are just a few examples of the exciting and diverse research that takes place all right here in the Hooker lab. We will continue to keep this blog updated with new intriguing details on what will be happening next, as well as any interesting news or results that may be found in this lab. 

Monday
Jul082013

Progress Update

Hello all who are reading this. This is William checking in to give an update on my progress, as I know I have not written a blog in a while now. As a part of my project I have to go through a series of organic synthesis steps in order to yield the final product that I will be using to analyze the brain via autoradiography. There is one reaction in the middle of the synthesis known as the Palladium-catalyzed Suzuki cross-coupling reaction. While reading background information on this reaction I learned that it won the Nobel Prize for Chemistry in 2010. Needless to say it is a very important reaction and a very key step in my overall synthesis. For the past two weeks I've had some trouble getting the reaction to work, as it is pretty tricky to set up. After trying the reaction 3 times and not being able to figure out why it wasn't working it was quite discouraging. My mentor Emily had to be in her other lab to complete further studies on her work in preparation for her dissertation committee meeting for graduate school, so I didn't have her around to ask direct questions and had to seek help elsewhere. Although, we did communicate often via phone and email and I'm thankful that she tried to help me as best as she could under her circumstances. That meant a lot. I consulted others in the lab for help, including Ramesh who has done this reaction before. I learned a lot and gained new understanding on this reaction and ways to ensure that the reaction works to completion. On the 5th try I finally reached product conversion! It wasn't much, but it gave me the motivation I needed to carry forward and improve my product yield. On the next try I acheived a better product yield and this was extremely exciting for me. I am now at the final step of my synthesis which looks even trickier than the Suzuki reaction. However, I am ready to take on the task and learn from this experience. After this step I will be able to radiolabel my compound and it will be ready for autoradiography analysis on rat brain samples. Hopefully all will go well. Don't you just love science?

-William Taylor 

Wednesday
Jun262013

Things I have Learned about Boston

1)      It is perfectly fine to jaywalk. Seriously. I’ve even seen a cop do it.

2)      But, be careful of the bikers. They usually do not stop for red lights, meaning that you can easily get run over. (Two close shaves thus far.)

3)      Once you look like you know where you are going, people will ask you for directions. (Four people and counting.)

4)      Pronunciation is everything. It makes out-of-towners stand out. (ex. Lechmere is pronounced Leach-mere).

5)      Eventually, someone will make fun of your southern accent – even if you only have a little one. (My favorite voicemail. Ever. : “Hey y’all, it’s Occupational Health. You must be from North Carolina….” Busted.)

6)      You can buy really cheap food at Haymarket – like 60 tomatoes for 6 dollars. (It weighs about 15 pounds in case you were wondering and, with the help of four girls, can make huge amounts of guacamole, salsa, and tomato sauce. It will take an entire day to cut them up.)

7)      The South End is not abbreviated as SouthE, but Southie. Strangely, there is not a similar rendition for the North End.

8)      Traffic is terrible - especially when it’s raining.  The worst traffic I’ve experienced is five blocks per hour. If I had walked it would have taken 10 minutes tops.

9)      The mayor of Boston is Thomas M. Menino. The only reason I know this is because his name is literally plastered on half of the signs and buildings I have seen. They mayor of Raleigh might want to look into that.

10)   Boston is a wicked fun city (wicked is a new word I am trying to pick up to hide my tendency to say y’all).  It’s united in so many ways and can be summed up in just two words: Boston Strong.

-Jaclyn

Friday
Jun212013

First Summer Subgroup Meeting

This week, we summer students had our first, full subgroup meeting with Jacob, and, while it was a little intimidating at first, it was such a great learning experience that I really enjoyed it. Since this was the first time we exposed to each other’s projects, we spent a good portion of our time explaining the background behind them. I volunteered to go first, and through Jacob’s questioning throughout the whole meeting, I learned three major things:

  1. I thought I knew the fundamentals of the technology with which I am working (fMRI, MR-PET, baseline and blocking scans, etc), but during my short presentation, I realized that there were certainly some holes in my understanding, and fortunately they were quickly filled in that time. Even after reading some papers and plenty of Wikipedia articles, at the beginning of the summer, my understanding of all of this was quite hazy, but as I keep gathering these points of understanding and insight, the picture is becoming clearer and clearer. That understanding is making me really appreciate the technology I’m working with, and as everything starts to clear, I feel like I’m developing a stronger sense of ownership over my projects, which is exciting.
  2. I’m beginning to work on my skills at explaining what I do in science in layman’s terms. Jacob urged us to start our talks with something wicked big picture—in his words: “one step below ‘the brain is important’”—and we all struggled with it. I think that is because most of the time when we talk about our work in science, we’re in the academic setting where everything is either currently studying something in the sciences or they’ve somewhat recently seen the basics in high school. Honestly, coming into the meeting, I thought my skills in this department were decent, as I’ve done a fair amount of tutoring both formally and just with my friends/classmates, and in those sessions I could break down concepts into simpler terms. However, once again, they had a general exposure to the material to begin with, so I really wasn’t testing my skills fully. As someone who hopes to be a physician, especially a pediatric physician, the ability to describe physiological concepts to patients who could have little to no science background knowledge is absolutely crucial. Patients will want to know what’s going on in their bodies (and/or their children’s bodies), so doctors need to be able to tell them in a way that they’ll understand.  By the end of the summer, I want to get better at this.
  3. Okay, confession—and this might be blasphemy considering I’m working in a heavily chemistry-focused research group: I did not like taking organic chemistry this past year. I struggled through that class. Hard. I was given several packages of notecards worth of reactions and mechanisms to memorize over the course of two semesters, and I had to somehow memorize them and translate them into use when given a synthesis or product prediction problem. My bridge between that input and output was shoddy at best because I was probably missing some fundamental bits of understanding. The result? A pretty miserable two semesters and some hard feelings between orgo and me. However, when we were going through some of the reactions that my fellow interns were running, I was able to both see a real application for those piles of notecards, and I think I started to learn organic chemistry—and really learn it this time. The result this time? It was actually pretty fun! Even though I am not doing a lot of chemistry (in terms of running reactions, NMRs, TLCs, etc) myself this summer, I am excited about keeping up with what my fellow interns are learning as they do their chemistry-focused projects.  

While subgroup meetings are typically an hour long, we occupied Jacob for about two hours this past week. To me at least, those two hours were the furthest thing from time wasted, and I’m looking forward to learning more at our next meeting next week.

-Steph Lie

Tuesday
Jun112013

Fishing for Targets

Following precedent, I will begin by introducing myself. My name is Stephanie Lie, and I am a rising junior at Boston University's Sargent College of Health and Rehabilitation Sciences currently pursuing a degree in Human Physiology. Upon graduating, I hope to attend medical school, and I am excited to use this summer with the Hooker Group as an opportunity to explore the development and basic science behind some of the technology that I will potentially be using, from a clinical standpoint, in my future career, while also supplementing some of the topics I’m learning in school with some real life experience. Unlike my fellow summer interns, I have not ventured very far from the nest, as I was born and raised in a suburb outside of Boston, and I now attend school and work in and around the city. Therefore, outside of work within the group, I will not have to face the intimidating challenge of navigating a new city; instead, my challenges will lie in transitioning to the life of a suburban commuter and tackling the monster that is Boston auto traffic and the MBTA.

However, I digress. This summer I will be working under the guidance of Ronald on peripheral MR-PET imaging. I am currently looking at data from full body, NHP scans utilizing some of Changning’s HDAC inhibitor tracers that he’s developing for the brain, and hopefully I will find that they specifically bind outside of the brain as well. From the literature, I’m learning that HDACs appear to play an interesting, epigenetic role in many different conditions, whether it be neurodegenerative diseases, psychological disorders, or, of particular interest to me while working in the periphery, cancer. Because these new compounds are focused on use in the brain, my exploration of their effects in the rest of the body are much like that of a fishing boat moving out into uncharted waters: I will make educated guesses as to where to drop lines (or in my case, Volumes of Interest in the images) based on literature and my mentors’ advice, but like with most research, I run the risk of pulling up empty. However, high risk yields high reward, right? The idea of finding an area where one of these compounds effectively binds means potentially finding a tracer for earlier cancer detection in places buried in the thoracic cavity and abdominal region; as someone who wants to go into the medical field, the idea of developing these types of diagnostic tools is pretty cool.

While the overall idea of what I will be doing this summer appears quite straightforward, in my first few weeks here, I have learned and experienced one of the hallmarks of research: translating those ideas into a reality can be far from straightforward. In order to reach the point of textbook perfection that I have seen in my undergraduate courses thus far, there are plenty of imperfections and challenges to overcome first. So far, I’ve had to tackle the learning curves of using various types of imaging software, finding alternatives when the preferred system broke down, and learning the new languages of radiology and computer science, all while facing the challenges of working around the imperfections that come with real-life data acquisition. While it’s certainly been challenging, by single-handedly keeping Google, PubMed, and Wikipedia in business and exploring different computer programs, I’m starting to get my sea legs underneath me, and I’m very excited to see what’s at the end of my lines.    

- Steph Lie