Let's Talk About It -- Week 12

This week marks my last one working at ASU. A few days ago in the SLG lab, Dr. Peter and I finished copying all the high CADD and polyphen score genes into a separate document. Today, I further organized this document, color coding the participants (red for speech impairment and dyslexia, orange for speech impairment, yellow for dyslexia, light green for typically developing monolingual, and dark green for typically developing bilingual). Finally, I marked all the male participants in blue so all our patient information was readily visible on the 1400 line spreadsheet.

The data we had received from the company Illumina included a number next to each genotype, always between 0 and 1. At first, Dr. Peter thought these numbers where quality scores; however, a bit of research proved quality scores are always whole numbers. As it turns out, these scores were Gencall scores, a grading scale similar to quality scores, but not as widely used.

My last day in the SLG lab proved I'd learned how to organize and analyze data quickly. My experience in this lab was amazing and helped me to see the world of what happens after the genetics samples are gathered. Overall, we haven't yet reached our conclusions in the SLG lab, but the work itself has taught me more than reading about genetics ever could.

For my final day in the CHILL lab, I was allowed to perform an assessment in Phoenix, meaning I didn't have to drive endlessly far for a simple hour and a half study. During this assessment, I watched a graduate student perform the three intelligence tests meant to check whether students qualify for the POWWER testing, and later we compared the scores we'd each assigned to make sure neither of us had made mistakes.

I also attended my team's poster presentation at ASU, where we talked through out experiment and evidence. Overall, the experience really helped me understand how research works and I'm excited to do my own at ASU!

The brochure and my name tag from the presentation. 

All the members of the CHILL lab and Dr. Gray with our poster.

A slightly blurry picture of our poster with the results and analysis. 

Let's Talk About It -- Week 11

This week in the CHILL lab, I drove out to Mesa to test new kids. The girl I tested became incredibly frustrated during her first word learning task.

I've noticed that it takes most sixth graders until the last of four rounds to remember the names and appearances of all the monsters whereas my tenth grade sister had everything down by the second round. This may seem obvious, but it supports the conclusions the CHILL lab has been trying to draw. Age affects working memory. The older a student is, the easier it is for them to remember a series of meaningless syllables.

On Wednesday, I continued assessments on the same students.

In the SLG lab, I continued my work from last week, copying the mutations with the highest CADD and polyphen scores to a new document. This process will likely take all of this week and most of next, so as of yet there aren't any new developments in the SLG lab.

Overall, week 11 wasn't particularly exciting, but as my senior project comes to a close - and the presentation deadline draws nearer - all my labs have started reaching conclusions that I'll be able to more accurately report on!

See you next week :)

Let's Talk About It -- Week 10

This week, the CHILL lab decided to train several new volunteers on how to administer the POWWER game. Though the school year is almost up, the POWWER tests will continue over the summer. It's hard to believe I'm one of the "senior" members of the CHILL lab crew, but this week, I took several trainees out into the field where they could watch me administer the test. This training proved a little stressful as the new lab members were encouraged to take notes on my procedure. The entire time I hoped I was doing everything according to the rules. Set up the computer, wipe down the touch screen, properly start up the game. Never had there seemed to be so many steps to the POWWER game!

In the SLG lab, I worked on narrowing down the genes in question from an annotated file Dr. Peter received from a program called Seattle Sequence. This process meant copying and pasting all the abnormalities the lab had found in each gene thought to be related to speech and language. Then, I would delete any repeats or any genes with abnormalities other than a "missense" mutation. A missense mutation occurs when a single nucleotide meant to code for a protein changes and instead codes for a different type of amino acid. These mutations aren't the only ones, but because we had so many mutations to work with, Dr. Peter insisted we only study the "worst of the worst." The missense mutations.

This process took me three days to complete and resulted in a 2,000 line excel document in which I had lovingly selected each pertinent line. Next week, we narrow down the document even more, searching for the worst CADD (combined annotation dependent deletion) and polyPhen (polymorphism phenotyping) scores.

CADD scores reflect errors in insertions and deletions in the human genome and polyPhen scores represent the probability that a mutation will do damage, so as Dr. Peter said, we will continue to narrow down our huge list of genes to find the worst of the worst.

Have a good week!

Let's Talk About It -- Week 9

Dr. Peter emailed me tuesday morning to say there was still data to regroup, so wednesday I headed back to ASU. We created a new annotated file for the genes and chromosomal regions we had narrowed down, meaning another spreadsheet full of information about each region. Where it was located and what a mutation was projected to affect.

Creating this file displayed all our data - which, because of our small sample size, was more of a hypothesis than a conclusion - in an easy to read manner.

But because of the upcoming play back at school, my availability was limited. Instead, I focused on analyzing the two books I had read to supplement my research. First, Working Memory and Learning, a practical Guide for Teachers by Susan Gathercole and Tracy Packiam acted more as a textbook. The authors included graphs of child test scores versus memory abilities to showcase not only the obvious existence of working memory impairment, but also the affect of such impairment on the education of elementary aged kids. Their observations proved sometimes kids who do poorly in school need help with their memory and not necessarily anything else. For example, students may forget what they're writing about and start a paragraph on the themes in To Kill a Mockingbird but conclude with a detailed description of their weekend. This problem doesn't only affect english problems, but math and science as well. Students with poor working memory skills can't hold numbers in their heads, forgetting the grams of carbon they have just calculated for their chemistry problem before they can convert this number to moles. 

The solution to this problem, which seemingly repetitive for typically developing children, is teaching students to write down every part of their instructions and each step of their work. This may force teachers to allow extra time for students with memory impairment, but such patience will help the affected children succeed. 

The second book, How to Learn Any Language Fast and Never Forget It, by Gabriel Wyner took on a far less clinical tone. Wyner, an opera singer, recounts the humorous stories of his quest to learn five languages fluently (and he hasn't stopped there!) but also gives serious tips for picking up vocabulary and grammar. 

Learning a second language isn't the main focus of my project, but the pursuit combines memorizing tactics and the nature of language. Wyner's advice focuses on how to quickly transfer information from the working memory to the long term memory and therefore proves interesting next to the research I've already completed. 

As all of our projects slowly wrap up, I'm looking forward to analyzing all my findings together. Only with the results from each lab and each book can I draw meaningful conclusions about the relationship between speech and working memory. 

Let's Talk About It -- Week 8

After spending week 7 enjoying spring break with my friends and family, I was ready to get back into my work in the CHILLL and SLG labs.

With data collection done and checked (over and over and over again), graphs made and conclusions drawn, the SLG lab drew to a close. Dr. Peter promised to send me the rough draft of the paper she has been writing about our findings, and that was it, at least for this project in the Speech and Language Genetics lab. We narrowed down genes and chromosomal regions that could possibly affect either speech abilities (leading to such things as speech impairment and dyslexia) or working memory (leading to low memory scores). We found, as we had predicted, that most of the children with dyslexia or speech impairment scored low on the working memory tasks as well.

My experience in the SLG lab was my first introduction to real life genetics.

But my time with Dr. Peter isn't over yet. She asked for my help in another project, one I don't yet know anything about but would be glad to work on, as I really enjoyed the genetics analysis of our previous project. As soon as the paper is proofread, I'll learn more about this new study!

There wasn't much to do in the CHILLL lab except continue our assessment of children. On friday, I drove out to Tempe to evaluate another student. She was much quieter than my first student had been, but at the end of the session she told me she had fun so it was worth it.

Next week marks the week before our school play, meaning my ability to work in the CHILLL lab will be limited. However, I still have plenty of material to read and hopefully I'll find out about this mysterious second project of Dr. Peter's.

Have a good week!

Let's Talk About It -- Week 6

Week 6 continued similarly to week 5. In the CHILLL lab, I met with Dr. Gray to discuss the lab's progress and signed up to RA further assessments over the weekend.

Tuesday and Thursday I spent most of my time in the SLG lab. Finally we were nearing the final pieces of our data analysis, which meant more spreadsheets. Karishma and I compiled a list of all genes thought to affect either speech and language or memory. We created a document with the gene names and the chromosomal regions they supposedly affect. Next, with a file so big Dr. Peter’s Mac couldn’t open it, we checked these specified regions against the information from our test subjects for possible point mutations. Next week we will try to narrow now specific genes/chromosomal regions that seem to affect only the children with low working memory scores, dyslexia, or speech impairment. 

Here is the desk I work at in Dr. Peter's lab, complete with three separate spreadsheets open on the computer. 

Though not much changed this week, I'm looking forward to finding and analyzing results from both labs in the weeks to come!

Let's Talk About It -- Week 5

As this week was ASU's spring break, I couldn't work in the SLG or CHILLL labs. However, I did have the computer at home, which weighs about half as much as I do and took up much of our dining room.

The keyboard and game lockbox 

(which contains all patient information as well

 as tape and touch screen wipes and 

other necessities) on my dining room table

Finally I could work on my skills as an RA by testing my siblings at home. My 15 year old sister's working memory was nearly impeccable, but with my brother...

My somewhat stressed brother playing the POWWER video game

...not so much. Still, between the two of them I was able to administer the tests for all "islands" and by Saturday felt prepared to enter the field!

My first true test occurred at Chandler sunset library. I drove the computer there, set up, and tested the first sixth grade student. He was surprisingly excited, even for the repetitive tasks. When learning the names of the monsters, he would repeat the nonsense syllables out loud, during the difficult tasks he kept assuring me he'd eventually get it, and at the end of the session, he exclaimed that the POWWER video game was "super cool!"

If only I had so much energy in sixth grade...

My preparation paid off, and my first experience as an RA was exciting.  Now I'm confident that I could administer the tests without any of the other researchers watching over me. I'm able to set up and pack up the monstrous computer, start and record the game, and even, with enviable speed, deliver to snotty children. Saturday was a success. 

Next week, ASU's classes will be back in session (meaning the buses will run again and I won't have to drive as far), and my own in the SLG and CHILLL labs will continue!