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!

Let's Talk About It -- Week 4

Week 4 continued on a similar note. Tuesday in the CHILLL lab, I finished testing myself on the POWWER game and learned how to pack up the computer cases. Finally I can practice supervising while a student takes the tests! This week, I practiced on my 15 year old sister, Jessica, who like me was a bit patronized by the pirate at first but later found the competitive nature of the game somewhat entertaining. This weekend I plan to finish my trial run with Jessica and report back to the lab.

The SLG lab too was a bit slower this week. I could only work thursday, but Karishma and I searched through detailed spreadsheets which listed all the genes found in each patient. We flagged specific genes known in previous studies to affect speech, language, and memory for further examination. Likely, we will finish this work next week.

Later this week I will attach pictures of the computer I had to bring home from the CHILLL lab. The case and computer together weight 50 pounds and would be quite a struggle to take on the bus! Until then...

Let's Talk About It -- Week 3

In the SLG lab we continued our quest for genes that could affect dyslexia (dsx) or speech impairment (si).

After searching two articles (“Genome-Wide Analyses of Working Memory Ability: a review” and “Understanding Language from a Genomic Perspective”), my lab partner Karishma and I highlighted any genes mentioned in the papers. Once we’d compiled a list, we checked the mentioned genes against our own data, flagging where patients with dsx or si showed deletions of duplication in these mentioned genes.

Despite our (>15000!!) lines in the spreadsheet mapping the chromosomal regions of the tested patients, we only discovered three genes with direct overlaps: COMT, SCN1, BCAS3. Six genes with nearly overlapped the mentioned regions, just close enough to still factor into our study.

As the head of the lab, Dr. Peter, left for Seattle on Wednesday, Karshima and I couldn’t begin searching for point mutations because neither of us had any clue what we were doing. With Dr. Peter back on Tuesday, we will begin investigating the data more deeply – especially data from dsx and si patients – for possible occurrences of point mutations in DNA. But due to

Dr. Peter’s absence, most of my work in week 3 occurred in the CHILLL lab.

On Tuesday I continued playing the POWWER computer game and finally learned what POWWER – the name of the computer game and our current study – stands for.

Profiles

Of

Working memory and

Word learning for

Educational

Research

Which makes sense, as the game is meant to test not only a child’s working memory, but also their language learning skills and reaction times.

After Tuesday, I’d learned enough of the POWWER game to begin testing myself without an RA present. I spent all day Thursday playing the game alone as both student and administrator. Being alone allowed me to take more pictures! So here’s me set up like a student would be to play the game:

In order to complete the trials, students press the touchscreen, record their responses in the microphone, or hit specific buttons on the key board. In order to accurately measure reaction time, students must return their hand to the green circle between each answer. In addition, two pieces of fishing wire attached to the touchscreen allow a consistent measurement of how far the green circle and the student are from the screen. All these added steps ensure higher accuracy when measuring results. 

Because I’ve now completed each of the tasks several times, I have a good idea as to how exactly the game functions.

Working memory tasks are fairly straightforward. Children hear a series of letters or numbers, or perhaps see a string of atypical polygons, and must repeat the information back. While these tasks aren’t simple, how they work and what they’re meant to test is easy to understand.

Most fascinating to me are the word learning exercises. On Sea Monster Island, for example, I was faced with four different “monsters,” each looking something like:

To ensure the students were truly learning the information and not just recalling facts, each monster was given a mashup of sounds as a name. Students had to be able to say the monster names, recognize the names when said, and match each name with each monster. As if this wasn't hard enough, the trials on the island also included recreating what each monster looks like!

I chose from four categories of details in an attempt to recreate the monster's exact features. After one or two rounds, the tasks became much easier.

Thanks to my now thorough understanding of the POWWER game, on Friday, I accompanied graduate student Melissa Sacchetta to a charter school in Chandler, where one sixth grade student had signed up to participate in the study. Melissa and I spent an hour in the schools only empty room - a robotics laboratory - assessing the participant's vision and hearing, as well as administering three separate kinds of intelligence tests. 

The first of these tests asked the student to form a sentence given a word and a picture to include. One such example was a picture of two children standing in front of a closed toy store in which the student was instructed to form a sentence with the word "until." Melissa and I wrote down each sentence and separately scored them, a "2" for a perfect sentence, "1" for a flawed but permissible sentence, and "0" for a lack of attempt, sentence that didn't make sense, or sentence without referencing the picture. Later we compared our scores in a process called "double scoring" to ensure neither of us made a mistake in our grading of the sentences. 

The next test assessed the students ability to solve word puzzles. When presented with a questions such as "what has a tail and barks?" students must answer "dog." While these puzzles appeared easy at first, the riddles became progressively more difficult to the point where I was impressed at the sixth grader's ability to answer! 

The final test was one I remember from elementary school in which the student read a series of unrelated words as quickly as possible, attempting to fit as many in to 45 seconds as he could. 

We perform all these tests to ensure each participant will fall within the first standard deviation of "intelligence" for children of this age before they begin the POWWER game. Now with this experience under my belt, I'm ready to travel and prepare more students for our research in the CHILLL lab!

Let's Talk About It -- Week 2

To begin week 2, we received data on our patients from a group working with the SLG lab. This group tested each patient’s working memory and assigned each a score – or working memory class – from 1 to 4, 4 being high performance and “good” working memory and 1 being the opposite end of the spectrum. However, we received this data only as the patient’s identification number and the working memory class they were assigned. My job was to fill in our master sheet with the data, adding the working memory class to the rest of the genome information for each patient. As could be expected, most of the typically developing children scores 3s and 4s while the patients with dyslexia, speech disorders, or both typically scored 1s and 2s.

Last week, we marked all the chromosomal regions our patients displayed against regions known in previously published studies to cause speech problems. Not that we have this data, week 2 consisted of analyzing our data for chromosomal regions not specifically mentioned in other cases in search of a genetic region that could be linked to speech disorders. To do this, I created a blank spreadsheet and copied over any regions in which there was an overlap between at least two affected individuals, giving us a long list of chromosomal regions that could possibly cause or worsen speech impairments.

The CHILL lab too began to get exciting. On Friday, I began playing the pirate themed computer game meant to test working memory. Even though these assessments were made for 6th graders, I found them difficult. The tasks I completed focused on two different types of memory. In the first and hardest trial, I was presented with atypical polygons paired with names made from random combinations of syllables, for example, a shape like this:

combined with the name: buvdape. After flashing six pairs of polygons and names across the screen, I would hear the name of a polygon and have to pick the correct shape from a lineup of the polygons I'd seen. 

This task was so difficult I had to repeat the introduction several times. 

However on other islands - as the game centers around a pirate moving from place to place and completing assessments for treasure - I performed more preferably. I best remember strings of  numbers and can repeat them back out loud, write them down, or even remember them for significant periods of time after initially hearing them. 

These tests in the CHILL lab proved interesting, and I hadn't even finished half of them. Hopefully next week I will be able to continue analysis of the genes thought to cause dyslexia and speech impairments in the SLG lab, and complete the rest of the islands in the CHILL lab. But first, I have hours of club volleyball to watch at the festival fiesta tournament!

Until next week :)

Let's Talk About It -- Week 1

The first official week has been hectic.

I've attended meetings in the CHILLL lab for several weeks, but now we're ready to start our data collection. This means an awful lot of folding, labeling, and sealing to get hundreds of information packets out to potential participants. Throughout the week I have helped compile, file, and style so we can get the most interest in our research project. Week 1 was slow, but thanks to the packets we made, the following weeks will become more exciting.

Beginning next week, an ASU grad student and I will lug around the 50 pound computers to various libraries. After teaching kids to play the computer games, we will assess their working memories. I have yet to get my introduction to the software, but hopefully I'll be able to play the game too!

My first few days in the SLG lab gave me a taste of the tedium behind research. A fellow student and I searched through an excel document of over 15,000 lines, examining the strings of digits denoting specific regions of chromosomes and searching for overlap between the tested regions and regions that other studies have concluded present speech and language impairments. Despite the repetitive nature of this work, finding a match proved extremely exciting, even when we only discovered four or five overlaps in one hundred regions.

However, after only half an hour, we noticed an error in the data. According to the spreadsheet, one of the minimal regions had a higher number than the maximal region. After reexamining all the data, we realized the program from which the data was translated into excel deleted every zero that followed a comma. This discovery rendered our current data invalid, so we spent the rest of the day manually reentering all the data with the correct number of zeros.

My first week afforded me experience with real research. Before my internship, I would never have considered the difficult process behind participant recruitment or even data analysis. In the upcoming weeks, we will begin data collection in the CHILLL lab and continue analyzing previously collected data in the SLG lab. I can't wait to start in earnest!

Let's Talk About It

Let's Talk About it: Understanding the Science Behind Speech and Language.

My name is Julia Guido, and instead of attending classes in the last ten weeks of my high school career, I plan to spend the last trimester of the year participating in BASIS Peoria's Senior project. I've always been fascinated with the brain and the process of research, and this independent project will allow me to explore these areas and conduct experiments outside of a high school setting. I will answer two questions:

What is the relationships between working memory and language acquisition? and What are the genetic causes of language abnormalities?

In order to learn about speech and language from as many angles as possible, I will intern in two labs. Thanks to Dr. Shelley Gray and Dr. Beate Peter for allowing me to work in their respective laboratories, the Child Language and Literacy Laboratory (CHILLL), and the Speech/Language Genetics Lab (SLG). These labs will give me experience in administering scientific tests and analyzing speech from a genetic perspective. In addition, thank to my advisor at BASIS, Mrs. Hagerman, and my college counselor Mrs. Estes.

SO

In the CHILLL lab, I will work with other students administering computerized tests to sixth graders meant to assess their working memory. We will analyze the development of language in 12 year olds via the results of these tests.

In the SLG lab, I will analyze genetic markers of language abnormalities, adding a more biological component to my project.

The goal of my project is to understand how working memory relates to language acquisition, and its implications are broad. With this research, schools will be able to tailor their programs more accurately to the minds of children, teachers will be able to create projects that capitalize on the abilities of the students, and even standardized tests will be able to reform around the abilities of the brain.

For the next ten weeks, I will share my learning and experience through this blog, starting now.