Status: Latest Events

Research in 2018

A lot has happened in this new year of 2018.  One of them is that I went to the Biophysical Society Meeting in San Francisco!  I met a lot of great people, and my friend Gokul dragged me out to see the Golden Gate Bridge, for which I am especially grateful.  I never would have done it without him.  My  research has focused on building on my published work, moving splicing of RNA using my nanozyme into cells.  I also have a second project looking at the mechanism of how DNAzyme functionalized particles work inside cells.

 

 

Family in 2018

Meanwhile, family has been busy too.  Isaiah has continued to grow.  He started walking on his own as of Superbowl weekend, when he took his first tentative steps.  My grandmother has moved in with my parents since she can no longer live on her own, due to some mild dementia.  So, my mom is watching both her and my son Isaiah while I go to work.  It’s a lot for her to handle, but so far we are making it. 

Weekly Update

Today:  This week, I’m giving group meeting, so I am preparing for that.  I had the pleasure today of meeting and speaking with former Mirkin graduate Dr. KiBum Lee.   We students took him to lunch to Saba, a popular Italian joint at Emory Point.  I really enjoyed meeting him and hearing about his research, as there is a lot of overlap between us.  I really hope we get to collaborate one day. 

Tomorrow:  Tomorrow, I am running a gel to verify some of Kevin Yehl’s work, and prepare for some of my own.  I’m salting gold nanoparticles (AuNPs) – which means – I am making more DNAzyme-AuNP conjugates.  I am also changing the media on my cells, in preparation for my attempts at validating my splicing reporter, once I can get the plasmid from Oskar, Emory’s cloning expert.  I am also discussing a piece of literature with a member of the Heemstra lab.  We may collaborate on a new idea that Khalid and I have been cooking up.  Finally, there is subgroup meeting at 4 p.m., where I am pitching this idea, and showing latest data.  It will be a busy day.

Isaiah is also having a check-up and more shots.  On April 14th, I give a 10 min talk at the Biomaterials Society Conference in Atlanta.  More soon!

Status: A Crazy Day

The experiments!

Today, Brendan showed me how to add DNA to my mammalian cells with lipofectamine.  I was also trying to spin down more particles at the same time, and make my own media for the cells.  Finally, I got the transfection going.  Then, I worked on spinning down and washing my particles for a kinetics assay.  These nanoparticles have a DNAzyme attached to them and I wanted to test their catalytic activity.  I did this by having the DNAzyme cleave a FAM / BHQ RNA / DNA hybrid substrate.  Essentially, what this means is that the DNAzyme would cut the substrate, releasing the two halves into solution.  When the two halves were released, the fluorophore (FAM) would glow more brightly because it was no longer near the quencher (BHQ).  Therefore, the activity of the DNAzymes can be measured as fluorescence over time.  I also added a toxin to some of my cells.  Why? Because.  It was necessary for my experiment.  

Fast paced all round!

Today was really fast paced.  I was constantly moving.  I got just enough time to eat lunch (leftover pizza) during one of the spins I was doing on my nanoparticles.  I noticed Khalid seemed extra busy today.  But he’s seemed busy all week.  However, today, loads of people were trying to talk to him constantly.  I made sure to leave him alone.  He has 17 students to watch over plus rotation students.  That’s just a lot of work. 

Tomorrow!

Tomorrow, I am doing flow cytometry sample prep from 8 a.m. – 10 a.m.  Then, I am doing flow cytometry training from 10 a.m. – 1 p.m.  Then, we have the nanozyme subgroup meeting at 1:30 p.m.  Then I have to do a spin of 70 tubes of nanoparticles for our collaborator.  Finally, I’m going to eat dumplings with Alisina, to celebrate his passing his second year report because dumplings are my favorite.  We are going to go to a dumpling restaurant!  Total fun.  More soon!

Keywords / Terms:  nanoparticles (NPs, 13 nm gold nanoparticles; that’s the size of viruses), DNAzyme (deoxyribonucleotide, a ~33 nucleotide piece of DNA that can act like an enzyme by cutting RNA), fluorophore (a dye molecule that glows), spins (centrifuging something), lipofectamine (a transfection reagent), transfection (adding DNA to mammalian cells), flow cytometry (instrument that measures the fluorescence of cells and can count them for you)

Status: A Normal Day in Grad School

I thought I would describe what today looked like — a normal day in the life of a grad student — written to science educated non-scientists.  Although I tried to write this to non-scientists, I realized, it still doesn’t make any sense to non-scientists.  I hope to one day improve this problem.  But for now, I may be limited to writing technical speech, if I give science updates.  Once my paper comes out, I hope to explain it in a truly STEM way.  We will see if I can do it!

Collaboration:  centrifuging nanoparticles

Last Friday, I centrifuged nanoparticles, forcing them all to pellet at the bottom.  I then washed them by removing the top layer of water and adding in fresh water, resuspending them by vortexing (a device that vibrates the heck out of small tubes).  I washed them four times.  Today, I checked the concentration of the nanoparticles by UV-Vis on a Nanodrop instrument.  I then had to get the proper concentration of nanoparticles by adding in more or less Nanopure water, until they were 100 nM.  These particles are for a collaborator.  I had a bunch of trouble with them, but I finally got them to work out.  The picture to the left is of a vortexer vortexing tubes.

Growing Mammalian cells

Today, I was growing some human embryonic kidney cells – they are a common cell line.  And, I am transfecting them with DNA, which means I am adding new DNA to the cells in the form of a plasmid.  I am new to culturing mammalian cells (I usually work with bacteria), so Brendan is helping me learn.  He and I plated these cells in a 24-well plate and they are now growing.  Tomorrow, I will add the DNA.  The picture to the left is of a 24-well plate full of media that mammalian cells like to grow in.

Reducing and purifying synthetic DNA

I also reduced some synthetic thiolated DNA strands from Integrated DNA Technologies with DTT.  I will be purifying these DNA on a nap-25 column full of a kind of gel that can separate out the small molecules (DTT and short linker strand) from the DNA.  The picture to the left is of a nap-25 column.

Making a TEM grid

I wanted to check how my gold nanoparticle synthesis went last week, so I put a 5 ul drop of AuNPs on a transmission electron microscope (TEM) grid, and gave it to our TEM expert, Hong, to image.  Han could have done it too, but he is busy this week.  I have not been trained yet, so I can’t use the instrument.

John goes to the dentist and other adventures

And that is what my day looked like today!  I have lots of things planned for this week.  But firstly, I am driving John to the dentist tomorrow to get his wisdom tooth out.  He hopes to get a crack in his molar fixed that was brought on by this bad wisdom tooth.  After I have dropped him off back home, I’ll go to Emory and do MORE SCIENCE!!  Alisina passed his second year report today.  I hope we can celebrate by going to the dumpling restaurant I’ve heard so much about by my other student friends.  More soon!

Science: 5th year and trying to graduate

Welcome to the new website!

Science Status:  My life recently has been complicated, but my immediate goal is to graduate with my PhD next year.  All my energy has been put into making that happen.  Right now, I have a paper in review, that I am hoping to hear word about soon.  I cannot wait to talk about that paper!  It consists of the work I have done the last four years.  In the aftermath of the paper, I am working on a mix of projects: a collaboration with a labmate and two different projects for my thesis work.

Personal life:  My mom most blessedly watches my son Isaiah while I’m at work, which takes a load off my mind.  I commute an hour to work each day, getting to work about 8 am and getting home about 7 pm.  My weekends are consumed with watching my son and cleaning the house, which perpetually seems to stay messy.

Free time:  After having a baby, I really don’t have free time any more.  However, when I do get some, I like to read, blog / write and play Star Wars: The Old Republic. I’m also a member of the Rebel Legion costuming group, who goes to events cosplaying Star Wars characters for fun.

I hope this blog provides some entertainment!  For my previous history in graduate school, take a look at my old website culurien.weebly.com.  I have officially switched over to WordPress website, since Weebly is consumed with spammers and blocked by most institutions.  Unlike my old website, this one will only have one blog, and all the different posts which used to be in separate tabs are combined together, separated by categories.