It has been a great week filled with learning and growing as a scientist! Even as a teacher, consider myself a lifelong learner. So, having the opportunity to strengthen my science skills and understanding has been tremendous!

In Dr. Xiao’s lab, We are working a project that is incorporating synthesized non-canonical amino acids (ncAA) (amino acids that are outside of the 20 that occur in nature) to enhance protein thermal stability.

So this week’s activities have included making various solutions, incubating, culturing and plating E.coli cells, sending plasmids samples out for sequencing, analyzing sequences of plasmids to look for incorporation of our mutant ncAA and comparing it to wild type amino acid sequences for the enzyme Beta Lactamase. There’s also many smaller steps in between, and in between each step,  I am learning new procedures, calculations and mindsets.

And even though I have been teaching science for years, I had never done something as routine in a lab as using an autoclave. I learned how to operate one this week.

So all around, I’ve been learning lots, and look forward to learning even more in the weeks to come.

This is a picture of me plating a culture of e-coli cells. (And if you at all concerned about the open flame in the picture, don’t be! It’s to sterilize the ethanol soaked tool that we use to spread the bacteria culture onto the plate smoothly.)

I recall many years ago when we all were so excited about the possibility of computers to crunch huge amounts of data and instantly deliver accurate results.  For instance, we could take a data set of 10,000 values, instantly visualize it, analyze it, and in a few minutes develop an in situ stoichiometry.  Or we could follow a signal and real time determine if we what was happening in a reaction was what we thought was happening.

I also recall  a time when everyone realized that computer code had bugs, and those bugs could significantly effect the accuracies of the results that we were taken on faith, trusting the computer in the same way that a student trusts a calculator to magically give them the correct answer on standardized test.

In many ways our faith in our equipment is the  same as the faith of the student in their calculator, as we use the results without understanding of the process.  In many ways, this is nothing new.  Researchers have been purchasing equipment for years without completely understanding what the equipment does.  However, the fact that we are now using closed code, or home brewed code, or code that we never review adds another level of uncertainty.

The fact that we worry about such things is not new.  In my senior lab class for physics my professor would not accept anything unless I explained what the computer was doing and verified results.  A major error in software was discover in the lab I worked in `as we compared out results with other labs doing the same work.  This is how science works.

Over the past decade or so there has been an increased realization that we have introduced error into our results not only by unfaithful actors in the research community, but also because our equipment has become so complex, our assumptions so ingrained, that we accept results as valid without verification.  In the work we are starting this week, I see this desire for clarity.  There are many researchers asking what can we really know by looking at the  Photoplethysmogram(PPG) waveform.  I also see manufacturers aggressively hiding the code and data, presenting results of their Pulse Oximeter, presenting the results as accurate with no transparency.

Week 1 in the Ball Lab: Chemistry Boogaloo

Hello all! Welcome to my blog. Okay, so the first week is just about over and what a doozie of a week it has been! Let me give you a little background about myself before we get started.

I got my Baccalaureate in Youth and Family Ministry from Lubbock Christian University back in 2010, and as you can imagine I did not have to take very many hard science courses for that particular degree. In fact I was able to substitute a science course for something completely different, thinking that I would never have a use for it. Boy, was I wrong!

Years later, I decided to teach elementary school math and science. I had to get my alternative teaching certification and struggled a bit at first with the material, but wound up enjoying myself immensely. It’s a bit strange teaching science when you’ve only experienced a laboratory environment in high school so when the RET applications opened up I jumped on the opportunity!

With all that being said, I want you to imagine a pool. One end is the shallow end, where I had been playing with my bright yellow floaties on. The other end is unfathomably deep and filled with grad students and it’s labeled “The Ball Lab”. I decided to jump into the deep end and figure things out as I went along, and it’s been quite the challenge! I’ve learned more about chemistry in the past week than I ever thought I would learn in my lifetime. Dr. Ball has instructed me to observe, and perhaps replicate some experiments for the first week and we will meet and discuss what to do after I’ve absorbed some lessons.

My mentor Katie has been instrumental to my progress, and has been letting me get a great feel for the process of what they do in the laboratory. Her project is to take a surface, and use existing chemistries to covalently bond a one-molecule thick layer of proteins in a predictable and easily replicated way. It’s all still a bit over my head, but I’ve put myself on something of a crash course in chemistry to get caught up and I’m starting to make sense of it all.

If there’s anything that I can take away from this week is that chemistry is sometimes a slow process, involving a lot of experimentation and trying several different things at the same time to see what works and what doesn’t work. I’m also learning that there’s a ton of dead-ends in science, and that those are very informative in that they help you narrow it all down.

First week summary:

Day 1: Learned how to operate atomic force microscopy, how to insert nano tips for scanning which was pain in the neck since I was dealing with a very fragile 0.1 mm silica material.

Then my mentor showed me more lab equipment. We created our first polymer – PDMS which is formed by mixing two materials.

Since the materials are stirred, there are billions of bubbles!

We placed the polymer in a vacuum where it is applied under low pressure to surface bubbles, and then shocked with nitrogen gas to break bubbles, repeated the procedure about 7-10 times to have super smooth surface that will be used under AFM.

Placed in an incubator to speed up curing process whihc will take about 36 hours.

Day 2:  Got a silica glass film, and placed gold pieces at the bottom, super vacuum and high voltage applied to evaporate gold on silica film. Super shiny, nice looking gold mirror created!

Double sided tape can be seen where the clear part was behind the glass and other parts were also coated with gold and titanium.

Took the gold coated glass to atomic dicing machine to create 5 mm by 5 mm pieces that polymers will be placed on this to be analyzed under AFM.

Cleaned these pieces with sulfuric acid to remove all residues, any tiny dust particle will cause fluctuations.

Day 3: Researched about polymers, best mixing ratio, and how & where to buy.

Created two more polymers with the ratio of 9.1./1 and 10.1/1 to see the best result. I did this part on my own!

Yaaayy! 🙂

Everything is super sensitive! 0.1 grams will mess up all!

Vacuumed to pop millions of bubbles and placed in incubator.

Next step is to place our first sample under AFAM and start taking data to be analyzed.

Got some questions answered from Mentors.

We are working on solving different problems and how we are going to attack them. Presentations are tomorrow.

Its only Wednesday and I know I have been at my internship for only 3 days, but I am extremely glad to be here! This program is definitely not like other internships.

As teachers, we usually are the ones that instruct, teach and enhance the minds of students. For the past three days I have been the one learning, taking notes, asking questions, and learning new things! My mentor has been super patient and kind to me and has taken the time to explain the laboratory procedures (which they call protocols) that we will be doing throughout my time in the lab. There are definitely no dull or boring moments. I am either in the lab learning a new procedure or reading/learning more on the research we are helping accomplish.

Everybody at the lab is very helpful and everybody seems to help and learn from each other. This is great because it creates a great atmosphere to be around. I think its awesome that the graduate students at the lab are so willing to take people under them and teach them all about their research. I thought at the beginning that I would be the only “outside” person there, but there are many undergraduate students and high school students learning all the procedures and the importance of the research we are doing.

I am super excited for the weeks to come and at the same time nervous to be able to produce a lesson that relates to the research we are doing.

Over the years, I have learned lots of different computing topics. I have never implemented any digital signal processing. The computing tasks, algorithmic complexity, and data analysis components are all the kind of thing I have done before. But I don’t know very much about human physiology.

This week I have learned about pulse oximeters, photoplethysmography, and human physiology related to the pulse and blood flow.

Here is what I can convey: the simple method for measuring the pulse using emitted light produces a signal that is anything but simple. The data is there, but so are artifacts and sources of noise. The sheer number of environmental and physiological variables makes this task daunting, but lots of great work has been done to attempt to divine the meaning of the signal and the reduction of the noise.

One of the most interesting and upsetting things is how little is known about what causes the waveform seen using photoplethysmography (PPG) and why some areas of the body exhibit bizarre effects when using the technique.

You shine a light onto a body part. Then you measure either the light re-emitted (scattered) off the body part or you measure the light transmitted through the body part. Then you analyze the signal and the noise and look for patterns. Or at least display the waveform (hopefully in real-time) so someone can offer therapeutic advice. A pulse oximeter can be used for this task. So far, I have ignored the capability of this device to read blood oxygen levels.

The hardest part has been getting up to speed on the biology material. The next hardest part has been diving into digital signal processing. But I feel like I have mastered these to a large enough degree to effective learn to process signal data and produce a useful GUI.

Once that task is mastered, the problem will be learning to use multiple pulse oximeter devices simultaneously. ^__^

We’ve started doing background research. We’ve also installed Python in our computers. We think we have solved the problems with the libraries. Tomorrow we should try again to run the collection process.
Musings: I think I want to research how to extract other variables from the wave form data, that can be used to predict health outcomes: Backward wave amplitude (Pb), reflection index (RI), Arterial Velocity Pulse Index (AVI), Brachial Finger Pulse Wave Velocity (BFPWV).

Nanosystems Engineering Research Center for Nanotechnology Enabled Water Treatment (NEWT) is applying nanotechnology to develop transformative and off-grid water treatment systems that both protect human lives and support sustainable economic development. NEWT is an interdisciplinary, multi-institution nanosystems-engineering research center (headquartered at Rice University) whose goal is to facilitate access to clean water almost anywhere in the world by developing efficient modular water treatment systems that are easy to deploy, and that can tap unconventional sources to provide humanitarian water or emergency response. NEWT also develops systems to treat and reuse challenging industrial wastewaters in remote locations, such as oil and gas fields to help energy production be more sustainable and more cost-efficient in regards to its water footprint.

This year NEWT is host 9 Research Experience for Teachers (RET) interns at our partner institutions (RICE, ASU, and UTEP). The goals of the program is for K-12 teachers to engage in current research NEWT research, develop project-based learning (PBL) lessons plans with an emphasis on the engineering design process, and to widely disseminate their research experience and lesson plans.

NEWT interns will share their research experiences over the course of 6-weeks throughout this Blog.

Happy Blogging

-Christina