Who knew that algae could be so cool and yet so gross at the same time?

This week, for the algae component of my research project, I was able to obtain an algae sample from a co-worker. He obtained this sample from Ascarate Park, a water source here in El Paso. The day that I brought it into the lab I felt like the coolest kid at show and tell. The graduate students were both amazed and a bit grossed out by the newest addition to the lab. (This is exactly how Jimmy Sanchez must have felt in the 2^nd grade when his mom let him bring his new puppy to show and tell.) :0) My next steps with the algae is to find an effective way to grow it in the lab. The idea then is to expose the algae to titanium dioxide to see if the algae growth and replication will be inhibited. Now, you may be asking yourself…why? Well, with the thousands of algae species that have been classified so far, there are a number of consequences to algae ranging from rashes, stomach and liver complications, respiratory problems, neurological affects and even death! Not to mention the negative consequences on the organisms that live in water sources polluted by algae.

Until an effective method of cultivating algae in the lab is found, I am currently assisting in an experiment to determine the effectiveness of titanium dioxide (Ti0₂) paint as a tool for purifying water. To date, a number of indicators have been used to identify if the chemical reactions (the formation of ROS: reactive oxygen species) used to identify effective water purification are taking place. So far methyl orange and blue have been used as indicators to test the effectiveness of the paint. An interesting addition to the use of methyl blue and orange is the use of food dyes? Why food dyes you ask? An extension to the application of the titanium dioxide is to coat plastic buckets with the titanium dioxide paint for individuals who do not have access to clean water sources. Then, after the buckets are filled, they can be exposed to sunlight. These individuals will then know when the water is clean based on the absence of the food coloring as its absence indicates that the water purification process is complete.

Below you will see the plates being used for this experiment. Each plate contains dioxide water and food coloring. The plates are then exposed to sunlight with samples taken every 20 minutes for an hour and 20 minutes.

From left to right: control, resin only, 1% Ti0₂, 2.5% Ti0₂, 5% Ti0₂ and 10% Ti0_2.

For the initial red food dye experiment you can see below how the 10% concentration of the Ti0₂ is the most effective but the 5% and the 2.5% concentrations are not lagging too far behind.

From left to right: control, resin only, 1% Ti0₂, 2.5% Ti0₂, 5% Ti0₂ and 10% Ti0_2.

…mind blown.

Until next week my nanopeeps!

:0)

We entered the week full of hope and confidence.  However, life in the lab is sometimes unpredictable. You live, learn, and move on.  Having done all the background research, we had established our plan for the week.  This week’s focus was all about refinement.  We were destined to move forward with leaps and bounds.  Geared with a new instrument, which would allow us to duplicate last year’s work within a few days.  This in itself would be a remarkable feat because we could validate our previous data and finally move on testing our samples via fluorescence.  However, the lab gods had other plans.

Last year’s design utilized TiO₂ solutions which had nanoparticles that averaged about 70nm in diameter.  One of the complications was each particle varied in size, thus producing some discrepancies.  In order to mitigate the variances, this year we would have two standardized nanoparticles TiO₂.  One being 18nm rutile and the other 30nm anatase.

We commenced the analysis by creating the two different colloid suspensions using the two different sizes of TiO₂.  Both solutions had approximately 1.6mg of their respective nanoparticle and 40mL of water, which were dispensed into two separate 50mL centrifuge tubes.  The two samples were then placed in a sonicator.  A sonicator applies sound energy to agitate the particles throughout the solution.  After sonication, the samples were allowed to rest for a day in order to evaluate their suspension. Day one was a success!!!!

Nonetheless, 24hrs later a good percentage of the TiO₂ remained in suspension with a small amount of precipitate observed at the base of both test tubes.  This was a delightful sign because last year a good amount of the particles did precipitate to the bottom of the tubes, which posed a major challenge when conducting further studies.

The following day came upon us.  Both my mentor and I knew this day would be critical.  We aspired to measure the zeta potential of both solutions at different pH’s.  The zeta potential is the potential difference (measured in mV) between the dispersed particle and the surrounding fluid.  The zeta potential measurement is key in determining the stability of a colloid in solution.

Meaning if the solution has an optimal zeta potential then there is an elevated resistance to aggregation (which is what we are looking for).  In regards to our nanoparticle solution, which is a small colloid, then a high zeta potential (+ or -) measurement shows an excellent resistance to aggregate.   On the other hand, small colloids with a low zeta potential tend to coagulate or precipitate out of solution.

We went ahead and proceeded to assess the zeta potentials of both the 18nm and 30nm TiO₂ in water and at different pHs in order to determine our next plan of action.

I carried this task out manually last year, which was time consuming, tedious, and took up most of my time in the lab.  This time around we were prepared with a titration instrument, which is linked to a zeta potential analyzer.  This instrument would complete 3-4 days worth of work into just several hours.  However, this would not be the case.

We attempted 3 trials and did not attain the results we were hoping to observe.  We had many difficulties with the titration of the acid and base solutions in order to reach our target pHs.  The instrument would not properly adjust the pH as we had set into the parameters.

Yet, this is what the research is all about.  A problem arises, you solve the problem, then move on to the next.   We spent two days troubleshooting and to no avail.  We are hoping this Monday that we can get through our obstruction and continue as planned.  Will keep you all posted!!!

This week I learned how we will be fabricating our membrane. Last week, I described how we want a membrane that has hierarchical roughness. Which means it will have an inner core with pores and an outer core with even larger pores. Like this 

So the method we will be using is called electrospinning. It is a technique that can create fibers with diameters as small as a few nanometers. You can really see how small the fibers are in comparison to a human hair below.

To gain an understanding of the process I read a review article about all the possibilities of electrospinning which include optoelectronics, sensor technology, catalysis, filtration, and medicine.    Well the setup seems quite simple, but there are several variables that can be manipulated  to change  the product made.

There is not a protocol yet for what he wants to accomplish so we are meshing together the procedures from a few articles on electrospinning polyvinylidene flouride (PVDF) membranes. So my mentor and I set out on an engineering adventure with a scientific article in hand to attempt to bring his plan to life.

This is how I would sum it.

Step 1.

Create a solution of  whatever you want your fibers to be composed of. In our case it is a PVDF solution. We are using this polymer because of its resistance to harsh chemicals. It took 2 days just to prepare the solution! We will be testing several variables and the concentration of the PVDF solution is one those. We prepared a 15% and a 10% solution.

Step 2.

Place your polymer solution in a syringe that is placed in an automatic pump. Set up the electricity. We set our electric field at 20  kV or 20,000 volts. The applied voltage causes the solution to be pulled from the positive to negative electrode. As you increase the voltage the shape of the polymer will change from a cone to a jet and cause your product to change.

Step 3.

Start the pump and when you see the solution exiting the nozzle of your syringe turn on the electricity. Watch and wait for your fibers to collect. The spinning process took about 3 hours total for 3 ml of solution.

Like I said the process seems very simple, but is very complex due to all of the variables that can be manipulated. The distance the nozzle is from the collecting plate, the humidity, the rate of the pump, the size of the syringe, the electric field all play a major role in the fiber formation.

Next,  we will use the Scanning Electron Microscope (SEM) to take images of our membranes to compare the two solution fibers.

We will also be trained on a special elctrospinning set up that will allow us to take control of many of the variable mentioned before.

This week I have learned to importance of the doing background research because we have had to rely heavily on the work of others. I have also learned the importance of my engineering notebook. Everything we do is recorded in the notebook and will not only help us but serve as a guide to others.  This experience has given me a concrete experience, so I can better teach my students the engineering process.

One of the things I try to always remind my students of when they are working on their research project is that you don’t always get the results you want and that’s okay. You often learn better from a failure than a success and I was reminded of that this week.

In my journey to learn about how silver nanoparticles remove bromide from water, I have also learned a lot about what it is like to be an engineer. This week we tried to run the column with the Granular Activated Carbon (GAC) that we are testing to see which GAC that was impregnated with silver nanoparticles worked the best. After loading all of my mini column with the GAC to our desired 8 in. mark, I tried running water through, but I could not get water to run through any columns. This is where the engineering came in and we had to figure out why.

We loaded our control GAC that didn’t have nanoparticles in the column one pipet (1 mL) full at a time and run the water. We repeated this until we could not get sufficient flow of water. We determined that it took 3 pipets full of GAC to a height of 2 inches to get 5 mL of flow at a low pressure. I loaded the other 5 columns with the silver impregnanted GAC the exact same way as our control and tried to get water to flow. We tested 2 commercial GAC, 2 GACs that were made by Clemsen University, and Zeolte (no silver nanoparticles were on the Zeolite). The two new GACs from Clemsen would not work during my runs and the rest of the columns did.

I decided to pipet the GACs into a 15mL conical tube to see if the amount laded was the same for each. I noticd that the GAC from Clemsen was lower than the rest of the GACs. Based off of this, my goal for the beginning of nest week will be to try and figure out why the Clemsen GAC is acting differently from the rest and figure out what it’s flow capacity is.

My lesson is coming along with great ideas about what materials the students could add to their column to try to remove glucose from water.

Have a good week everyone!

-Taylor

It is useful to approach a topic with which one is generally unfamiliar, or even  not generally interested in, such as  has occurred this summer.  I was trained in in science and research, but rebelled by studying physics instead of biology or medicine like much of my family.  Engaging in the opportunity to study the medical topics is provides not only valuable learning, but also a connection to the difficulty of my students who often are expected to engage with topics they may be uninterested in, often will much less background and opportunity.

In particular, the jargon for a particular topic can be jarring, not only new words but also refining the definition of existing words.  For instance, in physics we have to refine the definition of words such as heat, work, and especially temperature.  As an aside, this is why the overuse of sites such vocabulary.com worries me.  Sometimes words are not context sensitive, especially in math and science and computer science, and implying that some words can have more than one definition can be harmful.

In the current research, the jargon is extensive.  Words such as Dicrotic Notch and Diastolic Peak are unfamiliar and complex.  The methods and data needed to calculate each can be equally complex, not only to understand, but also to derive and gather.  One item I was told to focus on in the new year was to provide more scaffolding for students to help them in the problem solving process.

One thing I have learned over the past two weeks is that the various tools I have picked up over the years allows me to break up complex problems into small pieces, then put those pieces back together into a overall solution.  I can eliminate extraneous information for the current step, then put it back if I need to later on.  I can adjust my thinking to the current rules, like the fact that gol has no ‘a’, so that we can efficiently approach the problem at hand.

Duplicated making polymer and peptide with mentor. Now that supplies are more available, I starting making hydrogels of varied concentrations of polymer and peptide. First polymer hydrogel was too fluid to gel so to crosslink into gel. Next week will try a higher concentration of polymer. Did have success with the concentrations of K2 peptide hydrogels.  Met mentor on Saturday to run two of my peptide hydrogels on the Rheometer.  I even managed to take a one hour PD course online while data was being acquired. Next week will be busy as I am getting more independent with preparing hydrogels and running Rheometer. next week  I have to learn how to analyze data. z

Hi there,

I’m finding that coding is fun when the time into learning and trying to “crack the code” are invested. As I move through modules and units, each task has a particular code that needs precision and accuracy in order to “crack” it. Running code successfully makes me do a joyful shoulder bounce or “happy dance.”

Julius Emanuel

This week I have been learning how to do mini preps (plasmid purification)  independently. The process includes lots of pippetting, centrifuging many buffers that serve different purposes, but in the end help to purify our plasmid product. After the plasmid is purified, the concentration of nucleic acid in the sample is measured using a Nanodrop machine. Once this is completed, the sample is ready to be sent off for sequencing. This sequencing allows us to identify into which sites the plasmid has incorporated our non canonical amino acid (ncAA)  mutation.  Once those sites are known and isolated, it allows us to plate plasmid containing bacterial colonies with a single site mutation at different temperatures.  I must say, I love being in the lab and getting the privilege to play even a small part in this work because its broader implications could be massive, and the work is equally as fascinating as it is challenging.

The first photo below shows an apparatus that is hooked up to a vacuum where wash buffers are used for the plasmid purification. And the second picture shows the Nanodrop machine.

A series of if/elif statements or a fairly complicated if conditional?

For this program, I decided to go the first route. I decided it gives clarity to the code. The interesting point, and why this is making it into a blog, is that I have encountered actual discussions on the Pythonicity of different codes. That cracked me up.

I am working on improving my Python literacy. I am getting there.

We also  had good discussions on what the week with students will look like. Engaging and Inspiring is our goal.

I am really happy with the people in my group. We are good peeps.

MEETING TIME

We have weekly meetings to share what we have accomplished and to help give feedback to the other people in our lab.  I was able to say “I learned what nanotubes are and I started working on the aqueous two phase extraction except, I have not had success.” The follow up questions helped me to realize that the polymers that I am using come in different molecular weights. These molecular weights  indicate how large the polymer is. The larger the molecular weight the bigger the polymer is and the harder for the single walled carbon nanotubes (SWCNTs) to move in that solution. I think of it like trying to swim through water (low molecular weight) compared to trying to swim through through honey (big molecular weight).

Aqueous two phase extraction (ATPE) relies on the movement of SWCNT between the top phase (layer) and bottom phase (layer) to create a separation of SWCNTs. My large molecular weight of the bottom phase was preventing any SWCNT from moving into the bottom phase to separate from the top phase. This means I was not extracting a specific group of SWCNTs.

TIME TO WORK

I decided to run the same protocol but with the molecular weight of the polymers indicated in various articles. I also created a more concentrated solution of SWCNTs in a 2% sodium cholate solution.

Much to the relief of the undergraduate whose protocol I have been using.  Success! A “blue” top phase and “red/brown” bottom phase.

Riding my high horse I showed my sample to my mentor. She reminded me that just because the appearance seems right doesn’t mean that I have the correct result. Time to go get some data using the spectroscopy machine. Also, how cool is it that the professor in charge of the lab works on creating this machine! I analyzed my data with the help of the undergraduate student in the lab. It looks like I am doing an “okay” job of separating the semi-metallic SWCNT but not a great job of separating the metallic SWCNT.

Time to problem solve: I was probably extracting the bottom phase incorrectly getting part of the interphase with the bottom phase, my TCCA might have decomposed or be the wrong concentration necessary, the pH could have changed, or the solutions were not properly “mixed” before using the centrifuge.

After you problem solve you jump back in and try it again. It is important to have multiple successful trials before making conclusions and moving on.

HIGHLIGHTS

• I created a carbon nanotube dispersion on my own
• Independently I was able to correctly identify the solute and the molecular weight to create stock solutions
• I used articles to inform decisions
• I asked questions to clarify how to read the spectroscopy data
• I had some success and failures using the EXACT same protocol