I spent a lot of time catching up on my chemistry last week, and this week has been less observation and more making things helpful to our lab. My mentor has kept me busy and has been walking me through the math to make 50 Millimolar solutions to use in our reactions. Now I’ll be able to tell my students who complain about doing math during science that the two are one and the same, and give some great examples. Maybe it will inspire some of them to take math more seriously!
Making 50Mm Solutions
I was also given the task to study up on a process called “contact angle”, which is used to measure the angle of water droplets on a surface. We use it in the lab to see if some of our modifications have taken to that surface. Our lab uses a boronic acid modification that should change the angle of a water droplet when put onto whatever surface we’ve modified, so we have been doing quite a bit of experiments that involve the contact angle machine. So far our results haven’t been what we have wanted, but the testing continues.
My mentor Katie helped found a program called “Fun with Science” for younger students that visit Rice University. They get to see some of the more dramatic chemical reactions and changes that chemistry is capable of. She let me come to the show to take some pictures and get a few ideas that might benefit my school, and I got to see some fun chemical reactions as well! Students get really excited about chemistry when they see how fun it can be.
Elephant Toothpaste is always a hit
Yesterday while Katie was off in meetings, I made my way to the Library and read up on contact angle and spent quite a lot of time searching the stacks for some good books. I found quite a few and read up on the history and math involved with contact angle as well as how to properly implement the procedures involved. Hopefully all that study will come in handy next week as we dive even deeper into our project! I believe that we are making some good progress, and I’m excited to see what next week brings.
In my lab we are working with a virus called AAV9. They are currently using as a vector for gene therapy, specifically to the heart. The virus is currently able to identify inflammation but the goal is to make it specific to a cell. To do this, my mentor is working with adding locks that will allow for the virus to only attach to a specific type of cell. This is very challenging and there are many steps to the process- from the creation of a virus with specific locks to the actual delivery of the virus- in vitro or in vivo.
My job in the lab currently involves keeping my HEK 293T cells alive- this involves splitting the cells: lifting them, changing them to another plate and adding new media to keep them happy. This is the one process that I feel very comfortable doing by myself and my mentor has trusted me to do it already about 3 times without his supervision.. yay! The rest of the time my mentor has been teaching me new protocols with the end goal of being able to make virus! Last week we started by preparing the backbone and the inserts that we wanted in our plasmid. Once the plasmid is ready, we utilize it to transform E. coli. We then send our E.coli samples to a company that is in charge of sequencing them and checks to see if the bacteria did indeed take in the plasmid. We sent in 8 samples and 4 out of the 8 were great! This allowed us to go on to what we have been working on this week- Maxi Prepping our DNA.
A Maxi Prep works as follows: Making large amounts of bacteria, spinning down the bacteria to a pellet –> lysing the bacteria to release DNA and protein –> precipitating the protein –> get rid of the protein and load DNA solution onto column that can capture DNA –> elute DNA and precipitate DNA –> pellet DNA and redissolve DNA.
What you see there inside the bottle is the pellet which is part of the first step in a Maxi Prep- I love pipetting but never have I had to spend a good 3 -5 minutes trying to re-suspend pellets– My thumb is definitely getting muscular! After that all the steps to follow involve cleaning the DNA because we want to make sure that we don’t have any cell debris or RNA in our final products. The pictures below show some of the cleaning/precipitation steps used in cleaning DNA. Picture on the left has a layer of gel, DNA and phenol/chloroform/isoamyl alcohol, After spinning them, the layers rearrange as the picture on the right with the layer of the phenol/chloroform/isoamyl alcohol on the bottom, gel and then the DNA on top which is what we will extract.
After all the cleaning and precipitation steps are done we will carry out a gel to see if we have clean DNA we can then use for our virus!
This video compares the signal between 2 type of PPG. Read on for lots of details!
Circuit Playground Express with LED 1 at max brightness
This week, I have been tinkering with 3 different ways to read ones pulse. This technique is called photoplethysmography. Light is emitted into tissue with a capillary bed not far from the skin surface. One can measure how much light passes through the skin or how much light is reflected. Both type of photoplethysmography, transmissive and reflective, have pros and cons. Transmissive signals can provide information about blood oxygen content more accurately than reflective signals. But for digital signal processing (DSP) which is what I am after, they both work very well. The signal or pulse is called the photoplethysmogram or PPG. I want to display the signal in real time. Perhaps even provide some analysis of pulmonary physiological parameters such as heart rate variability or inter-beat interval.
FISCHER et al.: ALGORITHM FOR REAL-TIME PULSE WAVEFORM SEGMENTATION AND ARTIFACT DETECTION IN PPG (waveform from pulse oximeter)
A quick search on your favorite store or search engine will show you plenty of inexpensive, reliable home pulse oximeters (finger-in, transmissive photoplethysmographs.
Pulse Oximeter
But if the user wants access to the actual data without using a propriety software package, they are out of luck unless they find a way to crack the transmission protocol. I happen to have access to pulse-ox where the protocol has been cracked and the signal can be accessed directly. But if I want to share what I am doing with students, I feel like they should have access to the hardware and software information without fear of violating someone copyright. There are several different types of open hardware pulse sensors. Today I am going to compare a “raw” PPG to one provided by one of these open hardware sensors. I decided to use the Adafruit Circuit Playground Express as the platform for the “firmware”. This way, I can use both the on-board light sensor and the nearest LED to that sensor as one type of pulse sensor. I also added the Pulse Sensor Amped to the circuit as well. Then I plotted the PPG from both sensors on to one plot using the serial plotter in the Arduino IDE.
Code to take data from 2 sensors and plot them together.Pulse signal from 2 sources plotted simultaneously
The Pulse Sensor Amped circuit has some built-in filtering to ignore the so-called “DC” component of the signal. This low frequency signal is not useful for health purposes. The red signal has the DC component filtered out (and the AC component amplified too) whereas the blue signal which is the unfiltered signal directly from the light sensor built in the board is smaller and shows a secondary trend beyond the higher frequency pulse signal.
I began my research experience in the Alvarez lab last week, and I have already learned so many amazing things about research, nanotechnology, and the future of medicine. In the Alvarez lab, we are conducting research to develop bacteriophages that can effectively disrupt the biofilms that form on membranes in water treatment plants. This research is positively fascinating to me, especially since it has the potential to have broad-reaching applications far beyond the original intent of improving water treatment. While I have certainly learned a lot about the scientific content relating to my research, my biggest takeaways this past week were that I gained:
Confidence in my laboratory skills
Creative ideas for a maker activity for my biology class
Connections for my students & new considerations for my future
Confidence in my laboratory skills
On my second day in lab, my mentor introduced me to a multi-step protocol for measuring the effectiveness of the adsorption of viruses to their bacterial hosts. In reading the protocol on my own first, I felt a bit confused about a few parts but for the most part I felt excited to try something new. My mentor walked me through the procedure completely, and I was sure to take notes the whole time I was shadowing him. Once we reached the end, he turned to me and said, “Now that you know how to do it, why don’t you go teach your labmate so that he can know how to do it?” I felt my heart stop for a split second, uncertainty filling my brain. Then I chuckled to myself because I thought maybe he was kidding. Nope. He brings over my labmate and tells him that I will teach him how to do the protocol. The smile left over from my chuckle disappeared and I’m sure I looked white as a ghost. About one-hundred “what ifs” flooded my brain. What if I mess everything up? What if I ruin the experiment? What if I teach him incorrectly and then all of his subsequent experiments will be wasted? But all of the “what ifs” ended once I said to myself, “What if this means that he truly trusts you and believes in your ability to do it?” I held on to this thought, that my mentor must believe in me to give me this task, and I guided my labmate through the process. Were there still times that I needed to go over to my mentor to ask for clarification? Yes. Were there still times I felt uncertain? Of course. But I pushed through it and ultimately the experiment came out as a success. This experience truly helped me grow in my confidence in ways that wouldn’t have been possible had I not been given this chance. Anytime I feel uncertain or down on myself in the future, I know I can look back on this and think, “Laurel, if you could teach a lab protocol on your second day in lab, then you can do this.”
Creative Ideas for My Classroom
Since my blog post is already growing a bit long, I will save the details of my ideas for a future post; however, what I will say here is that I have loved reading the scientific literature from my lab and have already developed a few ideas for how I can use the concepts in my biology class. Since I am working with bacteria and viruses, there are clear applications to the viruses and bacteria unit. We can discuss how viruses infect cells using surface proteins that attach to cell receptors, and my mentor mentioned how I can use this as an opportunity to mention helpful viruses whenever we are discussing helpful vs harmful bacteria. Yet, the ideas that I am most excited about are the ones that model natural selection. In my lab, there are a couple clear instances of this. First, when preparing the magnetic nanoparticles, they isolate the most magnetic ones by exposing the solution to a magnet and removing all of the particles that stay suspended in solution rather than moving towards the magnet. After a couple rounds of washing the particles in this way, you will be left with only the most magnetic of the particles. Second, and perhaps most interesting in my opinion, my lab isolates polyvalent phages (viruses that can infect multiple strains of bacteria) through a process similar to natural selection. By sequentially exposing the phages to different hosts, you are ultimately left with only the phages that have the ability to infect all of the hosts. I will go into more detail about how I will model this in a future post.
Connections & New Considerations
My mentor has been truly amazing in helping me learn more about this research, and one of the ways he has helped me was by inviting me to a symposium on Friday. This symposium was not about water, but about combatting antibiotic resistant organisms in the gut, specifically C. diff bacteria. I am a huge nerd, so I absolutely love museums and conferences and symposiums of any kind, and this one was especially important to me as my grandfather passed away following complications with a C. diff bacterial infection. All of the talks were fascinating and exposed me to a wide variety of perspectives on the topic from pharmaceuticals in development to the biochemistry of antibiotic resistance to bioinformatics being used to predict how an individual’s gut microbiome may respond to certain antibiotics. While at this conference, I had the pleasure of meeting many fascinating and intelligent people whom I learned from. A couple of these people even offered to look into the possibility of visiting my school or having some of my students conduct research with them. I am really excited to see where these connections lead for my students. Additionally, this experience as a whole has made me consider perhaps earning a masters in biology sometime in the future. I had truly forgotten how much I love learning about science and conducting scientific research myself. I am looking forward to continuing to learn more this summer, and I will be sure to update you more on my lesson plan in the next post.
“Water, water everywhere and nor a drop to drink.” —-The Rime of the Ancient Mariner, by Samuel Taylor Coleridge
Wow! What a crazy first week! I hit the ground running with Dr. Caroline Masciello here in the Keith-Weiss Geological Laboratories. My situation seems to be a bit different in that I don’t have a mentor – which is actually ok. I’ve been working directly with Dr. Masciello and her colleague, Dr. Mark Torres. The very first day of research she was kind enough to sit with me one on one in her office to explain what it is she actually researches. She cleared her desk, whipped out a dry erase marker, and starting writing feverishly as she explained the Nitrogen Cycle and how this relates to her research.
Dr. Masciello’s notes on the Nitrogen Cycle
The whole time she was talking I was thinking I should be taking notes, right? Well, her explanation was so enthralling and I kept relating it to the case study we did in our orientation about the farmer and the DDT, I kept asking questions and she kept answering and continued explaining, and we were having the best time for almost two hours… and I didn’t take one note! So I snapped a picture instead before she erased it all off of her desk. Luckily, I was assigned an office in her building, and as soon as I got settled I rewrote notes based on this picture and her explanation.
Trying to understand the Nitrogen cycle
She also sent me several websites to read through in order for me to build my background into the research. Soon after our first meeting, she introduced me to her colleague, Dr. Mark Torres. They are working together on a project to test the waters of Buffalo and White Oaks Bayous. He gave me a tour of his lab and the amazing equipment inside. Unfortunately, I will not be working the equipment as it takes a lot of study and training in how to use them, but it is ok because that’s where Solana comes in. She is a rising Junior here at Rice and was hired to help Dr. Masciello and Dr. Torres with collecting, testing, and dissemination of data from the water samples of Buffalo and White Bayou. Each week, the four of us will meet here on campus bright and early on Fridays and then go together to collect water samples from three different locations: Buffalo Bayou, White Bayou, and Allen’s Landing (a point south of both bayous where they converge). On site, we will use equipment to test for some things (I’m still learning this part) but when Solana brings the samples back to the lab, I will get to observe as she uses the equipment to get detailed readings of Chloride, Nitrate, Sulfate, and Phosphates.
The second meeting with Dr. Masciello and Dr. Torres led to more notes (see below) and I had an Aha! moment while Dr. Masciello was talking. Through lots of reading and digging, I’m learning that the lack of oxygen causes the nitrification process to go crazy. As I was explaining that my goal was to figure out how to interpret all of this research and take it to kids in a way they understand, she said, “I just wish teachers could help kids to truly understand the importance of oxygen in water!” I told her, “Stop! Don’t stay anything else. I’m writing that down!” I did and I’ve looked at that in my notes this past week a million times thinking surely that is how my lesson will evolve. I’m not a 100% certain, but I do feel like it’s the beginning of an idea for my lesson plan.
More of Dr. Masciello’s notes about how oxygen and lack of plays into the nitrogen cycle.
My main assignment from Dr. Masciello is to research and dig up raw data on water samples from water sources around the Houston area (in particular Buffalo and White Bayous). With that raw data, she would like me to compile a spreadsheet of sorts for her to begin adding to as she collects her samples and tests them. Looking at reports is not easy because the raw data is not always given, so part of my job is to call, email, or contact in some way the authors of the reports to request the raw data. My time has been spent doing two main things: 1. researching to learn about the nitrogen cycle and what excessive levels of nitrates, phosphates, chlorides, and sulfates to do the environment as well as 2. reading through reports and digging up raw data. As I teeter between the two, I found myself asking lots of my own curious questions. I finally broke down and started a list which I’ve pinned to the board in my office. My hope is that through this experience, I will not only help Dr. Masciello in her research, but I’ll answer my own burning questions as well.
So many of my own questions!
I’m excited to be working with Dr. Masciello, Dr. Torres, and Solana. We will not only go out into the field to collect samples, we have discussed going on some field trips together to a few places such as Texas A&M Galveston, the Buffalo Bayou Cisterns, and maybe even to the San Jacinto River Authority on Lake Conroe (it doesn’t hurt that I have a boat and can take everyone out on the lake to the SJRA location). If you are interested in touring the cistern, it’s open to the public. Here’s the link: https://tinyurl.com/ybzux2qs
The Buffalo Bayou Cistern
An added bonus is the Tuesday luncheons hosted by Dr. Masciello. It’s pizza and a presentation from graduate students to an audience of undergraduate students. We get to hear about the field experience of graduate students and how it is they are putting their degrees in geology to good use. Check out this link to read about last week’s presentation from Andrew Moodie. He shared his research experience from the northeast coast of China. The article is actually written by his fellow researcher, Brandee Carlson, but they worked together. https://tinyurl.com/y8qmsvlb
China research article from the Rice magazine called “Outcroppings”
I’ve lived in the Houston area for close to 40 years. I’m fascinated with Texas History as it is one of the subjects I happen to teach. Being part of RET is going to be an amazing opportunity for me as a teacher to connect the dots for my students –from the early beginnings of the Houston area and the reliance on Buffalo Bayou as a major resource to the science behind why it is important we treat the water in certain ways so as to not pollute the water of today’s bayous. Even though we no longer rely on it as a drinking source, the bayous are a major part of our history and continue to impact our environment. Knowing what’s flowing downstream into the Galveston Bay and beyond because of what we are allowing to enter into the water is important information for everyone to know so we are making decisions that will not harm our amazing ecosystems.
The first week is down and not let the fun begin. It just happened that my mentor was out for most of the week. I was tasked to read several articles to get a grasp of what we will do these next few weeks and see how I will apply this to my lesson.
We will be attempting to develop a novel Titanium Dioxide detection protocol. This analytical technique uses organic ligands/chelates, which will associate with Nano-TiO2 in solution to form a molecular chelate complex. The formation of this chelate complex should display a shift or change in absorbance/fluorescence. This change will then be measured by the following instrument. This is a CUV-ALL-UV spectrometer and will be my best friend for the upcoming two weeks.
Once the organic chelate with best suspension stability is found then different manufactured water samples (brackish, freshwater, groundwater, oil and gas water, etc.) will be utilized to test the validity of this novel method.
Additionally, (time permitting of course) we will apply the new method with two different types of TiO2 nanoparticles: 18nm rutile and 30nm anatase. Although the plan for this model is in its early stages it is beginning to display great promise based on last year’s research. However, we all know that things in the lab are unpredictable, so with an open heart and an open mind, I enter our great adventure willing and ready to rock this summer.
Howdy! My name is Krystle Dunn and I am completing the Nanotechnology-Enabled Water Treatment System (NEWT) Summer Research Experience for Teachers (RET) program. The vision of NEWT is to ensure water access anywhere in the entire universe! The project that I am working on will help recycle water from astronaut urine, so that they have potable water for drinking, hygiene, and oxygen generation in space.
This week I feel like have been immersed in an intense 5 E Lesson Plan. So far, I have been engaged by reading article to build knowledge and expectations, exploring and receiving explanations when shadowing and working with mentors.
This first week I have completed a lot of background research to just wrap my head around the concepts and the problem that we are trying to solve. In space membrane distillation is the method for treating concentrated urine, but membrane scaling and fouling is a problem. So, the membranes get dirty with minerals and bacteria and need to be replaced sooner than expected. I am working in the Qilin Li Lab and her lab focuses on creating many types of membranes for water purification and keeping those membranes clean.
My mentor, Seth Pedersen’s goals is to create a membrane with low surface energy and hierarchical roughness(increased surface area) that that will make the membrane superhydrophobic. They will look similar to the images below.
The membranes we fabricate will look similar to these.
After the membrane is made we will coat it with silver nanoparticles to increase the roughness and then coat it with 1-dodecanetiol which will make the membrane more hydrophobic. The idea is very similar to the nano waterproofing activity we completed during our RET orientation.
Here is a breakdown of my week. (Engage, Explore, and Explain)
Day 1-3
There are several undergrad, grad, and postdoc students that work in the Li lab.I was introduced to another project that is taking place in the Li lab while my mentor attended and presented at a conference on membranes. I was able to work with Suping Yu who specializes in inhibiting and understanding the growth of biofilms on membranes. She does this by cultivating the bacteria and then she compares the genetics of normal strain and antibiotic resistant bacteria.
Biofilm cultivation of bacteria without antibiotic treatment and antibiotic resistant bacteria with treatment
Day 4
I was able to use the scanning electron microscope (SEM) with Seth and get images of the commercial membranes that he is currently using.
An SEM image of a commercial PVDV nanofiber membrane with biofilm fouling
Day 5
I attended the labs group meeting and heard updates on other projects that are taking place in the lab. I attended a meeting to determine the best practices for collecting urine on campus. I also helped with the modifications of the module that houses the membrane during the Membrane Distillation experiment.
Modifying the module or membrane chamber for the membrane distillation setup
I look forward to the upcoming weeks (Elaborate and Evaluate)
We will be ordering parts and chemicals to create our membrane and be trained on electrospinning (the process we will use to create our unique membranes) and begin creating the membranes. I will also narrow down my options for a lesson plan to bring back to school.
I have never used social media especially blogging about research. It was strictly prohibited so this is something new. I did enjoy reading everyone’s posts! I am in a lab that is researching polymers that can house cells. Most of the researchers are bioengineering graduate students. There are also two Rice University undergraduate students. I attended two lab meetings : The Collagen Group & the Polymer Group. I also attended their lab’s journal club meeting. As far as experiments … next week will be a repeat of last week … we will synthesize more peptides using the FMOC method (first picture) and prepare polymers (second picture). The content of the peptide will be determined using Mass Spectrometry. The polymer will be tested using a Rheometer. I just had a learning “experience” with blogging as site did not want to load the pictures of the equipment … likely because I cut the picture from my PowerPoint. Click here to see the Mass Spec and Rheometer … Equipment-2li5byu
My first week as a R-STEM RET intern has been an eye opening experience. Though this week was a lot of training, I enjoyed getting to know my mentor and the bits of what I am researching. For my research I am working with fruit flies and manipulating their environments and then isolating the mothers, fathers, and siblings. My hypothesis that the second born sibling will be more “bold”, which means they are more prone enter the new environment quicker than the other siblings.
The first day was definitely a mess. I got lost, nearly fell of my bike, and cracked my phone screen. Once I got to my lab it was a breath of relief. My mentor is such an inspirational person. She is so patient with me and is always ready to answer any questions I have. I learned how to make fly food from scratch and pour them into 32 petri dishes. After that I did a practice run of emergence trials.
The second and third day I “extended” the fly racks. Which means I make new subcultures and throw away old ones, so we will always have a sufficient amount of flies to work with. I then “cleared” 4 rows on 5 racks so I can have brand new flies to work with, since age will be a factor in my research.
The fourth day I began my experiment, I collected mothers from four different genotypes and then fathers from one genotype. Sadly there were not enough fathers for my mothers. I sat around and waited 2 hours for the flies to emerge. I ended up not collecting enough, but it was more for my back up vials.
The fifth day, my mentor gave me scientific papers to read so I could understand more of what my research was related to.
I definitely respect researchers, because what they do is to meticulous and you have to make your own protocols. You cannot follow a cook book recipe and that is probably what my students want to do when I ask them to do inquiry work. This experience so far is very humbling and I am so happy I’m here! I do however wish I didn’t crack my phone screen…
K-12 Educators Disseminating Research from Rice University, Arizona State University, and University of Texas-El Paso
