Fighting Antibiotic-Resistant Bacteria With Viruses

Bacteria. The single-celled organisms responsible for a range of diseases from food poisoning to the bubonic plague. Modern medicine, especially antibiotics, has allowed us to survive these bacterial diseases. Unfortunately, antibiotics are not working as well as they used to because bacteria are getting better at getting us sick.

The growing problem with using antibiotics, which are the first line of defense against infections, is that bacteria are becoming resistant to antibiotics. Due to the growing prevalence of pathogenic diseases, scientists are scrambling to come up with alternatives to diagnose and treat bacterial infections and diseases.

Undergraduate researcher, Colin Kim, is familiar with this problem, and he is working to help solve it. As a researcher under Chemistry Professor Irene Chen, Kim studies bacteriophages, viruses that infect bacteria. Although there are more bacteriophages on Earth than there are bacteria, the vast majority are uncharacterized. The Chen group aims to characterize bacteriophages so that they can be engineered to treat bacterial infections.

A typical wound contains a diverse community of microorganisms, and the Chen group hypothesizes that it contains bacteriophages. In order to figure out the different types of bacteriophages, you first need a way to collect them. Last summer, Kim helped develop a method of swabbing human skin to collect bacteriophages and determine the amount of bacteriophage present.

Kim is currently collaborating with researchers to develop a diagnostic tool to detect specific types of bacteria. Because bacteriophages have a high affinity for the types of bacteria they infect, researchers can chemically modify the bacteriophage protein coat so that the bacteriophage will fluoresce, or glow, when it binds to bacteria.

Kim uses the bacteriophage M13, which is well-studied and has a strong affinity for E. Coli. By modifying different parts of the M13 protein coat, researchers can make it have a high affinity for a different bacteria such as Methicillin-Resistant Staphlococcus aureus (MRSA), a pathogenic bacteria that is resistant to higher order antibiotics.

Studying bacteriophages may lead to new developments in how we treat bacterial infections and diseases.

The End of a Run

Wow! As this summer program comes to an end, I am exhausted…

Not the overwhelmingly sleep-deprived exhaustion. But instead, the kind of exhaustion that shows that you have accomplished something—like being out of breath after running.

At the end of a run, you know that you have earned not only the tiredness and soreness, but also the strength that ensues. So as I gear up to sprint the last couple of weeks of the MARC summer program, I know that I will be even more exhausted than I am now. But I also know that there is a great reward waiting for me on the other side of the finish line. I have struggled in workshops to improve my writing and presenting and labored in lab to develop my technique and skills. But there is satisfaction in knowing that you have challenged yourself, struggling through new obstacles and emerging stronger and wiser than before. There is fulfillment that comes with presenting work that you have invested time in and believe in. And there is gratification that comes with knowing you have worked on research that has helped not only your growth, but could also potentially benefit many others.

However, as I run my course, I am not alone. I have met second years that hold so much promise, my fellow third years that have offered encouragement as we run similar courses, and fourth years that are looking ahead to bright futures. As we run along side one another, my peers have seen me struggle when my stride faltered but have only given me positive support to continue. They have provided me with laughs to distract from my labored breathing telling me to slow. To sum it up, they have been pretty awesome!

So if you are looking at the CSEP programs and wondering if all the hard work is worth it… it is. The opportunities that these programs give you are so unique, and only a small group of undergrads gets to experience them each year. From workshops on conferences and graduate school to dinners with experienced scientists from academia and industry, there is always something new to learn, and there is always someone new to meet. So, if you are like me, you may be exhausted, but the soreness just means that you are getting stronger.

Developing Undergraduate Research Skills Outside of a Laboratory

As I’ve been working in my lab – making new bacterial culture media/buffers, running DNA extractions of bacteriophages, and compiling qPCR data for analysis – I realized that the tasks in lab are very similar to what we do on a daily basis. Whether you are already working as an undergraduate researcher, or if you are hoping to get started, here are some research skills and techniques you could develop outside of the lab as part of your daily routine!

Colin is currently about to enter his third-year working in the Chen Lab

About to enter my third-year working in the Chen Group!

 

  • Cooking

As a college student, cooking is one of the biggest tasks on my daily ‘to-do’ list. Even though eating at local food stores saves time and effort, I enjoy cooking. Cooking is an awesome opportunity for you to develop your research skills!

Cooking recipe for spicy chicken breasts –

Cooking recipe for spicy chicken breast

Protocols to make PBS buffer, LB, TB, 2xYT, and SB bacterial culture medium

Protocols to make PBS buffer, LB, TB, 2xYT, and SB bacterial culture medium

The way I run experiments in my lab is extremely similar to the way I cook at home. For example, the first time I cooked chicken breasts, I gathered all the ingredients and tools and followed the recipe carefully – exactly the same as following the protocol for extracting viral DNA from my bacteriophage samples. I did not succeed at either on the very first try, but I didn’t give up. It took a couple of failures to make the experiment work – just like it took a few tries for me to get the chicken breast recipe right. The point is, if you continue to practice, you will eventually become an expert at the specific techniques needed for your experiments/cooking.

  • Staying organized

I don’t know about you, but I can’t start studying unless my desk is clean. Staying neat and organized is a key point in research. As you go through your undergraduate research journey, you may forget to label tubes, or misplace or mix up your samples if you don’t pay enough attention to organization. It’s much easier to avoid these problems if you start clean on a daily basis. Your work space at home reflects the degree of organization you will have in the lab!

My desk at home

My workspace at home – a binder for research papers, a clipboard with documents for data analysis

My workspace in lab

My workspace in lab – buffers, tubes with samples, autoclaved pipet tips, and an ice bucket specific for my experiments to reduce contamination

 

 

 

 

 

 

 

Put on the desk only what you need for that specific task – if you are studying for Organic Chemistry,

A sample entry in my lab notebook on RT-PCR (experiment done on 5/9/2015)

A sample entry in my lab notebook on RT-PCR (experiment done on 5/9/2015)

then you shouldn’t be on your phone! Make sure to label things on your bench and stay organized. For example: since I work with microbes, my samples are extremely sensitive to contamination. To avoid contamination, I autoclave my reagents, tubes, and pipet tips.

It is also very important to get in the habit of annotating and recording your experiments because you never know what will happen in your experiments, even if you think you did everything right. You might need to repeat the experiment a couple months later, when you have forgotten the exact details of the experiment. This is why it is important to practice taking thorough notes in your introductory laboratory courses. In the same way during your daily routine, you could easily develop note-taking skills by making ‘to-do’ lists of your day.

Additional tips: 1) Google Calendar to organize events, lab work, school, etc. 2) Zotero and/or Mendeley to manage and share research papers

 

  • Building relationships

If you are an undergraduate student, you almost always will be working with a graduate student or a postdoctoral mentor. Besides the time you will be spending on experiments with your lab mentor, it is also very important to develop a personal relationship with them. It is so crucial to develop good relationships with your TAs and your professors because who knows what will happen in the future? Next thing you know – you might be spending most of your day running experiments with the TA that taught you about the basics of chemistry lab techniques. Fun fact: my graduate student lab mentor was actually my General Chemistry (Chem 1AL) Lab TA during my very first quarter in college!

Grabbing lunch with my Principal Investigator, Professor Irene Chen (Department of Chemistry and Biochemistry)

Lunch break with my Principal Investigator, Professor Irene Chen (Department of Chemistry and Biochemistry)

Me at CSEP's dinner with faculty with Professor Joel Rothman (Department of Molecular, Cellular, Developmental Biology)

At CSEP’s dinner with faculty with Professor Joel Rothman (Department of Molecular, Cellular, Developmental Biology)

If you are hoping to pursue graduate studies, and even a career in academia, what better way is there for you to learn about the research path than talking directly to your Principal Investigator (PI) or professors in your college? As an undergraduate, professors might seem intimidating, but many of them are actually very encouraging. I had the opportunity to ask Professor Joel Rothman in the UCSB Department of Molecular, Cellular, and Developmental Biology about his awesome journey to becoming a faculty member at UCSB. I was surprised that he became an expert in the wine making before he became a professor. I also got the chance to go to lunch with my PI, Professor Irene Chen, and to talk about how she began researching about the Origin of Life. It was fascinating and encouraging to hear their stories because they were once an undergraduate researcher like me!

  • Going on walks & enjoying life

One of the biggest advantages we have as UCSB students is that our school is on the beach, literally. It is important to take some time off doing your homework or designing your next experiment, and go on a walk at the beaches nearby. On my walk, I think about life, and how beautifully it was designed for us to enjoy… and where life first began (Origin of Life – main research topic of the Chen Group). For me, the most creative ideas pop up in my mind when I am de-stressing and appreciating the good things that were provided for me!

Taking a walk and enjoying the astonishing view of sunset at Sands Beach, Isla Vista

Taking a walk and enjoying the astonishing view of the sunset at Sands Beach, Isla Vista

U dub life

I am officially a University of Washington employee this summer! I will be working as a lab assistant this summer in Ferric Fang’s lab at University of Washington until early September. I am stoked. I’ve been working in the lab for exactly a month now and it has been nothing but positive.

First, I’m very excited to be in Seattle. I weigh location very heavily when choosing a school or establishment to work at, so, naturally, Seattle was a top choice for my destination this summer. I came to Seattle for a few days in November for the ABRCMS conference. Yes, I was a totally noob tourist, but I instantly knew this was a place I could fit in. Seattle is beautiful—so much green everywhere, such a cool city, so much to explore, moody vibes. I love it. Very similar to the bay area in California.

Second, I’m really looking forward to the research I’ll be doing this summer. My previous project at UCSB involved searching for peptides that can permeate bacterial outer membranes in order to facilitate antibiotic delivery. I learned a ton from that project, but I wanted to get more involved in some basic microbiology research. My current project at UW is just that. I am currently working on characterizing nitric oxide targets in Staphylococcus aureus, a Gram-positive bacteria. I’ve also never worked with Gram-positive bacteria so it’s been eye-opening learning how to handle different types of bacteria. We’re studying the target thymidine kinase, an enzyme involved in the salvage pathway of pyrimidine synthesis. It’s pretty cool because I just learned about this exact pathway in one of my courses, which means I’m actually applying what I learned in class, in real life. Imagine that…

Lastly, I love UW. The campus is gorgeous (see photos), the people are incredibly kind, and the microbiology program is ranked fourth in the nation. There are some amazing researchers here!! It feels great to be connected to so many resources and be a part of a school that is so heavily focused on research.

In a nutshell—really enjoying my time here this summer. I’m growing as a person and a scientist. I’m feeling more confident than ever that a research career is what I’m working towards.

Peace

B

IMG_4607 IMG_4638 IMG_4624 IMG_4515 IMG_4489^^^the magical house I’m subleasing at this summer

Research. What is it good for?

A few nights ago, my fellow CSEP scholars and I had dinner with faculty from STEM fields all across the UCSB campus, and we chatted about this very question: what is research good for? From these conversations, I got a lot of insight from people extremely well-qualified to answer such a question. So I am here to share this expert advice so that you may learn these lessons sooner than I did.

There is the more obvious answer to what the benefit of research is: resumé booster. Whatever it is that you want to do in STEM, research experience is helpful. Whether you want to go on to get your Masters, go to graduate school, or go straight into industry after your undergraduate education, previous lab experience, in my opinion, is an unspoken requirement for admission. This was reinforced by a conversation I had with a professor at dinner. He told me that research experience is often used as a filter to narrow down the pool of applicants. Therefore, many smart and capable candidates are not even given a chance—a sad reality. However, this is not done in malice. It is done because the amount of qualified candidates is so large (and growing every year) that they must narrow them down somehow. Now, I am not telling you this story to scare you or to say that those without research experience have no chance of progressing in their careers. I am telling you this as advice to seize all of the opportunities you can so that you are not tossed aside when you really are a smart and capable candidate. Therefore, research in your undergraduate career gives you a leg up, which is nothing but helpful in the competitive world we live in. Many of the skills and techniques that you need in both grad school and industry are taught through lab experience as an undergraduate, such as how to set up, purify, and analyze reactions. You learn what the research process is like and how to move forward when your reactions either do or do not work. It even teaches you what lab culture is like and how to navigate within it. This, among many other reasons, is why previous lab experience makes you a more desirable candidate.

While this may be a good enough reason to jump on board the undergraduate research train, it is not the only or most important answer to why research is good. Research (at all levels) teaches you about yourself. Personally, it has taught me what my passion is and, as a result, what I want to do with my future. It has forced me to carry on in the face of adversity, whether that adversity came from a project failing or from lacking role models for my education. From the people I have met and the experiences I have had, I strongly believe that research helps produce people that are driven and strong, as well as guides them to careers they love. At dinner, Professor Joel Rothman told me that he loved his job and would not want another one, and I believed every word. Not only because of the conviction in his voice but also because of his story. He had taken time off during graduate school and found his way into winemaking. After a few years, he had made it to the top of the winemaking industry. However, once there, he looked around and saw what his future would be like, and he saw a life that could not give him the excitement and gratification that research could. So he went back to graduate school, and although he did not take the typical path to get to where he is, Professor Joel Rothman is now a successful professor, mentor, and researcher. Therefore, I would like to leave you with this remark: while research makes future employers happy, it should, first and foremost, make you happy.