Ask a Microbiologist #2: Questions from a future scientist

Bacteriophage attacking a bacterial cell
Bacteriophage attacking a bacterial cell (Photo credit: AJC1)

This week I received my first piece of reader mail and it contained some great questions from an undergraduate student at what I’ll call Big U. Here’s the background:

“I’m currently still working on my bachelors, but it is my ambition to earn my PhD, become a microbiologist, and research virology and bacteriology, topics which I have found articles on in your blog. However, I am new to the world of research, and I would love to be able to get some of your insights into a potential future in this field.”

A couple of these I really wish I’d know to ask before jumping into graduate school myself. So without further ado I’ll go straight into the questions.

1. What made you choose Microbiology as a program to earn your PhD in?

My current position as a graduate student in microbiology has been influenced by many different events. During the process I wasn’t sure exactly where I was going, but with the benefit of hindsight I can see the big moments that led me down this path.

I was in high school during the final years of the Human Genome Project and I thought it was just the coolest thing around. Around this time I was also exposed to the book “Genome” by Matt Ridley, which was essentially a chapter-per-chromosome novel. Each chapter explained the function of a gene on each chromosome and some relevant story about its function. When I read this book it really opened my mind to the vast world of science taking place in genetics and biotechnology. I knew going into college that I wanted to go into some form of biotechnology or engineering-related field.

Four years later I got my bachelors degree in Biotechnology and a few of my upper-division courses were microbiology related. These were always my favorite classes and to me seemed the most interesting. I knew that I wanted to pursue graduate education and microbiology seemed like the right choice for me.  I initially wasn’t sure what sub-field I wanted; I just wanted to work in a field that I found personally both interesting and rewarding.  After taking virology and reading “The Hot Zone” I knew I wanted to pursue virology and those were the programs that I applied to my senior year. Part of my decision was influenced by all the news about pandemic flu that year; virology was a hot topic in the news and a common conversational item in classes.

After graduation, I worked as a research assistant for almost two years and during that time I kept somewhat current with virology in the news. I began to be drawn to neglected tropical diseases, emerging disease, and especially those that are transmitted by mosquitoes.  Now I work with West Nile virus, which is a great fit for my interests and a rewarding dissertation subject.

I know my interests will keep evolving and that this will determine where I go after my PhD, but these are the bigger trends are why I’m getting a PhD in microbiology. That and I really enjoy what I do. Apparently somewhere along the way I drank the science kool-aid.

2. Which scientist in this field most inspires you?

That I’ve personally met: John Alderete PhD.  I was fortunate enough to be referred to him and his lab at Washington State University by my adviser for a senior year internship. I didn’t know it at the time, but I managed to stumble into the lab of a fantastic mentor who really gave me the confidence to go forward with microbiology as a graduate and career pursuit. This for me is saying something as my path to graduate school was not direct and gave me many opportunities for attrition.

I am also very impressed by the fact that he has taken research from his lab and applied it to a real world problem: field diagnosis of the pathogen he studies, Trichomonas vaginalis. It inspires me to look of the translational applications of my work and how it can more directly benefit people. Without question I can say that working in his lab was a turning point in my early career and I am very thankful to have passed through his sphere of influence.

3. What magazines, newspapers, ect. do you find you information from?

I’m a big fan of the New York Times Science page despite the paywall for the online version.

Google news can be good if you set it for more science and health stories, but the sources aren’t always the best.

I highly recommend the WHO outbreak page, it’s really interesting to see what diseases are appearing where and what kind of impact they have.

What surprises me the most is that I get a lot of referred stories from my Twitter network. As I’ve followed more professional scientists on Twitter I’ve gotten access to great articles and studies through their tweets. I wasn’t expecting this, but Twitter really has become a great tool now that I know how to utilize it.

I also get a lot of my primary information from journal sources and I try to use these for the bulk of my research. Thanks to my university library access I can get almost any article I need from PubMed or similar sources. Having access to this primary literature is great because you can really begin to see what is happening right now, as opposed to referencing text books, which are always a little bit behind the cutting edge. I still use some textbook from my undergraduate and graduate courses for reference though.

4. What sort of professional writing do you encounter on a day to day basis in you career?

Day-to-day writing isn’t horribly intensive as a second year student and as a result it’s easy to ignore writing altogether outside of specific tasks. This is actually one of the main reasons that I blog: it forces me to write on a regular basis and pay attention to how I’m communicating my ideas. Even though I’ve been doing this a little over 6 months my writing has benefited immensely from consistent practice. I’m still working through my personal writing hang-ups, which I sure have been noticed here on the site, but I have made significant progress.

Course work is usually essay format, but coursework will make up very little of the overall writing in graduate school. The bulk, at least in my program, is directed towards the almighty thesis and anything that bows in supplementation such as grants, journal articles, and comprehensive/preliminary exams. Essentially these are all going to be large documents that are a product of extensive research and effort so becoming comfortable with more intensive and self-synthesized content is key.

What is fundamentally happening here is I am being trained to generate my own ideas and conclusions and support them at length, as opposed to the more fact-regurgitation formats that seemed to dominate my undergraduate experience. No more having to memorize the Krebs Cycle substrates; it’s more about understanding core concepts, how they influence systems, and how to use those functions in a way that make for understandable and valid experiments. So instead of knowing the chemical structure of a substrate at a specific point it’s more important to understand how to utilize that substrate as an experimental readout of a mutation in a key catalytic protein.

5. What sort of documents must you personally write, both in and out of the lab?

In the lab I primarily write protocols and will eventually be authoring journal articles and grant applications. I also try to keep as current with my bench notebooks as possible. In undergraduate courses  I can clearly remember hating to keep up with my notebook; I thought it was rather pointless. After nearly two years as a professional research assistant and another in graduate school I now keep it as up to date and as detailed as possible. Having my own notes to refer back to is invaluable because it is SO easy to forget the details that can make or break an experiment.

While it isn’t writing, I want to include putting together talks and research presentations for this because it is such an essential  part of modern science. You have to be able to communicate your positions and your research well and at this level writing and speaking are both necessary skills to have, so the more comfortable you are with this the easier parts of graduate school will be.

6. What sort of obstacles should I expect entering grad school? How should I overcome them?

Getting in to graduate school can be an involved process depending up the type of program that you apply to. Expect upfront additional standardized testing such as the GRE, and begin studying in weak areas a few months in advance if necessary. You mentioned that you’re a Junior, so I would recommend taking it earlier (late spring) rather than later if you need to study and take it again. Give yourself plenty of time because it really isn’t worth stressing and cramming for.  You just can’t cram for an exam like this and lead time can be an immeasurable help. There are tons of great test prep materials out there if you need them.

Far and above anything else you absolutely need research experience if you’re going for a PhD program. I won’t say that you absolutely have to be published (many people in graduate school publish their first first-author paper here, not undergrad) but you do need to know if the reality of laboratory work is what you want. Continuous work in a single lab over the course of many months looks good on an application; it shows that you can work in a research environment. This is also invaluable for generating the contacts you need for strong letters of recommendation. So the long and short is that lab experience is a must.

There is another obstacle with academia that is totally out of your control but you should be aware of: funding sucks right now. Many investigators are struggling to fund labs and opportunities in traditional academia are tight. However, don’t let this discourage you if you feel passionate about the field. Being aware of these conditions ahead of time will allow you to look for programs that are well funded and find those investigators who do have the financial resources to take on a student and minimize the negative impact of our difficult economic times. I cannot understate how much this impacting the climate in academia right now and will continue to do so. Those of us who feel that this is more of a calling than a career will keep finding ways to make the best of the situation, but it’s tough.

7. What sort of presentations do you have to give? How large is the audience?

So this answer is going to be based on my experience in my program which does not require me to teach. Right now I give a few presentations a year between various journal clubs, research presentations, and talks at small conferences. Audiences for my events have been small so far; 40 people tops. Hopefully over time I will begin to reach larger audiences as I move up to bigger conferences .

Most of this is centered about communicating my research (or another person’s work in the case of journal club) to people who may not have background in that area. Learning how to tailor a presentation to my audience and their general level of knowledge of my topic is one of the more difficult things I have to do but also one of my favorites as well.

8. Is there anything that surprised you when you starting working in this field?

Research is a slow process that takes a great deal of time and planning to do well and can have so many minute variables. You may think that something will be straightforward and it quickly becomes anything but that. Everything takes time and if you want to produce data on a regular basis you have to put in the hours. This wasn’t surprising so much as it was adjusting to the workload and understanding the necessity of replicates and repeats. You can’t rush a project and a large part of you time will be determined by the living systems you work with. For me right now this means coming in at odd hours for time points and working with my cell culture on weekends. You do adjust though.

Getting used to and even expecting setbacks has been valuable for me. I’ve had to learn to keep the failure of bench experiments from impacting my personal feelings because much of what research is consists of 90% failure and 10% success. Focus on growing the 10%, learn from the 90%, and keep moving forward.

I’ve mentioned before that I think I drank the science kool-aid early on in my career. However, my general enthusiasm isn’t always shared and I have difficulty resolving my passion for science with the general tone of cynicsm that seems to breed in certain parts of academia. Even I’m not immune to this phenomenon (that 90% does eventually get to me at times), so I work hard to keep a positive outlook and not let the day-to-day difficulties trip me up.

In Summary:

I think that if you are passionate about a subject and want to add to the body of human knowledge then a PhD program is probably the right choice for you. If you want to run your own lab someday it’s required. I won’t lie and say that it is an easy process taking place in times of plenty; its not. Funding is tight and the work can be long and difficult. However, I also believe that this is so far the most rewarding thing I have done for myself. I have grown as both a researcher and a person as a direct result of being in graduate school and pursuing my passion for microbes.

The fact that you’re asking these questions now means that you already have a head start. It heartens me to see young women in the sciences wishing to continue their education and follow their passions. I hope that some of what I have written here has helped you in finding your own career path, wherever it may take you.

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7 thoughts on “Ask a Microbiologist #2: Questions from a future scientist”

  1. Hi Katherine, glad to see you’re interested in my blog!

    It’s interesting that you cite “Genome” here. I also read that book before entering college and it definitely helped solidify my interest in biology, although I initially took the developmental route. It really is surprising how profound an impact good scientific writing can have!

    1. I love coming across good science writing, it has been such a huge part of my path to becoming a scientist on my own, not just reading about the science in the books.

      It has also taught me that you can get people interested in hard science with prose, which is something that I try to do. Right now I’m reading “The Panic Virus” by Seth Mnookin and it is fantastic. Great understanding of the science made highly accessible to people new to the issues.

  2. A 25 g sample of food was analysed and results declared as under:
    1.Enterobactericeae:”Not detected”
    2.Salmonella: Present/25g
    3.Cronobacter: Present/25g
    Is it possible that in same sample Enterobactericeae is declared “Not detected” and its other member (Salmonella & Cronobacter) are declared as present?

    1. If I understand the question correctly and that the detection methods are sound (IE they can distinguish between discreet species of bacteria) it is possible for a food item to be contaminated with Salmonella and Cronobacter but not Enterobacter. This is because while Enterobacter is a specific genus of microbe, Enterobacteriaceae is a large family of microbes that includes Cronobacter, Salmonella, and Enterobacter.

      My best understanding of the situation would lead me to believe that the test that you ran was on these individual members of the larger family. While all are technically Enterobacteriaceae only the genus Salmonella and Cronobacter are present.

      1. Hello,

        I would greatly appreciate any advice from an expert on eliminating candida from my body. My GI tract has been colonized by these fungi.
        Typically probiotics, digestive enzymes, and a candida diet are recommended.
        I realize though that candida may be able to adapt to foods recommended to help kill it off: garlic, oregano oil, coconut oil, grapefruit seed extract, etc
        Do you have any insights into this?
        Thankyou!

      2. Candida albicans (also commonly called yeast) is a normal part of your gut microbiota and shouldn’t cause disease in healthy individuals. As such, it is not necessary to completely eliminate it from our bodies. Who told you that you were colonized with these fungi? Was it an accredited physician or are you self-diagnosed by using the internet? If you believe you are having significant yeast issues please see a qualified physician, as this may indicate serious underlying conditions. An examples is when thrush (oral candida growth) is seen in undiagnosed diabetics.

        Do not go see some quack who is trying to peddle the newest neutraceutical or anti-yeast diets that you mentioned to cure this. Those people are modern snake oil salesmen and their claims are rarely backed up by any solid evidence.

        Hopefully this is a treatable condition that you can recover from swiftly with the aid of sound medical advice. I’m not a physician though, so I highly recommend you ask a professional.

  3. Is the Kv1.3 potassium channel receptor on EM Tcells the same as the cancer mitochondrial Kv1.3 receptor?

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