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Posted by Rebecca on October 24th, 2017  ⟩  0 comments

After finally writing and editing your thesis, it’s time to defend. Here we discuss what steps you can take to prepare for your defense and provide some tips on how to successfully defend in front of the thesis committee.

For many graduate students, the thesis defense can be scary and extremely nerve-wracking, but with the proper preparation, it can actually be an enjoyable experience. It is important to remember that you are the ultimate expert in your research project. While professors on the committee may know your field of study in a general sense, they have not spent the time you have studying your thesis topic. Keep in mind that the committee is not there to make you fail, but is there to ensure you are prepared and have the skills necessary to proceed independently as a scientist. Follow the guidelines below to understand what to expect, ease your nerves and show off what you have learned over the past few years. If you need to refresh your public speaking skills, be sure to check out our articles on public speaking  for the grad student and seasoned researcher.


What to expect

1. The Setting.

While most defenses are open to the public, some are closed door. This will depend on the department and institution so check with your program to see what type of defense you will have.

Since many defenses are seen as more of a formality and celebration, there is often food and drinks provided. Be sure to find out if you are responsible for providing refreshments for your guests and committee in advance.



2. Inviting Friends and Family.

Most programs allow you to invite guests such as friends and family. If your family and friends do attend, tailor your presentation to a wider audience so everyone can understand. Also, don’t forget to be prepared for embarrassing questions. Take them with a sense of grace, and they will brush right over. If you’re worried that your parent with a background in life sciences may try to stump you, remind yourself that it is okay not to know the answer—just stay professional and confident.

Pro Tip: Preemptively involve your family before the time of the defense. The best way to do this is to invite them to your presentation and give them an overview prior to the defense. Ask if they have questions, and if not, provide them with intelligent questions to ask. By charging them ahead of time, they’ll be too distracted by the honor of the task to try anything else, and you’ll already be prepared to respond to their questions.



3. The Committee.

The committee is usually made up of your advisor as well as other professors from your department. Occasionally, there may be a few professors from a related department, but a majority will be from yours. The advisor serves as the moderator for the defense and does not have a say in the outcome.



4. Format of the defense.

At most institutions, the event begins with a presentation by you—sometimes with interruptions for questions. At the conclusion of your talk, the committee may have you leave the room while they decide which questions they will ask you. You will be invited back into the room for the defense portion, and the committee will ask you a series of questions. Most questions are simple and not meant to stump you, but expect a few challenging ones.



5. Failure is rare.

As stated previously, at many institutions, the thesis defense is more of a formality that happens once the final revisions have been made to your dissertation. Therefore, failure is rare. The committee does not let people defend until they are ready. Common outcomes are passing and passing with revisions required. While failure is the third possible outcome, it is unusual.



Before your Defense

6. Reread your thesis.

Two weeks before you defend, set aside some time to reread through your thesis in its entirety. While it may seem like overkill since you already spent so much time writing it, going back over your thesis can help to bring the bigger picture back to mind before you present. This is very important when it comes to answering questions from the committee about the implications of your project. The details of your research will be freshly accessible in your mind after going over the paper one last time as well.



7. Pretend to be the examiner.

As you review your thesis/dissertation, try to do so from the perspective of your thesis committee. Look for the strengths and weaknesses of your research. Try to identify potential areas of confusion because the audience will likely ask questions about parts of your thesis that could have been expanded upon. Write out the questions that you come up with while rereading, and then go back and answer them to the best of your ability. Were you able to answer them thoroughly? If not, now is the time to brush up on current literature about the topic as well as the nuances of your own research study.



8. Attend other thesis defenses.

Perhaps one of the most intimidating aspects of the thesis defense is not knowing what to expect. You may have heard rumors about previous thesis defenses and how they were but if you weren’t actually there to see it, these rumors won’t be as helpful. At many universities, students are allowed to observe the thesis presentations of other students. Take advantage of this opportunity before you start preparing your presentation. Not only will this help to calm your nerves since you will have a better idea of what to expect, it will help you to form a list of dos and don’ts in your head for your own talk. Look for the strengths and weaknesses in each student’s defense and learn from their mistakes and successes.



9. Schedule a strategy meeting with your advisor.

Scheduling a time to meet with your advisor can be very helpful. Once you have outlined how your talk will go and what the points of your thesis are, share your plans with your advisor. He or she has been on defense committees in the past and can give you some insight into how you may want to alter the structure or content of your presentation based on common mistakes that other students have made. Remember that your advisor is rooting for you and was once in your shoes preparing for his or her own thesis defense.

Pro Tip: At most universities, you can meet with the committee before your defense as often as you can get them all in a room together—take advantage of this. Each time you meet with them, you will get more and more recommendations on how to make you thesis better and therefore have a better defense.



10. Get the most out of practicing.

There are a few ways you can optimize your practice time so you get the most out of it. Practice alone the first few times until you become more comfortable with your talk. When you feel like you are ready, record yourself giving your defense. One of the most convenient ways to do this is using the camera on your laptop or your cell phone. After you finish, take time to review your recording. Check out your body language and look for certain words or phrases that you use repeatedly—many of us do this when we are nervous. You can also use your recording to gauge the length of your presentation.

Once you have practiced enough, get a group of your colleagues together and practice giving your defense to them. By presenting to people with a background in your field, you have the opportunity to ask them to grill you with questions. Some of their questions may even be similar to questions the committee will ask you when it is time for your actual defense and will help you get used to answering questions about your project on the fly.

Pro Tip: In biology, there are many words that are hard to pronounce if you are not used to saying them on a regular basis. We often get accustomed to using acronyms and abbreviations in daily speech, but try to avoid this by practicing the pronunciation of any words you don’t know how to say. If you are unsure about how a word should sound, inquire with your advisor, look online for a pronunciation key, or check with your peers.


During your defense

11. Don’t assume everyone has read your entire thesis.

Even though you provided the committee with your thesis in advance, it is important not to assume that they were all able to read through the whole paper. Therefore, you should present the importance of your research project, what methods you used to complete your project, and what the outcomes of your research were. You should also provide the committee with an explanation of the implications of your study both to your field specifically and also to the wider body of scientific knowledge. Stating your recommendations for future research is also encouraged because you will probably be asked about it if it is not addressed during your presentation.

On the other hand, be prepared to answer questions that may come from your paper rather than your talk. Some of your committee members will have read your entire thesis and may reference a specific paragraph or page in it when posing a question. Be sure to have a paper copy with you just in case!



12. Be prepared for questions.

There are some questions that you can anticipate being asked. For example, if there are any weaknesses or limitations to your project, you can be almost certain that your committee will ask about them. Prepare for questions like this by creating slides with graphics and text that will help you answer any questions you suspect may be brought up. You can leave a blank slide between your presentation and extra slides or save them in an entirely separate file—just be sure they are easily accessible.

Remember that you are not expected to know everything, and if you don’t know the answer, it is best to be honest. Perhaps you hadn’t thought of that question before, but you can tell the committee that you will consider it in the future.

Pro Tip: When answering questions, first listen to the entire question. Next, restate the question back to the person who posed to be sure you understood it correctly. Lastly, answer the question to the best of your ability and provide a succinct close to your answer to minimize a long dialog. If you need to pause to gather your thoughts, that is OK.



13. Dress the part.

It can be easy to put off planning what you are going to wear for your thesis defense when you are caught up in preparing for the talk itself. However, don’t put this off until the last minute. Looking professional is important in making a great impression with your thesis committee. Remember that you are defending the fact that you deserve your master’s or Ph.D. as much as you are defending your thesis—so dress the part. Your outfit should be business professional. For men, wear dress pants along with a coat and tie. Women should wear a skirt or pant suit, but a dress can work, too. Try to steer clear of sleeveless dresses, low cut tops or anything that will make you feel uncomfortable. You don’t want to have to adjust your outfit constantly during your talk; this will appear fidgety and unprofessional.



14. Be confident, but not arrogant.

Body language plays a big role in all types of communication. In your thesis defense, it is imperative to speak with confidence about your research and your findings. If you speak as though you are unsure, it will be hard for the committee to believe what you are saying and it may come off as though you aren’t confident about your results. The defense committee is there to ensure you are capable of working independently after graduation. This is your time to prove to the committee what you have learned over the past few years and that you deserve a Ph.D. in your field.

Pro Tip: Minimize your use of qualifying words such as likely, may, might, could, should, probably and usually. Excessive use of these words will cause you to lose your authority. Add strength to your presentation by instead using works like will, always and won’t.



15. Record your defense.

During or after the question section of your defense, the committee will provide you with feedback, suggestions and revisions for your thesis. However, it can be difficult to remember all of the words of wisdom when you are nervous. If you set up a video or audiotape to record your talk, you will have a record of what was discussed so you can go back and make edits to your thesis as necessary after your defense is over.



These 15 tips can help you successfully deliver a thesis defense at any university, but remember that your institution will have its own guidelines to help you prepare your defense. Since the thesis defense varies between departments and schools, it will also be beneficial to talk to your peers who have already completed one. Gather as much information as you can and jump right in to the planning stages. Don’t get caught up in your fears and remember that you are the only expert on your research. Your advisor and defense committee would not let you defend if you weren’t ready. You can do it!


    
              Rebecca Talley
         GoldBio Staff Writer


Rebecca is a medical student at the University of Missouri.
She previously worked as a lab technician while studying
biology at Truman State University. As an aspiring
reproductive endocrinologist with an interest in global
health, Rebecca has traveled across Central America on
medical mission trips. With a passion for the life sciences,
she enjoys writing for GoldBio.

 

Category Code: 79108, 79109

Posted by Rebecca on October 12th, 2017  ⟩  0 comments

Applying for postdoc positions is an important process along your journey to academia. While there are many similarities to applying for jobs in general, there are a few very important differences. To provide you with a detailed guide on how to go about finding the best postdoc position for you, I will discuss the application process as well as the application itself. I will then give you a variety of tips on how to maximize your success and avoid common mistakes throughout the course of the postdoc application. Finding a postdoc position doesn’t have to be overwhelming; with this guide, you will be on your way to obtaining the job you want.


The Application Process

The application process for postdoctoral positions varies based on your field, interests and type of position you desire. There are also multiple directions you can take when looking for a positions that fits your interests. One option is to follow the formal process, which involves looking for an open position and submitting an application. However, there is also the option of identifying potential PIs that you wish to work with and contacting them directly about becoming a postdoctoral fellow in his or her lab. Oftentimes, Ph.D. students decide to take both approaches simultaneously. Having as many doors open to you as possible will increase your chances of finding a job that matches your interests and skills.

PostDoc Application Checklist


The Traditional Route

The traditional application route involves submitting a formal application for an open position. These positions can be found by searching through job postings on university websites or through job search databases. They can also be found through word-of-mouth, but this is easier accomplished by those who have done extensive networking.

The key to being successful with the traditional route is applying to positions which you are passionate about and qualified for. Applying to every position you come upon will not increase your chances of getting a job more quickly, but will instead lead to less time spent on each application. Identify positions in which you would be a great addition to the PI’s lab and where you think you can make a difference and be successful. A postdoc’s primary job is to assist in furthering the research of the PI, so having goals that align is imperative.



The Alternative Route

The alternative route to obtaining a position as a postdoctoral fellow involves contacting PIs directly—regardless of whether they have an advertised opening or not. This method will require a lot of research. First you will need to identify potential PIs with similar research interests as you. You can go about this in a few different ways such as networking during conferences, identifying authors of papers which align with your research, or even asking your advisor for potential leads. Once you have these contacts identified and you have read some of each PI’s publications, contact them via email (read below on sending a postdoc request letter)—your email will essentially be your cover letter, but be sure to attach your CV.



A Closer Look at the Application

Applying for a postdoctoral position through the traditional route is extremely competitive.

According to Times Higher Education, as many as 200 applications are received for each postdoc position at some universities. With statistics like these, your application must give

the best impression of you and your scientific experience. In this section, I’ll discuss the purpose of the application, what it tells the PI about you, and what should be included in a formal postdoc application.


Purpose

The purpose of your application is to give the reader enough information about you so that he or she can determine whether or not to invite you to interview for a postdoctoral position. This is usually the first impression the reader will get of you, unless you have previously met this person at a conference or other networking event.



Cover Letter

I like to picture the cover letter of your application as your personal abstract. It should give the reader all of the most important information in your application, and in many times, will help him or her decide whether to continue reading the rest of your submission or if you may not be the best fit for the position.

How you write your cover letter can vary, but the format below can help you keep it organized and efficient. Remember to address the PI by his or her appropriate title, likely Dr. (insert name) and to close your letter by thanking the PI for his or her consideration. It is a good idea to put your contact information with your signature at the end of the letter so it is easily accessible for the PI. Additionally, the recommended length of a cover letter is typically one page.

Paragraph 1—Introduction

  • Tell the PI why you are writing including what position you are applying for. The American Society for Biochemistry and Molecular Biology recommends using this format, “I am applying for the postdoctoral position available in your laboratory that was advertised (where).”
  • Provide a basic introduction about yourself, including your field of study. Describe your current position. If you’re still in school, provide your anticipated graduation date. Include where you are working or attending school as well as the name of your mentor.
  • End with a short explanation of why you are qualified and would thrive in this position.

Paragraph 2—Qualifications and Experience

  • In this paragraph, you want to inform the PI why you are the best candidate for this particular position; this means your cover letter must not be generic, but rather tailored to each position you apply for.
  • Include things such as past research experience and relevant skills and traits that make you a great candidate.

Paragraph 3—Stand Out

  • This is the place for you to talk about why you’re different from other candidates. What publication are you most proud of? Have you won any awards for presenting your research? Have you gotten any grants or previous fellowships?
  • Remember, this is not a place to outline your entire CV, but rather to highlight your key achievements.


Curriculum Vitae (CV)

The purpose of the CV in your application is to provide details of your credentials for the position and to outline your professional experience as a scientist. To start, you should make a list of all the potential experiences and qualifications you might want to include. I personally recommend starting your CV when you start your academic career, and adding to it as you accomplish something; this minimizes the chance of leaving something important off of your CV when using it to apply for postdoctoral positions or even academic jobs later on. However, if you are just creating your CV for the first time, here are some important things to include:

Name and Contact Information

  • This should be the first thing a reader sees when looking at your CV. It is typically formatted as a header to your page and includes your name, address, phone number and email.

Education

  • List universities you have attended, starting with the most recent.
  • Include the program you attended at each university, the dates you attended, and what degree or certification you received.
  • If you received any significant academic awards such as honors at graduation, you can include that in this section as well.

Research Experience

  • In this section, list out the research projects you have been involved in. For each project, include the associated university or other institution as well as a summary of the project and its results. If it has been accepted for publication, you can list that here as well.

Publications

  • Here is where you will list any and all publications that you want the reader to be aware of. They should be formatted like a citation, including the authors in order as listed on the paper, the name of the publication, the name of the journal, and you may also wish to include dates, volumes, and page numbers.

Awards and Honors

  • In this section, list any awards or honors you have received. Some examples of these include fellowships, grants, dean’s lists, and conference presentation or poster awards. Be sure to include the name of the institution giving the award and the year it was received.

References

  • An important part of your CV is the references you list at the end. These should include the contact information of about three people who know you well and speak on behalf of your professional career in science. This may be your mentor or another professor who you have done research with previously. Include their affiliation (i.e. university) and title as well as their address, email, and phone number.

Here are links to example CVs from different universities to help you understand what a general template of a CV should look like visually and to help you get some ideas for your own CV.



Research Statement

Some positions that you apply for will request that you provide a research statement with your postdoc application. This is a summary of your research with past, present and future components. You should discuss any accomplishments you have made in your research career this far as well as what your current project is, including the methods, results and conclusions of your project. You will also need to discuss where you see your research interests going in the future. Do you have any potential projects in mind? Do you see yourself continuing in the field you are currently in or branching out to another area of interest?

According to Cornell University, this statement should also address issues such as lab equipment that you may need, funding issues and possible collaborations on projects you foresee. They also suggest that “the strongest research statements present a readable, compelling, and realistic research agenda that fits well with the needs, facilities, and goals of the department”.



Letters of Recommendation

Some institutions will request that you submit letters of recommendation as part of your postdoctoral application. These letters should be from people who are comfortable writing you a strong recommendation, so ask them if they feel they can do so before choosing them to write your letters. Letters of recommendation can be a way for your potential PI to learn about how you contributed to research in the past and how you may add value to his or her research team, so choosing someone with whom you’ve done research before is a great idea. Provide your letter writer with adequate information about the position you are applying for as well as an updated CV and research statement. Each letter should be tailored to the position you’re applying for, if possible. It can often be time consuming for a letter writer to write a new letter for all of your applications, but at the very minimum, the writer may be able to tweak a few sentences here and there to make the letter more specialized to each position you are applying.



Application Tips

Making your application stand out is the one of the most important aspects of applying for postdoc positions. This can be very challenging, but there are a few simple steps you can take to boost your application.


General Tips and Resources

  • Finding a postdoctoral fellowship to apply for can be difficult. Some ways to find positions include word-of-mouth, looking at university job postings and searching sites like PubMed for potential PIs. Remember that looking at prior publications only shows you what the researcher has worked on in the past, so you may need to reach out to find out what their current projects are.
  • When you find positions to apply for, make sure you pick positions that meet all three of these categories: safety positions, target positons and stretch positions. Safety positions refer to those that you think you have a good chance obtaining. They may not be at a big name school, but they are something you can fall back on if you don’t get one of your more desired positions. Target positions are those that fit your skill level and experience. They are the ones you are likely to get an interview with and would be happy to have. Stretch positions are positions you don’t feel as confident about applying to. They may be with big name researchers or at top universities. Apply to some of each, because you never know what will happen over the next few months.
  • Follow the instructions of the application. I cannot stress this enough. The PI will notice if you do not follow the instructions as they are stated on the posting, and this can be an easy way to get your application removed from the potential candidates. This is an easy step, so follow it without exception.


Networking

Networking is a great way to get your foot into the door of someone’s lab. This can be done with others at your own university as well as throughout the country and beyond. Networking should begin at least two years before you graduate, but starting earlier is even better. Attending conferences and talks is a great way to get to know others in your field. Approach presenters and mingle with other students and researchers at these events. Exchange contact information and talk about projects you’re involved in or hope to get started. These people may later be able to help connect you with others in the field or even be a starting place to look when searching for the postdoc position that is right for you.

ProTip: Have a business card made with your contact information and field of study. This can be passed out to anyone you meet and can be a way for them to remember you or contact you later on.



Postdoctoral Request Letter

The postdoctoral request letter is intended for applicants who are using the alternative route of finding a postdoc position. Since you will be looking into working with a PI who is not currently advertising an open position, you will need to send a letter requesting that a position be created for you. This type of letter is typically sent via email to a PI who you wish to work with. It is imperative not to send blind emails to a list of PIs in your field—they will not respond if it does not appear that you have a strong desire to work in their specific lab. In his editorial letter in Analytical Chemistry, Dr. Jonathan Sweedler advises students to send fewer emails in higher quality. He suggests that students should “read about a faculty member’s research and tailor your letter to the group.”

Ultimately, your postdoc request letter should include why you are contacting the potential PI and why you want to work in his or her lab specifically. It should then outline your research interests and plans as well as a possible funding plan. Additionally, you should include a copy of your CV and a research statement.



Cover Letter

  • The cover letter is your first impression to a potential PI. In addition to what I have already discussed, you can use the cover letter as an opportunity to explain any gaps in your CV or publication experience. This is not a place for providing excuses, but it is a place to address these gaps and to help the reader gain a better understanding of any potential weaknesses your application may have. Turn your weakness into a strength. In an article published by Nature, author Jack Leeming discusses following a two-step approach when addressing gaps or weaknesses. First, state the weakness and “keep it realistic and surmountable”. Next, explain how you plan to use this position to grow and further develop your CV. This information can be included in the paragraph three of your cover letter.


Google Yourself

  • With social media thriving in our culture, potential employers now have a way to get more information on you than your application provides. By simply typing your name into a search engine, they may be able to find pictures and social media accounts you have. Before you submit an application, do some research on yourself and figure out what kind of online presence you currently have. Ensure that what others will find is presenting you in a positive and professional manner. Perhaps, creating a LinkedIn profile will allow you to provide links to prior publications and provide more details about your work experience. The goal is for your online presence to help you get a postdoc position and not deter you.


Common Application Pitfalls

One of the great things about applying for postdoctoral positions is that so many people have done this before you—some people successfully and some not so successfully. However, you now have the opportunity to learn from their mistakes and avoid repeating them. Here are some common application pitfalls to avoid throughout the process.


Sending a Generic Application/Cover Letter

  • Sending a generic application or cover letter is one of the most common mistakes applicants make. Of course, it takes less time and is easier to use a generic application, but this gives the impression that you are applying to any position that you find and are not truly interested in a particular job. Instead, put in the effort to research the institution, lab, and PI for each position you apply for. Include details that you find in the cover letter and tailor your application and CV to match what the PI is looking for. Getting a postdoctoral fellowship is a process of finding a PI and candidate that are compatible with one another, so it is essential that both you and the PI can evaluate how you will fit in his or her lab.


Randomly Emailing PIs

  • Following up on the last point, applying to or emailing random PIs is not beneficial. If you won’t be a great fit in the lab that you are seeking employment, you’re essentially wasting your time and the PI’s time. Research the type of work the PI is doing and determine if it fits within your research desires. Only seek out positions where you will be a good fit.


Only Applying to ‘Big Names’

Apply only to big names is a common mistake students make. Although, you may have a strong desire to work for a top research lab in the country or elsewhere, you should also apply for more reasonable opportunities. No matter how strong your application may be, you will have a lot of competition. You don’t want to end up without a job after graduation, so keep an open mind when it comes to deciding where to submit your application.



Lack of Proofing

This goes without saying—but having mistakes in your application is unprofessional and will give the PI a bad first impression. Have someone else look over your application before you submit it because it can be easy to miss small mistakes after you have spent so much time working on your application.



Now that you have a good idea of what the postdoc application entails and have read our guide on how to submit a great application, print out our  Printable Companion Checklist to help keep you on track throughout your application journey.  



References:

Kelsky, Karen. “The Postdoctoral Applicant”. https://chroniclevitae.com/news/1238-the-postdoctoral-applicant. (2016)

“How do I apply for a postdoc position?”. Emory University School of Medicine. https://med.emory.edu/postdoc/documents/How%20do%20I%20apply%20for%20a%20Postdoc%20Position.pdf

Powell, Kendall. “A foot in the door”. http://www.nature.com/naturejobs/science/articles/10.1038/nj7281-696a(2010)

Gould, Julie. “The postdoc search timeline”. http://blogs.nature.com/naturejobs/2014/12/05/the-postdoc-search-timeline/(2014)

Sullivan, Bill. “How to write a killer cover letter for a postdoctoral application”. http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=48927(2013)



    
              Rebecca Talley
         GoldBio Staff Writer


Rebecca is a medical student at the University of Missouri.
She previously worked as a lab technician while studying
biology at Truman State University. As an aspiring
reproductive endocrinologist with an interest in global
health, Rebecca has traveled across Central America on
medical mission trips. With a passion for the life sciences,
she enjoys writing for GoldBio.

 

Category Code: 79107, 79108

Posted by Megan on September 18th, 2017  ⟩  0 comments

Glowing petri dish - rendering



You don’t usually hear the word “beautiful” when discussing bacteria, but a trend among microbiologists has turned microbes into aesthetic wonders. A number of projects have repurposed bacteria for art. In one competition, the Agar Art Contest, scientists become artists by creating "paintings" with cultured bacteria and other microscopic organisms. The annual contest results in scientific "art" that is in every aspect beautiful.

Because anyone can appreciate a bit of innovation – scientific or artistic – we’ve decided to browse the theory of this inventive competition, expanding our perspective on the surge of petri dish paintings. We’ll conclude with strategies for how you can contribute to the art form.

Raise your monocles and magnifying glasses; let’s get cultured!



The Agar Art Contest

The American Society for Microbiology has held its Agar Art Contest for several years, encouraging competitors from around the world to express their artistic side through scientific modes. Members of the ASM create images on agar plates or similar artistic “media” with a palette of microbials like bacteria, fungi and yeast. The aggregation of microorganisms produces unique paintings that last as long as the colonies thrive.

Experts, students and hobbyists have participated in the competition. Some pieces are the collaborative projects of artists and research scientists blending their expertise. One example of cooperation came from microbiologist Dr. Mehmet Berkmen and artist Maria Peñil Cobo, a pair that matched complimentary skills to create 2015’s winning plate, “Neurons.” Other paintings are the work of entire lab teams that integrate distinctive organisms into pictures.

Agar paintings are judged on artistic presentation, originality and the artist’s scientific assessment of their culture. Guidelines are given for sizing but also safety, as some organisms can be hazardous if not treated with laboratory precaution. Any type of microbe and agar can be used. Minimal editing is suggested to prevent images from being unfairly enhanced, but the submissions become more impressive each cycle. Past examples of the art include a bacterial rendering of “Starry Night” by van Gogh. Another imitated Monet’s “Water Lilies.” Many artists generate original images as well.

This year’s winner was a stained plate of yeast rather than bacteria, but the art of Jasmine Temple and her colleagues was no less beautiful than an organic spread of bacterial colonies. Her process stippled nanodroplets of pigment-encoding baker's yeast on an agar plate. The media retained each drop’s position in a geometric landscape, producing an ocean-side sunset of pinks, blues and yellows. Although featured pieces may only survive a few days, the impact remains; the distinct tones dividing “art” and “science” coalesce in a new color.



Creating Microbial Art

Painting with bacteria isn’t entirely novel. Sir Alexander Fleming, the scientist responsible for discovering penicillin in the 1920s, began making “germ paintings” of bacteria during his career as a microbiologist. His use of pigmented strains as paint and lab loops as brushes didn’t attract much recognition at the time, but his pieces included portraits and cartoon-style images.

This passion may have led directly to the detection of his now famous antibiotic. A particular agar plate by Fleming demonstrated the bacteria-killing activity of Pencillium fungus. Another culture infused with nasal mucus showed similar activity and generated the theory of human lysozymes. Association to these discoveries make Fleming’s microbial paintings historically valuable to both fields.

In more recent years, laboratory technicians and artists alike have fashioned similar plates for the Agar Art Contest. The process remains based in microbiology. Participants must consider the organisms they’re using; species of bacteria require differing nutrients to successfully colonize a plate. Strains may also grow at asymmetrical rates or proliferate over one another if left unsupervised. Art and science must therefore be carefully coordinated to produce the most successful, aesthetically pleasing cultures.

ASM isn’t the only organization participating in the microbial art era. A collection of scientists provide material for Microbial Art, an online gallery and source of purchasable agar art. While some contributions are like those in the ASM contest, others expand the approach to microbial creations. Some artists feature organic patterns of bacteria imaged in adaptive response configurations. Another gallery uses colored agar to draw relief images of other macroscopic organisms like insects and birds. Bioluminescent bacteria bring further light to the mode. Beyond bacteria, eukaryotic algae and slime molds are employed to create “bioglyphs,” images composed of natural growth patterns. Every artist expresses individual talent and style; the final product is a microbe-based art museum.

Individuals also cultivate their own bacterial art displays. Zachary Copfer is a “bacteriograph” artist, a past microbiologist who discovered his passion for this specialized technique during his photography MFA program. The first step of the photo-printing process manipulates a culture of fluorescent protein E. coli or Serratia marcescens covering the plate. Radiation sterilizes some bacteria to imprint a photo negative on the gel. The true image is revealed after surviving colonies expand, and an acrylic-resin solution immobilizes them. Copfer uses this method to bacteriograph visuals of space as well as scientists like Albert Einstein. Similar to the ASM and Microbial Art projects, Copfer’s intent for bacteriographing is to reverse the division between art and science, annulling the boundaries posed on these fields.



Make Agar Your Canvas

Any curious researcher must now be wondering how they can participate in the microbial art trend. We have a few suggestions for how you can successfully (and safely) turn your agar gels into a canvas suited to bacterial painting.

How to raise a proper culture:

Your basic necessities are a petri dish for holding medium, agar, and inoculation loops. For your culture, you can purchase weak strains of bacteria like E. coli, fungi or yeast. Alternatively, swabs can be taken from objects or body parts to cultivate environmental species, though predicting what these colonies will look like is difficult. Relevant agar medium should be bought to adequately support whatever strains you’re raising.

If you have the resources to do so, bacterial color and luminescence is easily influenced. Low-demand genetic engineering can produce fluorescence and vibrant pigmentation. Heat shock transformation methods stress your bacteria with high temperatures, inducing their absorption of DNA additive in their environment. Kits provide the substances necessary for this technique, but equipment like centrifuges and incubators are also necessary. These are available to the average lab tech, but an artist home-growing their paintings must buy new or used machines.

Prepared microbes are collected and spread onto the agar layer surface. For artistic purposes, manipulate the growth pattern by applying them in the shape of an image. After application, allow a few days of growth. You can check progress at daily increments to decide when the image has been most accurately rendered. When you’re satisfied with the picture, seal the agar’s contents with epoxy. An oxygen seal prevents aerobic growth among bacteria and thus preserves your image.

As previously mentioned, creating agar art is possible outside of the laboratory setting. A cheap set of petri dishes, agar and swabs can produce a microbe painting. One consideration is an incubator. Because bacteria grow more readily in the heat, having a machine or environment that warms the agar plate will produce the best results. Incubators will also prevent unwanted strains from contaminating your art piece. If you don’t have an incubator, leaving the plate covered in a heated room should induce the same effect.

Safety precautions are recommended even when you’re working with household bacteria swabs for your cultures. Don’t unnecessarily expose yourself to whatever strains take up residence in your plate – you never know when a dangerous colony has occupied your colorful art experiment. Bacteria purchased from a manufacturer will come with safety instructions; read these to prevent any unsafe painting practices.

Creating a bacterial palette:

Keep in mind the different environmental and behavioral characteristics of each microbe you incorporate. Keep in mind that agar recipes differ depending on microbe, so some strains are not compatible with others. There are also varying rates of pigmentation between species. Some become vibrant upon generation while others require chemical processes to color. More advanced techniques engineer the protein expression of microbes to induce unnatural coloration or fluorescence.

Many types of bacteria, fungi and yeasts have entered the palette of agar art. Here are a few naturally colored microorganisms that can accentuate the aesthetic appeal of your project:

  • Bacteria:
    • Brown: Bacillus subtilis, Proteus mirabilis
    • Pink-red: Micrococcus roseus, Serratia marcescens
    • Orange: Streptococcus agalactiae
    • Yellow: Micrococcus luteus, Staphylococcus aureus
    • Blue-green: Pseudomonas aeruginosa, Pseudomonas fluorescens
    • Purple: Chromobacterium violaceum
    • Transparent: E. coli
    • Bioluminscent: Vibrio fischeri
  • Yeast and fungi:
    • Brown-black: Aspergillus fumigatus, Cladosporium herbarum, Cryptococcus neoformans
    • Red-orange: Penicillum marneffei, Rhodotorula
    • Yellow: Aspergillus ochraeus, Saccharomyces cerevisiae
    • Green: Aspergillus flavus
    • White: Candida albicans
    • Epicoccum nigrum comes in a variety of colors including brown, red, orange, yellow and black


Art can be integrated into science to craft remarkable projects and raise awareness of the research being conducted. Adding a bit of excitement to your agar promotes public interest in how microbes are being studied. The art grows not only bacteria but conversation – the general fear of bacteria is transformed into intrigue, sometimes even adoration. This is positive coverage for microbes as well as their human counterparts, researchers.

A few days of microbial growth is all it takes for a scientist to become an agar artist. Next time you have an extra plate, some viable bacteria and a few hours of time, you might consider making your own painting. If you’re inspired to join the artistic movement, share your creations with us!

For more on the relationship between art and science: Art and Science: An Eternal Relationship



References

Acharya, T. (2016, April 13). Pathogenic microbes with characteristics pigments production. Retrieved August 9, 2017, from http://microbeonline.com.

Blondin, J. (2016, March 26). Is it possible to create microbial art at home? If so, how? Retrieved August 9, 2017, from https://www.quora.com.

Bowerman, M. (2015, October 21). Van Gogh's 'Starry Night' recreated with bacteria in petri dish. Retrieved August 9, 2017, from https://www.usatoday.com.

Dunn, R. (2010, July 10). Painting With Penicillin: Alexander Fleming’s Germ Art. Retrieved August 9, 2017, from http://www.smithsonianmag.com/science-nature.

Howard, J. (2016, April 4). This Artist Paints With Bacteria, And It’s Strangely Beautiful. Retrieved August 9, 2017, from http://www.huffingtonpost.com.

Microbial Art. (n.d.). Featured Galleries. Retrieved August 9, 2017, from https://www.usatoday.com.

Palmero, E. (2015, October 22). Microbe Masterpieces: Scientists Create Cool Art from Bacteria. Retrieved August 9, 2017, from https://www.livescience.com.

Zhang, M. (2012, September 12). Bacteriograph: Photographs Printed with Bacterial Growth. Retrieved August 9, 2017, from https://petapixel.com.



                 Megan Hardie
           GoldBio Staff Writer

Megan Hardie is an undergraduate student at The Ohio State
University’s Honors Arts and Sciences program. Her eclectic
interests have led to a rather unwieldly degree title: BS in
Anthropological Sciences and BA English Creative Writing,
Forensics Minor. She aspires to a PhD in Forensic Anthropology
and MA in English. In her career, she endeavors to apply the
qualities of literature to the scientific mode and vice versa,
integrating analysis with artistic expression.

Category Code: 79101, 79102, 88221, 88231

Posted by Megan on September 5th, 2017  ⟩  0 comments

Buffers are a class of solution-stabilizing molecules which existed long before contemporary lab technology. Natural buffer substances like bicarbonate and carbonic acid are manufactured by organisms and molecular interactions, functioning to maintain pH equilibrium.

After natural buffer systems were discovered, their balancing effects became indispensable in scientific exploration. Synthetic buffers were developed over decades to produce reliable reactions in experimental models, enhancing biochemical reactions and medicinal products.

New buffers are introduced every year, built from the fundamentals developed over a century ago. This article explores buffers beginning with the foundation which made them inseparable from biochemistry. We’ll then follow the construction and replacement of buffering systems among individual studies as procedures are continually refined.



First developments: Quantifications and medicine

Quantifying chemical behavior is essential to experimentation, so calculations paved the buffer system’s entry into biochemistry. In 1908, Lawrence Joseph Henderson formulated an equation which described carbonic acid as a natural buffer. Karl Albert Hasselbalch later reformulated Henderson’s work logarithmically to create the Henderson–Hasselbalch equation, a formula that measures pH derivation in terms of acidity. It became a valuable tool for estimating the equilibrium pH in acid-base reactions and what pH a buffer would constitute.

Buffers applied to other mediums had their own mathematics developed soon after. Published by M. Koppel and K. Spiro in 1914, “On the action of moderators (buffers)” studied the effects of these substances “in the shift of the acid-base equilibrium of biological fluids.” The paper introduced our basic concept of buffer value (P, relating to strong acids) and gave revolutionary calculations to buffering activity among different substance types: weak and dibasic acids, bases, ampholytes and buffer mixtures.

Another contribution was made eight years later when Van Slyke published a simplified calculation for buffer values in a solution. His quantification using β, the amount of strong base, was similar to Koppel and Spiro’s and had identical assumptions. Van Slyke’s focus tended towards the physiological aspects of buffer solutions whereas the previous authors intended their calculations for physicochemical mathematics. This algorithm for acid-base variation has since been useful for blood-based chemistry and determining the relationship between buffer concentration and capacity.

Early buffers focused on medicinal purposes like stabilizing biofluid pH. The 1928 invention of Tums maintained pH ranges in the digestive system via neutralization of stomach acid. Alka-Seltzer, made available in 1931, is still used as a lab demonstration in university lectures. 



Foundational experiments: 1960-1990s

Basic reagents are used in combination to produce the most potent buffer solutions. Once buffers transitioned into biochemistry, researchers began to establish what chemical mixtures were most productive for equalizing the pH of certain reactions.

Between the 1960s and 80s, a project for determining the best buffers resulted in a list that remains crucial in modern laboratories. “Good’s buffers” were produced or collected by Norman Good and his colleagues, and selected on a number of criteria that qualified application to research in the biological field. Some of the requirements were pKa between 6 and 8, high water solubility, stability and a lack of exchange with membranes or biochemical reactions. Good also prioritized substances that could be prepared easily and safely.

One of the lab world’s most valuable buffer agents, Tris – was first recognized by Good in the early 1960s. Known in therapeutics as THAM, Tris quickly adopted scientific roles. Tris and other reagents identified by Good continue to act as the equalizing agents within buffer mixtures by adjusting pH to a specified range. 



Recent developments: 2000s

After Good’s buffers became common knowledge, researches took advantage of flexible buffer technology. The ease of inventing compounds gives each laboratory license to pioneer new buffer mechanisms; furthermore, new technology and experimentation methods expand research opportunities. Recent decades have demonstrated the creativity of researchers who seek better devices for validating experiments. Their initiative to revise past substances advances biochemical techniques. We can visualize buffer advancement through a few novel systems, invented to improve research activity.

Retrieving results is the first priority of scientific research. Two studies in 2007 used new buffers to optimize data recovery from biochemical tests involving DNA. In an article on real-time polymerase chain reaction (PCR) analysis, researchers intended to improve the quantification and yield of replicated DNA using a combination of buffers with Tris. By using HEPES, MOPS or TAE alone or together in addition to Tris, the reaction’s efficiency was improved in terms of detection and measurement. Another project identified a pair of new buffers for use in plant DNA flow cytometry. Termed “general purpose buffer” (GPB) and “woody plant buffer” (WPD), these buffers produced quality results from samples. GPB was more applicable to softer tissue plants and WPD worked better with recalcitrant tissue. These original substances had higher productivity than buffers previously used for this technique, indicating a possible replacement for other solutions.

Inventing buffers relevant to multiple techniques can result in overall enhancements to biochemical analysis. All chemical substances have qualities that prevent them from being functional in all test circumstances. For buffers, limits are posed by cooling processes that reduce their efficacy. Cold temperatures can degrade buffer-maintained pH and damage frozen or refrigerated samples, but a 2008 research project designed a buffer which could combat the constraint. Buffers become either more acidic or more alkaline when cooled, so researchers combined solutions until they found the correct proportions to have a minimal pH shift of 0.2 (reduced from the 2 pH change seen in other buffers). Biochemical tests need maximally stable pH from which results can be confidently validated, so having this buffer mix at a lab’s disposal could optimize their experimentation.



(Click the image for an expanded version of the timeline)



Today’s researchers use decades of assembled knowledge to develop new, better compounds for stabilizing biochemical reactions. With such a reliable foundation for implementation, it’s obvious why buffers have proliferated throughout the field. Old buffer systems can be applied to emerging techniques, but more often new solutions are created to replace outdated ones. As Good’s team encouraged safe, inexpensive buffers, science encourages the discovery of productive buffers for conducting each test. We have high expectations for this category of substances – with the direction of visionary scientists, our methods can only improve.

Buffers purchasable from GoldBio



References

Ahmad, A., & Ghasemi, J. (2007). New buffers to improve the quantitative real-time polymerase chain reaction. Bioscience, Biotechnology, and Biochemistry, 71(8), 1970-1978. doi:10.1271/bbb.70164.

Ambler, J., & Rodgers, M. (1980). Two new non-barbiturate buffers for electrophoresis of serum proteins on cellulose acetate membranes. Clinical Chemistry, 26(8), 1221-1223. Retrieved August 1, 2017, from http://clinchem.aaccjnls.org.

Loureiro, J., Rodriguez, E., Dolezel, J., & Santos, C. (2007). Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species. Annals of Botany, 100(4), 875-888. doi:10.1093/aob/mcm152.

Roos, A., & Boron, W. F. (1980). The buffer value of weak acids and bases: origin of the concept, and first mathematical derivation and application to physico-chemical systems the work of M. Koppel and K. Spiro (1914). Respiration Physiology, 40(1), 1-32. doi:10.1016/0034-5687(80)90002-X.

Sun, H., Lau, K. M., & Fung, Y. S. (2010). A new capillary electrophoresis buffer for determining organic and inorganic anions in electroplating bath with surfactant additives. Journal of Chromatography A, 1217(19), 3244-3250. doi:10.1016/j.chroma.2010.01.011.

Thomas, J. M., & Hodes, M. E. (1981). A new discontinuous buffer system for the electrophoresis of cationic proteins at near-neutral pH. Analytical Biochemistry, 118(1), 194-196. doi:10.1016/0003-2697(81)90178-0.

Williamson, J. D., & Cox, P. (1968). Use of a New Buffer in the Culture of Animal Cells. Journal of General Virology, 2, 309-312. doi:10.1099/0022-1317-2-2-309.



                Megan Hardie
           GoldBio Staff Writer

Megan Hardie is an undergraduate student at The Ohio State
University’s Honors Arts and Sciences program. Her eclectic
interests have led to a rather unwieldly degree title: BS in
Anthropological Sciences and BA English Creative Writing,
Forensics Minor. She aspires to a PhD in Forensic Anthropology
and MA in English. In her career, she endeavors to apply the
qualities of literature to the scientific mode and vice versa,
integrating analysis with artistic expression.

Category Code: 79101, 79102, 79105, 88221, 88241

Posted by Rebecca on August 23rd, 2017  ⟩  0 comments

When doing research, using existing protocols and modifying them to suit your experiment can save you a lot of time if you know where to search. Here are 10 great protocol databases to check out.

When doing life science research, the best way to save time and increase your efficiency is to use and modify existing protocols. It is rare that you will ever need to come up with your own protocol from scratch and preexisting protocols can save you time. Finding protocols when you don’t know where to look can be time consuming and monotonous. To save you the effort of searching the internet high and low trying to find a procedure to follow, I have compiled 10 sources for protocols here and a brief description of each that goes over cost. Many of the protocols can be found at little to no cost so take advantage of them and you can spend more time doing the science that you love rather than hunting for reliable protocols for your experiment.

     
     

1. Supplier Protocols

When searching for protocols, one of the first places to look is on your supplier’s website. At GoldBio, we offer a variety of protocol types ranging from how to use our products, to preparing stock solutions and a guide for using our buffers. Check out our growing database of protocols and to see if your other suppliers offer protocols on their sites as well.

   
 
     

2. Protocol Online

Protocol Online is a large database of life science protocols provided by suppliers, researchers and labs around the world. It was created by POL Scientific, which publishes a variety of journals, including the Journal of Biological Methods. Protocols are divided into categories and subcategories making them easy to find. There is also a search feature to help you locate a protocol you need even faster.

     
   

 

3. Nature Protocols/Protocol Exchange

Nature has two different databases of protocols available online. Nature Protocols is a collection of vigorously peer-reviewed protocols that have been approved for publishing. These protocols are not free to access; however, there are a variety of sponsored protocols available at no cost.

Nature also has a database known as the Nature Protocol Exchange. At this site, users can upload any type of scientific protocol, but there is a focus on protocols related to life science research. This is an open source database so there are no fees for accessing protocols that have been uploaded by other users. There is no peer-review process that protocols go through before being published on the protocol exchange.

   

 
     

4. Springer Protocols

Springer offers a variety of protocols divided into categories. These protocols require a subscription to access and can therefore become quite expensive. Protocols have been reviewed by the site’s editor of that particular subject area. Additionally, there are about 150 free protocols available in their free protocol library. Springer’s protocols are written in a step-by-step manner similar to a recipe from your favorite cookbook.

   

 
     

5. Journal of Visualized Experiments

JoVE is a peer-reviewed journal that publishes visual experiments such as videos or images. The idea behind JoVE is that using visualized science, the reproducibility of protocols will be increased. Moreover, it will decrease the amount of time scientists spend learning new techniques because they will be able to follow along with the protocol visually. Many of the video protocols published on JoVE require a subscriptions, but there are also some available as open-access experiments.

JoVE publishes a wide variety protocol videos. Some of the methodologies featured in their journal are newly discovered or updated, while others are standard, common techniques. JoVE publishes works related to both the life and physical sciences and they are organized by subjects such as biology, immunology, engineering, etc.

   
 
     

6. Hivebench

Hivebench is an electronic lab notebook with a feature available for users to upload protocols to an open-access protocol database. Anyone can post protocols for public viewing and the protocols are not peer reviewed before becoming accessible to users. Protocols can be copied and pasted, and then edited directly in the Hivebench notebook. If you don’t use Hivebench for your lab notebook, don’t worry—the protocols are freely accessible even without opening a Hivebench account.

   

 
     

7. OpenWetWare

OpenWetWare is a wiki page set up in 2005 by graduate students at MIT. It was created to share discoveries and information in biology among members of the scientific community. The page features various sections including protocols, labs, and courses. You can add your lab to OpenWetWare by submitting a request to join. More importantly, protocols are free to access without creating an account. They’re organized by categories, but the site also has an option to search through their protocols so it is easy to find what you’re looking for.

   
 
     

8. Bio-Protocol

Bio-protocol is a site created by a group of biologists from Stanford. They saw an area where life science research was lacking—the reproducibility of experiments. The protocols are published and accessed at no cost, but must be related to the life sciences. They are detailed and peer-reviewed to ensure accuracy and reproducibility. Furthermore, there is a moderated question and answer forum associated with each protocol so if there are any areas of confusion, they can be addressed in a collaborative manner. You can access protocols by field of research or organism.

   
 
     

9. Protocols.io

Protocols.io is an open-source database of protocols for the life sciences. Similarly to Bio-protocol, researchers and suppliers can upload details protocols outlining improvements to existing procedures or just sharing a completely new experimental process. Researches can comment and leave questions on protocols. What sets Protocols.io apart from other protocol databases is that users can clone and edit protocols when they find out something new and want to update what the previous author had written. There is also an application where you can access Protocols.io from your mobile device and follow the experiments step-by-step, marking each instruction complete as you go.

   
 
     

10. SciGine

SciGine is a scientific methods search engine designed to search the web and its database of updated protocols for scientific methods. After finding a protocol, you can edit it to match exactly how you performed your experiment. You can then save your new edited copy and share with colleagues at your own discretion. SciGine also features a blog that provides techniques and tips for some of the most common biologic procedures such as the Western Blot.

All of these online tools can help you find protocols quickly. If there is a protocol that you cannot find, you can also turn to books such as “Current Protocols in Molecular Biology.” Sometimes you will find a protocol that is for something similar to the experiment that you want to perform, but will have to tweak and alter it to find your needs. When compiling, writing and editing your own protocols, read our article Protocol Writing in the Life Sciences.

In the interest of sharing, feel free to submit your protocols to GoldBio if you feel they might help others in the field.

     
     

    
              Rebecca Talley
         GoldBio Staff Writer


Rebecca is a medical student at the University of Missouri.
She previously worked as a lab technician while studying
biology at Truman State University. As an aspiring
reproductive endocrinologist with an interest in global
health, Rebecca has traveled across Central America on
medical mission trips. With a passion for the life sciences,
she enjoys writing for GoldBio.

 

Category Code: 79107, 79108, 79109