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Ten Cardinal Rules For Being a Lab Scientist

Guest Post by Ania Wronski, PhD.

  1. Write everything down

Whether you are learning a technique from someone or you are running you thousandth PCR reaction, if you do something different or noteworthy – write it down. I assure you, when months down the line you need to repeat a similar reaction (and you will!) you will NOT remember the conditions that you thought were so obvious that you didn’t write it down. Even details that may not seem very significant – like, I had a longer lunch so my blot was in blocking solution for 2 hours instead of one, may make a big different to the end result and knowing why may vastly improve your reproduction of the results.

  1. Be organized

When you start a project, identify a storage structure and STICK TO IT. This sounds relatively simple, but it isn’t! Are you going to organize your scientific literature by topic? What if it covers multiple topics? What filename will you use to save it? How are you going to organize your data? By experimental type? Date? Project? You want to be able to find things relatively easily and NOT have multiple copies of the same or similar files floating around.

Same goes for labelling tubes. Please, for the love of the PCR fairy, please DO NOT label your tubes 1-8. At least put the date and some redeeming feature. One of the best things to do is to log it in a database with its details and location so you have the capacity to search for it electronically – but it does take time to establish these systems and it is often MUCH harder to go back and re-organize your samples once you have 4 boxes of plasmids and several boxes of primers…

  1. Be consistent

Science is already hard – why make life harder for yourself? When you get in stock solutions, make them to a nice, repeatable number. Dilute primers to 50 or 100uM every time you get a new primer tube. That way, you don’t need to look up what you did. It is a standard dilution for all your primers. This also leads to better science as consistency is often the best way to reduce variability and increase the reproduction of results. Passage cells a certain way? Why deviate? You could be introducing variability that may influence your downstream applications.

  1. Re write protocols for a dummies guide.

You could be a cloning god or goddess, but what happens when you don’t have to do a technique for an extended period of time? You forget. Re-write your protocols so they explain all the steps, including the little quirks that you discovered are the keys to success. This is especially important for logins to shared equipment that you may not access very frequently (I.e. the nanodrop password on level 5 is DropitLikeItsHot). I often write several versions of protocols: a lengthy “extended” protocol with explanations and detailed information and a short “mini” protocol that I can just fill out the blanks as I need for the experiment. One warning about having spreadsheet protocols: you can accidentally introduce errors and not even realize it! So it’s always good to check your spreadsheet or have some “control” calculations that will let you know if something is wrong.

  1. Make sure you use the appropriate controls!

If an experiment fails, controls can help you determine if it was a technical failure or a negative result (same with the inverse – a positive result or a technical glitch). Many may think that controls are a waste of time and reagents, however controls are more important than your experimental sample because it tells you if your result can be trusted. You are only as good as your positive and negative controls!

  1. Understand your techniques

Nowadays there is a kit for everything technique conceivable – the age of convenience has hit the world of scientific research. Although kits can make your experiments much easier, they are also a very easy way to become complacent. If you don’t know how an experiment actually works, you won’t know the limitations of your results and the conclusions you can or cannot draw from them. In addition, troubleshooting is MUCH easier if you understand the rationale behind how an experiment works.

  1. Never stop learning

The vast majority of scientists has an innate desire for knowledge – it’s why we are scientists to begin with! You can learn something from everybody, from the new grad student to the seasoned postdoc. This includes the lab down the hall working on a random organism that doesn’t seem related. Some of the greatest discoveries in science came about when multiple fields crossed paths. Never turn down an opportunity to learn, as your knowledge is your best asset as a scientist.

  1. Ask for helpEveryone is always busy so it can seem daunting to ask someone with a full plate for help. However, you are surrounded by incredibly skilled and intelligent individuals. If you do not ask, you cannot ever receive. When you do ask, try to be mindful of their time, maybe even email them to ask for a good time to sit down and chat with them. Know what you want to ask and make sure it’s not an answer that can be relatively easily answered by google or a lab protocol that is easily accessed. Much of the knowledge of science is passed down from lab member to lab member.
  1. Don’t think about the how, think about the WHY
    When you are the bench, it is very easy to fall into a pattern of simply doing experiments because that feels comfortable. A great scientist will consider why they are doing an experiment. Before you rush into anything new, sit down and consider all of your data. What is it telling you? What would the next logical step be? What question are you really asking? What is the big picture? It is pointless to mindless conduct experiments if they will not help further your question and the eventual result. Even if you know it is highly unlikely that you will achieve your end goal, you should still one in mind.
  1. Be prepared for change.
    Two years ago, CRISPR sounded like a type of cracker, nowadays it’s the hot new technique. Science is dynamic and is constantly changing. You need to be prepared for these and be amendable to changes, whether it be new techniques, a change in direction or even location. If you are working in industry, it is common for projects to suddenly be terminated or drastically change, even if everything is going well. In academia, we are not as efficient at culling projects and tend to beat the proverbial dead research horse because we really want a project to work out. One critical skill of a researcher is to know when they have hit a dead end and to move on. It is extremely difficult and you often need to convince powerful people (i.e. your PI) that it’s the right decision.

Originally published on AdageOfAnia.com

 Ania is a post-doctoral fellow in the Kupperwasser lab and blogs regularly about “Science!” at www.adageofania.com

Notes from the Library…Finding Journal Articles (November 2015)

How do I find journal articles about…?

The best place to search for journal articles is a bibliographic database, such as PubMed or Web of Science. Bibliographic databases index and organize citations to published literature, such as journal, newspaper and magazine articles or books and book chapters. Databases are often devoted to specific subjects, such as life sciences or engineering, and have sophisticated search features that allow you to retrieve relevant results.

How do I choose which database to search?

Tufts subscribes, or otherwise provides access to, hundreds of databases. When choosing a database, consider the subjects, dates and types of material (journal articles, books, conference proceedings, patents, etc.) that the database covers. The Find Articles page of the Biomedical Sciences Resource Guide (http://researchguides.library.tufts.edu/biomedical_research) provides a brief list of databases. A complete list of biomedical databases available at Tufts can be found here: http://www.library.tufts.edu/hsl/resources/dbases.html. Depending on your topic and purpose, you many need to search more than one database. When in doubt, just ask!

What about Google Scholar?

Google Scholar uses an algorithm to search scholarly literature available on the web. Like Google, results in Google Scholar are ranked and displayed according to relevance, with few options to filter the results. The careful selection of materials, indexing, and search capabilities of databases mean that you will usually get more precise results than a search in Google Scholar. I use Google Scholar to: supplement searches that I have done in databases; find grey literature (literature produced by government, academia, business or organizations and made available by means other than commercial publishers, for example, reports or white papers); find the full text of an article.

How do I find the full text of an article?

If you have found the article in a database, then look for the blue ‘Find It@Tufts’ button, which should take you directly to the full text if it is available through Tufts. Remember, you must access PubMed via the library homepage to see this button.

If you access Google Scholar from the library homepage, then you will see a ‘Get This Item at Tufts’ link if the article is available electronically through Tufts Libraries.

If you have the title of a journal article and want to know whether or not the full text is available through Tufts, simply copy and paste the title into JumboSearch (http://tufts.summon.serialssolutions.com/#!/; also accessible from the library homepage).

An article that I want is only available in print at a Tufts library. Does this mean that I have to go to the library to retrieve it?

No! If an article is available in print at any Tufts library (including Hirsh Health Sciences Library), then you can request that it be scanned and delivered to you electronically. This service is free and there is no limit to the number of requests that you may submit. Submit requests via ILLiad (https://illiad.library.tufts.edu/illiad/TFH/logon.html).

What if the full text of an article that I need is not available either in print or electronically at Tufts?

If an article is not available at Tufts, then you can submit a request for the article to be retrieved from another library and delivered to you electronically. Students have 20 free requests per academic year for items from non-Tufts libraries. A $4 fee per request will be charged once the 20 request limit has been surpassed (for more information, see: http://www.library.tufts.edu/hsl/services/docDelPolProc.html). Submit requests via ILLiad (https://illiad.library.tufts.edu/illiad/TFH/logon.html).

What if I want to browse the contents of specific journals?

The easiest way to browse and read journals available through Tufts is to use BrowZine, a mobile app that provides direct access to (most) of the journals that Tufts receives electronically. Available for free for both Apple and Android devices, this app allows you to: view current and past journal issues; create a bookshelf of journals of interest to you; and save articles for later reading. BrowZine recently released a web version of their service (http://www.browzine.com/). If you access this site from on campus, then you will be brought directly to the Tufts BrowZine Library. If you access the site from off campus, then select Tufts University and log in with your Tufts username and password. Eventually, you will be able to sync your bookshelf and reading lists between the web version and app. The library does receive some journals in print; current print issues can be found on the 4th floor of Sackler, older issues on the 7th floor.

-Laura Pavlech

PubMed Tip of the Month: Using MeSH Headings (October 2015)

Including MeSH terms in a PubMed search can help you get more precise results.

What is MeSH? Most of the more than 25 million citations in PubMed come from MEDLINE, the National Library of Medicine’s (NLM) journal citation database. Medical Subject Headings (MeSH) is a controlled vocabulary of standardized terms that indexers (actual humans!) apply to each article in MEDLINE to describe the publication type and topics covered in the article.

Why should you care about MeSH? Biomedical topics are often expressed in different ways. For example, chronic kidney disease may also be called end-stage renal disease, chronic renal failure, or abbreviated as ESRD. The MeSH term for this condition is kidney failure, chronic. Using MeSH terms in a PubMed search helps you find articles regardless of how an author referred to that topic. MeSH terms also allow you to search on all concepts in a broad category without having to enter every term. MeSH headings are arranged in a hierarchy of broader and narrower terms; when you search a broader term, all the narrower terms are automatically included in your search. For example, the MeSH term for cancer, neoplasms, can be used to search for all types of cancer.

How do I find MeSH terms? When you conduct a search in PubMed, the database will try to match your terms to MeSH headings in a process called automatic term mapping. To see how the PubMed translated your search, look for a box labeled ‘Search Details’ in the right column on the results page (you will need to scroll down the page). You can also search the MeSH database directly by choosing ‘MeSH’ from the dropdown menu to the left of the PubMed search box. See this example of the term meningitis in the MeSH database: http://www.ncbi.nlm.nih.gov/mesh/68008581.

Need help with MeSH? Contact me at laura.pavlech@tufts.edu or 617-636-0385.

-Laura Pavlech