Category Archives: November 2015

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

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

Techniques – Wild, Wild West(erns)

Need some help to tame that wild western blot? Here are some tips and tricks to help you along the way –

  • Always check ladder migration pattern based on specific gel and electrophoresis conditions, as these factors can shift the apparent molecular weights from the supposed “standard” ladder image given out by the company.
  • When testing a new antibody, leave the blot intact, opting to strip it and perform a control protein blot after probing for your target protein. Cutting the blot and using different pieces for your target and control protein on a first try may obscure alternative target protein isoforms or off-target background staining.
  • High background? Try a more stringent blocking condition than just BSA or milk by adding goat serum or fish gelatin to your solution. Blocking overnight also can help clean up your blots.
  • Is you gel “smiling” or “frowning”? This usually happens when your sample buffer has too much salt.
  • Make sure your PVDF membrane is pre-activated with methanol for 20 minutes before making gel sandwich. It’s also a good idea to mark which side of the membrane is facing the gel with a sharpie, on a top corner.
  • It’s always a good idea to do a Ponceau stain on your membrane after transfer to make sure your transfer went all right. Alternatively, you can also stain your gel with Coomassie blue.
  • It is possible to over-transfer, especially for low MW proteins (<10 kDa) – optimize transfer time or reduce voltage. On the other hand, high MW proteins will take longer time to transfer.
  • Have a dirty secondary? Consider adding a wee-bit of Tween-20 to your washes (0.01-0.5%).
  • When loading your samples, press on the pipet just enough to get any possible air bubbles out and run the tip through the running buffer in the tank before putting it in the well. And make sure your sample was denatured prior to running.
  • If power supply reading shows 0 when switched on, make sure your power cables are properly connected to the power supply. If that doesn’t work, check for broken electrodes or blown fuses. Lastly, try with a higher limit power supply.
  • As always, make sure you write down the protocol before-hand and check through every step when performing. This will help you track your steps back to see at which step things could have gone wrong.


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Meating adjourned?

Meat-eaters’ Misery and Vegetarians’ Victory? 

On 29th October of this year, the Lancet Oncology published a report on the carcinogenicity of red meat and processed meat [1]. The Working Group, consisting of 22 scientists from 10 different countries, recommended to the International Association of Research on Cancer (IARC) (part of the World Health Organization) to classify processed meat to be “carcinogenic to humans” (Group 1) and red meat to be “probably carcinogenic to humans” (Group 2). These recommendations were made after evaluation of more than 800 epidemiological studies.

Since the publication of the report, mainstream media has picked it up with a fervor that painted the report with a facade of novelty. However, as Tufts University’s very own Dariush Mozaffarian  (Dean of Friedman School of Nutrition Science) pointed out in an interview with National Public Radio (NPR), this report only served to solidify what has been known for quite a while now.

Given the significant associations made between cancer risk and consumption of red and processed meat, what is the public supposed to do?


Besides following Chik-fil-A’s advice, here is what you need to know before you decide get well done with meat.

Red meat include beef, lamb, pork, goat. Processed meat include anything that has been cured, salted, smoked, or preserved in some way, e.g. – sausages, bacon, hot dogs, etc.

What did the IARC find?
Colorectal/bowel cancer showed the strongest association with high red and processed meat consumption. Positive associations were also seen between red meat consumption and pancreatic and prostatic cancers, and between processed meat consumption and cancer of the stomach [1].

How scary are these findings?
The Working Group found that there is a 17% increased risk of colorectal cancer for those who ate the most processed and red meat compared to those who ate the least [1]. Is this number really big? As Cancer Research UK blogged, the “17%” represents a relative risk; out of every 1000 people in the UK, 61 people develop bowel cancer at some point in their lives compared to about 56 cases per 1000 low meat-eaters. Therefore, according to the analysis, a 17% increased risk translates to 66 people per 1000 would develop bowel cancer at some point in their lives [2].

However, labeling processed meat as cancer causing and red meat as probably cancer causing does little to soothe our worries. But! As Cancer Research UK points out, IARC does “hazard identification” and not “risk assessment” [2]. Therefore, IARC classifications can only provide a qualitative assessment and does not tell us how potent something is in causing cancer. This is exemplified when red/processed meat is compared to tobacco, which is also classified into Group 1. In the UK, excessive consumption of red/processed meat resulted in 3% of all cancer cases annually whereas smoking caused 19% of all annual cancer cases.

Credit: Cancer Research UK

How to balance your bacon
Dariush Mozaffarian suggests no more than, one or two servings of processed meat per month and of red meat per week.  For more customizable options, check out the awesome infographic from Cancer Research UK below –

Credit: Cancer Research UK

So, as with everything, MODERATION IS KEY! Unless, of course  you are Ron Swanson.

While the meat industry does not agree with the recommendations based on scientific evidence to eat less meat [3], nothing topped the Far Right’s claim that this must be a Muslim Conspiracy to establish Sharia Law [4].

1. Bouvard, V et al 2015 Lancet Oncology. doi:10.1016/S1470-2045(15)00444-1.
2. Dunlop, C. 2015. Processed meat and cancer- what you need to know. Cancer Research UK, Science blog.
3. Aubrey A. World Health Organization Report Links Red, Processed Meats to Cancer. National Public Radio.
4. Bartlett, E. 2015. The World Health Organisation says bacon is carcinogenic and right-wingers think it’s a Muslim conspiracy. Independent.–ZJLDa_0B_l


On the Shelf (November 2015)

For work…

Electronic Resource: Knovel

Location: Search for ‘Knovel’ in E-Resources Finder (

Collection of engineering and applied science reference books and databases. While this collection is designed for engineers, it does cover biochemistry, biotechnology and pharmaceutical topics. A unique search feature of Knovel allows you to find data within tables, graphics and equations. Two particularly useful resources in this collection are Knovel Critical Tables and the Biology Data Book. Knovel Critical Tables are a set of interactive tables of constants and physical, electrical and thermodynamic properties. The Biology Data Book is an old, but indispensable resource that provides basic biomedical data for biological substances and hundreds of organisms, including humans and common laboratory species.

And leisure…

Room cover

Room, by Emma Donoghue

Location: HHSL Leisure Reading Fiction D687

This 2010 novel, told from the perspective of a 5-year boy, tells the story of a woman and her son held captive in a single room. This riveting and thought-provoking book has recently been made into a movie.

-Laura Pavlech

Upcoming Library Events (November 2015)

Open Workshop: Using Images

Wednesday, November 4th & Thursday, November 5th, 12-1 PM

Sackler 510


This workshop will survey image collections licensed by Tufts and show you how to find images available in the public domain. Options for storing, displaying and citing images will also be discussed.


Open Workshop: Basic PubMed

Wednesday, November 18th & Thursday, November 19th, 12-1 PM

Sackler 510


This workshop will review: the structure of PubMed; planning and executing a search; narrowing search results; finding full text and exporting citations into citation management programs, such as EndNote and RefWorks.


Fun Fridays: Elementary School Throwback

Friday, November 20th, Time TBD

Library Service Desk, Sackler 4

Come make hand turkeys and other crafts that will remind you of your younger days!

-Laura Pavlech

PubMed Tip of the Month: Clipboard (November 2015)

The Clipboard feature in PubMed allows you to temporarily store citations for review; items are deleted after 8 hours of inactivity. To place citations on the Clipboard, check the box to the left of an article title on the results page. Choose Clipboard from the Send to menu at the top of the page. Click Add to Clipboard. An icon will appear at the top of the page with a link showing the number of items on your Clipboard. I use this feature in a two-step review process. When I am satisfied that I have a good search, I do a first pass through the results, quickly scanning the title of each article and checking the box for any citation that may be relevant. I send these items to the Clipboard. Once I have completed the initial review, I go to the Clipboard, change the view from Summary to Abstract (menu at the top of the page) and read the abstract of each article to decide whether or not it is truly relevant.

-Laura Pavlech

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 ( provides a brief list of databases. A complete list of biomedical databases available at Tufts can be found here: 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 (!/; 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 (

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: Submit requests via ILLiad (

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 ( 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