Tag Archives: November2015

April 2017, articles, arts & culture, Community, Events for Students

CMDB and Genetics Programs Come Together in Portland, Maine

For the first time, the Genetics and CMDB programs came together for a retreat in Portland, Maine for the snow and slush-filled weekend of April 1st. The retreat brought together students from different programs to interact and learn more about one another’s’ research, as well as students from different campuses. Both the Boston and the Bar Harbor Jackson Laboratories contingents made it to Portland to join the Scarborough Maine Medical Research Center Institute (MMCRI) folks for a weekend of science and camaraderie. Students and faculty gave brief talks on their work, followed by a poster session and a fantastic keynote speech on storytelling was given by Christine Gentry. Read on for details on the weekend, written by Jessica Elman (CMDB, Boston Campus), Jessica Davis-Knowlton (CMDB, MMCRI), and Alexander Fine (Genetics, JAX).  

We kicked off the retreat with a marathon of 16 talks given by students in year four and up from the CMDB and Genetics programs. Given the challenge to present a summary of their work in seven minutes or less, the students delivered with presentations that were brief but pointed. Three winners were selected by Philip HInds, Ira Herman, and Rajendra Kumar-Singh for their exceptional clarity, creativity, and concision.

In third place, Melissa LaBonty, a 5th year CMDB student in Pamela Yelick’s lab, presented on her work studying Fibrodysplasia Ossificans Progressiva (FOP). In this rare and severely understudied disease, an abnormal wound repair mechanism results in bone ossification in soft tissue after damage or injury. LaBonty is working with zebrafish to create a model of FOP, which will help to better characterize the disease and understand the underlying mechanisms that drive its progression. In her presentation, LaBonty spoke clearly and at an even pace, with assisting powerpoint slides that displayed only the most essential words: together this style helped keep the group focused on her story and contributed to her ranking as one of the best speakers of the day.

 

Siobhan McRee, a 5th year Genetics student in Philip Hinds’ lab, came in second among the student presenters. McRee talked about her work in which she is elucidating the roles of different Akt isoforms in BRAF-mutant melanoma. Though this cancer is initially responsive to the drug Vemurafenib, which specifically targets cells with a BRAF-mutation, cells with other driving mutations manage to survive the drug treatment and clonally expand, resulting in significant and potentially deathly relapse of disease. Ultimately, McRee’s work will help to better understand how the Akt signaling pathway is involved in this disease and may result in more therapeutically targetable molecules. McRee’s story logically built from general facts and understanding of BRAF melanoma to ultimately culminate on more specific data showing her findings thus far as well as their implications. Furthermore, her even pace and well-organized slides made her an especially great presenter that day.

Coming in first place was Kayla Gross, a 4th year CMDB student in Charlotte Kuperwasser’s lab. Gross’s work involves understanding how aging contributes to the breast cancer development, and why certain subtypes of breast cancer are more prevalent in the aging population. Given the prevalence of breast cancer, the impactfulness of Gross’ research is immediately obvious. She worked with an aging mouse model to characterize their mammary tissue as well as performed an RNAseq experiment to uncover molecular mechanisms that might be differentially expressed in young and aging mouse tissue. Gross presented her data in a logical progression, and used illustrative cartoons and animations to her advantage to keep her audience focused and to get her point across. Besides for her brilliant and captivating powerpoint, Gross stood out for her speaking style: she had clearly chosen her words to be concise and to the point, which allowed her to make the most of the seven minutes allotted to her.

All in all, the student presentations were remarkably impressive: in just seven minutes, all the participating students managed to convey the most critical and interesting components of their research. This was a great opportunity for everyone to learn a little bit more about what our colleagues are working on, as well as a chance to practice our “flash talk” skills, which will come in handy whether it’s at a job interview or at Thanksgiving table when your uncle asks you to explain what you’re doing in graduate school for the third time.

The Story Collider’s Christine Gentry, PhD as keynote

It was suggested by Terry Pratchett, Ian Stewart, and Jack Cohen in The Science of Discworld II: The Globe that perhaps Homo sapiens as a name for our species is a bit of a misnomer considering we are not omnipotent beings. They suggest Pan narrans, the storytelling ape, because we gain understanding by fitting facts into a larger narrative rather than collecting and storing millions of pieces of disparate information.

As communicators of new knowledge to the world (i.e. our scientific findings), it is important for us to keep the nature of our listeners in mind. In her keynote presentation to the retreat, Story Collider’s Christine Gentry, PhD encouraged us all to think about how to frame our narratives to be more approachable and demonstrated some methods of drawing in an audience.

She immediately captured our attention and sympathy by describing the challenges she faced in a wending career path that started with her geek excitement to bring a black widow spider to her Texas elementary school show-n’-tell, traversed through public outreach on the topic of zoology, and has landed at teacher/storyteller in Boston.

She required us to engage with her material by highlighting snippets of stories that we examined in small groups to find the element that made them compelling. We saw that admitting to vulnerability helps to humanize us to our audience in the story from a researcher who relies on fresh donor tissue, that self identity makes us more honest in the story from a researcher who decided not to cover her tattoos, and that we can surprise our audience by not sticking to script in the story from David who refused to tell the inspiration arising from conflict story that reporters sought to box him into. The thread tying all these stories together is that at the core they are about relationships with others, ourselves, our work, and with the larger community.

Perhaps the most memorable take-home point from her talk is that anecdotes do not equal stories. The response to most anecdotes is naturally “so what?” In order for an event or experience to be a story, it must have changed you: “I was callus, this event happened, and now I am more thoughtful” rather than “I am amazing, I did this, and I am still amazing!”

Scientific inquiry must be done in an objective manner and it is imperative that we remain unbiased as possible when we review scientific evidence, but there is room for us to inject our personalities into our presentations and relate our findings to the people who care. Now it remains to us to decide when to do so and to what degree.

On Sunday morning, we took a break from data and lectures; it was time to start working together. The purpose of this retreat was cross-program cooperation, and in our final event of the weekend, we put that goal into action. We separated into breakout sessions, not by program or campus, but by what we are interested in. These small group discussions were designed to get people together with various strengths and experiences to think about how to solve some of the challenges that graduate students face.

So what are graduate students at Sackler interested in discussing? The topics of these breakout sessions varied. Some sessions focused on day-to-day problems that a graduate student might face, like using CRISPR/Cas9 or selecting a sequencing platform. In the CRISPR discussion, participants came to the conclusion that there are no specific shared standards for all the applications of CRISPR and identified strategies to address potential off-target effects.

Other discussions centered on how to accomplish broader training goals, including grant writing, mentoring, and communicating in science. The grant writing section reviewed general writing strategies, like setting short-term, realistic goals, and shared a need for a formalized grant-writing course at Sackler. The mentoring/leadership session discussed existing programs at Sackler where a student can find a mentor, like the Tufts Mentoring Circles and the Tufts Biomedical Business Club. Students expressed a need for a more accessible alumni network, including cross-institutional resources. In the scientific communication group, students were urged to get on social media platforms like LinkedIn, Twitter, and ResearchGate.

In two of the largest breakout sessions, participants concentrated on solving larger scale problems: designing coursework for a modern graduate program in biology and bridging the gap between science and medicine. To help bridge the gap between scientific research and medicine at Tufts, the discussion group recommended that faculty members be identified that can connect labs with clinicians and tissue banks. In addition, access to a course that provides a basic orientation to clinical research would benefit many students at Sackler. In the session on coursework for a modern graduate program, one topic became the clear center of the discussion: computational biology! Whether students had struggled through teaching themselves or were currently stuck with a dataset they didn’t know how to analyze, everyone in the room agreed that coursework in computational biology was crucial for a graduate student’s success in modern biology. In addition to new coursework, students from both programs expressed a need for a revision and update of their first year coursework.

While all of the breakout sessions at the retreat were productive, they are meant to be starting points for continued discussion and collaboration. This retreat should be the springboard that leads to action across programs and institutions. Sackler students are lucky to be in programs that span multiple states, campuses, and research focuses. The cross talk between these groups will make each of our programs stronger and better prepare us for our careers in the future.

articles, November 2015

2015 Charlton Lecture and Poster Competition

The Charlton Lectureship, named in honor of Mr. Earle P. Charlton, has been held annually since 1975. This celebrated lectureship has evolved over the years to include a student poster competition. Held in conjunction with the lectureship, the poster competition is a platform to recognize outstanding research work being done by Tufts graduate, medical, dental, and veterinary students. The Charlton Poster Competition and Lecture are sponsored and hosted by the Academic Research Awards Committee of the Tufts University School of Medicine.

This year’s lecture was held on October 27, 2015, in the Sackler DeBlois Auditorium. The 2015-16 Charlton Lecturer was delivered by Virginia M.-Y. Lee, PhD. Dr. Lee obtained her PhD in Biochemistry from the University of California in San Francisco (1973) and an MBA at the Wharton School of Business (1984).

Dr. Virginia Y M Lee, 2015 Charlton Lecture Speaker
Dr. Virginia Y M Lee, 2015 Charlton Lecture Speaker

Dr. Lee is the John H. Ware 3rd Chair for Alzheimer’s Research, and directs the center for Neurodegenerative Disease Research at the University of Pennsylvania’s Perelman School of Medicine. Dr. Lee’s work was instrumental in demonstrating that tau, α-synuclein, and TDP-43 proteins form unique brain aggregates with a central role in numerous neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis.

The poster competition was held on October 26, 2015 with finalists competing again the following morning. Students with similar levels of training are evaluated with their peers:

Sackler Senior Category: Sackler biomedical PhD students in years 4 and above, MD/PhD students in Sackler years 4 and above, and Sackler CTS PhD students

1ST PLACE – Kevin Goncalves, CMP
Angiogenin promotes hematopoietic regeneration by dichotomously regulating quiescence and expansion of stem and progenitor cells

2ND PLACE – Jennifer Shih, NRSC
Partial genetic deletion of the astrocytic glutamate transporter GLAST disrupts organization of the cerebral cortex and causes network hyperexcitability

3RD PLACE – Brian Lin, CMDB
Neuronally committed progenitors can dedifferentiate, become multipotent, and generate nonneuronal cell lineages following injury

Sackler Junior Category: Sackler PhD students in years 1-3, MD/PhD students in Sackler years 1-3, and Sackler MS students

1ST PLACE – Joseph Sarhan, IMM
Basal levels of Interferon β Regulates Necroptosis in Macrophages

2ND PLACE – Danish Saleh, NRSC
Kinase activities of RIPK1 and RIPK3 are required for GNB-induced IFN-I synthesis

3RD PLACE – Payel Ghatak, GENE
Digital ELISA Based Ultrasensitive Strategy to Detect microRNAs at Subfemtomolar Concentration.

Professional Category: All Medical, Dental, and Veterinary Medicine students and MD/PhD students in TUSM years 1 and 2.

1ST PLACE – Mary Tam, Medical
The HBP1 Gene: A Pre-clinical Model for Genetic and De novo epilepsies

2ND PLACE – Seda Babroudi, Medical
A Novel Compound, Membrane-Tethered E2, Selectively Activates the ER Rapid Signaling Pathway – Implications for Vascular Benefit

3RD PLACE- Marianna Papageorge, Medical
Cyst Aspiration of Endometriomas Prior to In-Vitro Fertilization

Congratulations to all participants, finalists, and award winners.

Sackler Charlton winners 2015
Charlton Poster Award Recipients 2015. Left to right – top, Kevin Goncalves, Danish Saleh; bottom – Mary Tam, Jennifer Shih, Brian Lin, Mariana Papageorge.
articles, arts & culture, November 2015

2015 Nobel Prizes in the fields of Physiology or Medicine and Chemistry

First awarded in 1901; The Nobel Prize is widely regarded as the most prestigious award available in the fields of physiology or medicine, chemistry, physics, economics, and literature. Nobel Prizes are awarded annually in recognition of outstanding academic, cultural and/or scientific advances. Each Nobel Laureate receives a Nobel Foundation medal, a diploma, and a sum of money, which is decided by the Nobel Foundation. As of 2012, each prize was worth approximately $1.2 million (USD).

This year, Nobel prizes in the fields of physiology or medicine and chemistry were awarded for: discoveries concerning a novel therapy against malaria and infections caused by roundworm parasites; and mechanistic studies of DNA repair, respectively.

Novel Therapies for Parasitic Infections

Nobel-2015-Medicine-people
(Ill. N. Elmehed. © Nobel Media AB 2015.)

Diseases caused by parasites have plagued humankind for millennia and constitute a major global health problem. In particular, parasitic diseases affect the world’s poorest populations and represent a huge barrier to improving human health and well-being. This year’s Nobel Laureates for the field of physiology or medicine developed therapies that revolutionized the treatment of some of the most devastating parasitic diseases. The Nobel was awarded ½ to Youyou Tu and ¼ each to William C. Campbell and Satoshi Ōmura.

Youyou Tu is recognized for her discovery of Artemisinin, a drug that has significantly reduced the mortality rates for patients suffering from Malaria. William C. Campbell and Satoshi Ōmura are recognized for their discovery of Avermectin, the derivatives of which have radically lowered the incidence of River Blindness and Lymphatic Filariasis, as well as showing efficacy against an expanding number of other parasitic diseases. These two discoveries have provided humankind with powerful new means to combat debilitating diseases that affect hundreds of millions of people annually.

The discoveries of Artemisinin and Avermectin have fundamentally changed the treatment of parasitic diseases. Malaria infects close to 200 million individuals yearly. Artemisinin is used in all Malaria-ridden parts of the world. When used in combination therapy, it is estimated to reduce mortality from Malaria by more than 20% overall and by more than 30% in children. For Africa alone, this means that more than 100 000 lives are saved each year. Today the Avermectin-derivative Ivermectin is used in all parts of the world that are plagued by parasitic diseases. Ivermectin is highly effective against a range of parasites, has limited side effects and is freely available across the globe. The importance of Ivermectin for improving the health and well-being of millions of individuals with River Blindness and Lymphatic Filariasis, primarily in the poorest regions of the world, is immeasurable. Treatment is so successful that these diseases are on the verge of eradication, which would be a major feat in the medical history of humankind.

The discoveries of Artemisinin and Avermectin have revolutionized therapy for patients suffering from devastating parasitic diseases. Tu, Campbell, and Ōmura have transformed the treatment of parasitic diseases. The global impact of their discoveries and the resulting benefit to mankind are truly unfathomable.

 

 

 

The cells’ toolbox for DNA repair

lindahl-modrich-sancar-25
(Ill. N. Elmehed. © Nobel Media AB 2015.)

Each day our DNA is damaged by UV radiation, free radicals and other carcinogenic substances, but even without such external attacks, a DNA molecule is inherently unstable. Thousands of spontaneous changes to a cell’s genome occur on a daily basis. Furthermore, defects can also arise when DNA is copied during cell division, a process that occurs several million times every day in the human body. The reason our genetic material does not disintegrate into complete chemical chaos is that a host of molecular systems continuously monitor and repair DNA.

The Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich and Aziz Sancar for having mapped, at a molecular level, how cells repair damaged DNA and safeguard the genetic information. Their work has provided fundamental knowledge and insight into how a living cell functions.

In the early 1970s, scientists believed that DNA was an extremely stable molecule, but Tomas Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible. This insight led him to discover a molecular machinery, base excision repair, which constantly counteracts the collapse of our DNA.

Paul Modrich has demonstrated how the cell corrects errors that occur when DNA is replicated during cell division. This mechanism, mismatch repair, reduces the error frequency during DNA replication by about a thousand fold. Congenital defects in mismatch repair are known, for example, to cause a hereditary variant of colon cancer.

Aziz Sancar has mapped nucleotide excision repair, the mechanism that cells use to repair UV damage to DNA. People born with defects in this repair system will develop skin cancer if they are exposed to sunlight. The cell also utilizes nucleotide excision repair to correct defects caused by mutagenic substances, among other things.

These Nobel Laureates have provided fundamental knowledge and insight into how a living cell functions. Their respective breakthrough discoveries have been applied and used for the development and advancement of novel cancer treatments.

articles, arts & culture, November 2015

Movie Review: The Martian

Who wouldn’t want to be a space pirate? Granted, if you had to be stranded alone on a barren planet for over a year for that chance to happen, it might not be so appealing. Still, space pirate: think of the possibilities.

It is this optimistic, jocular tone that Ridley Scott’s The Martian, based on the book by Andy Weir, takes as it follows astronaut and botanist Mark Watney, played by Matt Damon, through the trials and tribulations of having to remodel rudimentary living conditions after being presumed dead and left behind by his crew during a mission to Mars. Stranded initially without means of communication to Earth, Watney’s life-saving ventures range from making water using hydrogen and oxygen gas (which almost gets him blown up) to growing potatoes in a homemade greenhouse (you don’t want to know where he got the fertilizer for that project, just saying). His life gets a little less difficult when an observant mission control operator notices a moving rover on the satellite surveillance of Mars’ surface late one night, giving those on Earth the first sign that Watney is in fact alive. With some quick thinking and teamwork, they rig up a way to communicate and suddenly Watney isn’t so alone anymore. They continue to help him survive in the harsh conditions of the planet, which he does all to the lively beats of disco hits, as that is apparently all his team’s commander, played by Jessica Chastain, loaded into the system during their stay, much to his chagrin.

The 1970s soundtrack calls back to the post-space race era, using the backdrop of where we have been to throw into sharp relief how far we have come, and also how far we can still go in exploring the stars. Still, The Martian, at its heart, is not a two-hour promotion for NASA and its programs. Though it does get ample on-screen time, political maneuverings and calculated public relations decisions made in board rooms rival the time spent problem solving in mission control or the Jet Propulsion Laboratory (JPL), giving the organization an almost ominous corporate vibe. Driven by Jeff Davis’ performance as the callous program director, NASA becomes the antagonist when the decision is made to keep the news of Watney’s survival from his crew, who are making their way back to Earth, in an attempt to keep their focus on the mission to return home safely.

It is this theme–balancing the lives of several versus one–that refracts throughout the back half of the film, making the humanity of this survival story begin to outshine the science in a subtle and heartwarming way. Thus it comes as no surprise that the returning Ares III crew chooses to risk their lives in a genius attempt, crafted by an eccentric but endearing JPL engineer, to change course and retrieve Watney even though NASA initially rejects the plan. As every pirate adventure should, mutiny and risky swashbuckling ensue, ending in a daring rescue attempt that requires the brains and particular STEM skills of all six members of the Ares III team. In a breathtakingly beautiful and nerve-wracking sequence, an injured, exhausted, and bearded Watney attempts to launch into Mars’ atmosphere with a jerry-rigged pod to reach his crew’s ship which is orbiting by, all while the whole world watches on.

Whether or not he makes it–well, you’ll have to go see The Martian yourself to find out the answer to that question. Though the AMC Loews Boston Common 19 will no longer screen the sci-fi adventure after this week, Regal Fenway Stadium 13 and AMC Assembly Row 12 have showings scheduled for the next two weeks, so catch it while you can.

Lastly, for those interested in how accurate Watney’s scientific efforts to remodel his surroundings are, NASA [1] and The Guardian [2] both addressed this question, and Neil deGrasse Tyson also weighed in on the matter via Twitter with some very amusing and pointed commentary [3].

 

  1. Fox, Steve. “Nine Real NASA Technologies in ‘The Martian’.” NASA. National Aeronautics and Space Administration, 11 Sept 2015. Web. 03 Nov 2015. https://www.nasa.gov/feature/nine-real-nasa-technologies-in-the-martian
  2. Zubrin, Robert. “How Scientifically Accurate Is The Martin?” The Guardian. Guardian News and Media, Limited. 06 Oct 2015. Web. 03 Nov 2015. http://www.theguardian.com/film/2015/oct/06/how-scientifically-accurate-is-the-martian
  3. Gettell, Oliver. “Neil deGrasse Tyson Tweets His Thoughts on The Martian.” Entertainment Weekly. Entertainment Weekly, Inc. 2 Oct 2015. Web. 03 Nov 2015. http://www.ew.com/article/2015/10/02/neil-degrasse-tyson-the-martian

 

articles, arts & culture, Events for Students, November 2015

Enjoy a classic cultural experience in Cambridge!

The Central Square Theater in Cambridge houses two award winning and professional theater companies; The Nora Theatre Company and The Underground Railway Theater. This vibrant hub of theatrical, educational, and social activity, is where artists and audiences can come together to create theater that is both vital and captivating to the community.

Live performances for the month of November include:

Einstein’s Dreams (ending Nov. 14th)

Switzerland, 1905: A modest, newly-married patent clerk struggles to make ends meet while re-conceiving time. What happens when Albert Einstein completes his Theory of Relativity? Absurd, comic, and poetic, Einstein’s Dreams captures the poignancy of the human condition. In celebration of the 100th anniversary of Einstein’s Theory of General Relativity, Underground Railway Theater reunites the original 2007 world premiere cast, adapted by director Wesley Savick from the novel by Alan Lightman.

 

Copenhagen (ending Nov. 15th)

Copenhagen, 1941: Two brilliant physicists – fast friends from enemy nations – famously confront each other at the height of WWII. This award-winning psychological mystery unravels what transpired on that fateful night. Werner Heisenberg and his mentor Niels Bohr meet again in the afterlife, goaded by Bohr’s wife, Margrethe. Who will remember the truth that changed the course of history? Commemorating the 70th anniversary of the dropping of the Atomic Bomb, Eric Tucker cracks open Michael Frayn’s contemporary classic play.

 

Arabian Nights (beginning Nov. 27th)

Become enchanted by the power of storytelling one final time! The Nora Theatre Company and Underground Railway Theater revive their award-winning production of Dominic Cooke’s Arabian Nights. Based on One Thousand and One Nights, a collection of folk tales from the Middle East and Asia, Arabian Nights is rich with suspense, romance and hilarity—stories irresistible for all ages, and at its heart, the power of the imagination to heal, inspire, and transform.

articles, November 2015

Dr. Victoria Seewaldt: Whole-Body Research, Whole-Community Medicine

We probably all remember elementary school science worksheets, those ink-marked copied pages with large Comic Sans text that asked us the most basic questions: What do you see? What do you smell? What do you hear? These are simple enough questions, with simple answers to simple experiments. As the science gets more complex, so do the questions, and the fact that a researcher’s daily bread-and-butter, the core component of our work, is merely observation often gets lost among that complexity. The importance of it, however, cannot be forgotten.

Dr. Vicky Seewaldt, formerly of Duke University and now a clinician and the Population Sciences department chair at City of Hope in California, and her work investigating the mechanisms of malignant progression in high-risk breast cancer patients highlight the crucial role that simple observation can play, and how it can lead to more tangible advances in how we conceptualize, research, and treat disease. When she made the move from University of Washington to Durham, North Carolina, she found herself treating a new patient population, the majority of whom were women of color. When some of her high-risk patients came to her and described their cancers as seemingly ‘appearing from nowhere’—a concept that, at the time, was at odds with her previous experience with breast cancer diagnosis—she did not dismiss them. Instead, she listened to their very personal experience with their very personalized disease. She listened, she observed, and then she began to wonder and plan.

For more than a decade, Dr. Seewaldt worked for and with her patients to delve more deeply into understanding why certain populations display such aggressive disease progression. Her main focus was on identifying biomarkers for short-term risk assessment within this subset of triple-negative breast tumors, as well as understanding how the breast microenvironment contributes to disease occurrence and development. Simply by listening, she launched a career that would benefit many and carve out new inroads to understanding breast cancer heterogeneity.

Yet her listening didn’t end with the disease, either. Dr. Seewaldt took note of her patients’ requests for wellness treatment beyond the one part of their anatomy that at the time needed it the most. Thus the Women’s Wellness Clinic came into play at Duke. Through the clinic, Seewaldt and colleagues not only sought to provide underserved women with access to information and services regarding breast health and cancer detection, diagnosis, and treatment, but also to encourage overall wellness within the community.

She reiterated this idea as she concluded her talk given for the 3rd Diane Connolly-Zaniboni Lecture in Breast Cancer at Tufts Medical Center earlier last month, commenting that clinicians should treat “the whole body, not just the breast.” Her work in Durham, which will no doubt be continued in the same enthusiastic and innovative capacity at her new position at City of Hope, demonstrates this idea of whole-body medicine and whole-body research, a reminder that a snapshot won’t do to truly eradicate disease. Rather, you need a mural, made up of bits and pieces of the many, in order to see the whole picture.

Photo credit: UC Davis M.D. Class Notes, Spring 2011

articles, 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 AdageOfAnia.com

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

articles, November 2015, Techniques

Techniques – Wild, Wild West(erns)

1 Comment

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.

 

Source - http://prooffreaderplus.blogspot.com/2014/05/one-of-my-favourite-memories-good-bad.html
Source – http://prooffreaderplus.blogspot.com/2014/05/one-of-my-favourite-memories-good-bad.html
Library, November 2015, On the Shelf

On the Shelf (November 2015)

For work…

Electronic Resource: Knovel

Location: Search for ‘Knovel’ in E-Resources Finder (http://www.library.tufts.edu/hsl/CentralDatabase/centraldatabase.html)

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

Events for Students, Library, Library Events, November 2015

Upcoming Library Events (November 2015)

Open Workshop: Using Images

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

Sackler 510

Registration: http://www.library.tufts.edu/hsl/education/workshops.html

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

Registration: http://www.library.tufts.edu/hsl/education/workshops.html

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