5 tips for your thesis defense

5 Tips to Pass Your Thesis Defense with Flying Colors


By Thalyana Vikos-Smith, PhD

If you are defending your thesis anytime soon, congratulations! Here are some tips for the big day:

1. Victory lap

The thesis defense is supposed to be a happy occasion and shouldn’t be looked upon with fear and dread. This is a day to celebrate! Depending on which university you attend, you have probably already completed writing the actual thesis and have gotten through multiple committee meetings to confirm that you are ready for this day. All of the hard work is done, so the defense is the opportunity to tell your friends, family and coworkers about all of this hard work.

2. Make it relatable

If you have invited non-scientists to your defense, then prepare the talk for a general audience, i.e. it should be different from a departmental research in progress talk. The introduction is especially important so that you don’t lose people right from the beginning. Also, the thesis defense should summarize all the research you have done but should relate this research back to your personal scientific interests; it’s a story about you! For example, my thesis defense was on the genetics of aging, so I began my talk by explaining my interest in research that has been done on a group of extremely long-lived people on the island of Ikaria in Greece; even though my thesis had nothing to do with Ikaria, my family is from Greece, so by introducing the topic of aging in this manner, I also provided a personal touch. Additionally, if you are doing a postdoc after your PhD, feel free to mention how your postdoc research relates to your PhD work and why you decided to do this type of research.

3. Keep it loose

For all the comedians out there, now is the time to exercise your skills! Again, the thesis defense is a celebratory occasion, so no one is going to mind a joke or two during the talk. For example, any difficulties that you encountered in your research can be introduced with a dash of humor. Other great opportunities to be funny are in the introduction and when you are giving your acknowledgements.

4. Make it flashy

The thesis defense should be a summary of all of the research you have done; you will definitely not have time to discuss everything in detail. Thus, making some attractive summary diagrams to include before you transition from one thesis topic to another and to reiterate everything at the end of the talk will be very helpful to the audience. Be adventurous with this presentation; this is your last opportunity to wow the audience with your professional PowerPoint skills. If you are super adventurous, try using Prezi, a very appealing alternative to PowerPoint. It will also be helpful to provide a flowchart at the beginning of the talk to outline which topics you will discuss, roughly how long you will discuss each topic, and any topics that you won’t have time to talk about.

5. Q & A

I have found that most questions asked at thesis defenses are “big picture” questions; it doesn’t make sense to scrutinize small points anymore. While “big picture” questions can be very insightful, they can also be difficult to answer, so be prepared to take a stab at trying to shed some light on the question by thinking on your feet, and also throw in this lovely phrase, “that’s a great question; I’ll have to think about that some more and get back to you.”


Follow Thalyana on Twitter @ThalyanaScience

Mitochondrial Clues for a Long Life


By Thalyana Smith-Vikos

Biological clocks that can predict an individual’s lifespan more accurately than chronological time alone have been proposed in multiple molecular, cellular and genetic contexts, but a single clock has yet to be identified. Mitochondria, however, have been identified as promising candidates for a biological aging clock in many organisms. Dong and colleagues report that mitochondrial function in Caenorhabditis elegans young adults provides a highly accurate predictive measure of eventual longevity of individual nematodes.

By visualizing quantal mitochondrial flashes, or mitoflashes, in vivo, the authors were able to show that this optical readout was specific to free-radical production and metabolic rate at the single-mitochondrion level. These mitoflashes exhibited a strong correlation with C. elegans aging and had similar attributes in a mammalian system. Mitoflash measurements in pharyngeal muscles peaked during active reproduction and when the first nematodes began dying off. The mitoflash activity on day 3 of adulthood during active reproduction explained up to 59% of lifespan variation. Day 3 mitoflash frequency was negatively correlated with future lifespan of individual C. elegans, and this negative correlation persisted in the face of various genetic and environmental alterations that extend or shorten lifespan. The authors further showed that day 3 mitoflash frequency was due to glyoxylate cycle activity, and they propose that mitochondrial activity not only predicts but also determines lifespan, as the lifespan of long-lived insulin receptor mutants was at least partially explained by decreased mitochondrial production of superoxide.

These findings indicate that mitochondria can function as a biological clock that predicts lifespan of individual C. elegans in various contexts. Importantly, this clock has already begun ticking very early in life, as mitochondrial flashes in early adulthood during active reproduction have been shown to be most potent predictors of future longevity.


Tumor-Suppressive microRNAs


By Thalyana Smith-Vikos

MicroRNAs (miRNAs) are short, noncoding RNAs that inhibit the expression of specific target genes. Certain classes of miRNAs have been identified as tumor suppressors, most notably miR-34. Studies have shown that miR-34 can be delivered as a tumor-static agent, including a 2012 report by Kasinski and Slack in Cancer Research. This report identifies miR-34 as a tumor suppressor in a Kras;p53 mouse model of lung cancer, the most potent cause of cancer deaths around the world. Tumors harvested from these mice had elevated levels of miR-34 targets, including Met and Bcl-2, indicating that miR-34 expression was inhibited. By adding exogenous miR-34, both tumor formation and progression of preformed tumors were prevented in the mice, and proliferation and invasion of lung tumor-derived epithelial cells were inhibited. This and other studies show promise for the use of miRNAs, especially miR-34, in clinical trials for cancer treatment and prevention.

The Most Scizzling Papers of 2013


The Scizzle Team

Bacteriophage/animal symbiosis at mucosal surfaces

The mucosal surfaces of animals, which are the major entry points for pathogenic bacteria, are also known to contain bacteriophages. In this study, Barr et al. characterized the role of these mucus associated phages. Phages were more commonly found on mucosal surfaces than other environments and adhere to mucin glycoproteins via hypervariable immunoglobulin like domains. Bacteriophage pre-treatment of mucus producing cells provided protection from bacterial induced death, but this was not the case for cells that did not produce mucus. These studies show that there may be a symbiotic relationship between bacteriophages and multicellular organisms which provides bacterial prey for the phages and antimicrobial protection for the animals.


Interlocking gear system discovered in jumping insects

Champion jumping insects need to move their powerful hind legs in synchrony to prevent spinning. Burrows and Sutton studied the mechanism of high speed jumping in Issus coleoptratus juveniles and found the first ever example in nature of an interlocking gear system. The gears are located on the trochantera (leg segments close to the body’s midline) and ensure both hind legs move together when Issus is preparing and jumping. As the insect matures, the gear system is lost, leaving the adults to rely on friction between trochantera for leg synchronization.


HIV-1 capsid hides virus from immune system

Of the two strains of HIV, HIV-1 is the more virulent and can avoid the human immune response, whereas HIV-2 is susceptible. This may be due to the fact that HIV-2 infects dendritic cells, which detect the virus and induce an innate immune response. HIV-1 cannot infect dendritic cells unless it is complexed with the HIV-2 protein Vpx, and even then the immune response isn’t induced until late in the viral life cycle, after integration into the host genome. Lahaye et al. found that only viral cDNA synthesis is required for viral detection by dendritic cells, not genome integration. Mutating the capsid proteins of HIV-1 showed that the capsid prevents sensing of HIV-1 cDNA until after the integration step. This new insight into how HIV-1 escapes immune detection may help HIV vaccine development.


Transcription factor binding in exons affects protein evolution

Many amino acids are specified by multiple codons that are not present in equal frequencies in nature. Organisms display biases towards particular codons, and in this study Stamatoyannopoulos et al. reveal one explanation. They find that transcription factors bind within exonic coding sequences, providing a selective pressure determining which codon is used for that particular amino acid. These codons are called duons for their function as both an amino acid code and a transcription factor binding site.


Chromosome silencing

Down syndrome is caused by the most common chromosomal abnormality in live-born humans: Trisomy 21. The association of the syndrome with an extra (or partial extra) copy of chromosome 21 was established in 1959. In the subsequent fifty years a number of advances have been made using mouse models, but there are still many unanswered questions about exactly why the presence of this extra chromosome should lead to the observed defects. An ideal experimental strategy would be to turn off the extra chromosome in human trisomy 21 cells and compare the “corrected” version of these cells with the original trisomic cells. This is exactly what a team led by Jeanne Lawrence at the University of Massachusetts Medical School has done. Down syndrome is not the only human trisomy disorder: trisomy 13 (Patau syndrome) and trisomy 18 (Edward’s syndrome), for example, produce even more severe effects, with life expectancy usually under one to two years. Inducible chromosome silencing of cells from affected individuals could therefore also provide insights into the molecular and cellular etiology of these diseases.


Grow your own brain

By growing organs in a dish researchers can easily monitor and manipulate the organs' development, gaining valuable insights into how they normally develop and which genes are involved. Now, however, a team of scientists from Vienna and Edinburgh have found a way to grow embryonic “brains” in culture, opening up a whole world of research possibilities. Their technique, published in Nature, has also already provided a new insight into the etiology of microcephaly, a severe brain defect.

[box style="rounded"]Scizzling extra: In general, 2013 was a great year for growing your own kidneyspotentially a limb and liver. What organ will be next? [/box]


Sparking metastatic cell growth

A somewhat controversial paper published in Nature Cell Biology this year showed that the perivescular niche regulates breast tumor cells dormancy. The paper showed how disseminated breast tumor cells (DTC) are kept dormant and how they can be activated and aggressively metastasize. Based on the paper, this is due to the interaction of interaction with the microvascularate, where thrombospondin-1 (TSP-1) induces quiescence in DTC and TGF-beta1 and periosstin induces DTC growth. This work opens the door for potential therapeutic against tumor relapse.


Fear memories inherited epigenetically

Scientists showed that behavioral experiences can shape mice epigenetically in a way that is transmittable to offspring.  Male mice conditioned to fear an odor showed hypomethylation for the respective odor receptor in their sperm; offspring of these mice showed both increased expression of this receptor, and increased sensitivity to the odor that their fathers had been conditioned on.  Does this suggest that memories can be inherited?


Grid cells found in humans

Scientists have long studied rats in a maze, but what about humans?  An exciting paper last August demonstrated that we, like out rodent counterparts, navigate in part using hippocampal grid cells.  Initially identified in the entorhinal cortex of rats back in 2005, grid cells have the interesting activity pattern of firing in a hexagonal grid in the spatial environment and as such are thought to underlie the activity of place cells. Since then grid cells have been found in mice, rats, and monkeys, and fMRI data has suggested grid cells in humans.  This paper used electrophysiological recordings to document grid cell activity in humans.


Sleep facilitates metabolic clearance

Sleep is vital to our health, but researchers have never been entirely sure why.  It turns out part of the function of sleep may be washing waste products from the brain, leaving it clean and refreshed for a new day of use.  Exchange of cerebral spinal fluid (CSF), which is the primary means of washing waste products from the brain, was shown to be significantly higher when animals were asleep compared to waking.  This improved flow was traced back to increased interstitial space during sleep, and resulted in much more efficient clearance of waste products.  Thus, sleep may be crucial to flushing metabolites from the brain, leaving it fresh and ready for another day’s work.

[box style = "rounded"] Robert adds: As a college student my friends and I always had discussions about sleep and it was also this mysterious black box of why we actually need to sleep. Studies could show the effects of lack of sleep such as poor cognition and worse memory but this paper linked it to an actual mechanism by which this happens. First of all I found it very impressive that the researchers trained mice to sleep under the microscope. On top of that showing the shrinkage of the neurons and the flow of cerebrospinal fluid which cleans out metabolites finally linked the cognitive aspects of sleep deprivation to the physical brain. [/box]


Poverty impedes cognitive function

People who are struggling financially often find it difficult to escape poverty, in part due to apparently poor decision making.  Investigators demonstrated that part of this vicious cycle may arise from cognitive impairment as a direct result of financial pressures.  The researchers found that thinking about finances reduced performance on cognitive tasks in participants who were struggling, but not in those who were financially comfortable.  Furthermore, farmers demonstrated poorer cognitive performance before harvest, at a time of relative poverty, compared to after harvest when money was more abundant.


Gut Behavior

2013 has definitely been the year of the gut microbiome! Studies have shown that diet affects the composition of trillions of microorganisms in the human gut, and there is also a great deal of evidence pointing towards the gut microbiome affecting an individual's susceptibility to a number of diseases. Recently published in Cell, Hsiao and colleagues report that gut microbiota also affect behavior, specifically in autism spectrum disorder (ASD). Using a mouse model displaying ASD behavioral features, the researchers saw that probiotic treatment not only altered microbial composition, but also corrected gastrointestinal epithelial barrier defects and reduced leakage of metabolites, as demonstrated by an altered serum metabolomic profile. Additionally, a number of ASD behaviors were improved, including communication, anxiety, and sensorimotor behaviors. The researchers further showed that a particular metabolite abundant in ASD mice but lowered with probiotic treatment is the cause of certain behavioral abnormalities, indicating that gut bacteria-specific effects on the mammalian metabolome influence host behavior.

Your skin - their home

A paper published in Nature examined the diversity of the fungal and bacterial communities that call our skin home. The analysis done in this study revealed that the physiologic attributes and topography of skin differentially shape these two microbial communities. The study opens the door for studying how the pathogenic and commensal fungal and bacterial communities interact with each other and how it affects the maintenance of human health.


Discovery of new male-female interaction can help control malaria

A study published in PLOS Biology provided the first demonstration of an interaction between a male allohormone and a female protein in insects.  The identification of a previously uncharacterized reproductive pathway in A. Gambiae has promise for the development of tools to control malaria-transmitting mosquito populations and interfere with the mating-induced pathway of oogenesis, which may have an effect on the development of Plasmodium malaria parasites.

[box style = "rounded"]Chris adds: "My friend chose this paper to present at journal club one week, because he thought it was well written, interesting etc etc. Unbeknownst to him, one of the paper’s authors was visiting us at the time. We sit down for journal club and one of the PIs comes in, sees the guy and exclaims (with mock exasperation) “you can’t be here!” Me and the presenter look at one another, confused. He presents journal club, and luckily enough, the paper is so well written, that he can’t really criticize it!" [/box]


Using grapefruit to deliver chemotherapy

Published in Nature Communications, this paper describes how nanoparticles can be made from edible grapefruit lipids and used to deliver different types of therapeutic agents, including medicinal compounds, short interfering RNA, DNA expression vectors, and proteins to different types of cells. Grapefruit-derived nanovectors demonstrated the ability to inhibit tumor growth in two tumor animal models. Moreover, the grapefruit nanoparticles used in this study had no detectable toxic effects, could be manipulated or modified to target specific cells/ tissues, and were economical to create. Grapefruits may have a bad reputation for interfering with drugs, but perhaps in the future we will be using grapefruit products to deliver drugs more effectively!



In May, a new technique called CLARITY to effectively make tissue transparent through a new fixation technique was published in Nature. This new process has allowed them to clearly see neuron connection networks not possible before because they can now view the networks in thicker tissue sections. This new advancement will help researchers be able to better map the brain, but this new technology can also be to create 3-D images of other tissues such as cancer. This new ability allows us to gain better insight into the macroscopic networks within a specific tissue type.


Crispier genome-editing

This year, the CRISPR technique was developed as an efficient gene-targeting method. The benefit of this method over the use of TALENS or a zinc-finger knockout is it allows for the rapid generation of mice that have multiple genetic mutations in just one step. The following review gives even more information on this new technique and compares its usefulness to that of TALENS and zinc-finger knockouts. Further, just couple of weeks ago, two back-to-back studies in Cell Stem Cell using the CRISPR-Cas9 system to cure diseases in mice and human stem cells.  In the first study the system was used in mice to correct the Crygc gene that causes cataracts; in the second study the CRSPR-Cas9 system was used to correct the CFTR locus in cultured intestinal stem cells of CF patients. These findings serve as a proof-of-concept that diseases caused by a single mutation can be “fixed” with genome editing using the CRISPR-Cas9 system.

What was your favorite paper this year? Let us know! And of course - use Scizzle to stay on top of your favorite topics and authors.

So What Is It You Do, Exactly?

Tips and anecdotes on how to explain your science over the holiday dinner.


The Scizzle Team


Pick your project carefully

Chris works on a malaria vector and how it survives by blood-feeding, so he usually just says he's trying to kill all the malaria mosquitoes. After that people rarely have follow up questions, since it’s a goal people can easily get behind!

[box style="rounded"]Scizzle tip: Work on a disease everyone knows[/box]

Be prepared

Stephanie says that everyone should have an elevator pitch ready to pull out of their back pocket at a moment's notice! Start working on your 3 minute miracle as soon as you've picked up a pipette and learned which way to point it.

[box style="rounded"]Scizzle tip: This doubles as a great networking tool![/box]

Try once (and you might never get asked again)

Robert's first lab experience was during a summer internship, and he shares: for the first month I was working there I was commuting from the suburbs to NYC to work. Since my dad was retired at the time he usually drove me in and would pick me up when I was done. When he picked me up he would always ask me about what I had done that day. In the beginning it was simple stuff to explain like sectioning kidneys, doing dissections, etc. One day I had done PCR for the first time and when my dad asked me what I did that day I went on the spiel about PCR. How you have DNA and primers and taq polymerase and dNTPs. I explained it as simply as I could think going one step at a time and slowly and ended with "basically, its like photocopying DNA and we use it to see what genes the mice have". After a pause my dad said to me "I have no idea what you were just talking about." I offered to try to explain again but he politely declined and that was the last time he asked me about what I did in lab.

[box style="rounded"]Scizzle tip: Don't use fancy words[/box]

Tell them what you do

Celine suggests to focus on what she does rather than what she studies: if I tell my people that I work on cortical interneuron circuits their eyes glaze over, but if I say that I use a tiny electrode to listen to neurons and observe their behavior, people are actually quite interested.  A good visual helps a lot too; for a long time I had a picture on my phone from my electrophysiology rig monitor showing neurons and a blood vessel, and even people who don’t care about science at all thought it was pretty neat.

[box style="rounded"]Scizzle tip: Have good visuals! (Just make sure it's not gross)[/box]

What's your model organism?

Thalyana's words of wisdom for those studying model organisms: be careful how you explain what organism you are studying. For example, I study the nematode C. elegans, and I made the mistake of saying "I study worms" at a family get-together. I spent the rest of the party explaining that I do not spend my day digging in the soil for earthworms! Also, if you study yeast, make sure to point out that you are not brewing beer in the lab (...unless you are!).

[box style="rounded"]Scizzle tip: Choose your words! C.Elegans sounds way more sophisticated than worms[/box]

Start with something they know

Joseph tells us the importance of a few key words: I recently tried to explain my research on the evolution of developmental mechanisms in moss, and found myself seeing an increasingly confused face in front of me.  I was then helpfully notified that, while delving into details about making mutant lines and tracking cell divisions, I had left the word “evolution” out of my explanation!  This was a great learning experience; there are words that your mother/father/aunt/cousin has probably heard in the news that relate to what it is you do, so make sure to use them!

[box style="rounded"]Scizzle tip: Use those buzzwords![/box]

Keep it Real

Zach tries to relate his work to human problems and interactions: as a computer scientist, my work often has broad applications, so I look for the human element - an analogy to a common problem or familiar pain often helps people to understand how my work is useful. It helps to anthropomorphize as well - presenting my work as teaching a silly, ignorant computer how to complete a useful task is often easier than trying to convey the set of abstractions and mechanical and electrical processes that are the true nature of my work.

[box style="rounded"]Scizzle tip: Find the human element[/box]


Do you have a tip on how to deal with the question or a funny story? Please share!

A New Approach to Publishing Science Research


Thalyana Smith-Vikos

By perusing a recent article published in the online journal eLife, I noticed a few aspects of the article that I definitely wasn’t expecting when scrolling to the bottom of the page. The decision letter, sent to the authors when their article was accepted for publication, is included, along with the names of the peer reviewers and their comments. Additionally, the authors’ response to the reviewers’ comments is also included.

eLife explains that the authors and reviewers have given their approval to include this information, and that only the major concerns identified in the reviewers’ comments are shown. Still, I was surprised to see that this information  was accessible! I then discovered that other journals, including EMBO Journal from Nature Publishing Group, also follow this format of transparency, in which all of the letters between authors and editors, including reviewers’ comments, are listed on the journal’s website for each accepted article. I’m not sure how often people carefully look through these letters or are just happy reading the paper, but the principle still stands that this information is now made public.

I immediately began to ponder why eLife and other journals have decided to include this information with published articles. As someone who has both received and written decision letters and peer review comments, I can attest that this is a very sensitive process that most scientists like to keep private. Every scientist knows that even if a paper is accepted for publication, there may still be some aspects that need to be ironed out, but for a non-scientist reading the decision letter online, this may generate confusion: they may think, why was this paper accepted if there were still issues with it?

However, displaying this information can provide more credibility to the peer review process in general: scientists and non-scientists alike can see that this paper was rigorously reviewed by experts in the field, and a lot of time and effort went into improving the manuscript based on these comments. With the rise of “predatory” journals that lack a real peer review process, we can clearly observe that eLife and other journals maintain the high standards of peer review. Sometimes it is easy to guess how long the peer review process took for any paper in any journal, because each journal will report the dates the article was received and accepted after review; however, eLife has taken it a step further and displayed the entire review process for us to assess. This extra information allows for the reader to develop a much more informed opinion of the article; readers now have the entire “backstory” of an article at their fingertips, and witnessing how the article has been revised prior to publication provides a deeper understanding of and greater appreciation for the final product.

Additionally, I was surprised that the reviewers’ names and comments were revealed. Anonymity of reviewers helps to keep the publication process more objective from the authors’ point of view. Sometimes authors may try to guess who the reviewers are, as the authors themselves can suggest or exclude potential reviewers, but that final anonymity also acknowledges that the reviewers’ comments must be respected without any personal bias. This also allows the reviewers to feel more comfortable with writing their analysis of the paper. On the other hand, as this new method  of peer review gains more visibility, I think scientists could also be accepting of this lack of transparency. If the status quo is not to give comments anonymously, then authors, reviewers and editors can be equally prepared to handle this scenario. By  revealing reviewers’ names, this provides assurance to the authors and to readers that the journal has indeed found experts who are appropriate reviewers for the manuscript.

I should also mention that F1000Research, the new open-access journal from Faculty of 1000, has developed a somewhat related publication process. F1000Reserach is truly the first “open science publisher”: after an article is submitted, it is almost immediately published online (with all of the raw data included) after a quick in-house check for any major concerns. Then, the post-publication peer review ensues, in which F1000 users can post comments on the paper using a forum-type discussion model. This certainly instills the principle that science is a community, and that any scientist’s work should be assessed by this community in order to draw the best conclusions from the data. Additionally, F1000 Research nominates experts in the field to be peer reviewers (whose names and affiliations are disclosed), as well.

Articles which are then revised based on peer review comments will be announced on the F1000 Research site, and only these revised papers will be indexed on PubMed and other databases. In addition to “revised”, articles can also receive the tag of “update”, if, for example, there is an update to a software release or other type of technology the paper describes. Articles can also be labeled as “follow up”, which are cited separately and provide new information to a review or opinion piece.  All in all, the F1000Research models allows work to be published much more quickly, and it increases the community of reviewers. As science is fast-moving, new updates and insights to previously published work can be quickly added to keep up with the pace.


What do you think? Do you think it's beneficial to have all the review information disclosed?

Follow Thalyana on Twitter @ThalyanaScience

Let’s turn up the heat and turn STEM into STEAM

Thalyana Smith-Vikos 


I recently had the pleasure of watching an amazing performance of the Pilobolus acrobatic modern dance troupe, and something in the program caught my eye: it said that the dancers had worked with MIT scientists to develop new dance routines! This was quite evident in the “Automaton” performance, in which the dancers were all arranged into different acrobatic positions and moved in unison to create the effect that they were all parts of a robot. It was really quite astonishing: at first, I was just watching the dancers on stage, but then suddenly it really looked like there was a robot moving across the floor. With many kids in the audience, there was definitely a lot of oohing and aahing at this moment.

Another example where it was evident that the dancers had worked with scientists was in the “Sextet” performance, in which the performers placed pieces of rope on the stage and then moved the rope (like doing double dutch) in sync with the music to mimic sound waves. As additional beats were added to the music, more dancers appeared with rope to start copying those specific sound waves, and suddenly there was an entire orchestra on the stage! The dancers moved with such grace and poise while still perfectly depicting sound waves with the rope; it reminded me of ribbon dancing at the Olympics. There were more oohs and aahs during this performance, and I thought to myself, “That’s not just the art of music, kids, that’s the art of science.”

Since its founding in 1971, Pilobolus has been devoted to establishing educational programs to encourage kids to develop an interest in dance, and hopefully they throw in some of what they learned from the MIT scientists, too. Using their platform, I think there are many more programs like this that could help encourage the STEAM (Science, Technology, Engineering, Arts and Mathematics) Educational Initiative, an addendum to the STEM Initiative.

The City University of New York (CUNY) has a Science & the Arts program funded in part by the National Science Foundation (NSF). Examples of recent performances include AstroDance, a multimedia dance performance illustrating the discovery of gravity waves at the Laser Interferometer Gravitational-Wave Observatory (LIGO), and DNA Story, a play that tells the story of how Watson, Crick, Franklin and Wilkins discovered the structure of DNA in the 1950s. While the NSF remains concerned about how to fund the “broader impacts” of science research, I think this is actually a great way for the NSF to promote science education, by funding groups that present the beauty of scientific discovery in an entertaining and approachable manner.

Here’s another example that the NSF could support: the Cambridge, MA game company Harmonix creates technology for the Xbox game “Dance Central,” which allows players to learn dance routines step by step without a controller. Students could be invited to spend the day in the music lab learning how to translate the K-pop hit “Gangnam Style” into an interactive game. Who doesn’t love “Gangnam Style”? And who doesn’t love video games? This would go over in a heartbeat.

And then there’s the initiative to have students rap about scientific principles, which has garnered a lot of support and been quite successful in getting students interested in science. The program was started when Christopher Emdin, a Columbia University professor, and GZA, a member of the Wu-Tang Clan, met with Neil deGrasse Tyson, an outgoing physicist and director of the Hayden Planetarium, at a radio show. Starting in New York City public schools, they launched a pilot project to bring hip-hop and rap into science classrooms. There’s a lot that can be learned from the success of Emdin and GZA’s program that could be implemented in schools across the country, namely teaching science using something that students already enjoy and can relate to. In fact, in a manner that deGrasse Tyson has termed “dropping science,” GZA will be rapping about the Big Bang in his upcoming album “Dark Matter;” hopefully his younger fans will take to the album and be inspired.

There’s really no limit as to how STEAM education can be accomplished, whether it be acting, dancing or rapping. Many scientists themselves have an artistic inclination, which could lead to initiatives where scientists visit classrooms and teach the artistic side of science. Take the winners of the annual “Dance Your PhD” contest (which Pilobolus dancers help judge): these are scientists who are conducting their thesis research in the lab and have found a way to illustrate their research using interpretive dance.

If you would rather scientists sing instead of dance in the classroom, I’m sure Indre Viskontas, a cognitive neuroscientist, professional soprano opera singer and TV host, could help with that. She has found a way to combine both scientific and artistic passions and studies the psychology of music, specifically how musicians can best use their practice time, and how they can find a way to connect with the audience. Viskontas is the perfect example of a scientist who has interests outside of science and can incorporate these interests into her research. Moreover, her artistic pursuits enhance her success as a scientist and vice-versa.

Overpowering all of these excellent STEAM initiatives, however, is the idea that while students may better appreciate science by using art in the classroom, this still does not mean they will want to become scientists when they grow up. Adding on to this is the misconception in the media that scientists are nerds, or that scientists plan to destroy the world in every Marvel or DC comic on the big screen. Have no fear, The Science & Entertainment Exchange is here! The Exchange is a program of the National Academy of Sciences that connects entertainment executives with scientists and engineers to develop accurate and engaging scientific concepts for TV shows and movies. The Exchange has consulted on over 500 projects, and while it still bothers me that they haven’t completely solved the misrepresentation of how scientists are portrayed, along with the scientific ideas that are being discussed in TV and film, imagine how worse “The Avengers” could have been without having an Exchange consult?

Bringing this back to STEAM education, wouldn’t it be great if The Exchange established an internship program? In this way, students with the Hollywood bug could rub shoulders with entertainment executives, while also learning that they could have super cool jobs as scientists who consult for these executives. Maybe being a scientist is not so nerdy, after all.

From Trials to Practice - Improving Health Outcomes of the Elderly


Thalyana Smith-Vikos


Disabilities that limit mobility diminish quality of life for many seniors and represent a major burden on the healthcare system. The Yale Claude D. Pepper Older Americans Independence Center

is investigating whether physical activity and exercise can prevent these disabilities as part of the largest clinical trial of its kind.

The trial is just the latest in more than two decades of research by the Pepper Center, which is dedicated to improving the lives of the elderly by studying the complex issues they face.

“This is a landmark study that could provide the evidence needed to establish exercise programs more widely throughout the country, in senior centers, YMCAs and other community settings,” stated Pepper Center Director Dr. Thomas Gill.

The Pepper Center, along with the Yale Program on Aging, has enrolled 200 participants and is one of eight LIFE Study sites around the country. Each of the participants has been enrolled for a minimum of two years, with some individuals receiving continuous exercise training or health education for four years.

The physical activity intervention primarily focuses on moderate-paced walking, but also addresses methods for improving gait, balance and muscle strengthening. The major assessment has been to observe improvements in mobility every six months by asking each participant to walk without assistance around a ¼ mile-long course.

Participants have been using exercise facilities at Southern Connecticut State University or Choate Rosemary Hall in Wallingford, CT, while the health education classes occur at either Albertus Magnus College or Ashlar Village in Wallingford.  The Program on Aging evaluates changes in participants’ cognition, risk of injury from falling, and risk of hospitalization due to myocardial infarction, congestive heart failure or other serious health conditions.

In total, the LIFE Study has been following 1635 men and women aged 70-89, who are receiving either a physical activity intervention or a health education intervention. The LIFE Study is in its third year, and Gill expects that the trial will be completed by the end of 2013. The research is funded by the National Institute on Aging (NIA) and the National Heart, Lung and Blood Institute (NHLBI).

The Operations Core reached out to participants through mailing lists for persons 70 years or older in the Greater New Haven, CT area.

“We received an excellent response for participation in the LIFE Study; in fact, we completed recruitment about one month earlier than expected,” Gill said. “Not only do we have an outstanding field operation to recruit people to the LIFE Study, but we have also had very few dropouts and are by far the top performing site out of the eight research sites. This is truly a testament to the Program on Aging’s dedicated research staff.”

Field research by the Operations Core is by far the largest component of the Program on Aging and the Pepper Center. As many as 60 researchers may be collecting data at any one time in a variety of field sites, although this fluctuates with the number of projects being simultaneously funded.

A large percentage of the research staff is composed of nurses who have an extensive background in clinical research. They are responsible for collecting data in many different venues, such as hospitals, nursing homes, participants’ homes, flu clinics, and a clinic assessment space in the Temple Medical Building. With direction from Peter Charpentier, data from dozens of studies are organized and delivered to the Biostatistics Core to be analyzed.

The Yale Pepper Center was first established in 1992 to investigate complex geriatric conditions. Researchers employ laboratory and clinical findings to discover root causes of geriatric conditions. The goal is to develop and test preventative treatments and to help doctors make better decisions when dealing with elderly patients.

The Pepper Center has been at the forefront of advancing the field of aging research, by instituting interdepartmental collaborations and publishing breakthrough research that has directly affected health outcomes of older individuals. True to its success, the Yale Pepper Center, currently one of 13 sites across the country, has been continuously funded by the National Institutes of Health (NIH) since its inception. Effective on June 1, the Pepper Center began its fifth consecutive renewal cycle from 2013-2018.

The new funding cycle will mark the beginning of an initiative to translate research findings from the Pepper Center into everyday practices to improve the welfare of older Americans. This research initiative, directed by Dr. Mary Tinetti, who also led the Pepper Center for its first 19 years, will focus on analyzing the findings generated by various field studies and applying these results to “real world” practices in the community, hospitals and nursing homes, so they can be of use for physicians, patients and their families.

Tinetti has extensive experience in implementing clinical findings into real world practice. An international expert on fall prevention research in older persons, Tinetti previously investigated the risk factors and precipitants that contribute to falls, and developed and tested interventions which successfully reduced falls in older persons participating in a clinical trial. Together with Dr. Dorothy Baker and other researchers, she then worked to incorporate these interventions into a variety of settings in the Greater Hartford, CT area, which resulted in significantly reducing the likelihood of serious fall injuries in these individuals.

“We are well-positioned based on Dr. Tinetti’s previous studies and expertise to develop an outstanding Dissemination and Implementation Core, which will distinguish the Yale Pepper Center from the 12 other Pepper Centers across the country,” Gill commented. “The other trials being conducted here will follow the model Dr. Tinetti has in place to translate research from traditional randomized clinical trials into real world clinical practice.”




Leafing through the Literature

Thalyana Smith-Vikos

Highlighting recently published articles in molecular biology, genetics, and other hot topics

Can I get some of your gut bacteria?

While there have been many reports popping up in the literature that demonstrate a connection between gut microbiome and diet, Ridaura et al. have elegantly showed how the mammalian microbiome affects diet in a specific yet alterable manner that can be transmitted across individuals. The researchers transplanted fecal microbiota from adult murine female twins (one obsess, one lean) into mice fed diets of varying levels of saturated fats, fruits and vegetables. Body and fat mass did depend on fecal bacterial composition. Strikingly, mice that had been given the obese twin’s microbiota did not develop an increase in body mass or obesity-related phenotypes when situated next to mice that had been given the lean twin’s microbiota. The researchers saw that, for certain diets, there was a transmission of specific bacteria from the lean mouse to the obese mouse’s microbiota.

Want to keep up with gut microbiota? Create your feed!


In vivo reprogramming

Abad et al. have performed reprogramming of adult cells into induced pluripotent stem cells (iPSCs) in vivo. By activating the transcription factor cocktail of Oct4, Sox2, Klf4 and c-Myc in mice, the researchers observed teratomas forming in multiple organs, and the pluripotency marker NANOG was expressed in the stomach, intestine, pancreas and kidney. Hematopoietic cells were also de-differentiated via bone marrow transplantation. Additionally, the iPSCs generated in vivo were more similar to embryonic stem cells than in vitro iPSCs by comparing transcriptomes. The authors also report that in vivo iPSCs display totipotency features.

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Connection between pluripotency and embryonic development

Lee and colleagues have discovered that some of the same pluripotency factors (Nanog, Oct4/Pou5f1 and SoxB1) are also required for the transition from maternal to zygotic gene activation in early development. Using zebrafish as a model, the authors identified several hundred genes that are activated during this transition period, which is required for gastrulation and removal of maternal mRNAs in the zebrafish embryo. In fact, nanogsox19b and pou5f1 were the top translated transcription factors prior to this transition, and a triple knockdown prevented embryonic development, as well as the activation of many zygotic genes. One of the genes that failed to activate was miR-430, which the authors have previously shown is required for the maternal to zygotic transition. Thus, Nanog, Oct4 and SoxB1 induce the maternal to zygotic transition by activating miR-430.


A microRNA promotes sugar stability

Pederson and colleagues report that a C. elegans microRNA, miR-79, targets two factors critical for proteoglycan biosynthesis, namely a chondroitin synthesis and a uridine 5'-diphosphate-sugar transporter. Loss-of-function mir-79 mutants display neurodevelopmental abnormalities due to altered expression of these biosynthesis factors. The researchers discovered that this dysregulation of the two miR-79 targets leads to a disruption of neuronal migration through the glypican pathway, identifying the crucial impact of this conserved microRNA on proteoglycan homeostasis.

Struggling to keep up with all the mIRs? Create your feed for miR-430 or miR-79.


Establishing heterochromatin in Drosophila

It is known that RNAi and heterochromatin factor HP1 are required for organizing heterochromatin structures and silencing transposons in S. pombe. Gu and Elgin built on this information by studying loss of function mutants and shRNA lines of genes of interest in an animal model, Drosophila, during early and late development. The Piwi protein (involved in piRNA function) appeared to only be required in early embryonic stages for silencing chromatin in somatic cells.  Loss of Piwi leads to decreased HP1a, and the authors concluded that Piwi targets HP1a when heterochromatin structures are first established, but this targeting does not continue in later cell divisions. However, HP1a was required for primary assembly of heterochromatin structures and maintenance during subsequent cell divisions.


The glutamate receptor has a role in Alzheimer’s

Um and colleagues conducted a screen of transmembrane postsynaptic density proteins that might be able to couple amyloid-β oligomers (Aβo) bound by cellular prion protein (PrPC) with Fyn kinase, which disrupts synapses and triggers Alzheimer’s when activated by Aβo-PrPC . The researchers found that only the metabotropic glutamate receptor, mGluR5, allowed Aβo-PrPC  to activate intracellular Fyn. They further showed a physical interaction between PrPC and mGluR5, and that Fyn is found in complex with mGluR5. In Xenopus oocytes and neurons, Aβo-PrPC caused an increase in intracellular calcium dependent on mGluR5. Further, the Aβo-PrPC-mGluR5 complex resulted in dendritic spine loss. As a possible therapeutic, an mGluR5 antagonist given to a mouse model of inherited Alzheimer’s reversed the loss in synapse density and recovered learning and memory loss.


Keep playing those video games!

Anguera et al. investigated whether multitasking abilities can be improved in aging individuals, as these skills have become increasingly necessary in today’s world. The scientists developed a video game called NeuroRacer to test multitasking performance on individuals aged 20 to 79, and they observed that there is an initial decline in this ability with age. However, by playing a version of NeuroRacer in a multitasking training mode, individuals aged 60-85 achieved levels higher than that of 20-year-olds who had not used the training mode, and these successes persisted over the course of 6 months. This training in older adults improved cognitive control, attention and memory, and the enhancement in multitasking was still apparent 6 months later. The results from playing this video game indicate that the cognitive control system in the brains of aging individuals can be improved with simple training.

Want to stay in the game? Create your feeds and stay current with what's sizzling.


Leafing Through The Literature

Thalyana Smith-Vikos

Highlighting recently published articles in molecular biology, genetics, and other hot topics


Aging is inherited maternally


Credit: Bob AuBuchon (Flickr)
Credit: Bob AuBuchon (Flickr)

Ross and colleagues investigated how mitochondrial DNA (mtDNA) mutations, which are exclusively maternally inherited, can contribute to aging. The researchers found that these mutations result in mild aging in otherwise wild-type mice, while decreasing fertility and accelerating premature aging in respectively heterozygous and homozygous PolgA mutants with increased mtDNA mutations. Additionally, maternal and somatic mtDNA mutations also resulted in brain developmental disorders. The authors posit that aging tissues may arise from the rapid expansion of mutated respiratory chain factors as mutated mtDNA replicates.


MicroRNAs regulate micro food portions

Vora et al. have identified a conserved microRNA (miRNA), miR-80, which regulates dietary restriction in C. elegans. Similar to dietary restriction-mediated effects, these mir-80 mutant worms are long-lived and maintain a healthy state for a prolonged period, regardless of the presence of food. Transcription factors DAF-16 and HSF-1 and transcription co-factor CBP-1 are required for these mir-80 mutant phenotypes. Expression of this miRNA is decreased when worms are subjected to a restricted diet, resulting in increased levels of CBP-1.


A fatty reward

Credit: Quinn Dombrowski (Flickr)
Credit: Quinn Dombrowski (Flickr)

Researchers have proposed that lowered dopaminergic function from a high-fat diet leads to obesity by promoting excessive food intake to restore this food-reward relationship. Tellez et al. further investigated how a high-fat diet can affect dopamine levels. The authors identified an intestinal lipid messenger, oleoylethanolamine, which is normally suppressed under a high-fat diet but can restore dopamine release upon administration. Additionally, administration of oleoylethanolamine increased consumption of low-fat foods, indicating that this signaling molecule may be responsible for promoting reward of low-fat foods.


Pathogen-host relationship therapy

C. albicans can exist as part of the non-pathogenic gastrointestinal microbiota or can be pathogenic to mammals. Pande and colleagues report that, while this pathogenic switch is due to the host’s suppressed immune system, a microbial genetic program is also at play. The researchers found that passage of C. albicans through the gut results in a switch to commensalism, driven by the transcription factor Wor1. These C. albicans cells that have transitioned into a commensal state are phenotypically different and express a unique transcriptome. The findings suggest that disrupting this genetic program results in reversion to a pathogenic state.


Breakthrough in wheat stem rust resistance

A highly resistant race of wheat stem rust, Ug99, has been plaguing wheat production areas all over the world for a number of years. Saintenac et al. report that the Sr35 gene cloned from T. monococcum provides near resistance to Ug99 and similar races, and the gene can be successfully transferred to polyploidy wheat. Periyannan et al. similarly identified a resistance gene, Sr33, which was cloned from another wild relative, A. tauschii. Both Sr33 and Sr35 encode coiled-coil, nucleotide-binding, leucine-rich repeat proteins that resemble other pathogen resistance proteins.


Transcribing autism genes

King and colleagues have provided a link to a recent correlation between mutated topoisomerases in individuals with autism and other autism spectrum disorders (ASDs). The researchers showed that a topoisomerase inhibitor, topotecan, reduces the expression of ASD-associated genes in a dose-dependent manner. Intriguingly, these ASD candidate genes are substantially longer than other genes on average. Topectan specifically prevents transcriptional elongation of extremely long genes (>200 kb), which was also achieved by knocking down topoisomerase 1 or 2b in neurons.

A Graduate Student's Browser History

Thalyana Smith-Vikos

We’re all guilty of having 10 internet browser tabs open at once on our laptops, but which websites should you be surfing while waiting for that incubation to finish? For “new” and “old” grad students alike, it’s important to balance researching specific details on your project with staying informed about the world outside of your bench. Take the time to give yourself perspective on how your research can be added to the body of scientific knowledge, as well as what is expected of you and what you should expect of yourself as a graduate student. Here are some tabs you can keep open that will meet these requirements:

Something outside your field of study

Staying up-to-date with the latest scientific publications (especially if they have nothing to do with your research) requires a lot of effort, but if you can put aside some time every day (or at least every week) to read about the latest news, it can be a pleasant experience! Start by taking note of which journals usually publish the most important articles in your field, and then browse the table of contents for these journals to see what other articles were published. Also, visit the homepages of Nature, Science, Cell, and other journals in these publishing groups to see which new research stories are highlighted. Lastly, visit the communications/public affairs website for your university to see which of your colleagues got published! (Obviously, these suggestions are in addition to using Scizzle and following our Scizzle Blog!)

Something outside of academia

As Science magazine is distributed by AAAS, the magazine’s website also contains the latest science policy news updates regarding decisions on federal grants, regulatory procedures, etc. It’s also worth your while to read Scientific American and the science sections of the New York Times, Huffington Post, and any other news sources you subscribe to, just to get a sense of how science research is portrayed to the public. This can also help improve your conservations about science with non-scientist friends and relatives! (Another plus for Scizzle Blog: in addition to highlighting the recent literature, we also have many other posts of interest for any scientist.)

Something career-related

It’s never too early to start thinking about your career, especially if you don’t want to stay in academia. Networking with professionals in other fields may seem intimidating, but never fear, LinkedIn is here! I am always surprised to learn how many PhD students are not on LinkedIn: everyone should be on LinkedIn! It’s the best way for you to display an abridged version of your CV for any potential employer to view. Yes, we are students, but we should also be establishing ourselves as professionals at the same time. Start by connecting with your friends and alumni from your PhD program, and you will quickly learn how large your networking circle actually is through 2nd and 3rd-degree connections. Join discussion groups and post on forums regarding your research interests or general scientific interests, careers outside of academia, alumni organizations, etc. Start following companies where you might be interested in working and make a note of how often they have job postings.

Something fun

Science can be very frustrating, especially after repeating that PCR for the third time and still getting a blank gel. To let off some steam and commiserate with other PhD students, I recommend visiting whatshouldwecallgradschool.tumblr.com. This website contains an extensive list of the many unhappy (and some happy) moments we experience as graduate students, accompanied by hilarious GIFs to illustrate these feelings. I also suggest visiting phdcomics.com, which is a comic strip (started by formed PhD student Jorge Cham) with recurring grad student characters who have to TA classes, write grants, perform experiments, attend happy hours, and anything else you can think of. Being able to laugh about all of these experiences will preserve your sanity throughout grad school!


Lessons Learned from the Science Fair

Thalyana Smith-Vikos

When I first started my PhD at Yale University four years ago, one of the program directors held a meeting for new students to learn about extracurricular activities on campus and around New Haven, CT. At first I was a little confused; how did they expect me to participate in all of these programs while still completing my course work and teaching requirements and working in the lab full-time?

However, once I began my lab rotations and had conversations with older graduate students, I quickly realized that many PhD candidates in our program devote a great deal of their time to volunteering for community-wide science activities outside of the lab, Read more

Image taken using ZEISS LSM 700 Cortical neurons and glia cells in culture. Green: Alpha-Tubilin-Alexa 488. Blue: Nucleic acids, DAPI.

Leafing Through The Literature

Thalyana Smith-Vikos

Highlighting recently published articles in molecular biology, genetics, and other hot topics

Battle of the Small RNAs

Sarkies et al. have analyzed gene expression in the nematode C. elegans upon infection with the positive-strand RNA virus Orsay. As RNAi is required for the immune response, the Argonaute protein RDE-1exhibits less repression of its endogenous small RNA targets to focus on its exogenous target. The authors also showed that a wild C. elegans isolate exhibits a reduction in miRNA expression and a consequent increase in miRNA target levels upon viral infection.

Read more

Leafing through the Literature

Thalyana Smith-Vikos

Highlighting recently published articles in molecular biology, genetics, and other hot topics

Small Molecules Achieve Pluripotency

Hou et al. have reached uncharted territory in stem cell research: rather than achieving pluripotency using the well-established transcription factor cocktail or recent advances in somatic cell nuclear transfer, mouse somatic cells were reprogrammed to generate pluripotent stem cells with a frequency of 0.2% using a cocktail of seven small molecules. These reprogrammed cells, termed chemically induced pluripotent stem cells (CiPSCs), were shown to resemble embryonic stem cells (ESCs) based on gene expression and epigenetic profiling, which is not case for other types of iPSCs.

Tissue and Organ Generation from Pluripotency

Takebe et al. report the first case of successful generation of a three-dimensional vascularized organ Read more

Leafing through the Literature

Thalyana Smith-Vikos

Avian Influenza Transmission in Mammals

Avian influenza viruses can reassort their genomes to infect mammals. To investigate how this is done, Zhang et al. generated all possible 127 reassorted viruses by combining the hemagglutinin gene of an avian H5N1 influenza virus with an H1N1 virus capable of infecting humans. The researchers examined the virulence of these viruses in mice, as well as their ability to transmit in guinea pigs, which, like certain livestock, have both avian and mammalian airway receptors. Certain H1N1 genes allowed the H5N1 virus to transmit between guinea pigs. The virus was transferred by respiration between guinea pigs without killing them, indicating that livestock could be carriers of this virus without the farmer even knowing. Read more