Just hook that little guy up to a generator, and boom! Electricity!

Sadly that’s not really how these scientists are making electricity from viruses. I mean, if I really think about it, there are several flaws to my idea: 1. How do you build a teeny tiny wheel? 2. How many teeny tiny wheels would you have to build to generate a sizeable amount of electricity? 3. How do you train the viruses to run on said teeny tiny wheels?

The way the authors of this Nature Nanotechnology paper did use their viruses, however, is pretty ingenious.

Their experiments were based on a phenomenon known as piezoelectric energy. This is the conversion of small amounts of mechanical energy, such as vibrations or strain, into electricity. For example, piezoelectric devices can harvest the vibrational energy produced by human footsteps if they are placed under a sidewalk. The amount of piezoelectricity generated is small, but there is potential for using it in small devices such as wristwatches and other hand-held devices. Harvesting this kind of energy relies on the specific physical and chemical properties of certain materials, and the major roadblocks to the widespread use of piezoelectric energy are the toxic chemicals needed to make these materials.

Enter biopiezoelectricity. There are several naturally occurring biomolecules that are known to possess piezoelectric energy generation potential. These include bone, collagen, and peptide nanotubes, all of which are inherently tricky to use. One of the key properties of a piezoelectric material is it needs to be organized into a regular, repeating, crystalline structure. Scientists have therefore been on the lookout for biological entities that naturally aggregate in this way. It is also important to be able to generate these molecules in large quantities; something that has also been an issue with previously characterized biopiezoelectric generators.

Lee and colleagues managed to overcome both of these problems by using a virus. The M13 bacteriophage (a virus that infects E. coli bacteria) is an 880nm-long rod-shaped particle that is made up of repeating protein building blocks called major coat proteins. These coat proteins self assemble, and the resulting rod has both rotational and screw symmetry, features that predispose a molecule to forming regular crystal sturctures. So what Byung Yang Lee and his pals at UC Berkeley did was to grow a large culture of E. coli in a liquid medium, infected the cells with M13, and let biology generate their starting materials for them. Then, they isolated the virus from the bacterial cells, and set about generating a structured crystal. But guess what? The viruses did that on their own too!

The researchers then set about testing this potentially piezoelectric material. They found that, with some genetic tweaking of the precise composition of the major coat protein, and by stacking the virus crystals into 7-layer deep arrays, they could generate up to 6 nano-Amps of current and 400 milli-volts of potential. Using this generator, they could power a small liquid crystal display, similar to those found in digital watches.

So, while this paper doesn’t describe the athletic properties of bacteriophage, it does provide a solution to the problems that have plagued the piezoelectricity field for some time. These self-assembling biomolecules could have direct real world applications in the not-too-distant future.

Piezoelectricity: Coming to an iPod near you soon!

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Katie Pratt is a graduate student in Molecular Biology at Brown University. She has a passion for science communication, and in an attempt to bring hardcore biology and medicine to everyone, she blogs jargon-free at www.katiephd.com. Follow her escapades in the lab and online on Twitter.

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Be the first one to mind the gap by filling in the bacteria name as a comment and get your name in the blog along with a sweet new BenchFly mug!

UPDATE – Congratulations to Michele Banks, winner of this week’s Mind the Gap!

About the winner: Michele Banks is a painter based in Washington, DC. Most of Banks’ artwork is inspired by science, particularly biology. Her work has been featured in The Scientist Online and Scientific American and has been exhibited at the National Institutes of Health. Check out her paintings and collages and follow her on Twitter.

About the prize: In addition to fame and glory beyond their wildest dreams, winners receive our new hot-off-the-presses large (15 oz) BenchFly mug to help quench their unending thirst for scientific knowledge… or coffee. Check out where the mug has traveled – will you be the first in your state or country to win one?

Miss a previous edition of Mind the Gap? Shame on you! Don’t worry – we’ve got you covered:

How is a Dormouse Like a Career Scientist?

With Great Power Comes Great Violin Strings

Tweet Tweet? TWEEEET!!

All the Better to See Sperm Whales With, My Dear

Saw VII: The Revenge of the Sawfish

Caution: Objects May Appear Larger Than They Really Are

Facebook Updates: The Good, The Bad, and The Vague

Scared of Dropping the Soap? Worry No More.

New Year’s Lab-olutions

A Social Network for Food: Why Won’t Vanilla Friend Garlic?

I’d Rather Die Fat and Young than Old and Skinny

Look Into My Wide, Vacant, Eyes

I’m Just Mad About Saffron

Sweet Relief: How Sugar May Help Reverse Climate Change

Recent findings by Henry Sauermann and Michael Roach suggest that while nearly 50% of life scientists and physicists regard an academic position as one of the most desirable career paths, the reality is that there aren’t enough academic job openings to fulfill the demand. As a result, many scientists end up working outside of the academic environment regardless of their initial career aspirations.

Although Sauermann and Roach find that many students feel their advisors preferentially support the academic path, departments on the leading edge of graduate education are beginning to offer support to students who will ultimately pursue a non-academic career. In many cases, this will be a majority of the class.

Given the realization that academic jobs are limited and a majority of students will find jobs outside of the university, does it make sense to refer to non-academic jobs as “alternative”? While some may argue it’s semantics and is splitting hairs, we feel it’s more than that. As our next generation of scientists contemplate a career in research, it’s only fair to help them understand where the career path leads. So if you were to describe what the “alternative career path” in science means, which profession do you feel most accurately fits the label?

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Any suggestions for other terms we may use instead of “alternative”?

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I maintain a line of particularly finicky cells as an integral part of my project. They need some kind of maintenance every 2-3 days, which isn’t a big deal other than the fact that finding vacation time is nearly impossible. I’m not sure I trust them to a lab mate and if I were to bleach them and go back to a frozen stock after the vacation, it would be about three weeks before I could start doing experiments again, which my boss makes me feel guilty about every time I bring it up. Any thoughts on how to get away?

Erin, graduate student

Dear Erin,

Welcome to the club ;)  I worked with rat liver cells in graduate school and I had to feed them every 2 days. In other words, I could not even take a weekend off.

If you want to trust them to another student, you need to implement appropriate controls, so you’ll be able to tell whether your cells are still OK when you come back. (e.g. microscopy or a viability test). Make sure to return the favor!

Taking an extended vacation can be a negotiation exercise with your boss, regardless of your field. Many universities have guidelines regarding the amount of vacation graduate students are entitled to. If your boss tries to make you feel guilty, remember that it is important for your mental and physical health to take a little break once in a while. On the long run, it will be to everyone’s benefit if you come back focused and rested.

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Dora Farkas, Ph.D. is the author “The Smart Way to Your Ph.D.:200 Secrets from 100 Graduates,” and the founder of PhDNet, an online community for graduate students and PhDs. You will find links to her book, monthly newsletters, and discussion board on her site. Send your questions to DearDora@benchfly.com and keep an eye out for them in an upcoming issue!

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Stay tuned for Dora’s next article in two weeks!  In the meantime, check a few of Dora’s recent posts:

Is a Publication Gap on Our CV a Job Killer?

How to Leave a Postdoc Quickly with Your Reputation Intact

How to Establish and Enforce the Chain of Command in Lab

Walking the Thin Line Between a Great Result and a Lie

Dear Boss: I Want to Graduate. Let’s Talk.

My Boss’ Spouse: A Spy or Civilian in Lab?

Bullying in the Lab: Are PIs Guilty

What Came First: The Grad Student or the PI?

Problems Communicating Science to Family? It’s Not Them, It’s You

How to Address the Funky-Smelling Lunch Problem

Does a Fellowship Yield Scientific Independence or Does the Boss Rule?

The Arrogant Labmate: Face ‘Em or Forget ‘Em

Is Grad School or Postdoc Success More Important for My Career?

Submit your questions to Dora at DearDora@benchfly.com, or use the comment box below!

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As anyone in academia knows, when to start a family is a really tricky decision. If you follow the traditional career path from college (4 years), to grad school (5-7 years), through a postdoc (3-6 years), perhaps another postdoc (3-6 years), into a tenure track position (5 years) which finally leads to a tenured faculty job (eternal) there really is no “good time” to pop out a baby or two.

After all, us mammals tend to reproduce at a time when we can ensure the survival of our offspring and ourselves, so we like to do so when there are plentiful supplies of food and water (and money), as well as reduced stresses such as predation or grant deadlines. While humans are not seasonal, the academic career is. There’s no way you want to have a baby while you prep for your qualifying exam, or get that paper submitted, or defend your thesis, or go on a gazillion post-doc interviews, or try to get that fellowship funded, or compete for tenure… Not to mention the fact that scientists have little to no financial security until they are tenured, a position few reach before the age of 40, at which point fertility can become a serious issue.

So what’s a baby-crazy scientist supposed to do?

In a recent paper published in Oecologia, Claudia Bieber and colleagues found that common dormice in Lithuania reproduce only once or twice a year, and the timing of these two litters was specific. The first peak in birth rate occurred in June, soon after the mice finished their hibernation period. Birth rate then dropped dramatically in July, only to rise again in late August, shortly before the mice returned to hibernation.

Having babies is a physical stress to the mother, but she in turn has to weigh her own discomfort against the survival of her offspring. Dormice often wait until their favorite diet of fruits and seeds are abundant in the late summer to have their first and only litter of pups. This allows the mother to fatten and provide rich and nutritious milk. It doesn’t, however, give her babies much chance to gain the fat stores they need to hibernate. On the other hand, if the mother can have her pups earlier in the year, she gives them a much greater chance of fattening up and surviving the winter.

Dormouse = Grad Student

But, as with all things in life, it gets more complicated than that when you take into account those pesky Tawny owls. In Lithuania, dormice make up almost 10% of their diet, thus posing a pretty serious threat to these little rodents. Indeed, dormouse life expectancy is much higher during hibernation than in the summer months, a factor that seems to play into the bimodal distribution of dormouse births; a pup born shortly before hibernation is much more likely to make it to sexual maturity than one born at the beginning of the active season.

So it is the balance between body mass and owl-attack-survival that appears to drive the reproductive strategy of the common dormouse. Is the same true for scientists?

In my cursory survey of the MCB department here at Brown, most people seem to have their babies while they’re post docs. While their job is temporary, the pay is better than a grad student stipend, and, in their late-twenties or early-thirties, it makes biological sense. So, if grad school and tenure track employment represent periods of hibernation, or sexual inactivity, then perhaps the postdoc represents a happy breeding season? A hypothesis to be tested, perhaps…

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Katie Pratt is a graduate student in Molecular Biology at Brown University. She has a passion for science communication, and in an attempt to bring hardcore biology and medicine to everyone, she blogs jargon-free at www.katiephd.com. Follow her escapades in the lab and online on Twitter.

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Be the first one to mind the gap by filling in the location as a comment and get your name in the blog along with a sweet new BenchFly mug!

UPDATE: Congratulations to Aaron – winner of this week’s Mind the Gap!

About the winner: Aaron is a post-doctoral fellow at the University of Michigan studying brain circuits involved in food intake and metabolism. He’s also a self-professed running junky, an amateur nutritionist and a coffee addict. You can keep up with the latest from him on Twitter or Facebook.

About the prize: In addition to fame and glory beyond their wildest dreams, winners receive our new hot-off-the-presses large (15 oz) BenchFly mug to help quench their unending thirst for scientific knowledge… or coffee. Check out where the mug has traveled – will you be the first in your state or country to win one?

Miss a previous edition of Mind the Gap? Shame on you! Don’t worry – we’ve got you covered:

With Great Power Comes Great Violin Strings

Tweet Tweet? TWEEEET!!

All the Better to See Sperm Whales With, My Dear

Saw VII: The Revenge of the Sawfish

Caution: Objects May Appear Larger Than They Really Are

Facebook Updates: The Good, The Bad, and The Vague

Scared of Dropping the Soap? Worry No More.

New Year’s Lab-olutions

A Social Network for Food: Why Won’t Vanilla Friend Garlic?

I’d Rather Die Fat and Young than Old and Skinny

Look Into My Wide, Vacant, Eyes

I’m Just Mad About Saffron

Sweet Relief: How Sugar May Help Reverse Climate Change

This quote from A Tale of Two Cities by Charles Dickens can perhaps sum up the feeling of anxiety we all experience at certain times, when our life flip flops between complete despair and a promise of success. This may be especially true if you are a graduate student or a post-doc dealing with work-related stress brought about by a number of factors.  As someone in a trainee position at the start of our scientific careers in the academic or corporate hierarchy, we are no strangers to stress. We work in the environment loaded with anxiety triggers: sometimes we feel powerless working in a state of perpetual uncertainty and lack of control, always exposed to extreme competitiveness and limited resources, long working hours, failed experiments, harsh criticism from reviewers or committee members, unrealistic demands from the adviser, and let’s not forget the “Publish or Perish” formula of the Ivory Tower. An article titled Grad School Blues published in The Chronicle Review reports that “Graduate school is gaining a reputation as an incubator for anxiety and depression.” As such, we are chronically exposed to anxiety triggers.

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Anxiety is a natural response

So what is the answer, you might ask. Should we sacrifice graduate education and a career in science to avoid all this anxiety?  For those of you who, after reading this article, decided to say goodbye to your graduate career, STOP! This, of course, is not what I am suggesting. Anxiety is a part of life and a natural response that by itself it is neither good nor bad. However, it is how we react under such situations that determines our ability to withstand stress. In fact, when faced with a challenge some anxiety is actually advantageous, because it provides the necessary push to work harder under duress. This is because anxiety is an ancient survival mechanism inherited from our ancestors: the fight-or-flight reflex. If not for our ability to increase performance under stress, human species might have never outlived cyber-toothed tigers or the ice age. However, our ancient survival system has not quite caught up with the modern world. Sometimes, triggers that are not necessarily life threatening, like presenting data to an audience or stress associated with a lack of job prospects, can eventually induce a chronic state of anxiety and diminish our work efficiency. Our inability to fine-tune the anxiety response eventually nips away at our resilience in the face of everyday challenges, leading to depression. With time, such stress can wear out our enthusiasm and mental state, leading to a state of “tunnel vision” in the workplace. Just remember how excited and idealistic you were when applying for graduate school?  Now fast forward to year 4 or 5 of your grad school experience … do you feel disgruntled and lack purpose? This dangerous trend and high burn-out rates, combined with a feeling of perpetual transition and instability, can sap even the most resilient and the brightest.

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How to deal with anxiety

So, if anxiety is a built-in response and can actually be helpful in moderate doses, we can do anything not to succumb to the downward spiral?   How do we minimize anxiety and develop resilience to shake off work-related stress?  While we may not control the factors that contribute to anxiety, we can try to be in control of how we react to and handle them. Here I am providing some advice on how to handle anxiety:

1) Minimize anxiety by setting achievable short-term goals. It does not hurt to plan far into the future. However, it is very helpful to plan bite-sized achievable goals that you can accomplish in a week, or a month. This way you will feel that you are making progress and identify areas that require more of your attention. This approach helps you feel more productive and positive when you achieve these goals, without setting yourself up for a long-haul goal that might not yield results.

2) Taking care of yourself and feeling positive is essential to the mental and physical health. Exercises is a good way to invigorate yourself, release stress, clear your head, and re-focus mentally because during exercise our bodies release endorphins that provide a natural boost of positive energy. For example, during my graduate studies I started training in Krav Maga, a very rigorous and practical self-defense system, which did wonders because it allowed me to refocus my mind from work-related issues and feel positive and re-energized (not to mention that I learned self-defense and improved my confidence!).

3) Establish work-life balance and change pace. We need to strive to establish a good work-life balance to avoid burnout. Taking breaks during the workday and going for walks can help prevent stress and tension buildup. Any sort of positive and reinforcing activity, such as travel, spending time with friends, hiking, going to a museum, etc, can help break up monotonous routine we sometimes face and combat anxiety.

4) Seek support from colleagues. Your colleagues may be experiencing the same stress and frustrations as you are, and may have found productive ways to cope and resolve them. You are not alone, and it helps to feel some solidarity and encouragement from your peers. You should not feel ashamed or embarrassed of what you are feeling, and reach out for peer support. There might already be support groups or networks established for this purpose. If not, then perhaps you can take initiate and organize a support group, which will address the work-related anxiety and also make you feel more positive and in control. However, it is important not to continuously dwell on negative emotions when sharing with your peers, because it could serve as an incubator for negativity and result in further demoralization and anxiety. Instead, try to be positive and supportive of other people, and you will feel positive yourself. Some institutions have complementary well-being and mental health services with trained professionals who address specific issues that scientists may have in the workplace.

5) Talk with your supervisor. Hopefully you are on friendly and professional terms with your boss, and they actually care about your well-being. It is important to talk to your supervisor if you feel unhappy about your current project or work direction. Often, they may be able to provide you with the perspective you need to feel like you are doing a better job, or redirect your efforts so that you feel more productive

6) Do not beat yourself up. It may turn out that much of your stress is self-imposed. Are you setting yourself up for unrealistic expectations? Are you pushing yourself too hard and not acknowledging your accomplishments? Refer to advise #1 on setting up achievable short-term goals. It could be that you are being too tough of a self-critic and cause your anxiety by never being satisfied with your work. Do not destroy your self-confidence by constantly denigrating yourself, but instead reward yourself for getting things done.  We can ruminate on negative thoughts and thus breed anxiety in our minds. Do not beat yourself up for making mistakes, we all make them, and remember to move on and focus on what is at hand.

7) Identify the causes of your anxiety.  Think carefully about what it is that is causing you to feel anxious. Is it anything that you can change? Is there anything that you can change about yourself to avoid feeling this way? You cannot worry about things over which you have no control. You may realize that some things you worry about are not problems at all, but rather that your mind just tends to over-think them and cause you to feel anxious. Ask yourself if you are getting as much satisfaction from your work as you once did and if you are as productive as you once were. If after realistically assessing your job satisfaction and workplace productivity, you determine that you are really unhappy and your goals are unattainable, then perhaps either your work setting is toxic, or your attitude is incompatible with the current work setting (or both). In this case you should seriously think about changing your line or place or work.  To avoid anxiety and work-related burnout, you should do what you love, which would allow you to grow as a person and feel positive about what you do, rather than causing you more pain and anxiety.

8) Avoid negativity. Avoid spending time around negative people, they are like black-holes for your well-being and will drain you of positive energy. If certain settings and people cause you to feel negative, minimize your exposure to them. Anything that causes you to feel negative emotions will only exacerbate your anxiety. This also extends to interactions outside your work, including personal relationships. You will end up bringing this negativity with you to work, which is likely to make you feel more stressed and susceptible to anxiety at work.  Same goes for any other sources that make you feel negative: news, TV, etc. Instead, try to spend time with people and visit places that make you feel positive and energized, as mentioned in advices 2, 3, and 4.

Hopefully these 8 simple suggestions will help you fight off and overcome anxiety issues that we face every day. Since I started this article with a quote, let me finish it with one: “Drag your thoughts away from your troubles … by the ears, by the heels, or any other way you can manage it.”  – Mark Twain

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Yevgeniy grew up in New York, but decided to transplant himself to the West Coast for his PhD studies at the Scripps Research Institute, where he studied mechanisms of gene regulation in the immune system. Recently, Yevgeniy again found himself in New York City, pursuing a post-doctoral research project in oncology. In his spare time Yevgeniy works as a Krav Maga self-defense instructor, and as a scientific writer to share his passion for fostering communication between the scientific community and the public.

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How do you manage anxiety in lab?

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Today we’re excited to announce our newest contributor, Yevgeniy Grigoryev, Ph.D. who will shed light on many of the shared challenges we face as scientists. In ‘PhD Tales from the Couch’ Yevgeniy will seek experiences from the broader community in order to identify solutions to help researchers move forward. We recently spoke with Yevgeniy about the roots of his passion for helping fellow scientists, the challenges he faced in his own career development and what’s at stake for science education if we don’t address the problems now.

BenchFly: As a kid, did you always know you wanted to be a scientist, or did that decision come later?

YG: As a kid, I demonstrated abundant curiosity for the world around me. I enjoyed asking questions, solving problems and tackling riddles. I think I just really wanted to know what made things work. I disassembled alarm clocks, old TV sets, anything that could tick, chime or beep and then tried to put it back together … the best I could. When I was 8 or 9, my parents bought me a small light microscope, and that’s when my foray into science began – I wanted to know what color eyes ants had, what happened when you dissolved different substances in water, if my dog could dream and what he dreamt about, etc. I did not think of this as a profession, it was just natural to want to know how things worked. I did not think too hard about what I would do when I grew up, I was too busy trying to piece back together my parent’s alarm clock.

Entering graduate school, did you have a particular career path in mind?

Entering Graduate school, I was such a visionary! I had everything planned out about how I will change the world and cure all the diseases, and become world famous for re-introducing space food to the public. Don’t we all feel this way when starting grad school? Honestly though, while in college, I was divided between a career as a medical doctor and a research scientist. Both were viable options. By then I had already developed a healthy fascination and interest in science. There were other subjects that I enjoyed as well, such as History, Literature, and Writing. But what really motivated me was my desire to be useful in this society, to help people around me, to make the old young again and the sick healthy and other such noble things. Yet, as I helplessly watched my grandmother succumb to the Alzheimer’s disease while the medical field was powerless to reverse the neurodegenerative damage it inflicted on her, I decided to choose a career of a research scientist, which seemed to me the most practical choice would enable me to address such challenges head on. I also realized that I wanted conduct research more on the clinical side (sorry, basic science, we had some good times, but it’s not you, it’s me … really!). I arrived at this conclusion after realizing that approximately 80% of my time in the lab, I transfer microscopic amounts of liquid from one tube to another, day in and day out. In order not to go crazy, I had to have a bigger picture in mind. That bigger picture to me is addressing current clinical issues, like investigating the immune mechanisms of organ transplant rejection, focusing on developing targeted cancer therapies, or promoting science communication between various sectors of society.

Yevgeniy Grigoryev, Ph.D.

Looking back on your experience at Scripps, what do you think were the most valuable components of your graduate education? 

I think the most valuable component of my graduate education was that it was unlike any other education I was used to. Most of the things that I learned in grad school were not taught in classes (which were few and not directly relevant to my research), or textbooks. The most valuable components involved developing an independent mindset, to be able to face questions that did not necessarily have answers, to dare to propose experiments even though they might fail. I think this was precisely it, not to be afraid to fail! In this world, we are all judged by our successes, and failure carries such a heavy stigma of shame. But in graduate school, failure was the driver leading to success. To quote the 1969 Nobel prize winner in Literature, Samuel Beckett, “Try again, fail again, fail better.” I learned more about the field, experimentation, and asking the right questions after my experiments failed (which happens 70-80% of the time … ever wonder why it takes 5 to 6 years to get that PhD?).

More importantly, in this unique and seemingly unstructured environment I learned a lot about myself. I would not be able to do it on my own, of course. I had the invaluable guidance of my colleagues, my graduate adviser, and my thesis committee, who challenged me, encouraged me, and occasionally criticized me (constructively, of course). Troubleshooting, learning on my feet, and thinking outside the box were just some of the skills I developed in graduate school, in addition to becoming more resilient, resourceful, and analytical in my thinking … but enough self accolades!

…and what were some of the pitfalls?

To me, the biggest pitfall in graduate school was feeling more and more alienated from the world around me. As I spent more time at the bench and increased my specialization, the fewer and fewer people around me understood, cared to understand or even bothered to understand what it is I did or why I did it. Such narrow path of specialization can make it hard for you to communicate with the rest of the world, which requires generalization. I was so used to dwell in the details of my PhD project that I lost touch with the outside world (world outside the lab, that is). This became especially noticeable when I started writing my dissertation. My friends would ask me what my work was about and I would immediately bombard them with such rods as “Genome-wide analysis”, “differential gene expression”, “post-transcriptional gene regulation”. They would quietly listen, pat me on the back and be on their way to find someone with whom they can actually have a conversation. So my biggest fear became that after so much hard work and time spent researching my project, my thesis would only be seen by a handful of people in this world: my graduate adviser, the three members of my graduate committee, and maybe a handful of graduate students who cite my work in their abstract. Isn’t it a shame that almost no living soul would care to open these pages that were saturated with my proverbial sweat, lack of sleep, and excess of caffeine? And just to think that my finest intellectual achievement would gather dust in the archives of some library until the sands of time have claimed its existence forever!

Another challenge that I became very aware of while in grad school was the question of what I should do and what path I should take once I graduate. Graduate School tends to make you feel very sheltered from the outside world. While my friends on the “outside” were getting laid off, looking for new jobs, going through the interviewing circuit and learning the ropes of what it takes to actually get a job, I was comfortably pipetting at my bench. Afterall, this is what is expected of you in grad school: you work hard, get your work published, write and defend your thesis and be on your way. The problem is, as I realized too late, is where exactly am I supposed to go with all these skills that I learned?  I was too busy working and writing to actually stop for a second and imagine where I want to be once this is all done. Do I want to continue with academic research and look for an academic post-doc? Am I interested in transitioning to Industry? What other aspects of science could provide an enjoyable career?

By asking these questions, I found a true passion for communicating science, for looking back at the big picture of why I do research. In order to communicate complex ideas and concepts, I had to become a generalist again, and find the common thread of humanity – something that unites us all and helps us relate to the big picture.  In doing so, I also was able to think more about my life’s work and how it relates to the public good and common/personal good.

How do you think these challenges will affect the future of science education and research left unchanged? 

Let’s admit it, no one wants to feel alone, alienated, and misunderstood in this world. We, as humans, have an inherent desire, nay, need to communicate, to tell stories, to relate to these stories (remember when you were just a kid and you loved listening to bedtime stories) … We simply love stories! With the current approach to graduate education, we are steadily producing hundreds of highly trained specialists each year. However, due to such rigid specialization, these highly trained PhDs may feel that they have lost that “common thread of humanity”. After all, let’s rewind back to when I was applying to Graduate School – I was young, full of zest and energy, ready to share my future discoveries and findings with the world.  Now let’s fast forward 3 or 4 years into my graduate education – I feel like a castaway … “Wilson! Wilson! I’ll do all the paddling. You just hang on”.  And then you start doubting yourself. Were you right to choose this path? Is it supposed to feel this way? Are you the only one going through such rocky experience?  I think it is important to remind these young researchers that they do not have to become isolated on this course, that while there is a trend for specialization, we should always see the big picture in front of us … otherwise we are just highly trained liquid carriers.

What are your goals with PhD Tales from the Couch? 

My goal with “PhD Tales from the Couch” is to connect people at different stages of the professional growth and specialization and create a portal where peers can shed some frustration, share a word of advice, stories of personal experiences, ask questions and remind each other that we are not alone.  There are hundreds, even thousands of us that go through this experience, and each one of us can still maintain that common thread of humanity. I see “PhD Tales from the Couch” as a portal where people involved in science and PhD studies can go for advice, guidance, and support – from their peers.

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Stay tuned for tomorrow’s launch of PhD Tales from the Couch!

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Yevgeniy grew up in New York, but decided to transplant himself to the West Coast for his PhD studies at the Scripps Research Institute, where he studied mechanisms of gene regulation in the immune system. Recently, Yevgeniy again found himself in New York City, pursuing a post-doctoral research project in oncology. In his spare time Yevgeniy works as a Krav Maga self-defense instructor, and as a scientific writer to share his passion for fostering communication between the scientific community and the public.

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That’s where off-site backup comes into play. Off-site can mean several things; for example, you can backup your data on an external hard drive and put it somewhere other than your home. But “off-site” can also mean online or “in the cloud.” There are countless online backup services — several of which have already been covered here at BenchFly — but in this article I’ll set my sights on so called “unlimited” online backup services. I’ll dig a little deeper and show you that not all “unlimited” data storage and backup services are created equal, and what you should keep in mind when choosing one.

Why use unlimited online backup in the first place?

Before we dive into the world of unlimited online backup providers, I’d like to explain why one would even need unlimited data backup. Nobody has unlimited amounts of data, right? While that is true, you don’t need hundreds of gigabytes to make those services worthwhile. Storage prices have decreased dramatically due to the high level of competition in this niche; and each company is doing their best to offer us as consumers attractive prices that are hard to resist. Nowadays, you can get unlimited online backup for as low as $5 per month, or even less if you’re willing to commit to a longer membership period. So for the price of a caffè latte per month, you can enjoy the peace of mind that comes with knowing that your data is safe.

How can those services offer unlimited storage space?

Another interesting question I hear a lot is: How is it possible for those providers to offer unlimited online backup? Obviously, offering unrestricted data backup is a nice claim that draws the attention of lots of customers. But it is based on the simple assumption that the majority of people will only backup a couple of gigabytes, while only a tiny majority will backup more than a terabyte. So, the company earns money off of one customer and loses money off the other. As long as the people backing up fewer files outnumber those who backup large quantities, this remains a sustainable business model.

Overview of unlimited online backup services

Now that we’ve covered our bases, let’s delve right into the thick of things by taking a look at the service providers that currently offer unlimited online backup, and what “unlimited” means to them. We’ll soon discover that the term “unlimited” can be interpreted differently as you look at it from different angles. The “unlimited” segment of the online backup market is still quite small, so I’ll only be looking at 5 services today.

Carbonite is one of the “big players” in online backup. In fact, you’ve probably heard about Carbonite on some radio commercial or seen it on the Internet, because they invest heavily in growth and thus do a lot of marketing. Together with Mozy, they were one of the first to offer unlimited storage of files; however, Mozy discontinued its unlimited offering a while ago.

Carbonite offers unlimited online backup for $59 per year. Unfortunately, there are no monthly plans available, but you can test the service for 15 days for free. And while it is nearly impossible to get a full initial backup done in 15 days, you can still access and restore your files before that initial backup is complete.

Now, is Carbonite really unlimited? Unfortunately, the answer is no. There are some caps built into the system which might be a deal breaker for those looking to backup more than 200GB — allow me to explain:

Carbonite implements a bandwidth throttle of 2 mbit/s, so even if you have a 10 mbit/s upstream, you won’t be able to use it all. Furthermore, they limit your upsteam even more aggressively to 512 kbit/s if you’re backing up more than 35GB; and if you surpass 200GB you can only upload at a measly 100 kbit/s. You see that “unlimited” comes with a catch here. While many users won’t ever backup more than 35 GB, the ones who do will be very unhappy to know that their backup will take a year to complete.

If you’re looking for cheap unlimited online storage then Carbonite might be an option; but only if you don’t care how much time it takes to complete your backup.

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Livedrive has one of the most interesting offers if you have more than one machine that needs backing up. While many services offer unlimited online backup, they only do so for one machine; any more requires an upgrade. With Livedrive, you get unlimited storage for as low as $7.95 per month for up to 5 machines, making it the cheapest option of the providers I’ve tested provided you actually have 5 machines you need backed up. They also claim to have neither bandwidth throttling nor file size restrictions in place.

So all in all Livedrive seems like a sound offer, right? Technically yes, but in my testing I found some reliability issues with restoring: sometimes it just wouldn’t restore my files correctly. That being said, they do offer a 14-day free trial, so you should certainly test this out for yourself.

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JustCloud is one of the youngest online backup services in this industry. They run (as many other online backup and syncing services) on Amazon servers, which makes them both fast and reliable in terms of upload speed and restore reliability. Currently, I have 400GB of data with them, and I have yet to experience any problems.

There are some downsides, however, that can’t be ignored: For example, they limit the maximum file size to 3GB, which can be a deal breaker for video producers or podcasters who frequently work with larger files than that. Also, they clearly state in their TOS that they reserve the right to charge for overages. The question is: what do they consider excessive use? and how much do they charge? There are, unfortunately, no answers available to these questions. As I said, I keep around 400GB with them and I haven’t run into problems; but this could be a slippery slope for people with lots of data.

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Like Carbonite, Crashplan is also one of the bigger players in this business, and rightfully so; their product is just great. Offering unlimited online backup for as low as $2.95 (if you’re willing to commit to a 4-year period) it is clearly one of the cheaper options out there. What I like about Crashplan is that I couldn’t find any restrictions. No bandwidth throttle, no file size cap — just easy backup, plain and simple.

Crashplan even offers some gems, such as the ability use their software for free to make a local backup to an external hard drive. Another feature that makes Crashplan unique is their free peer-to-peer backup, which allows you to backup to a friend’s machine if he also uses Crashplan. So you can get an onsite and off-site backup for free (unless your friend gets greedy and starts charging you).

The only downside I noticed is rather slow backup speed; but this is probably because I am based in Berlin, Germany while their servers are in the US. I never surpass 3 megabit/s, which is alright but translates to about 6 – 8 weeks for a 1 TB backup. If this is too long for you, you can send in an external hard drive (up to 1TB) to seed your backup in just a couple of days for an additional fee.

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Backblaze is the easiest online backup service out there. After downloading the software, it just backs up everything. If you don’t want to backup some files, you have to put them on a file exclusion list. This makes Backblaze the best backup solution if you don’t want to think about your backup or geek around with your setup (as I like to do). That being said, if you are a geek then you might find Backblaze “too easy” and a little restricting.

Backblaze is also very quick at both uploading and downloading (restoring) files. Backblaze (note the second lowercase “b”) used to have a file size limitation of up to 9 GB, but with their version 2.0 they’ve made it completely unlimited, doing away with bandwidth throttle at the same time. I have interviewed the CEO, Gleb Budman, in my podcast and I absolutely trust those guys with my data. I use it as my secondary backup, and it runs so quietly in the background that I often forget that it’s there.

What about sync?

Many people ask me: Mauricio, what about sync? It’s a good question, because it is very important to separate the concepts of backup and file sync. I would never use, for example, Dropbox as my main backup because it would be too expensive. However, it is the perfect companion to the unlimited online backup services I mentioned above. So here’s my recommendation: get a solid online storage and backup service, and combine it with a well known syncing service if you find yourself needing one.

There are providers like JustCloud and Livedrive that combine online backup and syncing, but I didn’t find it very smooth, and syncing was always a little laggy.

I hope I’ve provided you with some insight into the world of “unlimited” cloud storage and backup providers, and you now understand that they are not always as unlimited as they claim to be. In fact, in some cases the “unlimited” badge is downright misleading. So read carefully before signing up. A great tip is to search google by typing: “site:nameoftheprovider.com throttle”; What this does is search only on the provider’s domain for the word throttle, saving you the time it would take to scour through a lot of useless information and marketing talk.

Mauricio Prinzlau is the owner of Cloudbackuping.com, a website providing high quality reviews and video guides on a plethora of online backup companies, while also publishing daily news about the cloud storage industry.

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Disclaimer: BenchFly is not affiliated with any of these services and has no vested interest — other than making sure your data is safe — in your decision whether to use them or not.

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How do you backup your lab’s data?

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Dear FlyGirl,

Do you have any good hair grooming products to recommend? 

-Annie

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Dear Annie,

Now I’ve never been a fan of the deflection technique of answering a question with a question.  However, in this case, I am going to do precisely that with a few questions.   Your question requires clarification, as “grooming” refers to multiple zones on the body.  I will presume that you mean hair grooming.  But again, where?  Read on to find one some answers.

Do you have unruly leg hair?

If so, blame genetics, hormones, the cold weather, etc…  Though frankly, blaming is unproductive.  So here is how to retaliate against those prickly pests.

I actually learned this tip 13 years ago from a cyclist friend of mine who fancied himself a master of aerodynamics and needed his legs to be as smooth as silk.  I was initially skeptical.  But my scientific curiosity made me want to test his theory.  He claimed that using Johnson & Johnson Baby Oil gave the best and longest lasting shave.  It beat everything on the market.  Was he right?  ABSOLUTELY!!!!!  I discovered that lavender scent soothes while it smoothes.  And if you pat dry when toweling off, then you’ll retain the natural moisture from the baby oil.

Do you want your hair to be groomed without looking like you groomed it? 

I understand.  We all want to look effortless.  Fortunately, Bumble and Bumble keyed in on our pathologies and created Bumble and Bumble Texture hair (un)dressing crème.  It’s a rock star crème that can be used on both short and long hair to create an undone, yet clean and well-kempt coif.  If you need body for longer hair, then use it at the roots when the hair is damp and proceed with a blowdry.  If you need to give your short hair just a bit of style without it looking greasy or waxy, then rub a tiny drop around in your hands and then rub your hands through your dry hair.

Note:  Titrate this one, as a little goes a very long way!

Are you a Paul Bunyan on the outside and a teddy bear on the inside? 

Your strong and sexy scruff will never admit to needing sensitive TLC.  So anticipate its needs without bruising its ego.  Dude No.1 All-natural Beard oil conditions scruff using wonderfully woodsy fragrances that are not too overpowering.  It comes in a roll on, which you can either roll over hair directly (if the hair is short) or roll into your hands and then place on your beard (if the hair is a bit longer).

And here is my last question for you to answer:

Do you now feel empowered to tame your mane??

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Whether painting faces backstage at Victoria’s Secret, traveling the globe for her international clients or writing for magazines and style guides, our FlyGirl lends her hands to enhance beauty both inside and out.  She thinks creatively and approaches practically to create unique yet easy styles.  Send your questions to FlyGirl@benchfly.com and learn how to become your own artist! 

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[Disclaimer: FlyGirl nor BenchFly makes any money off of the products recommended in this column.]

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Need some help from FlyGirl? Send questions to FlyGirl@benchfly.com and don’t miss her recent articles:

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Bringing Style to Science, Literally. Introducing: FlyGirl

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Light switches on the wall: Concepts we take for granted

For much of my life, dealing with electrical lighting has been relatively straight-forward. Upon walking into a dark room, I flip a wall-mounted switch into the up position to turn the lights on. When I’m done in that room, moving that same switch into the down position turns the lights off. For the first 26 years of my life, turning something on or off had essentially become a “dogma” for me: up for on, down for off.

When I began working as a postdoc at Penn State, I moved into an apartment that had a few unique quirks. One of those was that a lot of the light switches moved in a horizontal direction (left or right) as opposed to almost all vertical switches that I had encountered in my life until then (up or down). Suddenly, “up” no longer necessarily meant “on”, and “down” no longer necessarily meant “off.” The dogma that I had memorized for 26 years prior had been broken!

Phosphoproteins: the light switch is always up-and-down… right? Wrong!

One of the questions I’ve encountered many times in my scientific career- usually coming from students- is how protein phosphorylation affects enzyme activity. Is phosphorylation or dephosphorylation what activates an enzyme? Or, in other words, is the “on” form of an enzyme the phosphorylated or unphosphorylated form, and is the opposite the “off” form? When someone asks me this, student or otherwise, I smile, take a deep breath (mostly to prepare for the onslaught of follow-up questions), and say that it depends entirely on the protein being phosphorylated. Moreover, it can even depend on the phosphorylation site, too; a phosphorylation of a serine residue over here can turn an enzyme on, whereas phosphorylation of a threonine right over there will turn the very same enzyme off. Just like that light switch, which I once took as being “dogma,” sometimes there is no universal answer that is guaranteed to cover every situation.

Mixing and matching: Pathways where phosphorylation is both activating and inactivating

I recently worked on a study which was particularly interesting in terms of phosphorylation activating or inactivating enzymes. This particular signalling pathway contained several protein kinases, some of which were activated by phosphorylation, and others which were inactivated, leading down to the final metabolic target of glycogen synthase (GS). Oh, and, insert shameless plug for my recent publication here.

Most scientists who have taken a biochemistry or molecular/cellular physiology course at the 4^th year level have at least a passing familiarity with the insulin signalling pathway. Insulin causes the insulin receptor to phosphorylate and activate the insulin receptor substrate-1 (IRS1). IRS1 interacts with and activates phosphoinositide 3-kinases (PI3Ks), which phosphorylate phosphatidylinositol phosphates (PIPs; for example, converting PIP₂ to PIP₃). PIP₃ recruits both phosphoinositide-dependent kinase-1 (PDK1) and Akt to the plasma membrane, allowing PDK1 to phosphorylate and activate Akt. The take home message, for the scope of this article, is that all of the aforementioned systematic phosphorylations- insulin receptor through Akt, inclusive- are activating. I’d draw you a diagram but when it comes to something so widespread like insulin signalling, I can’t compete with the commercial websites, like this one.

What happens after Akt gets to be even more interesting.

Opposite side of the same coin

Akt is turned on when it is phosphorylated by PDK1. However, Akt is now going to use the same trick- phosphorylation- to turn something off…

Only one protein kinase remains in the signalling pathway originating at the insulin receptor and ending with GS: glycogen synthase kinase-3 (GSK3). However, unlike all the kinases described thus far, GSK3 is actually inactivated by Akt phosphorylation; phosphorylation turns GSK3 OFF. Once inactivated, GSK3 cannot, in turn, phosphorylate its own downstream targets. That means that GS remains unphosphorylated. Like GSK-3, an unphosphorylated GS is an active GS; a phosphorylated GS is an inactive GS.

With some phosphorylations being activating and others being inactivating, while writing the manuscript for that publication I shamelessly plugged, even I admittedly had to keep a few post-it notes glued to my wall so that I could remember which phosphorylation patterns led to an activation or inactivation of the final metabolic target. For your benefit, dear readers, in short, here’s what can happen:

 1. Akt active, GSK3 inactive, GS active

When Akt has been phosphorylated and activated by its upstream signalling pathway, it phosphorylates and inactivates GSK3. A phosphorylated GSK3 is inactivated. An inactivated GSK3 cannot phosphorylate GS, and therefore GS remains active. Take a look at Fig 1.

2. Akt inactive, GSK3 active, GS inactive

Now assume Akt has not been phosphorylated by its upstream signalling pathway. An unphosphorylated Akt is inactive. It cannot phosphorylate its downstream targets. Unphosphorylated GSK3 remains active. An active GSK3 phosphorylates GS, inactivating it. Check out Fig. 2.

So the next time a student asks me “Chris, does phosphorylation turn an enzyme on or off?” I’ll refer them to this article. And now, you can do the same if a student asks you!

… oh, and go read my paper… please. Dieni, C.A., Bouffard, M.C., and Storey, K.B. (2012) Glycogen synthase kinase-3: cryoprotection and glycogen metabolism in the freeze-tolerant wood frog. J. Exp. Biol. 215: 543-551.

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Chris is originally from Montreal, and is a Comparative Biochemist and Physiologist. His educational and postdoctoral experiences have taken him from Montreal to Ottawa ON, State College PA, and finally back to Montreal’s biotech industry. In his spare time- as you would expect from a Canadian- Chris enjoys watching hockey and is a stalwart fan of the Montreal Canadiens and Ottawa Senators. You can keep up to date with the latest from Chris on Twitter.

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Have any kinase-related questions for Chris?

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“What does this have to do with science?” you ask. Not much. It does however explain why I found the following headline interesting:

Scientist fiddles with spider silk: Filaments are bundled, processed, and played on a violin. (ScienceNews.org)

Spider silk violin strings! Cool!

So I dug out the paper that was published this month in Physics Review Letters and sure enough, a scientist from Japan, Shigeyoshi Osaki, used spider silk to make violin strings.

There has been a lot of interest in using spider silk for various applications, including rope manufacturing and developing Kevlar-like fabrics that are exceedingly strong. Unfortunately a single spider doesn’t make that much silk, and housing a whole herd (I don’t think that’s the correct collective noun, but it conjures up a great visual) of spiders is more troublesome than you’d think, as they tend to eat each other, but there is a lot of work being done on the preparation of spider silk using molecular genetic techniques.

A cross section of the violin cable

In this instance, Osaki took spider silk from 300 female spiders (Nephila maculte), and arranged the 9,000 (for an A string) 3 feet-long strands in a parallel array. He then twisted the strands together to form a cable. This initial cable had lots of space between the strands, which would make it easily breakable, so he kept twisting and coated the strings with glycerol. When he looked at a cross-section of the resulting cable by electron microscopy he saw something surprising; the originally cylindrical silk strands had formed polyhedral shapes that fit together like crazy paving.

This in itself was a completely novel discovery in the world of spider silk research, and has the potential to change the way the material is used for other applications, but in the violin-string world there was still a crucial experiment left to do. Osaki needed to know if the strings sounded good.

So he manufactured a D string (12,000 strands) and a G string (15,000 strands) and assembled some professional violinists. He had them play either the Dancing Master’s Violin 1720 ‘‘Gillott’’ by Stradiviari (recognized as one of the best violins on the planet) or a run-of-the-mill violin strung with spider strings or conventional strings. While the professionals could perceive only a small difference on the Stradivarius, the spider strings made a vast improvement to the regular violin.

As to why these spider strings sound so great, Osaki suggests that “[t]he properties of spider violin strings can be ascribed to their elasticity, high modulus, and mechanically high strength that are characteristic of spider silk.” The timbre of the strings is affected also by their different and numerous overtones.

For the moment, spider violin strings are a novelty, and it will probably be a very long time before the likes of me get to string their violins with them. But we can search YouTube and find examples of them being played by others. Enjoy!

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Katie Pratt is a graduate student in Molecular Biology at Brown University. She has a passion for science communication, and in an attempt to bring hardcore biology and medicine to everyone, she blogs jargon-free at www.katiephd.com. Follow her escapades in the lab and online on Twitter.

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Be the first one to mind the gap by filling in the species of the spider as a comment and get your name in the blog along with a sweet new BenchFly mug!

About the prize: In addition to fame and glory beyond their wildest dreams, winners receive our new hot-off-the-presses large (15 oz) BenchFly mug to help quench their unending thirst for scientific knowledge… or coffee. Check out where the mug has traveled – will you be the first in your state or country to win one?

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