The Toughest Year in Grad School

By Susan Sheng

Dear Third Year Self,

You did it! You finished all your coursework, successfully presented and defended your thesis proposal, and are now officially a PhD candidate! You’re probably tired but relieved to have finished your qualifying exam, and excited to get started on those experiments you proposed. Better get working so you can stick to that timeline, find some novel and interesting data to publish, and be able to graduate in 3.5 more years right? Let me offer a few words of advice as you get ready to start your third year.

 

First, add at least 6 months to those proposed dates on that timeline. Your PI is right, they are overly optimistic, and even the most straightforward-sounding experiments will take longer to troubleshoot and optimize than you think.

 

While you’re troubleshooting and optimizing, talk to people. Talk to labmates or colleagues in other labs who may have experience with your procedure. Reach out to the technical support staff at the companies producing your reagents. If for whatever reason you think your yield from commercial kits is not as high as expected, and even if you have scoured their websites without finding anything useful, call technical support and they might be able to give you some tweaks that will make all the difference.

 

I’m not going to lie, third year is going to be tough. You will go months without seeing any positive data. You will have some promising results, and then fail to be able to reproduce them. In the spring, when it’s time to submit poster abstracts to the department retreat and to the big annual conference, you will remember that time in second year when you remarked to your friends, “Next year I’ll have data to present!” and you will wonder where you went wrong.

 

This year, some of your classmates will leave with their Master’s degree and pursue other career paths, and you’ll wonder whether you should do the same. Take the time to look at job postings and attend career panels. Again, talk to people. Learn about what is out there, see what types of jobs interest you and find out what skills are needed for those positions. Maybe it will make more sense to leave with the Master’s degree, or maybe not. Maybe you will need to learn new skills; make a plan and figure out how to best acquire and demonstrate those skills (i.e. online or in-person classes, volunteering, etc.)

 

Cultivate your life outside the lab. Yes you will spend many hours working in the lab, but make sure you step away from the bench to get some fresh air. Connect with your classmates and commiserate over the struggles of grad school. Find some hobbies, maybe a local recreational sports league, or some fitness classes. Get out into nature (fun fact, a recent PNAS study has suggested that nature walks may help calm the brain. Take care of yourself so that you can go into lab rested and recharged.

 

Things will get better. You may need to switch gears and try different approaches and techniques to get at the same question. While you don’t want to juggle too many experiments and projects simultaneously, it might also not be ideal to focus solely on one single experiment, so try and find some balance. Having multiple experiments increases your chance of finding something that works, but you don’t want to split your time and attention too much.

 

Make sure you take time to read. You will be reading anyway as you troubleshoot, trying to see what conditions other people have published successfully, but take some time to read other papers relating to your project, your field, or just science in general. Step back and think about how your experiments fit into the bigger picture. Read about new discoveries and remind yourself why you were so excited about your project in the first place, and why you are in science to begin with. Remember, grad school is a marathon, not a sprint.

 

Signed,

Soon-to-be Fourth Year Self.

 


Winter’s Sleep: Insights Into Neurodegeneration

 

By Susan Sheng

Winter has come for most places in North America, and for many creatures that means settling in somewhere and hibernating until the weather warms up. During hibernation, a number of physiological changes occur, such as decreased metabolic rates and lowered core temperatures, in order to conserve energy. Interestingly, the brains of hibernators also undergo morphological changes; specifically, scientists have shown that there is a loss of synaptic protein clustering in hibernating animals, and that upon rewarming to normal body temperatures, these synapses can be rapidly reformed. This process of synapse dismantling and reformation has been proposed as a model of adult synaptic plasticity.

Synapse loss is a hallmark of neurodegenerative diseases, so a group of UK scientists decided to investigate the mechanisms underlying synapse dismantling and reassembly in hibernating animals could give insight into the maintenance and subsequent loss of synapses in models of neurodegenerative disease.

First, Peretti and colleagues showed that laboratory mice demonstrated synaptic dismantling in the hippocampus with artificial cooling to core temperatures of 16-18C and subsequent reassembly with rewarming, similar to that of other small hibernators. Mechanistically, Peretti and colleagues linked an RNA binding protein, RBM3 (RNA-binding motif protein 3) to synaptic reassembly. RBM3 has previously been shown to be upregulated in hypothermic conditions and have neuroprotective effects. It plays a role in promoting global protein synthesis, and is expressed in both neurons and glia (Chip et. al., 2011). Here, Peretti and colleagues showed that RBM3 is upregulated following artificial cooling, and this upregulation persisted for up to 6 weeks in wild-type mice.

What is interesting is that RBM3 seems to be dysregulated in two mouse models of neurodegenerative disease: the 5xFAD model of Alzheimer’s disease, and prion disease (tg37+/- mice infected with Rocky Mountain Laboratory prions). Both models have a delayed onset of synaptic loss and associated behavioral and learning deficits under normal conditions (around 4 months in the 5xFAD model, and 7 weeks post infection in the prion model). In both models, prior to the onset of the disease symptoms animals that were cooled and rewarmed showed synaptic structural plasticity and upregulated RBM3 levels similar to that of wild-type mice. However, animals that were in the disease-stage showed a failure to reassemble synapses upon rewarming, as well as a failure to upregulate RBM3 after cooling. However, efforts to boost RBM3 levels, either through early therapeutic cooling to boost endogenous protein levels or through viral overexpression, showed a rescue of these structural deficits, and consequent behavioral changes. Additionally, viral knockdown of RBM3 accelerated disease progression. In all, it appears that RBM3 is important in synapse structure, either in the formation of new synapses or perhaps in the maintenance of existing ones.

In humans, therapeutic cooling is already used in certain clinical settings, such as cardiac arrest, stroke, traumatic brain/spinal injury, and neonatal encephalopathy, with varying amounts of evidence as to its efficacy. A 2009 study in human Alzheimer’s disease patients has shown that RBM3 mRNA is significantly downregulated compared to age-matched controls. It could be interesting to see whether RBM3 is a viable drug target for human treatments, given the effects of RBM3 overexpression in the rodent models. Alternatively, depending on when the downregulation of RBM3 occurs relative to disease progression, it could be a predictor or a diagnostic marker for the onset of Alzheimer’s disease.


New year's resoultions from scientists

Resolutions from the Bench

 

and some science to help you make your own!

Compiled and written by Evelyn Litwinoff and Katherine Peng

Like many of us out there, you may deem a New Year’s resolution a successful one if it lasts through January. To help create your own, the Scizzle staff is offering some tips backed by neuroscience (plus some science-y examples) that may help you to finally follow through in 2015.

 

Tip #1: Give yourself a pep-talk

Positive self-reflection boosts serotonin levels which is essential for proper functioning of the prefrontal cortex. The prefrontal cortex is our impulse control and decision making center, and plays the additional role of giving flexibility to habits ingrained in the basal ganglia. For example, subjects lulled into a conversation about their positive qualities prior to reading an informational packet developed a greater intention to quit smoking or eat healthier.

 

For inspiration, see this positive worded resolution (“I am!” “I will!”):

[quote]I am going to work on becoming better at networking. I will go to more networking opportunities, and I will not spend all of my time talking only to people that I know.[/quote]

S.S., Industry Research Scientist

 

Tip #2: Focus on one or few goals

Baumeister et al. have shown over and again that willpower is a limited resource. The effort it takes to complete one goal may render us too exhausted for the next. In fact, willpower depends on glucose levels, and a good dose of glucose helps to counteract willpower depletion (though admittedly not so helpful if your resolution is a diet).

[quote]This year, I will focus on the "existing" rather than "imaginary" problems in science; and I will try to address those by my solutions. The focus of the year will change from "providing solutions" to "identifying the right problems.[/quote]

Padideh Kamali-Zare, a new science entrepreneur and a Scizzle blogger

 

Tip #3: Give yourself a distraction

In a well-known series of marshmallow experiments, children were promised more marshmallows if they could resist the one marshmallow they were left in a room with. The most successful kids distracted themselves with singing or playing, and as a bonus had better SAT scores later in life.

[quote]For 2015, I will dedicate time every day to step away from the bench/paper I’m reading/experiment I’m designing to take a mental break, even if it’s only 5 or 10 minutes long. And I promise not to go on Facebook during those breaks![/quote]

E.L., Immunologist

 

Tip #4: Remind yourself

That the feeling of being in control is inherently rewarding. Imaging has shown that subjects making choices in which they control the outcome have greater activation in structures of the brain involved in reward processing.

 

[quote]For New Year's, my resolutions would be to 1) Actually finish one of those online statistics classes so I understand the statistical tests I will eventually be using to analyze my data (I keep starting the courses and then getting distracted and stopping about halfway), and 2) Come up with a better system to consolidate, organize and keep track of my paper reading/notes; currently things are spread across notes in PDF files, hard-copy notes, and Google Documents.[/quote]

- Susan Sheng,  neuroscientist and a Scizzle blogger

 

[quote]Read a paper a day (or at least an abstract) and be more efficient.[/quote]

– K.Z., neuroscienctist

 

[quote]My science New Year's resolution is to learn tissue culture techniques. And also, to be more careful with the ethanol around an open flame so I light fewer things on fire.[/quote]

E.O., Postdoc

 

Have a wonderful happy new year!!!

 


Robots to Replace Scientists

 

By Susan Sheng

[quote style="boxed" ]Life science research today is incredibly slow, error-prone, monotonous, and expensive with researchers spending many hours a day every day just moving small volumes of liquids from one place to another.[/quote]

Transcriptic

 

If I had to make a wish-list of things that would be helpful in my daily life, a robot to help me with the more repetitive and mundane lab tasks would be at the top of that list. Whether it’s pipetting samples to run a Bradford assay or running a western blot to look at changes in protein expression, there are many tasks in a typical biological sciences laboratory that are tedious and time-consuming, but necessary for answering scientific questions. While certain techniques, such as DNA sequencing, have benefited from advances in technology and automation, for many other techniques, either an automated option does not exist, or the machines necessary to run the protocols are too expensive for most research labs to consider. Luckily, as highlighted in a recent Nature commentary, there is growing interest in automating research in the hopes of improving its efficiency and reproducibility.

 

Two California companies, Emerald Cloud Laboratories and Transcriptic, are trying to offer cost-effective access to wet-lab experiments. Both offer web interfaces which allow scientists to design wet-lab experiments which are then carried out at a remote facility. Emerald Cloud Laboratories, which started as an internal system to streamline research at the biotechnology company Emerald Therapeutics, offers 40 common lab protocols, including western blotting, light and epifluorescence microscopy, and DNA/RNA extraction and downstream procedures such as gel electrophoresis and PCR, with plans to add many more procedures to the list. Similarly, Transcriptic allows users to program experiments using their application programming interface which are then carried out in their facility. They aim to transform basic research and lower the entry costs such that anyone with an idea and web access can start a biotech company, much like how the computer science world currently operates.

 

If companies like Emerald Cloud Laboratories and Transcriptic succeed in offering reliable, low-cost research services, it could revolutionize the way research is done. By outsourcing basic, repetitive tasks, scientists can be freed up to plan and design the next experiment, or carry out more technically challenging experiments. Additionally the increase in automation could help address the issues of reproducibility in science, which have been discussed here at the Scizzle blog  among other places. Automation would bring another level of standardization and documentation to experiment design and methods, and remove problems of human variability and error. I’m sure we all have received protocols that have worked wonderfully for other people, only to struggle to successfully repeat the protocol in ourselves. Of course, automated experiments will still need to be optimized and troubleshot for each specific condition or context, but at least the factor of human error is reduced. Additionally, automation could improve the efficiency and speed in which research is done; for instance, the Allen Institute for Brain Science was able to complete in situ hybridizations in adult mouse brain tissue for over 20,000 genes in a matter of weeks due to the automation of several steps in the process.

 

It’s unlikely that robots could replace research scientists, at least for the foreseeable future. We need trained scientists to come up with the questions and the experiments that will advance our knowledge. Tasks requiring a high level of precision and dexterity will likely still require human hands, at least until that level of precision can be achieved robotically. However, robots working alongside researchers could speed up the scientific discovery process. Whether automated processes take hold in the life sciences will likely depend on cost, reliability, and the ease it which standard protocols can be customized for different experimental conditions. I for one am excited to see what the future of research has in store.


Ancient Flyers and Gargantuan Creatures

 

By Susan Sheng

If you like dinosaurs and ancient reptiles, then this past month has been a real treat with major discoveries from land, sky and sea. On August 13, 2014, the discovery of a rare pterosaur fossil bed in southern Brazil was reported in PLOS One. Two weeks later, Drexel scientists described a fossil of a gargantuan land animal, possibly the largest ever discovered. Even more recently, on September 12, another group reported that the largest carnivorous dinosaur ever, the Spinosaurus, had adaptations that allowed it to swim.

 

Sky - Pterosaurs

Pterosaurs are an extinct group of flying reptiles which evolved on a separate branch of the reptile family tree from dinosaurs. They evolved over a period of approximately 170 million years, and ultimately became extinct during the Cretaceous period 66 million years ago, around the same time that Tyrannosaurus rex and other large dinosaurs died out. Pterosaurs are thought to be the first, and largest, vertebrates to fly under their own power; they had a wide range in size, from the very small, such as the Nemicolopterus with a 25cm  (about 10 inches) wingspan, to the very large, such as the Hatzegopteryx with a 12m (about 39 feet) wingspan  (to put that into perspective, that’s a larger wingspan than an F-16 fighter jet, which is around 32 feet!). They flew with their forelimbs, with the wing membrane supported by one digit, which would be the equivalent of our fourth finger.

 

Pterosaur fossils have been found on nearly every continent, but the fossils are rare, as like bird bones, pterosaur bones were thin and fragile and prone to being scattered or damaged before they could be preserved. The fossil bed found in southern Brazil by Paulo Manzig and colleagues  were of a new species of pterosaurs, Caiuajara dobruskiis. These pterosaurs were mid-sized, with estimated wingspans ranging from 0.65-2.35m. This fossil bed is interesting for several reasons. While many pterosaur fossils have been found in northeastern Brazil, this particular fossil bed is the farthest south of any find in the country. Additionally, these fossils were found in a region believed to be around an inland lake in the desert, which is also unusual as pterosaur fossils tend to be found near ancient coastal regions or shallow marine deposits, and fossil records from areas deep inside continents is limited. Furthermore, several pterosaurs were found together, and while it is difficult to determine exactly how many unique individuals there are in this fossil bed, the researchers believe there were at least 47 individuals and possibly hundreds of individuals, ranging in age from juveniles to adults. The close proximity of the fossils suggest that these pterosaurs may have lived in social groups, rather than as solitary creatures.

 

As an aside, if any readers out there are in New York City before January 4, 2015, I highly recommend visiting the American Museum of Natural History and checking out their pterosaur special exhibit!

 

Land - Titanosaurs

A team of scientists from Drexel University have reported a new member of the titanosaur family of plant eaters. The Dreadnoughtus schrani, meaning “fears nothing”, was unearthed between 2005-2009 from Argentina, and is “exceptionally complete, with over 70% of the bones, excluding the head, represented.”  It is estimated that this particular individual was 26m (85 feet) long, and weighed about 59,300 kg (65 tons); amazingly, based on the bone structure, scientists believe that this individual was still growing, meaning that in its fully matured adult form it would have been even larger!  Currently Dreadnoughtus holds ths record for largest land animal, breaking the previous record set by Elaltitan, another large titanosaur found in Argentina weighing in at 47 tons (approximately 42,600kg). Today, the largest land animal is the African bush elephant, weighing in at an average of 8,500kg.

 

Sea - Spinosaurus

Fans of Jurassic Park III might remember the fight scene between Tyrannosaurus rex and Spinosaurus; the two massive carnivores circle and charge at each other, until finally the Spinosaurus gained the upper hand and snapped Tyrannosaurus’s neck, killing it instantly.  Indeed, Spinosaurus was an enormous dinosaur, likely measuring in at over 15m (49 feet) long and weighing up to 20,000kg, making it possibly the largest carnivore ever; in comparison, Tyrannosaurus measured around 13m (43 feet) and weighed in around 7,000kg (http://www.walkingwithdinosaurs.com/dinosaurs/detail/tyrannosaurus/). Fossils of Spinosaurus aegytiacus were first found in Egypt in 1912, but were destroyed during the bombings of World War II. This most recent find is the most complete skeleton of Spinosaurus aegytiacus. Analysis of the size and bone density of the limbs suggested that Spinosaurus was better suited paddling and submersion in water, rather than running on land. Additionally the structure of the snout shows similarities to the pressure sensors in the snouts of modern-day crocodiles, with the teeth being suited for snagging fish. This makes Spinosaurus the first dinosaur known to swim. While a battle between Spinosaurus and Tyrannosaurus makes for good movie scenes, the reality is that Spinosaurus likely hunted for aquatic prey (additionally evidence suggests that Spinosaurus and Tyrannosaurus lived in different time periods and on different continents!)
I find it both amazing and somewhat terrifying that these giants once roamed the earth. Also, it is fascinating how much palaeontologists can deduce by studying rocks and fossils. While a part of me thinks it would be really cool to travel back in time and observe these creatures, another part of me worries about being crushed or eaten, given how miniscule we are in comparison. For now I’ll stick with documentaries and natural history museums.


choosing the right lab for you part 2

6 Top Tips For Choosing the Right Lab for You - Part 2

 

By Susan Sheng

Couple of days ago we shared with you the first top 3 tips for choosing the right lab for you, here are the other 3 tips.

 

4. Lab culture

The composition of a lab is always in flux, so it’s hard to say that your relationship with specific people in the lab should influence your decision whether to join or not. For instance, in the year since I officially joined my lab, about half of the members have left and moved on to other positions, and a new group of post-docs are scheduled to join by the end of the year.

 

One thing I did find very important, however, is the culture of the lab and the dynamics between members. I think this is something that stays relatively constant within a lab even as people cycle in and out, since prospective members would evaluate and be evaluated on their fit in the existing culture. By “lab culture” I’m referring to how people interact with each other in the lab. Do people discuss the latest papers (either related to the lab’s research, or just cool science in general) and work together to troubleshoot experiments, or do people tend to work on their projects in isolation? Is the lab generally collaborative or are multiple people working on closely related projects and competing to get data? This can be, although is not necessarily, related to the size of the lab.

 

In all three labs I rotated in, I knew I would have to learn new techniques (i.e. animal behavioral work, primary cell isolation, etc.) for my potential thesis project, so I wanted to be sure that I would be in an environment where I would feel comfortable asking my labmates for help and advice. I also wanted to be somewhere where I would have my own distinct project, but where there would be enough commonalities (either in topic or in approach/technique) where I could get ideas and suggestions from my colleagues.

 

5. Life after graduation…

Although it seems too early to be thinking about post-graduate school life right at the beginning, another thing I considered was the types of positions the lab alumni went to after their tenure in the lab, and the publications they had upon leaving. What I was looking for was whether the lab alumni were going into positions that I may want to follow and how, if at all, the PI helped the students and post-docs prepare for those positions. Initially I wanted to follow the academic track and try to become a professor with my own research lab, so I was mainly looking for PIs who were well-established and well-respected in their fields, in the hopes that their network would help me when I go out on the job market. Additionally I wanted to join a lab where the students graduated with first-author papers in bigger name journals. For those thinking about going into pharmaceuticals or biotech, or into non-traditional PhD paths, it can be helpful if other people in the lab have gone down that route, as they can provide helpful contacts in networking and learning more about those career options.

 

6. The project

Before I started my PhD, I thought the thesis project was going to be the most important factor in choosing a lab. It certainly is important, as graduate school often involves a lot of repetitive and tedious work so you need to find a question or topic that excites you and motivates you to get through those annoying pipetting/wash steps, and through all that troubleshooting you will inevitably have to do. However, I would argue it is less important than the above-mentioned “fit” criteria. Projects are malleable, and often there is a lot that can be explored within a given question, so you’re bound to find something that interests you. If you don’t get along with your mentor though, or are unhappy with the lab environment, even the most interesting topic may become impossible to tackle.

 

Lastly, try new things. Rotations are the best time to explore a new field of study, work on a new model organisms, or learn new techniques and approaches. It’s about the only time in your scientific career you can try something totally new with relatively little risk. My previous lab experience was primarily in the field of learning and memory, but I rotated in a developmental neurobiology lab as well as molecular signaling/transcriptional regulation lab and learned a lot of new techniques and approaches that I am now applying to my thesis work.


choosing the right thesis lab for your

6 Top Tips For Choosing the Right Lab for You - Part 1

 

By Susan Sheng

I’m still somewhat in disbelief that I’ve been in my thesis lab for nearly a year now, we’re halfway through summer, and my qualifying exam is fast approaching (eek!). A good friend of mine is getting ready to move across the country to start a PhD program of her own, and recently she has been asking me lots of questions about how to choose a rotation (and eventually, a thesis) lab. Looking back to my first year, I remember being overwhelmed with the number of rotation options, and worrying about “choosing the right one.” (one may recall the PhD Comic comparing PhD programs to marriage). After much discussion with more senior students and a few post docs, and meeting with potential PI mentors, I finally settled on three labs to rotate through. I was fortunate to have generally good experiences with all three labs, and it came down to weighing the pros and cons of each lab to decide which one I would ultimately be happiest in and do my best work. Below are some of the major factors that swayed my decision, and hopefully this will help incoming students narrow down their rotation/thesis lab options.

 

1. Don’t commit too early

First thing’s first though, don’t feel pressured into committing to three rotation labs right as soon as you arrive in the program. I remember talking to a few classmates on the first day of orientation, and they already had all three rotations lined up! When I started at NYU, I had a list of maybe 10 labs that sounded interesting. During the first month of grad school, I made appointments to meet with the PIs and discuss the possibility of rotating in their labs. From there, I narrowed down that list to about 4-5 labs. I decided my first rotation would be in a learning and memory lab, since it was an area I had worked in previously and thus it would be easier for me to hit the ground running while I adjusted to graduate school life. I told the other PIs that I was interested in possibly doing a second or third rotation with them, but that I would get back in touch with them at a later date to confirm. Luckily those PIs were amenable to this arrangement, and I realize this may not work in labs where there are a lot of other students interested in rotating/joining. However the advantage of not committing early meant that I had the flexibility to see how my interests developed through my work in the first rotation and through classes and seminars I attended in the first semester. I actually ended up doing my third rotation in a lab I had not even heard of prior to arriving at NYU, and in a totally different department (microbiology, instead of neuroscience), and that was based on chatting with a graduate student at a poster session I attended. Keep your options open!

 

2. Funding

As an international student, one major concern I had was funding. Because I’m not a US citizen or permanent resident, I don’t qualify for the vast majority of grants/fellowships in the US (i.e. institutional training grants, NRSA/F31, NSF, etc.). Additionally, I also found myself ineligible for funding from my home country (Canada), so I needed to find a lab that was well-established and well-funded enough that I wouldn’t be expected to bring in my own funding sources. Troubleshooting experiments and collecting good data is hard enough as it is without wondering whether you will have the funding to buy reagents or supplies!

 

When meeting with potential PIs, it’s good to be upfront and ask whether the lab can support a student, and be clear about what grants you are (and are not) eligible for. It seems a bit awkward at first but is a common question that comes up so don’t be afraid to ask! Another resource is NIH RePORTER  which lists active NIH grants held by a PI. Depending on the field, this database will be more or less useful, as it does not give any indication of other funding sources, such as NSF or private foundations, but it can be a good starting point to get a sense of a lab’s financial situation.

 

3. Mentoring style

In terms of mentoring style, PIs can range from micro-managers who want constant updates to very laissez-faire with only occasional check-ins, to everything in between. It’s important to consider your own working style and be honest about what kind of mentor would help you achieve your greatest potential and succeed in your program. For myself, I wanted a mentor who would check-in with me regularly to make sure I was making good progress (and give suggestions if I get really stuck), but would also allow me the freedom to explore my ideas. Too much leeway and I was worried I would either procrastinate horribly, or waste time wandering down paths that are less important or novel. On the other hand, one of my classmates remarked that if she was in my lab she would be too stressed and frustrated with weekly meetings, and instead prefers the greater freedom her PI allows her with monthly check-ins.

 

There is no right answer of course, but it’s important to be honest with yourself, and find the best fit. This is something you should be able to gauge from a lab rotation and from talking to current students in the lab. Generally I found that newer PIs tend to be much more involved with their students’ work (I have friends who are regularly in the lab until the wee hours of the morning, working alongside their PI!) and older PIs tend to be less involved and give more mentoring responsibility to the post-docs in the lab, but this is not always the case.

 

Want to know more? You can find the  other 3 top tips for choosing the right lab for you here!

 


Can I Have Some Beer with that BBQ?

 

By Susan Sheng

If you getting ready to fire up the grill this summer, be sure to grab some beer! Beer and barbecue often go hand in hand, and a Portuguese group recently showed that marinating pork in beer prior to grilling could potentially have some health benefits (in addition to being really tasty!).

Polycyclic aromatic hydrocarbons (PAHs) are hydrocarbons with multiple aromatic rings, and are found on many cooked foods, particularly smoked and charcoal-grilled food items. PAHs are ubiquitous in our environment, and some have been found to be carcinogenic. While one could give up barbecue meats entirely, a more ideal solution for some people would be to find a way to minimize exposure to and consumption of PAHs.

Isabel Ferreira and her colleagues at the Universidade do Porto in Portugal had previously shown that beer, wine (red or white), and tea marinades for meat could reduce levels of heterocyclic aromatic amines, another class of molecules which can have carcinogenic properties. In a recent paper published in the Journal of Agricultural and Food Chemistry  her group decided to look at whether beer marinades could also effectively inhibit PAH formation. In particular, they focused on Pilsner beer, nonalcoholic Pilsner beer and Black beer, and marinated loin pork steaks in each of the beers for 4 hours prior to charcoal grilling. First they tested the antioxidant activity of the three beers using the DPPH assay (DPPH is made of stable free radicals, and changes color from deep violet to colorless when it is neutralized). They found that the Black Beer had the highest DPPH-scavenging ability, followed by the nonalcoholic Pilsner. After the 4 hour marinade however, the black beer’s scavenging ability was significantly reduced, suggesting that the antioxidant compounds may have interacted with oxidative species on the meat.

After grilling the pork for 15 minutes, they took samples of the meat and ran it through an HPLC to analyze the PAH content (I hope they saved some of the meat for taste testing!) They focused on 8 PAHs (PAH8) which have been found by the EU Scientific Committee on Food to be “possible indicators of the carcinogenic potency of PAHs in food.” While all three beer marinades decreased PAH8 levels relative to control, the black beer marinade reduced PAH8 by more than 50% (Pilsner beer reduced PAH8 levels by 13%, and non-alcoholic Pilsner beer by 25%)

What does this all mean? Well, it’s unclear how exactly PAH exposure, especially in food, is related to cancer risk. Based on a 2008 report from the European Food Safety Authority, the average European consumes about 1700-3000ng of PAH8 per day. A single piece of grilled, unmarinated pork loin contains approximately 2000ng of PAH8, while a pork loin marinated in black beer contains approximately 1300ng, so the marinade certainly puts PAH8 levels below the average dietary intake and is something to consider when barbecuing this summer.

Now, if you'll excuse me, I’m going to the store to buy some Schwarzbier and steaks - all in the name of health and science of course!


Nine Star Wars-Inspired Creatures Found on Planet Earth

 

By Susan Sheng

If you think back to biology class when you had to learn about the official genus and species nomenclature to describe all living organisms, a lot of the names were Latin words usually describing where the organisms was originally found, or some physical characteristic of it. In fact, there is a (very long) set of rules laid out in the International Code of Zoological Nomenclature  governing how newly discovered species are named. Some mischievous scientists however have snuck in pop culture references when naming their discoveries, with Star Wars characters being one major influence.

Credit:  Jason Bond.
Credit: Jason Bond.

Aptostichus sarlacc (Bond, 2012)

n 2012, Jason Bond, a professor at Auburn University, discovered 33 new species of trapdoor spiders, all of which belonged to the Aptostichus genus. Aptostichus sarlacc was named for the Sarlacc creature in Star Wars: Return of the Jedi  and was found in the Mojave Desert in California. Much like the Sarlacc which lived in the desert planet Tatooine, trapdoor spiders live in underground burrows which are often covered by “trapdoors” made of soil, sand and plant material.

This genus also has many other “famous” members in its species, including Aptostichus angelinajolieae and Aptostichus barackobamai.

[hr]

Darthvaderum (Hunt, 1996)

While studying mites from eastern Australia, Glenn Hunt reported, “When I saw the SEM of the gnathosoma I immediately thought of Darth Vader, evil antihero of Star Wars.” Take a look if you can at Figures 12-14 in his report in the Records of the Australian Museum; the resemblance is certainly there! (Warning, it’s a big document!)

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Han Solo (Turvey, 2005)

Who says scientists don’t have a sense of humor? Trilobites are hard-shelled creatures which lived in the deep sea during the Paleozoic Era over 520 million years ago, and their fossils today can be found all over the world. In 2005, Samuel Turvey described the discovery and classification of three new species of agnostid trilobites found in southern China, one of which was named Han solo. In his paper in the Transactions of the Royal Society of Edinburgh, Turvey states that the name pays tribute to the place where the fossils were found (“Han,” after the Han Chinese) and the fact that this particular species “appears to represent the last surviving member of the Diplagnostidae” (hence, “solo”). Unofficially however, Turvey was reportedly dared by his friends to name the creature after a Star Wars character  (As an aside, in the same report Turvey named another trilobite, Geragnostus waldorfstatleri, after two characters from “The Muppet Show.”)

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Tetramorium jedi. Credit: antweb.org.
Tetramorium jedi. Credit: antweb.org.

Tetramorium jedi (Garcia and Fisher, 2012)

The Tetramorium jedi is an ant found on the island of Madagascar and was first described by Garcia and Fisher in 2012 Although Garcia and Fisher don’t describe why they were inspired to name this ant after the Jedis from Star Wars, I think it could have something to do with the spike on its back that could resemble a light saber…

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Yoda purpurata (Priede et al., 2012)

Credit: Carl Malamud (Flickr).
Credit: Carl Malamud (Flickr).

Named for the resemblance between its large lateral lips and Yoda’s ears, the Yoda purpurata was one of three new species of acorn worms reported by a team of researchers from the University of Aberdeen in 2012. The worm was found along the Mid-Atlantic Ridge between Iceland and the Azores. Acorn worms are particularly interesting to evolutionary biologists as some of its anatomical features are similar to those found in vertebrates, leading to debate over whether these worms are an evolutionary link between invertebrates and vertebrates.

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Albunione yoda (Markham and Boyko, 2003)

Yoda’s ears were the inspiration for the naming of this isopod parasite, found on sand crabs on the western coast of Taiwan. The female members of this species have long lateral extensions on their heads, which resemble Yoda’s long droopy ears.

 

Polemistus chewbacca, P. vaderi, P. yoda (Menke and Vincent, 1983)

Arnold Menke and David Vincent paid tribute to their favorite Star Wars characters when naming three new wasp species discovered in 1983.  These wasps are found in the southwestern United States and Central America.


Handheld Holographic Devices a la Star Wars?

 

By Susan Sheng

When I was very young, I remember being mesmerized by the holographic bird on my parents’ credit cards, how the bird seemed to flap its wings as you tilted the card at different angles. More recently, I was awed by the use of holograms in art in the “The Jeweled Net: Views of Contemporary Holography” exhibit at the MIT Museum. I thought it was really cool how three-dimensional objects rendered on a flat surface could be viewed from different perspectives and angles, as if the object was really sitting there.

 

Holograms are featured numerous times in the Star Wars movies, primarily as a form of telecommunication  (perhaps the early inspiration for telepresence robots  given that members of the Jedi Council could attend via holograms?). While traditional, real-life holograms rely on lasers and special photosensitive materials to capture physical objects, a 2013 letter in Nature  discusses current research to create 3D displays which could one day fit in devices as small as a mobile phone.

 

The 1971 Nobel Prize in Physics was awarded to Dennis Gabor for “his invention and development of the holographic method,” in 1947 while attempting to improve electron microscopes. With the invention of lasers, the first optical holograms are attributed to Yuri Denisyuk (Soviet Union), and Emmett Leith and Juris Upatnieks (both at University of Michigan, USA) in 1962. Holograms are created by splitting a laser beam in two and using mirrors and lenses, shining the beams onto an object. These reflected beams are then recorded on some recording medium, such as silver halide photographic emulsion. The light wave patterns generated by the two beams interfere with each other, and this interference pattern is what is ultimately recorded on the medium. Then to view the recorded hologram, a laser of the same frequency as one used to create the hologram is shone onto the developed film, and the resulting light pattern is projected onto our retinas as a virtual image.

 

Because we as humans have two forward-facing eyes, each eye receives a slightly different image of the world and our brains convert that into a 3 dimensional representation; this is known as stereoscopic vision. Currently 3D displays involve using some form of glasses to display slightly different images to each eye. This can be down by actively shuttering images between the left and right eye, or with different polarizing lenses.

 

A group at Hewlett-Packard Laboratories in Palo Alto, CA built on the idea of autostereoscopic displays to create a diffractive backlight system that could generate 3D images. Autostereoscopic displays are give the perception of 3D images without needing the viewer to wear any special headgear or glasses; an example of this type of display can be found in the Nintendo 3DS gaming system. Existing displays are limited in the viewing angles, and thus Fattal and colleagues sought to overcome this limitation with their new backlight display. They used standard LED lights for edge lighting, and this light is guided to a series of etched directional gratings which then scatter light across the viewing area. Due to physical hardware limitations, Fattal and colleagues were only able to build a prototype that allows 14 viewing directions, although in theory they could eventually build a device that has 64 viewing directions, allowing for smooth 3D renditions of objects (the number of viewing zones reflects the number of positions around the screen that would allow for the correct differential display of images on each eye resulting in the perception of three dimensional objects; outside of the viewing zone, the objects would appear two dimensional). Additionally what is promising about this new back light display is that it is small and compact.

 

Although there are many hardware and computational challenges that must be overcome before a device like this could hit the markets, perhaps one day instead of video conferencing, we could be virtually transported to our meeting site for an “in-person” conversation.


Real-life robocop?

Real-life Robocop?

 

By Susan Sheng

If you saw last summer’s science fiction/action movie Pacific Rim, then you will remember the  gigantic humanoid robots called Jaegers, which were created to fit the monsters which had emerged from the depths of the Pacific Ocean. The Jaegers are controlled by two human pilots through a “neural bridge.” While Pacific Rim is a science fiction movie, the technology to allow humans to control robots remotely is very much grounded in reality and is an active area of research. Recently, a group at Florida International University (FIU) teamed up with the U.S. Navy lieutenant commander to build a telerobotics system that could be used in law enforcement.
Telerobotics refers to the control of robots from a remote location, and is not a completely new idea in the field of robotics. In its more basic form, telepresence robots have been used in office settings to promote communication and collaboration when a person cannot physically travel to a location. Several companies have developed various forms of these robots, from robots that perch on a motorized stand on a table top and allow the user to “look” around the room, to movable displays that can actually drive and move around an office. More advanced forms of telerobots include remotely operated underwater vehicles which are used to explore the deep ocean. NASA is actively researching ways that telerobotics could be used for space and planetary exploration.
The TeleBot project at FIU began in 2012 when Lieutenant Commander Jeremy Robins of the US Navy Reserves donated $20,000 to the Discovery Lab, as well as secured the loan of two robots from the Institute for Human Machine and Cognition. Robins’ vision was to create a robot that would allow disabled law enforcement personnel and combat veterans to return to their former duties. A team made up mostly of undergraduate students worked for over 18 months to create a robot that could be controlled remotely and interact with other people. The students built a prototype that stands at 6 feet tall and weighs approximately 75 pounds. Cameras on the robot allow the user to see what the robot sees using an Occulus Rift headset, and specialized sensors allow the user move and control the robot.. While the Discovery Lab team has successfully created a working prototype, more work needs to be done before such a robot could actually be sent out into the streets. Given the number of disabled military veterans and police officers however (according to the Department of Veterans Affairs, in 2012 over 3.5 million veterans received disability compensation);  the TeleBot is a promising development towards helping injured personnel return to the workforce.


DIY Organs: Healing and Regeneration Through Printing

By Susan Sheng

3D printers are the latest trend in the recent “Do it yourself” movement that has seen the increase in popularity of spaces such as TechShop, FabLab, and MakerSpace. 3D printing is an additive process, where materials such as plastics are progressively layered to create different shapes, based on a digital model. Printers can be small enough to sit on a desk, or large enough to be able to build parts for turbines.

 

In science and medicine, 3D printing has had many applications. Recently at the University of Louisville, cardiothoracic surgeons used CT images to print a model of patient’s heart. The patient was born with 4 congenital heart defects and required a complex operation to repair the defects. The 3D printed model allowed the surgeons to study the heart defects that needed to be repaired and come up with a complete surgical plan before even picking up a scalpel.

 

Another recent application of 3D printing in medicine was the announcement of a collaboration between Ekso Bionics and 3D Systems. Ekso Bionics is a California-based company which builds exoskeletons both for military use and for medical purposes in the rehabilitation of patients who have lost the ability to walk. Up until now, their exoskeletons have essentially been a “one-size-fits all,” but on Feb 19, 2014, at a Singularity University conference in Budapest, Ekso Bionics unveiled their first customized exoskeleton suit. The advantage of such a suit is that it can be shaped to the contours of the user’s body, reducing the likelihood of bruising or abrasions from an ill-fitting suit. Given that the patient population using these suits includes paraplegics or stroke patients who may have lost sensation in their lower limbs, such bruising or abrasions may go unnoticed and result in infections.

 

In the spirit of the DIY movement, a recent story in CNET discussed one man’s year-long work in creating a prosthetic fingertip. The man, Christian Call, lost his right index finger tip through a work-related accident and was unable to afford a professional prosthetic. Given his background and interests in machining and mechanics, he decided to try making his own prosthetic. One and half years and several prototypes later, Call has created a prosthetic that behaves much like a real fingertip, complete with a magnetic tip to assist with picking up metal objects. He has been contacted by other people searching for fingertip prosthetics and has even started his own 3D-printing/design business.

 

As 3D printing technology becomes more advanced, the potential applications for 3D printing in science and in daily life are limited only by our imagination. 3D printing could be used to create customized lab equipment for specialized experiments, potentially at a fraction of the cost of purchasing from a commercial company. If bioprinting (printing with living cells) becomes more viable, miniature organs could be created for research and drug development purposes, or possibly combined with stem cell technology to grow whole organs in the lab for transplant purposes.


Why Re-invent the Wheel? Bio-inspired Robots

 

By Susan Sheng

Mother Nature has created some pretty incredible systems, and scientists and inventors have long looked to nature for inspiration. Robots are increasingly being utilized for tasks that are repetitive or dangerous for humans to do themselves, and naturally roboticists are looking to nature to overcome some of the problems in building these devices.

A recent paper in Science turned to termites, which are able to build large mounds with complex networks of tunnels. Each individual termite works autonomously and seemingly without guidance from a “master termite” or blueprints. As early as 1995, researchers have wondered whether such autonomous behavior could be replicated by computers or robots (Theraulaz and Bonabeau, 1995). Recently, researchers at the Harvard School of Engineering and Applied Sciences and the Wyss Institute for Biologically Inspired Engineering have finally successfully implemented this idea. Using liter-carton sized robots, Justin Werfel and his group programmed in the final desired structure and a series of rules. The rules did not give specific tasks to each robot, but instructed the robots how to react if the robot senses a block or another robot. As a proof-of-concept, Werfel and his team instructed three robots to build a three-pronged trident shape, which the robots were able to successfully completed in about 30 minutes. In theory, this type of collaborative work could be extended to more complex and larger structures, and with more robots, such structures could be completed even faster.

 

The major advantage of this type of algorithm, where no one robot is “in charge” and each robot is equally capable of completing the desired structure, is that the loss of any one robot would not halt the construction progress. If these robots were implemented for instance in disaster situations to build barriers or bridges, one would not want the success of the project to hinge on particular robots.

 

Another recent bio-inspired robot looked to the sea for inspiration on how to fly. Perhaps not surprisingly, it can be more difficult to design a small flying robot than a larger robot, as smaller robots can be tipped over or blown off course much more easily with changes in air flow. Dragonflies, bees and other insects have been the inspiration for many small flying robots, but Leif Ristroph and Stephen Childress of New York University decided to look to the jellyfish for inspiration. In an attempt to mimic the undulating motion of the jellyfish as it swims through the ocean, Ristroph and Childress designed small droplet shaped wings, about 5 cm wide, attached to a carbon-fibre frame. The entire device weighs about 2.1 grams, or about two paperclips, and is able to hover and fly horizontally, all the while maintaining its upright position. At this point, like the termite-inspired robots, this jellyfish robot is more a proof-of-concept device rather than something that can be used in real-world situations as is, however such a small robot could conceivably be used in the future for weather monitoring, surveillance, or even crop pollination.

Biomimetic robots are certainly not a new phenomenon, and as researchers develop more sophisticated robots to do more complex tasks, its likely they will continue to turn to creatures found in the natural world. After all, these organisms have already found a way to survive in the world, so why reinvent the wheel?