Let Us Eat Real Food

 

By Kelly Jamieson Thomas, PhD

Sugar, which is undeniably highly addictive, is the number one additive in our food. Food manufacturers are hiding added sugar in almost every food including pizza, juice, bread, ketchup, and even baby formula. Added sugar consumption causes several diseases, including obesity, cardiovascular disease, diabetes, gout, fatty liver disease, some cancers, and tooth decay. What are added sugars? Those not found naturally in foods. When you eat an apple, it’s sweet, but the sugar in an apple isn’t added. But, when you drink a soda or eat an energy bar, the sugar in both of those is added. Prior to 1950, there were no added sugars in food. Since then, with the onset of added sugar in our food, Americans consume 39% more sugar. On average, we are eating 152 pounds of sugar per year, which is 2/3 of a cup per day! With such an astounding increase in our sugar intake, it’s certainly not surprising we are seeing a hefty increase in diseases related to sugar consumption, specifically obesity.

 

Is there a true link between increased sugar intake and increased body weight, specifically, body fat content? In an attempt to answer this highly debated question, the World Health Organization (WHO) analyzed thousands of studies and selected the most reliable. They focused on identifying an overall indication of how population changes in added sugar consumption affects our health. The resounding results—yes, increased sugar intake leads to increased body fat (adiposity). In children, this was especially relevant to consumption of sugary beverages, such as soda. Just as Bloomberg faced backlash for attempting to rid New York of large soda bottles, WHO has also received similar resistance for encouraging us to consume 5% of our calories from added sugar. The guideline has been officially set at 10%, which is equivalent to approximately one 12-ounce soda per day.

 

With clear evidence linking excess added sugar intake to the rapidly growing obesity epidemic, it’s in our best interest to seriously consider how sugar may ruin our long-term health. If we don’t change our habit and instead continue to gorge on added sugar, we will continue to see a rise in obesity. Currently, in the US, about 78 million adults (more than 37%) and 12.5 million (17%) youths are obese. Obesity incidence has risen from 14.5% to 30.9%, more than doubling, between 1971 and 2000. Obesity, the leading cause of preventable death, poses a significant risk for decreased life expectancy, type 2-diabetes, heart disease, osteoarthritis and some cancers. Not only are we making ourselves fat, but we are also creating an enormous burden in healthcare costs. If the obesity rate continues to grow at current rates, healthcare costs attributable to obesity, which were $147 billion in 2008, are predicted to increase to $957 billion dollars by 2030, a startling 18% of total US health expenses.

 

What are we doing to make a change? Recently, the FDA has set new standards for food labeling. Information about added sugars will be required and serving size portions will be adjusted to reflect our larger portion size. Unfortunately, to our dismay, food manufacturers will not be forced to limit added sugars, nor will 20-ounce sodas and other sugary drinks be banned from the markets. With such strong evidence supporting the link between our increased consumption of added sugars and obesity, it’s time we wean off added sugars. Clearly, we can’t rely on processed foods to help us do this. The bottom line: let’s eat real food! Have some strawberries instead of strawberry ice cream. Ditch that soda for sparkling water with fresh lemon in it. If we consider that our food is our fuel, would you want to run on processed junk or naturally nourishing fuel?

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!

Is an Industrial Postdoc Right For You?

 

By Elaine To

In recent years, postdoctoral opportunities in industry have been on the rise. Notorious for higher pay, access to greater resources, and providing a leg up for future industry positions, these positions offer many advantages over traditional academic postdocs. However, they are not for everyone; certain aspects are cause for caution. Here’s a list of questions you need to answer when considering such a position and some tips for searching out opportunities.

Questions you need to answer:

1. Are you comfortable with closing the door to an academic career? Or do you want to leave it open?

Industrial postdocs are excellent opportunities if your goal is to stay in industry, but depending on the postdoctoral program and company, returning to academia may be difficult. Academic scientists need quality publications during their postdoctoral training, and not every project in an industrial setting may be designed to do that. Additionally, it is sometimes in the best interest of the company to dissuade publications, keeping discoveries and technologies confidential for profitable development. Thus many industrial postdocs get patents, which are a mark of success for the postdoc while also protecting the company’s business aspirations. However, publications tend to be more valuable to an academic hiring committee than patents. Patents often have a large number of authors and it can be difficult to discern each individual author’s contribution. Lastly, it is unlikely that you will be able to turn your postdoctoral research project into your lab’s research focus as a PI. This is not to say all industrial postdocs close the door to academia, but a warning to choose wisely with these caveats in mind.

2. What is the company’s goal in taking you on as a postdoc?

Be wary of companies that may just be trying to take advantage of you and pay less for what should be a full time employee position. Postdoctoral positions, whether in academia or industry, are meant to be training periods. Ensure that you are not being hired to perform a single specialized assay for the entire period of time. You should still be exposed to new techniques and concepts, even if you start out doing what you’re familiar with. Try to determine who you will be reporting to and gauge whether they have the time and scientific knowledge to mentor you in your chosen project(s).

An additional question that will help you understand the company’s goal is what are the differences between a postdoc and a full employee at this company? Will you be able to work on what interests you, or only what’s assigned to you? Are all the benefits the same?

 

3. After the postdoctoral position ends, is there the possibility to join the company afterwards?

Some companies actively refuse to hire their postdocs. In a roundabout way, this is actually beneficial for the postdoc. If a well-known company gains a reputation for hiring their postdocs, the postdocs they don’t hire may have the following stigma attached to their subsequent job search: “Well if XXX company didn’t hire you after your postdoc with them, you must not be very good.” Other companies will not guarantee a job after the postdoc, though it is likely if you perform well. These companies are viewing the postdoc period as a time to both train you and test you. While this state of affairs offers greater security, be wary and have a solid plan in case they do not hire you. If the company is small, it is entirely possible that they do not have a position open at the end of your postdoctoral training.

How to search out industrial postdoc opportunities:

If you read my previous post on how to jumpstart your non-academic job search, the major point I emphasized was the value of networking. That is just as applicable here, whether the company you’re targeting has a formal postdoctoral program or not.

Large companies including Genentech and Novartis have formal postdoctoral programs. The positions are often advertised online and easy to find. Compared to these announcements soliciting applications, the idea of networking into a position is scary, especially when we’ve spent our lives filling out such applications to advance our career (undergraduate, graduate, fellowships, etc). However, postdoctoral positions in industry, particularly at large reputable companies, are highly desired. Just like every other job announcement, the human resources department will be bombarded with hundreds of qualified applicants for that single position. Unlike the previous graduate or fellowship applications we’ve filled out, the human resources department may not have the scientific expertise required to adequately judge your fit for the position. If somebody in your network already works with the company, you can ask that individual to contact the scientist behind that advertised position and see if s/he is willing to do an informational interview with you. At the end of that interview, if you decide you still want to apply for that position, let the professor know to keep an eye out for your resume.

Smaller companies may not have formal programs and may have never even thought of taking on postdocs. Networking is also your way in here, though you could use it to ask for either a full time position or a postdoctoral position, depending on your career goals. Companies are sometimes more willing to take on a postdoc because it is a smaller investment with the same potential for gain. Even if they have no advertised positions online, ask if they are interested in discussing the possibility of a postdoctoral position. You may be able to inquire directly without a networking connection, though networking always helps. This cold calling method may also work with scientists in larger companies, if you’re able to identify who you’d like to work with.

My experience is an example of networking success and how much the job search relies on serendipity. Early on in my search, a chance met friend from an online dating site connected me to a biotech recruiter who worked closely with several companies in my targeted geographical area. After a brief rundown of my skills, she took my resume and passed it on to the company that ultimately offered me a postdoctoral position. Without my friend, or the recruiter (who I now consider a friend as well), the company and I would have never found each other. I’m both grateful and thrilled for the opportunity. Be on the lookout for further posts on the industrial postdoc experience after I start!

Pack Your Bags – We Have Found Another Earth!

 

By Knicole Colon, PhD

 

Okay, the title of this post is a bit misleading.  It is true that astronomers have discovered an Earth-size planet located in the “habitable zone” of a nearby star.  Note that the habitable zone is the region around a star where a planet has a temperature that allows it to sustain liquid water on its surface.  This definition implies that liquid water is required for habitability, but since all life on Earth seems to require liquid water (as far as we know), this is a reasonable assumption.  Still, I would not pack my bags to head to this new planet just yet.  Besides the fact that the shuttle program is no more (which means we have no means of transportation to go visit this “other Earth”), this newly discovered planetary system is located some 500 light-years from Earth.  To put that in perspective, a single light-year (the distance light travels in a year) is equal to about 6,000,000,000,000 miles.  I think we can all agree that 500 light-years is kind of far.  Regardless, the discovery of this potentially habitable, Earth-size planet (dubbed Kepler-186f) suggests that there are many Earth-like worlds hiding out there, we just haven’t been able to detect them until now!

 

The Kepler mission is responsible for this exciting discovery, and the related paper published in Science and led by Elisa V. Quintana (of the SETI Institute and NASA Ames Research Center) can be found here.  The Kepler mission’s goal was to detect an Earth-size planet orbiting in the habitable zone of a Sun-like star by searching for a transit of such a planet (i.e. an event where the planet passes in front of the star and therefore blocks some of the starlight, making the star appear dimmer).  However, the nominal mission ended once one of the reaction wheels that stabilized the pointing of the telescope died.   Regardless, the Kepler team was able to detect transits of Kepler-186f in the available data, which led them to determine that the radius of Kepler-186f is quite similar to Earth (within 1-sigma).  Furthermore, the planet orbits its star every 130 days, which suggests that the planet has a temperature capable of sustaining liquid water.

 

You might have noticed Kepler-186f has an orbital period that is almost three times shorter than the Earth’s, yet it is believed that it lies in the habitable zone.  This difference lies in the fact that Kepler-186f does not orbit a Sun-like star, which means it is not really “another Earth” after all.  It actually orbits a very cool M dwarf star (named Kepler-186).  There are several classes of stars, with the Sun being a G-type star and having a temperature of about 5800 K (or 9980 degrees Fahrenheit).  Being an M dwarf star, Kepler-186 is about half the size of the Sun and has a temperature of about 3800 K (or 6380 degrees Fahrenheit).  That difference is enough to “move” the habitable zone closer to the star, compared to the location of the habitable zone around the Sun.  That Kepler-186 and the Sun are different types of stars also has other repercussions.  Even if Kepler-186f does have liquid water on its surface, it receives different types and amounts of radiation from its star.  This suggests that the atmosphere is likely extremely different than what we are used to here on Earth.  That does not mean other types of life forms can’t exist on Kepler-186f, but humans might have some problems breathing there.  There’s one other major caveat to calling Kepler-186f an “Earth twin.”  Its mass, and therefore density and composition, are not known.  Some research suggests it is likely to be a rocky planet like Earth, but we do not know for sure.  Unfortunately, it is possible we will never know, because measuring the mass of a tiny object that is so far away is really, really, really difficult to do.

 

One other fun fact about this new planetary system is that Kepler-186f is named as such because there are four other planets in the system, known as Kepler-186b, c, d, and e.  All these planets orbit closer to their host star than Kepler-186f, making them way too hot to have liquid water (their orbital periods are just 4, 7, 13, and 22 days!).  As far as astronomers know, there are no other planets orbiting further out than Kepler-186f.  Even if there were, they would be too cold to be habitable.  So, Kepler-186f is really in the sweet spot, the so-called Goldilocks zone where it’s not too hot, and not too cold, but just right!

 

It is exciting to think about how many other potentially habitable planets like Kepler-186f might be out there.  Now that some 1500 (or more, depending what criteria you use) planets have been found around other stars, astronomers have even started cataloguing planets that come close to being an Earth twin.  For example, there is The Habitable Exoplanets Catalog  and The Habitable Zone Gallery.  Just remember that as we get closer and closer to discovering a true Earth twin, just because a planet is in the habitable zone does not mean it is inhabited.  It is my opinion that there is definitely other life out there somewhere, but so many conditions have to be met that it is not clear how much *intelligent* life may be out there.  Then again, some people believe there is not much intelligent life here on Earth either…  Still, I hold the belief that (to paraphrase a quote from Contact by Carl Sagan) because the universe is so darn big, it would be an awful waste of space if it is just us.

 

Marvelous Month of Immunology

 

By Stephanie Swift, PhD

 

Balancing modern and ancient anti-viral immunity

The human genome is stuffed full of ancient retrovirus genomes, a heritable legacy of ancestral infections. These pieces of DNA are dynamic elements, and can hop around the human genome and drive its ongoing diversification. Mostly, though, they are kept subdued by epigenetic changes that prevent them doing any damage. While identifying threatening new viral genetic material is an important job for our innate immune system, there is typically no reaction against these ancient endogenous benign retrovirus cDNAs that in modern terms are essentially a part of our own genome. Yet scientists have now implicated this evolutionary trade off between the immune system being able to sense and react against infectious DNA viruses (like retroviruses, adenoviruses, herpesviruses) while staying quiet against non-infectious ancient viral elements in certain autoimmune diseases, like Aicardi–Goutières syndrome (AGS). In AGS, mutations in the Trex1 exonuclease enzyme allow non-infectious ancient retroviral nucleic acids to accumulate and cause heart damage. They speculate that the immune system is almost inappropriately constrained against sensing these dangerous pools of foreign DNA, leading to autoimmune consequences. Happily, though, there is a potential treatment: using reverse-transcriptase inhibitors to prevent the formation of ancient retroviral immunostimulatory cDNAs in the first place. Learn more about anti-viral immunity here.

[hr]

Parasite proves proficient at immune scooping

As T cells bumble around our bodies, they are on constant stand-by to recognise pathogenic target proteins. These pieces of protein are presented to T cells for inspection by other immune cells, known as antigen-presenting cells (APCs). The T cells scoop up the pieces of protein being held up for inspection by the APC, along with a tiny bit of the APC membrance in a process known as trogocytosis. This leads to T cell activation and killing of infected target cells. Now, scientists have discovered that trogocytosis is also used by the gastrointestinal parasite, Entamoeba histolytica, to chew away at individual host cells in the gut until they die. Once that happens, the parasite moves on to the next tasty cell snack. It also appears that practise makes perfect: the parasite refines its killing skills and becomes quicker at ingesting target cells as it spreads from cell-to-cell. Now we know that trogocytosis is involved in this nasty, potentially fatal gastrointestinal disease, we can begin to design therapies that block this pathway and stop the parasite in its tracks.

[hr]

Childhood obesity linked to poor vaccine protection

Obese adults are at a greater risk of getting infected by – and dying from – influenza viruses like the pandemic H1N1. So, it’s probably very important for obese individuals to get their flu shot each year. Yet interesting research coming out of the lab of Melinda Beck at the University of North Carolina at Chapel Hill is starting to paint a rather startling picture showing that obese people don’t develop good responses to vaccines compared to healthy weight controls. Antibody levels in the blood decline more quickly over time, and T cells don’t get as robustly activated or produce the same quantity of toxic molecules designed to kill invading pathogens. Even more worryingly, these impaired vaccine responses are not just restricted to obese adults, but are seen in obese children as well. In Canada, an estimated 31.5% of children between the ages of 5-17 are overweight or obese. Since a number of serious childhood infections, including measles and whooping cough, are on the rise, obesity could be a modern risk factor contributing towards the development of serious disease, potentially even in vaccinated individuals where primed immune responses just aren’t as good at dealing with infections.

[hr]

Huge new database finds early transcriptional programs driving vaccine immunity

In recent years, scientists have made huge progress in furthering our understanding of how the immune system works, and applying this knowledge to vaccine design. Yet we are still pretty much in the dark about what makes a “good” vaccine. Are live replicating microorganisms better than dead ones? Is it better to generate an antibody or a T cell response? Are central memory or effector memory T cells better? Big data promises to help us get to the bottom of these questions, and ten thousand others just like them. By analysing huge data sets, we can begin to tease out correlations and signatures that predict if (and how) a vaccine will protect against its designated disease. Scientists at Emory University recently took the big data approach and created a hugely powerful database loaded with the molecular profiles of over 30,000 human blood transcriptomes from ~500 studies. They used this to look for a signature of protection across 5 successful human vaccines (2 against Neisseria meningitidis, 1 against yellow fever virus and 2 against influenza virus). Since their tested vaccines varied in their nature – some were conjugate vaccines made up of two distinct parts, while some were live attenuated vaccines – it was tricky to come up with a universal vaccination signature between all 5 vaccines beyond the basics of “B cell activation” or “leucocyte differentiation”. Happily, though, it was possible to see similar signatures of immunogenicity within a vaccine class. For example, vaccines that had a large carbohydrate component tended to induce stronger T cell responses, while live attenuated vaccines upregulated larger innate immunity and interferon responses. Very interestingly, they also observed that the two-part vaccines generated a dual-profile immune response established by two distinct molecular mechanisms.

[hr]

These posts were originally posted on the Stojdl lab blog.

5 Ways to Jump Start your Non-Academic Job Search

 

By Elaine To

So you’re nearing the end of your PhD. It’s a time for celebration, right? Unfortunately, the shining dream of becoming a professor in academia that you started with has faded. It’s no longer your career path, and all those seminars on how to land the perfect postdoctoral position no longer apply to you. Searching for a job in the real world sounds scary at first, especially in the current economy. Here are some tips for getting started:

1)     Build and update your LinkedIn profile

You should be able to copy/paste the statements from your resume into the “Experience” section. You can be more detailed and include more accomplishments than in your resume, but remember to use action statements and communicate things clearly. This is also the area to include the details of any volunteer work or leadership positions. Make sure to write a concise summary of your background and goals for the “Summary” section. This is what most people will read when deciding whether to delve deeper into your profile. Your current job title is just as important. Lastly, ensure the photograph is a professional well lit depiction of your smile.

2)     Build your network

Once your LinkedIn profile is setup, join groups in your field or that are associated with your university. Add individuals who you know in a professional or friendly capacity, but be wary of adding anyone you don’t know. In this way, you’ll increase the number of people you are connected with. Networking is crucial, as much of the non-academic PhD market is unadvertised. Leave no stone unturned, check your undergraduate and graduate alumni, friends, and colleagues. Talk to the career offices and use your PI’s network.

3)     Do informational interviews

Other people love talking about their experiences. You’d be surprised how many people are willing to help out somebody who was previously in their shoes! Within your network, alumni groups, or 2nd and 3rd tier connections, look for somebody currently working in a position or company you’d be interested in. Ask for a 10-15 minute phone chat to learn more about their experiences. Often the person you chat with will also ask about your background and career goals. During this chat, DO NOT ASK IF THEY KNOW OF AN OPENING. Ask about their day to day life, what skills are necessary to succeed in their position, how they got there, what it’s like to work for this company, etc. At the end, thank them for their time and ask if you can do anything for them, and also if they know of anyone else who might be a useful contact for you. The fact that you are asking about their current position lets them know that you are looking for a job, and they will keep an eye out. If you can, try to meet the individual over coffee; it will be a more personal connection.

4)     Search for job postings

If you match more than 70% of what a job posting asks for, it is worth applying to the job. Make sure to tailor your resume and cover letter for that specific announcement. If you do not match, job posting searches still let you know which companies are hiring. If it’s a company that interests you, return to LinkedIn and see if any of the employees in the company are a 2nd tier connection. Ask your shared connection for an introduction, and then follow up with an informational interview. Don’t be afraid to check smaller startup companies, who may be more willing to take someone without the specific skills on their specific instrument with this specific model system. Looking at the portfolios of venture capital firms will give you an idea of which startups are well funded and likely to be hiring.

5)     Keep an open mind

Through my informational interviews, I learned about many more career options for scientists. Before I began, I wasn’t aware that venture capital firms hired scientists to be analysts, some law firms hire scientists without patent bar registration to be technical advisors, that technology transfer existed as a field, and that there are many routes into science policy in addition to the AAAS fellowships. Learn as much as you can about any potentially interesting field before deciding not to pursue an opportunity within it.

There will be many cycles through these 5 tips, just like the many cycles that your resume and LinkedIn profile will undergo. As you continue, you will gain a greater understanding of which of your skills are desirable and how to market yourself, and use this knowledge to refine your approach. The informational interviews, whether over the phone or in person, are also excellent low pressure practice for real job interviews. Good luck! It won’t be easy, but there is a light at the end of the tunnel! Trust me.

Which Came First: the Enzyme or Metabolism?

 

By Elizabeth Ohneck, PhD

Where did we come from? How did life originate? These questions are perhaps the oldest form of “existential crisis,” and questions that science has long sought to answer. The path from simple elements to complex biological systems was dependent on the development of self-organizing, self-replicating systems, as well as generation of metabolic pathways and the enzymes that drive them. Much work has been done to build a map of this evolution, but we are far from a complete understanding.

 

Metabolism is the group of chemical reactions required for life, the processes that build our DNA, our RNA, and the proteins and fats that comprise us, as well as break down molecules to provide the energy for these activities. These reactions occur within cells and are driven by proteins called enzymes. Many of these reactions are conserved among all life, from tiny bacteria, to plants, to animals, including humans, suggesting these metabolic processes are ancient and likely arose before life as we know it; in fact, the origination of these processes likely allowed the formation of life. The consideration of the origins of metabolic networks presents a chicken-or-egg scenario: which came first, metabolism or enzymes? In an exciting paper published in Molecular Systems Biology, Keller et al. provide evidence for the former, demonstrating metabolic-type reactions can occur in the absence of enzymes in an environment that plausibly mimics earth before life.

 

Keller et al. selected a series of compounds that serve as intermediates of two universal metabolic pathways: glycolysis, which breaks down the sugar glucose to release energy, and the pentose phosphate pathway, which converts sugars to ribose-5-phosphate, a building block of RNA and DNA. Using ultra-pure water and chemical preparations, they first dissolved a known concentration of each chemical in water and heated the solutions to 70°C, a plausible temperature for early earth ocean environments near heat sources such as thermal vents. After 5 hours, they examined the chemicals in the solutions by liquid chromatography-selective reaction monitoring, a highly sensitive technique to measure the types and amounts of chemicals in solution. They discovered that many of the compounds were converted to other metabolic intermediates, with the most common being pyruvate, an important branch-point metabolite that can be used to generate energy or converted to sugars, fatty acids, or amino acids.

 

The researchers then repeated this experiment in an “Archaen ocean mimetic” – a solution of salts and metal ions at concentrations likely found in early earth’s oceans, as determined from geological data. While the salts alone did not change the reaction outcomes, the addition of metal ions resulted in a greater number of conversions, including the production of ribose-5-phosphate and erythrose 4-phosphate, a precursor for the formation of amino acids. In further studies, the researchers demonstrated that iron, which would have been at high concentration in early earth’s oceans, was the key metal ion in driving the conversion reactions. Additionally, they showed that an anoxic, or low-oxygen, environment, as would have been the state of early earth, facilitated these reactions.

 

The conversion of metabolites mimicked enzyme-catalyzed metabolic reactions that occur within our cells. The researchers ruled out the possibility of contaminating enzymes in their reactions in several ways. First, they conducted these reactions at a temperature that, while plausible for the early earth ocean environment, is too high for most metabolic enzymes. Importantly, these reactions were not observed below 40°C, temperatures at which common metabolic enzymes would be functional. Second, critical cofactors, or small molecules required for the function of some enzymes, were absent. Third, the researchers stringently assured purity of their reaction mixtures through physical and chemical means, including filtering the solutions through a membrane with a very small size cut-off that would exclude complex proteins such as enzymes, repeating experiments in different types of reaction tubes, and adding organic solvents that would denature or inhibit enzymes.

 

Thus, Keller et al. effectively demonstrated that metabolic reactions critical to life that we know today to be catalyzed by enzymes can occur in the absence of enzymes under conditions that mimic the environment of earth before life. These reactions include the formation of molecules that form the building blocks of RNA, DNA, and proteins, of which all living organisms are comprised. Their findings provide support for the hypothesis that metabolic networks arose first, leading to the subsequent formation of RNA and enzymes, which would eventually give rise to self-replicating systems that would evolve into the first cells.

 

Many questions remain, perhaps the most prominent being: where did the original metabolite compounds come from? One possibility is based on the Miller-Urey experiment, published in 1953. In this experiment, researchers combined water, methane, ammonia, and hydrogen, thought to be the primary components of the early earth’s atmosphere, and applied high-voltage electrical pulses, which, surprisingly, generated the amino acids alanine and glycine. Subsequent research refined the reaction set up to more accurately mimic the environment of early earth and was able to demonstrate the creation of multiple essential biomolecules. One might imagine, then, that the elemental and atmospheric conditions of earth pre-life allowed the generation of complex molecules, which, in the low-oxygen, high-iron conditions, underwent chemical conversions, creating the first metabolic networks that in turn allowed the generation of life.

 

These hypotheses are, of course, just that: hypotheses. Whether the occurrence of such a chain of events can be conclusively proven is debatable. But studies such as the Miller-Urey experiment and the research by Keller et al. present thought-provoking findings that stimulate careful consideration of the incredible set of circumstances that lead to the generation of life. To imagine how simple elements combined to form the diversity and complexity of life on our planet today can be overwhelming and awe-inspiring. The study by Keller et al. provides an important piece in the puzzle of understanding our past.

How I Nailed My Lab Rotation and Got in the Lab I Wanted

 

By Evelyn Litwinoff

From the first time I met with my now PI to discuss a possible rotation, I knew I wanted to end up in her lab. She took me seriously even as a lowly first year grad student, and valued my thoughts and input on the rotation project we discussed. I left that meeting super excited about the rotation to be, and I couldn’t wait to get started.

 

Arguably the best part about this rotation was that I made and had my very own project as a rotation student that had the possibility to become a thesis project if – I mean when – I joined the lab. And the project was all about autophagy – a topic I had been introduced to in undergrad, found super exciting, and wanted to learn all about. (A quick refresher: Autophagy is a cellular recycling mechanism used to degrade large proteins, organelles, aggregates, and other substrates. It is essential for cellular health, especially in times of starvation. As Bill Nye the Science Guy would say,Now you know!”)

 

Step #1: Taking initiative

 

I came in on day one ready to generate tons of data, eager to become friends with everyone in the lab, and “wow” them all with my super science skills. Then I hit roadblock #1: the person in the lab I was assigned to work under wouldn’t let me do anything myself. I would watch her as she plated the cells, changed the media, dissected the mice, etc, and all I was able to do was label tubes. Not exactly how I imagined this rotation would be. But instead of sulking around wishing things would be different – ok after doing that for 2 weeks and spending time looking up other labs to rotate in – I spoke with another post-doc in the lab, and she agreed to have me work with her instead. Later after I joined the lab, I found out from this post-doc that by taking charge of my situation and changing it for the better, I showed her (and therefore my PI) that I really wanted to be a part of the lab and I could take initiative with my own project.

 

Step #2: Learning and mastering new skills – Evelyn vs. the Western Blot

 

My undergrad research was all about Caenorhabditis elegans (C. elegans) genetics, so most of my science skills before grad school consisted of PCR, running DNA gels, sequencing, and C. elegans specific handling. Hence, I had never done a western blot myself before this rotation. But by the end of my 3 months in the lab, I was a western blot master! One of the main ways to assess if autophagy is upregulated is to look for increases in the autophagy specific protein, LC3. So the end points of all my cell culture experiments were western blots for LC3 and another autophagy specific protein, Beclin. I worked my butt off doing western blot after western blot, sometimes staying in lab until 1am, and was able to have new results at almost every meeting with the PI. At the end of my rotation, one of the research associates came up to me and said, “I can’t believe how much data you generated in such a short period of time.” I was very proud of how much data I was able to produce, but more importantly, I was happy I learned this new skill quickly enough that I didn’t have to take up a lot of my post-doc’s time when running my own experiments.

 

Step #3: Being a good labmate

 

When I used up my post-doc’s stocks and buffers, I always asked her for the recipe to make more, and I replaced whatever I took. Same thing goes for refilling the pipettes in the cell culture room, emptying the vacuum, etc. Doing these types of lab chores goes a long way in showing your commitment to the lab, and in convincing everyone that they want you to stick around. I didn’t realized how important these small things were until I joined the lab and saw everyone’s reactions to the, let’s say “absent-minded” summer students.

 

Step #4: Admitting mistakes

 

At one point in my rotation, I left some antibodies on the bench overnight. Major whoops. I apologized profusely to my post-doc. Although she was not happy with me, she understood it sometimes happens to everyone and appreciated my straightforwardness in telling her.

 

Step #5: The big finish!

 

One of the things my PI from undergrad engrained into my head was how to make a good presentation. She would never be happy with my slides until they were mostly pictures with very very very few words underneath. I used these skills to put together a presentation for the end of my rotation. In my now PI’s words, “Evelyn, these slides are gorgeous!” Cue the inner Cheshire cat grin. I left that rotation with good impressions on the lab and the PI, and I kept in touch with the post-doc I worked closely with. Sometime in the middle of my next rotation, I emailed this PI and asked to join her lab. To my delight, she said yes!

 

The Biomedical Research Crisis

 

By Neeley Remmers, PhD

 

Call it “woman’s intuition” if you will, but all throughout my graduate career I had this persistent voice in the back of my head trying to tell me something. It started as a gentle, lulling whisper in my first year that gradually grew into full-blown fire alarm screeching in my head. What was this alarm? My own growing concern over the sustainability of biomedical science and its job market. I had been exposed, to some degree, of the decline and volatility of research jobs in industry prior to attending graduate school and knew of the ever increasing influx of graduate students entering the biomedical field despite the fact that the number of available faculty and research positions had remained constant. My concerns were fully realized when I went to a career development conference in my 4th year, right about the time I needed to start making more concrete plans as to where I wanted to take my career. The recent article published in PNAS co-authored by Bruce Alberts, Marc W. Kirschner, Shirley Tilghman, and Harold Varmus eloquently highlights some of the concerns I have myself as well as additional faults of the current system used by the biomedical field and gives insightful recommendations as to how to remedy the situation to prevent our field from imploding.

 

The authors adequately identify the root cause of the looming implosion of biomedical research – the assumption that there will be continual, rapid growth in the field creating job security for those already established and creating a job market rich with opportunity for new scientists. This assumption had been frequently used as bait to persuade me into joining the field even though the NIH budget had already begun to diminish after experiencing a decade of growth by the time I entered college. This decline in available federal funds (thanks to recent economic hardships felt everywhere) has fully opened our eyes to our current situation of having a supply of highly-qualified scientists that surpasses the number of available research positions, more specifically academic research positions. This influx of skilled scientists was the catalyst needed to synthesize a number of other problems that have recently surfaced in biomedical research that hurt everyone in the field, particularly new investigators. I won’t spend time going into detail on these additional problems highlighted by the authors, but I do want to spend a few moments touching on a subject they missed that I feel could also be adding to our current dilemma.

 

One cause of our problem outlined by the authors is there being too heavy a focus on conducting “translational research.” First, neither the authors nor I are trying to downplay the importance of translational research. After all, for a many of us, advancing medicine is the main reason we decided to enter research. However, it does seem like these days many are over-looking the importance of basic research and that you need solid, basic foundation before you can jump into translational research. By doing quality basic research first, you can gain a firm grasp on the mechanisms that dictate whichever physiological process you are studying and can be more successful in translating that knowledge into clinically relevant studies. Part of the push towards doing more translational research, though, comes from Congress and support from the general public. In this day and age, people like to see immediate results, and translational research can provide the public with results that have a more direct correlation to patient care as opposed to basic science. These results may not always be positive, but even the negative results give a better appearance to the public that something worthwhile is being done with the money they have given us. The problem here is that the general public does not understand the scientific process and the time and effort that goes into discovering new, efficient therapies; a problem easily remedied by educating the public about the research process. Once they realize how important the basic science is to translational research, we can bring some focus back towards awarding investigators who propose long-term, high-quality science rather than on those who propose short-term, translational projects.

 

Back to the article, the authors give their recommendations for how to rescue biomedical research. I will refrain from commenting too much on how we might remedy the grants review process, selecting review panels, and such as addressed by the authors as I do not have much experience or knowledge in these areas. What I can comment on is their recommendations for altering the way we train new scientists. As mentioned earlier, there has been an inflation of graduate students and post-doctoral researchers in recent years that far surpasses the number of available jobs. This is in part due to the fact that it is cheaper for senior scientists to bring students and post-docs into their labs rather than hire staff scientists and restructuring grant guidelines in terms of salaries, as outlined in the article, could certainly help this. The authors suggest that by prohibiting payment of students from grants and increasing pay of post-docs will help to reduce the numbers of incoming graduate students, promote career advancement of post-docs, and encourage hiring staff scientists all of which can be beneficial in the long-run.

 

Aside from simply limiting the number of incoming graduate students, I feel it is necessary that graduate programs start implementing career development programs into student training. In the past, one’s career path in science was pretty clear and the apprenticeship scheme used to train current graduate students worked well. However, in today’s world only about 25% of current graduate students will be able to obtain a faculty position leaving the other 75% of current graduate students to find employment elsewhere rendering the apprenticeship scheme no longer a valid training model. Instead, we need to increase efforts to introduce students early on to the many other career options available to them in science by giving them opportunities to meet with professionals in these areas. Students can then begin to make valuable connections to establish relationships with a secondary mentor that can help them get into the fields of patents, policy, scientific writing, etc.

 

Change in the structure of the biomedical science enterprise is desperately needed to prevent it from collapsing. The reality is that the model currently in use may have worked well in the past but is severely out-of-date for today’s economy. Serious changes are warranted in order to get back to the days of exciting scientific discovery rather than living in the days of scientific survival.

The Uncertain Life of an Academic Scientist: Do We Quit or Do We Evolve?

 

By Lori Bystrom, PhD

 

I always thought I was meant to be scientist, even if I did not entirely understand what a scientist was as a kid. I loved to create, design, and understand how things worked. I also aspired to invent something; if I was not making some invisible potion to cure laughitis, I was imagining some kind of creation to make the bad monsters go away that were haunting my room.

 

Today, as I think about my next experiments in the lab (i.e., how can I selectively eliminate the cancer monsters?), I also wonder how much longer I can last as a scientist. If I continue along the academic path, do I have a sustainable future? Grants are hard to come by and tenure-track positions are few. Moreover, the amount of time you put into the work is not always rewarded sufficiently. As many postdoctoral researchers know, our salaries are often less than our peers who have bachelor’s degrees. Essentially, we invested lots of research time and got little return on our investment.

 

This dissatisfaction with academia is common feeling among many scientists in the academic world. This is apparent in the numerous blogs or articles by PhD graduates, postdoctoral researchers, and those who are lucky enough to begin tenure-track positions.

 

Although there is obviously a problem in academia right now, I do not think we have to stop being the scientists we once aspired to become. It is always good to know when to quit a specific job; however I think we can also adapt to the situation and evolve as a scientist either inside or outside of academia. Being a scientist today is not the same as being a scientist 20 years ago. There may be more PhDs to compete with than in the past, as well as more funding issues, but we also have new technology (e.g. the internet) that we can use to our advantage.

My experiences as a graduate student and postdoctoral researcher have made me view science much differently than I did as a kid or even since I began graduate school. There are several things that I have learned that may help academic scientists evolve and adapt to the current scientific environment.

 

1. Think outside the box

There are more than just government grants out there. If you are applying for such grants you have to realize that being smart and a good scientist is not always enough. What makes you special from the rest? You need to find that and emphasize that. I know my diverse scientific background has helped me obtain several grants. Find your niche. Explore unique types of grants.

 

 

2. Look beyond academia

Academia is not for everyone. A study by the American Institute of Research has shown that 61% of STEM PhDs pursue non-academic careers. There are jobs in science communication, science outreach, science education, science policy, industry, and the list goes on. There are many resources out there that explore life beyond academia. It may take a while but I have seen many people procure these kinds of jobs even after a long stint as a postdoctoral researcher. It is also possible that some people may even return to academia (one of my collaborators did this) or partner up with academic institutions after their experience outside academia.

 

3. Advertise your research

Get yourself connected and network with people at science events and even non-science events. Get the word out there. You never know who may be interested. This may not only make you feel good about your work, but it may also be beneficial to you in the future, whether you stay in academia or not. This may be one useful resource.

 

4. Collaborate

Start your own projects with other people you would like to collaborate with either at your institution or elsewhere. If your PI resists then explain how this could strengthen your research proposal and help you get funded. In fact, many grants require collaborations. Moreover, collaborations with industry or within academia may also lead you to other jobs in the future.

 

5. Continue your education

Gain expertise in a new field that might help you expand upon your research ideas. Ultimately, this may help you obtain more grants or find new job opportunities. You can do this by using tuition allowances you receive from grants or your institution. There are also online courses or MOOCs such as coursera  or workshops available at various institutions that you can take for minimal costs.

 

6. Start something new

Whether you start a bakery, a brewery, a science start-up, or anything that you are passionate about — you can still be a scientist. Many of the skills you acquired as a scientist (e.g., management, writing, etc.) will come in handy, and you can always use Scizzle to keep up with the science you care about.

 

Overall, I think if we want to continue to be scientists we can, but we need to utilize the technology that is available to us, keep our options open, and be mindful of both the current state of academia and what is beyond the academic world. Whatever we choose we have to continue to evolve.