Don’t be daunted–Anyone can parse through research literature

In case you missed why Open Access is awesome, the lack of open access is only one of many barriers that discourage the dissemination of scientific information to the public. Fortunately, more researchers are publishing in Open Access journals or with Open Access options thanks to requirements by various funding agencies. Although open access issues still remain a significant barrier to the dissemination of scientific information to the public; a greater barrier may be the lack of confidence for reading and understanding scientific articles. Reading scientific literature can be intimidating for many people. It’s full of scientific jargon, unfamiliar tools and techniques, and can feel more or less like reading text in a foreign language. While many people would be content with reading press releases of scientific discoveries by science communicators and journalists, only a small percentage of scientific literature actually receives significant press coverage. Hence, people miss out on discoveries relevant to them every day!

For care providers/patients dealing with rare diseases, wading into the murky waters of scientific literature is often mandatory. Rare disease don’t receive nearly the same amount of research or media attention as more common diseases, leaving little choice but primary scientific articles to keep informed of important discoveries.

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Finding buried treasure in shifting sand

The problem of keeping up with scientic literature is not new. In 1986, information scientist, Don R. Swanson, published an article about mining the wealth of knowledge buried in academic literature. In his article, “Undiscovered public knowledge”, Swanson investigated information that was not readily available simply because individual biomedical research papers were (and in many ways still are today) created “to some degree independently of one another.” By investigating literature that was “logically connected”, but was otherwise “non-interactive”, Swanson teased out a hypothesis essentially joining two small fields of research.

Since then, researchers are still trying to develop methods to wade through this ever-growing body of literature, only now there are about one million new biomedical research articles being published per year compared to the roughly 350 thousand published in 1986.

Finding the right information is a problem that's only going to get worse unless we do something
Finding the right information is a problem that’s only going to get worse unless we do something

Compound this issue with the growing amount of information that is now contained within biomedical research literature, but is not readily accessible due to lack of appropriate annotations.

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Neat Science Thursday – Call for Papers

We interrupt our regularly schedule post for this important announcement. There are only 7 days left to answer the call for papers and save a scientist.

Don’t leave Andrew and Ben to fend for themselves amidst to all that water, sun, and sand.

The 2015 Pacific Symposium on Biocomputing will be held from Jan 4-8 on Kohala Coast in Hawaii! Andrew and Ben (together with collaborators Robert and Zhiyong at NCBI) are organizing the session on Crowdsourcing and Mining Crowd Data. For the session to be remotely decent, they need manuscript submissions. Submissions will be vigorously peer-reviewed and accepted papers will be published in an archival proceedings volume (fully indexed in PubMed), with a number of the papers selected for presentation during the conference. Please consider submitting your manuscripts describing biocomputing applications and methodological advances in crowdsourcing techniques or learning from crowd data. Andrew and Ben are going to PSB for the research, but will be forced to hit the beach if their session is cut short due to insufficient entries. Don’t expose them to be excessive radiant heat of the sun when they would rather bask in the cool, comforting glow of countless compelling powerpoint presentations.

Here are the details on how to help them:
Visit the PSB session call for papers page for useful details to determine if your manuscript is right for this session. Instructions on how to format and submit your manuscript are also included on that page.

Key Dates:

  • Manuscript submission: July 31, 2014
  • Notification to authors: September 9, 2014
  • Camera-ready papers due: October 1, 2014
  • Abstract deadline for posters: November 17, 2014
  • Conference: January 4 – 8, 2015

Session Organizers

  • Robert Leaman, National Center for Biotechnology Information (NCBI)
  • Benjamin Good, Scripps Research Institute
  • Andrew Su, Scripps Research Institute
  • Zhiyong Lu, National Center for Biotechnology Information (NCBI)

Neat Science Thursday – Love thy soil chemistry

So much of science is really about understanding and appreciating the beauty of nature, hence it seems strange to me how some people or companies (or both in the US since companies count as people now) paint the two as polar opposites. Though many of my previous posts have been a bit microbe-centric, I want to emphasize that the different scientific disciplines all relate to one another since science is about explaining nature, and nature does not fit into neat little compartments or categories.

Previously, I briefly covered the importance of microbes in nitrogen cycling for aquaponics systems, but a lot more than just nitrogen cycling is needed to keep plants healthy. Many plants also have a preferred soil pH, so it’s time to pay some respect to the study of chemistry!

If you’re an avid gardener, you probably already know that pH is a measure of acidity or alkalinity and that different plants grow better when rooted in soils of specific pH ranges. For example, blueberry bushes prefer slightly more acidic soils.

Many plants not only require a number of transition metal elements as nutrients (iron, copper, manganese to name a few), but also for these nutrients to be in a form that enables their uptake by the plant. For example, manganese is an important part of photosystem II in the photosynthetic reaction center, while copper is an important part of photosystem I. Love that plants take carbon dioxide and release oxygen? The manganese is important for that.

Simple photosynthesis overview
You probably already knew that Plants use water and carbon dioxide to produce energy and oxygen via photosynthesis
But did you know that manganese and copper play an important role in this process? This is one of several reasons Mn2+ is so important for plants

Plants are able take up manganese in its ionic form (Mn2+). In the soil, Mn2+ will often form salts with anions present in the soil, and many of these solid salts will be more soluble in acidic as opposed to alkaline conditions. This means that in acidic soil, the manganese may be more readily taken up by plants, which may help to explain why fruiting plants (in general) prefer a slightly acidic soil pH. Considering the amount of photosynthesis needed in order to synthesize all the sugars the sugars stored in the fruits. Copper and many other micronutrients are also more readily available in slightly acidic soils than they would be in alkaline soils.

And because chemistry is an awesome discipline that deserves a bit more love, here’s how to create your own pH indicator using red cabbage. It was one of the coolest experiments in the 7th grade science class, and may come in handy if you can’t afford a real pH testing kit for your aquarium.

Adapted from How to make Red Cabbage pH Indicator by Anne Marie Helmenstine, PhD.

Red cabbage contains a pigment molecule called flavin (an anthocyanin). This water-soluble pigment is also found in apple skin, plums, poppies, cornflowers, and grapes. Very acidic solutions will turn anthocyanin a red color. Neutral solutions result in a purplish color. Basic solutions appear in greenish-yellow. Therefore, it is possible to determine the pH of a solution based on the color it turns the anthocyanin pigments in red cabbage juice.

The color of the juice changes in response to changes in its hydrogen ion concentration. pH is the -log[H+]. Acids will donate hydrogen ions in an aqueous solution and have a low pH (pH 7).


  • red cabbage
  • blender or knife
  • boiling water
  • filter paper (coffee filters work well)
  • One large glass container


  1. Chop the cabbage into small pieces until you have about 2 cups of chopped cabbage. Place the cabbage in a large beaker or other glass container and add boiling water to cover the cabbage. Allow at least ten minutes for the color to leach out of the cabbage. (Alternatively, you can place about 2 cups of cabbage in a blender, cover it with boiling water, and blend it.)
  2. Filter out the plant material to obtain a red-purple-bluish colored liquid. This liquid is at about pH 7. (The exact color you get depends on the pH of the water.)
  3. You can make your own pH paper strips using red cabbage indicator. Take filter paper (or coffee filter) and soak it in a concentrated red cabbage juice solution. After a few hours, remove the paper and allow it to dry (hang it by a clothespin or string). Cut the filter into strips and use them to test the pH of various solutions.

Red Cabbage pH Indicator Color Chart
pH – Color
2 – Red
4 – Purple
6 – Violet
8 – Blue
10 – Blue-Green
12 – Greenish Yellow

That’s it! Go forth and appreciate the wonders of acid-base chemistry. Visit for more awesome chemistry that can be done at home.

Neat Science Thursday – Sleep is awesome!

Unlike many untested dietery supplements that are marketed for improving your skin, memory, immune response, etc; there is a free aid that has actually be studied in the context of human health: Sleep!

According to the CDC more than 1 in 4 Americans report not getting enough sleep, and 1 in 10 Americans have chronic insomnia.

For many people, sleep is a luxury they cannot afford; maybe it’s the new baby in the house, maybe it’s the long work hours forcing, maybe they are procrastinators exploring new avenues to practice their craft. Regardless of the cause, the consequences of sleep deficiency can be severe. Think of missing sleep as getting a paper cut–it’s not a big deal once in a while, but when it’s routine, you are opening up yourself for illness, irritation, and accidents.

Although sleep has already been known to play an important role in synaptic plasticity in the developing brains of kittens and in imprinting (memory) of birds the cellular mechanism by which sleep strengthens learning had yet to be elucidated. Then, in last month’s issue of Science researchers discovered that sleep was important for the retention of dendritic spines that formed under the context of learning a new motor skill (at least in mice, anyway). If you are cramming all night for that final exam….you’re doing it wrong! Study well, but get plenty of sleep if you hope to retain anything by test time. Given the importance of sleep on memory, is it any wonder why many FDA-approved anti-dementia drugs also affect the quality of sleep? In a recent article, researchers examined the potential role of sleep as a mediating factor affecting the observed association between post-traumatic stress disorder and hippocampal size differences.

Sleep deprivation has such a profound effect on the mind that researchers are considering its use as a model for psychosis!

In addition to memory, sleep plays an important role in immunity as well. In one small study (actually involving humans), sleep deprivation was associated with alterations in neutrophil populations–resulting in a low-grade pro-inflammatory state consisting of potentially immature neutrophils. This pro-inflammatory state that could exacerbate the symptoms of asthma and other hyper-allergic responses, but still fail to fight off infectious invaders due to the insufficient production of reactive oxygen species (ROS) by the immature neutrophils. Sleep deprivation has been associated with increased levels of cortisol (and other glucocorticoids), which can affect inflammation. Low levels of inflammation have been associated with depression, so it should be no surprise that sleep disturbances have been associated with mood disorders as well. Insufficient sleep has also been found to interact with the perception of stress and pain, which can affect the ability to sleep and result in the need to self-medicate using alcohol or other drugs.

Because of its effects on immunity, sleep may play an important role in regulating the gut microflora and affect gut and skin health. Sleep disturbances have been associated with inflammatory bowel disease and preliminary research on circadian rhythms in mice suggest that alterations in sleep patterns can affect the gut microflora. If sleep status can affect asthma, it is likely to have an effect on dermatitis and other hyper-allergic skin conditions. One review has even examined the potential relationship between sleep, inflammation, stress, and acne. Don’t want bags under those eyes? Don’t buy eye creams, get more sleep!

If you eat plenty of awesome veggies in order to feed your gut microbes, get plenty of sleep to keep that immune system working properly to maintain your microflora. If you have trouble sleeping, click here for some tips to help improve your sleep.

Neat Science Thursday – Watch the Barbeque

July 4th is right around the corner so it’s time to bust out the BBQ grills which have seen no use since memorial day. On today’s menu…BBQ done right!

Cook meat thoroughly to kill pathogenic bacteria

Meats should be kept cold prior to cooking because the lower temperatures will help slow the growth of bacteria like Escherichia coli and Salmonella. Unfortunately, Listeria Monocytogenes still grows fairly well at lower temperatures which is probably why it is the 3rd leading cause of food poisoning death in the US.
Just look at how listeria can utilize actin in an infected cell to move around in it!

Although marinating your meats may help spread bacteria from contaminated cuts to uncontaminated cuts, the right marinade may also help to inhibit growth of illness-causing species of Clostridium, Enterobacteriaceae and Vibrio. Marinades can also affect the taste and texture of your meats so consider your choice of marinades very carefully. Marinades rich in salts, sugars, acids, or alcohols will be helpful in inhibiting the growth of microbes. Also, remember that pathogenic bacteria can contaminate vegetables as well, so be sure to wash those veggies well if you plan on eating them raw.

Click on the image to learn about detection methods for heterocyclic amines after an exposure event. Kataoka H et al. Analytical and Bioanalytical Chemistry Volume 406, Issue 8 , pp 2171-2178

After throwing the meats on the grill, use a food thermometer to ensure that foods are cooked to a safe internal temperature: 145°F for whole meats, 160°F for ground meats, and 165°F for all poultry. Remove the meats from heat as soon as they are thoroughly cooked because overcooking meat can induce the formation of heterocyclic amines (HCAs) and polycyclic aromatic hydrocarbons (PACs). Some heterocyclic amines like PhIP have been shown to induce DNA damage which may be why HCA’s have been associated with an increase the risk of developing colorecteral cancer.

Fortunately, anti-oxidant rich marinades have been found to reduce the formation of heterocyclic amines during cooking, so marinate away! However, if the prospect of cooking the meat just right in order to avoid pathogens and NOT increase risk of cancer seems to be more work than its worth, consider adding more veggies to your barbecue this July 4th–especially since (as we’ve seen before), veggies are awesome!


Neat Science Thursday – Engineered food

The high incidence of obesity and its related health risks has increased interest in diet, nutrition, “knowing your food”, and reducing the intake of processed food. While some entrepreneurs have been busy researching the perfect nutritional replacement for food others have been capitalizing on the recent food trends using the terms ‘organic’, or ‘natural’ in order to push their products (even though these labels can be meaningless). While it’s great that more people are paying attention to their diet and better monitoring their health, it’s not great that many companies are cashing in and contributing to the anti-science sentiment in food.

Science is not the enemy of food! Do you honestly think Chobani just leaves milk out to rot while waiting for the right bacteria to settle in to form yogurt? Of course not! Specific microbes are inoculated into pasteurized milk and allowed to incubate at a specific temperature range, because otherwise the product would turn out pretty darn gross. Science plays an important role in separating fact from fiction when it comes to food, nutrition, and health. So it is really silly to think that anything ‘scientific’ is the opposite of ‘natural’, considering science began with the observation of nature. What’s even sillier is how “all natural” has somehow become synonymous with “healthier” or “safer.” Would you drink “all natural” water from a slow moving creek and enjoy the health benefits of catching giardiasis or cholera or would you rather drink from your bottle of treated water?

If you insist on buying certain brands from specific food companies, do it because the brand/company has sustainability and social responsibility built into its supply chain, or because its locally produced, and do verify to be sure it’s not just green-washed. DON’T do it simply because it’s “all natural”, or “chemical-free.” Do these companies even understand what “chemical-free” means? Nothing! No elements, no atoms, nothing! Chemistry is a scientific discipline that studies the composition, structure, properties and changes of matter.

It’s great that people want to connect more with their food, but that’s not a reason to bash science. We need to consider situations outside of our own. Yes, a complete nutritional replacement for food may not be necessary where food is so ridiculously pervasive, but consider the fact that food is not pervasively available EVERYWHERE. There are people living in devastating poverty where highly processed, carefully designed Ready-to-Use Therapeutic Foods (RUTFs) help keep debilitating malnutrition at bay. It’s not the solution for poverty-associated malnutrition (the solution is to end poverty), but it doesn’t mean we shouldn’t use it until a better solution is found. Hopefully some researchers will find a way to improve the existing RUTFs to include colonizing gut flora gut microbes play a critical role in nutrient absorption. Because getting all these microbes at once by the “all natural” way (ie- eating poop) is just plain gross (no offense to the poop-eating baby rabbits trying to get nutrition and gut microbes from their parents).

And for those of us that enjoy gardening, aquaponics, and growing your own food…let’s acknowledge that science allows us to appreciate these hobbies/lifestyles/etc. even more. Soil chemistry is awesome and allows us to test our soil pH and ensure the blueberry bushes get the acidic conditions they love. Microbes, as we already know, are awesome