Storytelling in Science: The Cell as Your Favorite Restaurant Part I

Many say storytelling in science is a great way to describe complex material in an understandable way for the masses. In this post, I will try to use an analogy to illustrate the complexity of a typical motile bacterial cell.

Microbial Physiology through Storytelling

If there is anything Americans know, it’s food. We are a nation obsessed with food and frequent restaurants on a regular basis.

Imagine your favorite restaurant as one huge bacterial cell.

When I travel to another city, I can’t rely on habit to guide me to a restaurant for dinner. I have to search for it while driving down the road. In order to know when I have found the restaurant I am searching for, I must rely on signs telling everyone what the restaurant is. The sign is a way to recognize and identify the building as i) a restaurant and ii) the specific type of restaurant. Bacteria do the same. They have ‘signs’ (proteins and other molecules) attached to the outside of the cell that lets other cells around identify what the cell is. I go into the restaurant through a door that allows patrons to move in and out of the building like bacteria have gates or channels that allow molecules to move in and out of the cell. Almost always, patrons are different leaving than they were when entering the restaurant; filled with yummy food they consumed and perhaps stopping to make a deposit in the waste room before leaving. Many molecules that leave a cell are different than those that enter. The workers of the restaurant have to keep track of the number of patrons entering and leaving the building to efficiently serve the patrons. Each employee has a specific job to do for very specific patrons. The employees have to identify their patrons and serve them as described by the bosses. Bacteria have an array of workers (proteins and protein complexes) that have very specific job descriptions depending on the patrons (substrates and product molecules) present in the cell. The restaurant survives by serving as many patrons as possible efficiently and correctly just as a cell must survive by responding correctly and quickly to everything in its environment.


Images. The page has finally been updated to include my most valued pieces. Hope you all enjoy!

Imaging Cancer Tissue One Chemical At A Time

Since listening to a Gordon Research Conference talk several years ago, I have been simply amazed by the applications developing with use of the mass spectrometer. Imagine being able to ‘see’ a specimen or tissue without use of any lenses or cameras. Not only ‘see’ it but also know the chemical makeup of each point at high resolution.

A new study published online for the journal Proceedings of the National Academy of Sciences explains the application of mass spectrometry imaging (MSI) to cancer tissue. Researchers at the Imperial College London have described a process to make this more applicable in a clinical setting without waiting weeks for a histological assessment by a specialist. This new technique will move cancer histology from the analog to digital age by identifying the actual chemicals within a sample instead of relying on structure.


Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer. Veselkob et al. doi: 10.1073/pnas.1310524111

First Order of Business When Rich: One Microscope Per Child

animated GIF bacteria, animated GIF, microbiology
Azospirillum brasilense cells swimming in an oxygen gradient. Magnified 40X

It is really sad humans (that seem so determined to destroy this planet) show little regard to the majority of species, most of which are invisible to the naked eye. Most people go through life without knowing the splendor of Mother Nature in all its glory.

It’s hard to believe now the accepted knowledge of society before invention of the microscope around 1590 by Zacharias Janssen (disputed). Everyone had  to rely on their own eyes, while exquisite in their own right, but these are only reliable down to the size of a human hair width. Imagine a world where flies and maggots were thought to spontaneously generate from items such as rotting meat. This was the common knowledge and understanding. After human observation was enhanced by wonderful inventions such as the compound microscope, only then could the true understanding of all things small or distant be studied in acceptable depth.

Imagine if you will looking through a microscope for the first time. You have been told, and believe, you live in a clean world in which if you can’t see it, it does not exist. With true curiosity and virgin eyes, you place a drop of water on a small glass slide and focus upon it with a microscope. Small particles that appear to be moving as if they were swimming come into view. Suddenly, your whole world changes. At the intersection of ignorance and knowledge, powerful things happen.

Today, microscopes have evolved and improved to the point where we can visualize hydrogen bonds in molecules at the atomic scale. The invention of the electron microscope helped usher in the field of virology just as Antonie van Leeuwenhoek did so much for microbiology with his improvements to the light microscope. The gifted van Leeuwenhoek discovered red blood cells, cell vacuoles, and bacteria (among other things). Thanks to him, the use of a microscope became a useful technique in various types of research.

It is said that ignorance is bliss. However, I believe ignorance is…ignorance. The less a person knows and understands, the smaller their world and the less their ability to imagine and perceive new ideas. Seeing is believing and what better way to see beyond your means than with a microscope.

Now, imagine giving this enormous ability to see the unexplainable to the most curious and imaginative of us, children. Their innate curiosity and unobstructed ability to use their imagination makes the power of the microscope exponentially greater. Giving a child this portal to the unseen opens their eyes to endless possibilities, probing questions, and the ability to answer the questions themselves.

I support the One Laptop Per Child movement. Opening up the entire world of information to a child can open up new possibilities and lead to a better life. The laptop opens the world to the child, but a microscope opens the child’s world in which they live. The knowledge gained is not flat and two dimensional; it is in real 3D.

Yeah, when I’m rich, One Microscope Per Child is my first action.

Never underestimate clever bacteria: bacterial persistance

If there is anything I try to convey to anyone who will listen: never underestimate the intelligence of bacteria. A new case-in-point was published in the journal Infection and Immunity (Abstract only- Paywall) from researchers in Buffalo, New York to back up my claim. Former knowledge from two pathogens that cause strep throat, ear infections, and colds suggested they did not survive long outside the human body. However, a new study about Streptococcus pyogenes and Streptococcus pneumoniae suggests we were wrong and the bacteria were right.

Previous studies used unnatural conditions; i) cells grown in broth media and ii) free-living cells. These both are not encountered by bacteria which invade a human host. S. pyogenes and S. pneumoniae both infect humans as biofilms; very resistant, closely-connected bacterial communities. The present study used biofilm bacteria to test how long these bacteria could survive outside the body and still infect mice.

To drive the message home, researchers tested a day-care center for S. pyogenes and S. pneumoniae living on surfaces and capable of causing infection. Results indicate these bacteria were found at high levels and viable even after surfaces were cleaned before sampling.

Let me re-iterate: bacteria know survival. Don’t underestimate their ability to evade our most clever defenses and come out on top while we lay in bed recovering.

News Flash: Cook Your Chicken (like you have been)

I personally have a Google News section for “Bacteria”. I was shocked by the headlines I have read today:

After being told for years not to eat raw chicken, yet again, we are reminded why.
After being told for years not to eat raw chicken, yet again, we are reminded why.

How is this news? We have a general understanding around our house, “Raw chicken is the dirtiest thing you can bring into the house”. Even my four year old knows this. Through many years of research, countless studies have shown the quick adaptability of bacterial species to the over use of antibiotics. This has rendered most common drug treatments for bacterial infection useless.

However, bacteria have NOT adapted ability to resist some common treatments like alcohol, bleach, UV radiation, and heat. I do not recommend cleaning tomorrow night’s chicken with alcohol or bleach. I personally would go with heat. So, please, next time you want to make a chicken dinner, be safe and cook it as recommended.

Are we completely wrong about autism? Are we the abnormal ones?

I was home today with the TV on. It was Ingenious Minds day on the Science Channel. A majority of the people showcased on the shows hadAutistic Spectrum Disorder, or ASD. After watching/listening to several episodes, something occurred to me as I was making dinner, who is to say we are the ones with an abnormal brain? Historically speaking, it would be very unlikely for the majority of the population to be abnormal.

But what if this was looked at from a different perspective? The growing prevalence of diagnosed autistic children could be observed as a rapid evolution of the human. Let’s say Mother Nature’s evolution experiment with humans. I have written about autism elsewhere (here) and how much of this disorder is a huge question mark to researchers. Progress is being made with university PR departments and other ‘media’ proclaiming it is all just a intestinal flora imbalance and is curable. Evidence supports a link between gut bacteria and several disorders, but it is immature to call it case closed.

I am left looking at this as naivete on our part. The autistic are the abnormal ones because we don’t understand their physiology. I just hope our descendents don’t look back at us ashamed of our folly.