300th Post: Animated GIF of Shewanella extracellular electron transfer: periplasm edition

I can’t think of a better post to serve as my 300th. After a month and a half of teaching myself Autodesk Maya, I present my best animation yet, although it must’ve been by accident. I have two versions (two different file formats). But first, some background.

Many bacteria have developed strategies to grow and thrive within environments absent of oxygen. Instead of using oxygen to “breathe”, bacteria use alternative molecules (alternative electron acceptors) to dump the waste product from respiration (the electron). These molecules can range from bacterium to bacterium. Some of the most common alternative electron acceptors include nitrate, nitrite, and iron. Interestingly, these are some of the most prevalent land pollutants and our knowledge of the types of bacteria that can thrive under these conditions continues to grow. One of the most interesting observations, in my opinion, is the process of extracellular electron transfer, or EET. During EET, the bacteria with this property have devised a method to transfer their waste to their environment without having to actually import potentially dangerous compounds into the cell. Through a elaborate network of specialized proteins able to taxi electrons called cytochromes, bacteria like Geobacter and Shewanella are able to thrive within what we would consider extreme environments.

I’m only uploading one file due to file size, but if anyone is interested in the image sequence in .png to create their own animation with a background image, please feel free to let me know. So, here it is: Enjoy!

 

What I do: Parents edition with special animated GIF for Mom and Dad

One of my goals is to help the masses understand scientific discovery. More precisely, why should we care (i.e. spend money) about bacteria and/or plants. Visiting the parents this weekend, my mom and dad talked about some of my posts that I have on Facebook. Something dad said has stuck with me, I paraphrase: he starts reading then I lose him along the way. My response was that I need to try harder. I am not in a lab researching bacteria anymore, but I still do have a rich curiosity about what discoveries are coming out among the scientific community. As a practice for the future, I will now try to describe what I used to do; here it goes, dad.

animated bacteria GIF, microbiology, bacteria gif, animated gif
Why did the bacterium decide to avoid the fire and move towards the yummy cheeseburger? Decisions, decisions…

Learning Maya animation is not just a hobby, but hopefully will be a channel to help describe complex information in a easily understandable way. 

 

Like humans, bacteria have decisions to make. We can design experiments to watch them decide which direction to travel, towards something or away from it. My research was to help understand how bacteria are attracted or repelled by certain chemicals in their environment and exactly what these chemicals are since a lot of chemicals are ignored by the bacteria. Scientists can look at the genes of a bacterium (which are a parts list and instruction manual) and predict which genes code for proteins that are used to detect chemicals in the cell’s environment. If one of these genes are taken out (no longer an available part), we can observe changes in what chemicals that cell responds to. If this is successful, we can predict that that particular gene is responsible for the bacterium moving towards or away from a specific chemical. By chemical, I mean compounds, usually nutrients, that can provide energy for the cell. 

Soil bacteria love to live around plant roots. The roots leak chemical nutrients into the soil that attracts bacteria. This is a win-win for both plants and bacteria. Bacteria receive nutrients to survive while plants receive “help” defending themselves against disease as well as receiving some nutrients they can’t make themselves but the bacteria can. These bacteria can also produce plant hormones that help the plant grow. This is a big area of research as a way to increase crop yield, i.e. food or biomass for bioenergy fuels.

There you have it, what I did as a scientist in about 400 words instead of 300 pages like the dissertation.

A work in progress: scene 2 of extracellular electron transfer as animated GIF

animated bacteria GIF, electron transport chain gif

 

A definite work in progress. However scene 2 of extracellular electron transfer as an animated GIF is here. The green sphere is iron 3+ that is reduced by the glowing electron exiting the cell via, in this case, MtrB pore protein and MtrF extracellular cytochrome of Shewanella.

Stress: It’s not just for humans; animated bacteria GIFs

My wife is a kindergarten teacher. She always talks about how stressful her job is, and I believe her. Stress can have horrible effects to our bodies. However, humans are not the only species that experience stress, but we are the most vocal about it.

Bacteria can experience many different forms of stresses, depending upon their environment. Temperature, pH, and dryness (desiccation) are common forms of bacterial stress. When bacteria sense something is not right in their environment, they must decide what the appropriate action is to assure their survival. For example, many bacteria find high concentrations of oxygen harmful. Atmospheric oxygen (O2) can inhibit enzyme action for several vital enzymes including NiFe nitrogenase that converts atmospheric nitrogen (N2) into a usable nitrogen form (ammonium). In this case, the presence of oxygen competes with N2 for electrons from nitrogenase producing water instead of ammonium. This can lead to nitrogen starvation and the inability to synthesize new proteins. To avoid this, cells must change their lifestyle from loners to a well connected community via aggregation. Once cells are aggregated together, they can produce a protective layer of sugar polymers on the outside of the cells to buffer the cells themselves from oxygen. Crisis averted! Now the cells are able to survive but at a lower growth rate.

animated bacteria GIF, microbiology, bacteria gif, animated gif
In this sequence, bacteria cells exposed to higher than optimum oxygen levels begin to clump together as a stress response. Sticking together is a way to lower the effects of oxidative stress to individual cells. The light, refractive band of cells on the right side of images show the area of optimum oxygen concentration.
animated bacteria GIF, microbiology, bacteria gif, animated gif
Same sequence as before in binary mode

Shocking: animated preview of explaining bacterial nanowires

animated biochemistry gif
A model of the protein structure of a Geobacter pilus with the N-terminal phenylalanine in spacefill and colored blue.

I am working on a post about how huge the discoveries that bacteria can conduct electricity can potentially be. This is a simple animation showing a model of a Geopilus with the phenylalanine residues at the amino terminus of each subunit in spacefill and colored blue. It is suggested the electrons leaving the bacterial cell travel along these pili via aromatic amino acids, especially the phenylalanines.

Animated GIFs: cyclic-di-GMP binding to PilZ protein and a riboswitch

animated biochemistry gif
NMR structure of a PilZ protein from Pseudomonas aeruginosa binding to cyclic-di-GMP. Residues needed to bind c-di-GMP will appear, shown in orange. Lastly, a surface rendering of the complex.
animated GIF, cyclic-di-GMP dimer 20 conformations
The cyclic-di-GMP dimer from the previous figure in the 20 different conformations when bound to PA4608.

 

a riboswitch that regulates gene expression. This particular riboswitch binds very tightly to cyclic-di-GMP