New Image Page

Hi all. I have added a page to place my images I create in Autodesk Maya. The first one is of Anaeromyxobacter with a few pili.

  • MyTH: Week 6 focus: Anaeromyxobacter spp. (
  • 300th Post: Animated GIF of Shewanella extracellular electron transfer: periplasm edition (

Infographic: I’m glad we don’t have as much impact on the atmosphere as bacteria

As humans, we are contributing to global warming every time we breathe. Luckily, this contribution doesn’t amount to a hill of beans. The amount of carbon dioxide we excrete while breathing is easily converted to other molecules by other organisms on Earth. We, as humans, number roughly 7 billion. That is a lot of carbon dioxide. However, we are outnumbered by plants and trees by several orders of magnitude that consume this carbon dioxide and convert it back to the oxygen we so desperately need and make carbohydrates in the process.

Now, think about this: 7 billion humans converted to microbes living in the soil would amount to a pinch of soil. As you should know, there is much more than a pinch of soil on the planet, and that does not take into account the waters of Earth. So, doesn’t it make sense that what these microbes take in and “breathe” out has a much much greater impact on the composition of our atmosphere? Luckily, microbes, in the general sense, don’t breathe carbon dioxide under most conditions and some microbes like algae consume carbon dioxide like plants and give us oxygen in return.

bacteria, climate change
Affect of each domain of life on the composition of the atmosphere.

The figure above shows how simplistic plants and animals are compared to prokaryotes in regards to what we all “breathe”. This is not an exhaustive list of molecules microbes use; it’s just one small group of bacteria from the genus Geobacter. This complexity helps put things in perspective.

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.

MyTH: Week 7 focus: Pseudomonas fluorescens

Swimming bacteria
Swimming bacteria

My Tiny Highlight (MyTH) has been on hiedas for a while. However, I’m glad to introduce this week’s organism, Pseudomonas fluorescens. This will be the second highlight featuring a Pseudomonad (Week 5). For short hand, I will write the name Pfu. This is an interesting organism due to its effects on plants and other soil organisms. Pfu is a major constituent of the rhizosphere of plants. The rhizosphere is an active zone surrounding plant roots where soil microbes interact with the roots and each other usually in a symbiotic relationship. This is certainly the case for Pfu due to the benefits this microbe bestows upon host plants. First, Pfu produces many secondary metabolites that are probiotic for plants and can control bacterial and fungal plant pathogens. A major class of secondary metabolites produced are derivatives of phenol that display antifungal properties including 2,4-Diacetylphloroglucinolphloroglucinol, and phloroglucinol carboxylic acid. Secondly, Pfu also produces a type of antibiotics from phenazine that can be beneficial to both plant and microbe. Third, Pfu produces siderophores than can scavenge essential iron from the environment with very high affinity giving Pfu an advantage against other soil inhabitants that are less efficient at acquiring elemental iron. Siderophores are produced within the cell and excreted into the surrounding environment. Pfu contains outer membrane receptors that can transport iron-containing siderophores back into the cell. One specific siderophore, pyoverdin, has green fluorescent properties which give P. fluorescens its name.

Image of pyoverdin, also known as fluorescein.
Image of pyoverdin, also known as fluorescein.

In a later post, I will detail more about the rhizosphere and soil in general.