Answers to the Questions about the blog.

1. Refer to the last paragraph on page 1. The authors assert that B. anthracis forms three genetically homogenous clades within the B. cereus group, yet there is substantial pleomorphism in this group. First, define pleomorphism, and then describe how the authors explain this paradox.

Pleomorphism is defined in bacteria as the property of having a number of morphological forms. The authors explain how pleomorphism exists in the three homogenous groups by stating that there is very little genetic differences between the clades.  Therefore there are similar genes in the three groups but the genes still allow for different ways of life. This means that the genes of B. cereus can be regulated by their environment, and that it is mostly their environment that affects their differences. The authors give the example of the PlcR gene which is a transcriptional regulator and allows the organism to sense and respond to the environment.


2. State each of Darwin’s four postulates. Fully explain how the various populations (phage-infected vs. uninfected cells) of Bacillus anthracis in the “competitive microbial environment in the worm gut” (page 17) meet each of the four postulates for evolution by natural selection.
Darwin's four postulates are: 1. There is variation among individuals of the same species, 2. At least some of these variations are hereditary, 3. In every generation there are more offspring produced than can survive, and 4. Natural selection operates on populations (survival and reproduction are not random).

With regard to Darwin's first postulate, among the Bacillus anthracis there are specimens who, after being exposed to a group of bacteriophages, have emerged as lysogens. A lysogen is "a bacterial cell strain that has been infected with a temperate virus, one that does not cause destruction of the cell" (Dictionary.com). In this study specifically the exposure to a bacteriophage has given the anthrax unique "survival capabilities" including the ability to "block or promote sporulation"; "induce exopolysaccharide expression and biofilm formation"; and finally, "enable the long-term colonization of both an artificial soil environment and the intestinal tract of the invertebrate redworm, Eisenia fetida." Not all of the anthrax cells obtain every one of these characteristics when they are infected but even a single one could improve their survival. 

Darwin's second postulate is that some of this variation must be able to be passed on to the next generation. Once certain specimens have been infected by the phage, the bacterium can then takes over the "machinery" of the cell and can incorporate some of it's own DNA into the cell's genome. In the case of the Bacillus athracis, the bacterium "encoded bacterial sigma factors and the expression of at least one host-encoded protein predicted to be involved in the colonization of invertebrate intestines" into the anthrax cells allowing them to pass this on to the next generation. Also, the "shedding of phages by B. anthracis" scientists in this study theorized "could reflect a mechanism for DNA transfer (and thus niche expansion) among these organisms." 

When evolution is occurring, there will always be more offspring produced in each generation than can survive based on the resources or environment. This is Darwin's third postulate. In this study one of the most prominent abilities that the bacterium enabled the anthrax to do was to thrive in certain soil environments. The scientists conducted a test in which they placed Bacillus anthracis specimens into a soil environment "without a phage source as a control, [and there was] little or no survival was apparent at 24 weeks." When they placed anthrax cells that had been "co-cultured' with the bacterium, however, "there was a pronounced improvement in survival." As a result, they concluded that "B. anthracis phages that are either shed or added as free particles can lysogenize susceptible strains and confer the long-term survival phenotype in the soil milieu." The scientists also repeated this test in other environments and found that "regardless of the environment, all of the lysogenic derivatives tested survived up to six months while the parental ΔSterne strain declined steadily from the outset." 

And lastly, Darwin's fourth postulate is a little more difficult to apply to this scenario because this paper discusses a very controlled, detailed experiment. So natural selection is operating on the population of B. anthracis but survival is certainly not random as the scientists are choosing which specimens are infected with phages and which are not. However, the overall conclusion that they came to is that "B. anthracis phages that are either shed or added as free particles can lysogenize susceptible strains and confer the long-term survival phenotype in the soil milieu." So while survival was not random in this experiment, if the process were to occur naturally in a real-world environment it would agree with Darwin's last postulate. 

3. The bacteriophages described in this paper are able to confer “fitness genes” (page 2) to their Bacillus hosts. What do these genes allow B. anthracis to do ecologically? Compare Figures 1 and 10 to help address this question.
Figure 1:
Figure 10: 


Fitness genes, or lysogen conversion factors, are genes that are not essential for the phage lifecycle and are usually discussed with respect to virulence proteins and the evolution of pathogenic phenotypes.  However, they have recently been considered more with respect to "promoting environmental functions for bacteria and including metabolic enzymes, and transcriptional repressors for metabolic downshifts in nutrient-poor environments."  So basically, B. anthracis potentially goes through lysogeny as seen in Figure 10, which is the biological process where a bacterium is infected by a bacteriophage and the bacteriophage integrates its own DNA into the host sto that the host and the bacteriophage are not destroyed (dictionary.com).  The effects of this lysogeny with respect to ecological terms is that B. anthracis can be resistant to the soil antibiotic fosfomycin.  So, through this lysogeny, the B. anthracis become resistant to the fosfomycin antiobiotic and this would likely transmit to an animal that the anthrax was transferred to if it infects a host.


4. Think about the hosts for Bacillus species. Their anatomies serve as selection pressures on Bacillus populations. Apply Darwin’s four postulates to the coevolution of Bacillus anthracis and its hosts.
Darwin's four postulates are: 1. There is variation among individuals of the same species, 2. At least some of these variations are hereditary, 3. In every generation there are more offspring produced than can survive, and 4. Natural selection operates on populations (survival and reproduction are not random).

Among the hosts that are affected by Bacilus anthracis there are varying traits that affect the hosts probability of infection. One example of a trait that could vary and affect the Bacillus anthracis bacteria’s ability to survive is the intestine (specifically from the paper the red worm intestine). Bacillus antracis for part of its lifecycle resides in the intestine of its host.  The intestine could vary in surface area (number of folds) and this could affect how Bacillus anthracis is able to survive in the host. Bacillus anthracis for part of its lifecycle resides in the intestine of its host. There are no doubt variations in the intestines of species that are caused by genetic differences. These differences in the anatomy of the intestine will likely affect the bacteria’s ability to survive. These traits are encoded for by genes that are passed down from generation to generation. The hosts reproduce and produce more species than are capable of surviving. The hosts with the variations in their intestine that make it less susceptible to a Bacillus anthracis infection are more likely to survive and reproduce. The hosts that are more fit and do survive will mate with other fit hosts and will pass on their genes to their offspring. Meanwhile at the same time natural selection is operating on the Bacillus anthracis and the Bacillus anthracis that are able to reside in the intestine will survive and pass on their genes that allowed them to better adapt to the intestine.

Bonus: Biofilms are kind of a hot topic in multiple biological disciplines right now. Define and briefly discuss biofilms.

Biofilms are an assortment of microorganisms that grow on a surface. Biofilms have complex interactions within themselves between the varied organisms that they are made of. Biofilms begin with microorganisms adhering to a substrate. More and varying microorganisms that come along the substrate are then able to attach themselves to the substrate or, through some physical or chemical interaction, attach to the other microorganisms. The adhesion of one microorganism to another allows for a diverse amount of microorganisms to inhabit the substrate instead of only having microorganisms that are able to bind to the substrate directly. Secretions from these microorganisms can facilitate the transfer of nutrients to the microorganisms, protect the organisms or provide another avenue of attachment for microorganisms to the biofilm. The secretions, along with the layers of microorganisms help protect the biofilm as a whole. The secretions can protect the microorganisms from antibiotics and the outer layer of microorganisms help protect the inner layers from microorganisms as well. These forms of protection make biofilms resistant to conventional methods of disinfection. A common biofilm is the microorganisms in your mouth and teeth.

Additional Information:
Total credits as of 4/29/12: 7,622

An article that relates to our blog.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006532

Joe's Interview Response

1. Describe your feelings about or response to the interview.

 The interview was very interesting. Dr. Fisher is obviously a very intelligent person and I was very impressed with his vast knowledge on a variety of subjects. Although his knowledge of biology is superior to ours he did a good job of being able to explain things in a way we could better understand, and for the most part there was nothing that was completely above my head. I was also very interested to hear his background story and thought it was neat that he is originally from Kansas. Also I thought it was cool that his lab was the first to have images of the needle proteins.

2. What changes occurred for you as a result of your interview.

 One change that occurred for me is that I realized how complex the biological systems are that anthrax uses, and it also made me realize that in general that nearly all biological systems aren’t nearly as simple as they are sometimes made out to be in our textbooks.

3. Did anything about the interview disturb you?

 Somewhat related to my response to questions two is that it is kind of disturbing how complex these systems are. One thing that especially stood out as well was the fact that even if Dr. Fischer’s lab or other scientists figure out a way to stop anthrax (or any disease really) that it is possible (even likely) that anthrax would evolve and scientists would be forced to start their research all over again.

4. Describe the connections you found between the interview and your research & classwork.

 The connections Dr. Fischer made between genetics and evolution were very applicable to what we are talking about in class. It was cool to here him talk about some evolutionary concepts and think to myself “hey were studying that right now and I know exactly what he’s talking about”. It was especially relatable to class when Dr. Fischer talked about the genes evolving that code for the proteins and how its not the proteins that evolve but the genes that encode for them.

Claire's Interview Reflection:

1. Describe your feelings about or response to the interview.

Initially I was very nervous about the interview because we, a group of college students, were going to be interviewing someone with a Ph.D. and years of experience and research in his field about a topic that we had limited knowledge about. Dr. Fisher, however, was clearly very friendly and knowledgeable in his field but made a point to try and explain things in a way in which we could understand them. He even paused several times to make sure that he wasn't going too fast when he was discussing very complicated concepts.

2. What changes occurred for you as a result of your interview.

I really enjoyed talking to Dr. Fisher because it allowed me to see how someone took a childhood interest in science and made it into an interesting and successful career. Also, it is true that science classes tend to build upon each other but in general I've kept them separate and just focused on learning the material and succeeding in one at a time. Since doing this interview and studying the material in this class in particular, however, I've tried to look at how all these areas tie together, for example how crucially genetics and the things I learned last semester tie in to evolution.

3. Did anything about the interview disturb you?

Yes, the thing that disturbed me about this interview was just how "smart" diseases like anthrax are at invading your cells and taking over your body. Dr. Fisher's and many other scientists' work is trying to find a way to combat these, but it is still frightening how complicated it is to stop them and how efficient they are at their "job" and how long it will likely be before they can be eliminated.

4. Describe the connections you found between the interview and your research & classwork.

I'm hoping to continue my education after Rockhurst by entering a Masters program for Genetics, which I actually mentioned to Dr. Fisher (between Questions 5 and 6 of the interview), so hearing him discuss the field of genetics and how it can be applied to the evolution of diseases and all species having recently taken a Genetics course and being in an Evolution class currently was very interesting. It's always nice to see how concepts and theories that we learn in textbooks and in the classroom can be applied and used in the real world.

Misty's Blog Response

1. Describe your feelings about or response to the interview.
I really liked our interview for many reasons. Dr. Fisher was very nice and willing to help us and the things he had to say were very interesting and agreeable; however, a few of the things he talked about were above my comprehension level.

2. What changes occurred for you as a result of your interview?
I often times don't think about how diseases and other harmful factors affect more than just humans and he made me really thing about how anthrax affects animals besides ourselves in different ways.

3. Did anything about the interview disturb you?
Diseases and other harmful factors always disturb me when they are gone into in detail because of how easy it is for exposure to happen and infections to occur; however, it is just a fact of life that I obviously accept.

4. Describe the connections you found between the interview and your research & classwork.
Dr. Fisher went into a question about how evolution affects anthrax and other bacteria and viruses and how they can evolve to no longer be affected by vaccines or medicines intended to cure the affected organism so that they no longer are effective against the harmful factor.  He also went into how anthrax can affect two similar organisms in two different ways depending on their genetic make-up and these are all things we have gone over in class and done research for this project on.

Interview with Mark Fisher, Ph.D.

On February 17, 2012, we conducted an interview with Mark Fisher, Ph.D., a professor of Biochemistry and Microbiology at the University of Kansas Medical Center who has done a great amount of research on anthrax and the protein-folding of the bacteria that is responsible for the disease. He has also been published for his work with anthrax and more information on Dr Fisher can be found at http://www.kumc.edu/biochemistry/mfisher.html. Our interview is presented below:

1. Can you tell me a little bit about yourself and your background?

Dr. Fisher: I grew up in Kansas and was always interested in science from the time I was young, it thrilled me. I obtained a Bachelor's of Science from the Chemistry Department at KU and then went on to the University of Illinois where I received my Ph. D. in Biochemistry. From there I transferred to the National Institute, specifically the National Heart, Lung and Blood Institute. While I was there I first worked on oxidative modification in aging in proteins and then I formulated my own project and put that out to the world at the University of Kansas Medical Center.

At NIH I was one of the first researchers in a field that was a young field at that time and was involving the origin and the function of what they call "Heat Shock proteins" and it turns out these proteins are chaperone proteins. They help other proteins fold so they are "assistants" so to speak and they're called on when an organism is stressed. They're always around and they are a necessary component of the cell. They exist throughout life and they are absolutely essential and are involved not only in how proteins fold, they attempt to keep proteins from misfolding, but also how they disintegrate. They're pretty essential.

2. What lead you from there to specifically focusing on anthrax research with regard to proteins?

Dr. Fisher: Well one of the things that I noticed about these chaperone proteins is that they correct protein aggregation. And one of the most important aspects of bacterial toxins in particular is that these are all protein-derived toxins, from the diphtheria toxins to the botulism toxins to the tetanus toxins to even the anthrax toxins, exist in a free floating form that is soluble in water, but when they interact with cells they change their conformational state to a protein that can be inserted into the cell membrane.

And if they change their conformations outside the cell the proteins aggregate so we were interested in a) figuring out if we could capture one of these pre-aggregation forms and b) seeing if we could determine what these un-inserted forms look like. So we used the chaperone proteins initially to capture these forms that could puncture the cell membrane. And the protein that we are specifically interested in is one of the three proteins involved in toxin toxicity. It functions as a needle, it doesn't kill the cell outright but it helps to transfer the other two proteins into the cell and those two are the real cell killers. We are actually the first lab in the world to actually see a low-resolution structure of this needle protein.

3. So do you still currently work with anthrax? And what kind of research are you working on?
Dr. Fisher: Yes, I am still working with anthrax and actually we've gotten better at obtaining these images that we can now see large versions on the electron microscope. We've also been doing structural analysis, so under different pH conditions we can determine what kind of control regions are changing and if their conformation is the result of changing environmental conditions and so forth.

4. What kind of advances or progress do you hope the results of these tests will be able to lead to?
Dr. Fisher: Well these experiments will be very important in designing small molecule inhibitors that actually prevent the transition [mentioned above] from occurring. So our human health angle with this is that we need to understand how these bacterial toxins go from one form where they're non-lethal to another form where they have to unfold and refold into a new shape and insert into a cell membrane; and then those are the ones that we want to prevent from occurring. But in order to understand the transition from the one form to the other you have to capture the two pictures of the soluble and the membrane insertable form.

5. So understanding these transitions and how to prevent them is the key to fighting the toxins?
Dr. Fisher: Yes, and all of the work that we've been doing lately is involving not only being able to look at the transitions but understanding how fast these transitions occur. Which takes time obviously but we are very hopeful.

6. Evolution obviously occurs as the result of mutations in our genes so how can the theories of evolution be applied to your research with anthrax?

Dr. Fisher: Well when bacteria are confronted with something that can prevent their growth these bacteria then mutate. So you get different mutant strains of the same type of bacteria and understanding what regions can be variable and what regions aren't variable is important to understand because that's how proteins change. They change because of the genetics coding for them, the proteins themselves don't evolve it's the genes that evolve and allow the characteristics of the resulting protein be selected for.

It's important for us to understand not only the overall detailed mechanism of this but also the plasticity of these systems.  They are under genetic control and can actually evolve into a new form that is more highly infectious. An example of course is the HIV virus. You get infected with one virus but people don't die from that initial virus, it undergoes a microevolution and a person's system goes through a battle with it but cannot keep up and is eventually overwhelmed.  All of these micro-organisms, including the ones that cause HIV and anthrax, can change their "code" and as a result drugs that you've engineered so tediously can be circumvented by the viruses. 

7. And we've actually discussed in class how certain people's system are better at fighting HIV and how certain people, such as people with two copies of the CCR5 delta32 gene are basically immune to HIV; is this true of anthrax as well or does everyone's immune system pretty much equal in its resistance to it?

Dr. Fisher: Well anthrax is not as common a disease as HIV at least in humans, it's much more common in other animals, and there is variance in animals where you don't have as much of an effect of anthrax on one individual as you do on another. And these could be as subtle as just having more circulating proteins that are clipping enzymes like proteases that are clipping away at the toxins.

8. Have you ever worked with grid computing in your research?

Dr. Fisher: I know what it is very and I think it can be a very helpful tool but no I have never personally worked with it.

9. Finally, you are clearly well-versed in evolutionary processes and through your experiments have seen evidence of how organisms change; have you ever encountered someone who denied the existence of evolution and/or argued for the theory of Intelligent Design?

Dr. Fisher: Yes, I have many times and I do not avoid them, I confront them straight away. I usually approach it in the language that they're used to. The language of God, I explain, is written in a "book" of molecules not man-derived written word. This is where the ultimate aspects of God can come from because that is something that we as humans did not make. And an interesting thing about those people that believe in Intelligent Design is that they will accept microevolution in the form of bacteria and viruses evolving but they will not accept that macroscopic organisms can evolve. But evolution is the combination of numerous microscopic events which occur at the gene level all the time and I think one of the best arguments that one could make for the existence of evolution is there are virus proteins and viral genomes inserted into the human population. And the viral genes and human DNA co-evolve. Every human being on Earth has some so we are a walking history of evolution on this Earth. We are literally 3 billion years worth of information in books that are put on our genome.

And these enhanced retroviruses that insert themselves into our genome insert themselves into very precise regions of the DNA and these regions are the same for everyone across the population. And this insertion occurs at the exact same location in the genome of chimpanzees. So you can look at the "book" of the genome where the divergences and similarities occur among all organisms. So you can map evolutionary trees based on these enhanced retroviruses that have been inserted into the genome. Viruses have a huge impact on evolution and definitely affect how organisms move from one level to the next. And as I've mentioned, just like with HIV and anthrax, not all organisms are going to react to these viral proteins the same way. Some will be better at contending with them than others and that is the beauty of evolution.


Thank you so much for your time and all of these fantastic information.

Rosetta@home

At its center grid computing is a relatively simple concept that has extraordinary potential and power. It involves the linkage of multiple computers to form a singular network, which is then exponentially more powerful than any single one of those computer could possibly be on their own. Each grid is aimed at a specific goal that can vary wildly among different grids, from finding the next prime number to developing treatments for different diseases. Grid computing is becoming more and more prominent and it is an amazingly easy way for an ordinary person to contribute to amazing international and often philanthropic projects.


For our computer grid service learning project our group has decided to choose the grid Rosetta@home to connect to (http://boinc.bakerlab.org/rosetta/). This grid studies the 3-dimensional design of proteins, and ultimately hopes this information could help lead to the cure of several diseases. Proteins are known as the building blocks of life. And as we have been taught in numerous science classes, a protein’s function is greatly determined by the shape that it takes when it is folded by the golgi apparatus. However, scientists are not yet able to predict what shape proteins will take, but this is what the Rosetta@home computer grid aims to accomplish.

Images of examples of protein structure from the Rosetta@home grid.

The reason this breakthrough would be so incredibly significant is because if we are able to accurately predict the shapes proteins will take, it could lead to drug discoveries and cures for different diseases. Some of the diseases that the Rosetta@home group is focusing their research on include Malaria, Anthrax, HIV, Alzheimer's and Cancer. In the research of Malaria, for instance, a new development indicates that a newly discovered protein that stops cell movement by stopping the cell motor, could be a drug target for malaria treatments (Read more here: http://www.sciencedaily.com/releases/2011/05/110530152333.htm).

We will be focusing more, however, on Rosetta@home’s work concerning anthrax. In recent studies of anthrax, scientists have determined the structure of a protein involved in causing anthrax. It is one of several proteins that are secreted by the bacterium Bacillus anthracis, which can be seen below, known as oedema factor or “EF.” EF is able to “[hijack] one of the key intracellular proteins involved in calcium-triggered signalling pathways, at once disabling the protein and using it to stimulate its own catalytic activity” (Winstead). In doing this EF lowers the body’s ability to fight off foreign invaders and “[allows] infection to proceed” (Winstead). Additionally, scientists have discovered a “structural 'pocket' ” that they believe new drugs could be developed to attack (Winstead). This and other developments gives scientists hope of finding a cure for anthrax (Read more here: http://www.genomenewsnetwork.org/articles/02_02/anthrax.shtml).

Bacillus anthracis.

Now that we are connected to the Rosetta@home grid, we will keeping you updated on their work with anthrax and further detailing recent progress in this field of study.

Sources cited:
Winstead, Edward R. "Structure of the Third Deadly Anthrax Protein." Genome News Network - Home. 1 Feb. 2002. Web. 26 Jan. 2012. <http://www.genomenewsnetwork.org/articles/02_02/anthrax.shtml>.