CUDDLY ENOUGH TO KILL: LIMITED TIME DEAL!!!!!

(This is a collaborative project by Grace Lund and Connor Ito)

ARE YOU TIRED OF SCIENTIFICALLY INACCURATE PLUSH MICROBES?

DO YOU FEEL A NEED TO CUDDLE AN EBOLA VIRUS, BUT DON’T WANT THE LETHAL SIDE EFFECTS?

DOES YOUR LIFE NEED MORE TUBERCULOSIS?

THEN LOOK NO FURTHER!

Cuddly Enough to Kill is the most scientifically accurate plush microbe collection on the market! Featuring Ebola virus, Giardia lamblia (Giardia),  Mycobacterium tuberculosis (Tuberculosis),  Bacillus anthracis (Anthrax), and  Escherichia coli (E. coli)!

First up is Ebola!

Our Ebola plushes feature glycoprotein studding, represented in soft and huggable polyester! These Ebola also show twisted tube shape of the actual virus with none of the painful, life-threatening effects of the real thing!

Next up, one of the most common causes of waterborne disease- Giardia!

 Giardia are extremely transmittable microscopic parasites which cause gastrointestinal distress and can be lethal in the case of children, the elderly, or the immunocompromised! We have represented the shell of Giardia with machine washable fleece and their signature flagella in blanket yarn!

Now, Tuberculosis, affectionately known as TB!

Our TB are rendered in plush red fleece to represent the unique waxy cell coating, which must be dyed with acid fast stains, resulting in their red color! These microbes also feature Plasmid Pocketsâ„¢! Collect and share plasmids with all your microbe friends, transferring antimicrobial resistance, virulence factors, and more!

Now featuring Bacillus anthrasis, known commonly as Anthrax!

These cuties are the only obligate pathogens of the genus Bacillus! In our plushies, the wonderful purple color represents their Gram-positive cell coat! Now featuring Spore Sachelsâ„¢, the best way to store your spores in the case of poor growing conditions! If you or your friends both have Anthrax, you can form chains of the rods with the new feature  Streptobacilli!

Now, everyone’s favorite: E. coli!

 These fluffy little fellas are Gram-negative gastrointestinal bacteria covered in pili! Each one comes with four flagela that it’ll use to swim it’s way right to your heart! Or intestines! But be careful, these microbes have been known to be dangerous!

BUT WAIT, THERE’S MORE!  

No, really, we have a surplus of microbes! They’re replicating so fast, we can’t keep up with them! And we want to pass these pathogens on to you! Come look at our selection and take home a microbe today!

 

(All silliness aside, we set out to create accurate representations of microbes with the features of each organism in a hands-on method that could be used to demonstrate how diverse the microbial world can be. We thought about how to appeal to all ages, yet still be as accurate as possible while on a college budget, and decided to make plush microbes. Each microbe has its own unique feature, and we tried to cover a variety of different anatomies. All in all, this project took a long time to complete, with our final microbe count at 28.)

Researchers discover ‘switch’ that allows microbes to recognize kin

Researchers discover ‘switch’ that allows microbes to recognize kin

Published: March 27, 2017

https://phys.org/news/2017-03-microbes-kin.html

In our microbiology class, we learn a lot about how bacteria will interact with each other, but don’t really mention how they might be recognizing their own kind.   A plasmid shared among your species is much better than one shared with a competitor in the end.   And we also learned how beneficial a biofilm is, but not how a bacteria would know it can be a part of the biofilm.   In this article, we learn of TraA receptors —the cause of this recognition.   Digesting a study that looked at Mycococcus xanthus, this particular receptor was discovered to help recognition of M. xanthus cells for outer membrane exchange.   Additionally, different strains of bacteria have different TraA sequences, further supporting this receptor as a receptor to help with recognition of other bacteria of the same strain.   An interesting reason for the recognition receptor had to do with outer membrane exchange (OME).   The paper discussed that if different bacteria were to go through OME with each other, there might be toxins exchange that the recipient (being of a different bacterial strain) would then have no antidote to.

The article also discussed that the bacteria in question are phagocytes, and so they are of interest in the agriculture world.   So, as these would be great for getting rid of plants’ pathogens, it only makes sense that there would be interest in how they distinguish each other from other microbes.

One confusing part of the study is the way they present the ability to recognize different TraA sequences, saying one amino acid (AA) changed is enough to cause no recognition.   The way that the information was presented had me asking myself, “Is it a specific AA that when changed makes it so that the bacteria don’t recognize each other or is it that changing any AA would be enough?’

Waste-munching bacteria could make nuclear stores safer

Waste-munching bacteria could make nuclear stores safer

Published: 11 April 2017

https://www.newscientist.com/article/2127588-waste-munching-bacteria-could-make-nuclear-stores-safer/

As we learned about in class before, through research shown to us by Dr. Leigh, that some microbes use Uranium or other such things as a food source.   For that reason, when I was this article, I thought it might be interesting to see it there was any progress made.

As part of a radioactive waste disposal plan, the UK is hoping to put the radioactive waste deep underground and to cover it with cement.   The problem with cement (as stated by the article) is that it will create conditions too alkaline for microbes to grow.   To test this theory, a research team studied a similarly-conditioned site.   It was seen that there were microbes that were able to withstand such conditions.   In alkaline conditions, there is a possibility of the uranium to form soluble complexes with isosaccharinic acid and to leak out, but with the presence of microbes, the isosaccharinic acid would be degraded by them, which would help to stop these leaks.   An additional benefit of the microbes is that some break down H2, which would stop the gas from building up pressure and causing a radioactive gas leak.

One nice thing about this study was seeing the use of the words “carbon source,’ as well as the author describing that the bacteria that break down uranium and other metals (such as neptunium) use it “in place of oxygen’ thereby representing the use of oxygen as an electron acceptor.   The way it is presented is very interesting and makes me thing that it does a good job of making the information accessible to the public.   The paper also expands on the findings, suggesting using them for decontamination of drinking water, such as we saw in the study presented by Dr. Leigh.

One thing that is lacking in this paper is differentiation of microbes, albeit this might make the article harder for the general public to consume.   For this reason though, I wonder, are the microbes mentioned through the paper the same microbes or are different ones used in different scenarios (I find the latter more likely)?   Additionally, I wonder, are the microbes ones that would naturally be present and persist in the given environment or are they being introduced?

“Big Bang Theory Theme ‘ Microbiology Parody

The song I wrote for my art project was inspired by the Barenaked Ladies song from Big Bang Theory, one of my favorite TV comedies. I tried to incorporate a variety of material from throughout this semester, from before the atmosphere had oxygen to the power of our tears. If you want to listen to the actual song that inspired this work, here’s the link:  https://www.youtube.com/watch?v=CMSYv_Z4SI8

Below are the lyrics to my song (I’ll be presenting in class on Wednesday), I hope you enjoy it!

Microbiology Art Project Big Bang Theme Microbiology Parody

Microbes in the News Assignment: Post #3

Article and link: “Too Clean for Our Children’s Good? The Checkup’ by Perri Klass, MD, The New York Times, April 17, 2017.

https://www.nytimes.com/2017/04/17/well/family/too-clean-for-our-childrens-good.html?rref=collection%2Ftimestopic%2FBacteria&action=click&contentCollection=science&region=stream&module=stream_unit&version=latest&contentPlacement=3&pgtype=collection&_r=0

Summary: This article talks about the many various ways in which our children are protected from interaction with microbes, including giving birth by caesarian section, bottle-feeding, and possible exposure to antibiotics. Such protection on the one hand affords protection from disease but on the other hand offers greater risk that children may experience complications of the “built environment.’ It is a concern that living in such a clean, controlled environment could lead to an underdeveloped immune system and subsequent health problems which may have otherwise been avoidable had the body been exposed to a diverse array of microbes at a young age. In order to combat this problem, it is recommended that young children be introduced to these microbes in the outside environment through “controlled exposures’ in the form of either “natural exposure’ consisting of interaction with their environment or through a type of vaccine yet to be developed.

 

Connections: This article include discussion of the development of the human microbiome, its importance in the overall health of an individual, the avenues by which children are typically first exposed to microbes, and also the concept of vaccination with microbes in order to improve health. All of these are topics which have been mentioned or discussed over the course of the semester.

 

Critical analysis: I liked the contrast that the author provided between the microbes found outdoors as opposed to those found within the “built environment.’ While I had naturally assumed that the inside of a house or apartment may be “cleaner’ than the outside world, I had not given much thought to the members of the microbial populations to be found in each of the two environments; in reality, the inside of a dwelling is not necessarily any more microbe-free than the outside, it is instead simply inhabited by a different, and possibly narrower, variety of microbes. I did not detect anything scientifically inaccurate or confusing in this article, and think that it did perform an adequate job in relaying this information to the public. The author did not get too technical in any of their explanations, yet clearly stated the anticipated problem, reasons behind that belief, and also the possible solutions to the problem.
Question: Are researchers suspecting that the health problems mentioned are primarily due to inadequate exposure to pathogenic bacteria? Or do interactions with the non-pathogenic bacteria also play a role in shaping the immune system of children? What kinds of “natural exposures’ are parents advised to pursue in order to assist their child’s immune system to develop properly?

Microbes in the News Assignment: Post #2

Article and link: “New HIV reservoir discovered: Findings reveal a second target for cure research’, Science Daily (it should be noted that the article on Science Daily sites the University of North Carolina Health Care as their source and mentions that the original findings were published in Nature Medicine on this same date), April 17, 2017.

 

https://www.sciencedaily.com/releases/2017/04/170417114806.htm

 

Summary: This article describes scientists’ recent discovery that there is another cell within the human body which can act as a reservoir for HIV in addition to T cells: the macrophage. This discovery that macrophages are susceptible to infection by HIV is very important to current research focusing on the treatment of AIDS: this tells researchers that a successful treatment or cure would have to be effective in ridding the virus from both T cells and macrophages. One investigation found that viral replication within macrophages is effectively repressed when antiretroviral therapy is administered; however, the study also found that this effect is only temporary. Following treatment conclusion, macrophages still act as reservoirs for the virus and therefore remain capable of reinfecting the host. More research must be conducted in order to find the most effective way to resolve HIV infection of macrophage cells.

 

Connections: This relates to information we have discussed over the course of the semester in that it discusses a virus, HIV, and also cells involved in the immune response (T cells and macrophages). It also relates to the resolution of disease through treatment and also the ways in which viral cells can find ways to persist inside a host even following treatment; both of these are subjects which were briefly touched on in class this semester.

 

Critical analysis: I found it interesting to learn that HIV can also afflict host macrophage cells in addition to the host’s T cells. It has been known for some time that HIV targets T cells, but I had not heard of any other types of cells being specifically targeted by the virus. I also found it interesting that the antiretroviral therapy typically used in treating HIV infections in T cells does not work effectively on macrophages. I expect that the story is scientifically accurate as I have not seen indications to the contrary. I also did not find anything confusing in the article that would need to be corrected.  I believe that they did a good job in relating this news; it seemed as though they kept their audience in mind, and focused on relating the pertinent details and implications of this discovery without making the article too technical for those who may not have the background to understand a technical explanation.
Question: What are the most significant differences in terms of structure between T cells and macrophages which would cause antiretroviral therapeutic (ART) agents to be effective on T cells but ineffective in macrophages? Which ART’s were tested on the macrophages? What is their mechanism of action? Are scientists already aware of the specific reason that the ART does not work on macrophages?

A2: Microbes in the News – The ‘Dark Matter’ of the Microbial World

The ‘Dark Matter’ of the Microbial World

Sarah Zhang, March 7, 2017, The Atlantic

https://www.theatlantic.com/science/archive/2017/03/archaea-sequencing-challenges/518535/

Summary: Archaea have been historically understudied but they actually are an important part of the human microbiome. Since the genomes of archaea are widely unknown the use of common primers based on 16S rRNA gene sequencing has failed to identify the diversity of archaea that are present in the microbiome of primates, including humans. When sequencing was done on feces samples using archaea primers instead of universal primers, many more archaea species were identified –  in humans the difference was 37 species with arcane primers versus 1 species with universal primers. The most common archaea species found were methanogens. This difference is most likely due to the fact that universal primers are made with common bacterial species in mind. With metagenomics this scenario is likely to change in the near future –  we are now able to sequence the entire genomes of the species found in our samples so it is likely that the extent to which archaea are present in primates’ microbiomes will start to be more understood.

Connections: In class we briefly covered Archaea. This article cites an interesting cycle – the microbes that we cannot culture  are not studied as often. We base future studies on what we know (culture methods, genomes) so scientists tend to expand more on previous knowledge rather than studying completely new and unknown species. I believe that this will change soon, but when primers were the main tool in sequencing genomes I could see how this would happen. Scientists simply did not have enough information and tools to fully characterize Archaea.

This article did a good job of communicating the extent to which Archaea are not fully understood. They probably should have explained more about the fact that Archaea are not a type of Bacteria even though they are prokaryotes.

Question: What is the proportion of Archaea in the human microbiome? Are they essential in nutrient absorption and even production?

A2 Microbes in the news: Fungal infection ‘threat’ to human health

Fungal infection ‘threat’ to human health

James Gallagher, BBC News, July 5th, 2016

https://www.bbc.com/news/health-36702215

Summary: This article aims to describe the extent to which fungal infections can be pathogenic to humans. Often when people think of fungal infections, they may not necessarily consider that these type of infections kill one million people per year. Also, there are no vaccines available for fungal infections. Three major groups of fungi are responsible for the infections. People that are immunosuppressed are most vulnerable to these infections.

Connections: Fungi are eukaryotes, which means that they share many cellular mechanisms with the eukaryotic hosts that they infect, such as humans. This explains in part why it is so difficult to make vaccines against and treat fungal infections. Since antibiotics rely on differences between the pathogens and host for their targets, if the pathogen and host are similar, there are fewer cellular mechanisms available for the antibiotic to target.

Critical analysis: I though that the numbers in this story were interesting. I was not aware that approximately 1 million people are killed every year by fungal infections, and that there are three main categories of fungi that are responsible for these infections.

Question: Do any vaccines against fungal infections exist? What is their mechanism?

Getting antibiotics as a baby may have lasting effects on brain, behavior

Getting antibiotics as a baby may have lasting effects on brain, behavior

https://arstechnica.com/science/2017/04/getting-antibiotics-as-a-baby-may-have-lasting-effects-on-brain-behavior/

Published: April 5, 2017 at ArsTechnica

This article looks at a few different articles having to do with gut microbiome and their effects on the human brain in terms of behavior.   The main focus is a later paper in a series which looks as the exposure of baby mice to antibiotics given before and after birth.   The mice were split into two groups were one had penicillin introduced through the mother while in the womb and to themselves when they were born, with a later group added in which mice had the penicillin as well as were given a probiotic.   The group that had the penicillin had 42 percent of the population that were aggressive as opposed to the 9 percent in the control group.   Additionally, the antibiotic group appeared to be less social and a little less anxious.   The probiotic mice also had a thinner blood-brain barrier.   The group with the probiotics introduced had some of the effects of the antibiotic blocked.

Being that we talk a lot in class about how helpful a good gut microbiome is and how bad it is to overuse antibiotics —especially those that are more broad-spectrum, the contents of this article are no real surprise to me.   Even talk of cytokines being increased in the brains of exposed mice is a concept that I can understand thanks to learning about then with the immunology portion of class.

Overall, the article does a pretty good job at telling the story of the paper to the general public.   It goes as far as to include a section to discuss some of the limitation of the discussed study, such as the fact that the period of exposure to penicillin was quite long as well as the fact that the exposure before and after death was not differentiated in the study.   My only issue with the paper was that in one of their background statements, they say that, “gut microbes have been caught making most of the neurotransmitters our brains use to regulate themselves,’ but yet the link they provide leads to a paper that seems to more-so talk about the way that our neurotransmitters will influence the gut microbe, not vice versa (though the full paper was a paid paper and not free to view).

Question:   If there is a chance for the probiotics to help block the effects of the antibiotic use in infancy, would it be possible for probiotics to be used in a longer trial such that they eventually reverse the behavior issues that arise from the use of antibiotics?

A2: Microbes in the News – Amoeba can help kill bacteria protected by biofilm

Article:  Study finds amoeba “grazing,’ killing bacteria usually protected by film (April 17, 2017)

Source: University of Wisconsin-Madison

Study finds amoeba “grazing,” killing bacteria usually protected by film

Summary:

An Amoeba species called Dictyostelids  is capable of penetrating biofilm in order to eat the bacteria within. Bacteria tested were  Pseudomonas aeruginos,  Pseudomonas syringae,  Klebsiella oxytoca and  Erwinia amylovora.  All these bacteria are capable of creating biofilms and were harmful to humans or plants. This also opens up further studies of methods of killing bacteria without resorting to antibiotics, which the bacteria may grow resistances to.

Connection:
We’ve learned about how certain microbes can create biofilms to protect and help with survival. This article is about how we can get around that. Also my isolate happened to be a bacteria capable of creating biofilms (S.epidermidis)

Critical Analysis:

Most of the article was regarding the scientists’ steps in finding out about this amoeba rather than the actual science behind it. However, it did use many quotes by the scientists so it did give assurances on the accuracy of the report.

Question:

What is the molecular mechanism of how the amoeba can “eat” biofilm?

Will using amoeba to kill bacteria be safe for humans/plants in vivo?