A2: Microbes in the news

Article Title: Deepest Life on Earth May Be Lurking 6 Miles Beneath Ocean Floor

Author: Thea Ghose

Date: April 11, 2017

Source: Live Science

Link: https://www.livescience.com/58632-deepest-life-on-earth-possibly-found.html

Assignment author: Morgen Southwood

Summary-

There are mud volcanoes under the sea floor and they may be inhabited. Biological signatures in material that has risen to the surface could possibly be coming from microbial life 32,800 feet under the surface of the ocean floor. The organic matter are good indicators of the presence of life, but could also have been produced by abiotic processes.

Connections-

Reading this article reminded me of earlier in the semester when we discussed the origins of life and more recently in the semester when we discussed Bas-Becking’s idea. When we discussed the origins of life near under water vents we discussed the kinds of organic chemicals that could have been precursors for the first life forms, those same compounds were found in these mud deposits. When we discussed that life could/would be everywhere, I considered the presence of life beyond our atmosphere, but not beneath the crust of the earth. This article made me wonder what microbial super power could survive in those conditions.

Critical analysis. —

This article only spends one half of it’s very short article discussing the new discovery. I wish that there had been more details on the discoveries methods. Apparently the compounds came from rocks that were “spewed’ onto the surface, there was no explanation on how the scientists could be sure that any signs of life originated in the mud volcano, and wasn’t the product of contamination as the mud progressed to the surface.

My favorite sentence in this paper isn’t referring to the recent discovery; it’s within a paragraph summarizing other research on deep sub surface microbial life. The sentence reads, “ the deeper that scientists have looked the deeper life has seemed to go.’     I wonder if there is a limit to this, if scientist will one day conclusively say: no more life past this point. The researchers of the under sea mud volcano seem to think so. They made an estimate for the maximum depth that could support life. Considering a maximum temperature of 122 degrees Celsius and 1000x atmospheric pressure, the deepest Achaean environment would be about 32,800 feet below the surface.

This article was presented both scientifically, and in a way that could be digested by an interested member of the general public. Its lack of depth was compensated by links to relevant background information and relevant studies.

Question-

Will scientists ever be able to definitively state that an environment/ location is completely free of life without having to clarify “that we know of’?

 

A2: Microbes in the News- Scientists find a new treatment for antibiotic-resistant bacteria

https://www.ctvnews.ca/health/scientists-find-a-new-treatment-for-antibiotic-resistant-bacteria-1.3352187

CTV News

Article published April 3rd, 2017

Researchers from Birmingham University in the UK have developed an interesting alternative to using antibiotics for a certain rare lung disease that can be caused by several bacterium including P. aeruginosa. They would run a similar process to dialysis, called plasmapheresis, but instead of removing waste from the blood they would remove a certain antibody from the blood that was in excess, which prevented them from fighting the infecting bacterium. They would run this several times a week, replacing antibodies via blood transfusions, and this reduced hospitalization time and reduced the effects of it significantly, all without antibiotics. Research is being done to see if this is a viable replacement to some antibiotic treatments.

This relates to class material because we covered usage of antibiotics and how to prevent resistance. This would be a very good way to eliminate adding resistance to bacterium that can be fought this way significantly by not even using antibiotics.

I thought it was interesting how they are trying to find ways to avoid antibiotics completely, which would significantly decrease the worry of antibiotic resistance. It is a fairly new treatment, but it looks very plausible and accurate based on the reasoning in the article. It is fairly simplified for the public but is in depth enough so that the treatment process can be understood.

One question I would ask is how this could be expanded upon to more diseases beyond just filtering out antibodies from the blood. Could this be applied to other immune response diseases? People who are immune suppressed?

Parkinson’s Disease and Microbiome

“Gut microbe mix may spark Parkinson’s’

Science News Magazine online article

December 1, 2016

www.sciencenews.org/article/gut-microbe-mix-may-spark-parkinsons?mode=topic&context=60

 

This article describes several studies which, together, suggest that Parkinson’s disease is caused by the intestinal microbiome when it has a specific composition. It was found that the gut microbiome of diseased patients caused alpha-synuclein, the substance present in Parkinson’s patients, to clump in the brain compared to the gut microbiome of a healthy person transferred to mice with high levels of alpha-synuclein. In the second case, the mice did not show as many symptoms and the alpha-synuclein did not clump in the brain (this is what is believed to cause Parkinson’s disease).

We have discussed ideas of the human microbiome determining overall health. This has to do with the “ubiquity of microbes’, meaning they are found in all types of environments. We know that the bacteria in our gut produce byproducts while helping us break down and process our food. It is very interesting that they might be able to send signals to our brains. It seems like microbes must gain something beneficial by sending signals to the brain to make the organism act in a way that helps the microbe gain what it wants. We talked a little bit about microorganisms that infect insects to control them. The article was a summary of several peer-reviewed studies so I think they are credible. This is written in a very good way to communicate science to the general public since that is the purpose of this magazine. It pulls only the important parts of the methods and results to make it easy for the reader but also gives you enough information to critically think about it.

This topic makes me question many things like: What kind of chemical signals could microbes send to the brain to cause the symptoms of Parkinson’s disease? Is it a byproduct of their way of living or is it an intentionally released signal?

Microbes in the News: Researchers Uncover Clue about How Tiny Microbes Self-mutate.

Laboratory Equipment: Monday, April 3rd 2017 https://www.laboratoryequipment.com/news/2017/04/researchers-uncover-clue-about-how-tiny-microbes-self-mutate

Researchers just discovered a genetic element that enables a group of unidentified microorganisms to self-mutate. Researchers found genetic elements, called diversity-generating retroelements (DGRs), that enable the microbes to target their own genes for accelerated mutation. They found that a majority

An ultra-small cell of a bacterium that may be a relative of the self-mutating microbes.

of ac certain class of Archaea, as well as some yet-to-be-characterized categories of organisms closely related to bacteria, appear to have DGRs. The DGRs target the nucleotide adenine to initiate a new mutation. Much is still unknown about the newly discovered microorganisms.

This ties in with a lot of subjects that we have talked about in class, especially microbial evolution, because this shows how fast evolution and adaptation occurs in microbes.

I did find this story very interesting, and although much is still unknown about this subject, i think the article gave sufficient evidence and facts in order for the reader to understand the concept. I thought this was very interesting and i look forward to seeing further research on this subject.

The biggest question I had after reading this was, how? How can a microorganism self mutate? This is probably the biggest question that the researchers had as well.

 

A2: CRISPR

https://schaechter.asmblog.org/schaechter/2017/03/on-the-discovery-of-crispr-an-interview.html

In one day I had heard a clip on the radio about a thing called CRISPR that is a hot topic in genomics, and then I saw that radiolab had done a segment on CRISPR. So I figured I needed to look more into this  subject. The link above takes you to an interview with a microbiologist who played a role in discovering CRISPR and he talks about how he discovered the genetic sequences and talks about CRISPR’s role in microbes. The link below takes you to the radiolab podcast where you can listen to them explain CRISPR in a fun way, and they talk about its applications to human genetics. The rest of this post will refer to the link above: On The Discovery of CRISPR – An Interview.

https://www.radiolab.org/story/update-crispr/

Summary:  in 1992 Francisco Mojica was working on trying to sequence the genome of some type of halophilic archaea when he noticed a bunch of repeated, equally spaced sequences in the genome. Since genome sequencing was not very good at that time, they repeated there project many times and every time saw that the same regularly spaced sequences. He noticed this same pattern in the genome of E. coli  and continued to work with E. coli for this work. Mojica worked on other topics for 10 years before returning to study these repeated, equally spaced sequences. He talks about his difficulties publishing work, how hard it was for him to prove his hypotheses. He believes that CRISPR played an intricate role in the evolution of prokaryotes, and with the discovery of CRISPR  it opens up many area’s to study in the fields of genomics and biotechnology. (Radiolab references making super humans thanks to CRISPR)

Connections: In class we have talked about genome sequencing of microbes, microbial evolution, and characteristics of archaea. In lab we have actually gone through the process of DNA sequencing, and we are very lucky that we have the technology to sequences genomes faster, easier, and read them quicker.

Critical analysis: This subject is fun and interesting, and the fact that are so many places where you can find information on this topic means that this may be a big topic in science in the near future. CRISPR research involves many biological disciplines from microbiology, genetics, to possibly engineering. It will be really interesting to see what kind of work comes from these short, repeated sequences.

Question: Do you think it is a possibility that there could be CRISPR sequences in the genomes of our project isolates?

A Microbe Hunter Plies Her Trade In Space

Title: A Microbe Hunter Plies her Trade in Space

Date: March 14, 2017

Link: https://www.npr.org/sections/health-shots/2017/03/14/511891419/a-microbe-hunter-plies-her-trade-in-space

Summary: Microbiologist Kate Rubins has been investigating the unique microbiome of the International Space Station and establishing a microbiology lab in space. There has been 16 years of accumulation of the microbes brought by varying crews up from Earth, and microbes tend to stick around. While most of the microbes are harmless, some do have the potential to cause problems for crew, varying from infection to mold growing on the wall panels of the Space Station.

Microbiology in space is incredibly important to the future of space travel, be it for identifying alien life, preventing disease while in orbit, or simply improving the quality of life for spacefaring explorers.

Connections: We have been working to identify microbes from various environments and biomes, just as Rubins has, albeit from a less prestigious location. Being able to quickly and accurately identify microbes in all scenarios is something emphasized through the course, and Rubins is putting what we are learning to practical application whilst in orbit.

Critical Analysis: This article was actually a transcript of an NPR broadcast, and so read a little bit differently than most traditional news articles. It was filled with interview blurbs from Rubins, recollections of her time in space, and easy-to-follow explanations of her work. I know NPR works to tell stories as well as news, and this article was an interesting and engaging story. However, if you want the hard details about what Rubins was doing, or the specific microbial work done in the International Space Station, this is not the article for you. This is, more than anything, a story, and is not meant for conveying details. However, as a springboard for ideas, or an interesting illustration that your job can sometimes take you in strange and exciting directions, this is a good read or listen.

Questions: What other positions has NASA been searching for since it has stopped focusing on pilots? Rubins is a microbiologist, but what other branches of the sciences or other professions have gone to space?

Discovery of an HIV reservoir marker: New avenue toward eliminating the virus

Date: March 15, 2017

Source: CNRS (Délégation Paris Michel-Ange)

Summary:  A protein marker has been discovered that allows cells carrying dormant HIV viruses to be distinguished from healthy cells. This will allow the isolation, and hopefully the destruction of such HIV reservoir cells in order to make remission possible.

Link: https://www.sciencedaily.com/releases/2017/03/170315144033.htm

Connection: We have recently been discussing the reproductive cycles of viruses and how some varieties have the ability to go dormant for periods of time and remain undetected by the host.The dormant viruses inside of reservoir cells may reemerge at any given time.In the case of HIV, the ability of the virus to do so is the reason why patients must receive treatments for the rest of their lives in order to suppress the virus.

Analysis: This article is relatively short, but informative. The writing is easy to follow in layperson terms, but still conveys the discovery effectively. The journal is cited at the bottom of the page, so if one wanted to read the entire discovery in scientific terms, they would be able to. It appears to be scientifically sound, and considering it was published in Nature, that is another mark of its credibility. The fact that something like this has been discovered poses great possibilities in eventually curing HIV, and it was exciting to see this when I was looking up articles.

However, they did have a very small study group, and I hope to see this expanded upon in future studies. Only 12 HIV-positive individuals were checked for the marking protein, and while it was found in all the individuals, I think that for good  science it should have more verified successes before considering it a solidly proven fact.

Question: How long has this research been in progress? It states that the idea of identifying reservoir proteins has been around since 1996, so has this research been in progress for the last 21 years?

New Factors Contributing to Parkinson’s Disease

Source: Kateryna Kon/Shutterstock

Title: Even More Evidence Has Linked Parkinson’s Disease to Our Gut Bacteria

Source:  Mark McRae from Science Alert

Date:  March 4, 2017

https://www.sciencealert.com/evidence-piles-up-linking-parkinson-s-disease-with-the-bacteria-in-our-gut

Summary: Recent evidence has found that Parkinson’s disease may not only be influenced by the brain, but by gut bacteria too. Also, people’s bodies and the microorganisms they have may influence how they respond to the treatment provided to battle Parkinson’s disease. Even though studies are starting to make the link between microbes and Parkinson’s, these studies can help lead microbiologists and other scientists in the direction of making better medications and treatments for those fighting this disease.

Connections: There was a brief moment in the article that mentioned making medications specific to the individual that needs it based on the microbes within their system, which involved genetics. The bioinformatics lab gives us a glimpse into what goes into identifying bacteria based on their genetic sequence and the different functions that the bacteria’s genes carry out.

Critical Analysis: The title of the article caught my attention because I have been hearing more and more about Parkinson’s disease recently. Also, I was curious to see what the author had to say about other factors that play a role in this disease, instead of being just one component of the body. However, the way that the author wrote the article was a little confusing at times because it seemed as though the author would start to go into more details about the studies that they discuss, but then they would quickly become vague what the researchers were saying based on the results from the studies. Also, there were times that the author seemed to be a little disorganized when it came to presenting their thoughts and backing up their argument with a study.

Question:  Since more studies are starting to link bacteria with the cause of Parkinson’s disease, is there a way to protect against these specific bacteria increasing the chances of someone getting Parkinson’s?

What’s Going on With Our Phones?

Title: Scientists Discover 3 New Species of Microbes Growing on Mobile Phones

Source: Press Trust of India from Gadgets

Date: March 6, 2017

https://gadgets.ndtv.com/science/news/scientists-discover-3-new-species-of-microbes-growing-on-mobile-phones-1666732

Summary: A lot of people have their cell phones attached to their hands wherever they go, but what researchers have recently found is that phones are starting to become a home for a diverse array of microbes. In the midst of their research, scientists came across three new species of bacteria, as well as one new species of fungi. Not only that, but the researchers found that people’s phones contain more species of microbes than what they found on toilet seats. On the plus side, these scientists found that from the phones that they sampled, there were no dangerous bacteria species.

Connections: The microbial world is extremely diverse between the different species of bacteria, fungi, and archaea. Bacteria and fungi can flourish in any place that provides them with the optimal growing conditions, like temperature or amount of light. We have briefly explored how diverse the Bacteria domain is, as well as discussed different types of environmental conditions that assist with the growth and survival of bacteria based on their composition.

Critical Analysis: Reading through this article, I was surprised about how many species of bacteria and fungi grew on the surfaces of our phones. Not only that, but the fact that the researchers behind this study discovered 3 new species of bacteria and 1 new fungal species just further proves how diverse microbes can be. The article presented the findings from the study that would stand out and catch the audience’s attention, so I feel as though the article was scientifically accurate, even briefly including some of the methods used to obtain samples. The author even pointed out where the researchers could enhance the study by taking samples from phones that belong to those who work in the medical field. This article was easy to read and was written in a way that was somewhat entertaining and attention grabbing, which helps the audience stay interested in the material presented. I also liked how I was expecting the article to be all doom-and-gloom, but the authors had a positive tone.

Question: How would the microbial diversity be on phones that were sampled from people that work in healthcare locations, like a hospital? Would there be deadly bacterial strains and would this effect the sterility of an environment that is supposed to be completely sterile?