A2: Microbes in the News – Scientists Discover Nearly 200,000 Kinds of Ocean Viruses

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Article:

https://www.quantamagazine.org/scientists-discover-nearly-200000-kinds-of-ocean-viruses-20190425/

Summary:

Researchers have assembled data from a global sampling expedition using genomic analysis and have increased the number of known oceanic viruses twelvefold.

Connections:

This is a story of people using the tools which we have been using to study the viruses we have been studying and improve the body of knowledge we have in this field.

Critical Analysis:

While microbiology has been studied in some manner since the early days of science the changes in the accuracy or our tools and the price of using them can dramatically change what we are able to accomplish. This article is just one example of how much more there is to learn in this field.

Question:

With a single study able to make such a large impact on the amount known, the question becomes how much more is there to know? I would not be at all surprised to see another twelvefold increase with the next study and another after that. If there is one thing that I have learned from this class it is that the microscopic world holds a multitude of secrets yet to be discovered.

A2: Microbes in the news — Yeast produce low-cost, high-quality cannabinoids

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Article:

Yeast produce low-cost, high-quality cannabinoids

Summary:

Synthetic biologists at UC Berkeley have engineered brewer’s yeast to produce some of the main components in marijuana including THC and CBD among others.

Connections:

The developing field of synthetic biology is based on taking the tools that we are using in class, such as whole-genome sequencing, and our knowledge of how microbiology works to modify and create solutions to modern problems.

Critical Analysis:

Synthetic biology is an amazing and quickly developing field with the potential to take   a future we have only seen in science fiction and turn it into reality. This is an incredible technical achievement showcasing our developing mastery over the fundamental building blocks of life. I knew something like this was coming, I can see the economic incentives for this, I am sure the people behind this will end up fabulously wealthy, but I still can not stop myself from facepalming. Of all the amazing and wondrous potential synthetic biology holds… this had to be the top of my news feed today.

Question:

I cannot begin to imagine the legal ramifications, how the hell do you regulate something like this?

A2: Microbes in the News – New Anti-CRISPR Proteins in Soil Bacteria

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Article and Link: New anti-CRISPR proteins discovered in soil and human gut (ScienceDaily)  https://www.sciencedaily.com/releases/2019/02/190205144338.htm

Summary: CRISPR is a natural bacterial immune defence, but some bacteriophages (or viruses) have developed anti-CRISPR genes that cause bacteria to lose immune defence when infected. New anti-CRISPR proteins were discovered by using protein functionality tested across a variety of environments, rather than using DNA and culturing. Their discovery could lead to the development of better technologies in the emerging field of CRISPR gene editing.

Connections: This article demonstrates the prevalence and possible uses for bacteria in today’s medical world. If bacteria could be used to produce proteins that create more precise gene editing with CRISPR, gene editing may have a very real future in human society. The way the researchers discovered new anti-CRISPR proteins is also a testament to the diversity of microbial life and how not all microbes can be cultured.

Critical analysis:  I find this article fascinating, because I am very interested in how cellular function, protein production and genetics can be used in the medical world to produce new treatments, drugs and cures for disease. With improved CRISPR technology, it may be more realistic to use gene editing to treat diseases such as cystic fibrosis. Unfortunately, this article was not very well written and did not explain the methods of the researchers in a way that is accessible to the public. The writing was very hard to follow and I had to read it multiple times before I began to understand the premise of the article. However, from my level of understanding there were no factual inaccuracies even though it oversimplified genetic editing and the way CRISPR works.

Question: How does the presence of anti-CRISPR genes in bacteria affect their susceptibility to antibiotics? Could they be more susceptible since anti-CRISPR proteins target bacteria’s “immune systems’?

A2 Microbes in the News

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Article and link

“Gene expression study sheds new light on African Salmonella’
Science Daily, January 15, 2019 https://www.sciencedaily.com/releases/2019/01/190115144045.htm

Further Reading: https://www.ncbi.nlm.nih.gov/pubmed/30645593

 

Summary

A variant of Salmonella typhimurium (ST) 313 is responsible for the deaths of approximately 400,000 persons ever year in sub-Saharan Africa. Researchers at the University of Liverpool are attempting to understand how the genome of African S. typhimurium, which enters the bloodstream and spreads through the body, differs from the global strains of S. typhimurium which causes gastroenteritis.

By culturing the different Salmonella strains in different environments they could simulate differences of stages within the human infectious timeline. They then analyzed the transcriptome of these two strains and found a multitude of gene expression variations as well as RNA variations. These coincided with metabolic and plasmid differences within the two strains.

Connection

This correlates with the information that we have learned about variations in culture mediums in class. As well as what we will be going over in lab. The ability to culture this bacterium in different environments allowed for the researchers to study the gene expression at essentially different time frames in the bacterial life cycle. Say, from an environment similar to that outside of the human body, and then an environment within the human body.

Critical Analysis

What I found interesting in this article is that the phenotypic expression of genes within one strain has caused such a different in its ability to act as a pathogen. I also never thought of culturing microbes in different environments to simulate gene expression. I just thought you would culture them in their ideal environment and study them as such. Thinking about it now, it makes a great deal of sense to do this, not only to study the activity of pathogens, but to perhaps study microbes and why they fit into their respective niches.

The forum for this article is a scientific forum, and though it is technical it is written in a way that someone who isn’t specifically a microbiologist (such as myself) can understand what is being studied and the accomplishments that this group of researchers have made.

Question

The question that I have is a technical one. How is it that they were able to find out the gene expression of these bacterium from culture? I know that the genome can be sequenced using various methods, but how would one know or ascertain which portions of that genome are being expressed at any given time.

-Samantha Smith

A2: Microbes in the News Assignment

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Microbes in the News !

Over the course of the semester, post 3 different stories involving microbes  from the popular media and then read and comment on 3  posts by other students.

 

Points: Total possible = 30 points. Earn up to 8 pts for making a post and 2 points for posting a comment. Create 3 posts and 3 comments over the course of the semester.

Deadlines: Posts can be made as soon as you’d like, but for full credit you must post them by these deadlines:

Post 1: Feb. 8

Post 2: April 1

Post 3: April 15

All comments: April 15

 

Learning Objectives:

– Increase your awareness of microbiology and its role in society

– Expand and apply your knowledge of microbiology

– Practice critical thinking by analyzing popular news media for scientific accuracy

– Develop questions about microbiology

– Help your peers and yourself understand microbiology by answering their questions

 

Instructions:

Over the course of the semester, create 3 separate Microbes in the News posts on the course website, and then read and comment on 3 Microbes in the News posts by other students. Be sure to follow the guidelines below in order to qualify for  full credit.

 

Guidelines for creating a post:

– Article and link: Enter the title, source, and date of the article and create a link to it. Articles should be from any popular media source (newspaper, magazine, podcast, blog,  etc.) that others can access without hitting a paywall. Any relevant story is acceptable, but challenge yourself to find stories that are current (~within the last 3 months) and that haven’t yet been posted by your peers, whenever possible.

– Summary: Write a short summary of the story (just a few sentences is sufficient).

– Connections: Explain briefly how this connects to what we’ve covered in class.

– Critical analysis: Explain what you found interesting about this story, and what (if anything) you learned. Comment on whether you think the story was scientifically accurate or not. If you noticed any factual inaccuracies or aspects of the story that might inadvertently confuse or misinform readers, identify those and provide a more accurate explanation. Also comment on how this was written. Do you think it did a good job of communicating science to the public? Why or why not?

– Question: Write a question about microbiology that you had as a result of reading this story.

– Categorize: Categorize your post as “A2: Microbes in the News’ using the categories menu on the right. This will ensure I can find it and give you credit.

– Tag: Tag your post based on any relevant microbiological themes by choosing from the tag menu (below categories on the right). Use existing tags when possible, but you can add new ones if needed by clicking “+Add New Category’ link just below the list of tags. This will help us find stories on relevant themes. You can also use these tags to search for other students’ stories on themes that interest you.

Guidelines for commenting on a post:

– Read the news story and the students’ post about it

– Create a comment and write a response to their critical analysis. Do you agree, disagree, or have more to add?

– In your comment, answer their question to the best of your ability. This might require some independent research.