Assignment ll: Microbes in the News

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Can airborne viruses survive in water?

https://www.sciencedaily.com/releases/2017/04/170421091523.htm

This article discusses an equine herpes virus and its ability to survive in water. This causes a problem for shared water among animals. It also gives insight into viruses that can survive outside of their preferred conditions.

The first thing that came to mind after reading this article is the infectious game we played with the beach ball. This was the same lecture we talked about possible ways an infection can be passed: airborne, contact. However, for me, a combination was never considered.

An airborne virus also being able to survive in water makes the area spreading of that virus that much wider. The article mentions that even when the animal with the virus is absent, other animals were getting the infection through the shared water. This is important because trying to maintain the spread of an infection is only possible when you know all of the pathways of infection.

My question is: Have viruses always been able to survive outside of their ideal environment?

Assignment ll: Microbes in the News

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Bacteria’s DNA fingerprint suggests it could be spreading via food distribution

This article discusses the spread of Clostridium difficile, a microbe that causes gut infections. C. difficile  is an important topic of discussion because it appears to be transmitted through food, resistant in some people, seen in a lot of hospitalized patients, and it can be dangerous. To track the source of this bacterium, scientists have been using DNA fingerprinting. Dr. David Eyre, the researcher of this topic, has been promoting washing hands to prevent the spread however, he thinks it is beyond this because there are different strains appearing together in different countries.

This topic ties into a couple of our lectures. We’ve discussed resistance, the human microbiome, and washing hands (soap) as being a way to kill bacteria.

I find this topic important especially since Clostridium difficile appears to be widespread and affecting certain countries. DNA fingerprinting is a great method for finding the source of a spread and I think if scientists continue to practice this kind of research we could get to a place where we can stop a disease before it begins.

My question for you is: Will this be good enough? What other ways can we prevent the spread of an infection?

https://www.sciencedaily.com/releases/2017/04/170421210846.htm

 

Microbes in the News Assignment: Post #3

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— 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?

A2: Microbes in the News

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Antibody helps detect protein implicated in Alzheimer’s, other diseases

https://www.eurekalert.org/pub_releases/2017-04/wuso-ahd041417.php

Summary: The article discusses research looking to find less invasive ways to identify and then track the progress of neurodegenerative diseases like Alzheimer’s. They have accomplished the first step by crafting an antibody which binds to the protein tau, which is present in tangles when damage to the brain is occurring. The antibody allows tau to stay present in the blood and accumulate long enough to be observable via blood tests.

Connection: The article discusses the use of an human antibody, but in a way we didn’t really cover in class. The antibody is not used as a flag for the destruction of a microbe or “not-self” entity in the body, but rather keep an entity around long enough to track its concentrations.

Critical Analysis:  This article does an excellent job of explaining the issues related to diagnosing neurodegenerative diseases, as well as the way in which the protein tau is associated and was identified as a potential measurable product for blood tests. Though the study has only done limited preliminary human trials, they were able to magnify the presence of tau in the blood of individuals with known neurodegenerative diseases. I believe the article did a great job of translating the innovative way in which scientists approach problems like that of diagnostics, and the interdisciplinary cooperation and literacy that is at the command of these researchers to accomplish what was discussed.

Question:  Would this antibody have the ability to track damage as it accumulates in individuals like football players, perhaps as a longitudinal study to gain more data and a predictive model for brain damage?

A2 Microbes in the News

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A Taste For Pork Helped A Deadly Virus Jump To Humans

 

https://www.npr.org/sections/goatsandsoda/2017/02/25/515258818/a-taste-for-pork-helped-a-deadly-virus-jump-to-humans

In 1999, in a small town in Malaysia, a scientist named Dr. Kaw  Bing Chua made a discovery crucial for the restructuring of the agriculture and farming industry across Malaysia (as well as Singapore, the Philippines, and several other countries). Chua discovered the virus later to known by the name of Nipah. Chua, a grad student studying virology at the time pinpointed this virus as one spreading across the country, yet no one at the time believed it.  Over the course of the next year a disease more deadly than Ebola was spreading rapidly throughout the town of Nipah, Malaysia. It eventually caught the attention of the government, and since most common viruses were spread through mosquitoes, the government treated it that way. However, after months of efforts to decrease the rate of spreading, nothing was working. This is when Chua comes back into the story. Chua was adamant that the virus in question was not in fact spread through mosquitoes, but actually through pigs. He came to this conclusion when he observed that the only demographic of people not getting the disease were Muslim, and hence were not eating pigs. Chua connected with a lab in Fort Collins, Colorado where he was able to see the virus through a special camera at their lab. The virus was identified and confirmed to be one that spreads through livestock. This led to the researchers at the CO facility contacting the Malaysian government,  who then immediately switched procedures and began focusing on stopping the spread between pigs and pigs to people.

This relates strongly to what we’ve been discussing most recently in class.  Learning how a disease spreads is critical for studying how to stop or slow it. Once the Malaysian government realized that Chua’s observations were correct, they changed policies throughout their nation. The entire farming industry was turned over and reshaped in order to minimize the spread of infectious diseases, such as the deadly Nipah virus. It really struck me in this article that the key to reducing outbreaks is to start by preventing them in the first place. The article elaborates on how serious a threat diseases like measles pose for humans. Nipah, like measles, is a respiratory virus. It spreads through close proximity, like when the pigs lived in extremely close quarters, but it also can spread just through the air. This is why taking advantage of any available immunizations is key to reducing outbreaks of potentially deadly pathogens. One question that stuck with me after reading this article was how specifically is this virus adapting to its conditions? The first outbreaks of Nipah were only due to pig to human transfers, but as of late, the virus spreads from human to human.

 

 

A2: Microbes in the News!

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Fungi have enormous potential for new antibiotics

https://www.eurekalert.org/pub_releases/2017-04/cuot-fhe041917.php

Summary: This article explores recent research into the genome of 24 different fungal species in order to identify antibiotic and other bioactive compound production genes. This study has resulted in the discovery of over 1000 pathways for generation of bioactive compounds with pharmaceutical application.

Connection:  The article could be characterized as part history of the use of antibiotics and the rise of antibiotic resistance. We have at length discussed the prevalence and mechanisms for bacterial antibiotic resistance as well as the known pathways for antibiotic production in microbes like fungi.

Critical Analysis:  The studied referenced in the article shows the promise of new antibiotic and even anti-cancer medications as a result of identifying these genomic pathways in fungi. The researchers believe that the knowledge gained from these sequences will also improve the efficiency of production and efficacy of existing antibiotics. At one point in the article, they refer to the predictive capability of the researchers experiments with the new sequencing data, claiming that not only could they predict the chemicals these fungi were capable of making, but identifying new versions of the same antibiotic chemicals. The reader must infer from the phrasing of this part that the researchers were able to trace the gene and find fungi that were previously unknown to have the ability to produce that particular antibiotic. The implications of information like that open the door wide to not only new means of production, but new variants of chemicals that have otherwise been fighting an uphill battle against antibiotic resistance.

Question:  If it is true that the researchers found antibiotic production previously undiscovered in some fungi, they use the example of the chemical yanuthone, are these inactive genes that must be activated, and how are they accurately and consistently activating these genes to produce this chemical?

Microbes in the News Assignment: Post #2

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— 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

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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

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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?

Microbes in the news: Deadly, Drug-Resistant ‘Superbugs’ Pose Huge Threat, W.H.O. Says

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Deadly, Drug-Resistant ‘Superbugs’ Pose Huge Threat, W.H.O. Says

Feb 27, 2017, The New York Times

https://www.nytimes.com/2017/02/27/health/who-bacteria-pathogens-antibiotic-resistant-superbugs.html?_r=1

Summary: Superbugs, or antibiotic resistant microbes, have been declared a threat to human health by the World Health Organization. They kill approximately 25,000 Europeans and 23,000 Americans each year. The victims are usually patients who are either older or have some form of immunosuppression. As antibiotic use has emerged in medicine over the past 100 years, so has antibiotic resistance. Different antibiotic resistant strains of microbes can be restricted to certain geographic locations or even to particular hospitals. However, with air travel becoming more frequent and widespread there is a tendency that these strains will spread throughout the world.

Connections: Antibiotic resistance develops as microbes are exposed to antibiotics and spreads rapidly among microbial populations via plasmids. As we expose pathogenic microbes to antibiotics, those with resistance are selected for, which means that we must continually monitor antibiotic use so that resistance does not become too widespread.

Critical Analysis: I thought that it was very interesting that the World Health Organization has highlighted antibiotic resistance as a threat to global human health. There is a certain degree of social responsibility that comes with prescribing antibiotics to patients. Every time a pathogen is exposed to an antibiotic, it is possible that resistance will emerge. In addition, it is becoming increasingly difficult to find new antibiotics since they rely heavily on exploring mechanisms in the microbes that are different from the host. Eventually it will become more difficult to indemnify these mechanisms and antibiotic treatments may be less beneficial  to hosts.

Question: How prevalent are MRSA infections in the US? Is there anything that we can do to prevent their proliferation?