Biochemists' discovery could lead to vaccine against 'flesh-eating' bacteria

Necrotizing Fasciitis, also known as 'flesh-eating' bacteria, is a bacterial infection that damages tissues in a short period of time. This infection can cause death in the individual. One of the most common bacteria that causes this infection is group A Streptococcus.

There are some treatments that can be done against this infection, but it mostly involves antibiotics and surgeries (Necrotizing Fasciitis, 2016)

As with other bacteria, group A Streptococcus has a protein coating, and the reason that there is not a vaccine for it is that group A strep has different types of strains. These strains have different protein coatings. The protein coating is called the M protein.

When bacteria enters the body, the immune response of the body immediately tries to fight against the bacteria by using antibodies. The antibodies have to be specific for that bacteria's protein coating. Since there are many strains of group A strep and each have different M proteins, then the body that armed up with antibodies specific to a strain of group A strep will not work for another strain of group A strep. That made it hard for scientists to find a vaccine that fights against this bacteria. However, a group of researchers discovered C4BP. This is a human binding protein. This binding protein binds to not just one M protein, but the majority of M proteins of the group A strep. 

Knowing this, biochemist wanted to study the interactions between proteins of the M proteins and C4BP using computers. These studies allowed the biochemists to find patterns that were hidden between all the M proteins that they were studying. 

These biochemists now have the idea that a vaccine can be developed that gives antibodies that act like the C4BP in that it recognized many M proteins.

A vaccine is know being developed by chemists at the UC San Diego, and with collaborations of Nizet, an infectious disease expert.

The biochemists' published paper can be found at https://www.ncbi.nlm.nih.gov/pubmed/27595425

When I was younger I remember listening about a 'flesh-eating' bacteria on the news in Bolivia. I remember feeling really scared of it. For a while I was really scared that I would get something like that, or that anybody in my family would get it. Due to this worry of mine, I started reading all sorts of articles about it, but could not find a specific cure for it that does not include amputations. Seeing the title of this article then called my attention.

References

Biochemists' discovery could lead to vaccine against 'flesh-eating' bacteria. (n.d.). Retrieved March 27, 2017, from http://www.biologynews.net/archives/2016/09/05/biochemists_discovery_could_lead_to_vaccine_against_flesheating_bacteria.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A%2Bbiologynews%2Fheadlines%2B%28Biology%2BNews%2BNet%29

Necrotizing Fasciitis: A Rare Disease, Especially for the Healthy. (2016, June 15). Retrieved March 27, 2017, from https://www.cdc.gov/features/necrotizingfasciitis/

Study Reveals How Ionising Radiation Damages DNA and Causes Cancer

This article is focused on how ionising radiation in gamma rays and x-ray, which we are frequently exposed to can damage our DNA and cause cancer. Previously, the unfortunate thing is what has yet to be figured out is how tumors are actually cause by these harmful forms of radiation.

From the article it says, "Dr Peter Campbell from the Welcome Trust Sanger Institute who led the study, said: "To find out how radiation could cause cancer, we studied the genomes of cancers caused by radiation in comparison to tumours that arose spontaneously. By comparing the DNA sequences we found two mutational signatures for radiation damage that were independent of cancer type. We then checked the findings with prostate cancers that had or had not been exposed to radiation, and found the same two signatures again. These mutational signatures help us explain how high-energy radiation damages DNA.' " 

Often times when DNA is damaged, a mutational signature is shown. Dr. Peter Campbell, through these signatures was then able to track the patterns of the growth of tumors and how radiation reacted to the further growth of cancer is patients. 

One type of mutation found is a deletion in the DNA. Another is called balanced inversion. What this means is the DNA is cut in two places and the cut strand of DNA then spins and connects in an opposite orientation. This type of mutation does not occur naturally in the body but high-energy radiation could be strong enough to have this happen.

Of these mutations, Dr Sam Behjati, clinician researcher at the Sanger Institute and the Department of Paediatrics, University of Cambridge, said: "Ionising radiation probably causes all types of mutational damage, but here we can see two specific types of damage and get a sense of what is happening to the DNA. Showers of radiation chop up the genome causing lots of damage simultaneously. This seems to overwhelm the DNA repair mechanism in the cell, leading to the DNA damage we see."

These mutations cause by radiation and the signatures they leave could provide insight into how these tumors would rapidly grow. By following the mutations and looking into the damages cause to the DNA scientists have been able to see the harmful affects of ionising radiation and the affects it has on the body and the risks of cancer it can cause.

-Chad Lords

The Strange World of Nighttime Open-Ocean Diving

Will Ford
BIO 1610

The article that I chose focuses on what to me is a very interesting topic because it shows just how much we still have to discover in biology. It starts off by explaining how at night deep sea plankton migrate up closer to the surface than usual. Along with these plankton many of the othere deep sea fish who feed on them also go up closer to the surface. This causes a huge variety of fish to be much more easily observed by people because they are so much closer, all you need is your basic scuba diving skills. However with this "Blackwater Diving" even the most seasoned scuba diver can be thrown completely out of his element because you encounter animals that you would have never ever seen like that in their natural habitat.

This type of deep water diving started first in Hawaii and is currently practiced in only a handful of locations around the globe. In Hawaii dives are lead weekly just a short boat ride off the shore. However after arriving to the dive zone it usually still takes a while for someone to summon the courage to get in from the fear of the unknown below them.

This fear of the unknown has caused many to speak out saying that this type of diving should be avoided because there are so many potentially dangerous sea creatures that you may encounter and there is evidence of these encounters. The author gives an explanation of why he doesn't fear Blackwater Diving any more than regular writing how in reality we come in contact with just as many highly dangerous animals during the daytime when diving and just as in the light they are normally scared of us.Photographer Jeff Milisen is who gathered the data and he makes the claim that really what causes the fear of Blackwater Diving is really just the fear of so much that we are unfamiliar with.

I really enjoy this article in relation to biology because it goes beyond just looking at and studying things in a lab and takes us to what biology really is, it shows us life in its different forms. After all that what biology is all about, teaching us how life itself keeps functioning and with so many things that we still dont know in the ocean its really cool to see that we have access to some of that and that we have only scratched the surface with the studies so far.

A Virus, Fished out of a Lake, May Have Saved a Man's Life

The most common forms of medicine used to fight bacterial infections are antiobiotics; however, in the case of a man Dr. Ali Khodadoust, a virus was used to kill the serious infection that was nearly killing him. Clearly, a virus doesn't seem like the best form of medicine, but a virus-using method called phage therapy has actually been used for over a century. Back before antibiotics were discovered, bacteria-infecting viruses called bacteriophages were used to treat infections. This method became outdated and was never studied enough because of the submergence of antibiotics. But, when the bacteria killing Dr. Ali Khodadoust was resistant to antibiotics, the use of page therapy was turned to.

In 2012, Khodadoust had to have a coronary artery bypass, in which there was a piece of plastic mesh patching placed on his aorta. The mash patch end up having a bacteria on it called Pseudomonas aerugino that created a massive infection on the aorta. This bacteria is virtually harmless to healthy people, but can be extremely harmful to someone with a weakened immune-system, such as someone with cystic fibrosis, which we talked about in our first case study. 

Antibiotics were tried, but the bacteria was resistant to them. A fistula, which is essentially a hole, formed on his chest. The hole became infected by the bacteria as well. For three months he was on large amounts of antibiotics that were only helping a little bit, and carrying an IV port with him. The doctors didn't know what to do because they were scared of spreading the bacteria. Just as Khodadoust was falling into a "miserable medical limbo", a scientist named Benjamin Chan came with an idea. He wanted to try phage therapy on the infection. All they had to do was find bacteriophages that killed infections like Pseudomonas aeruginosa. 

After searching for weeks, a sample of water from a Dodge Pond in Connecticut came up. Bacteriophages from the water were tested and worked on the Pseudomonas aeruginosa sample! They called this perfect virus OMKO1. Chan and the other doctors made a plan to use this OMKO1 on the infection and then kill off any remaining bacteria with strong antibiotics. This plan was a risky one to be tried on Khodadoust, but something had to be done -- it was do or die for him. Chan and the other doctors got the operation approved by the FDA and did it. 

Five weeks after the surgery, Khodadoust was in his homeland of Iran and had to be rushed into surgery to stop massive bleeding from a bone poke in his fistula. After the surgery, they tested him for Pseudomonas, and there was no trace at all. The phage therapy had worked! Miraculously, the virus had worked against the bacteria and they concluded that OMKO1 was capable and worth studying much further. 

I found this article incredibly intriguing and awesome. I never knew that viruses, which are normally looked at in a negative aspect, could be used in a positive way. I think it shows how cool biology is -- how the medicine we may need could be all around us. This article and assignment definitely make me want to read more on these websites.


-Connor Lemmon

Can Facebook’s Machine-Learning Algorithms Accurately Predict Suicide?

Joshua Reber

Biology 1610

Can Facebook’s Machine-Learning Algorithms Accurately Predict Suicide?

            We as humans love our social media. Many of us are avid users-for example there are 1.23 billion active Facebook users daily. Why? Talking face-to-face is messy and emotionally involved–we don’t have time to think about what to say, we have to read facial cues and body language.

Online, we have time to construct and and be open. This gives us the opportunity to position ourselves the way we want to be seen. We hear daily about how the current generation is struggling with bullying, and how it has turned into something digital.

   This article begins by talking about a story of a young girl who through Facebooks new live video feature filmed herself talking, and even showing signs that she was about to commit suicide. Her friend saw this and alarmed the police, but they weren’t able to get there in time to save her life. This caused a lot of alarm in the Florida area, and Facebook is the first to start doing something about it.

The article says this: “To reach its at-risk users, Facebook says it is expanding its services that allow friends to report posts containing signs of any suicidal or self-mutilation plans and it provides a menu of options for both those individuals and the friend who reported them. Choices include hotlines to call, prompts to reach out to friends and tips on what to do in moments of crisis. This tool will now be available for Facebook live streams as well. Similar reporting systems exist on a number of social media platforms including Twitter, Pinterest and YouTube. Facebook is now also piloting a program that will let people use Messenger, its instant messaging app, to directly connect with counselors from crisis support organizations including Crisis Text Line and the National Suicide Prevention Lifeline (NSPL).”

Various programmers are working on developing software that acts as a robot to identify keywords and behavior expected from a victim of suicide. These robots and software will then be able to provide various hotlines and numbers and resources that lead to help. Facebook stated that tens of thousands cases are reported by friends who are concerned by a friend to see if they can get some help with suicide prevention.

“This ultimately is an effort that makes a lot of sense,” says Jessica Ribeiro, who is a psychologist at Florida State University. I am in complete agreeance with her. I really like this article because I know many people who really do struggle with these things, and are having hard trials with it all. This article also interests me because I am a social media user, and find it interesting to hear about what kind of protection the various platforms are offering their users so they can feel safer. I believe if they can dominate this software, without it being pushy on people, it really could be beneficial and serve a lot of people. It's also interesting to think on a biological level about the various chemicals that are being secreted when we post online, and how we react to reading posts from friends/family. Suicide in this nation is one of the top 10 reasons for death, and is now 2^nd overall cause of death for youth. I encourage everyone to read this article, not only to hear about this cool idea, but to also be aware of the issue.  

The reference came from Scientific American: http://biologyinthenewsspring2017-tuesday.blogspot.com/2017/03/joshua-reber-biology-1610-can.html

Ethical Guidelines on Lab-Grown Embryos Beg for Revamping, Scientists Say

Ethical Guidelines on Lab-Grown Embryos Beg for Revamping, Scientists Say, it may be time to update the currently observed 14-day rule as a benchmark

         This article was about synthetic biology and the growing of an embryo that passed the 14-day observation mark. Which is usually the time when the embryo is developing tissues and right before they start developing a nervous system. The article also explained that during this time it is the last time an embryo can divide. The article goes on with George Church who is a synthetic biologist and geneticist, he explains what he does in his lab. For example, growing organoids to function like hearts, lungs, kidneys, and the brain. He uses them to test out drugs and hoping one day they can be used for failing body parts. The idea of going over the 14-day mark triggered some opinions from the bioethicists. Insoo Hyun for example says, “Between synthetic biology and artificial intelligence a future might not be far off in which we have to ask whether something created in a lab is truly alive.” He goes on by saying that we are getting into experiments that question what it means, to be human and what it means to deserve moral respect. That being said there are some committees that regulate embryonic research, but lit it states in the article, “Synthetic biology falls between the cracks, though, with no one having such clear authority to regulate the work,” Finally the article comes to a close with church saying that from his experience he has seen more problems come from under regulation as oppose to overregulation.

I found this article really interesting, because of a few reasons. The first being that synthetic biology is growing day by day. New discoveries for synthetic organs that are being used was really interesting. Reading other scientist views on synthetic biology was interesting as well because, not all of them believe this new discovery is not ethical. I really liked reading this article, I liked seeing scientist tell share their own opinions and backing them up as well.

 -MS

https://www.scientificamerican.com/article/ethical-guidelines-on-lab-grown-embryos-beg-for-revamping-scientists-say/