AP Biology class blog for discussing current research in Biology

Tag: viruses

How the “unknown” of the human gut microbiome gets in the way of metagenomic studies…

Did you know that the greatest concentration of bacteria lives in your gut? At two or three years old we have a balanced microbiome. While we know a lot about the human gut microbiome, there is a lot that is unknown about it. There has been a lot of improvement in finding an “unknown microbiome” for example, shotgun metagenomics enables researchers to take a sample of all genes in all organisms and allows them to find an abundance of microbes in many different environments.

What we know: 25 Phyla, ~2,000 Genera, ~5,000 Species, ~80% Metagenome mappability, and 316 million genes

What is unknown?: Undetected unknowns, hidden taxa and strain-level diversity (~20% sequences not matching microbial genomes), functional unknowns (~40% genes without a match in functional databases)

For example, one study where researchers studied a stool sample from 2 lean African men and a stool sample from 1 obese European. In the stool, they found 174 new species never seen in the human gut before and 31 new genome species (which can help in later studies). Found within these new species was, Microvirga Massiliensis which has the largest bacterial genome acquired from a human, along with Senegalvirus which is the largest virus in the human gut. We definitely know a lot more about the human gut microbiome than we did, even though there is a long way to go.

However, organizing large numbers of draft genomes from uncharacterized taxa is challenging, and while performing well for bacteria, assembly-based metagenomic tools are less effective when targeting new eukaryotic microbes and viruses.

The human gut microbiome intestines in an obese person vs. a lean person

To make improvements in uncovering “hidden strain-level diversity” it is vital to alter sample-specific associations from the metagenomes and to additionally incorporate as many genomes for each species in reference databases. Most species are “open”, meaning they don’t have an upper bound on the size of accessory genomes and it may seem impossible to reclaim all strain-level diversity; however, preserving “the effort of cataloguing strain variants remains crucial for an in-depth understanding of the functional potential of a microbiome.”

The difficulty is that the microbiome contains viruses. The “functional unknown” of the human gut microbiome is the broadest and most challenging to delve and study further into because there is little known about understanding its pathways and genes. There is one creation though, that helped try and find out what was “unknown” about the microbiome, called the Integrated Gene Catalogue. The Integrated Gene Catalogue of the human gut microbiome which consists of 10 million genes. It groups genes into thresholds, thus the genes then fall into sub-units of gene-families. Locating these genes is only a small part of finding out what they actually do. For example, out of 60.4% of the genes that were annotated, 15-20% of the genes have been discovered, but are stilled labelled “function unknown.” These results show how little is known about genes, their functions, and what is current in microbial communities. There is not enough investment in microbiome research. It is difficult because there could be viruses that can be discovered; however, not enough time is being put into finding it.

Lastly, there is a lot of research going into the human gut microbiome. For example, Fecal microbiome transplantation is where stool from a healthy donor gets placed into the other patients intestine, this transplant usually occurs when more bad bacteria take over the good bacteria in the intestine. However, it could cause more disease which is why further investigation in the human gut can solidify that transplantation could overall prevent a bad bacteria take over. The microbiome field is open to all technologies. Understanding the function of the microbiome still remains the largest challenge researchers face, along with the biggest challenge that “targeting specific genes are irreplaceable”, technology should be able to provide solutions (including microbial transcriptome, metabolome, and proteome, and the automation of cultivation-based assays to scale-up the screening of multiple taxa and genes for phenotypes of interest.)


Alien DNA?

Our DNA has evolved over hundreds of thousands of years. This evolution was usually the result of natural selection. Scientists have discovered another way our genetics have been altered: virus DNA. Our DNA consists of 100,000 pieces of viral DNA and altogether those pieces make up about 8 percent of our DNA. Most of these genes are from endogenous retrovirus. Many viral genes produce proteins that affect our health in unexpected ways. Some of our ancient virus DNA may be protecting us from diseases and others may be raising our risks for cancer.

Viral DNA is neither good nor bad. It’s not that simple and the research being done on this part of our genome is just being started. In a recent study scientists engineered healthy cells to make a viral protein that is found in tumors. They concluded that the protein caused the cells to behave in a “cancer like way”. There are other viral proteins that play a crucial role in reproduction, known as syncytins.

This caused scientists to investigate other viral proteins. Five years ago Dr. Heidmann, a French cancer researcher, found a stretch of viral DNA that has gone overlooked and named it Hemo. She also found that versions of this protein was in other species and that the gene behind is have barley changed over thousands of years. The consistency of the gene throughout species shows that the protein must play an important beneficial role. Some preliminary research has shown it to be involved with helping the embryo develop a variety of tissue from stem cells.

Many things are still not known about this part of our DNA and how it affects us but researchers are working hard to find out everything they can. They are actively trying to figure out which viral proteins are beneficial and which are harmful. This research will help us understand a lot about our genome, evolution, and maybe even cancer prevention.

For access to other articles about this topic click here and here.


Ancient Viruses Do Good?

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Viral DNA. Sounds like something awful, but it isn’t. One type of viral DNA called endogenous retroviruses is something that can be passed down from generation to generation.

Recently a new protein, called Hemo, in the veins of pregnant women has been discovered. This protein is believed to be made by the fetus in the placenta. But, the effect of it is unknown. The cause of this is a gene from a virus that was formed more than one hundred million years ago. In fact, human DNA consists of 100,000 pieces of viral DNA. But, it is unknown exactly what the effect of viral DNA has overall.

Some are good as they protect from disease while others are believed to cause cancer. So, is it believed that Hemo is good or bad? Well, one theory is that it is a message from the fetus to the mother that dampens the mother’s immune system so that it does not attack the fetus, which is good. But, any mutations of Hemo could be harmful or even fatal. Other viral proteins play a role in the development of a fetus. Such as how viral proteins help embryos develop tissues. Early embryos may have come to depend on tricks that viruses once used to manipulate them. Scientists are currently trying to find out more about the topic themselves


Viruses are Like Felons, They Both Get Mugshots

Scientists at the Stanford University School of Medicine and three other schools have just discovered that a bacteria named Marinomonas mediterranea takes “RNA mug shots” to help recognize and defeat harmful viruses. The bacteria can take “RNA mugshots” or “DNA mugshots” depending on whether the invader is RNA-based or DNA-based.

Researchers want to use this technic to genetically form crops that have this virus-identifying property. Another use is to prevent viruses from infecting dairy products.

CRISPR is a new way of editing genomes that relates to this discovery. Bacteria takes pieces of DNA from cells and store them, also like “mugshots”.

RNA help DNA is coding, decoding, and expressing genes. By just getting a snapshot of a virus’ RNA or DNA, bacteria can identify this virus and destroy it in the future.

This finding is very new and so scientists are still studying how it exactly works and what its applications are. How do our readers think about it? Is this a surprising discovering or does it seem obvious? Were you aware that viruses have their own DNA and RNA? How do you think bacteria can apply this technic to other problems in the body, such as the regulation of cell production? Comment below on your scientific observations of this finding!

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Viruses: Good or Bad?

As we recently learned in class, scientists are attempting to use viruses to treat cancer and according to this article, scientists are inching closer and closer to success. The idea to use viruses to treat cancer stems from the discovery that when sick with a virus, cancer patients tended to go into remission.

Even though cancer cells can replicate quickly, they can’t defend against attacks as well as regular cells can. Thus the search is on for a virus that won’t damage normal cells but will attack cancer cells.  Many viruses were tried, for example, the “cat plague”  which was inserted into rural cats, and in most cases failed due to the return of the cancer or the development of a deadly infection.

However, in the 1990s, various steps were made by a few doctors that allowed this research to progress. First, in 1991, Dr. Martuza of Harvard Medical School  attempted using the HSV (herpes simplex virus) type 1 as a cancer fighter. He modified the virus by taking certain genes out and then injected the modified virus into mice with brain cancer. The mice first went into remission and then unfortunately died. Around the same time, Dr. Bernard Roizman of the University of Chicago found a master gene in the herpes virus that when removed could only slow tumor growth and could no longer overpower healthy cells. In 1996, Dr. Ian Mohr in NYU altered the crippled virus even more and attacked cancer cells with it until a mutant of the virus evolved and was able to replicate in those cells. Dr. Mohr and a student then made it so that the virus didn’t attack the immune system.

There are some great benefits using viruses to attack cancer. Viruses not only attack the cancer, but get stronger over time, unlike chemotherapy. They also produce an immune response that helps to attack the virus. The side effects of this viral treatment are less detrimental than those of chemotherapy . These side effects include nausea, fatigue, and aches.

Most recently, an engineered form of vaccinia by the name of  JX-594  is being tested against liver cancer and has already helped in doubling the survival rate of patients with this cancer. Though there are still hurdles to overcome, it is clear that great progress has been made thus far.

Intentionally making the flu deadlier?

In a recent New York Times article, research has been put into actually genetically enhancing viruses, specifically avian flu, to become more lethal by increaing its transmission. This might sound crazy but the scientists argue that being able to produce a more lethal virus will enable the scientists to come up with a better way of preventing a future epidemic. Other people are afraid that the enhanced viruses could accidentaly get out of the laboratory or be stolen by terrorists to cause an epidemic. Whatever the argument is, it is important for scientists to be able to better understand viruses and their ability to become a pandemic or not. From what scientists know already, the main factors for a virus to be lethal are how the virus is transmitted, what cells the virus affects, and where it enters the body.

Two seperate groups have been working on the avian flu virus, a group at Erasmus Medical Center in Rotterdam and the other at the University of Wisconsin. Dr. Ron Flouchier led the team at the lab in Rotterdam and they were able to modify the virus to transmit through the air for short distances to infect other animals, in this case ferrets because the flu behaves similarly to ferrets as it does to humans. Although they have begun to find ways to make the virus more transmissable, the number of modifications to the temperature the flu can withstand, the location where the virus attacks, and other factors to make the virus actually be threatening to humans is large. The avian flu has only infected 600 people since its discovery in 1997 and even though more than half of them died the chances of people actaully getting the flu is very low and there are vaccines for the flu.

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