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Interviewer: A new tool that could completely change how we diagnose infectious diseases, up next on The Scope.

Announcer: Examining the latest research and telling you about the latest breakthroughs, the Science and Research Show is on The Scope.

Interviewer: I'm talking with Gabor Marth, professor of human genetics at the University of Utah and co-director of the USTAR Center for Genetic Discovery.

Diagnosing infectious diseases is still a significant problem in medicine. Right now in the clinic, you either do a culture or maybe a PCR test to see what's infecting a person. You have co-developed a tool called Taxonomer that's taking a completely different approach.

Gabor: Taxonomer is a software tool that is able to look at DNA fragments, which is what current technologies are able to produce from blood from an infectious disease patient, and identify the organisms that are present in that sample.

These types of tools, in my opinion, are very likely to replace the tests that you mentioned, that are based on specific hypotheses. We have to know what the strains that we are looking for in these patients, whereas tools like Taxonomer will be able to look at the DNA sequences and tell you upfront what pathogenic organisms are causing the patients disease.

Interviewer: So if you have a patient that's sick, you take a little blood, you have to get the DNA from that blood sequence for all the genetic material, I guess. And then that sequence information goes in the Taxonomer, and Taxonomer catalogues everything that's in there.

Gabor: Yes, as you mentioned, in traditional clinical tests you would have to ask "Does this patient have this particular strain of, which specific pneumonia strain this particular patient has." Sometimes these experiments fail. Some of the strains go better in the media that are used in laboratory tests than others. When the same data goes to a Taxonomer you just get an unbiased view of which strains and what proportions are present in the patient. That will help the physician diagnose the patient much faster, and in a much more objective manner.

Interviewer: So there are some really stand-out characteristics of Taxonomer. These are based on the software called Iobio, which is what you developed, correct?

Gabor: Taxonomer itself is the engine, it is the software that is able to take a DNA fragment and tell you which organism that DNA fragment presents. And it's married to Iobio, which is a web-based analysis platform that my laboratory is developing, that allows interactive, real-time and high visual representation of the data.

Interviewer: So yes, one way I've heard it described is that it's like putting a super computer in the hands of your average user, it has that much power behind it. But it's accessible on the internet.

Gabor: This is actually an accurate description because the computational power that allows Taxonomer to run is enormous but all that is hidden from the user. It's what's called the backhand of the architecture, there is a powerful computer sitting in the background that performs the computation in very, very intensive classification job. But what the users see is almost immediate response and almost immediate results.

Interviewer: And so before, this type of analysis took a lot longer and probably had to be done by a specialist, right? A bio-informatic specialist. But now anybody could do it. Is that the idea?

Gabor: Many, many things that the average user will be able to do. Of course, this is not to say that there is no longer need to for a . . .

Interviewer: We don't need you anymore.

Gabor: More involved analysis and expert analysis, but what Taxonomer will be able to do, it will be able to give a scientist, or even a lay-person, an immediate view of what is the overwhelming characteristics of the data. For example, we have examples of an Ebola patient. And when you look at the viral composition of the blood taken from this Ebola patient, you will see that pretty much 100% of the viral load in this individual is Ebola. So that's a very, very obvious and easily interpretable answer to the question of what's making this person sick.

Interviewer: Well like you said, a lot of the strength of this tool is that it's very visual, and that helps people take in information in a different way. Can you talk about that a little bit? Why you think that's an important component.

Gabor: That's how the human mind works. Experts can be trained to look at large data files and textual outputs coming from software and interpret that data in a scientifically meaningful fashion. But our human brain doesn't quite work that way. We like to see things, we like to use the brains innate analytical abilities to start from an image to develop an understanding. And that is the underlying philosophy behind the Iobio project.

Interviewer: In a few years how do you envision Taxonomer, in particular, being used?

Gabor: I view this that its applicability is going to be very wide. This is going to be a very wide and generally applicable tool. Some of the applications that we can foresee today will be infectious disease identification in the clinic that will require expert review of the data. Moving forward, the obvious application will be pathogen identification in the field, under field conditions.

Once the technologies are developed for portable and faster DNA sequence can be used under field conditions. This is only scratching the surface, checking sanitary conditions in restaurants and many applications that we can think of now and many even more applications that will become clear in the future.

Announcer: Interesting, informative, and all in the name of better health. This is The Scope Health Sciences Radio.

Dr. Gellner: Your child really has chicken pox. Will old-fashioned home remedies work or do you need to take them to the pediatrician? That's our topic today on The Scope. I'm Dr. Cindy Gellner.

Announcer: Keep your kids healthy and happy. You are now entering The Healthy Kid Zone with Dr. Cindy Gellner on The Scope.

Dr. Gellner: So what is chicken pox? Chicken pox is a highly contagious disease caused by a virus. If your child has chicken pox then your child was exposed to the virus 14 to 16 days earlier. Symptoms of chicken pox include multiple small red bumps that become thin-walled water blisters. The classic appearance of chicken pox is what doctors describe as a dew drop on a rose petal.

Those clear water blisters become cloudy water blisters, and then they pop and they become open sores, and finally they dry out and are covered with brown crusts. This cycle all happens within the first 24 hours of this bump appearing. These bumps will crop up for four to five days and they usually start on the head, back and abdomen. They do not start on the arms and the legs. The rash will eventually spread to the arms and legs and possibly the mouth, eyelids and privates, but they start in the middle of the body.

There is usually a fever as well. The fever is usually the highest on the third or fourth day. Children start to feel better and stop having a fever once they stop getting new bumps. The average child gets a total of 500 chicken pox sores, and it may take two weeks for all the scabs to fall off.

Chicken pox rarely leaves any permanent scars unless the sores become badly infected or your child repeatedly picks off the scabs. However, normal chicken pox can leave temporary marks on the skin that can take 6 to 12 months to fade. Once a child has had chicken pox he will usually never get it again. Very rarely, a child may have a second mild attack of chicken pox.

If your child truly has chicken pox, they'll look pretty miserable. So how can you help them through this? The best treatment for skin itching is a cool or lukewarm bath every three to four hours for the first few days. Add four tablespoons of baking soda, oatmeal or cornstarch per tub of water. Don't worry. Baths don't spread the chicken pox.

Put calamine lotion on the itchy spots after the bath. If the itching becomes severe or interferes with sleep, give your child a single dose of an antihistamine. Acetaminophen may be given for a few days if your child develops a fever over 102. There is some controversy with giving ibuprofen to children with varicella but most doctors think it's now safe. Do not give your child aspirin ever. It's especially important not to give children and adolescents with chicken pox any aspirin because of the link with Reye's syndrome.

Chicken pox sores also will occur in the mouth and throat, so your child may be picky about eating. Don't worry. It's okay. Encourage your child to drink cold fluids and offer a soft bland diet, avoiding salty foods and citrus fruits.

Many parents ask about antiviral medications for their children. Antiviral medicines help only if started within 24 hours of the sores appearing, but it only slightly reduces the number of sores from 500 and may shorten the illness but only by one day. There are more risks to taking this medication than benefits, so most normal healthy children do not need them. To prevent the sores from becoming infected, be sure to trim your child's fingernails short and wash their hands with antibacterial soap frequently during the day.

Children with chicken pox are contagious five days before the rash begins and until all the sores have crusted over, which is usually about five to seven days after the rash begins. To avoid exposing other children, call your pediatrician to see if your child really needs an appointment. Usually, your child doesn't. If your pediatrician does want to see you, they will give you special instructions about how to check your child in. This is to protect all the patients in the waiting room who may not be old enough for the varicella vaccine. Once all the sores have crusted over, your child does not have to stay home anymore even though they may still have scabs. Remember, it may take two weeks for all the scabs to fall off.

Most parents who think they didn't have chicken pox as a child had a mild case. Only 4% of adults are not protected, meaning most of us have had chicken pox. If you as a parent lived in the same household with siblings who had chicken pox, consider yourself protected.

Siblings will come down with chicken pox in 14 to 16 days, and the second case in a family always has more chicken pox than the first. So if your child wakes up with spots, call your pediatrician who can help you determine if this is chicken pox or not and can help make the right call for the treatment your child needs.

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Interviewer: Eight percent of human DNA originally came from viruses. A new study published in "Science" reveals how our body is putting these viral remnant to work.

Announcer: Examining the latest research and telling you about the latest breakthroughs. The Science and Research Show is on The Scope.

Interviewer: I'm talking with the University of Utah Geneticists Dr. Cedric Feschotte and Ed Chuong, who've published a study in "Science" together with collaborator Nels Elde. Scientists for a while have known that some of our DNA comes from viruses. So I don't about you, but I actually find it kind of uneasy to think that I'm not just me, I'm part virus.

Dr. Feschotte: Eight percent of our genome is viruses, but then another 40% on top of that is actually other kinds of selfish genetic elements as well. So one might even say you're less human than you think. Definitely, a huge portion of the genome is represented by these kinds of selfish elements that most scientists often dust under the rug, so to speak.

Interviewer: What you've shown is that our body actually uses some of that foreign DNA for a very specific purpose. What did you find?

Ed: Yes, what we found is that some of these pieces of viral DNA being recycled to serve now some set of functions. Important for the defense of cells against pathogens including viruses.

Interviewer: How did the viral DNA get there in the first place?

Ed: There are remnants of past viral infections that have actually plagued our primate ancestors many, many millions of years ago. And they are descendants and they are been assimilated in the genome of the host and now what we are seeing still is that still some of these elements retain some of the properties, ancestral properties, regulatory properties of these viruses.

Interviewer: So tell me again what you think they're doing. How they're interacting with the rest of the defense system?

Dr. Feschotte: Your body has many ways to sense infection by virus or other kinds of microbes. And one of the first things that happen is that when you sense infections, cells will release, the signal, the warning signal called interferon. In the genomes of our cells there are hundreds of genes that are dedicated to fighting infection, fighting micros, fighting virus but they're normally turned off. Then what happens is when you have responses like the interferon response turned on, these cells sort of awaken from dormancy and then turn on and do their business and eventually sort of turn off. And what we found, basically, was that in addition to a lot of human DNA that gets activated by the signal, a lot of viral pieces are activated as well as thousands of viruses seem to be activated by the interferon response.

Interviewer: So these elements, these viral pieces are basically like triggers that help set off the immune weapons that they're sitting next to?

Dr. Feschotte: When we think about the switches, their original evolved function, so to speak, was to drive transcription of that virus. So I think, initially, 50 million years ago, that was the purpose. But clearly over time, some of these elements have been collocated or domesticated, you know there's different words for it by their host, in this case primates to act then exactly as you say, to act as switches that now instead of turning on viral genes, now they turn on genes that are pivotal for our own immune defenses.

Interviewer: Kind of the cool thing is that you're thinking of this as sort of a coordinated system.

Dr. Feschotte: You can imagine, no one protein is going to be enough against the pathogen. Our strategy is essentially the throw in hundreds of genes that together collectively make a very strong and robust defense system. And I mentioned earlier that the regulation of genes in response to interferon is governed by little molecular switches called regulatory elements. And our question was really, know how do these regulatory elements get there. How do they evolve in the first place? And one idea is that these regulatory elements can sort of evolve through mutation, the code necessary to turn on these genes or response interferon. But what we found was this potential mechanism where these endogenous retroviruses are actually providing these switches.

And what makes that mechanism so attractive is that these endogenous retroviruses have this built in ability to copy and paste themselves throughout the genome. And so if we are trying to think about how do you evolve a coordinative response? Well, it's a lot easier to take a pre bill switch provided by these viruses that are so common in the genome rather than to a sort of "rely" on random mutations to build these switches.

Ed: One reason why we think this mechanism of spreading these elements might be a good way to wire these networks and distribute these switches is that, indeed, the switches already existed. And again, they were serving probably viruses to begin with, but you didn't have to reinvent them.

Interviewer: Do you have evidence that this isn't a one-off thing? That this is happening kind of over and over throughout evolution and in different species too, right?

Ed: Yes, well, this was really another surprise that came kind of late into the study. And what we realized is that some of the elements that were similar are not identical. But very similar to the ones we would see in the human genome and in other primate genomes were actually also present in [inaudible] genome. Now a different location in the genome, but they had the same regulatory properties, it seems. That it contained some of these switches to respond to this infection, essentially. We see them present in multiple species and, indeed, we speculate that maybe the same mechanism has also spread some of these switches in other species to wire their own lineage-specific network of these immunity genes.

Interviewer: Do you think these viral DNA pieces might be impacting our health in other ways?

Ed: Yeah, so we think this is something really interesting that we need to follow up on. Because some of the genes that we found to regulated by this viral DNA have been implicated in cancer, autoimmune disease, they are themselves mis-regulating this disease. And we also know that some of this retroviral DNA is often activated in the same conditions. So now we've sort of connected the dots and are thinking that this provided mechanism can explain some of this mis-regulations of these genes in cancer and in autoimmune disease, but have been co-opted for a new regulatory function.

Announcer: Interesting, informative and all in the name of better health. This is The Scope Health Sciences Radio.