Category Archives: Strange but True

A Virus Lies in You

New Picture (4)Amanda Fierro (12:00 Micro) sent me this summary from Science Daily on the viral microbiome, which is something that scientists have begun to characterize only very recently. Identification of the bacterial flora is relatively straightforward–collect samples from people, and culture the organisms on microbiological media. The challenge with this approach is with organisms that might be present, but present in relatively small proportions, become difficulty to characterize; kind of like looking for a needle in a haystack. Viruses add another level of complexity since they are not able to be directly grown on microbiological media (you have to have the host cell that they infect), and as a result if you are trying to find them, it is kind of like looking for hay-colored needles in a haystack. It really ONLY became possible to do this type of experiment with the advent of cutting-edge DNA sequencing techniques. Here is Amanda’s summary:

The following summary is about an article found on Science Daily concerning viruses. We’ve learned about the bacterial flora of the human body in class but there also is a viral flora. The article is about the findings of a study researching the various viruses that may reside in the human body. The research was performed at the Washington University School of Medicine as part of the Human Microbiome Project. The study is the first comprehensive analysis to describe the variety of viruses in healthy people.

According to the researchers, healthy individuals on average harbor about five types of viruses. Researchers have discovered the standard viral flora to be rich and complex. The study performed consisted of 102 healthy adults between the ages of 18 and 40. Each volunteer was carefully screened to confirm health and the absence of symptoms of acute infection. The volunteers could not have been diagnosed with an HPV infection within the last two years or have an active genital herpes infection. Researchers split the human subjects as evenly as possible by gender. Researchers sampled five body habitats: nose, skin, mouth, stool and vagina. The results indicated an impressive number of viruses found in the sampled body habitats of the subjects. As one can guess, many more would have been discovered if the entire human body had been sampled.

In 92% of the subjects, at least one virus was found. Some of the individuals sampled were home to 10-15 viruses. Half of the subjects were sampled two or three times during the course of the study. Researchers observed some of the viruses created stable low-level infections in those individuals. While analyzing all of the collected samples, the researchers discovered seven families of viruses. Herpesvirus 6 and Herpesvirus 7, strains of the herpesvirus not sexually transmitted, were found in 98% of the mouth samples. Seventy-five percent of the skin samples and 50% of the nose samples harbored some strains of the papillomavirus. The researchers encountered novel strains of the virus present in both the skin and the nose habitats. The vagina was dominated by the papillomavirus—38% of the female subjects carried strains. Some of the women possessed high-risk strains that increase the risk of cervical cancer. The high-risk strains were more common in women whose vaginal bacteria had low levels of Lactobacillus and high levels of Gardnerella.  Lactobacillus is a good bacteria for humans that helps protect against bad bacteria. Gardnerella is the bacteria that produces bacterial vaginosis. Adenoviruses also were found in the various body habitats sampled. The common cold and pneumonia are caused by adenoviruses. In addition, the researchers had scientists at the university’s Genome Institute sequence the viral DNA of what was discovered by the study. They concluded each volunteer subject had a distinct viral fingerprint.

The study’s researchers admit they do not know whether the viruses have a positive or a negative effect on the overall health of the human body. They do hypothesize some viruses may keep the immune system prepared to respond to dangerous pathogens while other viruses may increase the risk of illness. The researchers also admit to the possibility the viruses discovered could have been latent viruses the subjects acquired years earlier, but they do not believe that is the case. They believe the viruses found to be active. Many of the viruses found during the study were discovered in body secretions where the presence of a virus is an indicator of an active infection. Latent viruses hide within cells and not in body fluids such as saliva and nasal secretions. The researchers plan to continue their research by distinguishing between the active viral infections not causing symptoms or illness and the active viruses that are.


Lyme Disease outbreaks, a positive benefit!

Via the Bad Ad Hoc Hypothesis competition, held at MIT last fall, a short video explaining a little bit about the range of Lyme Disease in the United States, and a surprising positive outcome from living in these areas:

Neanderthal Viruses Found in Modern Humans

English: First reconstruction of Neanderthal m...

English: First reconstruction of Neanderthal man Español: Primera reconstrucción del Hombre de Neandertal (Photo credit: Wikipedia)

Kelley Monaghan (12:00 Micro) found an article from Science Daily about a genetic sequence from a Neanderthal that is shared by modern humans. What makes this sequence particularly interesting is that it is a viral sequence that became incorporated into the genome as a provirus, at some point in human evolution where humans and Neanderthals shared a common ancestor. Here is Kelley’s summary:

Researchers at both Oxford University and Plymouth University recently discovered that in modern DNA there is an ancient virus that dates back to the Neanderthals. They came up with the theory that roughly half a million years ago this virus originated in our human ancestors. This was proven when researchers compared a cancer patient’s genetic data from modern day to the genetic data of fossils from both human ancestors the Neanderthals and Denisovans. Scientist plan to look into the relationship between modern diseases and ancient viruses could even help further our knowledge of the diseases such as cancer and HIV, and make us one step closer to finding the cure.

Endogenous retroviruses are simply viruses from our DNA sequence that can be passed down from one generation to the next generation, and they make up eight percent of our DNA. Scientists clump endogenous retroviruses into “junk” DNA, which has no known function yet and makes up 90% of our DNA. Medical Research Council (MRC) member Dr Gkikas Magiorkinis of Oxford University’s Department of Zoology say that, “’I wouldn’t write it off as “junk” just because we don’t know what it does yet,” concerning the recent discoveries. He believes this because under some circumstances disease has been caused from the combination of two “junk” viruses. This isn’t a new concept; we have seen this before in animals. For example, in mice endogenous retroviruses when activated by bacteria can lead to cancer. Dr Gkikas and his colleagues at Oxford University’s Department of Zoology have been studying the possible link between these ancient viruses to cancer and HIV. The link may be from the ancient viruses being apart of the HML2 family for viruses. Dr Gkikas and his colleagues are testing to see in humans today if these ancient viruses are active or the cause of diseases. To conduct these tests they are going to use 300 patients’ DNA sequences in order to see how common these ancient viruses are in the modern day human population. Dr Rober Belshaw, who is a former Oxford University staff member and currently at Plymouth University, said, “We would expect viruses with no negative effects to have spread throughout most of the modern population, as there would be no evolutionary pressure against it. If we find that these viruses are less common than expected, this may indicate that the viruses have been inactivated by chance or that they increase mortality, for example through increased cancer risk.”

Without the modern day technology, none of this research would have ever been able to happen. And, hopefully there will be upcoming technological breakthroughs that will be able to further fuel this research. Researchers are planning to see these technological advances as soon as 2014! They are hoping to have some solid proof for the connection between ancient viruses and modern human diseases, and what role the ancient viruses are playing concerning out modern day diseases within the next five years.

Fecal transplants even easier than before

"S#!t Sandwich"

“Our bactincinerators go to eleven!”

Long time readers of BIO230 know of my fascination with all things feces. One interesting idea is to use a fecal transplant from a healthy individual to someone with gastrointestinal disease as a potential treatment. There has been some excellent preliminary data that this is a useful approach, in particular for treatment of things like chronic Clostridium difficile infection. The premise is that an infusion of “normal” microorganisms will out compete and eliminate the pathogens in the digestive tract, resulting in recovery without the use of things like antibiotics. Indeed, the ability of C. difficile to form endospores makes that organism particularly resistant to antibiotic therapy, which is why some patients have problems clearing the infections even with long term antibiotic therapy.

The problems with fecal transplants have been several fold so far, and most have been related to collection and delivery. First, the organisms to be infused have to be to some degree tailored to the patient. It is better to acquire the normal microorganisms from a donor who would likely share a similar microbial makeup to the patient, and so a family member would be best. Quite frankly, I am pretty sure that I would not want a poop donation from a total stranger. Second, there is an “ick” factor associated with the process that requires either a feeding tube to bypass the stomach or else delivery via colonoscopy to put the donor organisms into the correct location. Passage of the donated material through the stomach would likely greatly reduce the viability of the microorganisms and diminish the effectiveness of the treatment.

A news update on Gizmodo reporting a CBSNews story details an innovation in fecal transplant technology, and summarizes research done by scientists at the University of Calgary.  (Editorial note: I would take off points if I graded the CBSNews report, due to their egregious failure to underline or italicize the names of microorganisms!)  The researchers treated 27 patients of persistent, antibiotic resistant C. difficile infections by administering donor microorganisms.  The novelty of this approach was that the donor microorganisms (taken from a relative at home) were brought into the lab to be cleaned of food and other non-bacterial fecal material, and packaged into triple gel capsules before administering orally to the patients. The gel capsule allowed the donated microorganisms to get past the stomach, so that the capsules could dissolve in the intestines. One patient, a retired nurse’s aide who reported two years of debilitating gastrointestinal disease due to C. difficile, has been cured by the donor bacteria pills.

Currently, the treatments are essentially tailored by specific donors for each patient. Other gastroenterologists foresee the potential for “universal” donors who might be able to contribute organisms that might help many different, unrelated patients. Since the donated fecal material can be frozen and stored to produce “poop banks”. Alternatively, people might go for the Do It Yourself approach in order to avoid needing to deal with health insurance companies.

A possible vaccine for breast cancer


In our current BIO230 discussion about viruses, we introduced the link between certain types of cancers and infection by a variety of different viruses. The first to be characterized by Francis Rous was a cancer of chickens, which had been infected with a virus that now bears his name, Rous Sarcoma Virus. The mechanisms by which viruses can induce cancer are rather complex, but the presence of an infectious agent as the causative agent allows the possibility of preventing the cancer by preventing the infection. Indeed, this is the premise behind the vaccine Gardasil which offers protection against infection by Human Papilloma Virus–a virus highly correlated with cancers in both genders. Of course, many cancers have no association with an infectious agent, which led me to be very surprised by this news alert pointed to me by Summer 2013 Micro student Dominique S. This was surprising because there was no indication that any infectious agent was involved with the cancer, so the mechanism of how a vaccine might protect was unclear.

The news alert references a primary research article by scientists at the Cleveland Clinic. The scientists used a model in mice to study the metastasis of tumors. A cancer cell line grown in tissue culture was injected into healthy mice, and the mice were observed to develop mammary tumors that resembled human breast tumors. The researchers noted that the tumors strip only expressed a protein called α-lactalbumin, a protein normally found only in breast tissue during milk production. Since the tumors cells in a non-lactating mouse would be the only cells to be making α-lactalbumin, the felt that this protein would make an attractive anti-cancer target. Consequently, they immunized mice with α-lactalbumin antigen, so that the mouse’s own immune system would start to produce an immune response against the protein, and hopefully against the tumor cells should they be present. This is essentially an induced autoimmune response (the body attacks an antigen that belongs to its own cells, in this case in lactating breast tissue), with the hope that the immune response would essentially be specific for the tumors. What they found was that the mice produced a strong T cell response against the tumor antigen, and it offered significant protective effect.

The work is currently progressing into clinical trials, and the Cleveland Clinic hopes to enroll human subjects into a pilot study in the near future. Phase 1 trials will be with women who have survived breast cancer using standard treatments but are at risk for recurrence, to determine the necessary vaccine dose to promote an effective immune response. Later trials will be with healthy, but at risk women, to see if the vaccine offers protection in humans as it seems to in mice. Some significant issues can still arise. First, the immune response of the mouse is not the same as the immune response of the human, and what works well in one animal may not work at all in the other. Second, the approach promotes an autoimmune response in the host. While α-lactalbumin expression in healthy women is only during active lactation, this likely means that it would be highly inadvisable for anyone receiving this vaccine to become pregnant.

Malaria and foot odor-the missing link!

Via and the LA Times, here’s a news alert that all college students should be mindful of. Researchers at the London School of Hygiene and Tropical Medicine have published in the medical journal PLOS One a new defense against malaria transmission. Malaria is a disease which affects a large proportion of the world’s population, with an estimated 220 million cases (nearly 1 in 20 people) worldwide in 2010. It is caused by the several species of the protozoan genus Plasmodium, and transmission requires specific species of mosquitoes that are essential for the life cycle of Plasmodium. There are treatments for malaria that can help infected patients to clear the parasite, but there is currently no vaccine. Main methods for control for the transmission of malaria have traditionally focused on controlling the reproduction of mosquitoes.

The experiments conducted by the researchers were simple; new adult female mosquitoes were fed human blood which was either infected or uninfected with Plasmodium. Following verification of infection, mosquitoes were introduced to socks (20 Den panty sock, HEMA, The Netherlands) that had been worn for 20 hours beforehand

…by a male volunteer of whom the relative attractiveness to An. gambiae s.s. compared to 47 other men is known…

Control socks, of course, were fresh right out of the package. The researchers constructed a mesh matrix, and measured the rate at which the mosquitoes landed on the matrix (landing rate).


As can be clearly noted from their data figure, infected mosquitoes were 4 times as likely to be attracted to the human odor than uninfected mosquitoes. The authors conclude that the presence of Plasmodium is altering the behavior of the mosquitoes, which may increase the rate of transmission as the population of infected vectors (the mosquitoes) rises. They suggest that current mathematical models for malaria transmission may be underestimating the rate at which the protozoan spreads through populations, as generally uninfected mosquitoes are used in behavioral studies and do not take into account the effects of the parasites themselves on vector-host interactions. Effective malaria control programs need to accurately model all aspects of parasite/vector/host interactions.

From the point of view of the pathogen (Plasmodium,) this is a perfect strategy. Plasmodium species depend upon the mosquito vector for the sexual portion of their life cycle, and this requires approximately 2 to 3 weeks to occur. As this occurs, it is advantageous for the organism not to be transmitted to a new host during a blood meal. However, after sexual maturation has occurred and the new sporozoites migrate to the salivary glands of the mosquito, modification of behavior will allow the subsequent transmission back into a new host during as the mosquito feeds. Long time fans of BIO230 will recall how another Apicomplexan protozoan, Toxoplasma gondii, has been found to potentially modify its host’s behavior, leading to the inappropriately named “Crazy Cat Lady Syndrome.”

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