Class blog for sharing and commenting on current events in biology.

Tuesday, November 26, 2013

Gut Microbes Affect Cancer Treatment Outcome in Mice

No author listed. (November 26, 2013). NIH mouse study finds gut microorganisms may determine cancer treatment outcome.  National Institutes of Health. Retrieved from:


            The term “microbiome” has become a buzz word lately in the fields of biology. Your microbiome consists of the native bacteria and other microorganisms that live in your gastrointestinal tract, on your skin, or around bodily orifices. For some time now scientists have understood that these microfauna are not merely harmless commensals, but actually provide many benefits to their human hosts. One such benefit is that they make it difficult for harmful microbes to invade, by crowding them out and altering the microenvironment, making it less hospitable. Our microbes also may play a role in helping us to digest certain foods. Scientists think that these microbes have a complex role with our immune system, but the relationship is poorly understood. Only recently have scientists begun to uncover the staggering numbers of microbes that live within us, and their remarkable diversity. 


This press release from the NIH describes a study conducted on mice in microbe-free, or nearly microbe free environment, and the negative impact that a lack of commensal gut microorganisms has on cancer treatment in mice. The “germ-free” mice were created using two different methods. One group of mice was raised in sterile conditions from birth, so they did not have any bacteria living within or on them. The other group of “germ-free” mice were born and raised in normal lab conditions, but then given a powerful antibiotic cocktail that results in a greater than 10,000 fold reduction in bacteria.
The next step was to give the mice cancer. Cancerous cells from tumors from lymphoma, melanoma, and colon cancers at similar stages of tumor progression. These cancers were selected based on their known ability to be transplanted and similar susceptibility to drug treatments. Tumors were inject subcutaneously, and allowed to grow to diameters of 0.2 inches or more. The mice were then treated with either an immunotherapy drug, which normally functions to ramp up the immune system and attack the tumors, or by traditional chemotherapy drugs oxaliplatin and cisplatin.
The germ-free mice (both groups) did not respond well to either immunotherapy or chemotherapy treatments demonstrating that the normal microbiota plays a significant role in the ability to respond to cancer treatment. The mechanisms underlying this are not yet well understood. However in this experiment scientists did measure cytokines production in the mice, and found them to be reduced. Cytokines are proteins secreted by cells and regulate cell activity and immune responses such as inflammation. So there may be some complex interaction between immune cells and the microbiome, that is necessary for drug-therapy effectiveness, and this signaling is interfered with when the microbes are not present.


            When antibiotics were first discovered, they were heralded as wonder-drugs capable of eradicating infectious disease and curing many illnesses. And antibiotics have saved millions of lives, stopping simple infections from turning lethal, and curing people of prolonged illnesses from the likes of gonorrhea and tuberculosis. However, there is an increasing concern that use of antibiotics is permanently altering our microbiome, killing off the good bacteria along with the bad. Ironically the result could be an impaired ability to fight off future infections, making people more disease-prone.
            The revelation that taking antibiotics could actually decrease your body’s ability to respond well to cancer drug therapies is a startling one. Because many cancer patients have a suppressed immune system and tend to get sick, they are precisely more likely than the average person to have received multiple rounds of antibiotics. The idea that taking antibiotics could make it harder to fight cancer is very worrisome. Understanding this could have huge implications for cancer-treatments. Perhaps we should be inoculating patients with good bacteria from healthy people before subjecting them to drug therapy treatments. Perhaps doctors should be more wary about prescribing antibiotics to cancer patients, or the public in general. This study should have a direct impact on oncologists and families coping with cancer. 

Critique & Conclusions

            This article was meant as brief overview and summary of a recently published scientific peer reviewed journal article. Since brevity was its aim, I found it acceptable that it glossed over many of the more complex details of the study. The article defined terms for the public such as “immunotherapy,” “cytokines,” and “tumor microenvironment,” which I found helpful. However, there were a lot of variables in this study: two types of “germ-free” mice, three types of cancer tested, two different types of therapies (immunotherapy and chemotherapy), with a total of three different drugs used. I would have liked to maybe see a data table or flow chart that listed out all these variables. Were the two groups of mice each given the three different types of cancer? (Thus creating essentially six experimental groups?) Which cancers were treated with which therapies? I am assuming there were control groups as well, but I would like the article to have mentioned the control groups and how great was the difference between the “germ-free” and the control? Although the article need not be too technical, one or two statistics or numbers would have strengthened the main points.  
            Because I do research on the role of immune cells in the tumor microenvironment of mice with pancreatic cancer, I believe this article may have a direct link to my own research. Perhaps the lack of microbes impacts the presence of macrophages and T-cells, which are known to play a role in tumor progression and immune response. I spent the last summer identifying macrophages and T-cells and reading this article is motivating me to look into this issue more deeply. I plan to read the full journal article on which this summary was based, and look into other recent publications that explore the role between the microbiome and immune cells in cancer.

Thursday, November 7, 2013

Hepatitis C Cure

Biology D Even
Caroline Schetlick

Works Cited
Pollack, Andrew. "Hepatitis C, a Silent Killer, Meets Its Match." New York Times. New York Times, 4 Nov. 2013. Web. 7 Nov. 2013. <>.

            There have been many experiments attempting to discover a medicinal cure for Hepatitis C, a deadly virus transmitted through the use of needles and occasionally sex. Hepatitis C can lead to severe liver damage or scarring of the liver, also known as cirrhosis, and liver cancer. Dr. Arthur Rubens, a professor of management at Florida Gulf Coast University, was striving to find a cure for his Hepatitis C infection that was gradually destroying his own liver. He continued trying treatment after treatment to try and solve this problem, however none of them worked and only led to horrible side effects, such as insomnia, depression, fever, anemia, and a burning rash. In spite of that, Dr. Rubens engaged in a clinical trial to test new pills against the virus. Taking the pill was easy and the virus was vanished after three months of treatment. Research has shown that Hepatitis C kills more Americans a year than AIDS and is the main cause of liver cancer and transplants. With this in mind, new drugs for this “silent plague” will be coming to markets in the next three years that will help victims of this virus in as little as eight weeks with few side effects. Despite that, the new drugs will cost $60,000 to over $100,000 for treatment, making access to the drug a problem, specifically for the uninsured and in developing countries. Differentiating from HIV, a patient taking these drugs will not have to take them for life. Once the virus is out of his system, he will no longer need to take the drug, whereas HIV victims need to take medication and treatment for life. Having said that, people are still at risk of liver cancer if the virus infected them. This positive energy is a new booster for the research and science world because the previous testing on these pills did not bring the results wanted. With this new drug, it impedes the enzyme of the virus and builds genomes out of the RNA, and the virus can replicate. But, the enzyme produces is somewhat like a decoy so the RNA cannot reproduce a chain, therefore stopping the virus. This was an amazing discovery and a very large step for Hepatitis C patients.
            This article definitely has a large affect on Americans, having said that four million have been infected with Hepatitis C. This article doesn’t only affect Americans, but people worldwide. Hepatitis C has negatively impacted the lives of 150 million people and counting. The discovery of this new pill can be a great thing if scientists figure out an easier way to distribute and find a better cost so it can be financially appealing to all. The fact that someone was capable of creating a “fake” enzyme to somewhat “trick” the virus is simply remarkable. I am truly amazed at the level of complexity scientists can test to today with the use of technology and extreme use of knowledge. This article stuck out to me out of all of the biology articles in particular, mainly because the science of medicine interests me and I love learning about new research and new ideas coming through in the world. I had not really heard of Hepatitis C previously, but I now realize what an impact this virus has made on so many lives. It is astounding, and quite frankly sad. But, things are looking up with this new medication.
            This article was very well written and easy to understand, however very lengthy. The author included many details, maybe too many. In addition, he included large scientific vocabulary in the beginning of the article, which was hard to follow because I had absolutely no idea what he was talking about until the next page where he then explains what the virus is, the side effects, long-term effects, and more. Pollack’s tone of voice in this article really pulled the reader in, creating a want to read more. Overall, a great piece that was very interesting and insightful. 

Baby’s Gaze May Signal Autism, a Study Finds

Freddie Reichel
Core Biology Honors
Block D Odd
Belluck, Pam. "Baby’s Gaze May Signal Autism, a Study Finds." Baby’s Gaze May Signal Autism a Study Finds., 6 Nov. 2013. Web. 07 Nov. 2013. <>.
            In a study just published in Nature, Warren R. Jones and Ami Klin of Emory University and the Marcus Autism Center used eye-tracking technology to show that children who were found to have autism at age three looked less in other people’s eyes when they were babies compared to normal children who did not develop autism.   Interestingly, despite what researchers hypothesized, the difference was not apparent at birth.  This suggests that the period in which autism develops could be able to slowed down or halted. Babies who gradually stopped looking into people’s eyes over a long period of time developed the most severe cases of autism.  Children who cannot maintain eye contact are the ones who display the most symptoms and are the most socially disabled.  This observation may lead to the early recognition of autism.   Autism treatment therapy has not yet been established for young infants and the number of cases of autism has severely increased in as short a period as six years.  The Centers for Disease Control and Prevention stated the number has increased from one child in 150 in 2002 to one in 88 in 2008.  Researchers speculate a growing number of older fathers could possibly be a factor. Dr. Jones and Dr. Klin, the directors of the autism center, studied two groups of babies.  One group was babies with a 20 times greater risk, having siblings with autism.  The other group was at low risk, with no direct relatives of autism.  The researchers tested 110 children, with a range of ages between two months and two years old.  The babies were instructed to watch a video of a friendly woman engaging in motherly behaviors.  Eye-tracking technology determined when the babies made eye contact with the women’s eyes, mouth and body and other objects in the background.  At age three, the children were evaluated for autism and eleven of the thirty-six children were diagnosed as autistic.  The researches determined that the children who developed autism looked more at the mouth of the woman past the age when a typical child lost interest.  In addition, the children who developed autism looked more at the objects in the background after the first year then children who did not develop autism.
            This article presents groundbreaking research.  Researchers and scientists still do not know the cause of autism, and the research conducted by Dr. Jones and Dr. Klin helps present a way to diagnose children at an age younger than three and may potentially lead to the development of ways to slow or reverse the development of autism.  Engaging babies in social environments can delay autism.  A major symptom is lack of eye contact, as demonstrated in the experiment, and the research may correlate to a better experiment to find autism in infants using eye-tracking technology.  I chose this article because over the past summer, I worked at The McCarton School, a school for children with autism.  The school was filled with hundreds of children, all on the autism spectrum.  Autism is a disorder that needs to be better understood, and the research conducted at the Marcus Autism Center is an original insight that may help lead to treatment.
            This article was written clearly and sequentially.  I liked the many quotes from a variety of people, ranging from doctors to researchers, who all gave a unique perspective.  Autism is complex and the author described the symptoms very lucidly.  In addition, I liked the graphs because they helped me visualize all the people affected by autism.  However, I feel the author could have provided more background on what is known about the disorder Autism and what other studies have revealed.  Some of the quotes included vocabulary that was too medical for the average person.  This research is an exciting find that is a significant advance in our understanding of autism, and will hopefully lead to more research and potential treatments. 

Wednesday, November 6, 2013

An Ocean Instrument Is Born Meet SID: the Submersible Incubation Device

An Ocean Instrument Is Born Meet SID: the Submersible Incubation Device

 Winner, Cherie. "An Ocean Instrument Is Born." : Oceanus Magazine. N.p., 5 Sept. 2013. Web. 06 Nov. 2013. <>.


Over thirty years ago, microbiologist Craig Taylor and engineer Ken Doherty started to create a way in which oceanographers could finally see exactly what was happening to the many microbes located in the deep sea. Taylor himself was most interested in finding out how fast single celled photosynthetic organisms converted Carbon Dioxide into organic carbon in the deep sea. At the time, the only way for scientists to see the phytoplankton was to spend many tough hours at very odd times of the day, bringing the phytoplankton up from the sea floor then incubating them in conditions that would allow them to continue with their regular photosynthesis. The problem with this was that the change in pressure, light,  and temperature when rising to sea level would most likely cause the phytoplankton to change it photosynthesis patterns which would lead to incorrect observations and conclusions.

The answer to this problem was a mechanism that could run, “In Situ,” or, “where the microbes exist,” incubation. Taylor and Doherty were faced with a challenge because this technology did not currently exist. The two set out to create the first ever submersible incubation device or SID for short. The problem with trying to build SID was how to stop the incubation process after the phytoplankton were collected. A normal incubator will run the microbes through a filter then apply a chemical to kill them and freeze their chemical reactions. Under water this wasn’t possible so SID instead uses a liquid preservative that when circulated doesn’t have any effect on the microbes, but then the circulation stops, the less dense preservative moves upwards through two small holes in the main tube of the incubator into a filter chamber with the microbes while the more dense salt water pushes downward and back into the main container without the preservatives or the microbes. Fifteen minutes after the circulation has stopped the microbes are all incased in preservatives on the filter without any moving parts having to be activated. The first SID was tested off the shores of Bermuda and was able to filter phytoplankton for a whole year.

News on SID spread and soon researchers worldwide were trying to improve the designs already made by Taylor and Ken. Taylor however had already invented deep SID which was about to dive and incubate at over 650 feet below sea level. After such success, Taylor and Ken were able to receive funding from the National Science Foundation to create an even more powerful model. With the new money the two developed a new filtration system that stored the preservatives away from the filters until they were needed for preservation. The MS-SID was first tested in 2011 with the new filtration system. The system worked well at the bottom of the Mediterranean Sea until a tube cracked and preservatives were lost. Improvements were quickly made and now the MS-SID works without problems up to two miles below sea level. Still, the two took the SID a step further and inverted the vent SID which can still work in temperatures up to 160°f. The SID continues to move forward allowing us to gain more and more information on the microbes that live in the depths of the sea.


This piece of machinery is very important to the scientific world because without it we wouldn’t be able to study microbes that dwell even a couple hundred feet below the sea level. Microbes are important because they’re the start of the food chain, the fist producer in the sea for bacteria. Without the microbes the chain would begin to die out and sea life as we know it could drastically change. Therefore, it is very important for us to know all that we can about these microbes so that we can protect them and make sure to not disrupt the balance found in the life cycle of all living things below the sea. I chose this article because I originally didn’t know much about this topic and I want to learn more about it.


This article was very well written and there are very few faults in it if any. One thing that I would like to know is what the SID is made out of so that it doesn’t combust or implode under the pressure two miles below sea level. Besides that, I felt like this article was wonderfully written and full of great detail. The author did a splendid job in describing all aspects of the mechanism, from its origin to its present.

Oarfish Offer Chance to Study an Elusive Animal Long Thought a Monster

Nick Sutherland
Core Bio
November 6, 2013

"Oarfish Offer Chance to Study an Elusive Animal Long Thought a Monster."

Off the coast of California two bodies of animals long thought to be sea monsters were discovered. One eighteen feet long and the other fourteen, these oarfish offer marine biologists a rare opportunity to study possibly the world’s most evasive fish. These enormous fish, eel-like in appearance, normally range from fifteen to thirty feet long and are notoriously bad swimmers. Oarfish, similar to lizards, have the ability to shed posterior parts of their body. They also have toothless jaws and a large red dorsal fin, which they use to propel themselves. The bodies of the oarfish were divided up among scientists in the area and were dissected for research. It was later found that the female oarfish was pregnant and had it not washed up would have spawned thousands of eggs. On the other hand, the stomach of the male oarfish contained several large tapeworms. This led researchers to believe he came from the West Pacific where these tapeworms are most common. Due to the fact that oarfish are seldom captured, there is very little knowledge about them; even oarfish experts disagree about various important details. Dr. Roberts, a marine biologist from the Smithsonian Tropical Research institute, believes that there are several species of oarfish and that during the course of their life, each oarfish changes its gender. Another important thing studiers of the oarfish disagree on is the depth at which the oarfish lives. Most scientists believe that the oarfish lives at depths between five hundred and one thousand feet. However, Dr. Roberts believes they reside near the surface.. The eyes dissected from the oarfish will be studied and from that study scientists think they will be able to uncover the true depth that the oarfish lives. In addition a team of biomechanists will be making a 3D model of this fish that people currently know very little about. The discovery of these oarfish will provide marine biologists with the missing pieces of our current scientific knowledge of the oarfish.

While the findings of this article are not necessarily pertinent to everyone, it still provides interesting context about how little we know about some species. This article personally drew me in because I am an avid scuba diver and am extremely fascinated by the numerous species of fish that exist.

Overall I, thought this article was extremely well written; however one thing that frustrated me was that some claims made in this article had absolutely no evidence. In the article it was stated that “Oarfish may have the capacity to change genders” (Roberts 2013), however no additional explanation or evidence was given. Other than that I felt the article was extremely informative and well written.

QUENQUA, DOUGLAS. "Oarfish Offer Chance to Study an Elusive Animal Long Thought a Monster." New York Times 2 Nov. 2013. Web. 6 Nov. 2013. <>.>.

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