BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: bacteria (Page 3 of 4)

Killer Cells Caught Red-Handed!

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On December 10, 2017

In Student Post

Antibiotics are most commonly used to treat bacterial infections, but bacteria are rapidly able to evolve and resist these drugs, contributing to superbugs. Immune killer cells or white blood cells, however, are seemingly more effective at destroying bacteria cells. How do our immune cells fight bacteria so efficiently? What exact mechanisms do killer cells use to track and destroy bacteria and can we replicate those mechanisms with drugs?

Image result for white blood cells

White Blood Cell (farthest to right)

A common way immune cells can the trigger death of bacteria is by oxidizing the bacterial cells. However, immune cells are still able to destroy bacteria in environments without oxygen leading scientists to believe other methods are also used in attacking bacteria.

Scientists have recently discovered that immune cells methodically kill cells without the use of oxygen. The immune cells do this by shooting enzymes into bacteria to program the bacteria to self-destruct. Scientists have discovered this by observing immune killer cells as they destroy E. coli and the bacteria responsible for Listeria and tuberculosis. They measured the protein levels of each different bacteria before, during, and after the immune cells killed the bacteria. Each bacterial strain started with about 3000 proteins and ended up losing around 10% of their proteins due to the immune cells injected enzyme called granzyme B. Those 10% of proteins destroyed, however, were necessary to the survival of each bacteria. Granzyme B also shuts down ribosomes preventing the bacteria from making new proteins.

This discovery is significant at a time where antibiotics are becoming less efficient and superbugs are becoming prevalent.  Scientists hope to design a new drug that will treat bacterial infections in a similar way to our own immune killer cells.

The SHOCKING Truth About Tattoos!

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On October 13, 2017

In Student Post

Dying to get a tattoo? You might want to hold that thought.

It might seem cool to have something permanently tattooed on your body, whether it represents an important symbol or not. People get tattoos for various reasons but many people see them as works of art that they want to display on their bodies. People spend much time to think about what images or symbols they want to display. However, few think about what happens after they get this tattoo. Yet, the after effects should be the most important consideration.

What effects does ink have on the body?

Tattoo artists inject ink into the dermis, the layer of skin under the epidermis, filled with blood vessels and nerves. But does the ink really just stay on the surface of the skin? Research and testing on rats has shown that some ink particles can travel through the bloodstream and enter the lymph nodes within minutes, which can cause major harm to the body. Ines Schreiver, a scientist who is part of a team of German and French scientists, found Titanium dioxide along with metal particles such as nickel and chromium (shocking) in the lymph nodes. These ink particles can cause complications such as enlargement of lymph nodes and blood clotting.

What about contamination of ink?

Furthermore, tattoo ink production is highly unregulated. So, no one knows for sure what companies are putting in the ink. According to Dr. Linda Katz, director of the FDA’s Office of Cosmetics and Colors, there is no fool-proof way of telling whether tattoo ink is contaminated. A study in Denmark showed that about 10% of unopened tattoo ink bottles were infected with bacteria.

So, what’s the verdict?

This study alone should make you think twice about getting a tattoo. Although tattooing has been part of human culture for countless years, these recent findings should create a more cautious attitude towards tattoos. There are many other ways to symbolize something that’s important to you or to make yourself look different.  You need to always think first about your health.

For more information click here.

The 450 Million Year Old Superbug

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On October 11, 2017

In Student Post

The first superbug may have occurred 450 million years ago when animals decided to leave the water and begin to live on land.  The scientists at the Broad Institute found evidence displaying a group of antibiotic-resistant bacteria which are as old as the first land animals. Like us humans, the animals possessed these superbugs in their guts. Since the bacteria has been around for so long it has given it time to adapt and develop necessary traits to make it resistant to antibiotics like penicillin. The specific superbug which has lasted since the first land animal is Enterococci.

Photo by Eric Erbe

They can be considered the “godfather” of superbugs. Enterococci were found during the 80’s and were one of the first pathogens to be known to resist antibiotics. Enterococci bacteria today is a major cause of hospital infections in the United States and infects up to 70,000 Americans and kills up to 1,000 each year. Enterococci is so special because it possesses a number of genes which are focused on “hardening and fortifying” the cell wall. The reinforced cell wall allows for the bacteria to fight off disinfectants and not dry out. Research also shows that the fortification was added around the same time that animals began to come ashore. Since the two events happened around the same time it is assumed that the new fortification was to assist the survival of the bacteria in the new environment.

Enterococci had to create new fortification against new elements on land which was not present in the water. Since Enterococci is located in the gut some are excreted through feces. In water, the excreted Enterococci would end up at the bottom of the ocean floor which was moist and filled with nutrients, similar to the guts of a marine animal. When the Enterococci was released on land it would meet a harsher environment where they were exposed to Ultra-violent light from the sun. This caused the bacteria to dry up and die. Eventually, the bacteria developed and picked up the fortification needed which now helps them to thrive in hospitals. Their shell from 450 million years ago allows them to be resistant to the typical effects of cleaning measures in hospitals. The protection the bacteria has is what causes it to be considered a superbug. Even though superbugs are becoming more prominent the understanding of the so-called “godfather” of superbugs may help us to find ways to defeat Enterococci and hopefully other superbugs.

Could a new bacterial test reduce the chances of new superbugs emerging?

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On October 11, 2017

In Student Post

We’ve all suffered from a nasty bacterial infection of some sort, like strep or a sinus infection. Usually, we go to the doctor and are prescribed antibiotics, and are cured in a few days. The problem with this is that bacteria are becoming multi-drug resistant and skipping over weaker antibiotics and immediately using stronger ones to increase the effectiveness. This is because to test out if an infection is resistant to antibiotics, a doctor would have to send a sample to a lab and wait 2-3 days for the results (Fore more information on standard bacterial lab tests, click here). The more antibiotics that are overused and misused, the more super-bugs (multi-drug resistant bacteria) will emerge.

Luckily, there is a new advancement in testing bacterias resistance to antibiotics. A new test has been developed at Caltech that can identify antibiotics resistant bacteria in as little as thirty minutes. The test was focused on UTI’s; they took a sample of infected urine and divided into two groups. One group was incubated, and the other was exposed to antibiotics for fifteen minutes. The bacteria were then lysed, or broken down, to release their cellular contents. The contents are then run through a process combining d-LAMP and Slip chips. This process replicates specific DNA markers which are imaged and counted as fluorescent spots on the chip.

This Photo is credited to Wikipedia

The logic behind this test is that antibiotics affects the DNA replication of bacteria, so there will be less fluorescent spots on the chip for bacteria that is not resistant to bacteria. If the DNA are resistant to bacteria, the DNA replication, fluorescent spots, will be the same in both groups. The tests had a 95% match with the standard two day test, (hyperlink info about standard test) and was tested on 54 subjects with UTI’s caused by the same bacteria, Escherischia Coli.

The creators of this test, Ismagilov, Schoepp, and Travis Schlappi, are continuing to test other bacterial infections, and hope to modify the test to be able to test blood infections. Blood infections are more difficult to test because the presence of bacteria in blood is significantly less than in urine. Having a test like this, for many types of different bacteria, which could be performed in one doctors visit would help reduce the overuse and misuse of bacteria, thus decreasing the chance of new superbugs emerging.

For more information and visuals click here.

 

Birthday Cakes: the New Bacterial Hangout

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On October 11, 2017

In Student Post

Various media outlets have been warning readers about the various unexpected places that germs like cold viruses and bacteria can be found: on a cellphone, the kitchen sink, and a toothbrush. Cake frosting can now find itself on that very list, because according to a study by food safety professor Paul Dawson, blowing out birthday candles can increase bacteria growth on the surface of cake icing by 1,400%.

Dawson conducted the study as a series around common questions regarding food safety. After preliminary tests showed that blowing on nutrient agar (edible sugar-based foods) may be a source of bacterial transfer, Dawson and his Clemson University students conducted a formal study in which the research objective was to “evaluate the level of bacterial transfer to top the of a cake after blowing out the candles”. Rather than using a real cake, they frosted a piece of foil over a cylindrical styrofoam base. In attempt to simulate an authentic birthday party, Dawson and his team had test subjects consume pizza in order to stimulate their salivary glands, then extinguish lit candles by blowing. This process was repeated multiple times Once the icing samples were sterilely recovered, they found that the bioaerosols in human breath led to a definitive increase in bacterial transfer. On average, the amount of bacteria on the frosting increased by 14 times. In one trial, it increased the number of bacteria by more than 120 times.

However, birthday cake lovers should not despair. Dawson says, “It’s not a big health concern in my perspective.” Human saliva is already abundant with bacteria, most of them harmless. If blowing out candles on birthday cakes posed a significant risk in the spread of bacterial diseases, it would be extremely apparent due to the popularity of the tradition. But if need be, especially paranoid germaphobes now have the option of “germ-proofing” birthday cakes with sanitary birthday cake covers especially equipped with holes for candles. So we can have our cake, and eat it too.

 

Source: http://www.huffingtonpost.com/entry/blowing-out-birthday-candles-increases-cake-bacteria_us_5989fde1e4b0f25bdfb31ffc?utm_hp_ref=health-and-wellness

Seagrasses: Benefitting the Ecosystem

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On March 1, 2017

In Student Post

Seagrasses have been known to improve water quality greatly, however it was only recently that scientists discovered other major benefits of the plants that reside in the ocean. The name seagrasses is a misnomer, for they are actually plants that grow in shallow ocean water. Seagrasses are one of the largest stores of carbon in the ocean, and they also remove excess nitrogen and phosphorous from the water.

A few years however, ecologist Joleah Lamb’s colleagues fell ill with amoebic dysentery. This is an intestinal illness that they contracted while conducting research on coral reefs in Indonesia. The illness can be caused by the release of raw sewage into the ocean by a city, which leads to a drastic increase in the populations of shoreline bacteria. The water collected close to the shore had been compared to offshore tidal flats and coral reefs with seagrass beds. The two different sites were very close to one another, yet the water where the seagrass was had a significantly smaller amount of Enterococcus bacteria. The bacteria in areas with seagrass was only 1/3 of that in other areas that did not have the plants. This bacteria is not only dangerous for humans, but is harmful for fish and other species as well.

While at this moment it is uncertain how the seagrasses clean the water, we know that seagrasses trap small particulates and prevent them from flowing on in the ocean. It is believed that the plants would catch the bacteria in the same way, or that the leaves might emit antimicrobial compounds that directly kill the bacteria. Another possibility could be that seagrasses release oxygen made during photosynthesis, and the oxygen is toxic to pathogens. Also, it is noted that seagrass meadows often are located next to coral reefs, so some suggest that they work together to protect one another from bacteria and other possible dangers.

 

Further reading:

http://www.smithsonianmag.com/smart-news/seagrasses-reduce-bacteria-polluted-waters-180962177/

https://www.newscientist.com/article/2121502-seagrass-meadows-help-remove-dangerous-bacteria-from-ocean-water/

https://www.health.ny.gov/diseases/communicable/amebiasis/fact_sheet.htm

Could A Computer Detect Your Sick Gut?

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On January 24, 2017

In Student Post

Photo by Nicola Fawcett (photo source)

 

The human gut microbiome is a system specially revolved around the genetic makeup of an individual person. These gut biomes are the subject of many studies by scientists who are interested in the small world of bacteria living inside of our stomachs and its relation to our health or illness. Many humans have the ability to recognize a healthy or unhealthy human gut microbiome, however, is it possible for a computer to have this same ability? According to the impressive research results developed by a group of scientists at the University of California San Diego, it is possible for a computer to be trained to differentiate a sick gut microbiome compared to an unhealthy one.

In order to reach this innovative conclusion, these scientists utilized metagenomics, a gene sequencing technique, to break up the DNA of hundreds of microbes residing in the human gut. The scientists took gut bacterial samples from the stool samples of thirty “healthy” and thirty “unhealthy” people. The unhealthy people whom had samples taken from them were either diagnosed with autoimmune Inflammatory Bowel Disease. With these 60 samples total, the scientists were able to sequence 600 billion DNA bases and put the information into a computer. After that, the scientists underwent a complex process of translating reconstructed DNA of the hundreds of microbes into thousands of proteins, which were then categorized into thousands of protein families. The tedious differentiation and categorization of certain proteins allows the scientists to see the activity of the bacteria and then program it into the computer so it, too, would be able to recognize these proteins and bacteria. Bryn C. Taylor, One of the scientists involved in this research says that, “You can try to categorize healthy and sick people by looking at their intestinal bacterial composition…but the differences are not always clear. Instead, when we categorize by the bacterial protein family levels, we see a distinct difference between healthy and sick people.” Incorporating this method of distinction with the storage of healthy and unhealthy patient data into computers is an effective way of “training” a computer how to detect a sick or healthy human gut due to a distinguishable difference in bacterial activity, protein presence, etc..

Overall, it seems that these scientists at the University of California San Diego have made groundbreaking progress in the future usage of computers in the detection of an unhealthy or sick human gut microbiome. Do you think the development of a computer’s ability to detect a sick gut will be ultimately more beneficial to the world of health and science, or will it just be an unnecessary new trick that computers can learn? The next time you feel like you’ve got a stomach bug, you just might be scheduling an appointment with a computer instead of your doctor.

https://commons.wikimedia.org/wiki/File:Wild_garden_of_the_gut_bacteria_3.jpg

 

Parents Take Warning: Antibiotics Can Be Harmful to Infants

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On January 18, 2017

In Student Post

Antibiotics are the marvel of modern medicine. They have brought about incredible medical advances, treating bacterial diseases and helping to prolong lifespans in modern times. But a new study conducted by researchers at the Massachusetts General Hospital and the Broad Institute has shined a light on the potential negative effects antibiotics can have on an infant’s health.

https://www.flickr.com/photos/herebedragons/2573487530

The study, conducted in partnership with a team of Finnish researchers, took monthly fecal samples from 39 children from birth until they were 36 months old and analyzed the sample using standard, RNA sequencing procedure to identify different microbes. During the study, 20 of the children had taken antibiotics for respiratory or ear infections ranging from 9 to 15 treatments over the course of the study. From this data, the researchers could analyze the diversity of the gut microbiome of these participants with respect to their antibiotic usage.

The researchers had chosen to analyze the effect antibiotics have on the gut microbiome in young children because of the pivotal role antibiotics appear to play in human health during early development. Low diversity in the early years of life of this collection of bacteria residing in the intestines has been linked to allergies and autoimmune diseases.

The results of this study show a decrease in the diversity of the microbial gut populations in infants who took antibiotics. This was even more pronounced when the infants were marked with a specific signature low in a bacteria known as Bacteriodes (this decrease in Bacteriodes has been speculated to be linked to Caesarean section births in the past but the researchers found this rationale to be inconclusive as well as another rationale that prolonged breastfeeding led to a stronger gut microbiome with higher levels of Bifidobacteria).

When the infants had taken antibiotics, a single strain of bacteria tended to rule their gut with only a few species surviving. On the whole, the gut microbiomes of these participants were less stable and had higher levels of antibiotic resistant genes.

Don’t get me wrong: antibiotics are an incredible innovation that has saved millions of lives. But, be careful in thinking they are a cure all. They’re side-effects might be more harmful than you think, especially in children.

How does this research change your perception of antibiotics?

 

Our Intestines Cure Cancer??

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On January 15, 2017

In Student Post

There are over one hundred trillion organisms- most are bacteria- living in our intestine today. These are referred to as the gut microbiota.

While trillions of bacteria sounds scary, they can actually be very helpful. Research has been done worldwide and the discovery has been that gut microbes actually can kill cancer cells all over the body. (Not just in the intestines) But how? Gut microbes and cancer actually cross paths. Gut microbes can manipulate the immune system and can either increase inflammation or lower it as needed. This means the bacteria can actually work with cancer treatments, boost T-cells, and control other factors that help cancer grow such as fungi, or viruses.

However, this is not all. While some cells help against cancer growth, others do the opposite. It varies cancer to cancer, and all have different results. As said by microbiologist and immunologist Patrick Schloss “What we really need is to have a much better understanding of which species, which type of bug, is doing what and try to change the balance.” So more research is still being done to decide how to control the microbiota, but a possible theory is that because it’s in the intestine it is related to our metabolisms and so what we eat controls the bacterium- this can also then effect the colon, thus effecting more cancer: colon cancer.

 

What’s Causing Your Migraine? The Answer May Be Inside Your Mouth.

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On October 24, 2016

In Student Post

photo by user "taennit" on on deviantart.com

photo by user taennit on on deviantart.com

Have you ever been going about your day and suddenly you’re hit with the feeling of needles ricocheting against the walls of your skull? Frustration grows inside you as you ponder what could’ve possibly triggered your migraine this time. Millions of Americans are struck with similar pain and turmoil every day, which makes the cause of migraines an in-depth and on-going research topic. Though the cause of migraines remains a bit blurry, it is believed that neurotransmitters, like serotonin, are involved in the development of a migraine. Known triggers of this hindering head pain are hormonal changes, stress, and our diets. Author Tim Newman’s article Could Migraines Be Caused by the Bacteria in Our Mouths?, published on MedicalNewsToday.com, suggests that migraines can be caused by the nitrate-filled foods millions of people consume on a daily basis.

Though you may resort to a glass of wine or piece of chocolate for relaxation after a hectic day, these two things can ultimately make your day into an all but relaxing evening. Both chocolate and wine possess high nitrate levels, as do processed meats and leafy, green vegetables. When nitrate is consumed through food, bacteria in the mouth converts nitrate into nitrite. Nitrites then enter the body and can be formed into nitric oxide which is helpful in reducing blood pressure and boosting cardiovascular health as a whole. Because of the benefits these forms of nitrate can have on the body, many people are given drugs containing nitrate in order to help with their health problems. Author Antonio Gonzales and programmer analyst Rob Knight found that four in five of the people that take these drugs also experience extreme headaches or migraines as a side effect. With this information, both Gonzales and Knight used information collected by the American Gut Project to further inspect the links between oral bacteria, diets, and migraines.

When someone takes drugs filled with nitrate or eat nitrate-sufficient food, their body must produce the necessary amount of bacteria or enzymes to break up the nitrate and turn it into nitrite or nitric oxide. Both Gonzales and Knight noted that people with migraines tend to have a significantly higher amount of nitrate-related bacteria located in the mouth, thus increasing the chance that the amount of nitrate-related bacteria in the mouth may correlate with the increased occurrence of intense headaches and/or migraines.

That all being said, the world of migraines is still a bit fuzzy to all of us and all we can do is continue to research the mysteries of this painful phenomenon. I won’t say that the results of these studies should be totally cast aside, but what I will say is that until nitrate-filled food and the presence of oral bacteria are a blatant cause of migraines, you shouldn’t flush those leafy, green vegetables, throw away the chocolate, or pour all the wine down the drain just quite yet.

http://www.huffingtonpost.ca/2016/10/20/migraines-bacteria-mouth_n_12573852.html

http://www.netdoctor.co.uk/healthy-living/wellbeing/news/a27149/bacteria-in-mouth-cause-of-migraine-study/

 

 

 

 

 

 

The Resurrection of “Dead” Bacteria

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On October 14, 2016

In Student Post

Many kinds of bacteria have the capacity to radically alter their metabolism in order to switch into a dormant state. This allows them to survive without any possibility of growth. One reason this might be advantageous to bacteria is if their microbes do not have a substantial amount of food. The cells’ revival process follows a strict genetic timetable. This is an important survival strategy.

One of the oldest types of bacteria are cyanobacteria – going back more than 3 billion years. Their activity released oxygen into the atmosphere, therefore enabling life on earth in its current state. When nitrogen, one of their major nutrients, is lacking, these cyanobacteria cease their growth and enter a dormant state. They dismantle their photosynthesis apparatus and lose their color. This allows them to survive long periods without requiring nutrients. If they become exposed to an accessible supply of nitrogen, they return to normal life within 48 hours. It is intriguing because the cells appear dead and then out of nowhere they return back to normal.

2000px-cyanobacterium-inline-svg

Diagram of Cyanobacteria

Through various experiments it was found that the cell revival process began almost immediately once nitrate was added. This is a highly organized process.

Phase One: Bacteria suppress all remaining photosynthesis activity and tap into reserves to obtain energy quickly

At First: Intake and processing of nitrogen. The production of protein synthesizing mechanisms are activated.

12-16 Hours Later: Photosynthesis begins

48 Hours Later: Full capacity reached. Cells begin to grow and divide again

 

There are copies of DNA that are not translated into proteins found in sections of uncoded RNA. These are important switches in the awakening process. This genetically coded program allows cyanobacteria to colonize environments where the nitrogen supply is inconstant. It also allows them to survive environmental stress and survive over three billion years of evolution. This is not the only bacteria that is capable of this phenomena. This can help scientists better control the spread of dangerous bacteria.

 

Source: https://www.sciencedaily.com/releases/2016/10/161006124409.htm

Other Resources (For More Information on This Topic):

http://phys.org/news/2012-02-bacteria-dead.html

Understanding how bacteria come back from the dead

We Eat What We Are: The Importance of Microbes in Our Gut

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On January 14, 2016

In Student Post

Unknown

Photo of microbes (licensing information here)

Ever since the discovery of the microbes, scientists have become very aware of the miniature world of microbes. This early awareness was later translated to an understating of how bacteria and other microbes effect the world we live in. Of course, early scientific and medical research often focused on microbes that cause diseases and how to treat them. However scientists have become aware that each individual is in fact a biome of microbes living on our exterior and inhabiting our interior organs.  Bacteria also play an important role in digestion helping us break down certain foods, producing vitamin and allowing for efficient absorption of nutrients. Increasingly, investigators have began exploring how the micro biome in our digestive track impacts our health and wellbeing.

Gut bacteria appear to play a role in matters of obesity, the development of certain types of cancer and ulcers. They do so by producing certain chemicals that affect a variety of health outcomes. Gut bacteria also produce a wide variety of neurology related chemicals that affect mental processes such as depression and anxiety disorders. Some studies now point to a relationship between autism and particular levels of gut bacteria.

The recognition of the importance of gut bacteria in health and disease have implications in a number of areas. First of all it suggests that a healthy diet should involve the encouragement of the development of good gut bacteria. It also suggests that gut bacteria diversity is a positive goal. Lastly, the results of many of these studies of the significance of gut bacteria in regard to disease point to the need to incorporate the study of an individuals gut bacteria as part of the treatment regiment to fight particular illnesses

 

 

You Are What You Eat

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On January 9, 2016

In Student Post

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Original Link To Image: https://www.flickr.com/photos/pnnl/8146322408

It has been known for some time by scientists that variations in food intake lead to various different gut floras.  However, that theory had only been tested on mice…Until now.  Lawrence David, assistant professor at the Duke Institute for Genome Sciences and Policy, led an experiment that resulted in the discovery that different foods not only lead to different bacteria, but the bacteria themselves experience gene variations.  Although the discovery itself is truly amazing, the celerity at which the changes occur is the most impressive.  University of Chicago’s professor of medicine Eugene Chang specializes in gastroenterology originally thought the changes would take months or even years but the study showed that the changes started to take place within a couple of hours.  There were also changes in the amount of bile acid secreted into the stomach and that microorganisms native to cheeses and cured meats were stronger against this.  The real question is “Why is this relevant?”  To Chang, the first is evolutionary.  Ancient humans who experienced rapid dietary changes could successfully switch from nuts and berries to meat with little gastric distress and maximum absorption of nutrients from even the most unrecognizable foods.  The second is the effects of diet on certain diseases.  Chang, who has been leading a research team to discover the connection between  B. wadsworthia and colitis in mice is yet to apply these tendencies to humans.  However, he believes there could be a connection.  His experiments show just how sensitive the body is to dietary change.  Dramatic changes in ones diet could lead to a brief exposure to harmful diseases such as inflammatory bowel disease.  The experiments are difficult to conduct however because according to David, it’s hard to find even 10 people willing to dramatically change their diets for science.

original article: http://www.scientificamerican.com/article/the-guts-microbiome-changes-diet/

similar article on the gut micro biome: http://www.medicalnewstoday.com/articles/290747.php

It’s Time to Re-program the Human Gut

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On January 9, 2016

In Student Post

(Photo of the human gut (licensing information here)

“What kind of water would you like? Tap or bottled?” “Bottled, please.”

It is known that when traveling internationally, it is typically unsafe to drink tap water. This is due to the lack of familiarity with the filtering systems used by other countries. This caution extends to certain foods as well. However, Dr. Pamela Silver, Dr. Jeffrey Way, and Dr. Donald Ingber, investigators at Harvard’s Wyss Institute for Biologically Inspired Engineering, may have found a solution to many acute gastrointestinal illnesses, such as this one, that affect the human gut microbiome.

Their goal is to create a bacteria that can detect and fight microbial invaders. This genetically engineered bacteria will specialize in detecting the chemicals given off by gastrointestinal inflammation. After the bacteria makes the detection, it will begin to attack all microbial invaders and restore normality within the gastrointestinal tract. The bacteria will be created in a probiotic pill form. In order to make sure that this probiotic pill does not have a negative impact on the environment after it exits the gastrointestinal tract, Silver and Way will ensure that it will not work unless it is in a specific environment and is triggered by specific chemical signals, both specific to the environment and signals found in the gastrointestinal tract.

Silver, Way, and Ingber will use the gut-on-a-chip technology to test this probiotic pill. The gut-on-a-chip technology will allow them to mimic gastrointestinal inflammation with living human cells. The team plans to study the response of invaders and pathogens, that are causing the inflammation, to the genetically engineered bacteria.

This research will allow for the treatment of a multitude of gastrointestinal illnesses, as well as the introduction to treating other diseases that negatively impact the human gut microbiome. I would love not having to worry about what I drink or eat on vacation! I am excited to see where this newly found research takes the discussion and the treatment of illnesses related to the human gut micobiome.

Source: Biology News

How Intestinal Microbiota Could Prevent Asthma

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On October 4, 2015

In Student Post

There are trillions of microbiota living in the average human intestine.  These microorganisms have formed a mutualistic relationship with humans and take on a number of functions including digestion, vitamin production, and the prevention of harmful bacteria growth.  In addition to these essential roles, new research shows that four types of these organisms may prevent asthma. 

Bacteria

 

The four types of bacteria are Faecalibacterium, Lachnospira, Veillonella, and Rothia.  Currently, some scientists think that these bacteria, FLVR for short, help prevent asthma by creating chemical byproducts.  These byproducts are thought to help train the immune system to attack harmful germs and to prevent inflamation.  Having these microorganisms is essential for the development of children. It is possible that the absence of the bacteria can lead to many health problems for people, including asthma.  Stuart Turvey, a pediatric immunologist at the University of British Columbia and a co-author of the study, thinks that being exposed to the FLVR microorganisms at very young ages is essential for preventing asthma and has said “Having the right bacteria in place at the right time is really important, especially in those early months of life.”  Despite their research, scientists do not know much about why the immune system possibly malfunctions when it is not exposed to the bacteria.  However they do know that the immune system becomes “confused” and creates inflammation in the lungs.

These new findings on asthma could possibly explain why asthma’s prevalence has tripled to quadrupled in first world countries in the past 30 years.  The advanced medical knowledge and technology in these countries could possibly be creating an over sterilized world.  Due to more and more doctors treating common sicknesses with antibiotics, human intestines are starting to become too clean and they lack the essential microorganisms including FLVR.  The absence of of these FLVR bacteria is likely to put more people at risk of developing asthma.  One study showed that many Canadian school children had very low levels of FLVR bacteria, putting them at high risk of developing asthma. Another study performed on mice strengthens the viewpoint that these bacteria prevent asthma.  The study examined new born mice by exposing some to FLVR and leaving the rest without the bacteria.  The results showed that the mice exposed to the FLVR at very young ages had much lower rates of inflammation in the airways.

Original Article

Animal Overdose and Its Effect on Humans

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On January 16, 2015

In Student Post

As we all know, antibiotics can be used to cure infections and kill bacteria, but the also often come with the many side effects that the infomercials so quickly warn us of. However, we often overlook aspects of antibiotics and rely on them to heal us in a variety of ways.

This then causes too much reliance on antibiotics, and in fact, humans are becoming immune to these medicines and too much use takes from their ability to have positive results.

This displays the alignment of veal that has been modified and undergone treatment to fight possiblebacteria.

This displays the alignment of veal that has been modified and undergone treatment to fight possible bacteria.

Animals have been receiving harsh treatment and experience weight gain as a result of being given antibiotics for growth promotion in order to sell more meat without disease.  However, animals experience the same resistance over time. The Environmental Working Group is concerned about this, because most of the meat sold in grocery stores is made up of a large amount of antibiotic-resistant bacteria. This, too, can easily be passed on to humans by consumption, as the Food and Drug Administration states.

Due to this resistance to antibiotics and its misuse, many are concerned that the amount of antibiotics served to both humans and animals needs to be lowered, which is much easier said than done. The ultimate goal would be to continue to fight bacteria as opposed to promoting its resistance, as one would assume. However, it is interesting to know how large of an affect antibiotics have on both the human and animal reactions in their bodily systems, and how misuse can alter the bacteria as well as the reason for their need.

Article Link:

http://www.scientificamerican.com/article/what-are-the-consequences-of-antibiotic-overuse/

Additional Links:

http://www.cdc.gov/narms/animals.html

http://www.pbs.org/wgbh/pages/frontline/shows/meat/safe/overview.html

http://www.fda.gov/ForConsumers/ConsumerUpdates/ucm378100.htm

Image Link:

http://en.wikipedia.org/wiki/Veal#mediaviewer/File:MIN_Rungis_viandes_de_boucherie_veau.jpg

 

Sensing neuronal activity with light

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On September 24, 2014

In Student Post

neurons

Researches have recently developed a tool that may help in mapping the neural networks of living organisms using light. Observing these electrical signals of neurons can lead to numerous advancements in our understanding of neural circuitry.

In a collaborative study between Viviana Gradinaru, Frances Arnold and Barbara Dickinson, they developed a method to sense neuronal activity with light. These researchers used a protein named Archaerhodopsin (Arch) and exploited its light responsive qualities. They were able to optimize Arch through a process known as directed evolution. Using this method they created a variant of the Arch protein, called archer1 that acted as a voltage sensor under a red light and an inhibitor under a green light, while generating a light intensive enough to detect. When this protein acts as a voltage sensor it can show which neurons are active and synaptically connected and which aren’t under certain stimuli.

These researchers were able to test Archer1 in the worm C. elegans, which was chosen for its near transparent tissue that made it ideal for observing the luminescent protein. This was the first place they were able to observe the circuits of the neurons light up if they were expressed and dim down if they were repressed. For future studies they hope to make Archer1 bright enough to be detected through opaque tissue and accurate enough to detect voltage changed in more complex, behaving mammals. This study can prove to help us in our understanding of neural networks.

Original papers:

http://www.pnas.org/content/111/36/13034

http://www.nature.com/ncomms/2014/140915/ncomms5894/full/ncomms5894.html  (You can only read abstracts; you have to pay to read the full text)

Are Antibiotics Killing More Than Just Infections?

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On September 24, 2014

In Student Post

What are in your antibiotics?

We all take antibiotics. Staph infections, Strep throat, etc. and they get the job done. Within two or three days, sometimes a week, you’re cured and infection-free. But is that really best for us?

Microbiomes are what make us so unique and individual. In fact, we have more bacteria cells that human cells in a 10 to 1 ratio. We have different microbiomes for different parts of the body; our mouth has a different microbiome than our skin microbiome which has a different microbiome than our gut microbiome. We can influence our microbiomes by what we eat, or rather they influence us based on what we eat. As part of an evolutionary benefit, our microbiomes adapt to newly introduced food within days, which we previously thought took years to change. In other words, if you didn’t eat carrots for three years and sporadically ate carrots one day, your microbiome would activate bacteria that was previously dormant to digest the carrots within days. Think for a moment: a bacteria your body hadn’t made in three years is suddenly recolonized and active in helping you digest within a few days. It’s truly amazing! However, the rest depends on how you were born.

If you were vaginally born, your first encounter with bacteria (bacteria from the placenta is still controversial as to whether babies acquire some of their intestinal bacteria before birth) was in the birth canal, which is exactly where you get your microbiota colonies from. If you were Cesarean born, you might find that you have a higher chance of chronic conditions like asthma or Celiac’s disease simply because you received your mother’s skin microbiome instead of her vaginal microbiome. If you were not breast fed, you are more likely to contract similar conditions because breast milk contains nutrients that cannot be broken down by your digestive track. Rather, they surpass your digestive track and nourish microbiota. Formulas were unaware of this and therefore did not contain everything necessary for your microbiota health, but formulas have been making adaptions to fully mimic these qualities of breast milk.

Say you did all of the right things: you eat whole, unprocessed foods that can nourish your microbiome, you were vaginally born and you were breastfed. It’s completely possible that you have a wonderful, flourishing microbiome. However, you likely do not.  Processed foods do not contain enough prebiotic nutrients (food for microbes). Although one associates Western civilization with nutrition and health, we are actually considered “impoverished” in the world of microbiomes.

The big problem with the Western diet is that it doesn’t feed the gut, only the upper G I. All the food has been processed to be readily absorbed, leaving nothing for the lower G I. But it turns out that one of the keys to health is fermentation in the large intestine. Stephen O’Keefe

Those with no contact to the Western world and its medicine, pesticides, sterility and processed foods have a rich and diverse microbiome. Not to mention the growth hormone in cows, which changes the microbiota for a hastened growth as well as the metabolism of the liver. They even stimulate an increase in body fat. Western medicine, however, affects us in less visible manner. Our antibiotics are too strong for our own good; they destroy the pathogenic bacteria, yes, but they also destroy the health-promoting ones. Therefore, some argue that we should improve our diagnostics to prescribe fewer and narrow-spectrum antibiotics to kill the harmful bacteria while reducing the collateral damage. (Dr. Blaser) These heavy duty antibiotics not only destroy the healthy, diverse microbiota, but have a permanent effect if used for a second course; the microbiome will bounce back but it will not be able to return to its original state. In addition to this, antibiotics have been trying to eliminate H. pylori since 1983 when they found it could lead to stomach cancer or peptic ulcers, when in fact its disappearance could be contributing to acid reflux and obesity. Due to our continual efforts to eliminate H. pylori from the microbiome, it is unlikely that we will see it in upcoming microbiomes due to antibiotics, and “each generation is [already] passing on fewer of this microbes.” Prevotella, for example, is a gut bacteria extremely difficult to find in Western society but relatively common in underdeveloped countries. One woman had unusually high levels of this bacteria in her microbiome, but after one course of antibiotics for oral surgery, her wonderful microbiome was reduced to the average American bacterial standards. 

One of the more striking results from the sequencing of my microbiome was the impact of a single course of antibiotics on my gut community. My dentist had put me on a course of Amoxicillin as a precaution before oral surgery. (Without prophylactic antibiotics, of course, surgery would be considerably more dangerous.) Within a week, my impressively non-Western “alpha diversity” — a measure of the microbial diversity in my gut — had plummeted and come to look very much like the American average. My (possibly) healthy levels of prevotella had also disappeared, to be replaced by a spike in bacteroides (much more common in the West) and an alarming bloom of proteobacteria, a phylum that includes a great many weedy and pathogenic characters, including E. coli and salmonella. What had appeared to be a pretty healthy, diversified gut was now raising expressions of concern among the microbiologists who looked at my data.

Her bacterial composition will return to something that somewhat resembles her original microbiome, but every course after that will decrease potential microbial recovery and also decrease invasion resistance (keeps pathogens from gaining a toehold by occupying potential niches or otherwise rendering the environment inhospitable to foreigners e.g. H. pylori regulates stomach acid to make the environment unfavorable to other bacteria that wants to colonize; vaginal pH is kept low so the environment is too acidic for foreign bacteria to colonize, etc.) So the next time you take an antibiotic, ask yourself: what am I doing to my microbiome?

Bacteria to become a new environmentally safe way to control invasive species?

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On March 9, 2014

In Student Post

 

source: http://commons.wikimedia.org/wiki/File:Zebra_mussel_GLERL_3.jpg

zebra mussels attached to a dock

Zebra mussels have, since 1991, become a huge problem in the hudson river. They devour the phytoplankton and disrupt the ecosystem, and, being an invasive species and having no natural predators in the americas, their population has soared uncontrollably. Until recently, Dr. Daniel Malloy has discovered a species of bacteria that is deadly to the shellfish, and to his knowledge, not to any other organism in the ecosystem. This solution might be just what the Hudson river ecosystem needs, a way to eradicate the aggressive zebra mussel without using chemicals that are harmful to the rest of the river’s inhabitants. This idea sprang from the use of the natural pesticide BTI (Bacillus thuringiensis israelensis) to control blackflies. Malloy has discovered a species of  Pseudomonas fluorescens called “Strain CL145A” that had the desired affect on zebra mussels. When ingested, the dead cells of the bacteria, emit a toxin that destroys the digestive tracts of mussels, the live cells, outside of the digestive system have little to no effect. Malloy and his team are working on finding a fresh water strain of the bacteria to start to eradicate invasive mussels in other bodies of water.

sources:

http://www.nytimes.com/2014/02/25/science/science-takes-on-a-silent-invader.html?ref=science

http://www.fish.state.pa.us/pafish/bass_black/smb2006/reebuck.pdf

The “Social” Bacteria

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On January 19, 2014

In Student Post

800px-M._xanthus_development        The Myxococcus xanthus is a bacterium found in soil that scientist identify as a “social” bacteria. Organized into multi-cellular and three-dimensional structures made of thousands of cells, the bacterium works together by hunting for food and surviving under difficult conditions. They form interesting structures and help each other survive, which are fascinating points of study for scientists who have been researching E. Coli (which has medical significance and influence) in test tubes. However scientists believe that this behavior in test tubes is obviously not as revealing as bacteria behavior in a social or spacial structure that they find in Myxococcus xanthus.

       Myxococcus xanthus eats other microbes and is therefore classified as “predatory”. The structural complex that the thousands of cells form interests scientists, because it is self-made and because it can hunt, kill, and digest various different microbes. By identifying the mechanisms that help the bacteria achieve their multi-cellular behaviors, scientists believe that this will answer questions about how individual cells break their symmetry to organize into these complicated many-celled compositions, teaching scientists about the evolution of multi-cellularity. “The most primitive form of life is single-cell life,” Igoshin, a scientific investigator, says. “The next step up would be going from single cells to multicellular organisms. These bacteria are somewhat in the middle.”

      The bacterium is capable of adopting various forms (ripples, segments, fruiting bodies) in order to hunt for food successfully as a unit and live for a long time together. These capabilities give researchers insight into designing future antibiotics by understanding its functions and methods, especially in embryonic development and other manifestations of this kind. 

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