BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: bacteria (Page 1 of 2)

New anti-CRISPR Proteins Serving as Impediments to this Miraculous System.

CRISPR-Cas9 systems are bacterial immune systems that specifically target genomic sequences that in turn can enable the bacterium to fight off infecting phages. CRISPR stands for “clusters of regularly interspaced short palindromic repeats” and was  first demonstrated experimentally by Rodolphe Barrangou and a team of researchers at Danisco. Cas9 is a protein enzyme that is capable of cutting strands of DNA, associated with the specialized stretches of CRISPR DNA.

Diagram of the CRISPR prokaryotic antiviral defense mechanism.

Recently, a blockage to the systems was found by researchers which are essentially anti-CRISPR proteins. Before, research on these proteins had only showed that they can be used to reduce errors in certain genome editing. But now, according to Ruben Vazquez Uribe, Postdoc at the Novo Nordisk Foundation Center for Biosustainability (DTU), “We used a different approach that focused on anti-CRISPR functional activity rather than DNA sequence similarity. This approach enabled us to find anti-CRISPRs in bacteria that can’t necessarily be cultured or infected with phages. And the results are really exciting.” These genes were able to be discovered by DNA from four human faecal samples, two soil samples, one cow faecal sample and one pig faecal sample into a bacterial sample. In doing so, cells with anti-CRISPR genes would become resistant to an antibiotic while those without it would simply die. Further studies found 11 DNA fragments that stood against Cas9 and through this, researchers were ultimately able to identify 4 new anti-CRIPRS that “are present in bacteria found in multiple environments, for instance in bacteria living in insects’ gut, seawater and food,”  with each having different traits and properties.  “Today, most researchers using CRISPR-Cas9 have difficulties controlling the system and off-target activity. Therefore, anti-CRISPR systems are very important, because you want to be able to turn your system on and off to test the activity. Therefore, these new proteins could become very useful,” says Morten Sommer, Scientific Director and Professor at the Novo Nordisk Foundation Center for Biosustainability (DTU). Only time will tell what new, cool, and exciting discoveries will be made concerning this groundbreaking system! What else have you guys heard? Comment below!

Microbial Tape Recorders: A new Application to CRISPR

Research in the new gene-editing technology CRISPR has raised many red flags and ethical dilemmas as its full capabilities prove to be more than what was thought previously possible. It is used by bacteria to combat viral infections, but now scientists have repurposed it to keep records of a given bacteria’s environmental conditions, which could have significant applications to accurate chronicling of biological changes. Scientific American’s article, “Bacterial ‘Tape-Recorder’ Could Keep Tabs on Bodily Function” outlines how CRISPR “is a DNA sequence that makes and keeps a genetic record of viruses the bacterium encounters, commanding it to kill any that try to reinfect the bacterium or its descendants”. This natural function of bacteria, though, can be manipulated so that instead of exclusively accounting viral encounters, any environmental abnormality can be captured by CRISPR. More specifically, the bacterial mechanism would sense a special signal from a change in its surroundings and create trigger DNA, which, according to the U.S. National Library of Medicine, is a noticeable sequence of DNA from the invaders, which could be used to identify what exactly caused the change.

Applications of this technology today are far-reaching. This technology can be theoretically used to measure contaminants in fresh water or saltwater, or the nutrient levels in topsoil, but the predicted first application will be in monitoring bodily function in humans, and other animals. Digestion problems seem likely to be the first human system monitored with this new tool. Fructose Malabsorption is a digestive disorder which results in high levels of fructose sugar remaining in the digestive system. This disorder results from damaged intestines, normally from serious infection. Sugar levels in the digestive tract can now be monitored precisely by using this application of CRISPR in Escherichia coli cells (bacteria which are naturally found in the human digestive system). The record of sugar can identify specific problems diseased patients, after the E. coli cells are recovered from a patient’s feces, and cause them no harm in the process.

This tool is not without its drawbacks. It is reported that millions of modified bacteria need to be placed in a given system to have an accurate reading of environmental surroundings, and these bacteria have to be in the region of interest for at least six hours. The magnitude and duration of this prospective tool leave much to be desired as initial costs would be enormous, and other limitations, which can only be found through proper testing, remain unknown. In all, this advanced tool still seems applicable for now on only a small scale, but it is an example of CRISPR as a tool for good, and shows much hope for the future.

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Escherichia coli bacteria which can be modified with CRISPR to become a “tape-recorder” of the human digestive system

First step to recovery after uncontrollable wildfires: Microbes?

As we all know, wildfires all around the world, especially out west have been burning uncontrollably. They are continuing to get larger and more unpredictable. But these fires are not only affecting humans and animals, rather they have narrowed down to affecting the tiniest of forest organisms—including bacteria and fungi– and researchers are now finding that some of the microbes are “thriving”.

A study last week reported that “that populations of several bacterial and fungal species increased after severe wildfires in the boreal forests of the Northwest Territories and Alberta in Canada.” Studies like these and others such as the effect of smoke on the distribution of microbes, “give researchers a clearer picture of how wildfires change microbial communities”, and can possibly help them predict how ecosystems will recover after blazing flames. “Microbes help to maintain ecosystem health by decomposing organic matter and readying nutrients for plants to absorb”. For example, because certain fungi and bacteria have specific relationships with plants, it makes it possible to predict which nutrients will be available in an area.

Image result for wildfireIn order to test what they had predicted researchers collected samples from 62 sites about a year after 50 of them had been damaged by fire in 2014 in forests of two Canadian provinces. They found that certain bacteria in the Massilia and Arthrobacter genera were more present after than before the fires. This bacteria usually shows up in cucumber root and seed, and some researchers are predicting that there might be some growth of vegetation of that kind in the future when the forests begin to recover.

It is predicted that microbes “use fire to colonize new territory is by hitching a ride on small particles of ash or dust in plumes of smoke”. In a study published last November, Leda and her team conducted a study and found that “the microbes present in the smoke differed from those lingering in ambient air”. The microbes getting caught in the smoke she predicts can help plant growth in faraway regions.

There is a downside. It has been detected that some fungus, such as Phytophthora ramorum, cause sudden oak death. Another negative is the smoke that the firefighters, other ER personal, and people inhale after and during the fires could contain hazardous microbes. These can lead to lung problems and allergens.

Microbes are not often spoken about when wildfires sweep through, but they surprisingly have more impact than you may think. When entire ecosystems are reduced to ash, microbes determine the first step on the road to recovery.

A Baby Beetle’s Nursery is.. In a Dead Mouse?!

Two Parent Burying Beetles in a Dead Rodent! Gross!

Typically, death for animals is experienced at the end of one’s life, but this is reversed for a certain species of carrion beetle, Nicrophorus vespilloides or burying beetle, in which infant beetles are born and raised within dead mice carcasses. In this mice carcass, parent beetles frequently tend to the dead animal by soaking it with their own oral and anal secretions, providing the baby beetle with a much needed dark microbial film. This bacterial goo actually closely resembles the parent beetle’s gut microbiomes, allowing for the baby beetle to truly thrive as an offspring of this beetle.

But why give these baby beetles this goo within a dead carcass? What benefit would that ever give to an insect?

In every living thing, there is sphere of personal bacteria that provide much needed life benefits as well as qualities like your own stench. Plus, bacteria can even join together through various forms of cellular communication, making an almost impenetrable microfilm biome for bacteria to live in, as seen in plaque on human teeth. This same function is what helps support infant beetles with necessary nutrients and life benefits by keeping the cadaver fresh and capable of sustaining youngster life. Plus, it even causes dead bodies to smell actually not terrible, but instead more pleasant! Crazy! “What burying beetle parents can do with a small dead animal is remarkable,” says coauthor Shantanu Shukla of the Max Planck Institute for Chemical Ecology in Jena, Germany.  “It looks different. It smells different. It’s completely transformed by the beetles.”

If these insects aren’t exposed to these microbiomes as a child, there could be some serious detrimental effects. As shown by Shukla’s lab work, larvae grown in cadavers that were swept clean of biofilm by Shukla and her colleagues used their food less efficiently and gained less weight (“roughly third less weight per gram than those who had their parents goo”).

But, the parents are not the only ones who manipulate the carcass, which can be seen here. As parent beetles and tended to their goo in the body and guarding their children, the infant beetles also add their own secretions to the dead mouse and also eat away the bacteria as well as the entire mouse body. “What will remain is the tail of the mouse,” Shukla says, “and the skull and a few pieces of skin.”

Isn’t it simply crazy how much bacteria can contribute to the growth of a baby insect as well as its impact on even a dead animal? Comment below about what YOU think about this!

Message Intercepted – Commence attack on bacteria!

Tevenphage – Photo credit to Wikimedia Commons

While experimenting, a group of scientists noticed that a A virus, VP882, was able to intercept and read the chemical messages between the bacteria to determine when was the best time to strike. Cholera bacteria communicate through molecular signals, a phenomenon known as quorum sensing, to check their population number.  The signal in question is called DPO.  VP 882, a subcategory of bacteria’s natural predator, the bacteriophage, waits for the bacteria to multiply and is able to check for the DPO.  Once there is enough bacteria, in the experiment’s case they observed cholera, the virus multiples and consumes the bacteria like an all-you-can-eat buffet. The scientists tested this by introducing DPO to a mixture of the virus and bacteria not producing DPO and found that that the bacteria was in fact being killed.

The great part about VP 882 is it’s shared characteristic with a plasmid, a ring of DNA that floats around the cell. This makes it easier to possibly genetically engineer the virus so that it will consume other types of bacteria. This entails it can be genetically altered to defeat other harmful bacterial infections, such as salmonella.

Ti plasmid – Photo credit to Wikimedia Commons

Current phage therapy is flawed because phages can only target a single type of bacteria, but infections can contain several types of different bacteria.  Patients then need a “cocktail” with a variety of phages, which is a difficult due to the amount of needed testing in order to get approved for usage.  With the engineering capability of using a single type of bacteria killer and the ability to turn it to kill bacteria, phage therapy might be able to advance leaps and bounds.

As humans’ storage of effective antibiotics depletes, time is ticking to find new ways to fight bacterial infections.  Are bacteriophages and bacteria-killing viruses like VP 882, the answers?

The Effects of Non-Antibiotic Medication on Human Gut Flora

This article focuses on the effect of non-antibacterial drugs on human gut flora. The study published by the European Molecular Biology Laboratory (EMBL) in Germany tested nearly 1200 drugs, some 835 of which were designed to target human cells, to see if they had any effect on the human gut flora. The team discovered that 27% of these drugs had an effect on the gut flora.

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Example of Human Gut Flora

However, these effects are not necessarily bad. They suggest that some of these changes may be some of the positive side effects of these drugs. The researchers also found a connection between the bacteria not directly affected by the drugs and antibiotic-resistant bacteria.

What are the consequences of such a discovery?

Although the results of the study did not answer the question directly, there could be a link between non-antibacterial drugs and antibacterial resistance. The study’s coauthor, Kiran Patil, says that such effects “should be looked at very seriously”.

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Ultimately the study highlights the importance of considering the drugs put into the human body and what effect they may have – positive or negative – on the human microbiome. Personally, I think that people in this day and age overuse drugs, popping anti-inflammatories and headache pills like they are candy. This has only decreased our sensitivity to these drugs and caused a need for stronger and stronger drugs. We often don’t consider what these powerful drugs are doing to our delicate and complex microbiomes.

What do you think of the results of this study? Is it something to be worried about or just trumped up malarkey?

An Exception to Microbiome Functionality

A recent study was developed to understand how HIV corresponds to the microbial communities of the female sex organ. Dr. David Fredericks- a physician and college professor that teaches “Allergy and Infectious Disease” at University of Washington, led a study on the relationship between the diversity of bacteria in the vagina and how it may lead to HIV. The research population specifically focused in on sub-Saharan African women, who make up 56% of the continent’s infected population.

HIV-infected T cell

Scientists have come to discover that the greater the diversity of a microbiome, the more equipped that region of the body is for combating infections. Although- this concept is strictly relative to the mouth, intestines, and nasal passageway because a variety of bacteria inhabiting a vaginal microbiome can be very detrimental to a woman’s health. One of the leading risks from having a diverse vaginal microbiome community is the “human immunodeficiency virus”.  This virus can be transmitted through sexual contact, childbirth, nursing, or the usage of unsanitary needles. One’s immune system is weakened after contracting HIV because CD4 cells are damaged, which makes it harder for the body to fight off illness. Dr. Fredericks has revealed that the presence of a microbe called Parvimonas Type 1 is usually not a dangerous bacteria, yet the microbe is linked to the virus when there is a higher concentration of it in the vaginal microbiome.

Dr. Fredericks accomplished making this new find by using a strategy called the “dose-dependent effect” to measure the amount of “bugs” in a microbiome community in correlation to the risk of contracting HIV. In doing so, the scientists took cultures from 87 women who were infected with HIV and 262 cultures from women who tested negative for HIV to compare the bacterias found in both microbiomes. During the second half of the study, biologists used screening through a method called “PCR“and identified 20 types of bacteria that could potentially be linked to the virus. The bacterias involved in generating the virus in the female reproductive system were narrowed down to seven specific strains of rogue bacteria. Since the discovery, the biggest question revolving around HIV is determining how to permanently reduce the concentration of these illness-inducing bacterias.

What are Biofilms?

 

Biofilm being formed. (Pixnio)

Medicine has made great advancements in patient care and treatment over the last decade. However, everyday viruses and bacteria alike have become stronger and more resilient – even to the latest antibiotics. One such threat that has led to “…thousands of deaths…” in “…American Hospitals alone…” are biofilms. These bacterial cells “…gather [together] and develop structures that bond them in a gooey substance…” insulating them from the outside world. Biofilms ability to become impervious to antibiotics at a moment’s notice has led biologists to wonder both how they develop, and how to stop them.

To find out how and why these bacteria form biofilms, researchers at the Levchenko Lab, at Yale University, as well as from the University of California – San Diego, “…designed and built microfluidic devices and novel gels that housed uropathogenic E. coli cells, which are often the cause of urinary tract infections. These devices mimicked the environment inside human cells that host the invading bacteria during infections.” From this experiment, the scientist discovered that the bacteria would multiply until physical constraints inhibited them from further reproduction. At this point, the bacteria would become “stressed” and thus this “stress would induce the formation of a biofilm.

With the numerous mimicking devices that the researchers utilized in the experiment, they can now create many biofilms in predictable ways, and further analyze their behavior in similar environments. “This would allow for screening drugs that could potentially breach the protective layer of the biofilms and break it down.”  It is an amazing solution to a stubborn and persistent biological threat, that has already robbed enough, otherwise healthy, people of their lives.

It is imperative that we continue to make great strides in the advancement of medical technologies and treatments, as this will enable us to live healthier, more disease-free lives for the future to come. As viruses and bacteria get stronger, we need to make sure to keep up.

This Easy Method Will Make Sure You Never Get Strep Again

More than 3 million people a year get diagnosed with strep throat, however since it is a minor illness that is very easily treated, people do not see the issue with getting sick almost every year. Because bacteria reproduce in just a few days, many generations of bacteria go by very quickly; and every time they reproduce, they are also evolve.  Meaning, every time one takes antibiotics, the bacteria becomes more and more resistant to it, until we can’t kill them anymore with the same antibiotic.

For many humans around the world, the thought of not being able to fix a simple bacterial infection with an antibiotic is quite frightening; however recent discoveries about the human microbiome puts this fear away.

Bacteria at the microscopic level

There are many helpful bacteria that live in the throat and mouth. Most of these helpful bacteria are probiotics.  The probiotic that specifically attacks strep, is actually another strain of strep called Streptococcus salivarius K12. This probiotic produces two lantibiotics that attack Streptococcus pyogenes, the species that are responsible for the known strep throat.

From this knowledge, scientists did an experiment that gave one group a tablet that, when chewed, released billions of colonies of S. salivarius K12 and gave another group a tablet that did nothing. The group that received the probiotic, showed a 90% reduction in strep episodes than the group that received nothing. This information also helped decrease the time on antibiotics for strep by 30 times.

You can buy doses of S. salivarius K12 here if you are interested in not only staying away from strep throat, but also improving your overall oral microbiome.

If you are interested in reading more about not just the mouth and oral human microbiome, but the whole entire human microbiome; click here!

 

Genetic Engineering will Create Super Humans?!

“Synthetic microbiome? Genetic engineering allows different species of bacteria to communicate”

Before seeking to analyze how genetic engineering enables the alteration of the microbiome, it is essential to understand the nature of the microbiome. Humans’ microbiomes consist of “trillions of microorganisms (also called microbiota or microbes) of thousands of different species.” Initially, peoples’ microbiomes are solely determined by their DNA; however, as time goes on, a person’s microbiome can be shaped by other factors, including the environment in which they live, or their diet. The microbiome contains both helpful and deleterious microbes, but “In a healthy body, pathogenic and symbiotic microbiata coexist without problem.”

According to researchers from the Wyss Institute at Harvard University, Harvard Medical School (HMS), and Brigham and Women’s Hospital, it may now be possible to create a “synthetic microbiome.” The team did a study in which they utilized a particular type of quorum sensing known as acyl-homoserine lactone sensing. Quorum sensing allows bacteria to regulate the expression of genes and to detect the size of bacterial colonies, through signal molecules. First, the team inserted “two new genetic circuits into different colonies of a strain of E. coli bacteria.” One of the circuits acted as a “signaler” and the other acted as a “responder.”

File:E. coli Bacteria (16578744517).jpg Picture of E. Coli bacteria

In short, the team inserted a single copy of luxl, a gene activated by the molecule anhydrotetracycline (ATC), into the signaling circuit. The signaling molecule formed by this gene then binded to the receptor circuit, which activated another gene, known as cro. The cro gene creates Cro proteins, and these proteins triggered a “memory element” within the responder circuit, in which two more genes, LacZ and another cro, were produced. If the signaling molecule is received (which it was), the presence of LacZ causes the bacterium to turn blue. Most importantly, the additional cro gene essentially keeps the “memory element” on, so this cycle continues.

To make sure that this system works in living organisms, the researchers tested it in mice. Signs of signal transmission in the mouse’s gut between the signaler S. Typhimurium bacteria and E. coli responder bacteria were detected. In other words, the engineered circuits allowed the bacteria to communicate with one another.

While these findings are extremely exciting, scientists have yet to discover whether or not other genetically engineered species of bacteria will also be able to facilitate communication between molecules. A Founding Core Faculty member of the Wyss Institute said that “[They] aim to create a synthetic microbiome with completely or mostly engineered bacteria species in our gut, each of which has a specialized function.” If this is achieved, we will move one step closer to becoming super humans!

Feature Image: “Free for Commercial Use” and “No attribution required”

60 Million Year Old Farmers

Microbial ecologist Cameron Currie of the University of Wisconsin-Madison has made an intriguing discovery about the lives of some South American leaf-cutter ants. He found that long before humans cultivated fruits and vegetables for food ancient leaf cutter ants where cultivating fungus. The ants farm the fungus as a food source, but there are pathogenic bacteria that can kill the fungus. To thwart these malicious bacteria, the ants have formed a symbiotic relationship with a different bacteria known as actinobacteria. These actinobacteria fight off the pathogenic bacteria and protect the fungus.

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Leaf Cutter Ant

But how could we possibly know if fungal-farming ants existed millions of years ago?

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Ant Trapped In Amber

Well, I am glad you asked. Curries research focused on a 20-million-year-old sample of amber that had a few of these green-thumbed ants trapped inside. The ants had specialized pockets in their heads called crypts where the ants store these actinobacteria. These leaf cutter ants are walking pharmaceutical factories.

It is intriguing that some of the smallest insects on the planet where farming and cultivating food millions of years before we even thought of it. Not only that, but they have been using anti-biotics for millions of years whereas humans have only started using them 60 or 70 years ago.

What lessons do you think humans today can take away from these ants? Could they be the key to our anti-biotic overuse crisis?

C. Difficile Colitis: How To Prevent It

What is Clostridioides difficile Colitis, or C. difficile Colitis, and how can you get it? C. difficile Colitis is an infection of the Colon caused by an excess amount of the Clostridioides difficile bacterium in your intestines. Some symptoms of the infection include diarrhea, stomach pain, nausea, vomiting, fever, and blood in stool. C. difficile Colitis is spread by feces, it usually comes from touching a contaminated surface, then touching your mouth. As repulsive as it sounds, it’s actually a lot more common than you might think. Statistics reported by the U.S Centers for Disease Control and Prevention estimated that in 2015, more than 148 out of every 1,000 people contracted C. Difficile Colitis.

Clostridium Difficile Bacteria

 

Experiment:

Confused and concerned by these findings, Kashyap, a Gastroenterologist at the Mayo Clinic in Rochester, Minnesota, alongside her team, decided to conduct an experiment on mice to get to the bottom of this infection. It is known that a disturbance in the combination of gut microbes within a mouse, can, in many cases, cause a C. Difficile infection inside of them. That being said, the researchers, at random, extracted and transported fecal matter from people’s colons with either normal or disturbed microbiomes, and transplanted the gut microbes into the mice’s stomachs.

Results of the experiment, as they predicted, showed that the mice that received transplants from people with disturbed microbiomes were not able to fight off the C. Difficile infection as well as the mice who received transplants from people with normal microbiomes, could. The results showed that, anteceding the experiment, the mice who had received the transplant of disturbed gut microbiomes, experienced an increase in a few specific amino acids found in their gut, especially proline. Proline is a major food source of C. Difficile bacteria, which in turn, strengthens the bacteria, giving it an advantage over other microbes found in the gut, that do not consume proline. This proved that proline-deficient people have much less C. Difficile bacteria in their intestines, thus making them far less susceptible to contracting the infection.

All that being said, the best way to prevent C. Difficile Colitis, is to avoid any and all antibiotics containing proline and to consider taking probiotics with proline-eating bacteria in order to hopefully outrun and weaken C. Difficile bacteria within the intestines, helping to restore the balance of microbes. Please don’t hesitate to comment what you think!

CRISPR Defends Bacteria, and Helps Scientists Discover New Bacterial Defenses

Although CRISPR is known for being a gene-editing tool, it can be used in other areas, such as a defense mechanisms in bacteria. This discovery “Probably doubles the number of immune systems known in bacteria,” according to a microbiologist at the University of California. Bacteria have to defend themselves against Phages, which take control over bacteria’s genetic machinery and force them to produce viral DNA. Bacteria use CRISPR to defend themselves against Phages because it stores a piece of past invaders DNA so bacteria can recognize and fight of those future viruses.

 

Photo By J LEVIN W (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

the researchers found that nine groups of bacterial genes were defense systems, and one system protected against plasmids. The data revealed a possible shared origin between bacterial defense systems and defense systems in more complex organisms. Some of the genes contained DNA fragments that are also  important parts of the immune system in plants, mammals, and invertebrates. The discovery of more bacterial defense systems poses the question of wether they will also be useful biotechnology tools like CRISPR is.Only 40% of bacteria have CRISPR, so scientists searched for other bacterial defense mechanisms. To do this, they looked at genetic information from 45,000 microbes, flagging genes with unknown functions located near defense genes, because defense-related genes cluster together in the genome. The researchers then used genomic data to synthesize the DNA and  inserted them into Escherichia coli and Bacillus subtilis, which can both be grown and studied in the lab. They then studied how well bacteria defended themselves during phage attacks with various genes detected. If eliminating certain genes deterred the bacteria’s defense, that determined that those specific genes were a defense system.

 

For more information, click here. For more information on CRISPR’s role in bacteria, click here.

Bacteria Not So “Bad”, After All?

Photo Link: Wild Garden of Gut Bacteria, By: Nicola Fawcett

Most of us are used to the common notion that bacteria may not be the most beneficial factor in maintaining your health.  Thats why the results of a recent research study conducted by scientists at Babraham Institute in collaboration with colleagues in Brazil and Italy, yielding evidence that in fact good bacteria in the gut can control gene expression in our cells, is game-changing!

The research team, led by Patrick Varga-Weisz, made this discovery by studying the gut bacterias found within various mice. Their attention was quickly drawn to the mice that had lost most of their gut bacteria. It became apparent that in the mice with a very low amount of the bacteria within their gut, contained increased amounts of the “HDAC2 protein”.  When investigating deeper into HDAC2, it was found that increased amounts of this particular protein are associated with increased risk of colorectal cancer.

This new research also resulted in the finding that the amount of chemical markers on our genes, are increased by short fatty acids. These specific chemical gene markers, known as “crotonylations”, were only recently discovered and are newly classified as genome “epigenetic markers”. The researchers then found that by shutting down the HDAC2 protein, short chain fatty acids increase the number of crotonylations.

Ingestion of fruits and vegetables into ones healthy diet are vital – ultimately determining how chemicals produced by gut bacteria, affect genes in the cells of the gut lining. In other words, the short fatty acids, which come from those dietary elements, have the ability to move from bacteria into our own cells, and from there cause changes in gene activity and cell behavior.

In the end, the scientists were strongly convinced that the ability to turn off and on genes, is determined by changes in crotonylation. This inferred that the existence of crotonylation in the genome of cells is vital to protect the body from cancer. Therefore, the pretense of good bacteria is very important for the prevention of disease and illness in the body!

As someone with a strong passion for the science, and also very influenced and intrigued by medicine, I very much enjoyed this study. As the boundary to curing cancer is still a hurtle doctors and scientists try to transcend everyday, studies like these, are both hopeful and fascinating, to me. Also, as someone curious about how the human diet ultimately affects the functions and inner workings of the body, this research again was very engaging and interesting!

Primary Source Article: How good bacteria controls your genes

Secondary Source: Wikipedia – Gut Flora (Gut Bacterias)

 

Bacteria may be more complex than we think

Photo by Wikimedia Commons

A common public misconception is that bacteria live alone and act as solitary organisms. This misconception, however, is far from reality.

Bacteria always live in very dense communities. Most bacteria prefer to live in a biofilm, a name for a group of organisms that stick together on a surface in an aqueous environment. The cells that stick together form an extracellular matrix which provides structural and biochemical support to the surrounding cells. In these biofilms, bacteria increase efficiency by dividing labor. The exterior cells in the biofilm defend the group from threats while the interior cells produce food for the rest.

While it has long been known that bacteria can communicate through the group with chemical signals, also known as quorum sensing, new studies show that bacteria can also communicate with one another electrically. Ned Wingreen, a biophysicist at Princeton describes the significance of the discovery; “I think these are arguably the most important developments in microbiology in the last couple years, We’re learning about an entirely new mode of communication.”

An entirely new mode of communication it is! Heres how it works:

Ion channels in a bacteria cell’s outer membrane allow electrically charged molecules to pass in and out, just like a neuron or nerve cell. Neurons pump out Sodium ions and let in Potassium ions until the threshold is reached and depolarization occurs. This is known as an action potential. Gurol Suel, a biophysicist at UCSD emphasizes that while the bacteria’s electrical impulse is similar to a neuron’s, it is much slower, a few millimeters per hour compared to a neuron’s 100 meters per second.

Photo by Chris 73 Wikimedia Commons

So what does this research mean?

Scientists agree that this revelation could open new doors to discovery. Suel says that electrical signaling has been shown to be stronger than traditional chemical signaling. In his research, Suel found that potassium signals could travel at constant strength for 1000 times the width of a bacteria cell, much longer and stronger than any chemical signal. Electrical signaling could also mean more communication between different bacteria. Traditional chemical signaling relies on receptors to receive messages, while bacteria, plant cells, and animal neurons all use potassium to send and receive signals. If these findings are correct, there’s potential in the future for the development of new antibiotics.

Learning about electrical signaling in bacteria has complicated our understanding of these previously thought to be simple organisms. El Naggar, another biophysicist at USC says, “Now we’re thinking of [bacteria] as masters of manipulating electrons and ions in their environment. It’s a very, very far cry from the way we thought of them as very simplistic organisms.”

 

 

Killer Cells Caught Red-Handed!

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!

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

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?

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

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

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