Punnett's Square

An article in ScienceDaily sheds some light on certain bacterial secretions. Bacteria protect themselves by secreting a slimy layer that we know as a biofilm. It is basically a whole strain of bacteria packed tightly to protect themselves from attack.  Biofilms have been known to cause many health issues especially on medical implants. They also cause a threat in ocean pollution due to their tendency to coat the outside of ships and boats. This article talks about a new technique that regulates the formation of biofilm by a molecular switch. SinR is known as the biofilm formation regulator protein in Bacillus subtilis. When SinR is bound to DNA, the proteins that are required to make biofilm are turned off. By the application of X-ray crystallography, it has been determined how SinR interacts with very specific DNA targets.

SEM imaging depicting the interaction of the cells of a mouse after exposure to biofilms

I think this is an astounding discovery. I am currently doing research in science about biofilms. I can genuinely see the importance of research in these fields. By knowing how SinR interacts with DNA and other proteins scientists would be able to interject molecules that can interfere with the process. This would stop biofilms from being produces. I also believe this would be a huge break through in the antibiotic field as well as an act against antibiotic-resistant bacterium.

A New York Times article written by Jon Mooallem discusses a science project created by students of City College of San Francisco.  The idea started when a student mentioned reconstructing the genes of an eel and making it an alternate source of energy.  Although a wonderful idea, it seemed to be an unreachable goal.  The idea was down sized and the team decided to create a battery powered by bacteria cells.  The students displayed their work in a competition at MIT.  Other school such as Harvard and Princeton competed as well.  The students wanted to display break away from the typical “cut and paste” gene alterations.  They wanted to create something that would never be seen in nature and would change the world of genetics.  This was the first time a two year college was able to compete at the iGEM.  They knew they would not win, but it was an honor to be able to display their work.

Discussed in a recent CNN article and Medical News Today article is the idea of where allergies come from. An allergy is brought about by the body’s reaction to an antigen. The body sees this antigen as a harmful invader instead of the harmless element it is. Allergens cause your body to produce Immunoglobulin E antibodies. These antibodies are responsible for identifying and destroying harmful invaders. However, in the process, they release histamine and other chemicals that create allergic reactions.

Sensitivity to the invaders is what brings on the allergic reaction. What is unknown is what causes  sensitivity. It is believed that this sensitivity develops even in the womb. It has been found that babies born by a Cesarean Section are 6 times more likely to be sensitive to allergies. Babies who are born via C-section have a different micro biome in their gastrointestinal tract. While in the womb, babies are sterile. As they pass through their mother’s birth canal, they are exposed to many bacteria, and the body can learn the difference between the good and bad bacteria. However, through a C-section, the baby is only exposed to bacteria found in skin cells. From this, babies born through C-section are more susceptible to allergens.

Recent New York Timesand CBS News articles are discussing a rise in a strain of bacteria that is resistant to even the strongest antibiotics.The spread is seen primarily- and mostly limited to- United States hospitals. There is a “limited window of opportunity” to control the spread. This bacteria is most often located in the gut of humans. The bacteria has acquired a lethal trait for the immunity to last resort antibiotics, including carbapenems. These antibiotics are responsible for inhibiting the cell wall synthesis and are a mainstay of therapy in patients with serious hospital acquired infections.

Director of the Centers for Disease Control, Thomas R. Frieden, nicknamed these organisms “nightmare bacteria.” This name stems from their ability to pass on the traits that leave them resistant to drugs. This case has been found in 42 of the 50 United States, and most commonly in the Northeast, specifically New York.

In order to reduce the spread of these infections, hospitals are urged to to ruthlessly scrub all work stations and have all employees and guests constantly wash their hands. They are also encouraged to identify infected people, isolate them, and assign dedicated care teams and equipment to only those infected. Any intravenous line or catheter should be removed as quickly as possible, because they are “avenues of infection.”

Researchers led by Dr. Craig Venter of the J Craig Venter Institute have successfully developed the first living cell that is entirely controlled by synthetic DNA. This team of researchers created a synthetic genome and placed it inside of a recipient cell. The recipient cell then took on the look and behavior of the type of cell that the synthetic genome was patterned after. The cell even underwent replication and made over a billion copies all of which were controlled by the synthetic genome. This is the first time that synthetic DNA completely controlled a cell.

The synthetic cell looks identical to the ‘wild type’.

Dr. Venter and his team have hopes of designing new bacteria that will complete different useful functions. Dr. Venter believes they could even help lessen the need for oil and reverse some of the environmental damage by capturing carbon dioxide. They are in collaboration with pharmaceutical and fuel companies to try to design and create synthetic genomes that could help to make vaccines and fuels that could possibly be used. However, there are those that say that these benefits are exaggerated. There are also risks associated with this type of science most of which are unknown. These would be entirely new organisms that upon being released into the environment could affect it dramatically, in ways that were never originally predicted. One of the potential dangers that can arise from this type of work is bioweapons. Various militaries or terrorist organizations could eventually utilize this technology to create extremely dangerous or powerful weapons that could do extreme harm in the wrong hands. As far as right now these dangers are not present, but with the development of this technology they are possible.

I believe that this technology could be very useful, especially if the technology can reach the potential that Dr. Venter has suggested. However, this does need serious regulation as the risks associated with this are very real with bioweapons. If the proper regulations can be put into place and enforced many good things could come from this.

This article details the findings of both the University of Copenhagen in Denmark and the Beijing Genetics Institute (BGI) of China in that though the study of “metagenomics” that results have displayed numerous ways in which gut bacteria in a person afflicted by type 2 diabetes are significantly discrete in comparison to individuals without the disease. Metagenomics is defined as the examination of DNA patterns within colonies instead of within individual organisms. It should be noted that the presence of these identified gut bacteria do not necessary mean that the bacteria are the cause of the disease itself, they merely note the presence of the disease. However, Danish researchers are examining this issue by injected healthy mice with these type 2 diabetes gut bacteria and examining the results. Experts note the shocking increase in diagnosis of individuals with type 2 diabetes, and believe that the numbers are even higher, masked by the fact that so many individuals do not even know that they are living with the disease.

The information that this research provides, even if it is found that the bacteria do not cause the disease, will have a resounding effect of the medical world. Having the ability to test and find if the individual has diabetes so much earlier would permit patients to more quickly react and change their lifestyle to prevent future heath repercussions. Even more so along this path, if additional research finds that these bacteria are indeed the cause of type 2 diabetes, I cannot  imagine how beneficial, though of course optimistically many years in the future, a medication or treatment would be that could eliminate or reduce the impact of such bacteria in afflicted individuals. I know many family members and friends who struggle with type 2 diabetes and can see how powerful such a discovery, and potential treatment, could be in their lives, not to mention for the thousands of other afflicted individuals worldwide.

According to a source at Sciencedaily researchers in a April 6 paper have discovered that bacteria may be going to through an evolutionary process much more similar to Eukaryotes.  MIT’s researchers from there department of Civil and Environmental Engineering have discovered evidence that beneficial mutations can progress through multiple organisms in a population at there own piece.  This process takes place by the genes exchanging between two bacteria. The way that the researchers are able to deal with conflicting results is that once the exchange has taken place the bacteria’s recombination frequency drops in till the recombination stops completely. Eventually leading to all the bacteria existing in population of cloning individuals. This shows that the bacteria really go through a process similar to Eukaryotes.  These ideas show that two of the Earth’s major organism have very similar method of evolution.

The second part of the paper deals about the implications of what the idea of how evolution works in bacteria may change how we view them. The general way bacteria are view is as ecological populations. Since the previous view of bacteria is as clones calling them species doesn’t make any sense at all. However, now that this new evidence has been brought to the forefront. Bacteria exchange genes and may create new types of completely different individuals which may give warrant to the term being used for Bacteria.

Credit: Manuel A. Palacios/Tufts University

According to the article posted by Robert F. on Science Magazine, scientists made an unusual kind of secret messaging code by using bacteria that show glowing proteins when specific things are added into it. David Walt, a chemist at Tufts University in Medford, Massachusetts, and his team worked on secret messaging that does not require electronics. Walt and his team combined different kinds of metal salts that gave a sequence of pulses of infrared light that encoded a message. Then, they decided to use bacteria instead of metal salts to code their secrets. They then combined seven colonies of Escherichia coli bacteria, injected with particular genes, which made different fluorescent proteins and showed colors such as yellow, green and red. This became possible when genes were expressed. By using seven bacteria with seven colors, they “…came up with 49 combinations, which they used to encode the 26 different letters and 23 alphanumeric symbols such as ‘@’ and ‘$’” (Robert F). The secret message was lined up in pairs of colored bacteria. Walt and his team used a method to “print” the message by pressing a sheet of nitrocellulose “paper” which immobilized the bacteria onto an agar plate (Robert F). A benefit to encode secret messages into bacteria is that only the receiver knows which color shows which character. Walt’s colleagues inserted genes for resistance to particular antibiotics and only those resistant bacteria would show the messages. The person who knows the right antibiotic would be able to see the secret code because the antibiotic will kill only nonresistant bacteria which would not be able to show color. To an unknowing person, it would be like a mix of colors which could not be understood. According to a Jan Sinnige report published on medGadget, Walt’s team was not the first team to hide secret messages in bacteria. Craig Venter, known for sequencing the first whole human genome, once embedded the names of three authors of their publication in a synthetic genome of Mycoplasma genitalium as a watermark. I was really surprised to read this new kind of invention code insertion into bacteria which can be helpful for military purposes and so on.

Knowing the three-dimensional shape of a cell’s chromosome can help in understanding genetic sequences and how genes are regulated; however, until now, it has been nearly impossible to analyze the shape and structure of a chromosome’s genome in its entirety.

Luckily, a group of researchers at University of Massachusetts Medical School, Harvard Medical School, Stanford University, and the Prince Felipe Research Centre in Spain recently deciphered the three-dimensional structure of the chromosome of the bacterium Caulobacter crescentus using both molecular and 3-D modeling technology, specifically high-throughput chromatin interaction detection (known as “5C” technology), advanced DNA sequencing techniques, computational modeling, and fluorescent microscopy.

C. crescentus, shown above, is a single-celled, Gram-negative, rod-shaped bacterium. (Image source: Yves Brun, courtesy of Indiana University)

In order to “create” the image, they used the 5C technology to map more than 28,700 contact points in the bacterium’s genome and used these points to then approximate spatial distance in the folded chromosome. In doing this, they discovered unique characteristics of a specific genetic sequence called the parS site, which helps to define the chromosome’s shape (which was found to be ellipsoidal with helically-arranged arms on both sides). They determined the importance of the parS site by creating mutant bacteria in which the site was in a different location, and observing that the entire genome had rotated clockwise, changing the shape of the entire chromosome.

This new experimental method is crucial because the previous technique used in analyzing genome structure – trying to form conclusions by studying the positions of genome loci – was not thorough enough to study any whole genome at once. As Dekker, one of the authors of the study, noted, “This study illustrates how an investigation of 3D genomic structure can provide insights into how the complex relationships between genome sequence and structure can impact function.” I think that these researchers’ approach was novel because they studied the chromosome in a three-dimensional, or realistic, way – biological structures, especially chromosomes, have complex shapes that are difficult to visualize.

The abstract of the original research article can be found here.

Recently at a speech in the Netherlands, Secretary of State Hilary Clinton warned that assembling genes could eventually be linked to biochemical weapons if the data got into the wrong hands. Clinton believes that further research in this field is beneficial as long as the information does not get leaked out. She believes a deadly organism could be created that could cause a global epidemic due to the genetic information becoming available. It has been noted that groups such as al_Qaeda have been trying to recruit scientists capable of growing genetic material which would decrease the time need to create artifical bacteria an viruses. Whether Republican or Democratic, hatred or love for Hilary Clinton, she brings a valid point to the table. If the genomes of Americans become accessable to the public a mass biochemical weapon could be created that easlily targeted specific sites in American genes.