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May 8, 2012

Posted by srstone in Biology, Evolution, Genetics, Health, Medicine, Science Education.
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Viruses: Friend or Foe?

What is invisible to the naked eye, can affect the Earth’s climate, has a tiny shell, and can causes cancer?  Viruses are considered non-living, but play a major role in our bodies and environment.  In fact, viruses kill half of the bacteria in the ocean every day.  To get an idea of how much bacteria that is, a teaspoon of water contains approximately a billion bacteria.  Recent estimates show there are 1031 viruses on this earth.  That reads, 10 billion trillion, trillion.  Although viruses are smaller than what the unaided eye is capable of viewing, if all viruses were stacked end to end, they would be lined up for about 100 million light years.

How Viruses Work


Viruses are constantly on the attack from the outside of our body desperately trying to get in, but 4 trillion viruses also reside inside our body.  While some viruses are trying to find a host cell and cause harm, many viruses are necessary for a healthy life.  Some of the viruses inside of us can protect us from detrimental bacteria, but can also help balance the population of bacteria vital to our health.  A similar phenomenon occurs in the ocean.  Without viruses consuming half of the bacteria day in and day out, the levels of bacteria in the ecosystem could hamper the living of certain species.  Also, bacteria contain carbon and lots of nutrients.  With the viruses consuming the bacteria, there is a constant recycling throughout the ocean.  There is a hypothesis that because of all the carbon that’s coming out, it could be affecting the Earth’s climate.  Any of the carbon that is sent back to the atmosphere is going to trap heat (greenhouse effect).  It may be an extreme thought, but these tiny, non-living viruses are partially responsible for the weather.

Bacteriophages: the lifeless killers

Viruses that attack and dispose of bacteria are known as bacteriophagesFelix d’Herelle discovered the extraordinary conclusion that viruses can kill bacteria through treating a dish of bacteria with fluid from patients with dysentery!  He actually began a business selling viruses that could cure bacterial infections.  Hypothetically, there are viruses that exist in nature that can kill the most severe bacterial infections, but it’s a matter of discovering the right viruses.  Each species of bacteria has a series of bacteriophages that can eliminate it.

Antibiotics and Viruses: An evolutionary arms race

Before antibiotics were discovered in the 1930s, a method called phage therapywas used to combat infections.  However, once these antibiotic “magic pills” were discovered, phage therapy stood in the distance.  The chemicals were reliable and scientists knew how to make them.  However, with the current widening spread of antibiotic resistance caused by bacteria developing resistance to modern medicine’s most well-used antibiotics, it’s beginning to look like phage therapy wouldn’t be a terrible idea.  One main argument phage therapy new found interest: antibiotics can’t evolve, while viruses can.  Scientists have reached the point where viruses can be engineered and genes can be strategically placed to enhance their effectiveness.  This genetic and evolutionary tinkering could allow scientists to develop viruses to strategically kill various bacteria that might be antibiotic resistant.

Genetic Engineering of Viruses


Viruses: Directors of Their Own Fate?

In the wake of the recent deadly avian flu virus, critics have questioned whether the spreading from mammal to mammal could have occurred on its own.  A study completed at MSU by Justin Meyer was started with the thought that it would be a wild goose chase.  Meyer wondered if lambda phages could evolve another way a new way to enter its host.

lambda was used to infect the gut bacterium E. coli.  It is harmless to humans.  The most common means for lambda to get into a cell is by attaching to its outer membrane.  The genes and proteins contained by the lambda are then injected into the microbe.  Meyer used E. coli that didn’t make the molecules necessary for the virus to grab onto.  This meant that the only viruses that would survive were ones that mutated to use a different surface molecule.  Shockingly, within 15 days, Meyer’s experiment showed that viruses were using a new channel in E. coli known as OmpF.

Meyer re-conducted the experiment with 96 lines of the virus and E. coli.  Of those 96, 24 of the lines began to use OmpF as the pathway into the host.  Because of the repeating phenomenon, the genomes of the evolved viruses were sequenced, finding that four mutations were required for the viruses to thrive.  All four were required, not a single one, or even three out of the four.  Meyer estimated the chance of all four mutations arising at once was nearly impossible: one in a thousand, trillion, trillion. However, the lambda viruses evolved to contain all four mutations in a couple weeks on a regular basis.

As incredible as this experiment is, it is somewhat frightening.  Meyer showed how easily viruses can evolve completely new traits, which can lead to new diseases.  This is exactly the reason why when treating a sickness with antibiotics, the patient MUST finish taking the dosage until it is gone, otherwise the virus can come back even stronger.



 Something in the Water: Tracing the Cholera Outbreak in Haiti April 13, 2012

Posted by srstone in Biology, Environment/Conservation, Evolution, Genetics, Health, Medicine, Policy, Science & Culture.
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 Something in the Water

Cholera Under the Microscope

When we go to the sink to get a glass of water from the sink, we trust that what the water is comprised of is safe for us to drink.  Most of us don’t give a thought as to what could be in it.  This is one of the luxuries of living in a first world country.  However, those in third world countries, such as Haiti, are not so fortunate.  Shortly after the earthquake in Haiti in 2010, a cholera outbreak occurred.  When an outbreak like this occurs, the goal is to not only check the spread of the disease among Haitians, but to prevent the bacteria from swapping DNA with other cholera strains in the country to form a more dangerous bug much harder to treat.

Antibiotic-resistant Cholera: Mechanisms explored

Bacteria reproduce asexually by a process called binary fission.  Binary fission causes two genetically identical bacterial cells to be produced.  If this was the only method bacteria had to procreate, treating a disease with antibiotics would be simple.  Antibiotics aim to either kill bacteria directly or hamper their ability to grow and reproduce.  This can be done by crippling the production of the bacterial cell wall and inhibiting protein, DNA, or RNA synthesis. 

However, when we put our bodies on the attack with the use of antibiotics, bacteria respond by playing their side with different defensive mechanisms.  Some of these mechanisms include changing the permeability of their membranes.  For example, bacteria can decrease the number of channels available for the antibiotics to enter the cell.  Another mechanism works by changing the actual physical structure of the antibiotic once it enters the cell so that the drugs can’t bind the way they were designed to in order to have an effect.  Although both of these mechanisms prevent antibiotics from carrying out their job, bacterial recombination is the most common form of developing antibacterial resistance.  When this happens, bacteria gain genetic variation by swapping DNA with other bacteria.  This allows the bacteria to acquire resistance to the drug.  A plasmid, which is a circular piece of DNA, can encode resistance to multiple antibiotics. Thus if one bacterial cell in the environment has evolved resistance to an antibiotic, it can easily share that information with other surrounding bacteria leading to an epidemic of widespread antibacterial resistance.   A transposon, known as a “jumping gene”, can jump ship from DNA to DNA molecule.  The transposon then becomes part of the plasmid.

Where did it come from?

Cholera, which had never been seen before in Haiti prior to the earthquake, had the advantage.  Nations offering their help focused on the earthquake recovery while cholera entered Haiti under the radar.  Reducing the fatality rate from cholera has been a success; however the response was slow to fully develop.  The most likely story is that cholera spawned from a Nepalese volunteer at the Minustah base.  Understandably, no one wanted to take responsibility for bringing an epidemic to a country that already needed all the help they can get. 

To resolve the “blame-game”, Danish and American scientists collaborated to determine where the cholera came from.  Haiti’s cholera strain and Nepal’s cholera strain of the bacteria were examined using the most comprehensive type of analysis: whole-genome sequence typing.  Virtually identical, the Nepalese were forced to accept blame.  Another method, pulse-field gel electrophoresis was also used as evidence.  Scientists found that cholera erupted in Nepal in July 2010, but was under control the following month in August.  Unfortunately, this was the same month that Nepalese soldiers left for a recovery mission in Haiti.        


Through the application of genetics, the cholera strain has been identified.  Unfortunately, this doesn’t solve Haiti’s problems.  Only 12% of the population has access to piped, treated water.  The rest find their water in rivers and wells.  These are the same rivers that contain feces and that Haitians wash their clothes in.  Vaccinations and supportive care will aid in the conquering of cholera, but until safe water is more readily accessible, the country needs to be prepared for round two.

A Typical Haitian Laundry Room

Effect of environmental toxins on GATC methylation in E. coli May 3, 2011

Posted by ljsteele in Biology, Chemistry, Ecology, Environment/Conservation, Evolution, Genetics, Health, Marian University curriculum, Physiology.
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With the end of the semester drawing near it is becoming that time again when the results are piling in from research you have been working on all semester. As we speak, the final data collection and analysis is taking place in biochemistry, a team of student researchers are exploring of environmental toxins of DNA methylation  in the bacterium E. coli. 

The Bacterial Genome

Bacteria exist throughout the world and can survive in almost any climate . Bacteria are unicellular and can consist in a wide range of environments such as a pond all the way to soil.  One unique attribute of the bacterial genome is that it contains adenine methylation , opposed to mammalian organisms which contain cytosine methylation at GpC islands.  Adenine methylation is when a methyl group becomes attached to the adenine nucleotide on the DNA. When a methyl group is donated from SAM to form a covalent attachment, it is made on the adenine which can cause steric hindrance of transcription factors and differential effects of DNA binding proteins, which can contribute to a change in gene expression.  In previous studies  it has been shown when E. coli is exposed to different carbon sources (ie glycerol or glucose).  Some areas of the genome become demethylated.  In the bacteria E. coli almost every adenine (A) in the GATC sequence is methylated.  To block the methyation at the GATC sequence, a protein must be present to inhibit the DAM methyltransferase from depositing a methyl group on the adenine.

What does Methylation do?

Adenine methylation has many roles in bacteria. Methylation can effect gene expression, cell cycle, virulence, and how proteins interact with the DNA. For the research we are performing, we are concerned with what effect the environment has on changing adenine methylation on the GATC repeats. There are about 20,000 GATC repeats in the E. coli genome and under normal log growth conditions almost every single repeat is methylated. It has been found that when bacterial cells are in a log growth phase there are 6-10 sites which are not methylated. These nonmethylated sites lie up and down stream of promoters of different genes. The lack of methylation may allow DNA binding proteins to modulate their function to allow a functional change in gene expression.

Pollutants and the Genome

In the study we are performing we wanted to see how three classes of chemicals pollutants commonly found in the Midwest affect adenine methylation at the GATC site. We choose three pollutants to represent chemicals that fit into the families of common water pollutants, which are heavy metals, chlorinated compounds and nitrogen rich compounds.Gel Electrophoresis

The above families of compounds will be compared to samples collected from different areas around the campus of Marian University, Indianapolis, IN. Supplements will be added to all the samples to generate a rich liquid media that will facilitate bacterial growth.  With 6 different test groups and 2 controls we are going to seek to determine if any of our known compounds or a compound present in our environmental sample has an effect on the methylation.  The determination of methylation can be done by using restriction enzyme digest with endonuclease selecting specifically for the nonmethylated site.  The enzyme we have chosen was MBO and AVI.  When all the genomic DNA from the bacteria is extracted and digested, then it will be ran on a gel to be imaged to determine if the bands of digested DNA differ depending on the chemicals present during growth.  This is a time efficient way to examine if any changes in methylation levels have occurred.

What Does It All Mean?

For conclusion, the relevance of this study includes a few things.  This study will provide evidence to show if environmental toxins have an effect on bacterial DAM methylation. One role bacteria play in an ecosystem is influencing the flow of nutrients which support plant and algae growth. The results of our proposed study may display that toxins have an effect on methylation patterns which could lead to an increase the mutation rate of the bacteria genome itself.   Destructive mutations may decrease bacterial populations leading to a disruption in the ecosystems nutrient flow, hence disruptions in plant and algae growth with effect additional aquatic and terrestrial organisms.

Using Fish to Detect Estrogen-like Endocrine Disruptors October 15, 2010

Posted by Grace Dible in Biology, Chemistry, Ecology, Environment/Conservation, Genetics, Health, Medicine, Physiology.
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Endocrine disruptors, according to the EPA, are substances which mimic a hormone, stimulate a body to over respond to a stimulus, cause hormones to respond at inappropriate times, or cause an under/over production of a hormone.  The EPA is most concerned with endocrine disrupting chemicals that end up in the environment and affect the environment and wildlife.  Chemicals of more recent concern are synthetic, natural, and mimic estrogens.  These chemicals include 17α-estradiol (found in birth controls) and herbicides like atrazine.  Much of the recent research is trying to determine whether or not these endocrine disruptors are causing intersex fish, which could possibly lead to population declines.

This flow chart shows how endocrine disruptors may lead to sex changes in a fish population.

One way to determine the estrogenic endocrine disruptors in an aquatic environment is to use different transgenic fish as biomarkers, specifically zebrafish (Danio rerio) and medaka (Oryzia latipes).  Current research is underway in order to determine the affects of these different endocrine chemicals on bioactivity.  Both Medaka and Zebrafish can be transgenic with different fluorescent proteins, which were originally found in bioluminescent jelly fish.    At Marian University in Indianapolis, I am currently trying to determine the best methods for determining the affects of estrogen-like endocrine disruptors in transgenic medaka with green fluorescent protein (GFP).  This GFP is expressed in the liver of the fish when a large amount of vitellogenin, an estrogen inducible promoter, is in its system.  Ordinarily, vitellogenin is found in the female medaka liver, but if an endocrine disruptor is in the environment, then a male medaka may be able to express the GFP as well; the GFP is these medaka have a 100% binding affinity to 17α-estradiol.

Medaka fish expressing GFP in the liver

According to recent review on the effects of a supposed endocrine disruptor like atrazine (A Qualitative Meta-Analysis Reveals Consistent Effects of Atrazine on Freshwater Fish and Amphibians – Jason R Rohr and Krista A McCoy – January 2010  Environmental Health Perspectives), they “found little evidence that atrazine consistently caused direct mortality of fish or amphibians, but we found evidence that it can have an indirect and sublethal effects.”  These sublethal effects in fish may include a decrease in motor skills, perceiving predator risk, olfactory sensitivity, and gonadal morphology.  Atrazine may also lead to the body’s production of aromatase, an enzyme that converts testosterone into estrogen.   Studies still need to be done to see if this supposed endocrine disruptor is causing the fish population sex ratios to change or the production of aromatase.

How could this research be beneficial to human health?  Waste water treatment plants currently don’t filter out estrogen-like endocrine disruptors. Right now Dr. Paul Winchester, at the Indiana University School of medicine, is trying to determine whether there is a correlation between the supposed endocrine disruptor atrazine and birth defects.  Another focus of the research is whether or not areas with high amounts of atrazine can lead to higher rates of breast, ovarian, and prostate cancer.   Dr. Paul Winchester recently did an interview with Indianapolis based NUVO magazine to help spread information on this endocrine disruptor so that people are more aware of what is in drinking water.

To see his Dr. Winchester’s full interview click here.  To view the EPA statements on endocrine disruptors click here.

Epigenetics May 3, 2010

Posted by zach in Biology, Genetics, Health, Medicine.
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Is it possible to find a way to fight a broad spectrum of human disease with a single break through in the in the biomedical world?  The emerging field of epigenetics is trying to lead the way in fighting a variety of human diseases, such as cancer, heart disease, and even neurological disorders.  The field of epigenetics was discovered at the conclusion of the human genome project.  When it was found that humans and chimpanzees genomes only differed by two percent, researchers knew something more than simply sequence differences had to be taking place.   Epigenetics was born, currently researchers are looking into all the mechanisms by which gene expression can be altered due to modifications of the DNA by using methyl groups and acetylation.

Epigenetic has had two major break throughs by showing how modification of the histones and methylation patterns can affect the organisms. The first study was done on pregnant agouti mice.  When there is a cross between two agouti mice the offspring usually comes out as an agouti, but scientist wondered if they changed the mother’s diet by adding meth donors, which could change the offspring phenotype by an epigenetic alteration. When the female agouti mouse was fed a high methyl donor diet the offspring showed a normal phenotype.  This means that there was some alteration at the agouti gene that changed the offspring to silence the agouti phenotype.

The other example of epigenetics in action is studies on monozygous twins (MZ).  Monozygous twins share the same DNA because they come from a single zygote, that divided early in development.  At a young age MZ are very epigenetically similar, but as they age their epigenetic patterns begin to diverge. This divergence is highly dependant on their lifestyle. Epigenetic patterns seem to change more when the two MZ twins experience very different environments in their lifestyles.  This shows that your environment can greatly influence epigenetics which can change your disposition towards disease.

“A Ghost in your genes” is a four-part documentary that explores many aspects of epigenetics and all the possibilities that can come from it.  I really recommend taking the time to watch it.   Give it a chance…you will not be let down.

From this clip you can visually see how HDAC’s function and what is being done to  prevent disease by blocking HDAC.

Epigenetics and HDAC are thought to play a key role in the development of cancer.  The National Cancer Institute agrees and pledged $8.5 million to Oregon State University to explore how diet, epigenetics, and cancer prevention can all be related.  The grant is going towards placebo-controlled human interventions trials on colon and prostate cancer.  In the future, researchers are hoping that there research on HDAC can be generalized to fight a wide range of degenerative disorders.

The “CSI-effect” May 3, 2010

Posted by Kyle in Genetics, Science & Culture.
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I recently found an interesting news article addressing an issue stemming from some popular television shows. As you have probably noticed, it is almost impossible to flip through the channels and not find at least one cop drama. While these shows may be interesting, some people are apparently having trouble separating reality from television.  According to the Marion County Crime Lab, there has been a dramatic increase in the demand for DNA evidence in criminal cases. This has been referred to as the “CSI-effect.” While this is not necessarily a bad thing, it has created an increased work load for the crime lab technicians, by roughly fifty percent.

"CSI-effect" based on the popularized TV series

Unlike the shows on T.V., there isn’t always DNA found at a crime scene. Also, it just simply isn’t possible to test every square inch of every crime scene. This has created issues in criminal cases when jurors want DNA evidence, but there isn’t any. When jurors confuse reality and television, they can begin to have unrealistic expectations of investigators. However, the positive side is the increased work load for the crime lab has led to the identification of many suspects, who may have never been identified otherwise.

DNA testing of firearm

A more recent article reported that prisons will begin to use DNA testing to determine the owners of items such as weapons and cell phones confiscated. Officials hope that this new tool will help cut down on the amount of contraband in Indiana prisons. An Indianapolis based company, Forensic ID,  has been contracted to run the program. With the advancement of science and technology many things are now possible that sound like they are from a science fiction movie. It is hard to imagine what will be possible in a few hundred years from now.

Gattaca… is it now a reality? April 30, 2010

Posted by Jill in Biology, Genetics, Health, Medicine, Policy.
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Lego DNA helix

For anyone who has seen the movie Gattaca, the concept is mind-boggling. Could molecular genetics really go as far as artificially selecting for so traits as specific as having an innate ability to speak or play the piano or be a world-class swimmer, not just choosing for a tall blond-blue eyed baby? In the movie Gattaca, Vincent is one of the last “natural” babies born into this genetically-enhanced world, where life expectancy and disease likelihood are determined at birth. Myopic and scheduled to die at 30, he has no chance of pursuing a career in a society that now discriminates against your genes, rather gender, race or religion. He assumes the identity of Jerome, a world-class swimmer who was crippled in an accident, in order to achieve prominence in the Gattaca Corporation, a spaceflight company, where he is chosen for his lifelong dream of being on a manned mission to Saturn.

Although this movie is fiction and was produced in 1997, how far away from this society are we really? The Stanford University School of Medicine analyzed a healthy person’s DNA in an attempt to predict the long-term diseases or medical conditions he would face in the years to come. The genome was of Stephen Quake, who is the Lee Otterson Professor of Bioengineering. The thought is that along with a family medical history, patients could potentially have a genetic component to their medical history that would help physicians in determining whether or not certain medications will work or have adverse side effects for that patient based on their genetic makeup. Patients that are at a potentially higher risk for a certain condition or disease will be able to have closer monitoring of that condition through testing or observation even if not present in the patient. Another benefit to this form of “pre-screening” of genetic disorders is that it will be more cost effective and be more economically sound because it will reduce the prevalence of unnecessary tests, making medicine more efficient.

In conjunction with bioinformaticians, Atul Butte, MD, PhD, assistant professor in bioinformatics, and his lab members have already done a lot of the necessary leg work for interpreting the genetic code into something meaningful, like what individual codons or even base pairs mean in a particular part of the genome. They spent 18 months cataloguing publications that associated particular genetic changes called SNPs (single nucleotide polymorphisms) with effects on specific diseases. It was the first time anyone had compiled all the information in one database.

Upon receiving the genome of Steve Quake, researchers were able to create an algorithm that analyzed all of the data they had compiled from previous studies against Quake’s genome to determine his risk factors for certain conditions such as obesity, Alzheimer’s, type-2 diabetes, and prostate cancer. They determined Quake’s risk of prostate cancer is about 23 percent, risk for Alzheimer’s diesease is 1.4 percent due to protection, and type-2 diabetes, coronnary artery disease, and obesity all at 50 percent. This information raises questions of patients actually knowing these alarming statistics because they are afraid of living their everyday lives. I’m sure this is similar to the idea of life insurance companies providing you the statistics for the likelihood that you will die if you walk across the street to your daily job. Most people do not want to know these things and if the problem arises, they will deal with it then instead of relying on knowing odds to predict what could potentially happen to them.

This new scientific research raises many ethical questions like should this be implemented to aid patients or should it be optional or is this an exploitation of personal information? As more of these findings are published, there will certainly be more controversial discussion in terms of what is right and wrong in exploring the meaning of our genomic fate.

The whole article can be found here.

Creationism vs. Evolution: How did we get here? April 30, 2010

Posted by Jill in Evolution, Genetics, History of Science, Science & Culture.
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Darwin's finches

I was in the library this week studying for finals and finishing up the rest of the work in my classes when I came across this book called Is God a Creationist, which contained many valid arguments for both scientific theory as well as theological explanations as to how life on this planet began. The age-old question of our existence has long been debated by both scientists and theologians.

Since Charles Darwin published his findings on the Galapagos finches and his theory about evolution, there has been an intense debate between scientists and theologians. Scientific evidence, such as carbon dating, dates the earth at about 4.54 billion years old, long before the existence of mankind. Theologians argue the biblical implications of the origins of the world saying that Earth was created by God and all living things were created by God. Literal interpretations of the Bible are difficult to comprehend for many reasons including the fact that the Bible was written 3,000 years ago so the interpretation and meaning of words could have been different than what they mean today and the fact that the Bible was not written as or intended to be a historical accurate account of the world because it is a book filled with symbolism.

The Bible contains two creation accounts in the book of Genesis. The first creation account can be found in Genesis 1-11. According to Michael D. Coogan, the first account of Genesis describes the “formation of the cosmos, an ordered universe, out of preexisting but chaotic matter—an unformed earth and unruly sea over which a wind from God swoops like a large bird” (Coogan 28)

The majority of evolutionary theorists believe that there was preexisting matter from which our universe has evolved. Besides the concepts of evolution, scientists are also known for having developed the “Big Bang Theory” to explain the origins of matter in a naturalistic framework, from which our universe was theoretically created. The Big Bang Theory is described as a moment 15 billion years ago when the total amount of matter in the universe exploded from a point and moved out to form the expanding universe today. The scientific perspective on the origins of the world can be described by: “the world had a beginning under conditions in which the known laws of physics are not valid, and as a product of forces or circumstances we cannot discover…the scientist’s pursuit of the past ends in the moment of creation” (Is God a Creationist 35)

Evolution and natural selection cannot be ignored even by theologians because there is significant scientific evidence that states that both do and have existed. At the very least, it is evident that at least artificial selection exists because of the domestication of animals such as horses, dogs, and cats. Humans were able to domesticate or breed certain characteristics of an animal, for example wolves that were friendlier to man than those that tried to attack, and cultivated these characteristics over thousands of years to produce the species we know as our four-legged friends, dogs.

Do chimps think and act like us because they are one of our closest ancestors?

Through molecular genetics, it is possible to find evolutionary pathways through the similarities in homology of DNA between different living species. Also, extracted DNA from fossilization records are the scientific equivalent of “paternity tests” of our earliest ancestors, determining how closely related we are genetically to other species, namely apes. Molecular geneticists as well as evolutionary theorists believe that chimpanzees and humans emerged from a common ancestor 6 million years ago, dating long before the creation of Adam and Eve (according to the Biblical timeline). The genetic evidence for humans being potential “cousins” of chimps is astounding in that approximately 99% of our DNA is identical to that of chimpanzees. The one percent variance between our DNA and that of chimpanzee DNA is what distinguishes us from apes, but in the genetic world one percent could potentially mean that all of the DNA in that one percent is what makes us distinctly different from say starfish. Although theologians refuse to believe that humans evolved from apes, how do we account for species such as the Geico Neanderthals or other upright-walking mammals that shared more behaviors with humans than chimpanzees do. Neanderthals looked more like humans today than modern apes do, so how does religion account for these differences?

An interesting view on the culmination of both the scientific and religious aspects concerning our existence can best be described by John MacArthur: “For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.”

The PCR song April 29, 2010

Posted by Dr. O in Biology, Fun, Genetics, Science & Culture, Science Education.
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To build on the post containing the rap song on photosynthesis, I thought I’d add this little music video montage put out by Bio-Rad. It’s hilarious.  See…scientists DO have a sense of humor.

Here is the original Bio-Rad link.

Bacteriophages have been found to have new uses–making car fuel! April 29, 2010

Posted by Jill in Biology, Chemistry, Environment/Conservation, Fun, Genetics, Science & Culture.
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hydrogen-fueled car

For those molecular geneticists out there, you will appreciate the new discovery of using a genetically modified M13 phage as a source for making hydrogen fuel out of water!

The M13 bacteriophage is often used in molecular genetics work as a cloning vector. The phage contains a single strand circular DNA genome of 6407 nucleotides that is released into a host cell as a result of the phage absorption. When used in a host cell, the, the host cell proteins will form the double-strand replicative form (RF). This new circular RF DNA is required for M13 packaging because the viral proteins are synthesized from mRNA transcribed off the strand of the RF molecule. From here, M13 DNA is packaged at the host cell membrane, and then releases the infectious particles.

Researchers have found a way to harness the M13 virus in such a way to break apart water molecules, producing hydrogen fuel. Researchers have been able to genetically modify the M13 virus, normally infecting bacteria, so that it would instead bind to a catalyst called iridium oxide and a biological pigment, zinc porphyrins. The viruses then will naturally arrange themselves into a wirelike structure while the catalyst and pigments will harvest sunlight to divide the oxygen from the water molecule. The virus works in this mechanism in that the pigment acts as an “antenna” to collect the sunlight and transfer the energy down to the virus, emulating photosynthesis.

Researchers have successfully been able to separate the oxygen from the water molecule, which is the hardest part of the water-splitting process. The hydrogen will then split into its parts (electrons and protons), but researchers are still attempting to harvest the hydrogen parts in order to collect the gas separately and then convert the gas eventually into hydrogen fuel.

The benefits to this are numerous, including finding a green way of obtaining hydrogen fuel without creating carbon emissions as well as making the process self-sustaining. The ability to harness the mechanisms of photosynthesis in order to control the electron transport in a system is one of the biggest problems in creating a system for artificial synthesis, but this approach allows the transfer of electrons to be controlled.

The full article can be found here: GM viruses offer hope of future where energy is unlimited

I have also included an entertaining rap dealing with photosynthesis: Photosynthesis Rap

And before you’re a skeptic and are thinking that no one would make up a rap about photosynthesis, I found another rap about ATP synthesis: ATP Synthesis Rap