Living in genetic comfort zone: How to avoid influence of genetic variation

As we have learned, the phenotype of organisms is not only shaped by their genetic make up, but by environmental stressors during development as well. A recent study conducted by a group of population geneticists at Vetmeduni Vienna showed the effect of canalization on two separate strains of fruit flies, Oregon and Samarkand. Canalization is a sort of buffering system that, regardless of genetic mutations or environmental stressors, is able to keep an organism healthy and stable throughout its development. This mechanism of canalization allows development to occur without recognizable changes in the phenotype of the organism. The article explains that the researchers subjected the flies to different temperatures (13°C, 18°C, 23°C and 29°C) to analyze the variation in their gene expression. Their results showed that the flies have a sort of “genetic comfort zone” at 18°C where the gene expression in both strains was unaffected by the temperature. However, when the temperature was above or below 18°C the phenotypes of the flies were altered significantly. As Christian Schlötterer, one of the researchers studying the flies explains, “Once an organisms leaves the canalized range, those hidden genetic variations can be expressed and become visible.” This phenomenon is known as decanalization.




I found this article interesting because the idea of decanalization shows how environmental stressors such as diet, smoking, air pollution or stress can cause the expression of disease in human beings during development. I also found it interesting that diseases such as diabetes, asthma, depression and cardiovascular disease can be the consequence of genetic decanalization as researcher Greg Gibson proposes.










Primary source: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004883


Secondary source: http://www.sciencedaily.com/releases/2015/02/150226141412.htm

The Bible and Science, fighting again

According to a new study, scientists from the University of Sheffield found that the "Y" chromosome in males is older than previously believed. Their studies show that the 'Y" chromosome is 8,300 years older than previously believed putting the age at 208,300 years old, while the Bible claims that the humans appeared a mere 6,000 years ago. The Bible also makes claims that there were originally only two humans, Adam and Eve, and all current humans are decedents of them. The article written by the scientists from University of Sheffield claim that there were groups of "Adams and Eves" living side by side wandering the Earth.

I found this article very interesting and I believe that it is very helpful as well. I believe that it helps to educate people who may have limited sources of knowledge about the development of humans over an extended period. I hope that articles like this continue to come out to educate people the history of humanity.




http://history.trendolizer.com/

Hybridization of Blue-winged Warblers and Golden-winged Warblers

   The Golden-winged Warbler, Vermivora chrysoptera, is warbler species that lives in North America, specifically in the northern states of the US and parts of southern Canada in the summer months. This bird then migrates to the northern countries of South America where it winters. The Golden-winged Warbler, due to its preference of early transitional habitat areas, has lost habitat to human development or humans lack of forest management. Its preferred habitat, which consist of early transitional species, is maturing and then is being protected by government agencies for conservation. However, the conservation of these areas leaves them untouched and allows them to mature into forests, which is not habitat suited for Golden-winged Warblers. This forces these birds to share this transitional area with the Blue-winged Warbler, Vermivora cyanoptera. 

This habitat sharing has lead to hybridization and two new species have emerged from it, the Lawrence's Warbler and the Brewster's Warbler. This causes problems because genetic lines between the two warblers become crossed and do not remain pure. In order to protect the future generations of the Golden-winged Warblers lands must be set aside that will consistently be maintained for the preferential habitat of each bird species independently. This will ensure its longevity and prevent further hybridization between these two species.  
   I found this article very interesting. It reenforces my belief in habitat management as well as habitat conservation. These two warblers show that conservation and management are not separate entities but rather go hand in hand.  

Sun Damages DNA in Skin Cells Long After Exposure

Each year, research on the sun's affect on our skin becomes more and more abundant. If you aren't wearing sunscreen by now or are still hitting the tanning beds, this new study may finally change your mind. Scientists have discovered that the sun's ultraviolet light can cause damage to DNA long after the physical effects of sun burn have stopped, and "certain damaging reactions that can lead to melanoma-causing mutations may take hours to evolve and mostly occur after you get out of the sun."

This study was led by Douglas E. Brash of Yale University, and included scientists from around the globe. They came to the conclusion that 'radical species' (superoxide and nitric oxide) that are generated from ultraviolet light, damage DNA even after irritation from being out in the sun ceases.

These radicals react and create peroxynitrite, which oxidizes and fragments melanin polymers (a pigment that protects mammals from harmful sun rays). They discovered this by using compounds found in melanin, to create lesions (or "dimers") in DNA, which in turn leads to mutations causing melanoma, a.k.a skin cancer.

The team of scientists found that at least half of the dimers you can be exposed to come in the dark, rather than daytime. While direct DNA damage happens almost instantly, the lesions can take hours to develop. This research gives a lot of information regarding melanoma. 

I thought this article was very interesting because too many people still think that even if you're in the shade you can't be affected by the sun's rays, or that it's unnecessary to wear sun screen. Also, tanning beds are a direct feed of UVA radiation; people go to great lengths to get a tan and will practically cook themselves alive in these beds, not to mention it's highly unsanitary. I, too, was once a naive beach-goer who didn't put on sunscreen due to the fact I do not burn. I have since learned that even if you do not get sun burn, it is still extremely important to protect yourself from the sun's harmful rays, or you run the risk of getting skin cancer. 

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Mystery Microbes Among DNA Diversity on NYC Surfaces

A recent study published in Cell Systems found that several organisms on the NYC subway and other places in the city, match no other known organisms. Over a 17 month period, Researchers at Weill Cornell medical college went throughout the city (above and underground) swabbing benches, handrails, poles, and doors. They found that almost half of the DNA they discovered had been completely unknown to science. 

Along with the mysterious DNA, researchers found recognizable DNA such as bacteria and viruses, both being mostly harmless. They also identified small particles of DNA from anthrax and the bubonic plague. Overall they found that only 12% of the thousands of Bacteria and virus samples discovered, were associated with diseases. The most common microorganism found was Pseudomonas studtzeri, a rod-shaped bacterium known for its flexible metabolism that can cause infection in humans.

         The researchers also found that human DNA found in subway stations aligned with the ethnicity of people living in that area. Samples taken in the subway near a neighborhood with high numbers of Hispanic residents, yielded a large amount of Hispanic and Asian genes. Samples from the Brooklyn neighborhoods turned out to host genes specific to British, Tuscan and Finnish heritage. These researchers now say that by understanding the normal population of microorganisms in the city, they now have a baseline to compare new samples against in the case of bioterrorism or a disease outbreak.

I find this study very interesting because of how much researchers can find out about a city just by looking at DNA swabbed from random places. Also, how they found a sample related to the plague was very interesting, (but also a bit scary). 

Original Article

New HIV Molecule Proven to Protect Cells from Virus

        Scientists have been conducting research on the HIV virus and its genetics and have created and begun testing a new vaccine that partially protects monkeys from an HIV-like infection. This article suggests that scientists are homing in on the ingredients for a HIV protective vaccine that could potentially be sent off for human trial. The Simian Immunodeficiency Virus (SIV) prime-boost vaccine offers partial protection  to monkeys from acquiring the disease by about 80%.  On the contrary, those individuals that became infected, the vaccine regimes reduced the amount of virus found in the bloodstream. Scientists are now working on a human-adapted vaccine for experimental trial. 

        I found this article to be very interesting and short, sweet and to the point. I know scientists have been researching HIV/AIDS for decades upon decades trying to find a preventative measure or cure. The risk of contracting HIV is real. I know many individuals personally who have been infected.  Could this be the cure?

Language Delay Linked to Chromosome Deletion

A article posted in Medical News Today talked about a research study led by CHOP which used a magnetoencephalography to look at the magnetic fields in 115 children. They believe that many children who have the deletion or duplication of the 16p11.2 chromosome who also usually happen to have autism are having more trouble with their language skills. They took 115 children, 43 with 16p11.2 deletion, 23 with 1611p.2 duplication and 49 healthy controls and found that children with the deletion have 23 millisecond, in a study done in 2010 Roberts found a 11 millisecond a brief interval of time, but it also meant that a child who heard the word elephant was still processing the 'el' sound as other students were moving on. With these finds Robert and his team are trying to figure out if this is a issue with the brain not sending information quick enough of information not getting to the brain quick enough. Many studies have been done on kids in terms of brain and behavior, but none so far on genetics and behavior. Robert's end goal is to try to make drug that can treat this 23 millisecond gap between processing and responding through further research and trials.

I personally think this research is ground breaking, children with autism have so much knowledge and understanding, but it is often hard for them to convey their intelligence. If Roberts can produce a drug that makes it easier for people to process and relay information quicker it would be ground breaking for many children. I also think that this kind of work will lay the ground work for other types of disorders like down syndrome in trying to alleviate symptoms due to chromosomal abnormalities.

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The Influence of Genes on Addiction

An article from the University of Utah Health Sciences Department, Genes and Addiction, discusses the role that genetics play on substance addiction. Genes are responsible for making an individual more vulnerable to substance dependence.  Research performed on laboratory mice has been helpful to determine the effects of similar traits in humans. When a certain gene was found to play a role in addiction in mice, the counterpart sequence of DNA was examined in humans.

I agree with the article that an individual’s environment is a much larger factor to addiction than genetics. If inheritance causes an individual to have higher withdrawal symptoms for a substance, but their environment does not put them in a position to experiment with this substance, then the genes would have no visible effect to the individual. However, if an addict has a genetic predisposition to have harsher withdrawal symptoms, than genetics could aid in the individual remaining addicted to the abused drug.

A goal of studying the genetic basis of addiction is to improve treatment for addicts. Identifying gene sequences that play a role in addiction allows scientists to develop drugs that are more effective in controlling this gene. This can begin a new wave of treatment, with drugs tailored specifically to your genetic make-up.

Potential Issues in Precision Medicine

The focus of this article was to bring up potential issues that could arise in medical genetic testing. The author of the article stated that there was a girl who had been misdiagnosed for DiGeorge Syndrome. After her misdiagnosis it was later determined that she did not have a missing fragment on chromosome 22.

The author then cited another incident where a women underwent extreme surgery to remove her uterus. It was later determined that the genetic test was read wrong and that the surgery was unnecessary. The risks for misinformation also included maternity care. Which according to the author is not a definitive as some doctors believe it is to be.The author then brings up the issue that medical doctors are not properly trained to diagnose genetic information because most of them were already practicing medicine while the first human genome was being sequenced.

In my opinion the the author brings up a pretty good point on potential malpractice incidents due to medical genetic testing. However I disagree with the author when they said that doctors should be trained in the field of genetics along with everything else they have to know. Doctors have to many things going on to effectively and accurately use genetic testing as a means of preventative healthcare.In my opinion this could and should open a new career path in the medical industry in the years to come.


http://www.newyorker.com/tech/elements/problem-precision-medicine

Bacteria Can Remember Viruses

     Researchers at Rockefeller University have provided more insight on how bacteria can "remember" viruses that have attacked them in the past. The basic idea is that the microbes' genome encodes viral DNA and stores it to create enzymes that can fight off the virus when it attacks again. One of the main enzymes produced is Cas9, and it is responsible for cutting viral DNA and embedding it into the bacteria's adaptive immune system, known as CRISPR. This system operates by altering the genome of the bacteria: "adding short viral sequences called spacers in between the repeating DNA sequences. These spacers form the memories of past invaders". Then, the Cas9 enzymes comes into play again because they destroy the DNA that resemble the ones found in the spacers of the bacteria's genome. The researchers at Rockefeller University have expressed that their research could potentially push action targeting and viral cutting into a more important role in biotechnology.
     I found this article to be a bit dry in terms of writing style. However, the idea within the article is pretty interesting. Being able to show that bacteria can memorize viruses for future protection is unbelievable. I didn't know viruses even bothered to infect bacteria, but this article is suggesting that bacteria are smarter than they appear. Furthermore, they have already adapted to this form of attack by outsmarting the viral DNA. In a sense, this article makes bacteria more likable (weird... I know) because they are able to protect themselves in a way that resembles the human immune system.

Original Article
Learn More About CRISPR

Epigenomics of Alzheimers Disease

     Alzheimer's disease is a very complex disease that not much is known about. There is no cure for Alzheimer's, it is a progressive brain disease that destroys the memories and the ability to think in the people it affects. Alzheimer's mostly affects people 65 and older, although in rare cases symptoms can appear anywhere from the age of 30 on.  Genetics plays a large role in Alzheimer's disease although it is likely that environmental factors are involved as well. It is said that damages to the brain can occur as early as a decade before symptoms become prevalent in an individual. Many studies have been done to try to shed some light on Alzheimer disease, one of which done by an interdisciplinary team at MIT and the Broad institute analyzed changes that occur in genes in regions that regulate the genes of Alzheimer's.

This study used mice that were engineered so that the gene for a protein called p25 would be overstimulated in the brain. This creates very similar symptoms to that of Alzheimer's in humans. With these mice they would be able to study changes that occur during early stages of Alzheimer's for the first time. The idea was that they would compare them to the later stages and symptoms. The study showed that "Neuronal plasticity processes that are involved in learning and memory were dampened, and immune and inflammatory pathways were activated." They found that microglia, a type of immune cell whose job it is to clear infected or damaged cells as well as secrete chemicals that produce inflammation, are a large part of the progression of Alzheimer's. They are still unsure of what exactly these cells do to further the development of Alzheimer's, however they play a large role in normal brain function and share a key cell surface marker with macrophages that infiltrate the brain during the progression of Alzheimer's.
   
     The results of this experiment showed that in both mice and humans the functional conversions were not restricted to protein coding genes, which opens up new doors for studying organs such as the brain in model organisms and how they respond to things such as disease. During this experiment they were able to map out the epigenome for Alzheimer's, this is a huge step for Alzheimer's, the research showed that genetic variants were associated with immune processes instead of neural processes. This means that Alzheimer's may not be a genetic predisposition to the repression of neural pathways, but a consequence of environmental factors as well as aging and altered immune pathways. This study will largely help the study of Alzheimer's and maybe one day help to prevent Alzheimer's progression.

Link to article: Epigenomics of Alzheimer's
Additional link: Alzheimer's Facts

Human DNA Placed Into Mouse Embryos

Evolution of the human brain has always been a topic of interest for scientists over the years. Many have wondered how human brains have become so complex and why chimpanzee brains have lagged behind even though chimpanzees have almost all of the same genes that humans have. Scientists at Duke University have tackled this question and obtained some interesting results. More specifically, these scientists have found differences between chimpanzee and human genetic codes and observed how these differences affected embryonic brain development in mice.

For the study scientists focused on shorts pieces of DNA called enhancers that are a part of every genome. These enhancers regulate gene activity and are sometimes human specific. Until now none of these human specific enhancers had been shown to influence brain development directly.  The scientists searched through chimpanzee and human genomes to find enhancers that are expressed in brain tissue and early in development. Enhancers that were largely different between the two species were of high importance. In the beginning, 106 enhancers were narrowed down as being potentially important for discovering the differences in chimp and human brains. Out of these 106, 6 were thought to be involved in brain development. The enhancers were named HARE1-6, standing for human accelerated regulatory enhancers.  HARE5 showed the most promise as it is located near a gene, Frizzled8, which is known for its role in brain development and disease. The researchers directed their attention onto this enhancer and postulated that it enhanced Frizzled8 since HARE5 and Frizzled8 make contact in the brain.  

The HARE5 in humans and chimpanzees only differ by only 16 base pairs. However, the human enhancer was active earlier and more active in general in the mouse embryos than the chimpanzee enhancer. The activity differences between the two enhancers were detected at a critical time in brain development. The mouse embryos with the human HARE5 ultimately ended up with more neurons than those with the chimpanzee HARE5. As the mouse embryos developed more and more and came closer to the end of gestation the difference in size of the brains became noticeable. The mice that had human HARE5 had brains that were 12% larger in area than those that had the chimpanzee HARE5. The part of the brain that was affected was the neocortex. This part of the brain is involved in language and reasoning. 

This feat was astonishing, just narrowing down the enhancers in itself was a difficult and cumbersome task. Many other scientists have tried to do what the Duke University researchers did and failed. As a result of this successful study, a genetic reason as to why humans have bigger brains than chimpanzees has been discovered.

I feel that this is so interesting and awesome that it has finally been discovered. Humans are so closely related to primates, yet so different. It is interesting to realize that all of the differences are most likely due to some small change in the genetic code. I mean if just one different enhancer could make mice brains larger then imagine what a few differences could amount to. It is astonishing to think about the complexity of genes and how they work together to produce many different characteristics. 

Link to Article: http://www.sciencedaily.com/releases/2015/02/150219133104.htm

Additional Link: http://www.latimes.com/science/sciencenow/la-sci-sn-dna-chimp-human-brains-20150218-story.html 

More than just male or female

Sex determination in placental mammals is described as needing the presence of a Y chromosome. Female cells contain two X chromosomes while male cells contain and X and Y chromosomes. According to an article in Nature, the boundaries between the sexes is much more ambiguous. Some people have conflicting sex chromosomes and gonads that show opposite characteristics of their sex. This is usually known as intersexed or disorders of sex development (DSDs). Researchers say they are about 1 in every 100 people with some form of DSDs.

There are many genes involved in the main forms of DSDs, and variations of the genes can have subtle effects on anatomical and physiological sex. Due to a large diversity within male and females, defining people with a binary dichotomy is difficult. Since sex is defined in a number of ways, the line between males and females can be ambiguous.

At the start of life, the differences between sexes physiologically are indistinguishable to at least five weeks of age. The development of the gonad into testes or ovaries determines the hormones produced to form the being into what is known to be a male or female. Changes in development can have dramatic effects on an individual's sex. Gene mutations that affect gonad development can cause a person with male XY chromosomes to develop female characteristics. Alterations in hormone signaling can also do the reverse with XX individuals developing male characteristics.

Studies with mice have shown that the gonad goes between male and female throughout life and needs maintenance to retain its identity. The gonad, however, is not the only source of sex diversity. DSDs have also come from changes in machinery that respond to hormonal signals from the gonads and other glands. Knowing that sex determination is not as black and white as we may think, makes me view this with wide eyes. There is so still so much we don't know in the realm of genetics, but there is also so much that we have learned that is changing the way we view the world and each other. 

Epigenetic's The New Frontier For The Fight Against Disease ?

An article published in Medical News Today talks about how researchers at the University School of Medicine in St. Louis have been working with epigenetic's. They talk about how every cell in the body has an identical genome and comes from the same instruction book, but what carries out the instructions from that book are different chemical markers. These chemical markers however, are not so methodical, they vary from cell to cell and vary in severity in terms of your health when disturbed. Ting Wang and other researchers at St. Louis figured out 111 of the epigenetic markers in different types of cell tissue. They have only started to scratch the surface with this type of work since epigenetic's is a very new and up coming idea. Ting Wang says there are only 20 other articles in publication like that of his. Which is very little compared to other more researched topics. Wang and his team also made a browser called WashU that allows for faster browsing through massive amounts of genetic and molecular data which has made it much easier on many researchers. Another, interesting thing that one of Wang's researchers was working on is the methylation of certain genes to turn on and off certain expressions. She found over 18,000 regions of the human genome that respond to methylation and this could be a huge break through in diseases like cancer.

This article was very interesting because epigenetics is such a new topic in the world of genetics and has been strongly fought against in the past. Epigenetics is especially interesting to me because I am very interested in Holistic health and it is wonderful to see that modern medicine is finally starting to look at the body as a whole and understanding that what you do today can greatly affect what you do tomorrow. The methylation of certain genes is also very interesting because if we could turn certain genes on and off it would change a lot in the world. We could stop devastating things like cancer and insignificant things that affect a lot of people like hair loss.

Primary Article
Secondary Article

Bedbugs and a Model of Evolution

Surprisingly Bedbugs have more importance than the itchy rash developed when bitten by one of these monsters or the infestation of your home. They have become a model of evolution showing how bedbugs are actually becoming a new species in front of our eyes. Warren Booth, a biologist at the University of Tulsa and a co-author of the new study, states, "For something that is so hated by so many people, it might just be a perfect model organism for evolutionary questions". Bedbugs basically dissapeared in the 1940s due to the creation of DDT. However, the pest has returned rapidly in the past decade because it has evolved resistance to pesticides. Researchers including Dr. Booth have teamed up with exterminators to extract and preserve the species of bedbugs in alcohol that can later be used to extract the DNA to observe how the species is changing. 

Cimex lectularius (the common bedbug) feeds on humans and bats. Dr. Booth collected bedbugs from human households as well as bedbugs from bat roosts in houses and churches over seas. DNA sequences from 214 bedbugs were compared and found that they were very genetically distinct from one another. The history dates back to the first encounter a human had with bedbugs in caves and served as the new hosts. As time went on humans left there cave dwellings and began settling in new environments which forced the bedbugs to adapt. Adaptations to feeding on humans include longer, thinner legs because the no longer had to hang on to bats or that bedbugs that have switched there attention to humans have shorter life spans than those who feed on only bats. According to Dr. Booth, "Many bedbugs that feed on humans carry a genetic variation that makes them resistant to pesticides but, the bedbugs on bats still carry a version of the gene susceptible to pesticides."

I consider this article very interesting because we are living in a time of advanced science allowing us to experience evolution. Whether it is bedbugs or human beings evolution is happening all around us. These little insects are close to evolving into a new species different from its bat-feeding ancestors. In our life-time how many times will we be able to add a new branch to Darwin's tree of life. Who's to say more species lacking the research are going through the same changes. Its all very exciting and I hope to experience more evolutionary changes in my life time.

Original Article: Click Here

Secondary Article: Click Here

DNA Hints to When We're Going to Die

DNA is the basis of genetics. It can be used for many things such as discovering what diseases run in our own genomes. Biologist Jonathan Alder and his recent observations of DNA, he has discovered that telomeres can tell us about the lifespan. The telomere is a great predictor of lifespan based on the size of the telomere. The shorter that the telomere was, the shorter the lifespan that person was going to have. This also indicates that the person has a greater chance of developing a disease. Within the last thirty years, they have tried mutating the telomeres to provide further research. Each and every time the cell divides the telomeres get smaller and get shorter as we age. When the telomeres are no longer present it can lead to disease.

This article is interesting because DNA can tell everything we need to know about the future. If we are able to predict how long we are able to live it might be possible to predict what else could happen to us. Considering the telomere is such a tiny part of DNA it is amazing that we can deduce so much information. It could help us better understand if the onset of a disease could be predicted. This research is important because as we progress into the future we may be able to prevent a short lifespan for the individuals with short telomeres.

Article

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111 New Tissues and Cells Mapped in Epigenome

The National Institutes of Health Common Fund's Roadmap Epigenomics Program has been supporting researchers in mapping different cells and tissues. This is a major step in understanding what the different DNA parts actually do.  It is now understood how over one hundred tissues and cells are coded for.

During the development of different cells, there are proteins that have the ability to turn genes on and off.  These regulatory proteins leave a chemical mark, which was examined and compared to by different researchers.  Cells from all different areas of the human body were studied to fully understand the human genome.  Understanding the variation has helped understand human biology at a cellular level, but also stand as a way to understand different segments of DNA.   

The human epigenome could even potentially explain how DNA and various diseases are connected.  By knowing the original genome and epigenome, witnessing a change in genetics can provide an understanding of where conditions like Alzheimer's and fetal growth abnormalities spur from.  The NIH is hoping to work on finding genetic signs to identify disease early.  This is really interesting because human genetics are about to be completely understood.  If this research keeps up, they'll probably find out what every piece of DNA codes! 

Primary Article

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All It Takes is One Mutation

A university research team from Scotland recently discovered a bacteria that has mutated and gained the ability to jump from humans to rabbits.  The scientists traced the evolution of a specific bacterium that causes skin infections in rabbits: Staphylococcus aureus (ST121).  Strangely enough, ST121 has been found in some humans as well and although it's relatively harmless, it can sometimes lead to meningitis or sepsis.  

This similarity allowed the scientists to track the evolution of the pathogen and discover that the rabbit-specific ST121 bacteria evolved from the human-specific version over 40 years ago and mutated enough to be able to jump from humans to rabbits.  One genetic mutation allowed this to happen.  One naturally occurring genetic mutation was enough to completely change the bacteria and let it change host species.  The fact that a genetic mutation this small can alter a pathogen so much brings up a lot of questions and a lot of places where more studies can be done to see what other bacteria, if any, may be able to jump so easily from another species to humans or vice versa.  This could also pose a problem for industrial animal businesses that keep many different species of animals in close quarters.

I think this is a very interesting topic because it's bizarre; a human probably wouldn't expect to get an infection from a rabbit.  I also think it's interesting how only one genetic mutation allowed the bacteria to do this.  Scientists know little about bacteria and viruses because they are all so complex and there are many variations of them so scientists may never learn everything there is to know about their makeups.  It's important that scientists research this in more detail with other species of animals if they ever want to help slow or stop the spread of these species-hopping pathogens for peoples' and animals' sake.

Nucleotide Excision Repair Nonexistent In Brain

Nova Southeastern University researchers discovered that tissues of different mammalian organs have very different abilities when it comes to repairing damaged DNA. The findings showed the heart has the greatest capability of repairing its DNA. This was followed by the intestines, kidneys, spleen, testes, and lungs. However, the brain showed no ability to repair its DNA. Although their study was conducted on mouse cell tissue cultures, they stated that the same results would occur in human tissue. They exposed growing cells to ultraviolet light to simulate sunlight and cause extensive DNA damage. They used skin cells as their control group and then exposed the other organs to ultraviolet light. The researchers then measured the amount of DNA repair performed by nucleotide excision repair.

Nucleotide excision repair requires a high level of metabolic investment by their respective cells. The brain cells use their energy to focus on more essential activities and are not commonly exposed to ultraviolet light. Lead investigator Jean Latimer, Ph.D., associate professor of pharmaceutical sciences at NSU's College of Pharmacy said, "The human body was not designed to live past 30 or 40 years, so our brains haven't prioritized DNA repair over other necessary functions. Our brains are frequently not physically prepared to last as long as medical science is now allowing our bodies to live. These findings could help explain a root cause behind memory loss and dementia."

I found this article intriguing due to its finding of a simple but incredibly important problem with the brain. I was surprised by the brain's inability to perform nucleotide excision repair, since it is a common DNA repair function and the brain is a highly complex organelle. This article made me wonder if the brain's inability to perform nucleotide excision repair was due to it never being present in its cells, or if it was an ability slowly lost through evolution. I hope that with this research, scientists may uncover new ways to possibly combat memory loss and dementia by finding  a way to make brain cells capable of this type of DNA repair.

Original Article: http://nsunews.nova.edu/nova-southeastern-university-researchers-discover-dna-repair-is-high-in-heart-nonexistent-in-brain/

Looking to Genes for the secret to Happiness

Scientists have long surmised that your mood can affect your health, but researchers at UNC and UCLA have recently discovered some of the cellular mechanisms behind the genetic effects of happiness. The researchers had 80 healthy volunteers complete an online questionnaire about why they felt satisfied with their lives, and then drew blood in order to analyze their white blood cells. They were looking for differences in gene-expression that controlled different aspects of the immune response, and they found that there was a big difference between individuals with either hedonic or eudaemonic reasons for their happiness. This whose happiness came from consuming things (hedonic) had increased markers for inflammation, while those whose happiness came from service to others, or a higher purpose (eudaemonic) had higher levels of antibody producing gene-expression. These shifts are most likely driven by an evolutionary strategy of working for the common good.

The researchers added that there is no real need to change your lifestyle based on these findings, since many types of happiness can coexist. It is however recommended to try to look past the simple gratification when performing a task. I find this very interesting that something as simple as our source of happiness can alter your life at the biological level. 

Main article link: http://well.blogs.nytimes.com/2013/08/23/what-our-genes-reveal-about-true-happiness/
Secondary link: http://www.livescience.com/46877-denmark-happiness-genetics.html

New Look on Life

     A research team from the University of Houston College of Optometry has designed a new strategy for prescribing glasses to individuals with Down syndrome. This strategy involves a newly constructed computer simulation program that fully examines the eyes of the individual. With this extensive examination, the individual's glasses can maximize their ability to see. In order for the strategy to be developed, the researchers needed to identify some of the physical defects Down syndrome does to the eyes. Also, the researchers needed to identify the genes responsible for causing these defects, especially the ones that contribute to eye development and function. The optical defects include "poor focusing abilities, misalignment of the eyes, and reduced visual acuity". Because of these effects, along with the intellectual disabilities, determining an accurate perscription is difficult. The researchers understand this difficulty, which is why they designed the new computer simulation. Their hope is to implement the system and distribute it across the country. In the future, the researchers hope this system will help patients with Down syndrome see better; thus, making them more independent. The new independence will allow these patients to live happier lives as well as make Down syndrome a little easier to live with.
     It is my hope that this system, or something like it, becomes a huge success. I know that people who suffer from Down syndrome do not like to feel dependent on others. With these new glasses, patients can have a sense of independence, and they can begin to live their lives on their own terms. I wish more research was done in this population of people to help them live more fulfilling lives.

Original Article

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An Increase of Cerebral Palsy Cases have been Linked to Genetic Mutations

For a very long period of time, it was believed that cerebral palsy was in no way shape or form linked to genetics due to the fact that as little as 1% of cases were likely caused by genetic mutations. However, new research conducted by the Australian Collaborative Cerebral Palsy Research Group has indicted that at least 14% of cerebral palsy cases are linked to a genetic mutation--one of the biggest discoveries into cerebral palsy in 20 years. Cerebral palsy is a congenital disorder marked by impaired muscle cooordination, and other disabilities caused by damage to the brain before or after birth. Typically, 70% of the brain damage that causes cerebral palsy takes place prior to birth (mostly in the second and third pregnancy trimesters).

Although it is still not relatively known what causes the brain damage--before it was believed that the damage was caused by the child experiencing a lack of oxygen before or after birth--this new discovery may open doors to find the source of the condition and help provide better treatments to children who have the disorder, as well. Being that now 14% of cases are due to genetic mutations, cerebral palsy in origin is at least partly genetic. For that reason, changes will be administered in the approach to diagnosis, treatment, and management of the condition. Additionally, the research group has gathered a unique DNA and clinical data cerebral palsy biobank which will be used to conduct further research on the matter.

It will be very interesting to see what further research may discover about the potential causes of cerebral palsy. Being that it took 20 years to make this ground-breaking discovery, it is very uncertain how long it would take to make another.

Original Article: click here.
Related Article: click here.

Gene that Shaped the Evolution of Darwin's Finches is Discovered

In light of Charles Darwin’s birthday a study that identified the gene that controls beak size in the Galapagos finches was published on February 11, 2015, just one day before Darwin’s birthday. The study, which was undertaken by researchers at Princeton University and Uppsala University, highlights the genetic aspects of evolution as well as gene flow and speciation. More specifically, it was discovered that evolution occurs in halting and disordered steps, allowing for genes to spread and create new lineages. Eventually the new lineages can evolve into entirely new species given the right set of circumstances.

DNA samples from 120 birds were collected and the genomes of the birds were studied. Each of Darwin’s 15 species of finches was represented in the population of the 120 birds. After studying the genomes the researchers noted a stretch of DNA that was different in finches with blunt beaks and in finches that had sharp, pointed beaks. A gene, ALX1, was found within that section of DNA. In humans and mice this gene influences the development of facial features. If this gene mutates and becomes inactivated then severe abnormalities in humans can result. However, mild mutations of this gene have the opposite effect in the finches. Instead these mutations lead to observable evolution in the finches. It was also found that individual birds of the same species sometimes had different forms of the gene. Of course, this finding is huge as natural selection runs off of genetic variation and cannot occur without it and natural selection is a means through which evolution happens.

Having studied the finches for forty years the researchers on this study know that the size and shape of the finches’ beaks plays an immense role in their survival, just as Darwin did.  They realized that the tough environment that these birds are exposed to made it essential that the finches had appropriate beaks that were suited to their habitat. However, until this study was conducted the researchers did not understand the genetic aspect of the evolution of these finches.  

Along with locating the gene that plays a role in the evolution of these finches the study also provides more information about what happens when genes are passed from one species to another (between two closely related species). Usually, the offspring of these two closely related individuals would be sterile, but that is not the case with the finches. The offspring can mate with individuals from either of the two parental species. The baby finch will conform to one of the parental species based on song and appearance. However, the finch still contains genes from both parents. This process, known as gene flow, has given the researchers a better picture of how genes move from specie to specie and create new species.

I think that this is really interesting and I haven’t thought much about it. It never really occurred to me that all of Darwin’s work was observed and he of course had no idea what genes were and which genes were playing a role in evolution. It is surprising to me that it has taken researchers so long to discover this about the finches, but it was nice that they published the study near his birthday. Honestly, I didn't think anyone still cared about the finches and didn't know that they were still being researched. It just shows that the Galapagos Islands offer many interesting species to study and that even though evolution has been studied so much there is still so much to learn. 

Link to Article: http://www.sciencedaily.com/releases/2015/02/150211153923.htm

Additional Links: http://beforeitsnews.com/science-and-technology/2012/08/scientists-sequence-genome-of-darwins-finch-2455302.html

http://www.sciencedaily.com/articles/e/evolution.htm

Darwin's Finches Get Their Genomes Sequenced

Among the most widely known scientific experiments is Charles Darwin's finches. In 1831-1836 aboard the HMS Beagle, Darwin traveled to the Galapagos Islands where he would study the variation in beaks in endemic bird species. This helped lead to Darwin's theory of evolution by natural selection. Researches have now been able to bring modern genetic technology to this timeless experiment and sequence the genomes of all fifteen species of Darwin's finches, and pinpoint the gene responsible for the renowned beak variations. The study has also redrawn a family tree of the birds.

As the story goes, Darwin observed the physical characteristics of the finches and noticed that their beaks were adapted to the types of food they ate; for example, some had thin, sharp beaks for collecting pollen and nectar (like the Cactus finch), while other had strong, thick beaks for cracking nuts (like ground dwellers such as the Large ground finch). It's a prime example of "adaptive radiation", where a species deviates from a single ancestor as a response to selective pressures, and new species emerge.

With the tremendous amount of progress made in DNA sequences and genetic testing, geneticist Leif Andersson along with a team of scientists, analyzed samples from 120 birds and were able to redraw the family tree of the finches, connecting the dots between branches and indicating gene exchange. The team discovered mixing of genes between species, indicating crossbreeding, and "were able to pinpoint the genes responsible for beak morphology." One of the genes, ALX1, is known to control facial development in vertebrates. This is one of the genes that helped finches rapidly adapt their beak structures to the environment. This was seen as recently as the 1980's, where a drought changed the food supply and the birds had to adapt. 

Other scientists have pointed out that beaks differ in many more ways than just being pointed or blunt. However, studying the ALX1 gene even further will reveal exactly what the gene controls, in this case, specialized beaks.

I really enjoyed this article because Darwin's finches experiment has always fascinated me and when combined with modern genetic technology, it's really exciting to find out what controls variation in beak types. Charles Darwin would be amazed at how far his initial study has come!

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An Apple a Day Gets Approved Any Day

The government has approved the commercial planting of genetically engineered apples that don't brown when sliced or bruised. The developer Okanagan Specialty Fruits, says the non-browning feature will make apples more appealing to consumers and food service companies. However executives in the apple industry worry the biotech apples will face controversy from some consumers along with them loosing exports in countries that do not like genetically modified foods. The Department of Agriculture has considered these issues, however under the law, approval is based on whether a genetically modified crop poses a treat to other plants. The apples do not pose any risk. The apples are genetically engineered to suppress the production of an enzyme that causes browning when the cells in the apple are injured, for example by slicing. But over time they will still rot a turn brown. 

In my opinion, although the browning of apples is not appealing to me in anyway, I'm not a fan of it being genetically altered to prevent it. There are other ways to prevent the browning for a bit more time, for instance, Lemon juice, which is natural. That's just my opinion though, I'm not going to be the guinea pig for an apple. 

Ice or Aliens?

Scientists have recently recreated interstellar ice, found to constitute most of the matter comprising the dense molecular clouds that lead to planetary and star formation. Within the ice, many simple sugars are formed with some help from ultraviolet radiation and cosmic rays, glycolaldehyde and glyceraldehyde being the two most important. What is their significance? These simple sugars are the backbone in the formation of nucleotides. As we now know, nucleotides serve as building blocks in the creation of DNA and RNA.
According to the LiveScience.com article, this explains that a comet colliding with early Earth and leaving these sugars behind, could have lead to the formation of complex life and eventually humans. Shifting now, from what we already know to speculation of the unknown, what could this mean? These new discoveries could mean that another life form exists somewhere in the universe. After all, if a comet carrying simple sugars suspended in ice is the source of our existence, what's to say this same mechanism hasn't created other societies of complex life?

Bacteria: The good and the bad

The human body is home to hundreds of different types of bacteria that we want and need. In a way we have a symbiotic relationship with many of the naturally occurring bacteria in our bodies. For example we benefit from them helping to maintain overgrowth of potential pathogens and they are able to reproduce and spread in our bodies. However as we all know too much of a good thing is not always good for us. Too many bacteria can become hazardous to us. "Ewa Chrostek and Luis Teixeira studied the symbiosis between a fruit fly and the bacterium Wolbachia to answer how benign bacteria become pathogenic"(Instituto Gulbenkian de Ciencia 1) It was found that a single genomic change in the bacteria can make them deadly. The bacteria originally protected the fly and other insects from numerous viruses, but if they grew and reproduced too fast they could quickly become deadly.

 Luis Teixeira said that there was "a region of the Wolbachia genome responsible for regulation of its densities in the flies. This is the first study linking genes and their functions in this bacteria and it provides a unique point of entry for the understanding of the widespread insect-Wolbachia symbiosis"(Instituto Gulbenkian de Ciencia 1) Since we have a better understanding of how bacteria can effect small creatures such as flies, we should start/continue researching what could happen if a single genomic change occurred in one of the many bacteria in our own bodies.

The Breast Cancer Gene

Mary-Clair King, the woman given the credit for discovering the breast cancer gene was recently interviewed by the New York Times. Her question/ answer interview style revealed some very significant medical break-through's. Not only was her and her laboratories accredited with the discovery for the breast cancer gene BRCA1 on chromosome 17, she also won a huge battle against a company called Myriad who tried to patent the rights to gene. Backed by her lab at the University of Seattle Washington, and The Attorney Generals Office she won the Supreme Court Ruling 9-0 because genes are natural and cannot be patented. King was also accredited in her contribution of using mitochondrial DNA testing to reunite displaced families in Argentina. Mitochondrial DNA testing can be used to identify parentage or lineage.
It seems as though Mary- Clair King made some extremely significant contributions to science and human rights. Locating the gene was very important, but perhaps even more important was her preventing the patenting of genes, which could have been a very terrible occurrence in the world of genetics.

Non-browning genetically modified apples

         The developer Okanagan Specialty Fruits recently developed a genetically modified apple  that is resistant to turning brown when it is bruised or even sliced. The U.S. government just recently approved this apple to be sold in the country and they believe it will reduce the amount of apples that are discarded due to browning significantly over the course of the next few years. A large amount of farming companies are already lining up to purchase trees to begin manufacturing these genetically modified apples in large amounts. Unlike most genetically modified  fruits or vegetables which have the genes of another species inserted into them, these 'Arctic' apples, as they are called, instead have the genes inside them modified as so to suppress the enzyme that causes the apple to brown.
        Many consumer and environmentalist groups however are opposed to these apples and believe they are unnecessary and will tarnish the name of an everyday fruit many people have come to enjoy. They also attempt to argue that these modified apples will not carry the same nutritional value of a regular apple and will make them less that suitable to attribute to a persons daily dietary needs. Specialists form the Okanagan Specialty Fruits  developing company have however proven that they do indeed carry the same nutritional value, and are optimistic that Arctic apples will be seen in supermarkets across the country by 2016.
         I believe these apples will become widespread in the near future and we will begin to see Arctic apples in American homes everywhere. The non-browning capabilities of the apple will make sliced apples more appealing to people, and allow it to become a more common snack that will be seen in restaurants, supermarkets, and even public schools.

The Genetic Link to Obesity

        With obesity rates at an all time high, researchers from the International Genetic Investigation of Anthropometric Traits (GIANT) have analyzed the DNA of over 300,000 individuals in the hopes to discover how genes affect obesity. There are several risk factors that can contribute to obesity. People with a higher waist to hip ratio, are more likely to have fat around their stomach. This can make them susceptible to more cardiovascular problems or diseases such as diabetes. By determining how genes can affect the location of fat deposits, researchers hope to better understand diseases that arise due to obesity. The genes that are thought to play a role in the location of fat deposit was previously understood as important in the creation of adipose tissue. Researchers have found 97 different regions within the human genome that can influence a person's obesity rates. However this is only the beginning. The next step for researchers will to see how these genes increase a person's chances to gain weight. 

I found this article to be interesting because many times we are focused on treatment rather than prevention. Over the summer I shadowed several doctors and they were all treating patients based on what they were presenting at the moment. Don't get me wrong, we need to help sick people when they are sick, but think of all the money we would save by catching an illness before it presented itself. Obesity is a growing problem in America. With research like this we can help patients that are at risk for obesity and help them to make lifestyle changes early in their life. 

Article Link: http://www.medicalnewstoday.com/releases/289343.php

Secondary Link: http://www.mayoclinic.org/diseases-conditions/obesity/basics/definition/con-20014834

Horizontal gene transfer in plants

Neochrome is a hybrid of two other plant genes which code for photoreceptor proteins that sense red and blue light. This gene is thought to have been responsible for the evolution of ferns. Most plants sense and grow toward blue light, but under the canopy, there is less blue and more red light. Researchers wanted to know where this gene originated in ferns. They searched through plant genomes and found a similar gene in hornworts.

They came up with 3 hypothesis for the involvement of neochrome in both ferns and hornworts: They could have had a common ancestor, they might have evolved their gene independently, or neochrome could have been moved across species by horizontal gene transfer.  In order to come to a conclusion, teams of scientists looked through land plants and algae and how their light sensitive genes were related. 

Because the ferns and hornworts diverged in evolution 400 million years ago, if neochrome had come from a common ancestor, it would have been passed on to other plants as well, but since no other plants seem to possess this gene that possibility was ruled out. Because neochrome is such an unique gene, it is also extremely unlikely for ferns and hornworts to have evolved the gene independently. Scientists came to the conclusion that the most probable origin of this gene in ferns was through horizontal gene transfer. Scientists are seeing more and more cases of horizontal gene transfer in plants, but they do not know how it is mediated as of yet.

This article was extremely interesting, up until now I only knew of horizontal gene transfer occurring exclusively in bacteria. It only makes me wonder how much we do not know about plants still and how we could use this recent discovery to our advantage.


http://www.sciencedaily.com/releases/2014/04/140414154444.htm    Main article
http://www.decodedscience.com/hornworts-loan-genes-ferns-shady-environments/44670 

DNA predatory device in the cholera bacterium

Scientists have studied more into the mechanism of how the cholera bacterium stabs and kills other bacteria in order to obtain their genetic material and possibly increase its antibacterial resistance in the process.

When this bacterium invades the small intestine it causes cholera, a disease with symptoms of acute watery diarrhea which eventually leads to dehydration.

This bacterium is naturally found in the sea attached to small planktonic crustaceans. It feeds on the chitin of their shells. When chitin is available, the cholera bacterium enters a phase known as “natural competence” in which it attacks surrounding bacteria regardless of species using a small spear like weapon called “type VI secretion system” in order to destroy them and obtain their genetic material afterwards.

Researchers conducted tests using this bacterium. They grew them on chitin surfaces to simulate natural environment. They observed that their “type VI secretion system” is also used in the transfer of genes. They used genetic and bio imaging techniques in order to identify which mechanisms are involved in this type of gene transfer as it happens in real time and observed that a cholera bacterium can obtain at least 40 genes from another bacterium.

This is important research because most bacteria use horizontal gene transfer which leads to an increase in antibacterial resistance and dispersal of virulence factors. If we can better understand the mechanisms that bacteria use in order to obtain genes for antibacterial resistance and virulence factors, we may be able to develop better ways to combat these disease causing bacteria.

http://www.sciencedaily.com/releases/2015/01/150101163629.htm Main article

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002778 

Controlling genes with light: Light-activating genes might be precisely controlled and targeted

By incorporating the use of light, a bacterium's viral defense system and a plants ability to detect sunlight, scientists are now able to turn genes on and off. As explained in the article, researchers from Duke University state that this new technology will allow scientists to pick a gene on any chromosome and activate or deactivate it with light. The future outlooks for this technology can allow researchers to further their understanding of gene's functions, potentially create systems for growing tissue, and, with a great sense of optimism, even create science fiction like healing technologies. The new technology works by targeting genes using a genetic engineering system called CRISPR/Cas9. CRISPR was discovered to be the system bacteria use to identify viral invaders, and through the manipulation of researchers, CRISPR can be used to target specific genetic sequences. As mentioned above plants play a major role in this technology. Two specific proteins located in the plants lock together when photons of light are present. The scientists attached the CRISPR system to one of the proteins, and a gene activating protein to the other. While shining blue light on the cells the research team was able to turn many genes on and off. The researchers went on to explain that this new technology will allow them to target specific genes in an easy, fast, and cheap way.


I find this article to be very interesting. It amazes me that the researchers were able to mesh differing biological pathways from bacteria and plants together to work as a functional unit. Not to mention that by doing so they could target and regulate specific genes just by using light. With the possibility that this technology may one day grow human tissue it seems like it could be a bright, science fiction like future.



found at:  http://www.sciencedaily.com/releases/2015/02/150209113249.htm
original research: http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1753.html

The Famous Colorful Coral Reefs

If you have ever seen the movie "Finding Nemo," then you will know about the famous and colorful coral reefs that line very small sections of the ocean floor. The coral reefs are home to about 25% of marine life world wide. But why are these coral reefs so famous and colorful? 

In a recent study conducted by scientists at the University of Southampton, the genetics of the colorful coral reefs have been studied. The study revels that the individual sections of living coral use one single gene to control pigment production to produce their colors. However, the corals do not just use one copy of the gene, the coral instead uses multiple copies of the same gene. The pigments act as sunscreen for the living organism and will create more or less depending on how much sun is on the reef. Another factor that affects the reefs are the many living organisms surrounding the coral. Most algae protect the coral from the sun through a symbiotic relationship.

This article was very interesting because I have always been fascinated with marine life and the coral reefs. The article does touch on why the coral reefs are dying out which I also thought was very interesting since part of it was related with the pigmentation.




found at: http://www.sciencedaily.com/releases/2015/01/150129094216.htm 

Attack of the Zombies!!!

Or I should say, attack of the wasps?

A ladybug being infected.

Parasitologist Nolwenn Dheilly at Stony Brook University in New York found a virus that actually turns ladybugs into a zombie by wasps.  Here's how it works:
The green-eyed wasp, Dinocampus coccinellae, lays its egg inside the ladybug (or various other beetles, but this is the most common). The larva eats the ladybug's internal organs for sustenance until it erupts from her abdomen after 3 weeks.  Then, it weaves a coccoon in between her legs and the ladybug turns into a zombie, warding off predators until the adult wasp emerges from the coocoon one week later. The ladybug is NOT zombified before the wasp emerges as a larva. Parasiologists and enthomologists wondered how this can even occur. Was it a toxin? Is it a mutation? Another parasite?  The answer may shock you.

A ladybug with a D.coccinellae cocoon.

Parasitologists, specifically Dheilly, found "unfamiliar viral RNA not present in healthy beetles."  Upon further study, a new species of Iflavirus (similar to the RNA virus that causes polio) was found and named DCPV (D. coccinellae paralysis virus). The wasp injects this virus into the ladybug when it is laying its egg into their abdomen. It then replicates rapidly but only moves to the brain right before the larva emerges from the egg (and the ladybug's abdomen). So far, they have not figured out why the virus is active in the brain at that point. One hypothesis is that the ladybug's immune system seems to be suppressed due to the wasp larva feeding off of her innards, and after the larva emerges as an adult, her brain returns to a normal function. The suppression may be a cause for her brain to not function appropriately, and once she is not being fed on, her brain can almost revive itself. This brain damage may be the cause of the zombie-like state that is timed right around when the wasp larva emerges from its egg. It is said that 25% o all infected ladybugs recover completely, some even become infected again!

While I do find this article extremely disturbing, I also find it quite amazing that animals have adapted over time to give them an upper-hand at evolution and survival. Many other animal species have parasitic components to their survival, but it's always a marvel to see a genetic evolution of a species to control brain function, even if it's not intentional! Perhaps now we can understand the real purpose of some species' existence, and how we can even attempt to reproduce those characteristics in modern science and medicine. What if there was a bioterroristic weapon that controlled the minds of people into doing what they wanted? What if governments were able to control your brain? One could only hope a success like this isn't used against us!

Original Article:Wasp virus turns ladybugs into zombie babysitters