AP Biology class blog for discussing current research in Biology

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Metagenomics will stare into your soul… and beyond?

If you ever feel lonely, take solace in the fact that at any given time there are thousands of bacteria cells living in your gut, (inside your skin!).

As it turns out, there’s a whole lot of ‘not you‘, living in you.

Admittedly, they don’t make the best company as they tend to be on the quieter side.

They make up for it by being fantastic listeners.

Improving Human Intestinal Health

Courtesy of Pacific Northwest National Laboratory.

They also serve as an essential part of our bodily systems, referred to by Valeria D’argenio in her essay The role of the gut microbiome in the healthy adult statusas “our forgotten organ”.

One great measure of how important something is is how wrong things go when the original thing isn’t doing it’s thing properly. Put eloquently by D’argenio “Quantitative and qualitative alterations in the composition of the gut microbiome could lead to pathological dysbiosis, and have been related to an increasing number of intestinal and extra-intestinal diseases”. The Human Gut micro biome is important to maintaining good health. Interestingly though (and somewhat alarmingly), the human gut micro biome has historically been fairly hard to study. as D’argenio puts it “microbial studies were based on the direct cultivation and isolation of microbes” and then later states that “it is estimated that up to 99% of microbes are currently uncultivable”. These facts make it clear that with old methods, the human gut micro biome has been extremely hard to study effectively. Which is crazy because the human gut micro biome is so important. Metagenomics are changing the game.

Recently new strategies  known as Metagenomics have been discovered that avoid the inefficient and ineffective cultivation step. Using the “Shotgun Sequencing” strategy, scientists have become able to sequence the DNA directly and have gained the ability to sequence entire microbial communities. This new method represents a significant step in understanding the human but microbiome but it is not perfect. D’argenio references limitations to current DNA sequence databases and difficulty in deciphering DNA function as obstacles that have yet to be totally overcome.

16s rRNA Sequencing is another form of metagenomics helping to illuminate the mysteries of the human gut micro biome. All bacteria contain the 16s rRNA. The 16s rRNA Sequencing gene takes advantage of this fact by identifying this gene in a large sequence and gaining a clearer view of which bacteria species are present in certain environments. This strategy is cost effective and can be performed rapidly but offers no insight as to bacterial function.

Metatranscriptomics succeeds where 16s rRNA Sequencing fails. In the words of D’argenio “Metatranscriptomics serves to analyze the entire transcriptome of an environmental site to obtain a comprehensive view of gene expression profiles and functional data”. Put simply metatranscriptomics, a form of metagenomics, is able to attain data on gene expression, not just sequencing. This is a major step in the analysis of the human gut microbiome as with this advancement we move closer to finding out exactly which aspects of the micro biome lead to which effects on the human body.

I’m personally excited about advancements in this field, because it seems like the human gut micro biome is important to our health and well being. The more we know about it the more we’ll be able to treat our bodies healthily. Which would be great!

Gut Microbes and the Brain

Neuroscientists are studying the idea that intestinal microbiota might influence brain development and behavior.

Neuroscientist Knickmeyer is looking to study 30 newborns and how they have grown into inquisitive, curious one-year olds through a series of behavioral and temperament tests. She is eager to see their faecal microbiota, bacteria, viruses and other microbes that live in their guts.

Studies of animals raised in sterile, germ-free conditions showed that these microbes in the gut influence behavior and can alter brain neurochemistry and physiology. Some research has drawn links with gut bacteria and their interactions with the brain.

Escherichia coli, a species of bacteria present in the human gut

Gut Reactions

Prior to recent research, microbes and the brain have rarely been known to interact, with the exception of when pathogens penetrate the blood brain barrier. When they do, there can be intense effects. For example, the virus causing rabies elicits aggression, agitation and a fear of water. The idea that gut microbes could influence neurobiology was not ever thought of, but this is changing.

One research study showed that IBS lead to issues such as depression and anxiety. This lead scientists to wonder if psychiatric symptoms are driven by inflammation or a whacky microbiome caused by infection.

One 2011 study showed that germ-free mice were less-anxious than mice with indigenous microbes. These studies also showed that many of these behaviors are formed during a critical period during which microbes have their strongest effects. Another problem is that “germ-free” is an unnatural situation. However, it allows for researchers to learn which microbial functions are important for development of organs or cell types.

Chemical Exploration

Recent studies have found that gut microbes directly alter neurotransmitter levels, enabling their communication with neurons.

Scientists are also studying whether or not altered serotonin levels in the gut trigger a cascade of molecular events, therefore affecting brain activity.

In 2015 research showed that myelination can also be influenced by gut microbes, at least in a specific part of the brain. Germ-free mice are protected from some conditions, for example multiple sclerosis, because it is characterized by demyelination of nerve fibers. These scientists wish to use these studies to help humans who suffer from MS.

A Move to Therapy

Tracy Bale, a neuroscientist, sought to study how microbes of pregnant mothers affect their offspring. Maria Dominguez-Bello, microbiologist, wants to see if babies born through Caesarean sections end up with microbiota similar to babies born vaginally if they are swabbed on the mouth and skin with gauze taken from their mothers’ vaginas.

For Knickmeyer, the amygdala and prefrontal cortex are the brain areas that interest her the most in her studies with the newborn infants. This is because both of these areas have been affected by microbiota manipulations in rodent models. Something she is worried might affect the study is the confounding factors such as diet, home lives and environmental exposure.


For more information:

The Human Gut Microbiome and Autism Spectrum Disorders

Researchers of the human gut microbiome have made connections to the autism spectrum disorder.  A gut microbiome involves the digestive tract microbes.  To learn more general information click here.  Studies tested DNA of children with gastrointestinal complaints.  Researches compared children with Autism Spectrum Disorder, and mainstream children.  It was found that children with Autism Spectrum Disorder had too many Clostridium or Desulfovibrio clusters.  To learn more about these gene clusters click here. Developing fever, receiving oral antibiotics, or ingesting probiotics are all likely to alter the gut microflora.  When children with Autism Spectrum Disorder do the above, they have exhibited improvement in their gastrointestinal pains; however, there hasn’t been scientific research, as it has only been found anecdotally. Research has been limited due to the difficult culture-dependent techniques; however, metagenomic technology could be used to discover and reduce the effects of the gut microbiome as a part in Autism Spectrum Disorder.

A longitudinal study completed in May 2016 shows more progress that scientists have made in discovering different aspects of autism in relation to the microbiome.  For two weeks, stool samples were collected from patients with autism and their siblings without autism in order to be compared. Sarcina ventriculi, Barnesiella intestihominis, and Clostridium bartlettii are organisms that are related to autism. They were found in the stool samples of children with autism, but not their siblings. Gastrointestinal symptoms were reported on days 6-8 of the study for children with Autism Spectrum Disorder, where Haemophilus parainfluenzae was detected at the onset. These patients also exhibited behavioral challenges during these days.

Though scientists have not found a diagnosis for Autism Spectrum Disorder yet, it is clear that the gut microbiome plays a role in the development. Further research that is not merely based off of a handful of patients needs to be completed to learn more.

Photo of Gut Flora

Number of strokes increased in children!

Sean Maloney stroke brainscan

Intel Free Press Image Link


According to new studies, strokes have been affecting younger generations more than ever. The average age for people having a first stroke has dropped from  71.1 in 2000 to 69.3 in 2012.What’s interesting is that in general, the number of strokes in the U.S. has actually gone down over the last few decades, according to Chengwei Li, an epidemiologist at the University of Michigan School of Public Health. However, Li’s study, shows that the rate of strokes in people under the age of 65 have not gone down, and that the rate of strokes in people under the age of 55 has actually increased.


According to a study on WebMD, it is in some ways easier to treat the younger patients affected. People who get to the hospital within 4 and a half hours of their episode, or attack, can receive a drug that breaks up the clot in the brain and restores the blood flow. However, studies have shown that this treatment is more likely to benefit younger patients opposed to elder patients. Although this may be the case, young adults and females in particular, are often not eligible for the treatment because they ignore early symptoms or wait until the symptoms get severe, before they seek help.

As stated in an article from Live Science  and a journal from NCBI, the increase in stroke incidents at younger ages has great significance because strokes in younger patients carry out for a greater lifetime burden of disability.

While the total number of strokes in the U.S. has decreased, the number and severity of strokes in younger generations has increased. As a result, researchers, doctors, and medical staff continue to work together in order to seek ways to treat the newer generation of stroke patients.

CRISPR/Cas9 Provides Promising Treatment for Duchenne Muscular Dystrophy

There are nine kinds of muscular dystrophy and of these, Duchenne MD is the most common severe form of childhood MD. It affects about 1 in 5000 newborn males, only in very rare cases has it affected females. DMD is a genetic disorder that causes progressive muscle degeneration and weakness. Patients usually die by age 30 to 40.

DMD is caused by the absence of a protein, dystrophin, that helps keep muscle cells intact. In 1986 it was discovered that there was a gene on the X chromosome that, when mutated, lead to DMD. Later, researchers discovered that the protein associated with this gene was dystrophin. From this information, we can tell that this disorder is sex-linked, which explains why women are mainly carriers.

No one has found an absolute cure for this genetic disorder until now. Even in recent years, people have discovered treatments that will make patients’ lives more bearable, but never reverse the disorder. As a result of these advances, mostly in cardiac and respiratory care, patients are able to live past teen year and as long as in to their fifties, though this is rare. Although there are still drugs being tested like Vamorolone (a “dissociative steroid,” is an anti-inflammatory compound), more treatments on the molecular level are now being considered. However, thanks to recent discoveries and research with the new genetic technology, CRISPR/ Cas9, scientists may have found a treatment for DMD.

This new approach to gene correction by genome editing has shown promise in studies recently. This particular correction can be achieved in a couple ways: one is by skipping exon 51 of the DMD gene using eterplirsen (a morpholino-based oligonucleotide). Studies over four years show prolonged movement abilities, and a change in the rate of decline compared to controls. The newest approach to gene correction using CRISPR/Cas9, which the article I’m writing about focuses on, was performed in this study as next described: the CRISPR/Cas9 system targets the point mutation in exon 23 of the mdx mouse that creates a premature stop codon and serves as a representative model of DMD. Multiple studies in three separate laboratories have provided a path and laid the groundwork for clinical translation addressing many of the critical questions that have been raised regarding this system. The labs also discovered by further demonstrations, that this is a feasible treatment for humans. Functional recovery was demonstrated in the mice, including grip strength, and improved force generation- all of which are very important and hopeful discoveries. It is estimated from these studies that this new method will pass clinical trials and go on to benefit as many as 80% of DMD sufferers. Even greater success rates are expected if this is performed in young and newborn DMD patients.

ANOTHER new study on Coffee

As students in high school, many of us are familiar with the immediate advantage of drinking coffee which is a decrease in fatigue and increase of alertness. Since I was young, however, I have heard many myths and hypotheses about the bad side effect of coffee, like how it stunts your growth and stains your teeth. I have also heard of other, positive side effect of drinking coffee. Some articles have said that caffeine has some positive effects against some diseases like Parkinson’s and Alzheimers. Multiple studies and published articles have come up throughout the years on the various side effects of drinking coffee daily and whether or not it is good or bad for you. An article published on explains the most recent research on this mysterious drink and its long term effects on us humans, while another article argues its bad effects.

This article describes a study and analysis of more than 200,000 professionals followed for almost 30 years. They concluded that drinking up to five cups of either decaf or caffeinated coffee a day has a strong correlation to reduced risk of early death from heart and brain diseases as well as suicide. This study had even accounted for lurking variables such as smoking, weight, and diet. By adjusting for these factors, the scientists discovered that the benefits were more pronounced for non-smokers. They also found that both decaf. and caffeinated coffee were had positive effects. This led the researchers to believe that the powerful components of coffee may stem from chemical compounds in the bean such as diterpenes and chlorogenic acids.

Another article I came across mentioned the known positive, as well as the harmful effects of caffeine. (On a side note, I find it relevant to point out that this article mentioned that studies proving harmful effects of caffeine are harder to find that the reported positive effects. This, I speculate, might have to do a little bit with the fact that people tend to want to hear reassurance on things that will permit them to continue on with habits or actions that might be seen as harmful or bad otherwise.) This website cited studies that were performed by the Mayo Clinic that found that coffee raised blood pressure, increased risk of heart attacks, caused headaches, reduced fertility in women, proved harmful to people with type 2 diabetes, worsened menopause symptoms, increased anxiety, and, most obviously, caused insomnia and more. Some of these correlations, like an increase in headaches due to drinking coffee, can be explained by obvious reasoning: caffeine is a diuretic, and therefore if you aren’t drinking enough water to compensate, your body will produce too much urine and you will become dehydrated which leads to headaches in some cases.

Because of this drug’s popularity, studies after studies have come out presenting new, or sometimes repetitive, information regarding the side effects of drinking coffee. Many people want to believe that it is good for them because they drink it on such a regular basis that if it proved to be very harmful they would be in real trouble. Therefore, people are looking for proof that it is good, so there are more articles, credible and not, showing proof that it is. Additionally, another potential issue with these studies is the amount of caffeine given to the patients. In study one, the subjects were given around 5 cups of coffee a day, which is 2 to 3 more than the average American, and therefore unrepresentative of what Americans actually consume. From this data, I have decided to continue drinking the relatively small amount of coffee I do on a weekly basis, paying attention to how my own body reacts and noting the changes with attention in order to learn more about how it affects me personally, as I feel I am the only reliable source of information to myself at the moment.

Cells Kill Cells—New Cancer Treatment Promotes Immune System response to Tumors

According to a recent article, oncological research has been a recent area of vast development. Cancer is a widespread form of disease that affects different areas uniquely and operates very subjectively. On a basic level, cancer is the uncontrolled growth and division of a cell.  This often yields a malignant tumor which can metastasize to other areas of the body.  When a tumor metastasizes and spreads beyond the primary site to other organs of the body, the cancer is considered to be Stage IV.  This is the most aggressive stage of cancer development and is often the most difficult to treat.  The new treatment revealed by Cornell University Engineers seeks to inhibit a tumor’s ability to metastasize.

Killer T Cells attacking a cancerous cell 


The paper explained the new approach in “annihilating” the tumors before they progress to a metastatic stage.  The key to this is not actually killing the cell, rather, inducing apoptosis of the cancerous cell.  Without the jargon, it means that the new treatment will not explicitly kill the cell, instead it will cause the cell to kill itself. The engineers accomplished this in model organism trials using mice.  The procedure involves injecting specialized liposomes in the lymph nodes, which commonly play a key role in metastasis.  The lymph nodes are parts of the lymphatic system where lymphocytes are formed. Lymphocytes are known as “killer cells” because they are a form of leukocytes (white blood cells).  The injection contains liposomes (membranous sacs of water) with a special “Tumor necrosis factor Related Apoptosis-Inducing Ligand” protein.  These will attach to the lymphocytes and target the cancerous cells, and effectively eliminate the tumor before it metastasizes.

The paper also references previous work by the engineering group where they created a similar approach for eliminating bloodstream metastases in January 2014.  This coupled with a lymphatic treatment can greatly reduce the rate of metastasis in patients with aggressive malignant tumors.  Recent developments in oncological treatments have suggested promising developments in the way of cancer treatments–and cures.

Img. Source

Original Article

Sewage Does More than Just Gross You Out… It Carries a Signal For the Microbiomes of Humans

Who knew that sewage would ever be useful. Well, it is a successful way to collect fecal bacteria from people. It can monitor, through gut microbes, the public health of a population without invading people’s privacy. The human gut microbiome consists of huge amounts of bacteria in the gastrointestinal tract. This gut bacteria has important functions in a healthy human. Recently, there has been much attention to the human microbiome, and more specifically, finding a “healthy microbiome” by identifying which bacterial communities are associated with healthy individuals. What has been hindering this experiment are financial concerns but also privacy concerns in terms of the individuals that can be screened.

Researchers from MBL (Marine Biological Laboratory) and the UWM (University of Wisconsin-Milwaukee) School of Freshwater Sciences proposed the idea of using sewage as a population that consists of a signal for human microbiomes. The scientists used oligotyping to compare 137 healthy people’s gut bacteria (provided by the Human Microbiome Project) to the bacterial communities of more than 200 sewage samples from 71 different U.S. cities. Researchers realized that geographically distributed populations consists of a similar core set of bacteria and its members symbolize many different communities within U.S. adults. The percent of obese people in a city is used by the study as a measure of a lifestyle difference which indicates that this bacteria community structure is accurate in detecting obesity in a city. Lifestyle differences are important because they can change the human gut microbiome and an indicator of obesity is the microbial community composition. This process of working with microbiomes of individuals is similar to drawing a map of a specific geographical area and fishing out new understandings and patterns. If it weren’t for the sewage, the scientists wouldn’t have been able to differentiate the cities based on their level of obesity. This type of approach can be effective when it comes to answering concerns about public health, without undermining the privacy of individuals.

I found it interesting how this profound yet relatively small experiment is even part of a bigger plan to create better water pollution and public health assessments. Do you think it can lead a better water pollution and efficient public health assessments? Overall, it’s amazing how new technologies can aid in decrypting information from complicated environments. I’m excited to see where this experiment takes us as it leads researchers and scientists in a more knowledgeable outlook on our environment and in public health.

The original article can be found here.

Elephant Trunks: The Most Convenient Way to Reach Food

New studies have indicated that elephants are using the air that they blast through their trunks to grasp for food in hard-to-reach areas. Way back when, Charles Darwin had even suggested that elephants might manipulate their breath to reach food. Scientists from Kyoto University and SOKENDAI decided to research this behavior in elephants. They predicted that the farther away the piece of food is, the more frequently the elephants would use their breath/air through their trunks to bring it near them. To test their hypothesis, they observed two captive, female elephants, Suzuko and Mineko at the Kamine Zoo. The researchers created this virtual grid in a ditch, enclosing the elephants. They placed food in different areas of the grid. The various types of food included: apples, bamboo, fallen leaves, potatoes, and hay. After spacing out these foods, they filmed the elephants trying to reach for them. 128 trials took place over 32 days; each trial started when it was audible that the elephants began blowing and ended when they finally got the food or gave up. Many other factors played a role in this experiment such as the position and shape of the elephant trunks, the frequency and duration of blowing, and the ability to track the movement of food across the area.

The scientist’s research concluded that on average, it took 3 blasts of air for an elephant to obtain inaccessible food and was less likely to use this technique if the food was nearby. Mineko was the dominant female who was much more skilled at altering the position of her trunk to aim more specifically at the food to push it in the correct direction. This particular behavior has brought up discussion of whether an elephant’s breath can be defined as a “tool” or not; similar to how chimpanzees use sticks to catch ants. It’s been concluded that this study creates a new possibility to rethink the term “tool” and to possibly redefine it. For this behavior to be defined as a “tool,” it shouldn’t solely be debated as whether it’s a physical object or not, but more of how it is a physiological process that promotes problem-solving. I thought this new finding was very interesting because I was unaware at how proficient an elephant can be with its breath. Furthermore, I love how this study promoted discussion on a different topic: what can be defined as a “tool” for animals nowadays. Do you think an elephant’s breath can be referred to as a “tool?” Please share your thoughts! In my opinion, I think it can definitely be referred to as a tool because it aids in carrying out a particular function. If only humans had this type of tool… we wouldn’t have to awkwardly reach across the dinner table ever again!

The original article can be found here.

For more information about the study, check out this article and video: Elephants Use Their Trunks as Leaf-Blowers to Reach for Food.

The Real Scoop on Artificial Food Coloring

Although artificial colors and dyes have been used in foods since the early 1900’s, the FDA has banned many of them due to health concerns. Thirty-seven artificial colors still remain approved for general food use in the USA, many of which are now prohibited in some European countries. Many of these chemicals have been researched and found to have harmful side effects, but they are still used in popular candies, soft drinks, cereals, and other processed foods.

Americans are now consuming more processed foods and drinks than ever before, and therefore more artificial colors and dyes. Many scientists have researched these common chemicals and found shocking results. The most common blue 1 & 2, citrus red 2, green 3, red 3 & 40, and yellow 5 & 6, have been found to cause a wide degree of side effects. Some have been found to cause cancer, ADHD, neurochemical and behavioral effects, allergies and more. Because of link between artificial dyes and the frequently seen side effects of cancer and ADHD, many European countries such as Norway, France, Finland, The U.K., and Sweden have banned a number of these chemicals from their foods.

It is no secret that these additives have harmful side effects, so why do companies still choose to use them? It is a very simple marketing tactic. “You eat with your eyes”, therefore companies will try to make their food look visually appealing to convince you to buy their products. Using artificial dyes and colors is just one method companies use to attract buyers. Artificial dyes like Yellow 5 have more vibrant and concentrated color than natural ones like saffron or turmeric. They are also much cheaper than natural dyes because companies do not need to use much in order to get the color they want. Artificial colors are also easier to use and their results are more reliable because they are much less sensitive to heat than naturally-derived food dyes are.

Silly Rabbit

(A bowl of Trix cereal made with artificial colors and flavors. The new Trix will go on sale later this year, without its blue and green puffs.)

This news may seem very alarming and upsetting to the average consumer, but there is hope. The FDA requires that companies put their ingredients on the food labels, so you know which foods are organic and which ones have artificial coloring. Research on artificial food dyes has led many consumers to cut out harmful processed foods and sodas from their diet and led to more awareness among buyers. And although there are companies such as Coca-Cola that use harmful cancer causing dyes such like 4-MEI, there are brands like General Mills that are promising to soon cut out all artificial dyes from their cereals by 2017. The new direction American consumers are taking now towards organic and health foods is slowly leading the food industry to change their foods in a healthy way. No longer are some food companies looking for the most vibrant look with their presentation, but rather the healthiest.



Epigenetics and Dopamine Activity

Researchers at the University of California in Irvine have correlated erratic dopamine activity as an underlying cause of complex neuropsychiatric disorders, specifically because of the epigenetic alterations caused by low levels of dopamine. This study, overseen by Emiliana Borelli, a UCI professor of microbiology & molecular genetics, provides clues to the possible causes of complicated disorders like schizophrenia.

Dopamine is a neurotransmitter (and hormone) that fuels our daily life, acting as our prime motivator and pleasure inducer, while also being linked to memory, and cognitive function. Many addictive drugs increase the amounts of dopamine released to exhausting levels, eventually wearing out the neurotransmitters notwithstanding the negative effects of the drugs themselves. High dopamine levels can also be achieved via everyday pleasures like exercise or sex, which can also spur addiction.


Dopamine, therefore, has an irrefutable role in our everyday lives, and according to Borelli, “Genes previously linked to schizophrenia seem to be dependent on the controlled release of dopamine at specific locations in the brain. Interestingly, this study shows that altered dopamine levels can modify gene activity through epigenetic mechanisms despite the absence of genetic mutations of the DNA.”

In short, it is quite likely that Dopamine is an epigenetic hub of sorts, that can cause powerful changes in gene regulation when functioning in a disrupted or excessive manner. Borelli, knowing the consequences of excess dopamine release, tested the opposite effect on mice, hindering dopamine release by turning off mid brain dopamine receptors in rats, leading to mild dopamine synthesis. The results were profound, as Borelli found there to be decreased expression in approximately 2,000 genes in the prefrontal cortex. This epigenetic surge of decrease in genetic expression was reinforced by the increase in change of DNA proteins called histones, which are associated with reduced gene activity. The now mutated mice suffered from ranging psychotic behavior and episodes, and were then treated with dopamine activators for a duration of time before seeing their behavior normalize.

Borelli’s and others’ work will provide useful clues for understanding these complex neurological disorders, while serving to reinforce the newfound importance of comprehending gene regulation and expression. These studies seem to point to a new era in which it is not just your genetic make up that determines your future, but also the regulation of your genes.



Genetics and Mental Illness

Brain Lobes

Scientists have tirelessly searched through the genetic makeup of people with metal illnesses trying to find a common variation(s) that could account for conditions such as schizophrenia and bipolar disorder. However this has been inconclusive so researchers have turned to epigenetics, the study of how experience and environment effect the expression of certain genes. Epigenetic marks regulate when and how much protein is made with out actually altering the DNA itself. It is believed that these “marks” can affect behavior, and thus may interfere with metal health. This idea was tested in a study with rats.  Researchers proved that affectionate mothering alters the expression of genes, allowing them to dampen their physiological response to stress, which was then passed on to the next generation. This is thought to be similar in humans and these markers develop as an animal adapts to its environment.  Epigenetic research led scientists to prove that offspring of parents who experienced famine are at a higher risk for developing schizophrenia. Additionally, some people who have autism, epigenetic markers had silenced the gene which helps produce the hormone oxytocin which helps the brain’s social circuit. And therefore a brain that lacks this hormone would most likely struggle in social situations. Thomas Lehner of genomics research at the National Institute of Mental Health says that studies and research have shown that epigenetic modifications impact behavior and he also believes that these effects can be reversed. By studying genes at the “epi” level, researchers are hoping to find patterns that were hidden at the gene level.  Finding and targeting these patterns can lead to more effective treatment of and management of certain mental illnesses. There are many projects and studies at some of the most prestigious institutes, such as Tufts and Johns Hopkins, that are focused on the study of things at the epigenetic level.

Original Article

Further Information:

Epigenetic Markers and Heredity

Epigentetics and Autism 

Genetics and the Brain





The New Source of Mental Illness

a three dimensional recreation of DNA methylation

a three dimensional recreation of DNA methylation

For years scientists were convinced that the root cause of diseases such as bipolar disorder and schizophrenia lay somewhere hidden in the human genome. But the particular genetic sequence that would supposedly be linked to these illnesses remained elusive.  So researches turned to the developing theory of Epigenetics.  Studies from King’s College in London and related in this article have shown that Epigenetic (changes in gene activity caused by the environment) changes might be responsible for bipolar disorder and schizophrenia.  Jonathan Mill and colleagues scanned the genome of 22 pairs of identical twins.  For each pair of twins, one of the twins was diagnosed with either bipolar disorder or schizophrenia. With the understanding that chemical methyl groups attached to particular sites on a genome are responsible for the “turning of” and “turning on” of genes, Mill and his team “scanned for differences in the attachment of methyl groups at 27,000 sites in the genome.”  The researches found variations in the amount of methylation of up to 20 percent in the gene ST6GALNAC1 (which has been connected with schizophrenia) and differences in the amount of methylation of up to 25% in the gene GPR24 (which had previously been linked to bipolar disorder).  Interestingly Mill’s team found that “a gene called ZNF659, showed over methylation in people with schizophrenia and under-methylation in those who were bipolar, suggesting that the conditions might result from opposing gene activity.  These findings certainly support the theory of Epigenetic’s being a real factor in behavior and mental illness.  They also serve to confirm that bipolar disorder and schizophrenia are related disorders.  This relates to our unit in the sense that Epigenetics deals with the expression of the DNA and genetic sequence we are learning about.  While we read about how the nucleotides are sequenced, Epigenetics could potentially be responsible for how DNA is expressed.

Related reading:

Does long-term endurance training impact muscle epigenetics?



Epigenetics translates to “above” or “on top of” genetics. To be more specific, Epigenetics is the study of how modification of gene expression can cause changes in many organisms.

A new study from Karolinska Institutet in Sweden explores the theory that long-term endurance training alters the epigenetic pattern in the human skeletal muscle. The team that conducted the research also explored strong links between these altered epigenetic patterns and the activity in genes controlling improved metabolism and inflammation.

The study was conducted using 23 young and healthy men and women. The men and woman would perform one-legged cycling – where the untrained leg would be the control of the experiment. Four times a week and over the course of three months, the volunteers would participate in a 45 minute training session. Though skeletal muscle biopsies, supervisors would measure their markers for skeletal muscle metabolism, methylation status of 480,000 sites in the genome, and activity of over 20,000 genes.

At the end of the study, the researchers concluded that there was a strong relationship between epigenetic methylation and the change in activity of 4000 genes in total. Epigenetic methylation is defined as the “addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. ” Moreover, it was determined that methylation levels increased when involved in skeletal muscle adaptation and the metabolism of carbohydrates. However, methylation levels decreased in regions associated to inflammation.

Furthermore, Carl Johan Sundberg found that “endurance training in a coordinated fashion affects thousands of DNA methylation sites and genes associated to improvement in muscle function and health.” He believes that this determination could be vital to understanding the treatment of diabetes and cardiovascular disease as well as how to properly maintain good muscle function throughout life.

This article relates very much to our work in class as we learn the Molecular Genetics Unit. It connects because we are learning what happens when mutations occur in one’s genome and the impacts those mutations have on someone. For example, cancer is one of the most researched and explored topics in regard to how modification of gene expression alters organisms. Oncogenes and Tumor suppressor genes have vital impacts on cellular division, changes to cellular function, and the growth of tumors.

Could There be Good Gene Mutations?

Is there an epic battle occurring within our bodies right now? The classic battle royale between good and bad? I suppose in the body’s case the fight between good and bad genes.  There is a new field in medical research in which researchers are on the quest to find good gene mutations that fight against the disease causing mutations.  One individual, Doug Whitney, sparked the interest of a few doctors because he has fought his genetic odds to be health at 65 years old.  Whitney has a gene mutation, presenilin, that causes early onset Alzheimer’s disease in those who has inherited it. Whitney’s mother and 9 out of his 13 siblings were killed by this mutation and so Whitney’s fate seemed to be sealed.  However when Whitney reached his 40s and 50s having no symptoms he assumed he did not have the gene.  At 62 years old, Whitney, decided he would get a gene test.  He did have the gene.  This was an anomaly, He was doomed to have early onset Alzheimer’s Disease but had absolutely no symptoms. Although Whitney still have changes of getting Alzhiemers but the effects of his bad gene have been greatly delayed by another gene in Whitney’s DNA.  Whitney joined a study at Washington University in St. Louis led by Doctor Randall Bateman which recruited people with the early onset Alzheimer’s disease gene. This attracted the attention of Doctor Eric E. Schadt and Doctor Stephen H. Friend.  Doctor Schadt said that searching for good genes that protect against bad gene mutations is completely turning genetic research on its head.  Researchers have found gene mutations that partially protect diseases like osteoporosis, Type 2 diabetes, heart disease, and Alzheimer’s.  These good gene mutation’s partial protect have help to develop drugs to help fight certain diseases. Finding good gene mutations are substantially more difficult to find than bad genes, but the search has gotten a little easier with fast and inexpensive methods of sequencing DNA. Doctor Schadt and Doctor Friend decided to start the Resilience Project and search for good gene mutations that counteract bad gene mutations to help develop new break though treatments and drugs. They have contacted the researchers at Washington University, the research that Whitney is currently participating in.

For more information:

Article from NYT

Prokaryotic positive genetic influences

Genetics used for intrusion protection

About genetic testing


Petri Dish Brain Models…Endless Possibilities.

Side View of the Brain

Who would have thought that modern science could develope a brain stimulation with actual brain cells in a petri dish? Well researchers led by Doctor Rudolph E. Tanzi have done just that.  They have made substantial steps in the field of medical brain research specifically in the Alzheimer’s research field. Rudolph E. Tanzi is a prominent neuroscientist at Massachusetts General Hospital in Boston. One of Tanzi’s colleagues and also a neuroscientist, Doo Yeon Kim, suggested that they grow brain cells in gel. From this suggestion researchers under Tanzi’s lead created a brain scenario in a petri dish and then gave this model Alzheimer’s disease. Tanzi and his group took embryonic stem cells, which have the potential to become any type of cell in the body, and grew them with a mixture of chemicals. Said chemicals cause the stems cells to become neurons, which they then gave those neurons Alzheimer’s genes and were all growing in a commercially available gel in a petri dish. Those genes then caused plaques and later tangles which are indicative characteristics of Alzheimers. Dr Tanzi was quoted, “Sure enough, we saw plaques, real plaques…We waited, and then we saw tangles, actual tangles. It looks like you are looking at an Alzheimer brain.” This manufactured real Alzheimer’s brain stimulation opens new doors for research that was hindered because previously on mice with imperfect formsof the human Alzheimer’s genes. Doctor P. Murali Doraiswamy of Duke University states, “It could dramatically accelerate testing of new drug candidates.” Although the Petri Dish Model lacks some real life qualities it can still be utilized as a start for quick, cheap, and easy drug testing. Doctor Sam Gandy of the Icahn School of Medicine at Mount Sinai in New York states that the new discovery is, “a real game changer.” Tanzi is now starting to test 1,200 drugs on the market and 5,000 experimental drugs, a project that was impossible to perform on mice. Tanzi also wishes to test a protein, amyloid, that clumps into the plaques. He found an enzyme, that when blocked prevents tangles from forming. Dr. Gandy wishes to use the the system to study the influence of genes, such as ApoE4, which contributes to about 50% of Alzheimer’s cases. Dr. Doraiswamy of Duke stated, “The lack of a viable model for Alzheimer’s has been the Achilles’ heel of the field.” Tanzi’s model is the first step towards defeating this “Achilles’ heel” which opens infinite new doors in the research of finding new medications to cope with the devastation of Alzheimer’s disease.

For more Information: 

Official Alzheimer’s Research Page

Neuroscience Research 

Actual Article




Dying Brain cells signal new brain cells to grow in songbird



Original article:

In a recent paper written by leading author Tracy Larson and co-authors Nivretta Thatra and Brian Lee, they discovered a brain pathway that replaces brain cells lost naturally. This study could further the progress of using replacement cells for the neurons lost during aging, Alzheimer’s Disease, and other natural causes.

These scientists used songbirds, specifically Gambel’s white-crowned sparrows, as a model and observed that the area of their brain that controls song increases during breeding season, and decreases during other times in the year. After breeding season the cells in the area of the bird’s brain that controls songs undergoes programmed cell death. What is noteworthy about these dying cells is that they are also releasing a signal that reaches certain stem cells in the brain that will eventually redevelop the singing part of the brain by the time the next breeding season arrives. This process of developing new neurons from stem cells called neurogenesis normally occurs in the form of “regenerative” neurogenesis post brain trauma in mammals; however, it also occurs in the hippocampus in small amounts.

These songbirds could provide insight on how the human brain can perform natural neurogenesis and help replace neurons lost because of aging and neurodegenerative diseases. These finding may pave the way to alternative treatment for repairing human brains using neurogenesis and replacement cells.

The Ebola Epidemic: When Will it End?

Ebola Virus

The Ebola epidemic in West Africa has captivated international audiences the last few weeks.  Ebola Virus Disease is an often fatal disease which is systemic meaning it attacks all organs and tissue in the body. It can be spread through any human to human contact, making this disease highly contagious. The countries of Liberia, Sierra Leone and Guinea have been heavily affected by this disease. On tuesday September 23th the Center for Disease Control (CDC) based in Atlanta Georgia released new projections on the Ebola epidemic in Africa based on computer modeling.  The CDC released a best-case scenario being that if proper measures are taken the disease could be eradicated by January 2nd and a worse-case scenario that if disease is left unmonitored and continues as is, there will be approximately 1.4 million cases by January 2nd.   Doctor Thomas R. Frieden, the director of the Ebola epidemic, has stated that since the data was received in August conditions have improved slightly due to increased aid to the affected regions. Another report was released by the World Health Organization (WHO) which stated more conservative figures but also acknowledged that there could possibly be more due to unreported cases. The WHO report brings about the idea that the epidemic may not end and the Ebola virus will perpetuate in West Africa. It is obvious to health officials, such as Dr. Jack Chow, that even in a medium case scenario the amount of hospital beds and aid are rapidly being surpassed by the number of cases. The CDC does acknowledge this impending lack of bed and isolation unit crisis. One solution to this problem is to educate citizens on home care and send home care packages to support this movement.  Although some are dubious, Frieden states that home care had been effective in the smallpox crisis in the 1960s in Africa.  In addition to homecare, Doctor D. A. Henderson explains that funds and food play a huge roll in the containment and elimination of disease because when you give victims money and food there is no need for them to beg or go out to the market for food where they might encounter other human contact. How should this epidemic be handled? Is homecare an effective solution? Where should money be allocated, homecare or hospital expansion?


Link to Article:


Sensing neuronal activity with light


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

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

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

Original papers:  (You can only read abstracts; you have to pay to read the full text)

What We Can’t See Is Just As Important As What We Can!

Taken by Ron Lute

Taken by Ron Lute

Many students of biology know that life comes in all shapes and sizes, and even though we can’t see some organisms, they are most certainly present.  If you don’t know this, and you are a biology student, you might want to go back and read the first chapter of your textbooks to learn a big chunk of information that will come around in either next week’s test or your midterm.  For now, you’ve already come this far, so you can just learn the basics later.

As it turns out, some of those little organisms, located just under the soil’s surface,  are vital to the health and safety of the the plant-life they surround.  In an effort to raise awareness of the many effects a microbiome can have on plant performance, Marnie Rout (University of North Texas Health Science Center) and Darlene Southworth (Southern Oregon University) brought together a series of works by different authors on the subject, all placed in a special section of the American Journal of Botany called “Rhizosphere Interactions: The Root Microbiome.”  As a basic understanding of the concept, the rhizosphere is the layer of soil around a plant root.  It contains microbes that affect the plant on basically every scale, from the genes to the ecosystem.  It’s important to note that the microbiome works through the rhizosphere, effectively turning this “metabolically diverse” collection of microbes into a supply source should the plant need anything.  Interestingly enough, the rhizosphere also can act as a type of self-defense grid, similar to how human microbiomes function, where in some cases plants have been known to shed their root’s outer cell layers into the rhizosphere in order to form a “layer of immunity” to the plant.

Perhaps, one day in the future, these microbiomes can offer different types of bacteria that can be used for “crop production… in areas likely to be affected by global climate changes.”  What do you think we still have to learn about microbiomes before uses like this are possible?  Do any of you know someone currently researching in this field?  Are you students who didn’t know that there were organisms that you couldn’t see ever going to look at your textbooks?



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