AP Biology class blog for discussing current research in Biology

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Taking care of your gut might be a pain now, but is definitely worth it!

Brain with Alzheimer’s

The contributions of microbes to multiple aspects of human physiology and neurobiology in health and disease have up until now not been fully appreciated.
Many people have said the human gut is like a “second brain.” With trillions of microbes, the digestive tract of the human gut can influence many things such as your metabolism, nutrition, immune function, and even your happiness. New research continues to show links between the brain and the health of the gut.

For example, a study from Lund University found that “unhealthy intestinal flora can accelerate the development of Alzheimer’s disease.” Alzheimer’s disease is an extremely common form of dementia or memory loss. It is caused by the death of many brain cells, which progressively decreases the size of the brain and the number nerve cells and connections. This study showed that mice with Alzheimer’s have a different bacterial profile in their guts than mice without this disease. Dr. Frida Fak Hallenius said that “Alzheimer’s is a preventable disease and in the near future we will likely be able to give advice on what to eat to prevent it. Take care of your gut bacteria, by eating lots of whole-grains, fruits and vegetables.”


After these discoveries, researchers are looking deeper into how bacteria can affect brain pathology. One of their ideas is that the bacteria may affect T-cells in the gut, which controls inflammatory processes both in the gut and brain. Therefore, if we can find a way to increase the health of the gut, we can reduce inflammation and brain damage. Alzheimer’s, while it is one of the most feared diseases, is preventable to in extent and if not preventable, there are several ways to delay it. The human gut microbiome has a huge impact on your health and your brain’s health. If scientists can continue to discover how to make your gut as healthy as possible, Alzheimer’s could soon be a thing of the past.

Battle of the Mongeese!

The Mongoose!

It turns out the banded mongoose also participates in the planned and systematic battle that humans are famous for! Lovely! The banded mongoose is a highly social, squirrel-like creature commonly found in the savannas and plains of western Africa and feeds on insects and small rodents. Families of mongeese stay very close, and remain together throughout their life spans. Because of this, the mongoose is very territorial and during breeding season will actually participate in full-scale warfare.


Unlike other animal conflicts, battle between groups of mongeese is highly organized, mimicking the warfare styles of humans. They will arrange themselves in lines facing each and charge forward as one, knocking rivals into bushes and killing each other mercilessly. This fighting actually promotes solidarity and closeness within groups. Similar to the “rape and pillage” technique of early humans, rival mongeese often mate with each other. This proves very beneficial to the groups as it eliminates the repercussions of inbreeding that can occur in small isolated groups of mammals.


A Strange Phenomenon!

Surprisingly, pregnant females are more likely to carry their litter to term in times of warfare. Females seem to find some way to better maintain their pregnancies. Perhaps this is due to the higher tensions and need for new “troops”. Scientists are unsure.


New Research Shows Possible Early Diagnosis of Autism

Normally autism in children is diagnosed at around ages two or three but studies have been done to try to predict autism before behavioral symptoms occur.  University of North Carolina partnered with other universities to experiment with MRI machines to see if they could diagnose autism earlier than 24 months (2 years)

Autism is a big problem in our country and the rest of the world.  About 3 million people have autism in the United States and millions more throughout the world.  The study focused on hyper-expansion of brain surface area in children of 6-12 months of age. According to this article “Brain overgrowth was tied to the emergence of autistic social deficits in the second year.” They found that 8 out of 10 kids with a hyper-expanded brain as well as an autistic sibling would be diagnosed with autism in the future.

The fact that MRI’s can show enlarged surface area of the brain at such a young age is important in predicting whether or not a child will be later diagnosed with autism.  This is an important experiment because if doctors can predict autism before symptoms occur there may be ways for them to intervene with brain growth before a child’s brain permanently has autism and behavioral changes occur at 24 months.



8 Genes That May Be Affecting Your Sleep Patterns

Have you ever wondered why you struggle to fall asleep at night, while your sibling has no issues sleeping soundly for eight hours? What causes your sleep patterns? While your sleep may occasionally be affected by a particularly stressful event, leading to irregular sleep patterns, for

While your sleep may occasionally be affected by a particularly stressful event, leading to irregular sleep patterns, for many, it is simply caused by the way their brains and bodies work. New research has identified for the first time eight specific genes that are linked to insomnia or excessive daytime sleepiness. The data also revealed that some of the genes associated with disturbed sleep identified in this study seemed to be linked to certain metabolic and neuropsychiatric diseases too, like restless leg syndrome, schizophrenia, and obesity.

Richa Saxena, one of the co-authors and assistant professor of  anaesthesia at the Massachusetts General Hospital and Harvard medical school, explained why this research was so important: while “it was previously known that sleep disturbances may co-occur with many diseases in humans, but it was not known that there are shared genetic components that contribute both to sleep problems and these conditions.” Furthermore, while studies have previously identified genes linked to some sleep disorders, this is the first study that has specifically linked genes to insomnia.

Link to Original Image

The study looked at the prevalence of insomnia, sleep problems and excessive daytime sleepiness in 112,586 European adults who had participated in a UK Biobank study. All participants had their genes mapped, as well as additional information like weight and diseases/chronic conditions. The results revealed fascinating linkages between certain genes. For example, the genes linked to insomnia were most strongly related to those associated with restless legs syndrome, insulin resistance, and depression, while the genes associated with excessive daytime sleepiness were also linked to obesity. Saxena remarked again that “it was not known until this study that there are shared genetic components- shared underlying biological pathways- that contribute to both sleep problems and these shared conditions.”

Of course, this study is not 100% conclusive- people who have trouble sleeping are not necessarily at higher risk for restless legs syndrome, schizophrenia, and obesity. In reality, it is likely that many different genes contribute to both sleep problems and these medical problems, Saxena said. But this new study does suggest that these problems share genes and underlying pathways.

So what does this research do for the average person? Well, not much. Right now, it’s just fascinating news that there may be a genetic reason people with these disorders are more likely to have troubled sleep. However, there is hope that in the future researchers will be able to design and test various drugs to target these genes. This would bring immense benefits to people who struggle to keep normal sleep patterns, as well as helping individuals proactively avoid diseases they may be more at risk for (for example, obesity).


Thylacine Brain Structure Reveals Predatory Lifestyle

The thylacine, also known as the Tasmanian Tiger, was the largest carnivorous marsupial of modern times. Native to Australia, Tasmania, and New Guinea, the thylacine quickly went extinct at the start of the twentieth century, following an increase of demand for its pelts. The last known thylacine died in 1936, in Beaumaris Zoo in Hobart, Tasmania, and little is known about the species’ natural behavior. New research however, gives humans a better glimpse into brains and programming behind one of Australia’s most fascinating predators.

Dr. Gregory Berns of Emory University and Dr. Ken Ashwell of the University of New South Wales scanned thylacine brains and reconstructed neural connections in an effort to better understand the specific functions of the thylacine brain and behavior. Only four surviving specimens of the brain exist, and their study gained access to two of them.

“One was provided by the Smithsonian Institution, taken from a male Tasmanian tiger after it died at the National Zoological Park in 1905. The other specimen, loaned to the researchers by the Australian Museum in Sydney, came from an animal that died during the 1930s.”, claimed researchers.

They compared the structure of Thylacine brains to those of Tasmanian devils. The researchers found that the thylacine brains had larger caudate zones than the Tasmanian devil brains. This suggests that thylacines devoted more of their brains to complex thinking, particularly action planning and decision making.

These findings match with what we know of the two animals. Tasmanian devils are known to be scavengers while thylacines were hunters. The neural rewiring done by the researchers provides anecdotal evidence that thylacines occupied a more complex predatory brain than their scavenger cousin, the Tasmanian devil.

These findings are fascinating because they give us new information regarding an animal less than 100 years extinct. It’s seems strange that we had never gathered much information about the thylacine prior to its extinction. However, the resurgence in fascination and curiosity about the animal is exciting to see. Hopefully new research and discoveries will be made in the near future, shedding more light on the thylacines life.



Image result for thylacine

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A Snap Shot of A Frog’s Slap Shot

Mix some water and cornstarch. We’ve all made it in science class: Oobleck! It’s that weird solid-ish liquidy substance that feels like wet putty in your hands. And it has more in common with a frog’s saliva than you think (partially because it’s a little odd if you’re constantly thinking about frog saliva, but you should be because it’s really cool!!!).

A Ph.D. student Alexis C. Noel and her supervisor David L. Hu at Georgia Tech studied and published their findings in Royal Society Interface. on how, by the laws of physics, a frog’s tongue catches its prey.

The duo was engaged in some hardcore, in-depth, scholarly research scavanging Youtube for the most ground breaking viral videos of the century when they had a spark of inspiration coming from an unlikely source: a video of a frog destroying all our high scores at a game of Ant Smasher with its long tongue (see this is why all homework should be to watch Youtube videos).

These two individuals became curious just how a frog’s quick and sticky tongue physically was able to catch its prey. They first had to find a high-speed camera, which they used at the Atlanta Botanical Garden and Zoo Atlanta, to record frog tongues in motion since the whole event takes place in the blink of an eye. They also tested saliva and tongue tissue samples and with data on the speed of the tongue and the viscosity of frogs’ saliva, developed a computer simulation to test their hypotheses.

Their results were as follows: frog saliva just like oobleck is a non-Newtonian Fluid!

Non-Newtonian fluids change their viscosity depending on the speed (shear rate) at which the liquid flows. Oobleck is a non-Newtonian fluid because when it is undisturbed it acts more like a liquid but if you squeeze it with a fist, it behaves more like a solid.

Frog saliva, which is usually 50,000 times stickier than that of humans, initially behaves less like a liquid. However, the force of the impact between the frog’s tongue and its prey is so great it causes the saliva to liquify more. Thus, the saliva gets into every crevice and covers the insect. When the saliva re-solidifies, the frog has a strong grip on the insect so it can reel it back in.

Of course, there is just one more issue. The frog now needs to release the insect from its tongue so that it can swallow it. To do so, it violently sucks in its eyes, creating a huge force that once again liquifies the saliva, releasing the insect.

So, there you go! That’s the secret to a frog’s saliva. But after reading this you might be thinking: that’s such a random thing to research! Well, the researchers note that this mechanism could be replicated in the development of robots made out of soft materials, a large technology field developing. They believe that this technology could help the robots made out of light and more flexible materials better grip items.

What other technologies do you think this research could aid?

Guppy Social Circles: The Evolutionary Benefit of Tight-Knit Groups

It is often said that humans are social creatures.  But why is this?  How do other species help substantiate the need for social interaction and friendship among humans?  What direct benefits result from strong ties between individuals?  To grapple with these questions, Rob Heathcote, an animal behavior researcher at the University of Exeter, conducted the following experiment.

Guppies swimming in a group of three by Per Harald Olsen, source

Heathcote and his team traveled to Trinidad, an island in the Caribbean that is home to the small freshwater Trinidadian guppy.  But why this place and this species you might be asking.  In response, Heathcote states that, “These guppies live in environments that have tons of predators around, so basically it really sucks to be a guppy. In some places they live, you’ll be watching these shoals of guppies and a predator is attacking them every twenty or thirty seconds or so.”  With the hypothesis that animals form social groups in order to reduce the risk of being preyed upon, the Trinidadian guppy was the perfect specimen.  However, Heathcote sought to investigate whether the benefits of communal living derived from individual relationships (as in humans) or simply safety in numbers.

The team divided 240 female Trinidadian guppies into smaller groups of fifteen, with each group having its own pool isolated from the rest.  Some fish were left alone while others were spooked with a doll version of a predator known as the pike cichlid.  It was recorded that the groups formed by the guppies exposed to the faux predator were smaller on average when compared to the groups that the unprovoked fish formed.  Therefore, one can conclude that the startled guppies fearing for their lives were more likely to establish stronger social connections between one another.  In other words “Fear of predation drives stable and differentiated social relationships in guppies” (Heathcote et al. in Scientific Reports).

So, guppies can congregate in massive groups to blend and reduce their chances of becoming dinner.  However, congregation itself attracts more and more predators.  Alternatively, as seen in the experimentation, they can hide in smaller social circles of three to four individuals, a sort of family where each guppy has each other’s best interest in mind and where the guppies can effectively communicate.  When drawing parallels between the Trinidadian guppy and humans, it is clear that both species form exclusive clans to ameliorate their lives.  In the words of Jason G. Goldman, “Spending time with a few close friends could outweigh the benefits of blending in with the crowd, particularly in dangerous situations.”

The research results in many follow up questions.  Why do some humans choose to isolate themselves from social interaction altogether?  How can this study relate to international relations?  What really makes humans different from more primitive species?

90 and Counting…

Life expectancy is continuously rising, and is expected to rise immensely in various countries around the world. The U.S however, is not increasing as drastically.

A recent study was done to predict the average life expectancy for 35 countries in the year 2030. The greatest increases were seen in females born in South Korea and males born in Hungary. The smallest increases were people born in Macedonia.

South Korean females are expected to live 6.6 years longer than they would have if they were born in 2010. Their life expectancy is 90.8 years old. WOW!

France had the second highest life expectancy for females, with 88.6 years.

Japan came in third with a predicted life expectancy of 88.4 years, not too far behind France.

The reason this news is so shocking is because scientists once believed that it would be impossible to have a life expectancy exceed 90 years, but South Korea has surpassed it. This barrier will be broken.

Professor Magid Ezzati said, “I don’t believe we’re anywhere near the upper limit of expectancy – if there even is one”.

For men, the greatest increase was in Hungary, with an estimated increase of 7.5 years more than 2010. The life expectancy is 78.2 years for boys born in 2030.

Like the females, South Korean males had the highest predicted life expectancy for 2030, with a whopping 84.1 years. Australia and Switzerland were not far behind with life expectancies of 84 years old.

The United States did not increase much. For women it was expected to increase by 2.1 years and for men it was expected to increase by 3 years. This would mean 83.3 years for women and 79.5 for men.

Researchers in the study noted that life expectancy at birth in the U.S. is already lower than most other high-income countries and that it is projected to fall further behind. Some reasons for this set back are that the U.S. has the highest homicide rates, highest death rates for women and children, and the highest average BMI of any high-income country. It is also the only country out of the 35 in the study that does not provide universal health care, so many people have unmet health care needs due to cost.


Additional Information:


More Than One Type of Giraffe?

It has recently been found that there are four distinct types of giraffes when we only thought there was one. This was found through an analyses that used several nuclear marker genes of more than 100 animals. The giraffe population has decreased by over 35% in the last 30 years so these animals are becoming endangered. And as it turns out these 4 species of giraffes only mate with giraffes of the same species. These giraffes are primarily located throughout Africa. This recent study has proved that we don’t know everything about these animals. In order to help increase the giraffe population people who mate giraffes now need to know that there are 4 distinct species of giraffes and that these 4 species only mate with the same species. hopefully this new data will help improve the population size of giraffes and help prevent them from becoming endangered.


Preferential Gene Expression: Not As Random As We Thought

Our conventional knowledge of genetics dictates that the activation of genes in our DNA is random. It is equally likely that our body will express our mother’s alleles as it is that our body will express our father’s. In the case that one parent donates a defective copy, it will be silenced; the other parent’s healthy set of DNA takes precedence and becomes activated.

However, a new study indicates that gene expression and activation is not as random as we thought. In certain regions of the body, our genes demonstrate preferential expression.

A team of scientists at the University of Utah found that almost 85 percent of genes in juvenile mice brains displayed preferential treatment. The mice brains activated one parent’s set of DNA over the other’s. This phenomenon was observed in other areas of the body, as well as in primates.

Although the preferential expression came to a close within ten days, it could provide explanations for vulnerability to brain diseases such as schizophrenia, ADD, and Huntington’s. The temporary preferential treatment to one parent’s copy of DNA could trigger a host of problems specific to that cell site that lead to such disorders, if the parent had given a defective copy of genes.

The study has the potential to alter our basic understandings of genetics, and how we are more prone to certain specialized diseases.

Image: (Public Domain,

The Grey Area of Human Gene Editing

The process of Human Gene Editing developed with the goal to prevent future generations from suffering from genetic diseases present in past generations, like our own. Human gene editing, provided it is done only to the correct disease, alters the DNA in embryos, eggs, and sperm to the when reproduction occurs, the gene for the disease or disability is not inherited. However, two weeks ago the National Academies of Sciences and Medicine issued a report stating that human gene editing is being used to enhance people’s health or abilities. This is considered unethical according to organizers of a Global Summit on human gene editing.

Human gene editing has been given a “yellow light” because the process is not yet approved to be done on people. There are high hopes that diseases caused by only 1 genetic mutation such cystic fibrosis and Huntington’s disease will be eliminated due to this process. Unfortunately diseases that are caused by more than one genetic mutation, such as autism or schizophrenia, are not curable by this process.

National Cancer Institute

Gene Editing on humans is such a controversial topic right now: is it ethical to change genes? should the practice be used to change physical appearances? Ultimately, if Human Gene Editing is approves, who decides when it becomes too much, or unethical. This grey area is presented to be somewhere between when it is appropriate to help aid the life of a human, ridding them of a disease, and when enhancements are made.


Bees Can Coach Soccer

Even a bee is better at playing soccer than I am. Ecologist Olli Loukola of Queen Mary University of London and his team have taught a number of bumblebees (Bombus Terrestris) to move a wooden ball to a specific point to be rewarded with food: AKA, Bee soccer (boccer?). The scientists had a number of bees in the stands, watching and cheering on the pro soccer players. After watching three intense games, the bees that had originally only attended the pro soccer games were put into the field. It’s a rags to riches tale of a bee that once only dreamed of playing soccer getting a chance to make it pro. Under pressure, the novice bees scored goals nearly every time, truly proving themselves to be professional bee soccer league material. However, bees that did not watch the soccer games beforehand only scored 30% of the time.

Graham Wise,

While this seems like simply a fun spin off of the bee movie, it was actually a productive use of the researchers time! The fact that the bees were able to learn how to perform a task shows that they have the ability to pick up on social cues. While it took a while for the researchers to teach the initial pro bee soccer players, the second group learned how to play much faster just by watching other bees perform the task.

In a second type of bee soccer, the researchers put three balls in front of the bees. Two of them were glued down to the table, and the third (which was farthest from the goal) was free to roll. While the untrained bees watched, the coach bees were only able to score using the third ball. However, when three balls that were free to roll were presented to the untrained bees, nearly all of them moved the closest ball to the goal, rather than the farthest one that they had seen the instructors use. This proves that the bees were able to actually think about their actions, rather than just imitate the actions of the bees before them. We may see bee olympics in the near future. Or they might take over the world. Be(e) prepared for both.

The Dangers of De-Extinction

uploaded by: FunkMonk

Our once ludicrous dream of resurrecting our dead animal friends, like the wooly mammoth, is transforming into a real possibility! According to David Schultz’s article on, due to human advancements made in the study of genetic engineering, scientists at Harvard University were able to reach new heights in the efforts to tackle de-extinction. However, now that it is almost within man’s capability to actually bring back extinct animals, there is a spark of skepticism sweeping the scientific world. “The conversation thus far has been focused on whether or not we can do this. Now, we are progressing toward the: ‘Holy crap, we can—so should we?’ phase,” states ecologist Douglas McCauley. McCauley shines light on the sudden realization of how resurrection may be exciting, yet also very demanding and potentially harmful. Due to tight funds, it is believed that resurrection of one extinct animal can harm the life that is already struggling to be sustained on earth.

In order to reach this financial conclusion, researchers sought out databases in New Zealand, Australia, and New South Wales that are responsible for tracking the cost of conserving endangered animals. With this information from the databases, the researcher team believed that it would cost just as much, if not more, to maintain a resurrected species as it would an endangered species. What this means is, that the already tight funds that conservationists have to support endangered animals would be stretched immensely in order to fund the conservation of a newly resurrected wooly mammoth species, for example. Schultz writes, “The result, the team calculates, would be an overall loss of biodiversity—roughly two species would go extinct for every one that could be revived.” Because of the world’s budget for species preservation, and as author and biologist Joseph Bennet says, “It’s better to spend the money on the living than the dead.”

With that being said, it appears that our excitement around bringing the dead back to life has been faded by the the reality of our world’s finances. Though the study of extinction is still vast, perplexing, and amazing, the application of our resurrecting abilities may not happen anytime soon. Would you like to someday walk on the earth with our old prehistoric animal friends or would you rather save the world’s endangered species first?


T Regulatory Cells Help Maintain Plasma Cells

Researchers at the University of Pennsylvania School of Veterinary Medicine, in February 2017, have discovered a trend in T regulatory cells and plasma cells, that explain why these “antibody-producing plasma cells” can last so long. They used a special microscope that shows “movement and interaction” of cells.  They found that regulatory T cells in the bone marrow support plasma cells, which disappear without the T cells.  Plasma cells are involved in the immune system, and can either be vital or detrimental. To learn more about plasma cells click here.  Scientists hope to use this new knowledge of the interaction between regulatory T cells and plasma cells to either increase the amount of plasma cells to fight off a virus, for example, or to decrease the amount in order to stop it from creating a disease.  This research also explains why vaccines can last so long. For example, the chicken pox vaccine is only given twice when the person is very young, but they will be protected against the disease even when they are much older. The regulatory T cells support the plasma cells in the bone marrow which create antibodies that fight off viruses, etc. Another article that explains this discovery can be found here. An article that describes more uses of regulatory T cells in the immune system can be found here.

With this discovery, scientists have more power to control, and have more insight into how plasma cells can be sustained over long periods of time.

Here is an image of an antibody that plasma cells create.

Seagrasses: Benefitting the Ecosystem

Seagrasses have been known to improve water quality greatly, however it was only recently that scientists discovered other major benefits of the plants that reside in the ocean. The name seagrasses is a misnomer, for they are actually plants that grow in shallow ocean water. Seagrasses are one of the largest stores of carbon in the ocean, and they also remove excess nitrogen and phosphorous from the water.

A few years however, ecologist Joleah Lamb’s colleagues fell ill with amoebic dysentery. This is an intestinal illness that they contracted while conducting research on coral reefs in Indonesia. The illness can be caused by the release of raw sewage into the ocean by a city, which leads to a drastic increase in the populations of shoreline bacteria. The water collected close to the shore had been compared to offshore tidal flats and coral reefs with seagrass beds. The two different sites were very close to one another, yet the water where the seagrass was had a significantly smaller amount of Enterococcus bacteria. The bacteria in areas with seagrass was only 1/3 of that in other areas that did not have the plants. This bacteria is not only dangerous for humans, but is harmful for fish and other species as well.

While at this moment it is uncertain how the seagrasses clean the water, we know that seagrasses trap small particulates and prevent them from flowing on in the ocean. It is believed that the plants would catch the bacteria in the same way, or that the leaves might emit antimicrobial compounds that directly kill the bacteria. Another possibility could be that seagrasses release oxygen made during photosynthesis, and the oxygen is toxic to pathogens. Also, it is noted that seagrass meadows often are located next to coral reefs, so some suggest that they work together to protect one another from bacteria and other possible dangers.


Further reading:

MRIs Catch Autism Prior to Symptoms

Mark Lythgoe & Chloe Hutton / Wellcome Images Image Link


By using magnetic resonance imaging (MRI), researchers are now able to accurately study and predict which infants, among those with older autistic siblings, will be diagnosed by the age of 2. According to an article on Science daily, in the past couple of years, researchers have correctly predicted 80 percent of these infants who would later meet criteria for autism at 24 months of age.

A study published in Nature, shows how early brain biomarkers can be very beneficial in identifying infants at the highest risk for autism prior to any symptoms. Joseph Piven, professor of Psychiatry at the University of North Carolina-Chapel Hill, explains how typically autism cannot be detected in infants until they ages 2-4, but for infants with autistic siblings, it can be determined at an earlier age.

People diagnosed with Autism Spectrum Disorder (ASD), experience social deficits and  demonstrate very specific stereotypical behaviors. According to this study, it is estimated that one out of 68 children develop autism in the United States and that  for infants with older siblings with autism, the risk may be as high as 20 out of every 100 births. Despite these high numbers, it remains a difficult task to detect behavioral symptoms prior to 24 months of age.

Piven, along with a couple of other researchers, conducted MRI scans of infants at six, 12, and 24 months of age. They discovered that increased growth rate of surface area in the first year of life was linked to increased growth rate of overall brain volume in the second year of life. This meant that brain overgrowth was tied to the emergence of autistic social deficits in the second year. The researchers then took the information they had and used a computer program that classified babies most likely to meet criteria for autism at 24 months of age, and developed an algorithm that they applied to a separate set of study participants.

The researchers found that there were brain differences at 6 and 12 months of age in infants with older siblings with autism and infants with older ASD siblings who did not meet criteria for autism at 24 months.

Plans for the Future

This research and test would be very beneficial to a family who already has a child with autism and has a second child who may or may not be affected. The ideal goal would be to intervene and provide as much assistance to the infant and family prior to the emergence of symptoms. By intervening at early stages and when the brain is most susceptible, researchers hope to improve the outcomes of treatment.

In the nature study, Piven describes how Parkinson’s and Autism are similar in that when the person is diagnosed, they’ve already lost a substantial portion of the dopamine receptors in their brain, making treatment less effective.

One mother who has benefitted from this discovery and is extremely grateful is Rachel O’Connor. When interviewed by News12, she shared how early intervention “has brought out some language in [her] daughter,” and how her daughter “can now say what she wants and she desires. She makes better eye contact.”


Long Island Sound May Be Getting a Timely Makeover

In its glory days, the Long Island Sound has supported many fisheries for lobsters, oysters, crabs, etc. It still boasts of 170 species of fish and more than 1,200 species of invertebrates. In recent years, however, the Sound has been plagued with excess nitrogen. The build-up causes eutrophication, in which the extra nitrogen feeds seaweed and algae blooms, causing them to use up more oxygen. As a result, the fish don’t have adequate oxygen and perish, and the ecology of the Sound makes it uninhabitable for shellfish.

Where does all of this nitrogen come from? The main sources of nitrogen are septic tanks and sewers, fertilizers from lawns and parks, certain agricultural practices, and atmospheric deposition from dust, rain, and snow. Because the severity of the problem is based largely on human practices, it is much worse in some areas than in others.

Bridgeport  Seaside Park looking over Long Island Sound 2011

View of Long Island Sound from Bridgeport Seaside Park (credit: 826 Paranormal)

Jamie Vaudrey and her team at the University of Connecticut wanted to make this issue a priority for people, so they made a model displaying the level of nitrogen runoff in the Sound. They painstakingly collected data for four years from each of the 116 estuaries, harbors, rivers, and bays of the Sound. This allowed people to see how this problem affected not only the Sound but their local beach or the coast they sail on.

The model is an Excel spreadsheet that can be easily downloaded. In addition, the “scenario” section of the model allows people to alter a communities’ settings (such as lessening fertilizer usage) to see how it can lessen the nitrogen runoff. Another feature of the model shows the places that are impacted the most by the issue.

The model is already in use by the Connecticut Department of Energy and Environmental Protection and the Nature Conservancy. Vaudrey is creating a second model to shed more light on how every bay is affected differently by the introduction of excess nitrogen.

Do you think that this model will prompt local governments to enact legislation to solve this problem? Will this model be extended to other bodies of water suffering from this same fate? Let me know in the comments!

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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!

Could A Computer Detect Your Sick Gut?

Photo by Nicola Fawcett (photo source)


The human gut microbiome is a system specially revolved around the genetic makeup of an individual person. These gut biomes are the subject of many studies by scientists who are interested in the small world of bacteria living inside of our stomachs and its relation to our health or illness. Many humans have the ability to recognize a healthy or unhealthy human gut microbiome, however, is it possible for a computer to have this same ability? According to the impressive research results developed by a group of scientists at the University of California San Diego, it is possible for a computer to be trained to differentiate a sick gut microbiome compared to an unhealthy one.

In order to reach this innovative conclusion, these scientists utilized metagenomics, a gene sequencing technique, to break up the DNA of hundreds of microbes residing in the human gut. The scientists took gut bacterial samples from the stool samples of thirty “healthy” and thirty “unhealthy” people. The unhealthy people whom had samples taken from them were either diagnosed with autoimmune Inflammatory Bowel Disease. With these 60 samples total, the scientists were able to sequence 600 billion DNA bases and put the information into a computer. After that, the scientists underwent a complex process of translating reconstructed DNA of the hundreds of microbes into thousands of proteins, which were then categorized into thousands of protein families. The tedious differentiation and categorization of certain proteins allows the scientists to see the activity of the bacteria and then program it into the computer so it, too, would be able to recognize these proteins and bacteria. Bryn C. Taylor, One of the scientists involved in this research says that, “You can try to categorize healthy and sick people by looking at their intestinal bacterial composition…but the differences are not always clear. Instead, when we categorize by the bacterial protein family levels, we see a distinct difference between healthy and sick people.” Incorporating this method of distinction with the storage of healthy and unhealthy patient data into computers is an effective way of “training” a computer how to detect a sick or healthy human gut due to a distinguishable difference in bacterial activity, protein presence, etc..

Overall, it seems that these scientists at the University of California San Diego have made groundbreaking progress in the future usage of computers in the detection of an unhealthy or sick human gut microbiome. Do you think the development of a computer’s ability to detect a sick gut will be ultimately more beneficial to the world of health and science, or will it just be an unnecessary new trick that computers can learn? The next time you feel like you’ve got a stomach bug, you just might be scheduling an appointment with a computer instead of your doctor.


Hunter-Gatherer to Westernized Human Gut Biomes

Somewhere between the time of early hunter-gatherer humans, and the present-day humans living in modernized Western societies, the human gut biome lost much of its diversity. New research has contributed another clue as to the evolution of the human gut biome.

An international team of scientists studied the fecal samples of an intermediary group between hunter-gatherers and Westernized humans. The Bantu community in Africa is a traditional, agricultural population that has incorporated some available Western practices, including the use of antibiotics and therapeutic drugs.


Bantu people; Steve Evans,

The scientists compared the Bantu gut biomes to those of the BaAka pygmy population, who resemble early hunter-gatherer populations and have no Western influences, and to the gut biomes of humans living in modern, Westernized societies.

By analyzing the sequence data of the three human biomes, the scientists placed the Bantu’s biome composition in between the BaAka’s and Westernized humans’. The Bantu shared similar bacterial species as the BaAka, but lacked many of the traditional bacteria that the BaAka possessed. In fact, the BaAka had such a different biome composition that their gut more closely resembled wild primate biomes!


Based on the functions of the variable bacterial groups between the three populations, the team hypothesizes that the boosted carbohydrate-processing pathways in Bantu and American biomes is a result of the sugars in our diet, whereas the BaAka do not have much access to such foods and thus do not have such bacterial populations.

Ultimately, the scientists have accepted that our diet contributes significantly to our gut biome composition.

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