Friday, December 30, 2016

Microbiome accelerates neurodegeneration


Parkinson disease (PD) is a neurodegenerative disease characterized by motor deficits and aggregates of a protein called α-synuclein (α-syn) in the brain (pronounced sin-NU-clee-in). Genetics plays a role in PD, because there are some early-onset forms of PD that are caused by mutations in α-syn that cause it to more readily clump together and form the protein aggregates. The purely genetic forms of the disease, though, are relatively rare, so the environment must also play a role in most cases. A recent paper published in Cell by Sampson et al. explores how the microbiome in the gut affects development of PD symptoms.

The microbiome is the community of bacteria and fungi living in and on us (watch this awesome video about the microbiome). It has previously been shown that the normal gut microbiome is disrupted in various diseases such as autism and in Parkinson’s patients. It’s always hard to know, though, what is the cause and what is the effect. Does the disease cause the microbiome to change, or does the change in the microbiome cause the disease? Maybe a little of both.

Mouse model

To address the role of the microbiome in Parksinson Disease, the authors relied on an established mouse model of PD. These mice overexpress the normal human form of α-syn in all their neurons. Even though this isn’t the mutant form of the gene, the fact that it is overexpressed all over the brain causes the characteristic α-syn aggregates. These mice are slow in motor tasks, including removing a piece of tape from their noses (sounds like a frustrating, but also adorable behavioral task). They also have impaired gastrointestinal function, which is to say they don’t produce as much poo as other mice. [An aside: normal mice apparently drop about 7 fecal pellets every 15 minutes!]

The researchers took these mice with mouse-Parkinson’s and raised half of them in a super sterile environment where they have no microbiome (called “germ free” mice), and the other half got all dirty so they had a microbiome (I will call these “dirty mice”). The PD mice with a microbiome had way more motor impairments than the mice without a microbiome! Yes, I wrote that correctly. I thought the microbiome was supposed to help its host? Well, not in these mice overexpressing α-syn.

Get this: if you give the dirty mice antibiotics from age 5-13 weeks old and then test them, they were more like the germ free mice – no motor impairments and better fecal output. Not that you would want to give humans antibiotics for their entire lives (that could cause some autoimmune diseases and serious digestive issues), but this does demonstrate that it is the gut microbiome that is affecting the symptoms of Parkinson Disease.

Short chain fatty acids

The bacteria living in our gut produce all sorts of chemicals that can get into our blood and nervous system. Bacteria produce short-chain fatty acids (SCFA), which are basically just little fats that can cross over the intestinal lining and get into our bodies. Parkinson’s patients produce more SCFAs, so the authors tested the role of SCFAs in their mouse model.

Germ free mice overexpressing α-syn are relatively normal, right? The authors fed these mice a bunch of SCFAs to mimic what the gut bacteria would be making and the mice became impaired like the dirty mice (can’t get that tape off their nose). This is amazing to me. So short-chain fatty acids that are normally made by the gut bacteria are sufficient to cause the Parkinson’s symptoms. Note that feeding SCFAs to normal mice without all that α-syn did not cause Parkinson's symptoms.

           α-syn mice no microbiome + SCFAs = impairments of α-syn mice with microbiome

Microbiome and the immune system

What are the short-chain fatty acids doing to the nervous system? One important role of the microbiome is to train the host’s immune system so it knows what to attack and what to ignore. This is why the microbiome plays a role in the development of autoimmune diseases, where the body attacks the wrong things (like a harmless pollen molecule or the body’s own cells like in type I diabetes). SCFAs can get up into the brain and regulate the immune cells of the nervous system, called the microglia (pronounced micro-GLEE-a). Indeed, the dirty mice with a full microbiome had more activated microglia in the brain than the germ free mice. Likewise, the germ free mice fed SCFAs also had activated microglia.

An overactive immune system promotes protein aggregation, so here’s the model: something causes the microbiome to become unhealthy, which causes the release of a lot of SCFAs, which activate the immune system in the brain, leading to neuron death and protein aggregation. The diagram below has some extra information in it, but the pathway in black is what they showed in this paper.


What about human patients?

Okay, so the microbiome plays a role in this one particular mouse model of PD, but what about in humans? Remember that the microbiome and the amount of short-chain fatty acids in Parkinson’s patients are different than in healthy humans. The authors took the microbes from human feces and transplanted it into the guts of the germ free α-syn mice. Amazingly, the germ free mice that got the bacteria from Parkinson’s patients had more severe motor impairments than the mice that got bacteria from the healthy humans. So there’s something going on in the microbiome of humans with PD that enhances the symptoms.

The authors raise the point that two things were needed for these mice to have the symptoms of Parkinson disease:
1) Overexpression of α-syn (genetics)
2) Disordered microbiome, also known as dysbiosis (environment)

This is a great example of a complex disease that is caused by the interplay of genetics and environment. Perhaps this information can be used to come up with new treatments to correct the dysbiosis and slow down the progression of Parkinson disease. 

Sunday, September 4, 2016

Human language in dog brains


Spoken language conveys meaning in two ways: the meaning of the words (semantics or lexical knowledge) and the intonation that the speaker uses. We can sense questions by the rising pitch at the end of the sentence. Likewise, we can tell if someone is upset or being sarcastic based on how they say the words. The patterns of intonation in language is known as prosody. There are areas of the brain that are specialized for decoding the semantic meaning of language and different areas for interpreting prosody. In fact, you can have damage to one area during a stroke, while the other area remains intact. There are great examples of this in “The President’s Speech” in Oliver Sacks' book The Man who Mistook his Wife for a Hat.

In most people, word meanings are processed by the left side of the brain and prosody is localized to the right side of the brain. Some animals also use the left side of their brains to understand meaningful and familiar sounds of their species (like alert calls or bird songs). What about for animals, like dogs, which can understand the sounds of another species (i.e. commands from humans). Is the dog brain really processing the intonations of praise “good dog!” or are they responding to the words? Do they process meaning and intonation separately like humans do?

Dogs in MRI machines

In the latest issue of Science, Andies et al. published their studies of language processing in dog brains. My first thought when I read the abstract was “how do you get a dog into an MRI machine?” We commonly study which areas of human brains are active during different tasks using a technique called functional MRI (or fMRI). fMRI was done on these dogs while they listened to their trainers speak. If you have ever had an MRI scan, you know they strap you in and you cannot move your head at all. Same thing with these dogs. Needless to say, they were very well trained dogs. If you still can’t believe it, check out this video the researchers made and the cute photo of dogs in an MRI machine below.

Really well trained dogs lying still before their MRIs. (Image from phys.org)
Dogs process language like humans

Okay, so they got the dogs in the MRI machine and scanned their brains while they heard their trainer say different things. The trainer would either say words of praise, like “good boy” (in Hungarian), or neutral words. And they used either a neutral, flat intonation or they raised the pitch of their voice to create a praising intonation. This created four possibilities:
  • Praise words with praising intonation
  • Praise words with neutral intonation
  • Neutral words with praising intonation
  • Neutral words with neutral intonation
They compared the brain responses to each combination and found that the left side of the brain responded to words of praise regardless of the intonation. This is amazing, right? The dogs have heard “good boy” enough times that their brains responded specifically to that phrase regardless of how it was said. It’s like they sort of know what it means. It would be interesting to see if they respond to the same phrase spoken by a stranger.

The researchers also found that the right side of the brain had active areas when praising intonation was used, regardless of the word meaning. So dogs also understand how our voices change when we praise them.

Finally, the researchers looked at areas of the brain associated with reward. These areas are active in a variety of animals when they receive natural rewards like food or during sex, but the reward pathways are also active if the animal is given an addictive drug like cocaine. Alternatively, you can put an electrode into a mouse brain that stimulates the reward pathway and the mouse will push a lever to receive an electrical shock in this area of the brain over and over until it starves.

Andies et al. found that praising words spoken in a praising intonation activated the reward pathway in the dogs. Praise words alone and praise intonation alone had no effect. So dogs really do feel good when you say “good dog” in a high pitched voice.

Notice the organization of language processing in the dog brain. Just like in humans, language semantics (praise vs neutral words) was processed on the left side and prosody (praise vs neutral intonation) was processed on the right side. What does this tell us about the evolution of language? Language lateralization has likely been around a long time and is not uniquely human. The authors end the article with this gem: “What makes lexical items uniquely human is thus not the neural capacity to process them, but the invention of using them.”

Saturday, May 21, 2016

No Y genes? No problem, bro.


The Y-chromosome is one of the smallest chromosomes in the human genome and contains genes involved in male development and production of sperm. Previous research has shown that just two genes on the Y chromosome are necessary to make male mice who can sort of produce sperm. By “sort of” I mean that the mice make things called “round spermatids”, which genetically are the same as sperm, but are underdeveloped, so they can’t naturally fertilize an egg. A lab in Hawaii took these round spermatids and injected them into oocytes to demonstrate that the resulting zygotes are viable and develop into normal mice. In other words, the experimental mice have only one X chromosome and the two Y genes, and they develop into males who can reproduce with a little help from scientists.  That is pretty amazing that only two genes can make a male.

The necessary Y genes
So what are these two genes? One of them is called Sry, which encodes for a transcription factor that regulates expression of other genes important for the development of the male reproductive system (see the figure below). The other necessary gene is Eif2s3y, which is involved in protein synthesis and somehow necessary for the production of sperm. There is a similar gene on the X-chromosome, which may serve the same function. Normal XY males express both Eif2s3y and Eif2s3x, the version on the X-chromosome.

 
In a paper that came out earlier this year in Science, Yamauchi et al. asked whether they could replace the function of Sry and Eif2s3y with other genes that are found on other chromosomes. Instead of a male mouse with Eif2s3y, what if you made a mouse that was overexpressing Eif2s3x?  Could the X version compensate for the Y version? And instead of Sry, could you overexpress one of its target genes to replace its function?

Through the power of mouse genetics, the researchers created a mouse line with one X-chromosome and no Y-chromosome, which overexpressed Eif2s3x and Sox9, one of the Sry targets. In other words, these mice do not have any genes that are normally found on the Y-chromosome.

A male mouse with no Y
The mice with no Y-chromosomes and no Y genes, but overexpression of Sox9, developed into males, with male reproductive systems (though smaller and less developed). When Eif2s3x was overexpressed along with Sox9, the males were able to produce the round spermatids (precursors for sperm). The researchers did their artificial fertilization with these round spermatids and were able to produce healthy offspring. 

 

So just to repeat: the mice without a single gene from the Y-chromosome developed into males and produced sperm that are good enough for successful in vitro fertilization. Just by overexpressing two genes found on other chromosomes. That’s amazing!

Sunday, July 19, 2015

Pandas are lazy!


Pandas are closely related to carnivorous mammals (like all the other bears), but they consume mostly bamboo.  Their digestive tracts are short and adapted for digesting meat, not cellulose that is found in plants.  In fact, they only digest about 20% of all the bamboo they eat, and they eat a lot of bamboo (30-60 pounds a day)!  How are these large, adorable bears able to get enough energy to function from their inefficient digestion of bamboo?  Researchers in China and Scotland addressed this question by studying captive and wild pandas, described in a recent Science article.

Low energy expenditure
Nie et al. measured the daily energy expenditure of the pandas and found that they used an unusually low amount of energy, only 37.7% of the predicted value based on their body mass.  In fact, pandas are expending energy at levels similar to the three-toed sloth, the epitome of a low-energy mammal.  The measly amount of nutrients they get from all that bamboo would be able to sustain such a low energy expenditure, so that’s how the panda is able to get by with such a maladapted digestive system.

How do the pandas manage to spend so little energy?  There must be some adaptations that are allowing the panda to survive without expending so much energy.  The authors found a number of these adaptations:

1) Pandas have a thick layer of fur, so they can maintain their internal body temperature with less heat loss through the skin.  The researchers measured temperature at the surface of various animals and the pandas consistently were cooler than other mammals (like a cow or dog).  Their internal body temperature would be considerably warmer because the fur helps insulate them, so they don’t have to spend as much energy on maintaining their body temperature.

2) Pandas are lazy.  No surprise: pandas spend more time inactive and when they do move, it is slowly.  So that is less energy needed for muscle contractions.

3) Pandas have small brains, livers and kidneys, so their organs need less energy.

4) Pandas have a low resting metabolic rate, which is driven by the thyroid hormones, T3 and T4.  In fact, levels of these two hormones were considerably lower than for other mammals of the same body mass, even lower than a hibernating bear.  The thyroid hormones regulate protein, carbohydrate and fat metabolism, as well as growth and development.  If the pandas don’t need to produce as much heat or energy, then there is no reason to have a high metabolic rate.

Interestingly, pandas have a single mutation in a gene called DUOX2, which is not found in any other mammals.  DUOX2 encodes for a protein that is necessary for the production of T3 and T4.  The mutation causes a premature “stop” in the protein, so it likely affects the function of DUOX2. 

In other words, pandas cannot synthesize T3 and T4 as well because of this mutation, so they have a reduced metabolic rate.  But that’s okay, because they are good at maintaining their body temperature and they have developed an enjoyable lifestyle of relaxing and eating.  The fact that their digestive tracts have not evolved for plant digestion is alright given the fact that they don’t really need that much energy from their food.  So it all works out: pandas are able to survive on their diet of bamboo and we can watch them sit around.