Sleep. Zzzzz… Why?

We spend almost 30 years of our lives asleep, however, we still have limited understanding about the function of sleep. Scientists and philosophers have been trying to understand why animals need sleep for more than 2000 years. In his book “On Sleep and Sleeplessness”, Aristotle wrote:

“With regard to sleep and waking, we must consider what they are: whether they are peculiar to soul or to body, or common to both; and if common, to what part of soul or body they appertain: further, from what cause it arises that they are attributes of animals, and whether all animals share in them both, or some partake of the one only, others of the other only, or some partake of neither and some of both”


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Of Planes, Microbes and Clocks Human microbiome is definitely one of the trending topics in biological science right now (admittedly, I also have been caught up in this trend and blogged about microbiome before). Each week new research announces it discovered a new role of the microbiome (last week there was a nice paper studying a link between alcohol dependency and gut microbiome) and many researcher now consider the microbiome to be another organ in our body, the functions of which we are only beginning to understand. And here is another great story about the gut microbiome but this time, maybe somewhat unexpectedly, it involves the jet lag. jet_lag Continue reading

A Wrinkly Purpose

Recently I was river tracing here in Taiwan. It’s basically hiking but in the water, you just jump into some kind of a stream and go upstream, it is very fun, especially when rocks are slippery because then you always feel like a very bad ballerina. After several hours spent in the water, our fingers became very wrinkly, you know, as they always do after a long bath, a swim or any prolonged water activity. And during the lunch brake people started discussing why does that happen, why do fingers get wrinkly in the water? Most of us started to mumble something about osmosis, i.e. water entering or leaving the skin. Yes, it’s very smart of us to say ‘osmosis’ and pretend that we know something about it but really this was just another case of what episode #293 of This American Life called ‘Modern Jackass’: situations in which people act as if they are knowledgeable about something but they actually have no clue. As Nancy Updike put it, “The thing about Modern Jackass is, it’s usually not something about which you know nothing. It’s something about which you know a little bit, enough to sort of get yourself into trouble.” And to be honest osmosis doesn’t really make sense if you think about it, I mean shouldn’t then all of our body turn wrinkly in water not just the fingers, and at least I haven’t notice any particular differences about wrinkling in fresh and salt water, but clearly the osmotic pressure in the two must be quite different (it’s easy for me to speak post factum).

Fig.1 Wrinkly Fingers
Fig.1 Wrinkly Fingers

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How to Employ a Microbe?

For many people microbes are associated with infections, diseases and in general mainly negative things but some microbes actually do more good than bad for us. We often take for granted that without microbes we would not have many things that we eat and use everyday and, as a matter of fact, humans would not even survive without these little creatures :)

Microbiome, Obesity and Diet

Even though we have started to appreciate the importance of human microbiome relatively recently, it is no longer a question’ if the microbiome is important?’ but rather ‘how the microbiome affects us?’. I define human microbiome as the total diversity of microbes in and on human body, however, this definition is definitely simplified version and for those interested in the subtleties of its use can go and read some of the debate in here.
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Fear in Slow Motion

Some people report that in fear-related situations time seems to slowdown. That is to say, for example, during a car crash the event takes much longer from the point of a person experiencing the crash than the observer. But how and why the brain creates this slow motion experience is not completely understood. Recently, on the World Science Festival panel called ‘The Deceptive Watchman: Mind, Brain, and Time’ David Eagleman mentioned his study on the subject, which both intrigued and amused me, so let me tell you why.

In his study Eagleman asked if in a fear situation time slows down because of increased temporal resolution of an experienced event (as when in slow-motion videos a better movement discrimination is seen because of increased number of frames in it). In other words, are people in life-threatening situations somehow able to increase their visual recording of an event, which leads to a more detailed recall and consequent slow motion-like experience?

Here comes the amusing part. To answer the question one obviously needs to place a person in a fear-inducing environment and what is better a way of doing it than a 31m freefall. The participants in this study were dropped from a huge tower in an amusement park and asked to preform a task while free falling (apparently no incentives where given, so I have a suspicion that the study is biased towards fear-junkies ☺ ).
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When Octopuses and Spaghetti Collide: why octopus’s arms don’t catch themselves

I suppose many of us would like to have a pair of extra hands, you know, just to hold that cup of coffee in one hand, a book in another and maybe an iPhone in the third. Although, then we might also require an extra pair of eyes too… But it’s not all that easy, apart from the fact that clearly under the specific circumstances of human evolution two hands proved to be an optimal option, too many hands can pose a problem: when it comes to managing them all at the same time they might end up just tangling all over the place!

But there are animals that do have quite a few hands and not just any hands but hands full of suckers that will stick and hold on to anything in their path. Yes, I am talking about cephalopods, which include octopuses, squids, cuttlefishes and others. So how and do these animals manage to distinguish between their own hands and other objects and prevent the suckers from catching the limbs of their own?

Well, this is the question that a recent paper called “Self-Recognition Mechanism between Skin and Suckers Prevents Octopus Arms from Interfering with Each Other” has attempted to answer.

Octopus verrucosus From: Report on the Cephalopoda collected by H. M. S. Challenger during the years 1873-76
Octopus verrucosus
From: Report on the Cephalopoda collected by H. M. S. Challenger during the years 1873-76
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The Forgetful Young Brain

Formation of new neurons (called neurogenesis) is considerably reduced in adults compared to infants. Considering the fact that new neurons would have to compete with the old ones for the space and connections (i.e. synaptic connections that are present between neurons), it makes sense that the old connections might sometimes be replaced by the new ones during neurogenesis. Consequently, if the old connections were storing memories then their replacement would fragment or completely delete those memories. If we take a step further this would imply that, compared to adult mice, the young mice would not be very good at making long-term memories because in their brains active neurogenesis is taking place, old neurons are replaced, and new connections are made- a process which should delete all the things that were stored in the old neuronal network.

Dentate gyrus imaged using brainbone technique. From: Livet, Jean, et al. Nature 450.7166 (2007): 56-62.
Dentate gyrus imaged using brainbone technique.
From: Livet, Jean, et al. Nature 450.7166 (2007): 56-62.

Consistent with these ideas is the observation of ‘infant amnesia’ in many animals. Namely, animal infants, including human, forget things more readily than adults (can you remember your first, second or third birthdays?). With these premises scientists decided to investigate if neurogenesis could be the cause of infant amnesia in mice and other animals.

Firstly, to prove that the adult mice have reduced neurogenesis in dentate gyrus (part of brain within hippocampus that is linked to memory formation and storage) they injected a retrovirus into dentate gyrus (the retrovirus is a type of virus that will stably integrate into cell’s DNA). The retrovirus was carrying a green fluorescent protein gene (GFP), which after integration will be expressed by the cell. If neurons are dividing then the number of neurons with GFP signal will increase because it will be passed on to new cells from their progenitors but if cells don’t divide then the signal remains stable. The scientists show that in infant mice GFP signal increases and in adults it does not.

Next the study looked at formation of dentate gyrus-dependent memory in young and old mice. Old mice and young mice were trained by placing them in a specific room and giving a series of foot shocks. 28 days later the two age groups were placed in the same room (but no shock was given) and their reaction was observed. The old mice all froze in place in that room indicating the recollection of the shock-memory, however, the younglings showed no response suggesting that they have forgotten the link between the room and the foot shock training.

Okay, so now we know that old mice have little neurogenesis and that they remember the past events better than young mice. But no link between the two events has yet been shown. So, the next step is to increase the neurogenesis in old mice and see if they start forgetting things. As it turns out, neurogenesis in old mice can be increased by as much as 50% simply by making them exercise, namely running in a scroll-wheel. So after several days of exercise , the amount of neurogenesis was measured in the old mice by the same GFP method and an increased neurogenesis was found. Now again the same foot-shock experiment was done: mice are given foot-shocks, put into space with scroll-wheel (mice like to run so they are sure to exercise on it) and placed back into the same room where the foot-shocks were given. As predicted adult mice showed reduced freezing behaviour because of increased neurogenesis, moreover, if the mice exercised before foot-shock training the old mice were still able to recall the training well, indicating that the neurogenesis after the training prevented stable memory formation. The same results were also confirmed by administering drug that induces neurogenesis (and therefore led to forgetting in old mice) and using transgenic mice in which neurogenesis can be inhibited with a drug (the inhibition led to higher rates of remembering in mice that were allowed to exercise as well as the infant mice).

Different animals are born at different stages of brain maturity depending on the length of gestation period. For example, in guinea pigs gestation takes 65 days compared to 21 days in mice, so therefore, guinea pigs should have lower neurogenesis rates as their development after birth is already quite advanced in time. And indeed, when scientists used the same foot-shock experiment to test patterns of memory recall in young and old guinea pigs they found no difference between them. Not surprisingly, injection of drug that increases neurogenesis in guinea pigs led to decreased memory formation.

Neurons in mice hippocampus imaged using CLARITY technique. From: Chung, Kwanghun, et al. Nature (2013)
Neurons in mice hippocampus imaged using CLARITY technique.
From: Chung, Kwanghun, et al. Nature (2013)

In conclusion, the study has determined that neurogenesis contributes to the loss of dentate gyrus-linked memory formation. Other studies, however, have previously shown the reverse effects of neurogenesis, i.e. suggesting that it improves memory. Overall, the picture now seems to be that neurons at different neurogenesis stages might play different roles in memory formation; for example, sufficiently mature neurons could provide more space for new memories. It sort of make sense, I mean if we extrapolate it to humans (and I know that from animal models this might not always be the best thing to do), for infants long-term memories are not as important because parents will provide the missing context for them. As we mature neurogenesis decreases and memories become more stable, while a low amount of new neurons formed contribute to an increased requirements for memory storage space. And for those who might now be scared to exercise because they might start forgetting stuff, well again the neurogenesis in adults is very low and a bit of increase in it thus far seems to be only a good thing. This study, for example, shows that exercise caused increase in hippocampus volume reverses the effects of ageing-linked memory loss and even improves it!

Akers KG, Martinez-Canabal A, Restivo L, Yiu AP, De Cristofaro A, Hsiang HL, Wheeler AL, Guskjolen A, Niibori Y, Shoji H, Ohira K, Richards BA, Miyakawa T, Josselyn SA, & Frankland PW (2014). Hippocampal neurogenesis regulates forgetting during adulthood and infancy. Science (New York, N.Y.), 344 (6184), 598-602 PMID: 24812394