Factors underlying variable DNA methylation in a human community cohort. L.L. Lam et al. PNAS October 16, 2012 vol. 109

The effect of environment on genes can be very profound. Our surroundings may not directly change our DNA sequence but it can surely dictate how our genes are transcribed. Epigenetics studies heritable changes in gene expression caused by non-genetic mechanisms, i.e. mechanisms other than the changes in the DNA sequence itself. DNA methylation is one of the major epigenetic modifications to regulate the gene expression. The addition of methyl groups on DNA sequence acts like a dimmer on a light bulb switch, which will turn certain genes on or off. A recent study showed that a person’s early life experiences shape their DNA methylation patterns. The research team discovered that childhood poverty (not socioeconomic status as an adult) is highly correlated to distinct methylation marks left on genes. Although children in rich and poor households have identical sets of genes, the degree of adversity or stress at home determines which combinations of those genes are activated or silenced through differential DNA methylation. One can imagine that such epigenetic changes might cause some alterations in the gene expression program of blind people to certain environmental signals or make them even more sensitive. Perhaps such changes could make some people more adaptive to harsher life conditions, hence enhance their survival. These findings suggest that environmental conditions early in life shape our epigenomes permanently thereby influence our life experiences, health and probably many other things that we are not yet aware of.

An alien planet next door

An Earth-mass planet orbiting α Centauri B. X.Dumusque et al. Published online 17 October 2012, Nature

Astronomers have just discovered an earth-size alien planet right next to our solar system. A new earthlike planet, named Alpha Centauri, is just 4.4 light-years away. That’s 40 trillion km away from earth! Although this rocky planet’s mass is similar to Earth’s, it orbits much closer (25 times closer than the Earth) to host star Alpha Centauri B. As a result, a year lasts 3236 days and the surface temperature of the planet reaches around to 1200 °C, which makes the planet incapable of supporting any life form we know. However, solar systems with a rocky world are usually predicted to have multiple planets. One possibility is that that Alpha Centauri A, the bigger sibling of Alpha Centauri B, might host some yet to be discovered unknown planets with more habitable zones. Although this recent discovery has sparked people’s dreams to travel to another star system outside of our planetary system, such an exploration mission unfortunately seems impractical in the near future. Even a cell phone-sized probe that is accelerated to 10% of the speed of light would need to travel non-stop for 40 years to reach the target. So, what is the next best thing to do? Will it be taking photos or dropping probes on the planet’s surface to study a potentially modified atmosphere? It seems like while astronomers work hard on the identification and characterization of this new star system, scientists should focus on developing super-fast propulsion systems, which will perhaps include new concepts like nuclear rockets and antimatter fusion drives.

Bad memories, substitute or suppress

Opposing Mechanisms Support the Voluntary Forgetting of Unwanted Memories
Benolt RG et al., Neuron, Volume 76, Issue 2, 450-460, 18 October 2012

For the nervous system, forgetting a memory is almost as complicated as creating one. A recent study probed the mechanism of how the brain allows us to voluntarily forget unwanted memories. Researchers utilized functional magnetic resonance imaging (fMRI) to examine the brain activity of participants who had learned associations between pairs of words and subsequently attempted to forget these memories by either blocking them out or recalling substitute memories. The fMRI results showed that two separate forgetting strategies looked equally effective yet they seemed to use different neuronal circuits in different parts of the brain. For memory suppression, dorsolateral prefrontal cortex inhibits neural activity in the hippocampus which is a critical region for recalling past memories. On the other hand, memory substitution specifically activates caudal prefrontal cortex and midventrolateral prefrontal cortex that are known to bring specific memories into awareness in the presence of distracting memories. These findings can help us to better understand the mechanisms of memory disorders such as posttraumatic stress disorder, and may ultimately help to develop effective treatments. At a more personal level, this study may direct us to explore how we deal with our unpleasant or unwanted memories. We might be surprised to realize that one approach might be working much better for us than another one. In other words, neuronal wiring in our brain might simply favor one approach over another.

Original Article: Ichinohe T. et al., PNAS (published online before print 2011).

Influenza, also known as seasonal flu, affects up to 5 million people annually. Flu viruses infect and damage the animal respiratory tract, especially the lungs. Upon flu virus infection, a life or death battle between an animal’s immune system and the flu virus begins. To defeat the flu virus, the animal’s immune system synthesizes important flu-fighting molecules. Researchers at Yale University discovered that mice on the antibiotic regimen, a treatment that wipes out certain bacteria which normally live in the guts of the animal hosts, showed deficiency in immune responses against flu virus in the lungs compared to mice that had not been treated. This finding suggests an unexpected link that the bacteria living in the animals seem to control the production of these flu-fighting molecules. These commensal bacteria, or good bacteria, prime the immune system in making flu-fighting molecules even before infection, and this priming is important for subsequent flu-fighting strategies. The exact bacterial species that helps fight the flu are yet to be identified. It is interesting to contemplate why the immune system trusts bacteria with such an important job. Whatever that reason might be this finding warns against misuse or abuse of antibiotics. We don’t want to kill the good bacteria that might just protect us in the next flu season.

2- Less talking with longer words

Original Article: Piantadosi S.T. et al., PNAS 108, 3526 (2011).

What factors affect the length of a word? Do we prefer to use short words or long words while we are talking? For many years, researchers believed that the most frequently used words tend to be short in order to make the language more efficient. It is intuitive when we think of words such as “a,” “the,” “but” and their popularity in our everyday life. However, according to a recent study done by Piandatosi and coworkers in the Department of Brain and Cognitive Sciences at MIT, the length of a word reflects the amount of information it contains. They observed that people use many words in predictable sequences along with other words in their daily life. Most of the time a short word may not contain information per se, but carry information as a collection with other familiar words. This observation led the researchers to look at the problem from an ‘information content’ perspective. A word is said to have more information if it is less predictable in a sequence. An analysis was done on the Google text database in 11 different languages. The results show that word length closely correlates to information content. Once again, it is not important how much you talk. It is important how much you mean.

3- Ups and downs of sleep with alpha waves

Original Article: McKinney S.M. et al., PLoS One 6, e17351 (2011).

Why do we randomly wake up in the middle of the night? Searching for an answer for this question, researchers at the Massachusetts General Hospital (MGH) discovered a brain rhythm that determines one’s susceptibility to disturbance by the outside world while asleep. Scott McKinney and his colleagues conducted a study where they analyzed the electroencephalographs (EEGs) of 13 volunteers, who spent 3 nights in MGH’s Sleep laboratory. EEG devices use electrodes on the scalp to detect electrical activity in the brain. There are four major brain waves that can be detected by EEG: alpha, beta, delta and theta waves. Alpha waves usually emanate from the back of the head during relaxed wakefulness, particularly when your eyes are closed, and they are thought to gradually disappear when a person goes to sleep. Researchers developed a special computational method that can probe EEGs in much deeper data resolutions. Their analyses revealed that alpha waves never disappear during sleep; they just go below conventional detection levels. Moreover, when alpha wave activity spikes just before an obnoxious auditory stimuli (e.g., loud talking or traffic noise) is played, volunteers seems to wake up more easily than when alpha wave activity was low. These findings suggest that maybe the alpha wave activity is the brain’s way of keeping us aware of our surroundings during sleep, and perhaps it enables us to wake up quickly in case of danger. Of course, too much alpha activity might also have a downside: it can make you a light sleeper and give you restless nights.

4- Killer whales imitate enemies and friends

Original Article: Wei B.M. et al., Marine Mammal Science (published online before print 2011).

In marine mammals, as individuals frequently cannot see each other, sound is particularly important for communication. Killer whales live in groups or clans, and these different clans have their own dialects. A recent study showed that whales can do more than just talk in their own language: they can mimic calls from other groups with a different dialect. While analyzing the social behavior of wild orcas living near Vancouver Island in British Colombia, a group of researchers from the University of Vienna discovered that resident whales occasionally produce call types from the repertoires of other vocal clans. The calls resemble the calls of foreign groups that the original group interacted with before. When different clans are in close proximity, it is quite challenging to reliably distinguish original calls from resembling calls. For this reason, researchers recorded calls that resemble call types of a different clan in the absence of that clan and compared them to the originals of the respective call types by analyzing their sonograms. Sonograms reveal distinctive information about the structure of the sound waves, i.e. the spectral density of these signals, and this information can be used to classify animal sounds. The comparative analysis clearly shows that killer whales can imitate calls from other groups even when members of that group are not around. Researchers suggest that this could be a way of labeling outsiders or keeping tabs on their location. Maybe by impersonating the calls of a group, they are conveying a message about that group to their own family members. It is exciting to see that vocal mimicry is not limited to songbirds and dolphins, and that killer whales have more complex social lives than we previously thought.