Aurelia Butler

From tiny fruit flies to human beings, all animals on Earth maintain their daily rhythms based on their internal circadian clock. The circadian clock enables organisms to undergo rhythmic changes in behavior and physiology based on a 24-hour circadian cycle. For example, our own biological clock tells our brain to release melatonin, a sleep-inducing hormone, at night time.
The discovery of the molecular mechanism of the circadian clock was bestowed The Nobel Prize in Physiology or Medicine 2017. From what we know, no one centralized clock is responsible for our circadian cycles. Instead, it operates in a hierarchical network where there are “master pacemaker” and “slave oscillator.”
The master pacemaker receives various input signals from the environment such as light. The master then drives the slave oscillator that regulates various outputs such as sleep, feeding, and metabolism. Despite the different roles of the pacemaker neurons, they are known to share common molecular mechanisms that are well conserved in all lifeforms. For example, interlocked systems of multiple transcriptional-translational feedback loops (TTFLs) composed of core clock proteins have been deeply studied in fruit flies.
However, there is still much that we need to learn about our own biological clock. The hierarchically-organized nature of master and slave clock neurons leads to a prevailing belief that they share an identical molecular clockwork. At the same time, the different roles they serve in regulating bodily rhythms also raise the question of whether they might function under different molecular clockworks.
Led by Prof. KIM Jae Kyoung and KIM Eun Young, researchers at the Institute for Basic Science (IBS) and Ajou University used a combination of mathematical and experimental approaches using fruit flies to answer this question. The team found that the master clock and the slave clock operate via different molecular mechanisms.
In both master and slave neurons of fruit flies, a circadian rhythm-related protein called PER is produced and degraded at different rates depending on the time of the day. Previously, the team found that the master clock neuron (sLNvs) and the slave clock neuron (DN1ps) have different profiles of PER in wild-type and Clk-Δ mutant Drosophila. This hinted that there might be a potential difference in molecular clockworks between the master and slave clock neurons.
However, due to the complexity of the molecular clockwork, it was challenging to identify the source of such differences. Thus, the team developed a mathematical model describing the molecular clockworks of the master and slave clocks. Then, all possible molecular differences between the master and slave clock neurons were systematically investigated by using computer simulations. The model predicted that PER is more efficiently produced and then rapidly degraded in the master clock compared to the slave clock neurons. This prediction was then confirmed by the follow-up experiments using animal.
Then, why do the master clock neurons have such different molecular properties from the slave clock neurons? To answer this question, the research team again used the combination of mathematical model simulation and experiments. It was found that the faster rate of synthesis of PER in the master clock neurons allows them to generate synchronized rhythms with a high level of amplitude. Generation of such a strong rhythm with high amplitude is critical to delivering clear signals to slave clock neurons.
However, such strong rhythms would typically be unfavorable when it comes to adapting to environmental changes. These include natural causes such as different daylight hours across summer and winter seasons, up to more extreme artificial cases such as jet lag that occurs after international travel. Thanks to the distinct property of the master clock neurons, it is able to undergo phase dispersion when the standard light-dark cycle is disrupted, drastically reducing the level of PER. The master clock neurons can then easily adapt to the new diurnal cycle. Our master pacemaker’s plasticity explains how we can quickly adjust to the new time zones after international flights after just a brief period of jet lag.
It is hoped that the findings of this study can have future clinical implications when it comes to treating various disorders that affect our circadian rhythm. Chief investigator Kim notes, “When the circadian clock loses its robustness and flexibility, the circadian rhythms sleep disorders can occur. As this study identifies the molecular mechanism that generates robustness and flexibility of the circadian clock, it can facilitate the identification of the cause of and treatment strategy for the circadian rhythm sleep disorders.”
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The time a person spends on different smartphone apps is enough to identify them from a larger group in more than one in three cases say researchers, who warn of the implications for security and privacy.
Psychologists Dr Heather Shaw, Professor Paul Taylor and Professor Stacey Conchie from Lancaster University, and Dr David Ellis from the University of Bath analysed smartphone data from 780 people.
Their paper is published in the journal Psychological Science.
They fed 4,680 days of app usage data into statistical models. Each of these days was paired with one of the 780 users, such that the models learnt people’s daily app use patterns.
The researchers then tested whether models could identify an individual when provided with only a single day of smartphone activity that was anonymous and not yet paired with a user.
Dr Ellis from the University of Bath said: “Our models, which were trained on only six days of app usage data per person, could identify the correct person from a day of anonymous data one third of the time.”
That might not sound like much, but when the models made a prediction regarding who data belonged to, it could also provide a list of the most to the least likely candidates. It was possible to view the top 10 most likely individuals that a specific day of data belonged to. Around 75% of the time, the correct user would be among the top 10 most likely candidates.
Professor Taylor from Lancaster University added: “In practical terms, a law enforcement investigation seeking to identify a criminal’s new phone from knowledge of their historic phone use could reduce a candidate pool of approximately 1,000 phones to 10 phones, with a 25% risk of missing them.”
Consequently, the researchers warn that software granted access to a smartphone’s standard activity logging could render a reasonable prediction about a user’s identity even when they were logged-out of their account. An identification is possible with no monitoring of conversations or behaviours within apps themselves.
Dr Shaw from Lancaster University said: “We found that people exhibited consistent patterns in their application usage behaviours on a day-to-day basis, such as using Facebook the most and the calculator app the least. In support of this, we also showed that two days of smartphone data from the same person exhibited greater similarity in app usage patterns than two days of data from different people.”
Therefore, it is important to acknowledge that app usage data alone, which is often collected by a smartphone automatically, can potentially reveal a person’s identity.
While providing new opportunities for law enforcement, it also poses risks to privacy if this type of data is misused.
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Although solar cells are typically designed to turn light into power, researchers have shown that they can also be used to achieve underwater wireless optical communication with high data rates. The new approach — which used an array of series-connected solar cells as detectors — could offer a cost-effective, low-energy way to transmit data underwater.
“There is a critical need for efficient underwater communication to meet the increasing demands of underwater data exchange in worldwide ocean protection activities,” said research team leader Jing Xu from Zhejiang University in China. For example, in coral reef conservation efforts, data links are necessary to transmit data from divers, manned submarines, underwater sensors and unmanned autonomous underwater vehicles to surface ships supporting their work.
In the Optica Publishing Group journal Optics Letters, Xu and colleagues report on laboratory experiments in which they used an array of commercially available solar cells to create an optimized lens-free system for high-speed optical detection underwater. Solar cells offer a much larger detection area than the photodiodes traditionally used as detectors in wireless optical communication.
“To the best of our knowledge, we demonstrated the highest bandwidth ever achieved for a commercial silicon solar panel-based optical communication system with a large detection area,” said Xu. “This type of system could even allow data exchange and power generation with one device.”
Optimizing solar cells for communication
Compared to using radio or acoustic waves, light-based underwater wireless communication exhibits higher speed, lower latency and requires less power. However, most long-distance high-speed optical systems are not practical for underwater implementation because they require strict alignment between the transmitter emitting the light and the receiver that detects the incoming light signal. More

University of Wisconsin-Madison physicists have made one of the highest performance atomic clocks ever, they announced Feb. 16 in the journal Nature.
Their instrument, known as an optical lattice atomic clock, can measure differences in time to a precision equivalent to losing just one second every 300 billion years and is the first example of a “multiplexed” optical clock, where six separate clocks can exist in the same environment. Its design allows the team to test ways to search for gravitational waves, attempt to detect dark matter, and discover new physics with clocks.
“Optical lattice clocks are already the best clocks in the world, and here we get this level of performance that no one has seen before,” says Shimon Kolkowitz, a UW-Madison physics professor and senior author of the study. “We’re working to both improve their performance and to develop emerging applications that are enabled by this improved performance.”
Atomic clocks are so precise because they take advantage of a fundamental property of atoms: when an electron changes energy levels, it absorbs or emits light with a frequency that is identical for all atoms of a particular element. Optical atomic clocks keep time by using a laser that is tuned to precisely match this frequency, and they require some of the world’s most sophisticated lasers to keep accurate time.
By comparison, Kolkowitz’s group has “a relatively lousy laser,” he says, so they knew that any clock they built would not be the most accurate or precise on its own. But they also knew that many downstream applications of optical clocks will require portable, commercially available lasers like theirs. Designing a clock that could use average lasers would be a boon.
In their new study, they created a multiplexed clock, where strontium atoms can be separated into multiple clocks arranged in a line in the same vacuum chamber. Using just one atomic clock, the team found that their laser was only reliably able to excite electrons in the same number of atoms for one-tenth of a second. More

Researchers from the RIKEN Guardian Robot Project in Japan have made an android child named Nikola that successfully conveys six basic emotions. The new study, published in Frontiers in Psychology, tested how well people could identify six facial expressions — happiness, sadness, fear, anger, surprise, and disgust — which were generated by moving “muscles” in Nikola’s face. This is the first time that the quality of android-expressed emotion has been tested and verified for these six emotions.
Rosie the robot maid was considered science fiction when she debuted on the Jetson’s cartoon over 50 years ago. Although the reality of the helpful robot is currently more science and less fiction, there are still many challenges that need to be met, including being able to detect and express emotions. The recent study led by Wataru Sato from the RIKEN Guardian Robot Project focused on building a humanoid robot, or android, that can use its face to express a variety of emotions. The result is Nikola, an android head that looks like a hairless boy.
Inside Nikola’s face are 29 pneumatic actuators that control the movements of artificial muscles. Another 6 actuators control head and eyeball movements. Pneumatic actuators are controlled by air pressure, which makes the movements silent and smooth. The team placed the actuators based on the Facial Action Coding System (FACS), which has been used extensively to study facial expressions. Past research has identified numerous facial action units — such as ‘cheek raiser’ and ‘lip pucker’ — that comprise typical emotions such as happiness or disgust, and the researchers incorporated these action units in Nikola’s design.
Typically, studies of emotions, particularly how people react to emotions, have a problem. It is difficult to do a properly controlled experiment with live people interacting, but at the same time, looking at photos or videos of people is less natural, and reactions aren’t the same. “The hope is that with androids like Nikola, we can have our cake and eat it too,” says Sato. “We can control every aspect of Nikola’s behavior, and at the same time study live interactions.” The first step was to see if Nikola’s facial expressions were understandable.
A person certified in FACS scoring was able to identify each facial action unit, indicating that Nikola’s facial movements accurately resemble those of a real human. A second test showed that everyday people could recognize the six prototypical emotions — happiness, sadness, fear, anger, surprise, and disgust — in Nikola’s face, albeit to varying accuracies. This is because Nikola’s silicone skin is less elastic than real human skin and cannot form wrinkles very well. Thus, emotions like disgust were harder to identify because the action unit for nose wrinkling could not be included.
“In the short term, androids like Nikola can be important research tools for social psychology or even social neuroscience,” says Sato. “Compared with human confederates, androids are good at controlling behaviors and can facilitate rigorous empirical investigation of human social interactions.” As an example, the researchers asked people to rate the naturalness of Nikola’s emotions as the speed of his facial movements was systematically controlled. They researchers found that the most natural speed was slower for some emotions like sadness than it was for others like surprise.
While Nikola still lacks a body, the ultimate goal of the Guardian Robot Project is to build an android that can assist people, particularly those which physical needs who might live alone. “Androids that can emotionally communicate with us will be useful in a wide range of real-life situations, such as caring for older people, and can promote human wellbeing,” says Sato.
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Researchers from The University of Tokyo calculated the optimal search strategy for organisms that employ run-and-tumble motion when looking for a food’s odor. They determined that the chemotaxis demonstrated by E. coli closely resembles this system when accounting for the costs of control and the noise of the environment. This work may lead to new methods of designing chemical-seeking drones or nanobots.
The aroma of a favorite dessert can tempt almost anyone to follow the scent. By moving in the direction of increasing smell, one can often locate the desired confection. It turns out that even simple organisms, like the single-celled E. coli bacterium, can use a similar method to detect and move toward food. Now, researchers have developed a theoretical model for the best possible search strategy when searching for source of the scent, which may help in the design of new drones or nanobots that can find their own way to a chemical target.
Scientists from the Institute of Industrial Science, The University of Tokyo have studied the odor-searching strategy used by organisms ranging from bacteria to multicellular eukaryotes, which perform “chemotaxis.” Chemotaxis is the process of attraction in the direction of a chemical gradient, and it takes several forms. E. coli bacteria use the common approach called “run-and-tumble,” in which periods of forward swimming are interrupted by rotations that randomly change the direction of motion. Although linear control theory has become part of the established practice of engineering, it does not suffice to handle the nonlinearity and large noise seen in biological systems. A more tailored theory is needed to better understand this phenomenon.
The research team used stochastic optimal control theory to find the best possible fully nonlinear sensing and control strategy of run-and-tumble motion in environments with noisy chemical gradients. They modeled the internal control using a partially observable Markov decision process. In this framework, agents cannot directly observe the correct solution, but they can update their beliefs by sensing their environment.
To make the model as realistic as possible, the researchers included a control cost that represents the physical limitations of regulating when tumbling occurs. “The correspondence between our optimal solution and biochemical bacterial models demonstrates the applicability of our theoretical framework to the understanding of biological search systems,” says first author Kento Nakamura. The primary way that organisms control their motion and progressively move toward a target is by inhibiting tumbling when sensing that the chemical concentration is increasing along their current direction.
This work opens the way for new kinds of autonomous pathfinding algorithms that can be employed to find specific targets, even if their exact locations are unknown. “Understanding the internal control mechanisms of biological organisms would be helpful when designing biomimetic robots that can take advantage of these systems,” says senior author Tetsuya J. Kobayashi.
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Simulations have led to the fabrication of a polymer-DNA gel that could be used in tissue regeneration and robotics.
Scientists in Japan have made a tuneable, elastic and temperature-sensitive gel by using complementary DNA strands to connect star-shaped polymer molecules together. The gel, and the method used to develop it, could lead to advances in tissue regeneration, drug delivery and soft robotics. Xiang Li at Hokkaido University led the team of researchers who reported their findings in the journal Polymer Science.
Scientists have long been looking for better ways to develop gels that can be used in a variety of applications, including in the fields of medicine and engineering. Ideally, such gels need to be predictable in their behaviour, self-healing and durable enough for the rigorous jobs they are intended for.
“Gels are made by using bonds to link polymer molecules together,” explains Li. “When the bonds are connected, the material is more solid, and when they break in response to stress, the material turns to liquid.”
Owing to their high biocompatibility, water solubility and temperature sensitivity, DNA strands would be highly suitable for linking polymer molecules by taking advantage of their ability to form complementary bonds. However, scientists have so far found it difficult to use DNA links to develop homogeneous gels with on-demand elastic properties.
Looking to solve this problem, Li and his colleagues used software programs to simulate the formation of different DNA sequences and their complementary strands, and to determine how these double strands respond to changes in temperature. Their aim was to identify complementary DNA sequences that would only disconnect above 63°C in order to ensure a potential gel’s stability in the human body.
Based on the software simulations, they chose a pair of complementary DNA sequences to link four-armed molecules of polyethylene glycol (PEG). They prepared the gel by dissolving DNA strands and PEG separately in buffer solutions before mixing them in a test tube immersed in a hot water bath that was then cooled to ambient temperature. Finally, they conducted a series of experiments and analyses to evaluate the resulting gel’s properties.
The gel performed as predicted by the simulations, remaining elastic, self-repairing and solid until its melting temperature of 63°C over multiple testing cycles. The experiments also showed that the PEG molecules were homogeneously linked together by the DNA double strands and that liquid formation happened when the strands separated.
“Our findings suggest that we will be able to fabricate DNA gels with on-demand viscoelastic properties by making use of already available data on DNA thermodynamics and kinetics,” says Li. “The aim will be to improve the understanding and applications of this class of gel.”
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