Artificial photosynthesis transforms CO₂ into liquefiable fuels

Yu and Jain. Plasmonic photosynthesis of C1–C3 hydrocarbons from carbon dioxide assisted by an ionic liquid. Nature Communications, May 2019.

Scientists have recently established a reliable “artificial photosynthesis” paradigm to produce fuels from water, carbon dioxide, and visible light. With the help of sunlight, chemical reactions between water and CO₂ are catalyzed in plants to generate and store solar energy in the form of glucose. This process is called photosynthesis. In the new study, the researchers developed an artificial process that uses the same mechanisms of natural photosynthesis to convert CO₂ and water into liquid fuel by using electron-rich gold nanoparticles as a catalyst. Gold nanoparticles function in the same role as chlorophyll in natural photosynthesis in the absorbing of light and transferring electrons and protons to catalyze the chemical reactions between CO₂ and water. They are known to be efficient at absorbing light and do not break down or degrade like other metals. The energy stored in the bonds of the hydrocarbon fuel can be freed by the conventional method of combustion or by new-generation, environmentally-friendly power fuel cells, thus producing electrical current. By converting CO₂ into more complex molecules like propane, green-energy technology is now one step closer to using excess CO₂ to store solar energy for use when the sun is not shining and in times of peak demand. While the development of this CO₂-to-liquid fuel may be exciting for proponents of green-energy technology, the artificial photosynthesis process is nowhere near as efficient as it is in plants. New methods should be developed to increase the efficiency of the catalysts and downstream chemical reactions at much higher scales.

Brain area that watches for walls identified

Henriksson et al. Rapid Invariant Encoding of Scene Layout in Human OPA. Neuron, May 2019.

Neuroscientists have identified the part of the human brain whose duty is to help us perceive the barriers which define the navigable space around us, such as walls or ceilings, so that so we can avoid bumping into things and navigate safely through our environment. By way of vision we have an almost instant sense of where we are in space. Although this process feels effortless, it requires the coordinated activity of multiple brain regions and neurons working together to give us this sense of our surroundings. This process has remained unknown. But thanks to a new study, we are a step closer to solving the puzzle. Using cutting-edge brain-imaging technologies, researchers examined the mental responses of volunteers as they were shown images of various three-dimensional scenes. The images depicted a typical room with three walls, a ceiling, and a floor, but then were abruptly changed by the removal of a wall or a ceiling. By doing this repeatedly, the team could pinpoint how the participant’s brain encoded every scene. In the brain scans of the volunteers, one brain area called the occipital place area (OPA) clearly stood out. OPA activity represented the geometry of the scenes and activity patterns, reflected the presence or absence of each component, such as a ceiling or a wall, and projected a detailed picture of the overall configuration. Interestingly, OPA seemed to ignore the surface appearance of the various components such as colors or textures in order to focus only on the geometric patterns. The OPA managed to perform all the necessary computations needed to get a sense of a room’s layout extremely fast – in just 100 milliseconds. In the future, the research team plans to incorporate virtual reality technology to create more realistic 3D environments for participants to experience, hopefully achieving much deeper insights into how our brains process and makes sense of the visual information.

Gut segments are organized by function

Esterházy D. et al. Compartmentalized gut lymph node drainage dictates adaptive immune responses. Nature, April 2019.

As food enters our intestine, it goes through a windy and lengthy journey. A new study provides new insights into how our intestines maximize nutrient uptake while protecting the body from potentially dangerous invading microbes. At first glance, the intestines appear to have a uniform tissue structure. But when scientists looked at them closer, they found that our food-processing canal seems to consist of multiple compartments that pace the immune system’s reactions to the food passing through. Scientists uncovered these functional intestine segments in mice when they examined the intestinal structures called gut draining lymph nodes, which orchestrate immune responses. The researchers found that nodes in different parts of the intestines had different cell composition, and they saw different immune responses between segments when they challenged the mice with a pathogen. They observed less aggressive defenses in the first segments where nutrients are absorbed, and more forceful responses at the end, where pathogens are eliminated. Researchers plan to exploit these immunological differences between the gut segments for treating gastrointestinal disorders. For example, by targeting immune-suppressing drugs to the specific gut segment where they’ll have the most effect, it might be possible to dampen their side-effects. The spectrum of immune responses along the intestines could also be used to make new and better oral vaccines. Thus far, scientists’ efforts to design oral vaccines have been hampered by the difficulty of generating a robust immune response; it is possible that the muted immune response at the beginning of the intestines might be part of the reason why oral vaccines tend to be less effective than injections. Thus, targeting the distant end of the intestine might be much more efficient way of inducing the immune response required.

Microbes, in particular bacteria, are associated with many diseases, being the deadliest pathogens along with viruses. But, this doesn’t mean that all bacteria are harmful. Indeed, most bacterial colonies that reside in our gut have mutualistic relationship with humans. Our intestines carry approximately ten times more bacteria than the total number of cells in human body. This vast number of bacteria residing in our intestines are not only harmless, but they are also beneficial for us in many ways, by digesting food to supply energy for the body, by outcompeting the disease-causing bacteria in the intestines, and by producing vitamins and hormones. This study brings a new dimension to our understanding of the interactions between the host immune system with the gut microflora. The main components of immune system are the T cells that can recognize the pathogens. Each T cell recognizes one particular pathogen and distinguishes self-cells from the pathogens. In the thymus, T cells that recognize self-molecules are either eliminated or transformed into a special category of T-cells called regulatory T cells (Tregs), whose job is to maintain tolerance towards self-antigens. Lathrop and colleagues demonstrated for the first time that naïve T cells are developed into Tregs in the gut upon encounter of commensal gut bacteria. What is striking is that these Tregs responded to the bacterial antigens, unlike the thymus originated Tregs that were generated by self-antigen recognition. These data suggest that gut bacteria train host’s immune system to be silent against themselves and act only against invading pathogens. Mechanisms involved in distinguishing harmful vs. beneficial bacteria by the immune system may provide new ways of tackling with bacterial diseases.

2- Cancer meets memory

Original Article: Odajima, J. et al., Developmental Cell 21, 655 (2011).

The recent discovery in the field of neuroscience reminded us the phrase “context is everything.” A study conducted by the scientists of Dana-Farber Cancer Institute and Harvard Medical School addressed somewhat contradictive observation that why human brain has high levels of cyclin E protein, a well-known culprit in many cancers. Cyclin E protein plays an important role in cell cycle where it helps to regulate the timing and the frequency of cell division in normally growing cells. However, overexpression of cyclin E has been associated with uncontrolled cell growth in various cancer types. It is surprising that the human brain, which has a group of non-dividing cells, also express cyclin E at high levels. The study showed that when cyclin E deficient mice were analyzed, there was a serious defect in the formation of nerve connections as well as the formation of memory. “It is overexpressed in many different cancers, but it also is expressed in high levels in the human brain. We have found that cyclin E is needed for memory formation and is a very important player,” said senior author Peter Sicinski, PhD, a cancer biologist at Dana-Farber. The study showed that cyclin E achieves its functions in the brain by binding to Cdk5 enzyme whose activity is associated with Alzheimer’s disease. “There is good evidence that hyperactivity of Cdk5 contributes to Alzheimer’s disease and inhibiting this enzyme can ameliorate symptoms in animals,” said Sicinski. “Manipulating cyclin E levels might be another way to accomplish this,” he added.

3- Designing perfect plastic 

Original Article: Read, D.J. et al., Science 333, 1871 (2011).

Plastic is used everywhere in our daily lives. Up until now, production of different types of plastic was done by trial and error. Only a small fraction of these trials give rise to a usable product. After ten years of hard work, scientists have now developed a computer program that can predict properties of plastic without actually manufacturing it. The program has two parts. The first part can predict how a specific polymer will flow based on the connections between the macromolecules that make up the polymer. The second part predicts the shape of these macromolecules when they are made at a chemical level. Using this code, one can effectively construct a recipe book for plastic. This will make it possible to design plastic that can better handle a specific job. It will also be possible to make plastic out of renewable materials instead of oil based materials which will be easy to recycle.

4- The key to long life?

Original Article: Kim, E.B. et al., Nature (published online before print, 2011).

Who would want to live a long life at the cost of looking ugly? One type of rodent species, naked mole rat, seems to have said “yes” to this intricate question. While an average rodent, a house mice or a rat living on streets, can live up to 4 years, naked mole rats can live up to 30 years. Mole rats are hairless, buck-toothed and almost blind rodents that are only found in dry sections of the Horn of Africa. They live in underground colonies with a social structure similar to ant colonies. There is a queen rat that chooses to mate with only few males, and rest of the colony takes the big responsibility of maintaining and protecting the colony. Scientists have always been puzzled with the extraordinary life span of these exotic animals and they finally generated the complete gene map of these intriguing animals. A quick look of the genomic map revealed that many genes associated with vision, circadian rhythms, perception of pain and perception of bitter tastes seem to be completely turned-off. Perhaps, these specific modifications allow animals to tolerate harsh living conditions and help them to adapt a lifestyle which lacks so-called the luxuries and expectations of a normal animal. Scientists believe that comprehensive analyses of naked mole’s genetic map might shed light on fundamental cellular mechanisms that are disrupted in aging and aging-related diseases.

Original Article: Akashi M. et al., PNAS 107, 15643 (2010).

Feeling sleepy during the day after a long flight? Internal body clock genes are to blame. Circadian (Latin: “around” “the day”) rhythm genes take part in a time dependent cycling of an organism to carry out daily physiological processes. These signals include very basic needs such as feeling sleepy at nighttime and waking up during the day and repeats about every 24 hours. Malfunctioning circadian rhythm genes are implicated in several sleep disorders. According to a recent study done by Makoto Akashi and his colleagues at Yamaguchi University in Japan, hair follicle cells were found to closely follow the gene expression pattern of the internal circadian rhythm of the human body. Gene expression patterns can be extracted from hair follicles from pulled hair. Studying the circadian rhythm genes and expression profiles has been quite an inconvenience for researchers up until now. This study provides a new alternative method for tapping into this machinery. Don’t be surprised if you are asked for a couple of hairs pulled from your scalp if you go to a doctor complaining about your sleep disorder in the future. This method could have implications in the field of diagnostic medicine as a less invasive method for diagnosing problems since it allows us to conveniently gain access to the gene expression profiles of a person. We are not at a stage where we can control our sleep cycle at our convenience, but this is a step towards facilitating our understanding of this mechanism.

2- Western diet disturbs our bacterial guests

Original Article: De Filippo C. et al., PNAS 107, 14691 (2010).

Did you know that there are 100 trillions of microbes living happily ever after in your gut? This is about 10 times as many cells as make up the whole human body. But, no need to panic, because the sole purpose of their presence is to serve us by aiding in our daily digestion, metabolism and improving our immune system overall. A recent study shows that our friendly inhabitants are drastically affected by the human diet. A research group at Meyer Children Hospital in Italy analyzed and compared the fecal microbiota of children from Europe to that of children from rural African village of Burkino Faso (BF). When they examined the diets of each group closely, they saw that the BF diet is rich in cereals, vegetables and legumes, whereas the European diet is usually rich in animal protein, sugar, starch, and fat. Thus, children from Africa typically have a high-fiber diet and the children from Europe have a low-fiber diet. Next, researchers characterized the gut microbiotas of each group from fecal samples. The results revealed that gut microbiota was drastically different between these groups. Interestingly, BF children had several types of bacteria that seem to produce substantial amounts of short chain fatty acids (SCFAs) as a result of fiber-rich diet. The high levels of SCFAs are known to result in high energy levels and an increased anti-inflammatory capacity. The fact that African populations have almost no non-infectious colonic diseases may be attributed to the enriched diversity of gut microbiota due to the high-fiber diet of African children. This study once again emphasizes the importance of a fiber rich diet and it becomes clear that the adoption of such a diet and refraining from fast food culture would be beneficial to all of us.

3- Eat more, enjoy less

Original Article: Stice E. et al., The Journal of Neuroscience 30, 13105 (2010).

Why do obese people tend to overeat? A new study suggests a vicious cycle stemming from an obese individual’s desire to compensate for reduced pleasure from food. Degree of pleasure derived from eating correlates with the amount of released dopamine, which is associated with food intake. The researchers studied 26 overweight and obese volunteers, who were subjected to fMRI brain scans to identify brain regions that became active as they sipped both sugary milkshakes and a flavorless liquid. Every participant was tested twice over a six month period. Participants who gained weight showed significantly less activation in response to the milkshake intake upon a six-month follow-up relative to their baseline scan and relative to participants who did not gain weight. According to these results intake of palatable food results in down regulation of D2 receptors, reduced D2 sensitivity, and decreased reward sensitivity, implying that overeating may contribute to reduced striatal responsivity. These results will likely be important in developing programs to prevent and treat obesity, and also help us understand why obesity typically shows a chronic course and is resistant to treatment. Here is another reason to eat less: to get more pleasure from the food we eat.

4- Tough Malagasy spiders

Original Article: Agnarsson I. et al., PLoS one 5, e11234 (2010).

There are 40,000 kinds of spiders. They have little bodies, but the webs that they knit with their long thin legs using the silk from their tiny bodies are examples of great talent. Among the 200,000 types of silk which spiders produce, each have different combinations of properties, such as stickiness, durability or thickness, etc. A recently discovered spider found in Madagascar has an even more amazing talent. This kind of spider with its 3–5 cm long body size can make a web that can cross a river 2.5 meters wide with the ends of the nets attached to trees on either bank of a riverside. These nets have been found to be the strongest biological material ever known. After careful measurement, it was discovered that these webs are 10 times stronger (350 MJ/m3) than Kevlar, which is the material used in bulletproof vest, and some threads become even more durable (520 MJ/m3), which means that this spider beats even the most talented scientists and engineers with its skinny small legs and tiny little brain by developing material which is more than ten times tougher. It is believed that these spiders need to have strong nets in order to bare the extreme weather conditions above the river and catch the bugs flying over the river. There are still investigations that have yet to be done in order to find out further properties of such webs. “Verily in these things there are signs for those who consider.”

I am not a tailor, I do not make or sell clothes for a living, I am not in the textile business in any way. Even so, what had brought me to this exhibition was curiosity about such devices as stitches, stitching needles, scissors and the like. More precisely, I had come to see what I could find out about the history and development of such devices in relation to cutting and joining in surgical procedures, especially sutures. 

Every display in the great hall was presented by a team of experts who were there to answer questions. I asked many. In the end, rather to my surprise, I met one expert who was able to give me the kind of help I was looking for. He was Paul Breuer from Aachen, representing the German company SNF MANF, who, as it happens, manufacture surgical needles. Paul Breuer astonished me with his knowledge of a wide range of methods for sewing skin, including the use of ants. Naturally, I was intrigued, and Paul promised to post to me a photograph of an ant being used as a skin stitch, after his return to Aachen.

An embroidery equipment specialist, Caroline Sayers, of the company DATA STITCH, said she could design an ant stitch, if I could supply her with a suitable photograph. The very next day after I had supplied the photograph, the ant was scanned, digitized and an embroidery machine executed for us the amazing ant stitch.

My curiosity about this unusual suture technique led me to further investigations which finally bore fruit when I came across Welcome Institute for the History of Medicine’s 1973 publication, Albucasis on surgery and instruments. This book is a definitive edition of the original Arabic text with English translation and commentary by MS. Spink and G.L. Lewis.

In Book 2, Chapter 85, on suture materials used by the Arab surgeons, Albucasis (the Latinized version of Abu l-Qasim) mentions two techniques. Spink and Lewis, 1973, p.538, comment:

1. Ants’ nippers. This is not a classical method; but is said to be used by African tribes as a way of bringing skin edges together (modern Michel clips); evidently the Arabian ant-nippers acted in the same way.

2. Gut sutures. Gut was used by the earliest Greeks for bow-strings; but it is not mentioned as used for surgical purposes until the Arab era of surgery. Albucasis then describes it as ‘rubbed-down gut, well cleansed’. This may be the earliest reference to this now universal suture material.

Abu l-Qasim’s own account (ibid., p.550) is a vivid description of sutures using ants and cat gut:

Some men of experience have said that when a wound occurs in the intestine and it is small, it should be sutured in this manner, namely: ants with large heads are taken; then the edges of the wound are brought together and one of these ants is applied by its jaws then the head is cut off, and it will stick and will not loosen. Then another ant is applied near the first; and you proceed after this manner with a number of ants according to the size of the wound. Then reduce the intestine and sew up the wound; for the heads will remain sticking to the intestine until it is healed up; and no harm will come to the patient.

The intestine may be sewn up with fine suture which is extracted from an animals gut and sticks to it after being threaded in a needle. The method is that the end is taken of this suture made of gut, well scraped; and to this end is fixed a linen thread, twisted, and then that thread is passed through the needle affixed to the suture of animalis gut, with which the intestine is sewn and then replaced in the abdominal cavity (Abu l-Qasim al-Zahrawi, Al-Tasrif, Book 2 Chapter 85).

Abu l-Qasim Al-Zahrawi (936-1013) wrote his remarkable surgery manual Al-Tasrif during the period of Arab/Islamic rule in Spain about a thousand years ago. I felt a curious and wonderful sensation at the link between an ant stitch, mentioned and talked about in an exhibition of textile craftsmanship in Manchester near the end of the twentieth century, and the dedication and craftsmanly skills of the Muslim scholar who, a millenium before, had adapted the use of ants, and invented the use of cat gut, for making sutures. This was not the only contribution this extraordinary man made to the development of modern surgery techniques, nor was he the only Muslim to have made significant and striking advances in the field of medicine.

It is hard not to feel awe (and, naturally, some pride) at the achievement of the Muslims in that great period of Islamic civilization. I have no doubt that their success was owed to the excellence of their faith and their consequent commitment to working for the improvement of human well-being and the advancement of learning. And I realize that I am merely at the beginning of a long quest for information about what was achieved by Muslims dedicated to Islam in the broadest sense-namely, a way that improves the quality of human life and the quality of our understanding of the world we live in.