Jacobs J. et al. Direct recordings of grid-like neuronal activity in human spatial navigation. Nature Neuroscience, 2013

Do you happen to have a poor sense of direction? Do you often find yourself holding a map upside-down? Well, now you can blame your grid cells. Using direct human brain recordings, researchers have identified a novel type of cell in the brain that helps people keep track of their relative location while navigating through an unfamiliar environment. Scientists got this rare opportunity to identify these unique cells while they studied brain recordings of epilepsy patients via electrodes implanted deep inside their brains. These cells have been called “grid cells” because they are activated in a triangular grid pattern. The “grid cell” is distinct among brain cells because its activation represents multiple spatial locations, which allows the brain to keep track of navigational cues, such as how far you are from a starting point or your last turn. This type of navigation is called path integration. During brain recordings, 14 study participants were asked to play a video game where they ride a virtual bicycle to navigate from one point to another to retrieve objects and then recall how to get back to the places where they found the objects. While participants were playing the game, researchers examined the relation between navigation and the corresponding activity of individual neurons. Results were striking: each grid cell responded at multiple spatial locations that were arranged in the shape of a grid suggesting that the navigation information is principally encoded in our brains through this triangular grid pattern. Without grid cells, humans would frequently get lost or have to navigate based solely on landmarks. Differences in how well the grid cells work could potentially explain why some people have a better sense of direction than others. In addition, grid cells are located in the entorhinal cortex which is a critical component of human memory. The entorhinal cortex is also the first brain region affected in Alzheimer’s disease. Thus, understanding how grid cells work could potentially help us to understand why people with Alzheimer’s frequently become disoriented as well as to develop new strategies to improve brain function in the affected individuals.

Giant viruses open Pandora’s box

Philippe N. et al. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science, 2013 Jul 19

On a fairly ordinary day, two French biologists were analyzing water samples collected off the coast of Chile. What they saw under the microscope was quite amazing: a previously unidentified organism, about the size of a bacterial cell, appeared as a large dark spot. Astonishingly, these new organisms seemed to be infecting and killing the amoeba in the water. Later, another group of researchers found a similar organism in a pond in Australia. Both groups soon realized that they discovered a type of “giant” virus which is at least twice as big as the largest known viruses. The biggest virus discovered so far was called Mimiviruses, with a size of 700 nanometers and carrying more than 1000 genes. The newly discovered viruses are called Pandoraviruses, which are 1 micrometer long and 0.5 micrometers across. Pandoraviruses are visible under a light microscope and contain more than 2500 genes. A viral genome consisting of 2500 genes is extremely large compared to known viruses, such as the Influenza or HIV, which only contain 10 genes or less. More importantly, 93% of the genes did not resemble any known lineage in the natural world, suggesting Pandoraviruses are not related to any known virus family and may represent a new life form. These findings generated new perspectives about how scientists see viruses. It raised the possibility that there might be many different kinds of giant viruses out there to be discovered. Some biological features in these giant viruses could easily blur the line between life forms and viruses, which are considered to be non-living. Although Pandoraviruses do not infect human cells, there might be other giant viruses out there that could infect human cells. There are still a lot of human diseases known to have an infectious component but for which no infectious agent has been identified yet. This study will definitely encourage people to actively look for the role of giant viruses in some diseases.

See through the Ears

Haigh A. et al. How well do you see what you hear? The acuity of visual-to-auditory sensory substitution. Frontiers in Psychology, 2013 Jun 18

Scientists have created a revolutionary device for the blind that allows them see the world through their ears. The device “vOICe” trains the brain to invoke mental images of what they are hearing around them. The first test trial of vOICe has been performed on blindfolded sighted people. The participants took a standard eye test where they were asked to view the letter E turned in four directions and in various sizes. The best visual acuity is considered 20/20 (distance in feet/size of the E) and the majority of participants were able to achieve the best performance possible, nearly 20/400 sight. This is an impressive result when compared to an alternative stem-cell based sight restoration technique, which only yielded 20/800 visual acuity. In addition, the affordable and non-invasive nature of vOICe would offer a unique option. But, how might this work in practice? One can imagine that visually-impaired people would wear a discreet head-mounted camera such as Google Glass and receive wireless audio information through mini earbuds. As the person turns to look in various directions, the device scans images and correlates those with soundscapes, then the person’s brain would momentarily translate those into mental images of the objects — like braille for the ears. These sensory substitution devices could potentially be employed in combination with other alternative invasive techniques to train the brain to see again, or even to see for the first time.

Each creation is a work of art. All animals and plants, as well as every human being, are unique and priceless. And those who appreciate their value are like antique dealers as in the passage above. I recently had the chance to listen to such an “antique dealer,” Joanna Aizenberg of Bell Laboratories/Lucent Technologies, and witnessing the appreciation of the valuables she presented to us helped me better understand Said Nursi. Both the valuable object she was talking about and her appreciation of it were equally inspiring for me, and this is the reason why I have decided to share this story with you. Without any further ado, here is the story of a sponge species called the Venus’ Flower Basket and its “eternally” incarcerated residents: a pair of shrimp. Now, you must find what is hiding behind all this; after all, it is the eyes that look but the heart that perceives.

Venus’ Flower Baskets (Figure 1a) are vase-like sponges that grow upright on the sea floor of the Pacific Ocean, mostly around Japan. They have a very sophisticated mesh structure which caused medieval Europeans to assume they were glasswork made in China. In Japan they are called Kairou-Douketsu (together for eternity) and given as wedding gifts, since they generally house a pair of mated shrimp which are trapped in their cavity. As you have probably already understood, our story is about the engineering secrets of these sponges and their relationship with their guests.

The design

The skeleton of the Venus’ Flower Basket is made of silica, which is a very brittle material (remember the glass windows that you broke with your football when you were a kid; they were made with silica). How can these amazing creatures withstand the pressure and the currents present at the sea floor or the disturbance caused by two shrimp? The secret lies in the hierarchical construction of their cylindrical cage-like structure. As can be seen in Figure 1b, their skeleton is made up of beams that run perpendicular and parallel to the axis of the sponge, which forms a rectangular grid. This grid is further supported by beams that run diagonally in both directions. Finally, this whole structure is reinforced by ridges that spiral around. But these are just the macroscopic hierarchical levels of the construction. Now let’s start from the very first level of this hierarchy and try to understand how each level adds to the stability of the sponge.

The basic building block of the Venus’ Flower Baskets is a fiber composed of silica nano-spheres (Figures 1i and 2a) that grows around an organic filament (the black dots at the center of the circles in Figure 1f). Though this fiber is not very stress tolerant, due to the size of the spheres from which it is made, in the next level of hierarchy it is toughened by alternating organic and silica sheets that form a concentric lamellar (fine, alternating layers of different materials) fiber structure. The thickness of each layer in the fiber decreases from 1.5 (: 1/1000 mm) at the center to 0.2 towards the periphery (Figures 1f, 1g and 2b). Hence any crack that is initiated at the periphery is halted at the organic interlayers and while the thinner outer layers lessen the depth of crack propagation, the thicker inner layers enhance mechanical rigidity (in addition to their mechanical stability, these silica fibers are endowed with optical properties which are superior to man-made fibers, which will be discussed later on in the article).

Figure 1. Structural analysis of the mineralized skeletal system of Euplectella sp. (a) Photograph of the entire skeleton, showing cylindrical glass cage. Scale bar, 1 cm. (b) Fragment of the cage structure showing the square-grid lattice of vertical and horizontal struts with diagonal elements arranged in a chessboard manner. Orthogonal ridges on the cylinder surface are indicated by arrows. Scale bar, 5 mm. (c) Scanning electron micrograph (SEM) showing that each strut (enclosed by a bracket) is composed of bundled multiple spicules (the arrow indicates the long axis of the skeletal lattice). Scale bar, 100 mm. (d) SEM of a fractured and partially HF-etched (25) single beam revealing its ceramic fiber-composite structure. Scale bar, 20 mm. (e) SEM of the HF-etched (25) junction area showing that the lattice is cemented with laminated silica layers. Scale bar, 25 mm. (f) Contrast-enhanced SEM image of a cross section through one of the spicular struts, revealing that they are composed of a wide range of different-sized spicules surrounded by a laminated silica matrix. Scale bar, 10 mm. (g) SEM of a cross section through a typical spicule in a strut, showing its characteristic laminated architecture. Scale bar, 5 mm. (h) SEM of a fractured spicule, revealing an organic interlayer. Scale bar, 1 mm. (i) Bleaching of biosilica surface revealing its consolidated nanoparticulate nature (25). Scale bar, 500 nm. Figure and captions from ref. 2.

Fibers of different diameters reinforced this way are then bundled loosely in a silica matrix (Figure 1d and 1f). The different diameter of the fibers in the bundle and the weak lateral bonding between them are essential for increasing the strength of the bundle against crack propagation. At the next level of hierarchy, these bundles are used as building blocks of the cylindrical cage of the sponge, being arranged horizontally and vertically into a square grid. This grid in turn is reinforced by diagonal bundles that run in both directions along every second square lattice. The minimum number of pin-jointed struts (i.e. ones that are free to rotate at the joints) per node needed in order to form a rigid two-dimensional grid has been shown to be six; this is the number present in the skeleton of the Venus’ Flower Basket. In fact, if the diagonal bundles were to run along every square lattice, the number of struts per node would be 8, which would be redundant for the stability in the skeleton.

At the early stages of the growth of the Venus’ Flower Basket the struts are not connected at the nodes. However as the sponge gets older the struts are joined by a silica cement which itself also has a lamellar structure (Figure 1e). Hence, while the younger sponges are flexible, the older ones are stiff; this also has important implications for the symbiotic relation that the sponge has with its guests, the shrimp. (This issue will be discussed in detail when the lifecycle of the shrimp is examined.) While the resulting grid is stable in two dimensions, in three dimensions it may still suffer from exterior effects, such as ovalization. This problem however is solved at the next level of hierarchy by the helical ridges that surround the grid (Figure 1b). The absence of the ridges at the base of the skeleton of the sponge where the cage diameter is small, and their increased density further up the cage where the diameter is much greater is proposed as evidence supporting this argument. Finally, this whole cage structure must be anchored to the sea floor in a way that will withstand the bending stresses caused by the currents. This is managed through the use of the fibers that have been discussed earlier; they are used as connectors between the base of the sponge that is anchored to the sea floor and the vertical struts of the skeleton, resulting in a flexible connection that enables the cage to swing freely in the currents (Figure 1a).

As a conclusion, it can be said that “The resultant structure might be regarded as a textbook sample in mechanical engineering, because the seven hierarchical levels in the sponge skeleton represent major fundamental construction strategies, such as laminated structures, fiber-reinforced composites, bundled beams, and diagonally reinforced square-grid cells to name a few.”

Now let’s concentrate more on the fibers (or spicules) that anchor the cage to the sea floor. These anchorage spicules (a term used for describing the skeletal structures of sponges which comes from the Latin word speculum, meaning the head of a spear or arrow)* are 5-15 cm in length and 40-70 um in diameter. In the above discussion we have briefly discussed the cross-sectional structure of these fibers that gives them their flexible, but resistant nature. Here we will focus on the optical properties of these spicules. But before doing so, let’s briefly explain how optical fibers work.

Optical fibers are silica fibers of a 5 to 80 um diameter that are coated with a cladding layer; light waves can travel in these for long distances by constantly bouncing off the cladding. The reason for this is the refractive index difference between the silica core and the cladding layer. Refractive index (n) is a measure of the ability of a medium to change the phase velocity of light and cause the light waves to bend while leaving one medium and entering another (refraction); in the case of fiber optics, leaving the core and entering the cladding. However, if the refractive index of the second medium is lower than that of the initial one, the incident light waves that have an incidence angle higher than a critical value or critical angle can be reflected back to the first medium and this is what happens in fiber optics (See red ray in figure 2). If the core diameter is small (5-10 um), light rays can propagate only through a single path in the fiber (which runs parallel to the fiber axis), hence these type of fibers are called single-mode fibers (See Figure 2a). If the core diameter is larger however, (60-80 um) several paths are accessible, and more paths will have incidence angles that are greater than the critical angle, hence they are called multi-mode (See Figure 2b).

Now with this information in mind, let’s have a look at the characteristics of the anchoring spicules of the Venus’ Flower Basket. First of all, as mentioned in the previous discussion, the lamellar structure of these spicules prevents crack propagation, which is the main failure mode of commercial silica fibers. This lamellar structure, however, also determines the dependence of the optical behavior of the spicules on the environment in which they are embedded. For instance if the spicules are embedded in an epoxide medium with a refractive index of 1.57, the spicule as a whole would not be able to act as an optical fiber, due to the smaller refractive index of the cladding. However, since the core region of the spicules has a slightly higher refractive index than that of the cladding, the core acts as a single mode fiber in such an environment (see Figure 2a). In sea water-the spicules’ native environment-which has a refractive index of 1.33, the whole spicule acts as a multimode fiber, since the refractive index difference between the core and the cladding is much smaller than that between the cladding and the surrounding sea water.

Another advantage of these spicules over man-made fibers is their formation/production parameters, which are ambient temperature and pressure; these enable the introduction of impurities into the silica. Though at first it may not sound as if impurities are a positive characteristic, these impurities are very important for increasing the refractive index of silica and act as dopants (impurity elements added to a semiconductor lattices in low concentrations in order to alter the optical/electrical properties of the semiconductor). The core section of the spicules, for instance, shows increased sodium concentration, which is the cause of the higher refractive index of this section. Such dopant introduction in the silica during the fabrication process, however, is not possible in the case of man-made fibers, due to the very high processing temperatures.

In addition to this, the spicules have crown-like caps at their base and thorn-like structures throughout their middle section. While the crown-like termini most probably are used to anchor the sponge to the ocean floor, it has also been shown that the waveguiding efficiency of the spicules increases when the illumination comes through the end that has the crown-like structure. Hence, it has been proposed that this structure may be acting as a light harvesting lens. The thorn-like structures, on the other hand, share the lamellar construction of the spicule body, and the light guided through the body branches out to these spines and emerges at the tip. Since sea water comes into contact with the tip at an almost perpendicular angle to the guided light, the coupling is pretty efficient. Hence the combination of crown-like ends and thorn-like structures forms optical networks that collect and distribute light. However, at the depths inhabited by the Venus’ Flower Baskets there is no accessible light source. If one accepts the fact that there is no waste in nature-whether one believes in “creation” or “evolution”-the existence of such an advanced network-like structure as a part of a sponge-the most primitive animal-is at least thought-provoking. In the case of sponges that dwell in shallower waters with similar spicules, it has been postulated that such spicules gather and provide sunlight for the sponge’s endosymbiotic algae. However, at the depths at which the Venus’ Flower Baskets live, direct sunlight is not available. However it has been suggested that if light sources, such as bioluminescent microorganisms (bioluminescence is the production and emission of light by a living organism as the result of a chemical reaction during which chemical energy is converted to light energy) or chemiluminescence (emission of light as the result of a chemical reaction) exist, their light may be efficiently distributed by the sponge and act as an attractant for juvenile shrimp that are searching for a host. But for now these suggestions are just speculation and merit further investigation.

Before concluding this section, we should also note that, as a natural outcome of their construction/composition, these spicules do not have as great a transparency as their industrial counterparts and light cannot be transferred over long distances with them. However, it seems this is not a problem for the Venus’ Flower Basket as, apparently, they just need fibers of 5-15 cm to survive and it is the scientists who need to figure out a way to incorporate the traits of the Venus’ Flower Basket into industrial fibers.

The love

As mentioned in the introduction, the Venus Flower Basket hosts a pair of mated shrimp. These belong to the family of Spongicolidae, the Spongicala japonica. These shrimp, which can be as “big” as 9 mm in length, spend most of their lives in their host sponge. Though studies about them are limited, it is believed that before permanently being entrapped in their host, the shrimp have two free- living periods. The first one is just after hatching when they are small enough to exit through the mesh of the sponge. During this period they exit and re-enter their cages and live in a group with their parents and other juveniles. Studies suggest that the females generally stay with their parents until sexual maturity, whereas the males tend to leave their original host and live a solitary life until they reach a length of about 4 mm.

The second free-living period comes at the time of sexual maturity, when it is believed that the male and female mate outside and then invade a host, or the female searches for a host that is already occupied by a solitary male. During this stage, the shrimp have a body length of 3.5 to 6.5 mm which is bigger than the mesh size of the host sponges. Though this seems puzzling, it is thought that the mated shrimp enter the sponge in its flexible stage-when it may be easier to penetrate through the mesh-and get trapped there “forever” as the sponge grows older and stiffer. In fact this theory is supported by the finding that several flexible sponge specimens host solitary and young mated shrimp, whereas in the stiff specimens only very few solitary and young mated shrimp have been observed.

References

1. “Biological glass fibers: Correlation between optical and structural properties.” J. Aizenberg, V. C. Sundar, A. D. Yablon, J. C. Weaver, and G. Chen, Proc. Nat. Ac. Sci. 101 3358 (2004).

2. “Skeleton of Euplectella sp.: Structural hierarchy from the nanoscale to the macroscale.” J. Aizenberg, J. C. Weaver, M. S. Thanawala, V. C. Sundar, D. E. Morse, P. Fratzl, Science, 309 275 (2005).

3. “Fibre-optical features of a glass sponge – Some superior technological secrets have come to light from a deep-sea organism.” V. C. Sundar, A. D. Yablon, J. L. Grazul, M. Ilan, J. Aizenberg, Nature 424 899 (2003).

4. “Skeletal growth of the deep-sea hexactinellid sponge Euplectella oweni, and host election by the symbiotic shrimp Spongicola japonica” (Crustacea: Decapoda: Spongicolidae). T. Saito, I. Uchida and M. Takeda J. Zool., Lond. 258 521 (2002)

5. “Pair formation in Spongicola japonica (Crustacea: Stenopodidea: Spongicolidae), a shrimp associated with deep-sea hexactinellid sponges.” T. Saito, I. Uchida and M. Takeda J. Mar. Biol. Ass. U.K. 81 789 (2001).

Note

*. Also defined as, one of the minute calcareous or siliceous bodies that support the tissue of various invertebrates (Merriam-Webster’s English dictionary)