Day: 05/07/2015

Missing link in the evolution of complex cells discovered

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In a new study, published in Nature this week, a research team led from Uppsala University in Sweden presents the discovery of a new microbe that represents a missing link in the evolution of complex life. The study provides a new understanding of how, billions of years ago, the complex cell types that comprise plants, fungi, but also animals and humans, evolved from simple microbes.

Cells are the basic building blocks of all life on our planet. Yet, whereas the cells of bacteria and other microbes are small and simple, all visible life, including us humans, is generally made up of large and complex cell types. The origin of these complex cell types has long been a mystery to the scientific community, but now researchers from Uppsala University in Sweden have discovered a new group of microorganisms that represents a missing link in the evolutionary transition from simple to complex cells.

In the 1970s, the acclaimed biologist Carl Woese discovered a completely new group of microorganisms, the Archaea, and showed that these represented a separate branch in the Tree of Life—a finding that stunned the scientific community at the time. Despite that archaeal cells were simple and small like bacteria, researchers found that Archaea were more closely related to organisms with complex cell types, a group collectively known as ‘‘. This observation has puzzled scientists for decades: How could the complex cell types from eukaryotes have emerged from the simple cells of Archaea?

In this weeks’ edition of Nature, researchers from Uppsala University in Sweden, along with collaborators from the universities in Bergen (Norway) and Vienna (Austria) report the discovery of a new group of Archaea, the Lokiarchaeota (or ‘Loki’ for short), and identify it to be a missing link in the origin of eukaryotes.

“The puzzle of the origin of the eukaryotic cell is extremely complicated, as many pieces are still missing. We hoped that Loki would reveal a few more pieces of the puzzle, but when we obtained the first results, we couldn’t believe our eyes. The data simply looked spectacular”, says Thijs Ettema at the Department of Cell and Molecular Biology, Uppsala University, who lead the scientific team that carried out the study.

Researchers discover missing link in the evolution of complex cells
Hydrothermal vent field along the Arctic Mid-Ocean Ridge, close to where ‘Loki’ was found in marine sediments. The hydrothermal vent system was discovered by researchers from the Centre for Geobiology at University of Bergen (Norway). 

“By studying its genome, we found that Loki represents an intermediate form in-between the simple cells of microbes, and the complex of eukaryotes”, says Thijs Ettema.

When Loki was placed in the Tree of Life, this idea was confirmed.

“Loki formed a well-supported group with the eukaryotes in our analyses”, says Lionel Guy, one of the senior scientists involved in the study from Uppsala University.

“In addition, we found that Loki shares many genes uniquely with eukaryotes, suggesting that cellular complexity emerged in an early stage in the evolution of eukaryotes”, says Anja Spang, researcher at Department of Cell and Molecular Biology , Uppsala University, and one of the lead-authors of the study.

The name Lokiarchaeota is derived from the hostile environment close to where it was found, Loki’s Castle, a hydrothermal vent system located on the Mid-Atlantic Ridge between Greenland and Norway at a depth of 2,352 meters.

“Hydrothermal vents are volcanic systems located at the ocean floor. The site where Loki is heavily influenced by volcanic activity, but actually quite low in temperature”, says Steffen Jørgensen from the University of Bergen in Norway, who was involved in taking the samples where Loki was found.

“Extreme environments generally contain a lot of unknown microorganisms, which we refer to as microbial dark matter”, says Jimmy Saw, researcher at Department of Cell and Molecular Biology, Uppsala University, and co-lead author of the paper.

By exploring microbial dark matter with new genomics techniques, Thijs Ettema and his team hope to find more clues about how complex cells evolved.

“In a way, we are just getting started. There is still a lot out there to discover, and I am convinced that we will be forced to revise our biology textbooks more often in the near future”, says Thijs Ettema.

Spiders sprayed with carbon nanotubes spin superstrong webs

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A team of researchers working in Italy has found that simply spraying a spider with a carbon nanotube solution can cause the spider to spin stronger webs. In their paper they have uploaded to the preprint server arXiv, the team describes their experiments with both graphene and nanotube solutions and what happened when they sprayed it on ordinary spiders.

Spiders sprayed with carbon nanotubes spin superstrong webs

As the researchers note, while using silkworms has been quite successful, doing the same to harvest from has not, (because of their territorial traits, the complex nature of the silk they make and their cannibalistic tendencies) which is frustrating as the silk they make to spin their webs has so many outstanding qualities. Intrigued by prior research efforts that investigated the possibility of enhancing spider silk by spraying the spiders or feeding them different materials (titanium, zinc, aluminum, lead, etc.) to improve the mechanical, electrical, magnetic or even fluorescent properties of the silk, the researchers wondered what would happen if they sprayed the arachnids, with a graphene or carbon nanotube solution.

To find out, they wandered out into the natural environs near their lab and collected a host of cellar spiders and carefully brought them back to their lab. They then proceeded to spray ten of them with a solution and five with a graphene solution (the particles were 200 to 300 nanometers in width). Sadly, four of the spiders died shortly thereafter, and some produced poor quality webs, but a few of them produced webs that were actually stronger than their normal webs. Testing showed that some of the silk with nanotubes in it was 3.5 times as strong as giant riverine orb spider silk, which is considered the strongest natural . Also closer examination using Ramen spectroscopy revealed peaks in the silk where the nanotubes were present.

The researchers do not know how the carbon in either form wound up in the silk, but have excluded the possibility that it became drenched with it as it exited the spider’s body, the uniformity of the silk was too fine—they think that the spiders pull materials in from their immediate environment and use it as an ingredient in their silk making. Their results suggest it should be possible to produce such silk in small quantities, though it is not clear to what use it would be put.

Here, we report the production of silk incorporating graphene and carbon nanotubes directly by spider spinning, after spraying spiders with the corresponding aqueous dispersions. We observe a significant increment of the mechanical properties with respect to the pristine silk, in terms of fracture strength, Young’s and toughness moduli. We measure a fracture strength up to 5.4 GPa, a Young’s modulus up to 47.8 GPa and a toughness modulus up to 2.1 GPa, or 1567 J/g, which, to the best of our knowledge, is the highest reported to date, even when compared to the current toughest knotted fibres. This approach could be extended to other animals and plants and could lead to a new class of bionic materials for ultimate applications.

New chip architecture may provide foundation for quantum computer

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New chip architecture may provide foundation for quantum computer
A photograph of the completed BGA trap assembly. The trap chip is at the center, sitting atop the larger interposer chip that fans out the wiring. The trap chip surface area is 1mm x 3mm, while the interposer is roughly 1 cm square. Credit: D. Youngner, Honeywell

Quantum computers are in theory capable of simulating the interactions of molecules at a level of detail far beyond the capabilities of even the largest supercomputers today. Such simulations could revolutionize chemistry, biology and material science, but the development of quantum computers has been limited by the ability to increase the number of quantum bits, or qubits, that encode, store and access large amounts of data.

In a paper appearing this week in the Journal of Applied Physics, from AIP Publishing, a team of researchers at Georgia Tech Research Institute and Honeywell International have demonstrated a new device that allows more electrodes to be placed on a chip—an important step that could help increase qubit densities and bring us one step closer to a quantum computer that can simulate molecules or perform other algorithms of interest.

“To write down the quantum state of a system of just 300 qubits, you would need 2^300 numbers, roughly the number of protons in the known universe, so no amount of Moore’s Law scaling will ever make it possible for a classical computer to process that many numbers,” said Nicholas Guise, who led the research. “This is why it’s impossible to fully simulate even a modest sized quantum system, let alone something like chemistry of complex molecules, unless we can build a quantum computer to do it.”

While existing computers use classical bits of information, quantum computers use “” or qubits to store information. Classical bits use either a 0 or 1, but a qubit, exploiting a weird quantum property called superposition, can actually be in both 0 and 1 simultaneously, allowing much more information to be encoded. Since qubits can be correlated with each other in a way that classical bits cannot, they allow a new sort of massively parallel computation, but only if many qubits at a time can be produced and controlled. The challenge that the field has faced is scaling this technology up, much like moving from the first transistors to the first computers.

New chip architecture may provide foundation for quantum computer
Fluorescence images of calcium ions confined in the BGA trap. 

Creating the Building Blocks for Quantum Computing

One leading qubit candidate is individual ions trapped inside a vacuum chamber and manipulated with lasers. The scalability of current trap architectures is limited since the connections for the electrodes needed to generate the trapping fields come at the edge of the chip, and their number are therefore limited by the chip perimeter.

The GTRI/Honeywell approach uses new microfabrication techniques that allow more electrodes to fit onto the chip while preserving the laser access needed.

The team’s design borrows ideas from a type of packaging called a ball grid array (BGA) that is used to mount integrated circuits. The ball grid array’s key feature is that it can bring electrical signals directly from the backside of the mount to the surface, thus increasing the potential density of electrical connections.

The researchers also freed up more chip space by replacing area-intensive surface or edge capacitors with trench capacitors and strategically moving wire connections.

New chip architecture may provide foundation for quantum computer
SEMs of the trench capacitor and TSV (thru-substrate via) structures fabricated into the trap chip. These make electrical connections to the trap electrodes while filtering out RF pickup.
The space-saving moves allowed tight focusing of an addressing laser beam for fast operations on single qubits. Despite early difficulties bonding the chips, a solution was developed in collaboration with Honeywell, and the device was trapping ions from the very first day.

The team was excited with the results. “Ions are very sensitive to stray electric fields and other noise sources, and a few microns of the wrong material in the wrong place can ruin a trap. But when we ran the BGA trap through a series of benchmarking tests we were pleasantly surprised that it performed at least as well as all our previous traps,” Guise said.

Working with trapped ion currently requires a room full of bulky equipment and several graduate students to make it all run properly, so the researchers say much work remains to be done to shrink the technology. The BGA project demonstrated that it’s possible to fit more and more electrodes on a surface trap chip while wiring them from the back of the chip in a compact and extensible way. However, there are a host of engineering challenges that still need to be addressed to turn this into a miniaturized, robust and nicely packaged system that would enable , the researchers say.

In the meantime, these advances have applications beyond quantum computing. “We all hope that someday quantum computers will fulfill their vast promise, and this research gets us one step closer to that,” Guise said. “But another reason that we work on such difficult problems is that it forces us to come up with solutions that may be useful elsewhere. For example, like those demonstrated here for ion traps are also very relevant for making miniature atomic devices like sensors, magnetometers and chip-scale atomic clocks.”