How the zebra gets its stripes: A simple genetic circuit

ScienceDaily (Oct. 14, 2011) — Many living things have stripes, but the developmental processes that create these and other patterns are complex and difficult to untangle.

Now a team of scientists has designed a simple genetic circuit that creates a striped pattern that they can control by tweaking a single gene.

"The essential components can be buried in a complex physiological context," said Terence Hwa, a professor of physics at the University of California, San Diego, and one of the leaders of the study published October 14 in Science. "Natural systems make all kinds of wonderful patterns, but the problem is you never know what's really controlling it."

With genes taken from one species of bacterium and inserted into another, Hwa and colleagues from the University of Hong Kong assembled a genetic loop from two linked modules that senses how crowded a group of cells has become and responds by controlling their movements.

One of the modules secretes a chemical signal called acyl-homoserine lactone (AHL). As the bacterial colony grows, AHL floods the accumulating cells, causing them to tumble in place rather than swim. Stuck in the agar of their dish, they pile up.

Because AHL doesn't diffuse very far, a few cells escape and swim away to begin the process again.

Left to grow overnight, the cells create a target-like pattern of concentric rings of crowded and dispersed bacterial cells. By tweaking just one gene that limits how fast and far cells can swim, the researchers were able to control the number of rings the bacteria made. They can also manipulate the pattern by modifying how long AHL lasts before it degrades.

Although individual bacteria are single cells, as colonies they can act like a multicellular organism, sending and receiving signals to coordinate the growth and other functions of the colony. That means fundamental rules that govern the development of these patterns could well apply to critical steps in the development of other organisms.

To uncover these fundamental rules, Hwa and colleagues characterized the performance of their synthetic genetic circuit in two ways.

First, they precisely measured both the activity of individual genes in the circuit throughout the tumble-and-swim cycle. Then they derived a mathematical equation that describes the probability of cells flipping between swim and tumble motions.

Additional equations describe other aspects of the system, such as the dynamics of the synthesis, diffusion and deactivation of one of the cell-to-cell chemical signal AHL.

This three-pronged approach of "wet-lab" experiments, precise measurements of the results, and mathematical modeling of the system, characterize the emerging discipline of quantitative biology, Hwa said. "This is a prototype, a model of the kind of biology we want to do."

Co-authors include Jian-Dong Huang, associate professor of biochemistry at the University of Hong Kong additional researchers at Hong Kong Baptist University, the University of Marburg, and the University of Hong Kong including members of the 2008 iGEM team, which Hwa co-advised as a Distinguished Visiting Professor at UHK.

Hwa is a senior scientist with UC San Diego's Center for Theoretical Biological Physics.

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Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of California - San Diego.

Journal Reference:

C. Liu, X. Fu, L. Liu, X. Ren, C. K. L. Chau, S. Li, L. Xiang, H. Zeng, G. Chen, L.-H. Tang, P. Lenz, X. Cui, W. Huang, T. Hwa, J.-D. Huang. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science, 2011; 334 (6053): 238 DOI: 10.1126/science.1209042

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Nanotechnology circuits for wireless devices: First wafer-scale graphene integrated circuit smaller than a pinhead

ScienceDaily (June 11, 2011) — IBM Research scientists have announced that they have achieved a milestone in creating a building block for the future of wireless devices. In a paper published in the journal Science, IBM researchers announced the first integrated circuit fabricated from wafer-size graphene, and demonstrated a broadband frequency mixer operating at frequencies up to 10 gigahertz (10 billion cycles/second).

Designed for wireless communications, this graphene-based analog integrated circuit could improve today's wireless devices and points to the potential for a new set of applications. At today's conventional frequencies, cell phone and transceiver signals could be improved, potentially allowing phones to work where they can't today while, at much higher frequencies, military and medical personnel could see concealed weapons or conduct medical imaging without the same radiation dangers of X-rays.

Graphene, the thinnest electronic material consisting of a single layer of carbon atoms packed in a honeycomb structure, possesses outstanding electrical, optical, mechanical and thermal properties that could make it less expensive and use less energy inside portable electronics like smart phones.

Despite significant scientific progress in the understanding of this novel material and the demonstration of high-performance graphene-based devices, the challenge of integrating graphene transistors with other components on a single chip had not been realized until now, mostly due to poor adhesion of graphene with metals and oxides and the lack of reliable fabrication schemes to yield reproducible devices and circuits.

This new integrated circuit, consisting of a graphene transistor and a pair of inductors compactly integrated on a silicon carbide (SiC) wafer, overcomes these design hurdles by developing wafer-scale fabrication procedures that maintain the quality of graphene and, at the same time, allow for its integration to other components in a complex circuitry.

How it Works

In this demonstration, graphene is synthesized by thermal annealing of SiC wafers to form uniform graphene layers on the surface of SiC. The fabrication of graphene circuits involves four layers of metal and two layers of oxide to form top-gated graphene transistor, on-chip inductors and interconnects.

The circuit operates as a broadband frequency mixer, which produces output signals with mixed frequencies (sum and difference) of the input signals. Mixers are fundamental components of many electronic communication systems. Frequency mixing up to 10 GHz and excellent thermal stability up to 125°C has been demonstrated with the graphene integrated circuit.

The fabrication scheme developed can also be applied to other types of graphene materials, including chemical vapor deposited (CVD) graphene films synthesized on metal films, and are also compatible with optical lithography for reduced cost and throughput.

Previously, the team has demonstrated standalone graphene transistors with a cut-off frequency as high as 100 GHz and 155 GHz for epitaxial and CVD graphene, for a gate length of 240 and 40 nm, respectively.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by IBM Research.

Journal Reference:

Y.-M. Lin, A. Valdes-Garcia, S.-J. Han, D. B. Farmer, I. Meric, Y. Sun, Y. Wu, C. Dimitrakopoulos, A. Grill, P. Avouris, K. A. Jenkins. Wafer-Scale Graphene Integrated Circuit. Science, 2011; 332 (6035): 1294 DOI: 10.1126/science.1204428

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Nanotechnology circuits for wireless devices: First wafer-scale graphene integrated circuit smaller than a pinhead

ScienceDaily (June 11, 2011) — IBM Research scientists have announced that they have achieved a milestone in creating a building block for the future of wireless devices. In a paper published in the journal Science, IBM researchers announced the first integrated circuit fabricated from wafer-size graphene, and demonstrated a broadband frequency mixer operating at frequencies up to 10 gigahertz (10 billion cycles/second).

Designed for wireless communications, this graphene-based analog integrated circuit could improve today's wireless devices and points to the potential for a new set of applications. At today's conventional frequencies, cell phone and transceiver signals could be improved, potentially allowing phones to work where they can't today while, at much higher frequencies, military and medical personnel could see concealed weapons or conduct medical imaging without the same radiation dangers of X-rays.

Graphene, the thinnest electronic material consisting of a single layer of carbon atoms packed in a honeycomb structure, possesses outstanding electrical, optical, mechanical and thermal properties that could make it less expensive and use less energy inside portable electronics like smart phones.

Despite significant scientific progress in the understanding of this novel material and the demonstration of high-performance graphene-based devices, the challenge of integrating graphene transistors with other components on a single chip had not been realized until now, mostly due to poor adhesion of graphene with metals and oxides and the lack of reliable fabrication schemes to yield reproducible devices and circuits.

This new integrated circuit, consisting of a graphene transistor and a pair of inductors compactly integrated on a silicon carbide (SiC) wafer, overcomes these design hurdles by developing wafer-scale fabrication procedures that maintain the quality of graphene and, at the same time, allow for its integration to other components in a complex circuitry.

How it Works

In this demonstration, graphene is synthesized by thermal annealing of SiC wafers to form uniform graphene layers on the surface of SiC. The fabrication of graphene circuits involves four layers of metal and two layers of oxide to form top-gated graphene transistor, on-chip inductors and interconnects.

The circuit operates as a broadband frequency mixer, which produces output signals with mixed frequencies (sum and difference) of the input signals. Mixers are fundamental components of many electronic communication systems. Frequency mixing up to 10 GHz and excellent thermal stability up to 125°C has been demonstrated with the graphene integrated circuit.

The fabrication scheme developed can also be applied to other types of graphene materials, including chemical vapor deposited (CVD) graphene films synthesized on metal films, and are also compatible with optical lithography for reduced cost and throughput.

Previously, the team has demonstrated standalone graphene transistors with a cut-off frequency as high as 100 GHz and 155 GHz for epitaxial and CVD graphene, for a gate length of 240 and 40 nm, respectively.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by IBM Research.

Journal Reference:

Y.-M. Lin, A. Valdes-Garcia, S.-J. Han, D. B. Farmer, I. Meric, Y. Sun, Y. Wu, C. Dimitrakopoulos, A. Grill, P. Avouris, K. A. Jenkins. Wafer-Scale Graphene Integrated Circuit. Science, 2011; 332 (6035): 1294 DOI: 10.1126/science.1204428

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

'Biological circuit' components developed; New microscope technique for measuring them

ScienceDaily (June 9, 2011) — Electrical engineers have long been toying with the idea of designing biological molecules that can be directly integrated into electronic circuits. University of Pennsylvania researchers have developed a way to form these structures so they can operate in open-air environments, and, more important, have developed a new microscope technique that can measure the electrical properties of these and similar devices.

The research was conducted by Dawn Bonnell, Trustee Chair Professor and director of the Nano/Bio Interface Center, graduate students Kendra Kathan-Galipeau and Maxim Nikiforov and postdoctoral fellow Sanjini Nanayakkara, all of the Department of Materials Science and Engineering in Penn's School of Engineering and Applied Science. They collaborated with assistant professor Bohdana Discher of the Department of Biophysics and Biochemistry at Penn's Perelman School of Medicine and Paul A. O'Brien, a graduate student in Penn's Biotechnology Masters Program.

Their work was published in the journal ACS Nano.

The development involves artificial proteins, bundles of peptide helices with a photoactive molecule inside. These proteins are arranged on electrodes, which are common feature of circuits that transmit electrical charges between metallic and non-metallic elements. When light is shined on the proteins, they convert photons into electrons and pass them to the electrode.

"It's a similar mechanism to what happens when plants absorb light, except in that case the electron is used for some chemistry that creates energy for the plant," Bonnell said. "In this case, we want to use the electron in electrical circuits."

Similar peptide assemblies had been studied in solution before by several groups and had been tested to show that they indeed react to light. But there was no way to quantify their ambient electrical properties, particularly capacitance, the amount of electrical charge the assembly holds.

"It's necessary to understand these kinds of properties in the molecules in order to make devices out of them. We've been studying silicon for 40 years, so we know what happens to electrons there," Bonnell said. "We didn't know what happens to electrons on dry electrodes with these proteins; we didn't even know if they would remain photoactive when attached to an electrode."

Designing circuits and devices with silicon is inherently easier than with proteins. The electrical properties of a large chunk of a single element can be measured and then scaled down, but complex molecules like these proteins cannot be scaled up. Diagnostic systems that could measure their properties with nanometer sensitivity simply did not exist.

The researchers therefore needed to invent both a new way of a measuring these properties and a controlled way of making the photovoltaic proteins that would resemble how they might eventually be incorporated into devices in open-air, everyday environments, rather than swimming in a chemical solution.

To solve the first problem, the team developed a new kind of atomic force microscope technique, known as torsional resonance nanoimpedance microscopy. Atomic force microscopes operate by bringing an extremely narrow silicon tip very close to a surface and measuring how the tip reacts, providing a spatial sensitivity of a few nanometers down to individual atoms.

"What we've done in our version is to use a metallic tip and put an oscillating electric field on it. By seeing how electrons react to the field, we're able to measure more complex interactions and more complex properties, such as capacitance," Bonnell said.

Bohdana Discher's group designed the self-assembling proteins much as they had done before but took the additional step of stamping them onto sheets of graphite electrodes. This manufacturing principle and the ability to measure the resulting devices could have a variety of applications.

"Photovoltaics -- solar cells -- are perhaps the easiest to imagine, but where this work is going in the shorter term is biochemical sensors," Bonnell said.

Instead of reacting to photons, proteins could be designed to produce a charge when in the presence of a certain toxins, either changing color or acting as a circuit element in a human-scale gadget.

This research was supported by the Nano/Bio Interface Center and the National Science Foundation.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Pennsylvania.

Journal Reference:

Kendra Kathan-Galipeau, Sanjini Nanayakkara, Paul A. O’Brian, Maxim Nikiforov, Bohdana M. Discher, Dawn A. Bonnell. Direct Probe of Molecular Polarization inDe NovoProtein–Electrode Interfaces. ACS Nano, 2011; 110603081000090 DOI: 10.1021/nn200887n

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

'Biological circuit' components developed; New microscope technique for measuring them

ScienceDaily (June 9, 2011) — Electrical engineers have long been toying with the idea of designing biological molecules that can be directly integrated into electronic circuits. University of Pennsylvania researchers have developed a way to form these structures so they can operate in open-air environments, and, more important, have developed a new microscope technique that can measure the electrical properties of these and similar devices.

The research was conducted by Dawn Bonnell, Trustee Chair Professor and director of the Nano/Bio Interface Center, graduate students Kendra Kathan-Galipeau and Maxim Nikiforov and postdoctoral fellow Sanjini Nanayakkara, all of the Department of Materials Science and Engineering in Penn's School of Engineering and Applied Science. They collaborated with assistant professor Bohdana Discher of the Department of Biophysics and Biochemistry at Penn's Perelman School of Medicine and Paul A. O'Brien, a graduate student in Penn's Biotechnology Masters Program.

Their work was published in the journal ACS Nano.

The development involves artificial proteins, bundles of peptide helices with a photoactive molecule inside. These proteins are arranged on electrodes, which are common feature of circuits that transmit electrical charges between metallic and non-metallic elements. When light is shined on the proteins, they convert photons into electrons and pass them to the electrode.

"It's a similar mechanism to what happens when plants absorb light, except in that case the electron is used for some chemistry that creates energy for the plant," Bonnell said. "In this case, we want to use the electron in electrical circuits."

Similar peptide assemblies had been studied in solution before by several groups and had been tested to show that they indeed react to light. But there was no way to quantify their ambient electrical properties, particularly capacitance, the amount of electrical charge the assembly holds.

"It's necessary to understand these kinds of properties in the molecules in order to make devices out of them. We've been studying silicon for 40 years, so we know what happens to electrons there," Bonnell said. "We didn't know what happens to electrons on dry electrodes with these proteins; we didn't even know if they would remain photoactive when attached to an electrode."

Designing circuits and devices with silicon is inherently easier than with proteins. The electrical properties of a large chunk of a single element can be measured and then scaled down, but complex molecules like these proteins cannot be scaled up. Diagnostic systems that could measure their properties with nanometer sensitivity simply did not exist.

The researchers therefore needed to invent both a new way of a measuring these properties and a controlled way of making the photovoltaic proteins that would resemble how they might eventually be incorporated into devices in open-air, everyday environments, rather than swimming in a chemical solution.

To solve the first problem, the team developed a new kind of atomic force microscope technique, known as torsional resonance nanoimpedance microscopy. Atomic force microscopes operate by bringing an extremely narrow silicon tip very close to a surface and measuring how the tip reacts, providing a spatial sensitivity of a few nanometers down to individual atoms.

"What we've done in our version is to use a metallic tip and put an oscillating electric field on it. By seeing how electrons react to the field, we're able to measure more complex interactions and more complex properties, such as capacitance," Bonnell said.

Bohdana Discher's group designed the self-assembling proteins much as they had done before but took the additional step of stamping them onto sheets of graphite electrodes. This manufacturing principle and the ability to measure the resulting devices could have a variety of applications.

"Photovoltaics -- solar cells -- are perhaps the easiest to imagine, but where this work is going in the shorter term is biochemical sensors," Bonnell said.

Instead of reacting to photons, proteins could be designed to produce a charge when in the presence of a certain toxins, either changing color or acting as a circuit element in a human-scale gadget.

This research was supported by the Nano/Bio Interface Center and the National Science Foundation.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Pennsylvania.

Journal Reference:

Kendra Kathan-Galipeau, Sanjini Nanayakkara, Paul A. O’Brian, Maxim Nikiforov, Bohdana M. Discher, Dawn A. Bonnell. Direct Probe of Molecular Polarization inDe NovoProtein–Electrode Interfaces. ACS Nano, 2011; 110603081000090 DOI: 10.1021/nn200887n

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here