life inspired

"Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers." Full paper @ Science

"People have a deep desire to communicate with animals, as is evident from the way they converse with their dogs, enjoy myths about talking animals or devote lifetimes to teaching chimpanzees how to speak. A delicate, if tiny, step has now been taken toward the real thing — the creation of a mouse with a human gene for language." Full article @ NYTimes.com

"The adaptive immune system, which can recognize, attack, and remember potentially harmful microbes, may have appeared on the evolutionary scene millions of years earlier than scientists thought. The immune system of the sea lamprey, a primitive, jawless fish, contains two cell types that recognize and respond to characteristic molecules associated with invading pathogens". Full article @ The Scientist

"Researchers have overturned the long-standing notion that lymph nodes are always necessary for launching the mammalian immune response." (though B-cell mediated immune response seems to require lymph nodes). Full pice @ The Scientist

"Tailed bacterial viruses (bacteriophages) are ubiquitously distributed in nature and are likely the most abundant organisms on the biosphere ( 1 1 ). Spending most of their time outside of the host, a bacterial cell, in often hostile external environments, they come to “life” upon encountering the receptor molecules on the host cell surface. The virus consists of a head (capsid) into which the DNA (genome) is packaged and a tail that delivers the genome into the bacterium. The capsid is pressurized because of packing of highly negatively-charged, relatively rigid dsDNA to near-crystalline density (≈500 μg/mL). The internal capsid pressure, ≈6 MPa or >10 times that of bottled champagne ( 1 2 ), provides a driving force for delivery of viral genome into host cell. One of the longstanding questions in phage biology has been how these viruses contain the DNA pressure and trigger release only upon recognition of a specific host cell. In this issue of PNAS, a study by Lhuillier et al. describes the pseudoatomic structure of a DNA gate from the Bacillus subtilis bacteriophage SPP1, which “zips” the capsid after the genome is packaged and unzips it when the virus is ready to infect the host. It is a compelling story, which began with the first in vitro virus assembly experiments described by Edgar and Wood >40 years ago ( 1 4 ) and is applicable not only to phages but also to large eukaryotic viruses such as herpes viruses." Full commentary @ PNAS

The paper: "Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating".

Labels: molecular machinery, virus

"Orthogonal, parallel and independent, systems are one key foundation for synthetic biology. The synthesis of orthogonal systems that are uncoupled from evolutionary constraints, and selectively abstracted from cellular regulation, is an emerging approach to making biology more amenable to engineering. Here, we combine orthogonal transcription by T7 RNA polymerase and translation by orthogonal ribosomes (O-ribosomes), creating an orthogonal gene expression pathway in Escherichia coli. We design and implement compact, orthogonal gene expression networks. In particular we focus on creating transcription–translation feed-forward loops (FFLs). The transcription–translation FFLs reported cannot be created by using the cells' gene expression machinery and introduce information-processing delays on the order of hours into gene expression. We refactor the rRNA operon, uncoupling the synthesis of the orthogonal 16S rRNA for the O-ribosome from the synthesis and processing of the rest of the rRNA operon, thereby defining a minimal module that can be added to the cell for O-ribosome production. The minimal O-ribosome permits the rational alteration of the delay in an orthogonal gene expression FFL. Overall this work demonstrates that system-level dynamic properties are amenable to rational manipulation and design in orthogonal systems. In the future this system may be further evolved and tuned to provide a spectrum of tailored dynamics in gene expression and investigate the effects of delays in cellular decision-making processes." Full paper: Synthesis of orthogonal transcription-translation networks — PNAS

Labels: engineering, gene circuits, systems biology

"The reaction–diffusion system is one of the most studied nonlinear mechanisms that generate spatially periodic structures autonomous. On the basis of many mathematical studies using computer simulations, it is assumed that animal skin patterns are the most typical examples of the Turing pattern (stationary periodic pattern produced by the reaction–diffusion system). However, the mechanism underlying pattern formation remains unknown because the molecular or cellular basis of the phenomenon has yet to be identified. In this study, we identified the interaction network between the pigment cells of zebrafish, and showed that this interaction network possesses the properties necessary to form the Turing pattern. When the pigment cells in a restricted region were killed with laser treatment, new pigment cells developed to regenerate the striped pattern. We also found that the development and survival of the cells were influenced by the positioning of the surrounding cells. When melanophores and xanthophores were located at adjacent positions, these cells excluded one another. However, melanophores required a mass of xanthophores distributed in a more distant region for both differentiation and survival. Interestingly, the local effect of these cells is opposite to that of their effects long range. This relationship satisfies the necessary conditions required for stable pattern formation in the reaction–diffusion model. Simulation calculations for the deduced network generated wild-type pigment patterns as well as other mutant patterns. Our findings here allow further investigation of Turing pattern formation within the context of cell biology.". Interactions between zebrafish pigment cells responsible for the generation of Turing patterns — PNAS

Labels: modeling, self-organization, turing

"The advantage of mutual help is threatened by defectors, who exploit the benefits provided by others without providing benefits in return. Cooperation can only be sustained if it is preferentially channeled toward cooperators and away from defectors. But how? A deceptively simple idea is to distinguish cooperators from defectors by tagging them. It clearly is in the interest of cooperators to use some distinctive cue to assort with their like. Such an assortment, however, conflicts with the interests of the cheaters, who have every incentive to also acquire that tag. This makes for an inherently unstable situation. The history of evolutionary thinking on this issue is long. An article in this issue of PNAS by Antal et al. opens new ground by providing an in-depth analysis of a selection-mutation model." Full discussion by Karl Sigmund @ PNAS.

Full paper by Antal et al @ PNAS

Labels: cooperation, evolution

"An early DNA extraction experiment paved the way for James Watson and Francis Crick's discovery of the double helix". Full article @ The Scientist [2009-05-01]

"Direct comparison of alternatives isn’t always the best way to make a decision – at least if you’re an ant. House-hunting rock ants collectively manage to choose the best nest-site without needing to study all their options, according to new research from the University of Bristol." Full press release @ Bristol University

"You can drive yourself crazy trying to multitask and answer every e-mail message instantly. Or you can recognize your brain’s finite capacity for processing information, accentuate the positive and achieve the satisfactions of what Ms. Gallagher calls the focused life.". Fulla rticle @ NYTimes.com

RNA is supposed to silence genes, not boost gene expression. So why are scientists seeing just that? Full article @ The Scientist

"The title question is echoed by electrical engineers and consumers alike. It has now been 15 years since quantum computing came to the forefront of popular science with its promise of superpowered computers for the future, so it is natural to be wondering when the first commercial products will appear on the market." Full article @ Science

"When two plants are grafted together, they share much more than water and minerals: They also swap genetic material, according to a study published in [...] Science. These findings muddy the distinction between naturally-occurring gene transfer in plants and the human-mediated mechanisms we generally refer to as genetic engineering." Article @ The Scientist

The full paper in Science.