SynBio Wetware http://www.synbio.org.uk/ Sat, 09 Feb 2013 03:03:55 GMT FeedCreator 1.8.1 (obRSS 1.8.11) http://www.synbio.org.uk/images/ SynBio Wetware http://www.synbio.org.uk/ News about the use of DNA for design and engineering in biological systems. A Triple Helix-Loop-Helix/Basic Helix-Loop-Helix Cascade Controls Cell Elongation Downstream of ... http://www.synbio.org.uk/plant-biology-news/2689-a-triple-helix-loop-helixbasic-helix-loop-helix-cascade-controls-cell-elongation-downstream-of-multiple-hormonal-and-environmental-signaling-pathways-in-arabidopsis.html Environmental and endogenous signals, including light, temperature, brassinosteroid (BR), and gibberellin (GA), regulate cell elongation largely by influencing the expression of the paclobutrazol-resistant (PRE) family helix-loop-helix (HLH) factors, which promote cell elongation by interacting antagonistically with another HLH factor, IBH1. However, the molecular mechanism by which PREs and IBH1 regulate gene expression has remained unknown. Here, we show that IBH1 interacts with and inhibits a DNA binding basic helix-loop-helix (bHLH) protein, HBI1, in Arabidopsis thaliana. Overexpression of HBI1 increased hypocotyl and petiole elongation, whereas dominant inactivation of HBI1 and its homologs caused a dwarf phenotype, indicating that HBI1 is a positive regulator of cell elongation. In vitro and in vivo experiments showed that HBI1 directly bound to the promoters and activated two EXPANSIN genes encoding cell wall–loosening enzymes; HBI1’s DNA binding and transcriptional activities were inhibited by IBH1, but the inhibitory effects of IBH1 were abolished by PRE1. The results indicate that PREs activate the DNA binding bHLH factor HBI1 by sequestering its inhibitor IBH1. Altering each of the three factors affected plant sensitivities to BR, GA, temperature, and light. Our study demonstrates that PREs, IBH1, and HBI1 form a chain of antagonistic switches that regulates cell elongation downstream of multiple external and endogenous signals.

A Triple Helix-Loop-Helix/Basic Helix-Loop-Helix Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways in Arabidopsis: "

(Via The Plant Cell current issue.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T16:11:42+00:00 http://www.synbio.org.uk/plant-biology-news/2689-a-triple-helix-loop-helixbasic-helix-loop-helix-cascade-controls-cell-elongation-downstream-of-multiple-hormonal-and-environmental-signaling-pathways-in-arabidopsis.html
Evolution from the Prokaryotic to the Higher Plant Chloroplast Signal Recognition Particle: The ... http://www.synbio.org.uk/microbe-news/2688-evolution-from-the-prokaryotic-to-the-higher-plant-chloroplast-signal-recognition-particle-the-signal-recognition-particle-rna-is-conserved-in-plastids-of-a-wide-range-of-photosynthetic-organisms.html The protein targeting signal recognition particle (SRP) pathway in chloroplasts of higher plants has undergone dramatic evolutionary changes. It disposed of its RNA, which is an essential SRP component in bacteria, and uses a unique chloroplast-specific protein cpSRP43. Nevertheless, homologs of the conserved SRP54 and the SRP receptor, FtsY, are present in higher plant chloroplasts. In this study, we analyzed the phylogenetic distribution of SRP components in photosynthetic organisms to elucidate the evolution of the SRP system. We identified conserved plastid SRP RNAs within all nonspermatophyte land plant lineages and in all chlorophyte branches. Furthermore, we show the simultaneous presence of cpSRP43 in these organisms. The function of this novel SRP system was biochemically and structurally characterized in the moss Physcomitrella patens. We show that P. patens chloroplast SRP (cpSRP) RNA binds cpSRP54 but has lost the ability to significantly stimulate the GTPase cycle of SRP54 and FtsY. Furthermore, the crystal structure at 1.8-Å resolution and the nucleotide specificity of P. patens cpFtsY was determined and compared with bacterial FtsY and higher plant chloroplast FtsY. Our data lead to the view that the P. patens cpSRP system occupies an intermediate position in the evolution from bacterial-type SRP to higher plant-type cpSRP system.

Evolution from the Prokaryotic to the Higher Plant Chloroplast Signal Recognition Particle: The Signal Recognition Particle RNA Is Conserved in Plastids of a Wide Range of Photosynthetic Organisms: "

(Via The Plant Cell current issue.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T16:10:56+00:00 http://www.synbio.org.uk/microbe-news/2688-evolution-from-the-prokaryotic-to-the-higher-plant-chloroplast-signal-recognition-particle-the-signal-recognition-particle-rna-is-conserved-in-plastids-of-a-wide-range-of-photosynthetic-organisms.html
Elasticity and wrinkled morphology of Bacillus subtilis pellicles. http://www.synbio.org.uk/microbe-news/2687-elasticity-and-wrinkled-morphology-of-bacillus-subtilis-pellicles.html Wrinkled morphology is a distinctive phenotype observed in mature biofilms produced by a great number of bacteria. Here we study the formation of macroscopic structures (wrinkles and folds) observed during the maturation of Bacillus subtilis pellicles in relation to their mechanical response. We show how the mechanical buckling instability can explain their formation. By performing simple tests, we highlight the role of confining geometry and growth in determining the symmetry of wrinkles. We also experimentally demonstrate that the pellicles are soft elastic materials for small deformations induced by a tensile device. The wrinkled structures are then described by using the equations of elastic plates, which include the growth process as a simple parameter representing biomass production. This growth controls buckling instability, which triggers the formation of wrinkles. We also describe how the structure of ripples is modified when capillary effects are dominant. Finally, the experiments performed on a mutant strain indicate that the presence of an extracellular matrix is required to maintain a connective and elastic pellicle.

Elasticity and wrinkled morphology of Bacillus subtilis pellicles.: "Publication Date: 2013 Jan 22 PMID: 23341623
Authors: Trejo, M. - Douarche, C. - Bailleux, V. - Poulard, C. - Mariot, S. - Regeard, C. - Raspaud, E.
Journal: Proc Natl Acad Sci U S A

(Via PNAS.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T16:07:25+00:00 http://www.synbio.org.uk/microbe-news/2687-elasticity-and-wrinkled-morphology-of-bacillus-subtilis-pellicles.html
Redirector: designing cell factories by reconstructing the metabolic objective. http://www.synbio.org.uk/microbe-news/2686-redirector-designing-cell-factories-by-reconstructing-the-metabolic-objective.html Advances in computational metabolic optimization are required to realize the full potential of new in vivo metabolic engineering technologies by bridging the gap between computational design and strain development. We present Redirector, a new Flux Balance Analysis-based framework for identifying engineering targets to optimize metabolite production in complex pathways. Previous optimization frameworks have modeled metabolic alterations as directly controlling fluxes by setting particular flux bounds. Redirector develops a more biologically relevant approach, modeling metabolic alterations as changes in the balance of metabolic objectives in the system. This framework iteratively selects enzyme targets, adds the associated reaction fluxes to the metabolic objective, thereby incentivizing flux towards the production of a metabolite of interest. These adjustments to the objective act in competition with cellular growth and represent up-regulation and down-regulation of enzyme mediated reactions. Using the iAF1260 E. coli metabolic network model for optimization of fatty acid production as a test case, Redirector generates designs with as many as 39 simultaneous and 111 unique engineering targets. These designs discover proven in vivo targets, novel supporting pathways and relevant interdependencies, many of which cannot be predicted by other methods. Redirector is available as open and free software, scalable to computational resources, and powerful enough to find all known enzyme targets for fatty acid production.

Redirector: designing cell factories by reconstructing the metabolic objective.: "Publication Date: 2013 Jan PMID: 23341769
Authors: Rockwell, G. - Guido, N. J. - Church, G. M.
Journal: PLoS Comput Biol

(Via PLoS Computational Biology.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T16:06:06+00:00 http://www.synbio.org.uk/microbe-news/2686-redirector-designing-cell-factories-by-reconstructing-the-metabolic-objective.html
Robust one-tube ohm-PCR strategy accelerates precise sequence modification of plasmids for ... http://www.synbio.org.uk/wetware-news/2685-robust-one-tube-ohm-pcr-strategy-accelerates-precise-sequence-modification-of-plasmids-for-functional-genomics.html Functional genomics requires vector construction for protein expression and functional characterization of target genes; therefore, a simple, flexible, and low-cost molecular manipulation strategy will be highly advantageous for genomics approaches. Here, we describe a ohm-PCR strategy that enables multiple types of sequence modification, including precise insertion, deletion and substitution, in any position of a circular plasmid. ohm-PCR is based on an overlap extension site-directed mutagenesis technique, and is named for its characteristic ohm-shaped secondary structure during PCR. ohm-PCR can be performed either in two steps, or in one tube in combination with exonuclease I treatment. These strategies have wide applications for protein engineering, gene function analysis and in vitro gene splicing.

Robust one-tube ohm-PCR strategy accelerates precise sequence modification of plasmids for functional genomics.: "Publication Date: 2013 Jan 17 PMID: 23335613
Authors: Chen, L. - Wang, F. - Wang, X. - Liu, Y. G.
Journal: Plant Cell Physiol

(Via Plant and Cell Physiology.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T16:03:47+00:00 http://www.synbio.org.uk/wetware-news/2685-robust-one-tube-ohm-pcr-strategy-accelerates-precise-sequence-modification-of-plasmids-for-functional-genomics.html
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs http://www.synbio.org.uk/wetware-news/2684-metabolic-engineering-of-escherichia-coli-using-synthetic-small-regulatory-rnas.html Small regulatory RNAs (sRNAs) regulate gene expression in bacteria. We designed synthetic sRNAs to identify and modulate the expression of target genes for metabolic engineering in Escherichia coli. Using synthetic sRNAs for the combinatorial knockdown of four candidate genes in 14 different strains, we isolated an engineered E. coli strain (tyrR- and csrA-repressed S17-1) capable of producing 2 g per liter of tyrosine. Using a library of 130 synthetic sRNAs, we also identified chromosomal gene targets that enabled substantial increases in cadaverine production. Repression of murE led to a 55% increase in cadaverine production compared to the reported engineered strain (XQ56 harboring the plasmid p15CadA). The design principles and the engineering strategy using synthetic sRNAs reported here are generalizable to other bacteria and applicable in developing superior producer strains. The ability to fine-tune target genes with designed sRNAs provides substantial advantages over gene-knockout strategies and other large-scale target identification strategies owing to its easy implementation, ability to modulate chromosomal gene expression without modifying those genes and because it does not require construction of strain libraries.

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs: "

Nature Biotechnology. doi:10.1038/nbt.2461

Authors: Dokyun Na, Seung Min Yoo, Hannah Chung, Hyegwon Park, Jin Hwan Park & Sang Yup Lee

(Via Nature Biotechnology - AOP - nature.com science feeds.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T16:01:28+00:00 http://www.synbio.org.uk/wetware-news/2684-metabolic-engineering-of-escherichia-coli-using-synthetic-small-regulatory-rnas.html
Autonomous bacterial localization and gene expression based on nearby cell receptor density http://www.synbio.org.uk/microbe-news/2683-autonomous-bacterial-localization-and-gene-expression-based-on-nearby-cell-receptor-density.html Escherichia coli were engineered to enable programmed motility, sensing and phenotypic response to the density of epidermal growth factor receptor expressed on the surface of cancer cells. Bacteria were engineered to display targeted motility through AI-2-mediated chemotaxis. Recruitment of motile bacteria was achieved by site-specific synthesis of quorum sensing autoinducers using anti-EGFR nanofactories. Threshold-based switching of bacterial gene expression was controlled by AI-2 quorum sensing. The engineered ‘bacterial dirigible’ represents a new means for targeted drug delivery and may have multiple applications wherein bacterial cells are designed to carry out specified tasks. Top of page Abstract Escherichia coli were genetically modified to enable programmed motility, sensing, and actuation based on the density of features on nearby surfaces. Then, based on calculated feature density, these cells expressed marker proteins to indicate phenotypic response. Specifically, site-specific synthesis of bacterial quorum sensing autoinducer-2 (AI-2) is used to initiate and recruit motile cells. In our model system, we rewired E. coli’s AI-2 signaling pathway to direct bacteria to a squamous cancer cell line of head and neck (SCCHN), where they initiate synthesis of a reporter (drug surrogate) based on a threshold density of epidermal growth factor receptor (EGFR). This represents a new type of controller for targeted drug delivery as actuation (synthesis and delivery) depends on a receptor density marking the diseased cell. The ability to survey local surfaces and initiate gene expression based on feature density represents a new area-based switch in synthetic biology that will find use beyond the proposed cancer model here.

Autonomous bacterial localization and gene expression based on nearby cell receptor density

Hsuan-Chen Wu, Chen-Yu Tsao, David N Quan, Yi Cheng, Matthew D Servinsky, Karen K Carter, Kathleen J Jee, Jessica L Terrell, Amin Zargar, Gary W Rubloff, Gregory F Payne, James J Valdes & William E Bentley

Molecular Systems Biology: "Citation: Molecular Systems Biology 9:636, 2013.

]]>
[email protected] (Jim Haseloff) 2013-01-26T15:56:37+00:00 http://www.synbio.org.uk/microbe-news/2683-autonomous-bacterial-localization-and-gene-expression-based-on-nearby-cell-receptor-density.html
Shared control of gene expression in bacteria by transcription factors and global physiology of ... http://www.synbio.org.uk/microbe-news/2682-shared-control-of-gene-expression-in-bacteria-by-transcription-factors-and-global-physiology-of-the-cell.html Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA-binding transcription factors and other specific regulators. We present a model-based approach to distinguish between these two effects using time-resolved measurements of promoter activities. We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E. coli. Our results show that the transcriptional response of the network is controlled by the physiological state of the cell and the signaling metabolite cyclic AMP (cAMP). The absence of a strong regulatory effect of transcription factors suggests that they are not the main coordinators of gene expression changes during growth transitions, but rather that they complement the effect of global physiological control mechanisms. This change of perspective has important consequences for the interpretation of transcriptome data and the design of biological networks in biotechnology and synthetic biology."

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell.

Sara Berthoumieux, Hidde de Jong, Guillaume Baptist, Corinne Pinel, Caroline Ranquet, Delphine Ropers & Johannes Geiselmann

(Via.) Molecular Systems Biology 9:634, 2013.

]]>
[email protected] (Jim Haseloff) 2013-01-26T15:50:02+00:00 http://www.synbio.org.uk/microbe-news/2682-shared-control-of-gene-expression-in-bacteria-by-transcription-factors-and-global-physiology-of-the-cell.html
Genome-scale engineering for systems and synthetic biology http://www.synbio.org.uk/wetware-news/2681-genome-scale-engineering-for-systems-and-synthetic-biology.html Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targetedgene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.

Keywords:directed evolution; genome engineering; metabolic engineering; synthesis; synthetic chassis

Introduction The phrase ‘genome-scale engineering’ invokes a future in which organisms are custom designed to serve humanity. Yet humans have sculpted the genomes of domesticated plants and animals for generations. Darwin’s contemporary William Youatt described selective breeding as ‘that which enables the agriculturalist, not only to modify the character of his flock, but to change it altogether. It is the magician's wand, by means of which he may summon into life whatever form and mold he pleases’ (Youatt, 1837). Selective breeding has transformed aurochs into Holsteins, wolves into Chihuahuas and Great Danes, and teosinte into maize. All of these examples involved genomic changes at a scale dwarfing any attempted through rational design. Understanding why genomes have been more readily shaped by evolutionary principles than conventional design-based approaches is important for current and future genome engineering endeavors.

Engineering is a human enterprise consisting of iterative cycles of design, construction, and testing. Optimizing this iterative process involves balancing the relative time, costs, and expected benefits gained at each phase. However, rationally designing and building a genome to produce the desired phenotype has proven exceedingly difficult. Designing organisms to specification requires accurately predicting phenotype from genotype, a complex problem that is worsened by our incomplete knowledge of biomolecule production, degradation, and interaction rates. Moreover, the computational resources required to run bottom-up molecular-level simulations are daunting even for simpler systems (Karr et al, 2012; Koch, 2012). Nevertheless, models have been useful for generating new hypotheses and targeting promising areas for engineering. Yet, even with the best in silico predictions, we are still limited by our ability to construct the designed genome. More than any other factor, the absence of molecular tools for manipulating genomic sequences has forced us to rely on selective breeding and evolutionary optimization (Conrad et al, 2011) rather than rational genome design.

Recent breakthroughs in genomics and genome editing have promised a greater role for rational design in biological engineering (Figure 1), offering new opportunities for systems and synthetic biologists aiming to reverse-engineer naturally evolved systems and to build new systems. In particular, advances in high-throughput DNA sequencing and large-scale biomolecular modeling of metabolic and signaling networks represent two important new frontiers that aid genome-scale engineering. Over the last few years, thousands of bacterial genomes have been sequenced from a wide variety of natural species and numerous laboratory-generated strains (Pagani et al, 2012). These efforts have illuminated many essential features of the core genome (Lukjancenko et al, 2010), the extent and importance of genetic heterogeneity across populations (Avery, 2006), the ubiquity of horizontal gene transfer (Smillie et al, 2011), and the evolution and selection of functional genetic elements (David and Alm, 2011). At the same time, new computational tools have used the flood of data to model metabolic processes and signaling networks across the entire cell, generating many new testable hypotheses (Lewis et al, 2012). Most importantly, emerging advances in de novo synthesis and in vivo gene targeting allow empirical validation of these model-driven hypotheses. By building and testing synthetic variants of biological systems, we have a unique opportunity to decipher the constraints imposed by the complexity of evolved systems and develop strategies for engineering living systems more conducive to quantitative modeling and rational design.

Figure 1 A historical timeline of selected advances leading to genome-scale engineering.

Here we review recent technologies that empower design-based genome engineering approaches, identify potential bottlenecks, discuss strengths and limitations of strategies employing rational design versus evolution, and consider future applications of genome-scale engineering. We advocate a synergistic engineering strategy that adopts the best aspects of rational genome design and evolutionary optimization."

This paper is part of the series on Systems Biology Technologies.

Genome-scale engineering for systems and synthetic biology. Kevin M Esvelt & Harris H Wang

(Via.) Molecular Systems Biology

]]>
[email protected] (Jim Haseloff) 2013-01-26T15:46:22+00:00 http://www.synbio.org.uk/wetware-news/2681-genome-scale-engineering-for-systems-and-synthetic-biology.html
Clues to Early Age of Exploration Found in Sweet Potato Genome http://www.synbio.org.uk/plant-biology-news/2680-clues-to-early-age-of-exploration-found-in-sweet-potato-genome.html Clues to Early Age of Exploration Found in Sweet Potato Genome

Europeans raced across oceans and continents during the Age of Exploration in search of territory and riches. But when they reached the South Pacific, they found they had been beaten there by a more humble traveler: the sweet potato. Now, ..."

Clues to Early Age of Exploration Found in Sweet Potato Genome

(Via Wired Science.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T15:37:43+00:00 http://www.synbio.org.uk/plant-biology-news/2680-clues-to-early-age-of-exploration-found-in-sweet-potato-genome.html
The Most Amazing Photos Of Flowers You've Ever Seen http://www.synbio.org.uk/plant-biology-news/2677-the-most-amazing-photos-of-flowers-youve-ever-seen.html

Floriculture Photography Andrew Zuckerman
A peek at some of the shots in Andrew Zuckerman's gorgeous coffee table book Flower

Flowers aren't everyone's cup of tea, but the latest project from minimalist filmmaker and photographer Andrew Zuckerman could make even the biggest skeptic fall in love with blooms. His book of photography, Flower, renders some familiar species so crisply they're almost unrecognizable as something you'd see in your neighbor's garden.

In Flower, Zuckerman says he aims 'to translate the essential nature of his subjects and unearth qualities that have previously escaped scrutiny.'

The hefty coffee table tome is the result of an investigation of over 300 species, providing an intimate, pared-down look at the botanical world. Filmmaker David Lynch sings his praises on the book's back cover: 'These photographs of flowers taken by Andrew Zuckerman are pure.' And everyone knows you can't argue with a book blurb from David Lynch.

You can check out more multimedia associated with the project on the Flower website.
Click here to enter the gallery

The Most Amazing Photos Of Flowers You've Ever Seen

(Via Popular Science -.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T15:15:41+00:00 http://www.synbio.org.uk/plant-biology-news/2677-the-most-amazing-photos-of-flowers-youve-ever-seen.html
Darwin's Neon Orange Balls http://www.synbio.org.uk/plant-biology-news/2663-darwins-neon-orange-balls.html

If you're wondering what in the world are those neon orange balls growing on a beech tree, you're in good company. See, it was Charles Darwin himself who first encountered the strange balls when he landed in Tierra del Fuego during his voyage on the HMS Beagle.

Turns out, the neon-colored balls known as 'beech orange' are actually a fungus named Cyttaria darwini (yes, named after the biologist in his honor). But that's not the strangest thing about the fungus. Turns out, you can make an alcoholic drink out of them!

Darwin himself noted they made up a substantial portion of the diet of the natives of Terra del Fuego and grew ‘in vast numbers on the beech trees’. He observed that the women and children collected their beech oranges when ‘tough and mature’, and that they had a ‘mucilaginous, slightly sweet taste, with a faint smell like that of a mushroom.’

Another South American group — the Araucans of Chile — discovered and capitalized upon the happy fact that Cyttaria harioti contains up to 15% fermentable sugars and that, like grapes, come naturally coated with the yeast Saccharomyces. This would be the same Saccharomyces that has made the fortunes of Fleischman’s, Budweiser, and half of France.

After drying, grinding, and mixing beech oranges with warm water and allowing nature to take its course, the Araucans enjoy an alcoholic beverage called chicha del llau-llau made from the ripe fruiting bodies, according to Bryce Kendrick’s The Fifth Kingdom.

Jennifer Frazer of Scientific American's The Artful Amoeba blog has the post: Link

Darwin's Neon Orange Balls

(Via Neatorama.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T11:48:31+00:00 http://www.synbio.org.uk/plant-biology-news/2663-darwins-neon-orange-balls.html
Photographing a Giant Sequoia http://www.synbio.org.uk/plant-biology-news/2661-photographing-a-giant-sequoia.html

Photo: Michael 'Nick' Nichols/The National Geographic

How do you photograph a 3,200-year-old giant sequoia that rises 247 feet from the ground? Michael 'Nick' Nichols did it by stitching together 126 images into one fantastic photo of an absolutely majestic tree.

The next question is how did he take those individual pictures? For the answer to that question, you have to watch the video clip:

The National Geographic has the fascinating article by David Quammen about these forest giants: Link | Photo Gallery

Photographing a Giant Sequoia

(Via Neatorama.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T11:41:19+00:00 http://www.synbio.org.uk/plant-biology-news/2661-photographing-a-giant-sequoia.html
Macro photos of coral take us to underwater alien worlds http://www.synbio.org.uk/wetware-news/2659-macro-photos-of-coral-take-us-to-underwater-alien-worlds.html Click here to read Macro photos of coral take us to underwater alien worlds Felix Salazar's macro photography of a coral reef offers a serene and colorful tour through an almost alien universe. Seen up close and in such brilliant colors, it's each to forget that these are creatures from our own planet. So head over to Salazar's website, scroll through the photos, and forget about Earth for a minute or two. More »

Macro photos of coral take us to underwater alien worlds

(Via io9.)

]]>
[email protected] (Jim Haseloff) 2013-01-26T11:36:23+00:00 http://www.synbio.org.uk/wetware-news/2659-macro-photos-of-coral-take-us-to-underwater-alien-worlds.html
How To Make Your Own Grow Lights http://www.synbio.org.uk/plant-biology-news/2637-how-to-make-your-own-grow-lights.html

DIY grow lights The Big Book Of Hacks
Create a light system to keep houseplants thriving during winter's short days.

Setting up specialized grow lights that mimic the sun's rays is a good solution, but you can get similar results with LEDs. We connected three inside a clear plastic tube to make a 'light spike' that you can stick into a pot for direct exposure, and added a controller that adjusts the brightness.

MATERIALS
Project box
Drill
2.1-mm power-connector jack
10-position header
100k-ohm slide potentiometer
Soldering iron and solder
Electrical wire
10k-ohm resistor
Wire strippers
White LED design kit
Five clear plastic tubes with endcaps
Five two-position connectors
15-volt 1A wall-mount power supply

STEP 1
Drill six holes in your project box to accommodate the various components, then assemble the controller by mounting the power-connector jack inside the box and the 10-position header and the 100k-ohm slide potentiometer on the box's sides.

STEP 2
Wire the box according to the circuitry diagram.

STEP 3
Cut the wire inside the LED design kit into five equal lengths. Attach the red wire to the red connector, and the black wire to the black connector, on each LED strip. Slip each strip inside a clear tube, and seal it with the endcaps so that it's watertight.

STEP 4
Add the two-position connectors that will hook up the tubes and the box. Attach each one to the red and black wires from each LED strip.

STEP 5
Press a spike into your plant container. Keep all wiring, electrical connections, and the LED strips away from soil and moisture.

STEP 6
Plug the spikes' two-position connectors into the control box's 10-position header, and connect the power supply to turn the LEDs on.

STEP 7
Adjust the slide potentiometer to control the brightness of the spikes, and watch your garden grow.

This project was excerpted from The Big Book Of Hacks: 264 Amazing DIY Tech Projects, a compendium of ingenious and hilarious projects for aspiring makers. Buy it here. And for more amazing hacks, go here.

(Via Popular Science -.)

]]>
[email protected] (Jim Haseloff) 2013-01-20T02:07:51+00:00 http://www.synbio.org.uk/plant-biology-news/2637-how-to-make-your-own-grow-lights.html
Chemical Synthesis of Arabidopsis CLV3 Glycopeptide Reveals the Impact of Hyp Arabinosylation ... http://www.synbio.org.uk/plant-biology-news/2628-chemical-synthesis-of-arabidopsis-clv3-glycopeptide-reveals-the-impact-of-hyp-arabinosylation-on-peptide-conformation-and-activity.html Chemical Synthesis of Arabidopsis CLV3 Glycopeptide Reveals the Impact of Hyp Arabinosylation on Peptide Conformation and Activity.: "Publication Date: 2012 Dec 19 PMID: 23256149
Authors: Shinohara, H. - Matsubayashi, Y.
Journal: Plant Cell Physiol

Arabinosylation of hydroxyproline (Hyp) is a posttranslational modification often found in secreted peptide signals in plants. The physiological importance of this modification was highlighted by the finding that CLAVATA3 (CLV3), a key peptide signal for regulating the fate of stem cells in shoot apical meristem (SAM) in Arabidopsis, contains three L-arabinose residues linked via linear beta-1,2-linkages. However, understanding the functions and properties of arabinosylated peptides have been hindered by difficulties in synthesizing the complex arabinose chain. Here we report the stereoselective total synthesis of beta-1,2-linked tri-arabinosylated CLV3 peptide ([Ara(3)]CLV3). Chemically synthesized [Ara(3)]CLV3 restricted stem cell activity more effectively than did unmodified CLV3 peptide. Comparison of mono-, di- and tri-arabinosylated CLV3 glycopeptides revealed that the biological activity increased progressively as arabinose chain length increased. Thus, arabinose chain length of CLV3 is important for its biological activity. NMR spectroscopy and NOE-based structure calculations further revealed the structural impact of the arabinose chain on peptide conformation. The arabinose chain of [Ara(3)]CLV3 extends toward the C-terminal end of the peptide, and its non-reducing end is positioned proximal to the peptide backbone. Consequently, the arabinose chain causes distinct distortion in the C-terminal half of the peptide in a highly directional manner. The established synthetic route of [Ara(3)]CLV3 will greatly contribute to our understanding of the biology and biochemistry of arabinosylated peptide signals in plants.

post to: CiteULike"

(Via Plant and Cell Physiology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:33:40+00:00 http://www.synbio.org.uk/plant-biology-news/2628-chemical-synthesis-of-arabidopsis-clv3-glycopeptide-reveals-the-impact-of-hyp-arabinosylation-on-peptide-conformation-and-activity.html
Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. http://www.synbio.org.uk/wetware-news/2627-single-molecule-analysis-of-gene-expression-using-two-color-rna-labeling-in-live-yeast.html Single-molecule analysis of gene expression using two-color RNA labeling in live yeast.: "Publication Date: 2012 Dec 23 PMID: 23263691
Authors: Hocine, S. - Raymond, P. - Zenklusen, D. - Chao, J. A. - Singer, R. H.
Journal: Nat Methods

Live-cell imaging of mRNA yields important insights into gene expression, but it has generally been limited to the labeling of one RNA species and has never been used to count single mRNAs over time in yeast. We demonstrate a two-color imaging system with single-molecule resolution using MS2 and PP7 RNA labeling. We use this methodology to measure intrinsic noise in mRNA levels and RNA polymerase II kinetics at a single gene.

post to: CiteULike"

(Via Nature Methods.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:27:24+00:00 http://www.synbio.org.uk/wetware-news/2627-single-molecule-analysis-of-gene-expression-using-two-color-rna-labeling-in-live-yeast.html
A Triantagonistic Basic Helix-Loop-Helix System Regulates Cell Elongation in Arabidopsis http://www.synbio.org.uk/plant-biology-news/2626-a-triantagonistic-basic-helix-loop-helix-system-regulates-cell-elongation-in-arabidopsis.html A Triantagonistic Basic Helix-Loop-Helix System Regulates Cell Elongation in Arabidopsis: "

In plants, basic helix-loop-helix (bHLH) transcription factors play important roles in the control of cell elongation. Two bHLH proteins, PACLOBTRAZOL RESISTANCE1 (PRE1) and Arabidopsis ILI1 binding bHLH1 (IBH1), antagonistically regulate cell elongation in response to brassinosteroid and gibberellin signaling, but the detailed molecular mechanisms by which these factors regulate cell elongation remain unclear. Here, we identify the bHLH transcriptional activators for cell elongation (ACEs) and demonstrate that PRE1, IBH1, and the ACEs constitute a triantagonistic bHLH system that competitively regulates cell elongation. In this system, the ACE bHLH transcription factors directly activate the expression of enzyme genes for cell elongation by interacting with their promoter regions. IBH1 negatively regulates cell elongation by interacting with the ACEs and thus interfering with their DNA binding. PRE1 interacts with IBH1 and counteracts the ability of IBH1 to affect ACEs. Therefore, PRE1 restores the transcriptional activity of ACEs, resulting in induction of cell elongation. The balance of triantagonistic bHLH proteins, ACEs, IBH1, and PRE1, might be important for determination of the size of plant cells. The expression of IBH1 and PRE1 is regulated by brassinosteroid, gibberellins, and developmental phase dependent factors, indicating that two phytohormones and phase-dependent signals are integrated by this triantagonistic bHLH system.

(Via The Plant Cell current issue.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:20:08+00:00 http://www.synbio.org.uk/plant-biology-news/2626-a-triantagonistic-basic-helix-loop-helix-system-regulates-cell-elongation-in-arabidopsis.html
Molecular mechanisms of robustness in plants. http://www.synbio.org.uk/plant-biology-news/2625-molecular-mechanisms-of-robustness-in-plants.html Molecular mechanisms of robustness in plants.: "Publication Date: 2012 Dec 29 PMID: 23279801
Authors: Lempe, J. - Lachowiec, J. - Sullivan, A. M. - Queitsch, C.
Journal: Curr Opin Plant Biol

Robustness, the ability of organisms to buffer phenotypes against perturbations, has drawn renewed interest among developmental biologists and geneticists. A growing body of research supports an important role of robustness in the genotype to phenotype translation, with far-reaching implications for evolutionary processes and disease susceptibility. Similar to animals and fungi, plant robustness is a function of genetic network architecture. Most perturbations are buffered; however, perturbation of network hubs destabilizes many traits. Here, we review recent advances in identifying molecular robustness mechanisms in plants that have been enabled by a combination of classical genetics and population genetics with genome-scale data.

post to: CiteULike"

(Via Current Opinion in Plant Biology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:12:23+00:00 http://www.synbio.org.uk/plant-biology-news/2625-molecular-mechanisms-of-robustness-in-plants.html
Computational modeling of epidermal cell fate determination systems. http://www.synbio.org.uk/plant-biology-news/2624-computational-modeling-of-epidermal-cell-fate-determination-systems.html Computational modeling of epidermal cell fate determination systems.: "Publication Date: 2012 Dec 31 PMID: 23287386
Authors: Ryu, K. H. - Zheng, X. - Huang, L. - Schiefelbein, J.
Journal: Curr Opin Plant Biol

Cell fate decisions are of primary importance for plant development. Their simple 'either-or' outcome and dynamic nature has attracted the attention of computational modelers. Recent efforts have focused on modeling the determination of several epidermal cell types in the root and shoot of Arabidopsis where many molecular components have been defined. Results of integrated modeling and molecular biology experimentation in these systems have highlighted the importance of competitive positive and negative factors and interconnected feedback loops in generating flexible yet robust mechanisms for establishing distinct gene expression programs in neighboring cells. These models have proven useful in judging hypotheses and guiding future research.

post to: CiteULike"

(Via Current Opinion in Plant Biology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:09:33+00:00 http://www.synbio.org.uk/plant-biology-news/2624-computational-modeling-of-epidermal-cell-fate-determination-systems.html
Control of root meristem size by DA1-related protein 2 in Arabidopsis thaliana. http://www.synbio.org.uk/plant-biology-news/2623-control-of-root-meristem-size-by-da1-related-protein-2-in-arabidopsis-thaliana.html Control of root meristem size by DA1-related protein 2 in Arabidopsis thaliana.: "Publication Date: 2013 Jan 7 PMID: 23296689
Authors: Peng, Y. - Ma, W. - Chen, L. - Yang, L. - Li, S. - Zhao, H. - Zhao, Y. - Jin, W. - Li, N. - Bevan, M. W. - Li, X. - Tong, Y. - Li, Y.
Journal: Plant Physiol

Control of organ growth by coordinating cell proliferation and differentiation is a fundamental developmental process. In plants, postembryonic root growth is sustained by the root meristem. For maintenance of root meristem size, the rate of cell differentiation must equal the rate of cell division. Cytokinin and auxin interact to affect the cell proliferation and differentiation balance and thus control root meristem size. However, the genetic and molecular mechanisms that detemine root meristem size still remain largely unknown. Here we report that dar2 mutants produce small root meristems due to decreased cell division and early cell differentiation in the root meristem. dar2 mutants also exhibit reduced stem cell niche activity in the root meristem. DAR2 encodes a LIM domain-containing protein and shows an expression peak in the border between the transition zone and the elongation zone. Genetic analyses show that DAR2 functions downstream of cytokinin and SHORT HYPOCOTYL2 (SHY2/IAA3) to maintain normal auxin distribution by influencing auxin transport. Further results indicate that DAR2 acts through the PLETHORA (PLT1/2) pathway to influence root stem cell niche activity and therefore control root meristem size. Collectively, our findings identify the role of DAR2 in root meristem size control and provide a novel link between several key regulators influencing root meristem size.

post to: CiteULike"

(Via Plant Physiology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:05:08+00:00 http://www.synbio.org.uk/plant-biology-news/2623-control-of-root-meristem-size-by-da1-related-protein-2-in-arabidopsis-thaliana.html
ERISdb: a Database of Plant Splice Sites and Splicing Signals. http://www.synbio.org.uk/wetware-news/2622-erisdb-a-database-of-plant-splice-sites-and-splicing-signals.html ERISdb: a Database of Plant Splice Sites and Splicing Signals.: "Publication Date: 2013 Jan 7 PMID: 23299413
Authors: Szczesniak, M. W. - Kabza, M. - Pokrzywa, R. - Gudys, A. - Makalowska, I.
Journal: Plant Cell Physiol

Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans. There are numerous factors that affect the process but splice sites themselves along with the adjacent splicing signals are critical here. Unfortunately, there is still little known about splicing in plants and, consequently, further research in some fields of plant molecular biology meets difficulties. Keeping this in mind, we performed a large scale analyses of splice sites in eight plant species, using novel algorithms and tools developed by us. The analyses included identification of orthologous splice sites, polypyrimidine tracts, and branch sites. Additionally we identified putative intronic and exonic cis-regulatory motifs, U12 introns as well as splice sites in 45 microRNA genes in 5 plant species. We also provide experimental evidence for plant splice sites in the form of EST and RNA-Seq data. All the data are stored in a novel database called ERISdb and are freely available at http://lemur.amu.edu.pl/share/ERISdb/.

post to: CiteULike"

(Via Plant and Cell Physiology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T17:02:31+00:00 http://www.synbio.org.uk/wetware-news/2622-erisdb-a-database-of-plant-splice-sites-and-splicing-signals.html
Identification of direct targets of FUSCA3, a key regulator of Arabidopsis thaliana seed ... http://www.synbio.org.uk/plant-biology-news/2621-identification-of-direct-targets-of-fusca3-a-key-regulator-of-arabidopsis-thaliana-seed-development.html Identification of direct targets of FUSCA3, a key regulator of Arabidopsis thaliana seed development.: "Publication Date: 2013 Jan 11 PMID: 23314941
Authors: Wang, F. - Perry, S. E.
Journal: Plant Physiol

FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box binding factor. LEC1, LEC2 and FUS3 are essential for plant embryo development. All three loss-of-function mutants in Arabidopsis thaliana prematurely exit embryogenesis and enter seedling developmental programs. When ectopically expressed, these genes promote embryo programs in seedlings. We report on ChIP-chip experiments to globally map binding sites for FUS3 that, along with other published work to assess transcriptomes in response to FUS3, allow us to determine direct from indirect targets. Many transcription factors associated with embryogenesis are direct targets of FUS3 as are genes involved in the seed maturation program. FUS3 regulates genes encoding miRNAs that in turn control transcripts encoding transcription factors involved in developmental phase changes. Examination of direct targets of FUS3 reveals that FUS3 acts primarily or exclusively as a transcriptional activator. Regulation of miRNA encoding genes is one mechanism by which FUS3 may repress indirect target genes. FUS3 also directly upregulates VP1/ABI3-LIKE1 (VAL1) encoding a B3 domain protein that functions as a repressor of transcription. VAL1, along with VAL2 and VAL3, is involved in the transition from embryo to seedling development. Many genes are responsive to FUS3 and to VAL1 VAL2 but with opposite regulatory consequences. The emerging picture is one of complex cross-talk and interactions among embryo transcription factors and their target genes.

post to: CiteULike"

(Via Plant Physiology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T16:57:16+00:00 http://www.synbio.org.uk/plant-biology-news/2621-identification-of-direct-targets-of-fusca3-a-key-regulator-of-arabidopsis-thaliana-seed-development.html
Bacillus: Biofilms grow with the flow http://www.synbio.org.uk/microbe-news/2620-bacillus-biofilms-grow-with-the-flow.html Bacillus: Biofilms grow with the flow: "

Nature Reviews Microbiology 11, 73 (2013). doi:10.1038/nrmicro2964

Author: Christina Tobin Kåhrström

Biofilm growth relies on the transport of solubilized nutrients and waste largely by diffusion, but the mechanism of transport over large distances, when diffusion is limited, has been unclear. A recent study reports the discovery of an integrated network of channels that transport liquid through

(Via Nature Reviews Microbiology.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T16:55:54+00:00 http://www.synbio.org.uk/microbe-news/2620-bacillus-biofilms-grow-with-the-flow.html
Cell-to-Cell Movement of Two Interacting AT-Hook Factors in Arabidopsis Root Vascular Tissue ... http://www.synbio.org.uk/plant-biology-news/2619-cell-to-cell-movement-of-two-interacting-at-hook-factors-in-arabidopsis-root-vascular-tissue-patterning.html Cell-to-Cell Movement of Two Interacting AT-Hook Factors in Arabidopsis Root Vascular Tissue Patterning: "

The xylem in Arabidopsis roots develops as a single row of cells neighboring the undifferentiated procambium. This work determined that two closely related AHL3 and AHL4 transcription factors regulate the boundaries between the xylem and procambium. AHL4 moves from the procambium to xylem in the root meristem, likely as a heteromeric complex with AHL3.

(Via Plant Cell Preview Papers.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T16:51:39+00:00 http://www.synbio.org.uk/plant-biology-news/2619-cell-to-cell-movement-of-two-interacting-at-hook-factors-in-arabidopsis-root-vascular-tissue-patterning.html
Infographic: Study Shows World’s Oldest Trees Are Dying Off Rapidly http://www.synbio.org.uk/plant-biology-news/2608-infographic-study-shows-worlds-oldest-trees-are-dying-off-rapidly.html Worlds Oldest Trees, Michael Paukner, ecological research, tree declining, trees dying off fast, australia university, sustainable design

The world’s oldest trees are dying off at an alarming rate, according to recent study by Australian National University professor David Lindenmayer. Research conducted on some of the world’s greatest forests – from Yosemite National Park and the Brazilian Rainforest – shows that the die-off rate of trees between 100 to 300 years is a grave concern, and climate change is one of the biggest reasons for their decline. This beautiful infographic by Michael Paukner shows the locations of some of the world’s oldest – and most at risk – trees.

+ Michael Paukner

Via Kateoplis

Worlds Oldest Trees, Michael Paukner, ecological research, tree declining, trees dying off fast, australia university, sustainable design (Via INHABITAT.)

]]>
[email protected] (Jim Haseloff) 2013-01-19T14:10:44+00:00 http://www.synbio.org.uk/plant-biology-news/2608-infographic-study-shows-worlds-oldest-trees-are-dying-off-rapidly.html
Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli. http://www.synbio.org.uk/wetware-news/2581-tuning-promoter-strength-through-rna-polymerase-binding-site-design-in-escherichia-coli.html Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli.: "Publication Date: 2012 Dec PMID: 23271961
Authors: Brewster, R. C. - Jones, D. L. - Phillips, R.
Journal: PLoS Comput Biol

One of the paramount goals of synthetic biology is to have the ability to tune transcriptional networks to targeted levels of expression at will. As a step in that direction, we have constructed a set of [Formula: see text] unique binding sites for E. coli RNA Polymerase (RNAP) [Formula: see text] holoenzyme, designed using a model of sequence-dependent binding energy combined with a thermodynamic model of transcription to produce a targeted level of gene expression. This promoter set allows us to determine the correspondence between the absolute numbers of mRNA molecules or protein products and the predicted promoter binding energies measured in [Formula: see text] energy units. These binding sites adhere on average to the predicted level of gene expression over [Formula: see text] orders of magnitude in constitutive gene expression, to within a factor of [Formula: see text] in both protein and mRNA copy number. With these promoters in hand, we then place them under the regulatory control of a bacterial repressor and show that again there is a strict correspondence between the measured and predicted levels of expression, demonstrating the transferability of the promoters to an alternate regulatory context. In particular, our thermodynamic model predicts the expression from our promoters under a range of repressor concentrations between several per cell up to over [Formula: see text] per cell. After correcting the predicted polymerase binding strength using the data from the unregulated promoter, the thermodynamic model accurately predicts the expression for the simple repression strains to within [Formula: see text]. Demonstration of modular promoter design, where parts of the circuit (such as RNAP/TF binding strength and transcription factor copy number) can be independently chosen from a stock list and combined to give a predictable result, has important implications as an engineering tool for use in synthetic biology.

post to: CiteULike"

(Via PLoS Computational Biology.)

]]>
[email protected] (Jim Haseloff) 2013-01-14T20:02:23+00:00 http://www.synbio.org.uk/wetware-news/2581-tuning-promoter-strength-through-rna-polymerase-binding-site-design-in-escherichia-coli.html
Design, implementation and practice of JBEI-ICE: an open source biological part registry ... http://www.synbio.org.uk/wetware-news/2580-design-implementation-and-practice-of-jbei-ice-an-open-source-biological-part-registry-platform-and-tools.html Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

Nucleic Acids Res. 2012 Jun 19;

Authors: Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, Keasling JD

Abstract
The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

PMID: 22718978 [PubMed - as supplied by publisher]

(Via pubmed: "synthetic biology".)

]]>
[email protected] (Jim Haseloff) 2013-01-14T20:01:13+00:00 http://www.synbio.org.uk/wetware-news/2580-design-implementation-and-practice-of-jbei-ice-an-open-source-biological-part-registry-platform-and-tools.html
A synthetic biology framework for programming eukaryotic transcription functions. http://www.synbio.org.uk/wetware-news/2575-a-synthetic-biology-framework-for-programming-eukaryotic-transcription-functions.html A synthetic biology framework for programming eukaryotic transcription functions.: "

Related Articles

Cell. 2012 Aug 3;150(3):647-58

Authors: Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ

Abstract
Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks.

PMID: 22863014 [PubMed - in process]

(Via pubmed: "synthetic biology".)

]]>
[email protected] (Jim Haseloff) 2012-12-09T16:52:16+00:00 http://www.synbio.org.uk/wetware-news/2575-a-synthetic-biology-framework-for-programming-eukaryotic-transcription-functions.html
Visualization of auxin-mediated transcriptional activation using a common auxin-responsive ... http://www.synbio.org.uk/plant-biology-news/2574-visualization-of-auxin-mediated-transcriptional-activation-using-a-common-auxin-responsive-reporter-system-in-the-liverwort-marchantia-polymorpha.html Visualization of auxin-mediated transcriptional activation using a common auxin-responsive reporter system in the liverwort Marchantia polymorpha.:

J Plant Res. 2012 Feb 4;

Authors: Ishizaki K, Nonomura M, Kato H, Yamato KT, Kohchi T

Abstract
The phytohormone auxin plays a pivotal role in various developmental aspects in land plants. However, little is known of the auxin response and distribution in non-vascular plants. In this study, we made transgenic plants of the liverwort Marchantia polymorpha which express the uidA (GUS) reporter gene under control of the soybean auxin-inducible promoter, ProGH3, and used it to indirectly monitor auxin-mediated transcriptional activation in planta. Transgenic plants carrying ProGH3:GUS showed GUS activity in an auxin-dependent manner. Histochemical GUS staining was observed at the bottom of gemma cups in the process of vegetative propagation. Significant GUS activity was also detected around the gametophyte-sporophyte junction as well as the developing sporophyte after fertilization. These results suggest that the activity of auxin is crucial in both gametophyte and sporophyte development in M. polymorpha, and that the mechanism for auxin-mediated transcriptional activation had already been established when plants emerged on the terrestrial environment.

PMID: 22311005 [PubMed - as supplied by publisher]

(Via pubmed: marchantia.)

]]>
[email protected] (Jim Haseloff) 2012-12-09T16:38:16+00:00 http://www.synbio.org.uk/plant-biology-news/2574-visualization-of-auxin-mediated-transcriptional-activation-using-a-common-auxin-responsive-reporter-system-in-the-liverwort-marchantia-polymorpha.html
Characterization of 12 polymorphic microsatellite markers in the liverwort Marchantia inflexa ... http://www.synbio.org.uk/plant-biology-news/2573-characterization-of-12-polymorphic-microsatellite-markers-in-the-liverwort-marchantia-inflexa-marchantiaceae.html Related Articles

Characterization of 12 polymorphic microsatellite markers in the liverwort Marchantia inflexa (Marchantiaceae).

Am J Bot. 2012 Nov;99(11):e440-2

Authors: Brzyski JR, Adams KJ, Walter CM, Gale KH, McLetchie DN

Abstract
• Premise of the study: Microsatellite markers were developed in Marchantia inflexa, a haploid liverwort with unisexual individuals, to identify clonal genotypes and measure population genetic variability. • Methods and Results: Twelve polymorphic primer sets were developed from three enriched genomic libraries. Primers were fluorescently labeled, and alleles were identified by fragment analysis. These primers were tested in four natural populations and revealed a moderate level of genetic variation within four populations, as indicated by the number of alleles per locus (range = 1-5). • Conclusions: Development of polymorphic markers is crucial to the identification of individuals and will allow additional research into this species, particularly on its population genetics and metapopulation dynamics.

PMID: 23108461 [PubMed - in process]

(Via pubmed: marchantia.)

]]>
[email protected] (Jim Haseloff) 2012-12-09T16:37:16+00:00 http://www.synbio.org.uk/plant-biology-news/2573-characterization-of-12-polymorphic-microsatellite-markers-in-the-liverwort-marchantia-inflexa-marchantiaceae.html
PPR protein molecular code cracked http://www.synbio.org.uk/wetware-news/2564-ppr-protein-molecular-code-cracked.html Molecular code cracked: "The code determines the recognition of RNA molecules by a superfamily of RNA-binding proteins called pentatricopeptide repeat (PPR) proteins.

When a gene is switched on, it is copied into RNA. This RNA is then used to make proteins that are required by the organism for all of its vital functions. If a gene is defective, its RNA copy and the proteins made from this will also be defective. This forms the basis of many terrible genetic disorders in humans.

RNA-binding PPR proteins could revolutionise the way we treat disease. Their secret is their versatility - they can find and bind a specific RNA molecule, and have the capacity to correct it if it is defective, or destroy it if it is detrimental. They can also help ramp up production of proteins required for growth and development.

The new paper in PLOS Genetics describes for the first time how PPR proteins recognise their RNA targets via an easy-to-understand code. This mechanism mimics the simplicity and predictability of the pairing between DNA strands described by Watson and Crick 60 years ago, but at a protein/RNA interface.

This exceptional breakthrough comes from an international, interdisciplinary research team including UWA researchers Professor Ian Small and Aaron Yap from the ARC Centre for Excellence in Plant Energy Biology and Professor Charlie Bond and Yee Seng Chong from UWA's School of Chemistry and Biochemistry, along with Professor Alice Barkan's team at the University of Oregon. This research was publicly funded by the ARC and the WA State Government in Australia and the NSF in the USA.

'Many PPR proteins are vitally important, but we don't know what they do. Now we've cracked the code, we can find out,' said ARC Plant Energy Biology Director Ian Small.

'What's more, we can now design our own synthetic proteins to target any RNA sequence we choose - this should allow us to control the expression of genes in new ways that just weren't available before. The potential is really exciting.'

'This discovery was made in plants but is applicable across many species as PPR proteins are found in humans and animals too,' says Professor Bond. Source : University of Western Australia"

]]>
[email protected] (Jim Haseloff) 2012-08-29T19:39:12+00:00 http://www.synbio.org.uk/wetware-news/2564-ppr-protein-molecular-code-cracked.html
A synthetic biology framework for programming eukaryotic transcription functions. http://www.synbio.org.uk/wetware-news/2563-a-synthetic-biology-framework-for-programming-eukaryotic-transcription-functions.html A synthetic biology framework for programming eukaryotic transcription functions.

Cell. 2012 Aug 3;150(3):647-58

Authors: Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ

Abstract
Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks.

PMID: 22863014 [PubMed - in process]

(Via pubmed: "synthetic biology".)

]]>
[email protected] (Jim Haseloff) 2012-08-29T18:23:07+00:00 http://www.synbio.org.uk/wetware-news/2563-a-synthetic-biology-framework-for-programming-eukaryotic-transcription-functions.html
Modular control of multiple pathways using engineered orthogonal T7 polymerases. http://www.synbio.org.uk/wetware-news/2561-modular-control-of-multiple-pathways-using-engineered-orthogonal-t7-polymerases.html Modular control of multiple pathways using engineered orthogonal T7 polymerases.

Nucleic Acids Res. 2012 Jun 28;

Authors: Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA

Abstract
Synthetic genetic sensors and circuits enable programmable control over the timing and conditions of gene expression. They are being increasingly incorporated into the control of complex, multigene pathways and cellular functions. Here, we propose a design strategy to genetically separate the sensing/circuitry functions from the pathway to be controlled. This separation is achieved by having the output of the circuit drive the expression of a polymerase, which then activates the pathway from polymerase-specific promoters. The sensors, circuits and polymerase are encoded together on a 'controller' plasmid. Variants of T7 RNA polymerase that reduce toxicity were constructed and used as scaffolds for the construction of four orthogonal polymerases identified via part mining that bind to unique promoter sequences. This set is highly orthogonal and induces cognate promoters by 8- to 75-fold more than off-target promoters. These orthogonal polymerases enable four independent channels linking the outputs of circuits to the control of different cellular functions. As a demonstration, we constructed a controller plasmid that integrates two inducible systems, implements an AND logic operation and toggles between metabolic pathways that change Escherichia coli green (deoxychromoviridans) and red (lycopene). The advantages of this organization are that (i) the regulation of the pathway can be changed simply by introducing a different controller plasmid, (ii) transcription is orthogonal to host machinery and (iii) the pathway genes are not transcribed in the absence of a controller and are thus more easily carried without invoking evolutionary pressure.

PMID: 22743271 [PubMed - as supplied by publisher]

(Via pubmed: "synthetic biology".)

]]>
[email protected] (Jim Haseloff) 2012-08-29T18:19:49+00:00 http://www.synbio.org.uk/wetware-news/2561-modular-control-of-multiple-pathways-using-engineered-orthogonal-t7-polymerases.html
Visualization of auxin-mediated transcriptional ... [J Plant Res. 2012] - PubMed - NCBI http://www.synbio.org.uk/plant-biology-news/2560-visualization-of-auxin-mediated-transcriptional--j-plant-res-2012-pubmed-ncbi.html J Plant Res. 2012 Sep;125(5):643-51. Epub 2012 Feb 4. Visualization of auxin-mediated transcriptional activation using a common auxin-responsive reporter system in the liverwort Marchantia polymorpha. Ishizaki K, Nonomura M, Kato H, Yamato KT, Kohchi T. Source Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan. Abstract The phytohormone auxin plays a pivotal role in various developmental aspects in land plants. However, little is known of the auxin response and distribution in non-vascular plants. In this study, we made transgenic plants of the liverwort Marchantia polymorpha which express the uidA (GUS) reporter gene under control of the soybean auxin-inducible promoter, ProGH3, and used it to indirectly moni"

Visualization of auxin-mediated transcriptional ... [J Plant Res. 2012] - PubMed - NCBI

(Via.)

]]>
[email protected] (Jim Haseloff) 2012-08-29T18:17:34+00:00 http://www.synbio.org.uk/plant-biology-news/2560-visualization-of-auxin-mediated-transcriptional--j-plant-res-2012-pubmed-ncbi.html
Botanicus Interactus turns plants into multitouch controllers http://www.synbio.org.uk/plant-biology-news/2559-botanicus-interactus-turns-plants-into-multitouch-controllers.html The Botanicus Interactus system allows plants to be used to control electronic devices suc...

It is now possible to control a computer by touching a house plant – touching the plant in different places can even cause the computer to do different things. While using a mouse or touchscreen still might be more intuitive, Disney Research’s experimental Botanicus Interactus system does hint at what could be possible down the road. .. Continue Reading Botanicus Interactus turns plants into multitouch controllers


Related Articles:

(Via Gizmag Emerging Technology Magazine.)

]]>
[email protected] (Jim Haseloff) 2012-08-29T18:10:13+00:00 http://www.synbio.org.uk/plant-biology-news/2559-botanicus-interactus-turns-plants-into-multitouch-controllers.html
Agri-Cube grows mass quantities of vegetables in a one-car parking spot http://www.synbio.org.uk/plant-biology-news/2558-agri-cube-grows-mass-quantities-of-vegetables-in-a-one-car-parking-spot.html Bountiful harvest fills the trays of a Daiwa Agri-Cube prefab garden factory

Daiwa House, Japan's largest homebuilder, has introduced a line of prefabricated hydroponic vegetable factories, aimed at housing complexes, hotels, and top-end restaurants. Called the Agri-Cube, these units are touted by Daiwa as the first step in the industrialization of agriculture, to be located in and amongst the places where people live, work, and play. .. Continue Reading Agri-Cube grows mass quantities of vegetables in a one-car parking spot
(Via Gizmag Emerging Technology Magazine.)

]]>
[email protected] (Jim Haseloff) 2012-08-29T18:07:45+00:00 http://www.synbio.org.uk/plant-biology-news/2558-agri-cube-grows-mass-quantities-of-vegetables-in-a-one-car-parking-spot.html
Visualization of auxin-mediated transcriptional activation using a common auxin-responsive ... http://www.synbio.org.uk/plant-biology-news/2557-visualization-of-auxin-mediated-transcriptional-activation-using-a-common-auxin-responsive-reporter-system-in-the-liverwort-marchantia-polymorpha.html Visualization of auxin-mediated transcriptional activation using a common auxin-responsive reporter system in the liverwort Marchantia polymorpha.

J Plant Res. 2012 Feb 4;

Authors: Ishizaki K, Nonomura M, Kato H, Yamato KT, Kohchi T

Abstract
The phytohormone auxin plays a pivotal role in various developmental aspects in land plants. However, little is known of the auxin response and distribution in non-vascular plants. In this study, we made transgenic plants of the liverwort Marchantia polymorpha which express the uidA (GUS) reporter gene under control of the soybean auxin-inducible promoter, ProGH3, and used it to indirectly monitor auxin-mediated transcriptional activation in planta. Transgenic plants carrying ProGH3:GUS showed GUS activity in an auxin-dependent manner. Histochemical GUS staining was observed at the bottom of gemma cups in the process of vegetative propagation. Significant GUS activity was also detected around the gametophyte-sporophyte junction as well as the developing sporophyte after fertilization. These results suggest that the activity of auxin is crucial in both gametophyte and sporophyte development in M. polymorpha, and that the mechanism for auxin-mediated transcriptional activation had already been established when plants emerged on the terrestrial environment.

PMID: 22311005 [PubMed - as supplied by publisher]

(Via pubmed: marchantia.)

]]>
[email protected] (Jim Haseloff) 2012-08-29T01:17:15+00:00 http://www.synbio.org.uk/plant-biology-news/2557-visualization-of-auxin-mediated-transcriptional-activation-using-a-common-auxin-responsive-reporter-system-in-the-liverwort-marchantia-polymorpha.html
Nature's weird foods http://www.synbio.org.uk/plant-biology-news/2520-natures-weird-foods-.html  

buddha's hand (kaldian), miracle berries (Hamale Lyman), durian (AFP), pluot (BMRR)

Related Stories

 

British consumers have a new treat: the "papple". Described as a cross between an apple and a pear, it is actually a cross between different pear varieties. But it is just one of an array of oddly shaped, strangely flavoured and strikingly colourful fruits grown around the world.

For centuries, humans have taken the wild fruit that nature has to offer and cultivated its most desirable features by cross-breeding different varieties, or by simply selecting the best fruits of a native variety to seed another crop.

Here are some of the most tempting and bizarre results.

Pluots, plumcots and apriums

Fruity mash-ups:

Lemon

Lemons: Originating in India, lemons are a natural hybrid of a citron and an orange. Use them to make homemade mint lemonade

GrapefruitCreated by happy accident when an Asian pomelo tree was transported to a Barbados glasshouse. It naturally hybridised with a native sweet orange producing what was called at the time, the "forbidden fruit". Use it to create adevilled mackerel with orange and grapefruit salad

Loganberry : Dark red, large and juicy, this berry is a child of the raspberry and wild blackberry. This is perfect in a summer pudding

Yuzua Japanese citron hybrid that is very acidic, so used in moderation. The lemon-lime sour flavour has hints of tangerine and pine. It's a key ingredient in chicken goujons with yuzu mayonnaise

The pluot, the plumcot, the apriplum and the aprium are all types of what Americans call "interspecific plums".

Hybrids between different prunus species, they tend to have a much higher sugar content than their parents.

Half plum and half apricot, the plumcot hybrid was named by the botanical pioneer Luther Burbank in the early 20th Century, who created 11 varieties of plumcot.

Sometimes called apriplums, plumcots are a first generation cross between a plum and an apricot. They are shaped like plums with a smooth skin and typically have a red or purple flesh.

By contrast, pluots and apriums are complex combinations of later generations and are trademarks of fruit geneticist, Floyd Zaiger's company.

Whereas pluots are mostly plum with a smooth skin and a fleshy core, apriums are mostly apricot, resembling their dominant ancestor from the outside.

They have a flavour that has been compared to a sweet blend of fruit juices.

Buddha's hand

Buddha's hand fruit

Buddha's hand originates from north-eastern India or China and is one of the oldest known citrus fruits in cultivation.

With its long protruding fingers and thick rind, this strongly scented fruit has no internal flesh and is considered inedible in many parts of the world.

The plant produces dark green foliage and small white flowers with a heady scent of citrus blossom which fruits from late spring to late summer. It can be grown in a well-drained pot or in a sheltered area outdoors.

In China the fruit has been used for centuries as a medicinal herb to treat indigestion and sore throats. It can also be used in marmalades and to flavour sweet and savoury dishes. The Chinese also pickle the fruit in salt to remove its bitterness and then wash it, steam and dry it, so that it can be candied in a similar way to lemon zest.

Buddha's hand symbolises happiness and a long life in China and is traditionally given as a New Year's offering to household gods.

Durian

It is known for its pungent aroma, which is loved by some and loathed by others. But it's not just the smell that keeps people away from this fruit, which is native to south-east Asia.

It's also hard to get close to the edible flesh of the durian fruit due to its spiky exterior, making it difficult to handle if you don't know how.

In countries like Malaysia where it is found, it has been nicknamed the "king of fruit" because its flesh has a complex taste, which is said to be similar to caramel and fine French cheese.

The BBC's Juliana Liu demonstrates how to eat a Durian

In fact food journalist Fuchsia Dunlop, a self-confessed "fan of durian" says it has a "bewitching succulence".

There are 30 described species, and it is rich in potassium as well as other minerals and vitamins. It actually has the same nutritional and bio active properties as avocado and mango, and can be recommended as part of disease-preventative diets, a study in the International Journal of Food Science and Technology found.

Australian finger limes

Australian finger lime

If you've ever seen what looks like green caviar, chances are it's the fruit of microcitrus australasica.

The delicacy is also known as "citrus caviar", the juicy spheres are full of lime flavour, and "pop" in you mouth when eaten.

From the outside, finger limes look longer than traditional limes and are shaped like gherkins.

They come in an array of colours, not just green, but also black, orange, yellow and pink.

Discovered by early settlers, the finger lime is now commercially cultivated in Australia and in the United States as demand for "gourmet bush tucker" grows.

Top chefs and mixologists have begun incorporating the fruit in dishes and drinks around the world.

Miracle berry

Miracle berry plant

The miracle berry plant originates in Ghana, West Africa where it has been grown for centuries.

The plant is better known for its taste enhancing berries which make sour or bland foods taste sweeter after eating.

The effect is produced by the glycoprotein miraculin contained within the flesh of the fruit, which tricks the tongue's taste-bud receptors into experiencing a much sweeter flavour.

The "sugar hit" is said to last between 30 minutes to an hour after eating.

In 1968 an attempt was made to extract and sell the plant's miraculin protein in tablet form.

However, in the 1970s the US Food and Drug Administration put a ban on the commercialisation of the berry until further research was carried out.

The miracle berry has no legal status in the EU but is sold in tablet form as a dietary supplement in the US. In Japan, the berry is popular amongst dieters who use it as a sweetener in rosehip tea and desserts such as lemon gelato.

From: http://www.bbc.co.uk/nature/18340216

]]>
[email protected] (Jim Haseloff) 2012-07-08T01:59:02+00:00 http://www.synbio.org.uk/plant-biology-news/2520-natures-weird-foods-.html
A Phage Tubulin Assembles Dynamic Filaments by an Atypical Mechanism to Center Viral DNA within ... http://www.synbio.org.uk/wetware-news/2544-a-phage-tubulin-assembles-dynamic-filaments-by-an-atypical-mechanism-to-center-viral-dna-within-the-host-cell.html Publication Date: 2012 Jun 22 PMID: 22726436
Authors: Kraemer, J. A. - Erb, M. L. - Waddling, C. A. - Montabana, E. A. - Zehr, E. A. - Wang, H. - Nguyen, K. - Pham, D. S. - Agard, D. A. - Pogliano, J.
Journal: Cell

Tubulins are essential for the reproduction of many eukaryotic viruses, but historically, bacteriophage were assumed not to require a cytoskeleton. Here, we identify a tubulin-like protein, PhuZ, from bacteriophage 201phi2-1 and show that it forms filaments in vivo and in vitro. The PhuZ structure has a conserved tubulin fold, with an unusual, extended C terminus that we demonstrate to be critical for polymerization in vitro and in vivo. Longitudinal packing in the crystal lattice mimics packing observed by EM of in-vitro-formed filaments, indicating how interactions between the C terminus and the following monomer drive polymerization. PhuZ forms a filamentous array that is required for positioning phage DNA within the bacterial cell. Correct positioning to the cell center and optimal phage reproduction only occur when the PhuZ filament is dynamic. Thus, we show that PhuZ assembles a spindle-like array that functions analogously to the microtubule-based spindles of eukaryotes.

(Via Cell.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T01:08:05+00:00 http://www.synbio.org.uk/wetware-news/2544-a-phage-tubulin-assembles-dynamic-filaments-by-an-atypical-mechanism-to-center-viral-dna-within-the-host-cell.html
Discover Interview: Tullis Onstott Went 2 Miles Down & Found Microbes That Live on Radiation http://www.synbio.org.uk/microbe-news/2543-discover-interview-tullis-onstott-went-2-miles-down-a-found-microbes-that-live-on-radiation.html Tullis Onstott in his lab

The first time Tullis Onstott ventured underground, he squeezed into an elevator with dozens of South African gold miners and descended a mile into a pit called Mponeng. His goal: Finding the bizarre, hardy microbes that survive in sweltering, inhospitable rock. A geologist by training, Onstott spent his early career studying the Earth’s crust—until he heard a talk in 1993 about colonies of bacteria living thousands of feet below the surface. Ever since, he has made dozens of deep expeditions, sometimes paying his own way, and discovered bacteria living more than two miles beneath the surface in 140-degree-Fahrenheit heat. By investigating microbes in these harsh environments, Onstott is gleaning clues about how life could have begun in Earth’s hot, chaotic early days—and about what it might look like on other worlds. Even his office is underground, in the basement of Princeton University’s geology building, where Onstott met with DISCOVER reporter Valerie Ross.

The first time you went underground to look for life, in 1996, you had no idea what to expect. What was that trip like?
The miners took me into the stopes, the tunnels where they mine gold, to sample the rocks. We were looking at an organic rock layer just millimeters thick that had lots of carbon, because we 
figured somewhere with a lot of carbon was a good place to look for life. The stopes are a meter high and they tilt downward at a steep angle, so you go down them almost like a slide, passing from one tunnel to the next. I basically slipped into a rabbit hole and got this big chunk of rock. I put it in an autoclave bag [normally used for sterilizing equipment], stuffed it in my knapsack, and then I went down the stope further until I came out the bottom into another, deeper tunnel.

What did you do with the sample you collected?
We measured the rock’s radioactivity. The Geiger counter showed it was hot as a pistol, so we sealed it up in a steel canister and filled the canister with argon gas, which pushed out all the oxygen. Organisms that live deep down are not normally exposed to oxygen, and in fact it could be toxic to them. So we sealed the rock away until we could get it back into the lab. I checked this radioactive rock inside a steel thing as baggage on a plane. This was 1996. Airport security was not like it is today.

When you analyzed the sample back at your lab, did you find any life?
We found one bacterium species similar to one previously identified from a hot spring in New Mexico. But the surprise was that this particular species could do something the other hot spring organisms could not: reduce [i.e., transfer electrons to] iron, which is present in minerals that are abundant in the mine’s rocks, and uranium, part of soluble compounds found in water in the mine. That helped us understand how they got their energy...

Image: Onstott keeps a carefully sealed workspace in his lab at a high temperature and free of oxygen—just like home for the bacteria he studies. Photo: Jess Dittmar

(Via Discover Magazine.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:55:25+00:00 http://www.synbio.org.uk/microbe-news/2543-discover-interview-tullis-onstott-went-2-miles-down-a-found-microbes-that-live-on-radiation.html
Bacterial signaling systems as platforms for rational design of new generations of biosensors. http://www.synbio.org.uk/microbe-news/2542-bacterial-signaling-systems-as-platforms-for-rational-design-of-new-generations-of-biosensors.html Publication Date: 2012 Jun 1 PMID: 22658939
Authors: Checa, S. K. - Zurbriggen, M. D. - Soncini, F. C.
Journal: Curr Opin Biotechnol

Bacterial signal-responsive regulatory circuits have been employed as platform to design and construct whole-cell bacterial biosensors for reporting toxicity. A new generation of biosensors with improved performance and a wide application range has emerged after the application of synthetic biology concepts to biosensor design. Site-directed mutagenesis, directed evolution and domain swapping were applied to upgrade signal detection or to create novel sensor modules. Rewiring of the genetic circuits allows improving the determinations and reduces the heterogeneity of the response between individual reporter cells. Moreover, the assembly of natural or engineered modules to biosensor platforms provides innovative outputs, expanding the range of application of these devises, from monitoring toxics and bioremediation to killing targeted cells.

(Via Current Opinion in Biotechnology.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:46:40+00:00 http://www.synbio.org.uk/microbe-news/2542-bacterial-signaling-systems-as-platforms-for-rational-design-of-new-generations-of-biosensors.html
The ParA/MinD family puts things in their place. http://www.synbio.org.uk/microbe-news/2541-the-paramind-family-puts-things-in-their-place.html Publication Date: 2012 Jun 4 PMID: 22672910
Authors: Lutkenhaus, J.
Journal: Trends Microbiol

Bacteria must segregate their DNA and position a septum to grow and divide. In many bacteria, MinD is involved in spatial regulation of the cytokinetic Z ring, and ParAs are involved in chromosome and plasmid segregation. The use of the MinD/ParA family to provide positional information for spatial organization continues to expand with the recognition that orphan ParAs are required for segregating cytoplasmic protein clusters and the polar localization of chemotaxis proteins, conjugative transfer machinery, type IV pili, and cellulose synthesis. Also, some bacteria lacking MinD use orphan ParAs to regulate cell division. Positioning of MinD/ParA proteins is either due to self-organization on a surface or reliance on a landmark protein that functions as a molecular beacon.

(Via Trends in microbiology.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:27:33+00:00 http://www.synbio.org.uk/microbe-news/2541-the-paramind-family-puts-things-in-their-place.html
BioWord: a sequence manipulation suite for Microsoft Word. http://www.synbio.org.uk/wetware-news/2540-bioword-a-sequence-manipulation-suite-for-microsoft-word.html Publication Date: 2012 Jun 7 PMID: 22676326
Authors: Anzaldi, L. J. - Munoz-Fernandez, D. - Erill, I.
Journal: BMC Bioinformatics

ABSTRACT: BACKGROUND: Manipulation, editing and basic processing of DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein manipulation tools. RESULTS: BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office Ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. CONCLUSIONS: BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms.

BioWord: a sequence manipulation suite for Microsoft Word.

(Via BMC Bioinformatics.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:23:19+00:00 http://www.synbio.org.uk/wetware-news/2540-bioword-a-sequence-manipulation-suite-for-microsoft-word.html
'Shotgun DNA synthesis' for the high-throughput construction of large DNA molecules. http://www.synbio.org.uk/wetware-news/2539-shotgun-dna-synthesis-for-the-high-throughput-construction-of-large-dna-molecules.html Publication Date: 2012 Jun 16 PMID: 22705793
Authors: Kim, H. - Han, H. - Ahn, J. - Lee, J. - Cho, N. - Jang, H. - Kim, H. - Kwon, S. - Bang, D.
Journal: Nucleic Acids Res

We developed a highly scalable 'shotgun' DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin biosynthetic gene cluster were assembled into numerous random fragments, and tagged with 20 bp degenerate barcode primer pairs. An optimal set of error-free fragments were identified by high-throughput DNA sequencing, selectively amplified using the barcode sequences, and successfully assembled into the target gene cluster.

(Via Nucleic Acids Research.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:14:57+00:00 http://www.synbio.org.uk/wetware-news/2539-shotgun-dna-synthesis-for-the-high-throughput-construction-of-large-dna-molecules.html
Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL ... http://www.synbio.org.uk/wetware-news/2538-iterative-capped-assembly-rapid-and-scalable-synthesis-of-repeat-module-dna-such-as-tal-effectors-from-individual-monomers.html Publication Date: 2012 Jun 26 PMID: 22740649
Authors: Briggs, A. W. - Rios, X. - Chari, R. - Yang, L. - Zhang, F. - Mali, P. - Church, G. M.
Journal: Nucleic Acids Res

DNA built from modular repeats presents a challenge for gene synthesis. We present a solid surface-based sequential ligation approach, which we refer to as iterative capped assembly (ICA), that adds DNA repeat monomers individually to a growing chain while using hairpin capping oligonucleotides to block incompletely extended chains, greatly increasing the frequency of full-length final products. Applying ICA to a model problem, construction of custom transcription activator-like effector nucleases (TALENs) for genome engineering, we demonstrate efficient synthesis of TALE DNA-binding domains up to 21 monomers long and their ligation into a nuclease-carrying backbone vector all within 3 h. We used ICA to synthesize 20 TALENs of varying DNA target site length and tested their ability to stimulate gene editing by a donor oligonucleotide in human cells. All the TALENS show activity, with the ones >15 monomers long tending to work best. Since ICA builds full-length constructs from individual monomers rather than large exhaustive libraries of pre-fabricated oligomers, it will be trivial to incorporate future modified TALE monomers with improved or expanded function or to synthesize other types of repeat-modular DNA where the diversity of possible monomers makes exhaustive oligomer libraries impractical.

(Via Nucleic Acids Research.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:10:24+00:00 http://www.synbio.org.uk/wetware-news/2538-iterative-capped-assembly-rapid-and-scalable-synthesis-of-repeat-module-dna-such-as-tal-effectors-from-individual-monomers.html
Design, implementation and practice of JBEI-ICE: an open source biological part registry ... http://www.synbio.org.uk/wetware-news/2537-design-implementation-and-practice-of-jbei-ice-an-open-source-biological-part-registry-platform-and-tools.html Publication Date: 2012 Jun 19 PMID: 22718978
Authors: Ham, T. S. - Dmytriv, Z. - Plahar, H. - Chen, J. - Hillson, N. J. - Keasling, J. D.
Journal: Nucleic Acids Res

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

(Via Nucleic Acids Research.)

]]>
[email protected] (Jim Haseloff) 2012-07-08T00:06:30+00:00 http://www.synbio.org.uk/wetware-news/2537-design-implementation-and-practice-of-jbei-ice-an-open-source-biological-part-registry-platform-and-tools.html
Glandular trichomes of Ceratotheca triloba (Pedaliaceae): morphology, histochemistry and ... http://www.synbio.org.uk/plant-biology-news/2531-glandular-trichomes-of-ceratotheca-triloba-pedaliaceae-morphology-histochemistry-and-ultrastructure.html Publication Date: 2012 Jun 14 PMID: 22696008
Authors: Naidoo, Y. - Karim, T. - Heneidak, S. - Sadashiva, C. T. - Naidoo, G.
Journal: Planta

This study was initiated to characterize the distribution, morphology, secretion mode, histochemistry and ultrastructure of the glandular trichomes of Ceratotheca triloba using light and electron microscopy. Its leaves bear two morphologically distinct glandular trichomes. The first type has long trichome with 8-12 basal cells of pedestal, 3-14 stalk cells, a neck cell and a head of four cells in one layer. The second type has short trichome comprising one or two basal epidermal cells, a unicellular or bicellular stalk and a multicellular head of two to eight cells. There is a marked circular area in the upper part of each head cell of the long trichome. This area is provided with micropores to exudate directly the secretory product onto the leaf surface by an eccrine pathway. The secretory product has copious amount of dark microbodies arising from plastids which are positive to Sudan tests and osmium tetroxide for unsaturated lipids. The secretion mode of short trichomes is granulocrine and involves two morphologically and histochemically distinct vesicle types: small Golgi-derived vesicles which are positive to Ruthenium Red test for mucilaginous polysaccharides; the second type is dark large microbodies similar to that of long trichomes with low quantity. These two types are stored in numerous peripheral vacuoles and discharge their contents accompanied by the formation of irregular invaginations of the plasmalemma inside the vacuoles via reverse pinocytosis. These two secretion modes of long and short trichomes are reported for the first time in the family Pedaliaceae. The long trichomes have more unsaturated lipids, while the short trichomes contain more mucilaginous polysaccharides.

(Via Planta.)

]]>
[email protected] (Jim Haseloff) 2012-07-07T23:30:42+00:00 http://www.synbio.org.uk/plant-biology-news/2531-glandular-trichomes-of-ceratotheca-triloba-pedaliaceae-morphology-histochemistry-and-ultrastructure.html
Ajinomoto, Bridgestone in bio-isoprene http://www.synbio.org.uk/plant-biology-news/2530-ajinomoto-bridgestone-in-bio-isoprene.html

The race for bio-based synthetic rubber development continues with new players - Japan-based specialty chemical firm Ajinomoto and tire company Bridgestone Corp.  


According to Ajinomoto's press release, the two companies will jointly developed isoprene ( a key chemical intermediate for synthetic rubber manufacture) using biomass for feedstock. The companies have been jointly doing research since June 2011.

Ajinomoto said it has already successfully manufactured bio-isoprene at a laboratory-scale using fermentation process, and that Bridgestone has also succesfully produce polyisoprene rubber using the material.

Ajinomoto and Bridgestone said they plan to decide on the potential for commercialization in 2013. It seems Ajinomoto has been especially active this year in the bio-based chemicals arena such as its partnership with Toray on the development of nylon raw material 1,5 pentanediamine using plant-based amino acid lysine.

Back to isoprene, another tire and rubber company working on bio-based isoprene is Goodyear with its partner DuPont Industrial Biosciences. Goodyear said in March that the two companies have already demonstrated proof of the technology through the production of a prototype tire made with DuPont and Goodyear's BioIsoprene monomer.

The two companies said they expect additional investments to establish pilot plant operations and manufacturing infrastructure. Unfortunately, no timeline has been disclosed.

AND ONE MORE!

European rubber and tire company Michelin is also working with US-based Amyris for the development of bio-isoprene using Amyris' farnesene. Amyris expects to begin commercialization of the bio-isoprene in 2015, with Michelin reportedly committing off-take columes on a ten years basis.

Amyris is also working with Japan chemical firm Kuraray to develop high-polymers by replacing petroleum-based butadiene and isoprene feedstock with Amyris' farnesene molecule.

Other companies working on bio-based chemical feedstock for synthetic rubbers includes:
Glycos Biotechnologies - bio-based isoprene
Aemetis - bio-based isoprene
Genomatica - bio-based butadiene
Global Bioenergies - bio-based butadiene in collaboration with Synthos. Bio-based isobutene (which can be converted to isoprene) in collaboration with LanzaTech.
Elevance - bio-based rubber compounds in collaboration with Hutchinson Worldwide
Gevo - bio-based rubber compounds in collaboration with Lanxess

(Via ICIS Green Chemicals.)

]]>
[email protected] (Jim Haseloff) 2012-07-07T23:19:09+00:00 http://www.synbio.org.uk/plant-biology-news/2530-ajinomoto-bridgestone-in-bio-isoprene.html
TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. http://www.synbio.org.uk/wetware-news/2528-tal-effector-nucleotide-targeter-tale-nt-20-tools-for-tal-effector-design-and-target-prediction.html TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction.: "Publication Date: 2012 Jun 12 PMID: 22693217
Authors: Doyle, E. L. - Booher, N. J. - Standage, D. S. - Voytas, D. F. - Brendel, V. P. - Vandyk, J. K. - Bogdanove, A. J.
Journal: Nucleic Acids Res

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0; https://boglab.plp.iastate.edu/) that enables design of custom TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites, ranked by likelihood, in a genome, promoterome or other sequence of interest. Search parameters can be set by the user to work with any TAL effector or TAL effector nuclease architecture. Applications range from designing highly specific DNA targeting tools and identifying potential off-target sites to predicting effector targets important in plant disease.

(Via Nucleic Acids Research.)

]]>
[email protected] (Jim Haseloff) 2012-07-07T23:14:47+00:00 http://www.synbio.org.uk/wetware-news/2528-tal-effector-nucleotide-targeter-tale-nt-20-tools-for-tal-effector-design-and-target-prediction.html