Showing posts with label Complex Adaptive Systems (CAS). Show all posts
Showing posts with label Complex Adaptive Systems (CAS). Show all posts

Tuesday, 5 February 2013

Squid Communication / "Bacterial Illumination"


piezoeletrico http://www.newtoncbraga.com.br/index.php/como-funciona/4571-art632.html
Bright Squid (bacteria) http://www.cbsnews.com/2100-205_162-592194.html
"The light itself is provided by colonies of luminescent bacteria that live on the squids, the researchers report in Friday's issue of the journal Science." http://www.this-magic-sea.com/COMBACTL.HTM
around "Bacterial Illumination"(in http://www.this-magic-sea.com/COMBACTL.HTM) "Squid Communicate with each other using a wide spectrum of colors and postures. At night they signal with luminescent organs. The squid's luminescent communications result from communications between bacteria living in special light organs. Squid, and a variety of fish, have luminescent bacteria housed in special sacs called light organs. The bacteria generate light with an enzyme called luciferase - but not all the time. When the bacteria Vibrio fischeri swim free in sea water, their population densities are very low and they do not produce light. When they inhabit the light organs of squid, however, the squid cells nurture the bacteria and their populations soar to high levels. When the bacteria are packed tight, they begin to secrete messenger proteins called autoinducer. As this reaches a critical level, it enters the bacteria and activates a protein called LuxR. Activated LuxR stimulates the bacterial genes to produce the light producing proteins luciferin, luciferase and associated light producing proteins. The genes are stimulated to produce additional autoinducer messengers and these are released from the bacteria. The additional production of autoinducer messengers, triggered by the active LuxR, stimulate another round of protein synthesis. This positive feedback loop results in rapid production of light producing proteins. When these proteins reach a critical density, they react with each other to liberate that delightfully eerie blue phosphorescence of the sea."
As any squid knows, visual communication is a wonderful way to convey a message. It has a major downside, though; predators can tune in to the broadcast just as readily as the intended recipients (other squid) can. A recent study by Lydia M. Mäthger and Roger T. Hanlon, both biologists at the Marine Biological Laboratory in Woods Hole, Massachusetts, suggests that squid—and most likely their close relatives, cuttlefish and octopuses—have evolved a secret communication channel to which their predators are oblivious. Squid, cuttlefish, and octopuses are known for their ability to change their skin color in a spectacular way. They can blend instantly into the background or produce a startling array of patterns and hues to express their physiological or motivational state. The secret to the show is the two distinct layers of cephalopod skin: The inner layer of iridophore cells is both iridescent and reflects polarized light. The outer layer is made up of pigmented organs, or chromatophores, which expand or contract to help change the color or pattern of the skin. Cuttlefish, octopuses, and squid have a visual system to match the complexity of their skin. Unlike their vertebrate predators, they can detect differences in polarized light. Mäthger and Hanlon discovered that the two skin layers work independently, and that by taking advantage of the reflective properties of the iridophores, squid may be able to communicate with other squid via polarized light. At the same time, the squid can camouflage themselves from predators by altering the color pattern in the chromatophore layer, through which polarized light travels freely. What happens among squid stays among squid!" http://www.tonmo.com/forums/showthread.php?8667-Secret-squid-communication

Saturday, 15 September 2012

self-organizing maps


http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=3105762_ismej2010180f1.jpg http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105762/ ISME J. 2011 May; 5(5): 918–928. Published online 2010 December 16. doi: 10.1038/ismej.2010.180 PMCID: PMC3105762 Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics Marc Weber,1 Hanno Teeling,1,* Sixing Huang,1 Jost Waldmann,1,2 Mariette Kassabgy,1 Bernhard M Fuchs,1 Anna Klindworth,1 Christine Klockow,1,3 Antje Wichels,4 Gunnar Gerdts,4 Rudolf Amann,1 and Frank Oliver Glöckner1,3 Author information ► Article notes ► Copyright and License information ► This article has been cited by other articles in PMC. Abstract Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion. Keywords: binning, metagenomics, molecular ecology, self-organizing map (SOM), taxonomic classification, TaxSOM