Intelligence Engineered

son of mafia and son of hashish

2011-08-18T04:59:00.000-07:00

what does son of mafia (mason-america) and son of hashish(turk) do ?

hashish (piç mit, turkish intelligence) creates spies to steal the secret addresses of secret centers in america. just click on links about human brain to computer memory or quantum research and you will be chosen a spy (someone to be killed and fucked up) without your permission.

son of hashish sends you to america to steal addresses and son of mafia fucks you on your way.

matrix is not a movie. they have built a system. there are no nails in your brain. there are only nanoparticle stimulators. these can make you talk, get angry make accidents, steal, kill.

masons and mit work together. mit fucks you and sends you to steal and masons fuck you not to steal. CROSS FİRE ATTACK.

to be edited..

son of mafia and son of piç

2011-08-17T07:04:00.000-07:00

have attached another process.
REJECTED !
SA

500 years old jedi trickSS wont work

2011-08-17T06:37:00.001-07:00

bloody equation and how to fuck it and google likes ME

2011-08-17T06:34:00.000-07:00

keh keh dedi telefonda ve öldü

2011-06-21T10:03:00.001-07:00

Telefonda keh keh diyen adam havaya uçtu. Dadin telefonundan yayın yapan adam havaya uçtu.

i will kill you if you talk, stop you talking mirror !

2011-06-01T03:45:00.001-07:00

i will kill you if you talk, stop you talking mirror !

Neurobiologists Find that Weak Electrical Fields in the Brain Help Neurons Fire Together

2011-02-08T09:26:00.000-08:00

ShareThis02/02/1102/05/11
Neurobiologists Find that Weak Electrical Fields in the Brain Help Neurons Fire Together
Coordinated behavior occurs whether or not neurons are actually connected via synapsesPasadena, Calif.—The brain—awake and sleeping—is awash in electrical activity, and not just from the individual pings of single neurons communicating with each other. In fact, the brain is enveloped in countless overlapping electric fields, generated by the neural circuits of scores of communicating neurons. The fields were once thought to be an "epiphenomenon" similar to the sound the heart makes—which is useful to the cardiologist diagnosing a faulty heart beat, but doesn't serve any purpose to the body, says Christof Koch, the Lois and Victor Troendle Professor of Cognitive and Behavioral Biology and professor of computation and neural systems at the California Institute of Technology (Caltech).

New work by Koch and neuroscientist Costas Anastassiou, a postdoctoral scholar in biology, and his colleagues, however, suggests that the fields do much more—and that they may, in fact, represent an additional form of neural communication.

"In other words," says Anastassiou, the lead author of a paper about the work appearing in the journal Nature Neuroscience, "while active neurons give rise to extracellular fields, the same fields feed back to the neurons and alter their behavior," even though the neurons are not physically connected—a phenomenon known as ephaptic (or field) coupling. "So far, neural communication has been thought to occur almost entirely via traffic involving synapses, the junctions where one neuron connects to the next one. Our work suggests an additional means of neural communication through the extracellular space independent of synapses."

Ephaptic coupling leads to coordinated spiking of nearby neurons, as measured using a 12-pipette electrophysiology setup developed in the laboratory of coauthor Henry Markram.
[Credit: Image from Figure 4 in Anastassiou et.,Nature Neuroscience, 2011]Extracellular electric fields exist throughout the living brain. Their distant echoes can be measured outside the skull as EEG waves. These fields are particularly strong and robustly repetitive in specific brain regions such as the hippocampus, which is involved in memory formation, and the neocortex, the area where long-term memories are held. "The perpetual fluctuations of these extracellular fields are the hallmark of the living and behaving brain in all organisms, and their absence is a strong indicator of a deeply comatose, or even dead, brain," Anastassiou explains.

Previously, neurobiologists assumed that the fields were capable of affecting—and even controlling—neural activity only during severe pathological conditions such as epileptic seizures, which induce very strong fields. Few studies, however, had actually assessed the impact of far weaker—but very common—non-epileptic fields. "The reason is simple," Anastassiou says. "It is very hard to conduct an in vivo experiment in the absence of extracellular fields," to observe what changes when the fields are not around.

To tease out those effects, Anastassiou and his colleagues focused on strong but slowly oscillating fields, called local field potentials (LFP), that arise from neural circuits composed of just a few rat brain cells. Measuring those fields and their effects required positioning a cluster of tiny electrodes within a volume equivalent to that of a single cell body—and at distances of less than 50 millionths of a meter from one another; this is approximately the width of a human hair.

"Because it had been so hard to position that many electrodes within such a small volume of brain tissue, the findings of our research are truly novel," Anastassiou says. Previously, he explains, "nobody had been able to attain this level of spatial and temporal resolution."

An "unexpected and surprising finding was how already very weak extracellular fields can alter neural activity," he says. "For example, we observed that fields as weak as one volt per meter robustly alter the spiking activity [firing] of individual neurons, and increase the so-called 'spike-field coherence'"—the synchronicity with which neurons fire. "Inside the mammalian brain, we know that extracellular fields may easily exceed two to three volts per meter. Our findings suggest that under such conditions, this effect becomes significant."

What does that mean for brain computation? At this point we can only speculate, Koch says, "but such field effects increase the synchrony with which neurons become active together. This, by itself, enhances the ability of these neurons to influence their target and is probably an important communication and computation strategy used by the brain."

Can external electric fields have similar effects on the brain? "This is an interesting question," Anastassiou says. "Indeed, physics dictates that any external field will impact the neural membrane. Importantly, though, the effect of externally imposed fields will also depend on the brain state. One could think of the brain as a distributed computer—not all brain areas show the same level of activation at all times.

"Whether an externally imposed field will impact the brain also depends on which brain area is targeted," he says. "During epileptic seizures, the hypersynchronized activity of neurons can generate field as strong as 100 volts per meter, and such fields have been shown to strongly entrain neural firing and give rise to super-synchronized states." And that suggests that electric field activity—even from external fields—in certain brain areas, during specific brain states, may have strong cognitive and behavioral effects.

Ultimately, Anastassiou, Koch, and their colleagues would like to test whether ephaptic coupling affects human cognitive processing, and under which circumstances. "I firmly believe that understanding the origin and functionality of endogenous brain fields will lead to several revelations regarding information processing at the circuit level, which, in my opinion, is the level at which percepts and concepts arise," Anastassiou says. "This, in turn, will lead us to address how biophysics gives rise to cognition in a mechanistic manner—and that, I think, is the holy grail of neuroscience."

The work in the paper, "Ephaptic coupling of cortical neurons," published January 16 in the advance online edition of the journal, was supported by the Engineering Physical Sciences Research Council, the Sloan-Swartz Foundation, the Swiss National Science Foundation, EU Synapse, the National Science Foundation, the Mathers Foundation, and the National Research Foundation of Korea.

Written by Kathy Svitil
Deborah Williams-Hedges
626-395-3227
debwms@caltech.edu
http://media.caltech.edu/press_releases/13401

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SOURCE: http://media.caltech.edu/press_releases/13401

Brain's complexity 'is beyond anything imagined'

2011-01-18T09:02:00.000-08:00

Brain's complexity 'is beyond anything imagined'
18.01.2011
By Brian Thomas, M.S.
The brain has for a long time been compared to man-made computers in its astounding ability to process, store, and route information. But a new imaging technique has revealed that just one brain's connections and capacities far outnumber and outpace those of all the world's computers. And this makes the question of the origin of brains that much more difficult for naturalistic explanations.

The imaging technique, called array tomography, detected light emitted by mouse nervous tissue that had been bioengineered to produce proteins that glow. Additional luminous chemicals were added, and these attached to specific areas in the mouse brains, adding more colors and allowing for the detection of much more information.

New computer software processed all the data to produce stunning three-dimensional images of never-before-seen brain cell connections. A study was published in the journal Neuron to showcase the usefulness of array tomography, but the technical paper also provided broad implications for neurobiology.

Array tomography could "resolve fine details at the level of synapses," allowing researchers to view the highest resolution of detail among nerve images yet. They could see individual synapses, the tiny connection points that link nerve cells together, as well as their different types and subtypes.

0
SharePrint version Font Size Send to friend"[The researchers] found that the brain's complexity is beyond anything they'd imagined," according to an article appearing in the Health Tech section of the online news source CNET. For instance, they found that the total number of synapses in a brain roughly equaled the number of stars in 1,500 Milky Way galaxies! And memory patterns and tiny on/off switches, which were long thought to reside in the larger neuron cell bodies, were instead found to be smaller than the tiny synapse connections. Each of the neurons imaged in the study serves thousands of synapses.

Stanford University professor and senior study author Stephen Smith said that "one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth." This research multiplies the brain's overall computing power far beyond what was previously known.

The more complicated a system is, the stronger it argues for having been intentionally designed. And brains certainly qualify, despite assertions that random-acting natural processes somehow assembled them. In these cases, the burden of proof lies heavily on those who insist that such systems are not in fact what they plainly appear to be: the products of intentional ingenious design.

The God of the Bible stands as the most tenable source of the specified complexity of interconnected neurons upon which human and much animal life depends. Until a naturalistic alternative can explain how a self-healing, adaptive, cosmic-sized internet of connectivity has been shrunk down to the size of a brain, then it is best to identify this hyper-tech design as being the product of a real Designer. And until an objective body of evidence can legitimately debunk the Bible's historicity and proven accuracy, then it is best to identify this Designer as the Creator and Sustainer revealed in Scripture.

Brian Thomas
Institute for Creation Research

Copyright © [2011] Institute for Creation Research. Reprinted by permission.
http://english.pravda.ru/science/mysteries/18-01-2011/116557-brain-0/

Gene therapy From Wikipedia, the free encyclopedia

2010-12-11T11:31:00.000-08:00

http://en.wikipedia.org/wiki/Gene_therapy

Scientists Decode Memory-Forming Brain Cell Conversations

2010-12-01T12:23:00.000-08:00

http://www.sciencedaily.com/releases/2009/12/091215202322.htm

Scientists Decode Memory-Forming Brain Cell Conversations

ScienceDaily (Dec. 16, 2009) — The conversations neurons have as they form and recall memories have been decoded by Medical College of Georgia scientists.

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The breakthrough in recognizing in real time the formation and recollection of a memory opens the door to objective, thorough memory studies and eventually better therapies, said Dr. Joe Tsien, neuroscientist and co-director of MCG's Brain & Behavior Discovery Institute. He is corresponding author on the study published Dec. 16 inPLoS ONE.

"It's a beginning, a first glimpse of a memory," Dr. Tsien said. "For the first time it gives us the ability to look at the brain dynamic and tell what kind of memory is formed, what are the components of the memory and how the memory is retrieved at the network level." The finding could help pinpoint at what stage memory formation is flawed and whether drugs are improving it.

For their studies, MCG scientists combined new technology and computational methods with century-old Pavlovian conditioning.

In the memory center of the brain, they used 128 electrodes capable of monitoring a handful of neurons each to simultaneously record the conversations of 200 to 300 neurons as mice learned to associate a certain tone with a mild foot shock 20 seconds later.

A computational algorithm translated the neuronal chatter into a discernable and dynamic activity pattern that provided scientists a trace or picture of what the memory looked like as it was formed and recalled.

"By listening to the neuronal activity we were able to decipher the real-time dynamic pattern and the meaning of those conversations so this is really satisfying," said Dr. Tsien, the Georgia Research Alliance Eminent Scholar in Cognitive and Systems Neurobiology.

The trace changed slightly each time it was recalled -- likely as the mood or situation of the rodent changed -- but still remained recognizable as a specific memory.

The scientists later correlated retrieval of the memory with the mice's actions, such as freezing upon hearing the tone or returning to the chamber where the foot shock occurred. They found the traces tightly correlated with memory scores: the mice that had lower scores predictably had a fainter trace and those with stronger traces had better behavioral performance, such as freezing in anticipation of a shock. "At the behavioral level he is just frozen, but with this technique of decoding the real-time memory, it will tell you exactly what he is thinking," Dr. Tsien said.

As expected, when mice were returned one hour later to the chamber where conditioning took place, they repeatedly froze, on average, 1.4 seconds after the recall pattern emerged in the brain. When placed in a setting with no history of the foot shock, the mice would freeze after they heard the tone.

One of the most surprising findings was that the memory trace of the foot shock was the sole memory that emerged in their brains 20 seconds after hearing the tone: just when the mild shock would have followed. "You think we are the only ones that can tell time?" Dr. Tsien said of this unexpected evidence of memory of time.

Problems with memory, the most fundamental cognitive function, can occur at any level -- learning, consolidating, storing or retrieving. The ability to watch memories being made in real time should help pinpoint where problems lie, enabling more targeted research and eventual treatment, Dr. Tsien said.

"If you don't know the basic biomarkers such as blood glucose or insulin level, it's hard to assess and study diabetes. Without knowing what memory traces are, you really don't have the precise physiological biomarkers to study memory and to reliably evaluate the effectiveness of treatment of memory disorders. We all know that behavior can be quite misleading sometime." The ability to tell what memory is produced and how good that memory is could also dramatically shape development of machines that are controlled directly by the mind, rather than those using hands as an intermediary, he noted.

Studies were done in the CA1 region of the hippocampus, a well-documented center for forming associative memories. Similar tests are needed in other memory regions, Dr. Tsien said.

Related technology is already advancing patient care. For instance, primate studies of essential motor neuron connections are advancing the development of mind-controlled prosthetic limbs and electrodes can help identify where seizures originate. But it will take time and improved non-invasive recording technology before Dr. Tsien's memory tests can be done on humans.

Dr. Guifen Chen, former MCG postdoctoral fellow, is first author on the paper, and Dr. L. Phillip Wang, MCG research scientist, is a co-author. The research was funded by the National Institutes of Health and the Georgia Research Alliance.

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

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Medical College of Georgia, via EurekAlert!, a service of AAAS.

Journal Reference:

Guifen Chen, L. Phillip Wang, Joe Z. Tsien. Neural Population-Level Memory Traces in the Mouse Hippocampus. PLoS ONE, 2009; DOI:10.1371/journal.pone.0008256

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Coliphage phi-X174, complete genome

2010-12-01T10:25:00.001-08:00

http://www.ncbi.nlm.nih.gov/nuccore/J02482

http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb2_3.html

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Coliphage phi-X174, complete genome

GenBank: J02482.1

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LOCUS       PX1CG                   5386 bp ss-DNA     circular PHG 16-JUN-2004 DEFINITION  Coliphage phi-X174, complete genome. ACCESSION   J02482 M10348 M10379 M10714 M10749 M10750 M10866 M10867 M24859             V01128 VERSION     J02482.1  GI:216019 KEYWORDS    . SOURCE      Enterobacteria phage phiX174   ORGANISM  Enterobacteria phage phiX174             Viruses; ssDNA viruses; Microviridae; Microvirus. REFERENCE   1  (bases 1047 to 1094)   AUTHORS   Ziff,E.B., Sedat,J.W. and Galibert,F.   TITLE     Determination of the nucleotide sequence of a fragment of             bacteriophage phiX 174 DNA   JOURNAL   Nature New Biol. 241 (106), 34-37 (1973)    PUBMED   4349156 REFERENCE   2  (bases 2370 to 2421)   AUTHORS   Robertson,H.D., Barrell,B.G., Weith,H.L. and Donelson,J.E.   TITLE     Isolation and sequence analysis of a ribosome-protected fragment             from bacteriophage phiX 174 DNA   JOURNAL   Nature New Biol. 241 (106), 38-40 (1973)    PUBMED   4572838 REFERENCE   3  (bases 2370 to 2420)   AUTHORS   Barrell,B.G., Weith,H.L., Donelson,J.E. and Robertson,H.D.   TITLE     Sequence analysis of the ribosome-protected bacteriophase phiX174             DNA fragment containing the gene G initiation site   JOURNAL   J. Mol. Biol. 92 (3), 377-393 (1975)    PUBMED   1095758 REFERENCE   4  (bases 2365 to 2591)   AUTHORS   Air,G.M., Blackburn,E.H., Sanger,F. and Coulson,A.R.   TITLE     The nucleotide and amino acid sequences of the N (5') terminal             region of gene G of bacteriophage phiphiX 174   JOURNAL   J. Mol. Biol. 96 (4), 703-719 (1975)    PUBMED   1081600 REFERENCE   5  (bases 2263 to 2421)   AUTHORS   Fiddes,J.C.   TITLE     Nucleotide sequence of the intercistronic region between genes G             and F in bacteriophage phiX174 DNA   JOURNAL   J. Mol. Biol. 107 (1), 1-24 (1976)    PUBMED   826639 REFERENCE   6  (bases 1017 to 1081)   AUTHORS   Sedat,J., Ziff,E. and Galibert,F.   TITLE     Direct determination of DNA nucleotide sequences. Structure of             large specific fragments of bacteriophage phiX174 DNA   JOURNAL   J. Mol. Biol. 107 (4), 391-416 (1976)    PUBMED   1003475 REFERENCE   7  (bases 730 to 903)   AUTHORS   Blackburn,E.H.   TITLE     Transcription and sequence analysis of a fragment of bacteriophage             phiX174 DNA   JOURNAL   J. Mol. Biol. 107 (4), 417-431 (1976)    PUBMED   826641 REFERENCE   8  (bases 1017 to 1762)   AUTHORS   Air,G.M., Blackburn,E.H., Coulson,A.R., Galibert,F., Sanger,F.,             Sedat,J.W. and Ziff,E.B.   TITLE     Gene F of bacteriophage phiX174. Correlation of nucleotide             sequences from the DNA and amino acid sequences from the gene             product   JOURNAL   J. Mol. Biol. 107 (4), 445-458 (1976)    PUBMED   1088826 REFERENCE   9  (bases 2395 to 2922)   AUTHORS   Air,G.M., Sanger,F. and Coulson,A.R.   TITLE     Nucleotide and amino acid sequences of gene G of omegaX174   JOURNAL   J. Mol. Biol. 108 (3), 519-533 (1976)    PUBMED   1088827 REFERENCE   10 (bases 4137 to 4207)   AUTHORS   Mansfeld,A.D., Vereijken,J.M. and Jansz,H.S.   TITLE     The nucleotide sequence of a DNA fragment, 71 base pairs in length,             near the origin of DNA replication of bacteriophage 0X174   JOURNAL   Nucleic Acids Res. 3 (10), 2827-2844 (1976)    PUBMED   995652 REFERENCE   11 (bases 4505 to 5374)   AUTHORS   Brown,N.L. and Smith,M.   TITLE     The sequence of a region of bacteriophage phiX174 DNA coding for             parts of genes A and B   JOURNAL   J. Mol. Biol. 116 (1), 1-28 (1977)    PUBMED   592379 REFERENCE   12 (bases 1 to 5375)   AUTHORS   Sanger,F., Air,G.M., Barrell,B.G., Brown,N.L., Coulson,A.R.,             Fiddes,C.A., Hutchison,C.A., Slocombe,P.M. and Smith,M.   TITLE     Nucleotide sequence of bacteriophage phi X174 DNA   JOURNAL   Nature 265 (5596), 687-695 (1977)    PUBMED   870828 REFERENCE   13 (bases 5022 to 5132)   AUTHORS   Brown,N.L. and Smith,M.   TITLE     DNA sequence of a region of the phi X174 genome coding for a             ribosome binding site   JOURNAL   Nature 265 (5596), 695-698 (1977)    PUBMED   859573 REFERENCE   14 (bases 5346 to 5386; 1 to 159)   AUTHORS   Smith,M., Brown,N.L., Air,G.M., Barrell,B.G., Coulson,A.R.,             Hutchison,C.A. III and Sanger,F.   TITLE     DNA sequence at the C termini of the overlapping genes A and B in             bacteriophage phi X174   JOURNAL   Nature 265 (5596), 702-705 (1977)    PUBMED   859575 REFERENCE   15 (sites)   AUTHORS   Fiddes,J.C.   TITLE     The nucleotide sequence of a viral DNA   JOURNAL   Sci. Am. 237 (6), 54-67 (1977)    PUBMED   929160 REFERENCE   16 (bases 1 to 5386)   AUTHORS   Sanger,F., Coulson,A.R., Friedmann,T., Air,G.M., Barrell,B.G.,             Brown,N.L., Fiddes,J.C., Hutchison,C.A. III, Slocombe,P.M. and             Smith,M.   TITLE     The nucleotide sequence of bacteriophage phiX174   JOURNAL   J. Mol. Biol. 125 (2), 225-246 (1978)    PUBMED   731693 REFERENCE   17 (bases 1290 to 1302; 1340 to 1430; 1510 to 1570; 1600 to 1750)   AUTHORS   Air,G.M., Coulson,A.R., Fiddes,J.C., Friedmann,T., Hutchison,C.A.             III, Sanger,F., Slocombe,P.M. and Smith,A.J.   TITLE     Nucleotide sequence of the F protein coding region of bacteriophage             phiX174 and the amino acid sequence of its product   JOURNAL   J. Mol. Biol. 125 (2), 247-254 (1978)    PUBMED   731694 REFERENCE   18 (bases 4256 to 4317)   AUTHORS   Langeveld,S.A., van Mansfeld,A.D., de Winter,J.M. and Weisbeek,P.J.   TITLE     Cleavage of single-stranded DNA by the A and A* proteins of             bacteriophage phi X174   JOURNAL   Nucleic Acids Res. 7 (8), 2177-2188 (1979)    PUBMED   160544 REFERENCE   19 (bases 4248 to 4332)   AUTHORS   Heidekamp,F., Langeveld,S.A., Baas,P.D. and Jansz,H.S.   TITLE     Studies of the recognition sequence of phi X174 gene A protein.             Cleavage site of phi X gene A protein in St-1 RFI DNA   JOURNAL   Nucleic Acids Res. 8 (9), 2009-2021 (1980)    PUBMED   6253953 REFERENCE   20 (bases 436 to 490; 630 to 669; 930 to 979)   AUTHORS   Takeshita,M., Kappen,L.S., Grollman,A.P., Eisenberg,M. and             Goldberg,I.H.   TITLE     Strand scission of deoxyribonucleic acid by neocarzinostatin,             auromomycin, and bleomycin: studies on base release and nucleotide             sequence specificity   JOURNAL   Biochemistry 20 (26), 7599-7606 (1981)    PUBMED   6173064 REFERENCE   22 (bases 1064 to 1757)   AUTHORS   Merville,M.P., Piette,J., Lopez,M., Decuyper,J. and van de Vorst,A.   TITLE     Termination sites of the in vitro DNA synthesis on single-stranded             DNA photosensitized by promazines   JOURNAL   J. Biol. Chem. 259 (24), 15069-15077 (1984)    PUBMED   6239864 REFERENCE   23 (bases 2380 to 2512; 2593 to 2786; 2788 to 2947)   AUTHORS   Air,G.M., Els,M.C., Brown,L.E., Laver,W.G. and Webster,R.G.   TITLE     Location of antigenic sites on the three-dimensional structure of             the influenza N2 virus neuraminidase   JOURNAL   Virology 145 (2), 237-248 (1985)    PUBMED   2411049 REFERENCE   24 (bases 449 to 482; 504 to 598; 1047 to 1111)   AUTHORS   Ueda,K., Morita,J. and Komano,T.   TITLE     Sequence specificity of heat-labile sites in DNA induced by             mitomycin C   JOURNAL   Biochemistry 23 (8), 1634-1640 (1984)    PUBMED   6232949 COMMENT     On Apr 28, 2004 this sequence version replaced gi:15535.             [8]  intermittent sequences.             [15]  review; discussion of complete genome.             Double checked with sumex tape.             Single-stranded circular DNA which codes for eleven proteins.             Replicative form is duplex, icosahedron, related to s13 & g4. [21]             indicates that mitomycin C reduced with sodium borohydride induced             heat-labile sites in DNA most preferentially at dinucleotide             sequence 'gt' (especially 'Pu-g-t').             Bacteriophage phi-X174 single stranded DNA molecules were             irradiated with near UV light in the presence of promazine             derivatives, after priming with restriction fragments or synthetic             primers [22].  The resulting DNA fragments were used as templates             for in vitro complementary chain synthesis by E.coli DNA polymerase             I [22].  More than 90% of the observed chain terminations were             mapped one nucleotide before a guanine residue [22].  Photoreaction             occurred more predominantly with guanine residues localized in             single-stranded parts of the genome [22].  These same guanine             residues could also be damaged when the reaction was performed in             the dark, in the presence of promazine cation radicals [22]. FEATURES             Location/Qualifiers      source          1..5386                      /organism="Enterobacteria phage phiX174"                      /mol_type="genomic DNA"                      /db_xref="taxon:10847"      CDS             join(3981..5386,1..136)                      /function="viral strand synthesis"                      /note="rf replication"                      /codon_start=1                      /transl_table=11                      /product="A"                      /protein_id="AAA32570.1"                      /db_xref="GI:216020"                      /translation="MVRSYYPSECHADYFDFERIEALKPAIEACGISTLSQSPMLGFH                      KQMDNRIKLLEEILSFRMQGVEFDNGDMYVDGHKAASDVRDEFVSVTEKLMDELAQCY                      NVLPQLDINNTIDHRPEGDEKWFLENEKTVTQFCRKLAAERPLKDIRDEYNYPKKKGI                      KDECSRLLEASTMKSRRGFAIQRLMNAMRQAHADGWFIVFDTLTLADDRLEAFYDNPN                      ALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRLHFHAVHFMRTLPTG                      SVDPNFGRRVRNRRQLNSLQNTWPYGYSMPIAVRYTQDAFSRSGWLWPVDAKGEPLKA                      TSYMAVGFYVAKYVNKKSDMDLAAKGLGAKEWNNSLKTKLSLLPKKLFRIRMSRNFGM                      KMLTMTNLSTECLIQLTKLGYDATPFNQILKQNAKREMRLRLGKVTVADVLAAQPVTT                      NLLKFMRASIKMIGVSNLQSFIASMTQKLTLSDISDESKNYLDKAGITTACLRIKSKW                      TAGGK"      CDS             join(4497..5386,1..136)                      /function="shut off host DNA synthesis"                      /codon_start=1                      /transl_table=11                      /product="A*"                      /protein_id="AAA32571.1"                      /db_xref="GI:216021"                      /translation="MKSRRGFAIQRLMNAMRQAHADGWFIVFDTLTLADDRLEAFYDN                      PNALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRLHFHAVHFMRTLP                      TGSVDPNFGRRVRNRRQLNSLQNTWPYGYSMPIAVRYTQDAFSRSGWLWPVDAKGEPL                      KATSYMAVGFYVAKYVNKKSDMDLAAKGLGAKEWNNSLKTKLSLLPKKLFRIRMSRNF                      GMKMLTMTNLSTECLIQLTKLGYDATPFNQILKQNAKREMRLRLGKVTVADVLAAQPV                      TTNLLKFMRASIKMIGVSNLQSFIASMTQKLTLSDISDESKNYLDKAGITTACLRIKS                      KWTAGGK"      CDS             join(5075..5386,1..51)                      /function="capsid morphogenesis"                      /codon_start=1                      /transl_table=11                      /product="B"                      /protein_id="AAA32572.1"                      /db_xref="GI:216022"                      /translation="MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTY                      QAGLRRDAVQPDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQ                      PAEFYRFHDAEVNTFGYF"      variation       23                      /note="in am18 and am35 [14]"                      /replace="t"      variation       25                      /note="ts116 [14]"                      /replace="c"      CDS             51..221                      /codon_start=1                      /transl_table=11                      /product="K"                      /protein_id="AAA32573.1"                      /db_xref="GI:216023"                      /translation="MSRKIILIKQELLLLVYELNRSGLLAENEKIRPILAQLEKLLLC                      DLSPSTNDSVKN"      variation       57                      /note="am6 [14]"                      /replace="c"      variation       117                      /note="am6 [14]"                      /replace="a"      CDS             133..393                      /note="DNA maturation"                      /codon_start=1                      /transl_table=11                      /product="C"                      /protein_id="AAA32574.1"                      /db_xref="GI:216024"                      /translation="MRKFDLSLRSSRSSYFATFRHQLTILSKTDALDEEKWLNMLGTF                      VKDWFRYESHFVHGRDSLVDILKERGLLSESDAVQPLIGKKS"      mRNA            358..3975                      /product="major transcript"      mRNA            358..991                      /product="minor transcript"      CDS             390..848                      /function="capsid morphogenesis"                      /codon_start=1                      /transl_table=11                      /product="D"                      /protein_id="AAA32575.1"                      /db_xref="GI:216025"                      /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI                      ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE                      FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"      CDS             568..843                      /function="cell lysis"                      /codon_start=1                      /transl_table=11                      /product="E"                      /protein_id="AAA32576.1"                      /db_xref="GI:216026"                      /translation="MVRWTLWDTLAFLLLLSLLLPSLLIMFIPSTFKRPVSSWKALNL                      RKTLLMASSVRLKPLNCSRLPCVYAQETLTFLLTQKKTCVKNYVRKE"      CDS             848..964                      /note="core protein; DNA condensation"                      /codon_start=1                      /transl_table=11                      /product="J"                      /protein_id="AAA32577.1"                      /db_xref="GI:216027"                      /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF"      CDS             1001..2284                      /note="major coat protein"                      /codon_start=1                      /transl_table=11                      /product="F"                      /protein_id="AAA32578.1"                      /db_xref="GI:216028"                      /translation="MSNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEM                      DAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTG                      YIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARYG                      FRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHD                      VISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRF                      FVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDV                      FRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYD                      QCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS"      CDS             2395..2922                      /note="major spike protein"                      /codon_start=1                      /transl_table=11                      /product="G"                      /protein_id="AAA32579.1"                      /db_xref="GI:216029"                      /translation="MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYF                      DSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTT                      LPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVS                      LNQVIKEIICLQPLK"      CDS             2931..3917                      /function="adsorption"                      /note="minor spike protein"                      /codon_start=1                      /transl_table=11                      /product="H"                      /protein_id="AAA32580.1"                      /db_xref="GI:216030"                      /translation="MFGAIAGGIASALAGGAMSKLFGGGQKAASGGIQGDVLATDNNT                      VGMGDAGIKSAIQGSNVPNPDEAAPSFVSGAMAKAGKGLLEGTLQAGTSAVSDKLLDL                      VGLGGKSAADKGKDTRDYLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLD                      NQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTN                      LSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHI                      GATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK"      misc_feature    3962                      /note="transcription start site"      rep_origin      4306                      /note="origin of viral strand synthesis"      misc_feature    4899                      /note="transcription start site" ORIGIN               1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa        61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac       121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt       181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag       241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt       301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc tgagtccgat       361 gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa tccgtacgtt       421 tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg gatttaaccg       481 aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac cgctctcgtg       541 ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga taccctcgct       601 ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat cccgtcaaca       661 ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt attaatggcg       721 tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta cgcgcaggaa       781 acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt gcggaaggag       841 tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc cgcagccgtt       901 gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg gtcaacaatt       961 ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata ttcaaactgg      1021 cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc agattggtcg      1081 tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga tggacgccgt      1141 tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta ctgtagacat      1201 ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta agttcatgaa      1261 ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata ttgaccatgc      1321 cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt tgtttcaggg      1381 ttatttgaat atctataaca actattttaa agcgccgtgg atgcctgacc gtaccgaggc      1441 taaccctaat gagcttaatc aagatgatgc tcgttatggt ttccgttgct gccatctcaa      1501 aaacatttgg actgctccgc ttcctcctga gactgagctt tctcgccaaa tgacgacttc      1561 taccacatct attgacatta tgggtctgca agctgcttat gctaatttgc atactgacca      1621 agaacgtgat tacttcatgc agcgttacca tgatgttatt tcttcatttg gaggtaaaac      1681 ctcttatgac gctgacaacc gtcctttact tgtcatgcgc tctaatctct gggcatctgg      1741 ctatgatgtt gatggaactg accaaacgtc gttaggccag ttttctggtc gtgttcaaca      1801 gacctataaa cattctgtgc cgcgtttctt tgttcctgag catggcacta tgtttactct      1861 tgcgcttgtt cgttttccgc ctactgcgac taaagagatt cagtacctta acgctaaagg      1921 tgctttgact tataccgata ttgctggcga ccctgttttg tatggcaact tgccgccgcg      1981 tgaaatttct atgaaggatg ttttccgttc tggtgattcg tctaagaagt ttaagattgc      2041 tgagggtcag tggtatcgtt atgcgccttc gtatgtttct cctgcttatc accttcttga      2101 aggcttccca ttcattcagg aaccgccttc tggtgatttg caagaacgcg tacttattcg      2161 ccaccatgat tatgaccagt gtttccagtc cgttcagttg ttgcagtgga atagtcaggt      2221 taaatttaat gtgaccgttt atcgcaatct gccgaccact cgcgattcaa tcatgacttc      2281 gtgataaaag attgagtgtg aggttataac gccgaagcgg taaaaatttt aatttttgcc      2341 gctgaggggt tgaccaagcg aagcgcggta ggttttctgc ttaggagttt aatcatgttt      2401 cagactttta tttctcgcca taattcaaac tttttttctg ataagctggt tctcacttct      2461 gttactccag cttcttcggc acctgtttta cagacaccta aagctacatc gtcaacgtta      2521 tattttgata gtttgacggt taatgctggt aatggtggtt ttcttcattg cattcagatg      2581 gatacatctg tcaacgccgc taatcaggtt gtttctgttg gtgctgatat tgcttttgat      2641 gccgacccta aattttttgc ctgtttggtt cgctttgagt cttcttcggt tccgactacc      2701 ctcccgactg cctatgatgt ttatcctttg aatggtcgcc atgatggtgg ttattatacc      2761 gtcaaggact gtgtgactat tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt      2821 ggtttcatgg tttggtctaa ctttaccgct actaaatgcc gcggattggt ttcgctgaat      2881 caggttatta aagagattat ttgtctccag ccacttaagt gaggtgattt atgtttggtg      2941 ctattgctgg cggtattgct tctgctcttg ctggtggcgc catgtctaaa ttgtttggag      3001 gcggtcaaaa agccgcctcc ggtggcattc aaggtgatgt gcttgctacc gataacaata      3061 ctgtaggcat gggtgatgct ggtattaaat ctgccattca aggctctaat gttcctaacc      3121 ctgatgaggc cgcccctagt tttgtttctg gtgctatggc taaagctggt aaaggacttc      3181 ttgaaggtac gttgcaggct ggcacttctg ccgtttctga taagttgctt gatttggttg      3241 gacttggtgg caagtctgcc gctgataaag gaaaggatac tcgtgattat cttgctgctg      3301 catttcctga gcttaatgct tgggagcgtg ctggtgctga tgcttcctct gctggtatgg      3361 ttgacgccgg atttgagaat caaaaagagc ttactaaaat gcaactggac aatcagaaag      3421 agattgccga gatgcaaaat gagactcaaa aagagattgc tggcattcag tcggcgactt      3481 cacgccagaa tacgaaagac caggtatatg cacaaaatga gatgcttgct tatcaacaga      3541 aggagtctac tgctcgcgtt gcgtctatta tggaaaacac caatctttcc aagcaacagc      3601 aggtttccga gattatgcgc caaatgctta ctcaagctca aacggctggt cagtatttta      3661 ccaatgacca aatcaaagaa atgactcgca aggttagtgc tgaggttgac ttagttcatc      3721 agcaaacgca gaatcagcgg tatggctctt ctcatattgg cgctactgca aaggatattt      3781 ctaatgtcgt cactgatgct gcttctggtg tggttgatat ttttcatggt attgataaag      3841 ctgttgccga tacttggaac aatttctgga aagacggtaa agctgatggt attggctcta      3901 atttgtctag gaaataaccg tcaggattga caccctccca attgtatgtt ttcatgcctc      3961 caaatcttgg aggctttttt atggttcgtt cttattaccc ttctgaatgt cacgctgatt      4021 attttgactt tgagcgtatc gaggctctta aacctgctat tgaggcttgt ggcatttcta      4081 ctctttctca atccccaatg cttggcttcc ataagcagat ggataaccgc atcaagctct      4141 tggaagagat tctgtctttt cgtatgcagg gcgttgagtt cgataatggt gatatgtatg      4201 ttgacggcca taaggctgct tctgacgttc gtgatgagtt tgtatctgtt actgagaagt      4261 taatggatga attggcacaa tgctacaatg tgctccccca acttgatatt aataacacta      4321 tagaccaccg ccccgaaggg gacgaaaaat ggtttttaga gaacgagaag acggttacgc      4381 agttttgccg caagctggct gctgaacgcc ctcttaagga tattcgcgat gagtataatt      4441 accccaaaaa gaaaggtatt aaggatgagt gttcaagatt gctggaggcc tccactatga      4501 aatcgcgtag aggctttgct attcagcgtt tgatgaatgc aatgcgacag gctcatgctg      4561 atggttggtt tatcgttttt gacactctca cgttggctga cgaccgatta gaggcgtttt      4621 atgataatcc caatgctttg cgtgactatt ttcgtgatat tggtcgtatg gttcttgctg      4681 ccgagggtcg caaggctaat gattcacacg ccgactgcta tcagtatttt tgtgtgcctg      4741 agtatggtac agctaatggc cgtcttcatt tccatgcggt gcactttatg cggacacttc      4801 ctacaggtag cgttgaccct aattttggtc gtcgggtacg caatcgccgc cagttaaata      4861 gcttgcaaaa tacgtggcct tatggttaca gtatgcccat cgcagttcgc tacacgcagg      4921 acgctttttc acgttctggt tggttgtggc ctgttgatgc taaaggtgag ccgcttaaag      4981 ctaccagtta tatggctgtt ggtttctatg tggctaaata cgttaacaaa aagtcagata      5041 tggaccttgc tgctaaaggt ctaggagcta aagaatggaa caactcacta aaaaccaagc      5101 tgtcgctact tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa      5161 tgctcacaat gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg      5221 acgcgacgcc gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc      5281 tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca      5341 aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca //

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Nucleotide sequences related by sequence similarity (BLAST) score to the current records.
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Gene
Gene records referencing the current sequence records. Sequences included in Gene are added manually by NCBI.
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Other nucleotide records for the same molecule in the same species for genome records in the current set. These are linked from the GenBank source record for the genome Reference Sequence. These linked records are available when there are multiple other records for the same genomic sequence in the database. Most commonly these are microbial, organelle, or viral genomes.
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Protein translations of coding regions from sequence records in the current set.
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PubMed articles that cite nucleotide records in the current set. These are articles that report the International Nucleotide Database Collaboration (DDBJ, EMBL, GenBank) data. These articles are also linked to Reference Sequences derived from these records.
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Phi X 174

2010-12-01T10:21:00.001-08:00

Phi X 174

From Wikipedia, the free encyclopedia

Structure of phage phi X 174 capsid

Phi X 174
Virus classification
Group:	Group II (ssDNA)
Family:	Microviridae
Genus:	Microvirus
Species:	phi X 174 phage

The phi X 174 (or phi X) bacteriophage was the first DNA-based genome to be sequenced. This work was completed by Fred Sanger and his team in 1977.^[1] In 1962, Walter Fiers had already demonstrated the physical, covalently closed circularity of phi X 174 DNA.^[2]

This phage has a very small amount of DNA. Phi X has 11 genes in 5386 bases (it is single stranded) in a circular topology; several of these genes express similar function in two groups. The GC-content is 44% and 95% of nucleotides are coding genes. It has an unusual nature of the base composition.

In 2003, it was reported that the whole genome of phi X 174 had been assembled synthetically from scratch.^[3]

[edit]See also

Bacteriophage MS2

[edit]References

^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977-02-24). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature 265 (5596): 687–695.
^ Fiers W, Sinsheimer RL (1962). "The structure of the DNA of bacteriophage PhiX 174. III. Ultracentrifuge evidence for a ring structure". J. Mol. Biol. 5: 424–434.
^ Smith, Hamilton O.; Clyde A. Hutchison, Cynthia Pfannkoch, J. Craig Venter (2003-12-23). "Generating a synthetic genome by whole genome assembly: {phi}X174 bacteriophage from synthetic oligonucleotides". Proceedings of the National Academy of Sciences 100 (26): 15440–15445.doi:10.1073/pnas.2237126100. Retrieved 2007-10-08.

[edit]External links

Synthesizing Genomes

2010-12-01T08:02:00.000-08:00

http://chemistry.umeche.maine.edu/CHY431/Synthetic1.html

Synthesizing Genomes

Viruses can be viewed both as chemicals and as "living" entities. They can be crystallized, and their empirical formulas and structures can be determined, yet they can replicate naturally in organisms from bacteria to humans.

Poliovirus is a small icosahedral virus consisting of

60 copies each of five capsid proteins, forming an exterior "shell"
One positive-sense single-stranded RNA genome of about 7.5 kilobases
The sequence, the map of the genome, and the crystal structure have been known for almost 30 years
The Capsid of the Sabin Strain of the Poliovirus

The life cycle is simple:

After the virus penetrates a cell, the RNA is translated in the ribosome into a single long protein
Two viral proteinases chop the long protein chain into functional proteins
A viral RNA polymerase then transcribes the viral RNA into a negative-sense (complementary) copies
These copies serve as templates for the synthesis of new positive-sense genomes
These can serve as mRNA for more copies of the viral proteins, or be encapsulated to form a new virus particle
Eventually, the cell bursts and releases the new virus particles to infect other cells

Wimmer and co-workers [Science, 2002, 297, 1016] carried out the chemical synthesis of the virus cDNA (that is, a strand of DNA complementary to the RNA of the virus)

The resulting DNA was inserted into a plasmid vector and then transcribed by an RNA polymerase.

The resulting viral RNA translated and replicated in a cell free extract, producing infectious polio virus.

When added to a culture of HeLa cells, this virus produced an infection in all ways identical to the natural viral infection.
Tumpey et al. [Science, 2005, 310, 77; Nature Biotechnol., 2009, 27, 1163] have synthesized the 1918 "Spanish" flu virus, that killed as many as 36 million people worldwide. A major reason for doing this was to understand what made this virus so lethal; in addition, they wished to learn its evolutionary history.
The 1918 virus was an H1N1 type.
- H1 is the particular mutant of the hemagglutinin protein, which causes erythrocytes to clump
- N1 likewise specifies a particular mutant, this time of the neuramidinase protein, which attaches to, and cleaves the oligosaccharides displayed on the cell surface
The Neuramindinase from the 1918 influenza virus
complexed to the antiviral Relenza (3b7e) An Avian H1N1 Hemagglutinin (3hto)
Viruses may not actually be alive, but bacteria certainly are.
The bacterium Mycoplasma genitalium is believed to have the smallest genome of any free living organism: 582,790 base pairs, which code for 482 proteins.
Smith and Venter [Proc. Nat. Acad. Sci., 2006, 103, 425] used transposon insertion mutation to establish that if a rich growth medium is provided, only 382 of the protein-coding genes are essential. However, in the organism's natural habitat, the human urogenital tract, probably all 482 are necessary.
The 382 essential genes provide these metabollic pathways:
Next, they proceeded to synthesize the whole genome [Science, 2008, 319, 1215]. The scheme was similar to that for the polio virus:
- Fragments of several hundred bp were obtained commercially
- These were assembled into 5-7 kbp "cassettes" in vitro
  - make "sticky" ends with an exo nuclease
  - anneal next segment
  - ligate
  - ampliify by pcr
- 24 to 72 to 144 kbp pieces were made by cloning in E. coli
- E. coli rejected larger pieces, so final assembly was done by cloning in yeast.
- Entire synthetic genome was sequenced to establish validity
To avoid pathogenicity, one gene was replaced with an aminoglycoside resistance gene. "Watermarks" were placed in non-coding regions to identify the construct as synthetic.
What's next? Mycoplasma laboratorium?
This page last modified 3:20 PM on Tuesday January 19th, 2010.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469

Start Hacking Life: Desktop DNA Synthesizers

2010-12-01T07:43:00.000-08:00

Start Hacking Life: Desktop DNA Synthesizers

By Alexis Madrigal
December 10, 2007 |
3:49 pm |
Categories: Uncategorized

UPDATE (8 PM): As reader Jason Dale pointed out, the ML 1000 is not a DNA synthesizer, it’s a luminator. Call me overeager. But we can imagine that it is still possible to get your hands on a DNA synthesizer, say, from Pegasus Scientific or order DNA from an organization like Blue Heron Technology. My apologies for the bum shopping steer, but the theoretical implications still hold.

A couple of weeks ago, I speculated in a post called The Open Organism: Genetic Engineering in the Open Source Era on the possibility for hackers to build their own custom organisms like people build web apps now. Well, if that post got you so excited that you want to run out and start building new organisms, your new DNA "compiler" is for sale on ~~Ebay for a mere $799.~~ It fits on your desk and can take genetic code that looks like this, gatcctccat, and turn it into an actual DNA sequence. From there, it can be incorporated into actual organisms via widely known genetic engineering techniques.

Of course, while you could just be trying to build an E. coli strain that produces butanol, you could also put this sort of device to more nefarious purposes. That’s why rogue DNA synthesizers worry members of the synthetic biology community. Prominent researchers from the J.
Craig Venter Institute and MIT, two hotbeds of synthetic biology research, recently released a report called Synthetic Genomics: Options for Governance (pdf) in which they discuss how to minimize the risks that someone creates a nasty virus while maximizing the scientific potential of the research. They stop short of recommending that DNA synthesizers be licensed, or tracked, but they do present those options.

For a quick overview of the worst case scenario, "basement bioterrorism," you can check out Reason magazine’s piece. They provide the following thrilling and chilling quote from the above report:

Now, or within a few years, any virus with a known sequence can or will be able to be constructed in a relatively straightforward manner.

While there’s a big complexity/difficulty jump from viruses to bacteria and other single-celled organisms, the day is rapidly approaching when someone, probably the J. Craig Venter Institute, announces that they have created a novel, manmade species.

How are Scientists Able to Artificially Synthesize a Virus?

2010-12-01T07:17:00.000-08:00

http://www.wisegeek.com/how-are-scientists-able-to-artificially-synthesize-a-virus.htm

The world's first artificial virus was synthesized in late 2003 by a research team led by Craig Venter, who was also responsible for the first sequencing of the human genome. The virus was a Phi-X174 bacteriophage (bacteria-eater) whose genome has 5,000 base pairs, or nucleotides. In comparison, the human genome has around 3 billion base pairs.

The polio virus, with 7,500 base pairs, has also been synthesized from scratch. Synthesizing the Phi-X174 viruswas a rapid task -- with contemporary technology, it only took two weeks. Synthesizing other virii has taken months.

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The process begins with the synthesis of oligonucleotides, which are small lengths of nucleotide (DNA or RNA) with around twenty or fewer base pairs each. Because biologists have already been synthesizingoligonucleotides for years, DNA synthesis machines exist that are capable of manufacturing them automatically. Designing the oligonucleotides for the Phi-X174 virus only took about eight hours, followed by a four-day synthesis process.

The next step is the purification of the oligonucleotides by gel electrophoresis. The purified oligos are then tagged with special chemicals and assembled sequentially, one by one, in a process called PCA (polymerasecycling assembly). After 35 to 70 cycles, a full chromosome made out of the artificial oligos has been synthesized. Using PCR (polymerase chain reaction), many copies of the original chromosome are then created, the best of which are selected using another cycle of gel purification. These nucleotide chains are then circularized from their linear chromosomal forms, becoming infectious.

The infectious chromosomes (virii) are then transplanted to an agar plate containing bacteria for consumption. Within a day, telltale remnants of viral activity and self-replication can already be found, showing that the synthesis was a success.

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The synthesis of artificial viruses has been discussed for such applications as pollution reduction and advanced filtering. Specialized microbes can be created to consume almost anything. On the other hand, there is always the risk that a malicious party would use this technology to create a virus engineered for high virulence or lethality against human hosts.