bacteria conjugation based communication

7/28/2019 bacteria conjugation based communication

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Multi-Hop Conjugation

Based BacteriaNanonetworks

SUMAS2.MTE

R


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Nanotechnology

Study of the control of matter on an atomic

and molecular scale.

Enabling the miniaturization and fabrication

of devices in a scale ranging from one to afew hundreds nanometers


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Nanoscale communication

An emerging research paradigm that aims to p

communication capabilities between nanoscale ma(nanomachines).

The first publication at 2005

Nanomachine

The most basic functional unit in nanoscale systems.

Scale: one to a few hundred nanometers.

Consists of biological materials (e.g., molecules

perform very simple computation, sensing and/or act

tasks.


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Top-Down

Main Challenge: Achieve

molecular

and atomic precision

Examples:

* Photolithography,

* Micro-contact

printing.

Design of Nano-Machines

Bottom-Up

Main Challenge:

* Controlling the assembly

process

* Obtaining complexstructures.

Examples:

* Molecular self-assembly

* Molecular recognition.

Bio-Hyb

Main Challeng

* Isolation of

biological

nano-machines

* Hybridization

Examples:

Bacteria transpor


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Design of Nano-machines

Nano-Material based

Nano-MachinesBiologically Inspired

Machines


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Biological nano-machines

CELL

The most sophisticated existing

nano-machine:

- Efficient energy consumption +

Harvesting Mechanisms

- Multi-task computing + DNAprocessing

- Multi-sensing + Actuation(Source:Ian F.Akyildiz,2008)


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Nanonetworks vs Traditional Communicat

Networks

Molecular

Communication

Traditional

Communication

(Source:Ian F.Akyildiz,2008)


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Molecular Communication

Defined as the transmission and reception of

information encoded in molecules

A new andinterdisciplinary field

that spans nano, ece, cs,

bio, physics, chemistry,

medicine, and

informationtechnologies


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Short Range(nm to m)

Wired

MolecularMotors

Wireless

Ion

Signaling

(e.g., calcium,

sodium,potassium,chlorine)

Medium Range(m to mm)

Wireless

Flagellated

Bacteria

Catalytic

Nanomotors

Long Range(mm to m)

Wired

Axons

Capillaries

Wireless

Pheromones

Lighttransduction

Pollen/Spores


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Nanonetwork architecture

Ion Sign

Molecu

Flag

bact

Cata

nano Pheromones

Pollen & Spores



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Bacteria based nanonetwork

Nodes-DPU(DNA processing unit)

-Emits attractants-

Reception attractant RA &

Transmission attractant TA

Carrier

-flagellated bacteria


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Flagellated Bacteria

Bacteria are microorganisms composed only by oneprokaryotic cell.

Flagellum allows them to convert chemical energy intomotion.

Escherichia coli (E. coli) has between 4 and 10 flagella, which

are moved by rotary motors, fuelledby chemical compounds.

E. coli bacteria is approximately

2 m long and 1 m in diameter.

(Source:sasitharan balusubrahmanian2013)


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Why Bacterial Communication?

Spans medium range to long range (m to tens of cm)

No need of infrastructure

Better than molecular motors

Transfer of huge amount of information

Up to 100Kbyte per bacteria (400K base pairs) using a plasmid.


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Basic communication steps

DNA packet is

introduced inside the

bacterias cytoplasm,

using:

Plasmids

Bacteriophages

Bacterial ArtificialChromosomes(BACs)

Encoding Transmission Propagation Reception Deco

Information is expressed as a set of DNA base pairs, the DNA packet,

inserted in a plasmid.

Bacteria sense gradients ofattractant particles.

They move towards the direction and

finds more attractants (chemotaxis).

The receiver releases attractants so thebacteria can reach it.

DNA packeextracted fr

plasmid usi

Restric

endon

enzym


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Message Plasmid Plasmids : circular sequences of DNA

Length between 5.000 and 400.000

base pairs First, the plasmid is cleaved in the

restriction sites by restrictionendonucleases.

Second the DNA packet containing the

desired information is added andlinked to the plasmid by means ofDNA ligase.

Finally, the plasmid is inserted insidebacterias cytoplasm usingtransformation or electroporation

techniques. (Source:sasitharan balusubrahmanian201


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Encoding

Nodes contain a DNA Processing Unit (DPU), which will be ato encode an arbitrary strand of DNA

This DNA forms a plasmid it is divided into 3 parts

the transfer region

the routing region

the message region


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The transfer region:

is present in typical plasmids as factor of E. coli and

33kbp (kilo base pairs) long . This region contains the genes and structures nec

for self-replication and transmission of the plasmid.


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The routing region:

contains a set of genes that implement the behavioral diff

between empty bacteria, with no data to deliver, and laden b

carrying a DNA message.

These genes encode new proteins or inhibit genes in the b

DNA for

Deactivate chemotaxis towards transmitters.

Activate chemotaxis towards the receiver.

Inhibit bacterial replication .

Enable programmed death on timeout


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The message region:

contains the destination network address and the

message body, which occupies most of the length of theplasmid.


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The DNA nucleotides -Adenine, Thymine, Cytosine and Guan

T, C and G) .

The information that the emitter nano-machine wants to send i

expressed as a set of DNA base pairs - the DNA packet.

The short-range packet is composed of different blocks .

The wrapper

The gateway .

The cleaving sequence

Receiver nano-machine address block

Information. A single-stranded sequence


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PROPAGATION

Conjugation involves the transfer of a plasmid between donor and recipient

that are normally in close contact

Genetic transfer is operated by a protein complex called tsecretion systems, which forms the transferosome.

the plasmid needs to be prepared by another complex crelaxosome. The relaxosome makes a cut at a precise positionplasmid sequence called origin of Transfer

the bacterium attracts another bacterium by joining the pili, and thplasmid is passed through the pili connection

HOW BACTERIA TRANSFER INFORMATI


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HOW BACTERIA TRANSFER INFORMATI


ROUTING OF DNA PACKET


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ROUTING OF DNA PACKET

A routing process that is usually applied to wireless networks.

The concept relies on intermediate nodes that have good immedqualities to forward packets to a destination node, in the event source to destination node link is poor or not within range.

One form of opportunistic routing is based on the concept oTolerant Networking (DTN) .

In DTN, mobile nodes opportunistically meet and passmesseach other,where eventually this message will reach the destinatio

Opportunistic Routing


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DELAY TOLERANCE NETWORK(DTN)


Conjugation Based Opportunistic Routin


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Conjugation Based Opportunistic Routin

the combined process of conjugation and

chemotaxis



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node 1 wants to transmit a message to node 3, by using the rela

2.

The chemoattractant from node 2 will attract bacteria travelingnode 1, while the chemoattractant from node 3 will attract bact

from node 2.

As the two groups of bacteria approach each other, a conjugati

process occurs, leading to messages of bacteria from node 1 toconjugate with bacteria from node 2.

The message will be transmitted to the destination node 3.

RECEPTION AND DECODING


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Once the plasmid is in the receivers gateway, the DNA pack

must be extracted from the plasmid.

This is done by restriction endonucleases enzymes that cleave

plasmid inrestriction sites.

DNA computers are able to separate different DNA strands b

lengths.

This allows the gateway node to recover the DNA packet am

the solution containing both the cleaved plasmid and the

DNA packet. Then, the gateway is able to process the DNA packet as requir

MAPPING OF NETWORK PROCESS TO BACTERIA


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PROCESS

ADVANTAGES


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ADVANTAGES

Less noise

Does not need external source of raw molecules

Low message delivery delay


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APPLICATION

Biomedical applications

Industrial applications

Security/Safety applications

CO C S O


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CONCLUSION

Here we have described a definition of molcommunication and its characteristics, and have

described initial designs for a molecular communi

system that uses bacteria as carrier for perfo

communication.


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REFERENCE


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REFERENCE[1] Sasitharan balusubrahmanian, multihop cojugation based nanonetworks C

Netw., vol. 52, pp. 22602279, Jun. 2013.

[2] I. F. Akylidiz, F. Brunetti, and C. Blazquez, Nanonetworking: A communi

paradigm, Comput. Netw., vol. 52, pp. 22602279, Jun. 2008.

[3] T. Nakano and J. Q. Liu, Design and analysis of molecular relay channels

information theoretic approach, IEEE Trans.NanoBiosci., vol. 9, no. 3, pp

221, 2010.

[4] S. Balasubramaniam, N. T. Boyle, A. Della-Chiesa, F. Walsh, A. Mardinogl

D. B. A. Prina-Mello, Development of artificial neuronal networks for mo

communication,Nano Commun. Netw., vol. 2, no. 23, Jun./Sep. 2011.

[5] L. C. Cobo-Rus and I. F. Akyildiz, Bacteria-based communication in

nanonetworks,Nano Commun. Netw., vol. 1, no. 4, pp. 244256, Dec. 20

[6] P. Lio and S. Balasubramaniam, Opportunistic routing through conjugatiobacteria communication nanonetwork, Nano Commun.Netw., vol. 3, no. 1

3645, 2012.


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Thank you..


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bacteria conjugation based communication