Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> This article discusses how DNA might be used to store data. It is argued that, at present, DNA would be best employed as a long-term repository (thousands or millions of years). How data-containing DNA might be packaged and how the data might be encrypted, with particular attention to the encryption of written information, is also discussed. Various encryption issues are touched on, such as how data-containing DNA might be differentiated from genetic material, error detection, data compression and reading frame location. Finally, this article broaches the difficulty of constructing very large pieces of DNA in the laboratory and highlights some complications that might arise when attempting to transmit DNA-encrypted data to recipients who are a long period of time in the future. <s> BIB001 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> AbstractIntegration, excision, and inversion of defined DNA segments commonly occur through site-specific recombination, a process of DNA breakage and reunion that requires no DNA synthesis or high-energy cofactor. Virtually all identified site-specific recombinases fall into one of just two families, the tyrosine recombinases and the serine recombinases, named after the amino acid residue that forms a covalent protein-DNA linkage in the reaction intermediate. Their recombination mechanisms are distinctly different. Tyrosine recombinases break and rejoin single strands in pairs to form a Holliday junction intermediate. By contrast, serine recombinases cut all strands in advance of strand exchange and religation. Many natural systems of site-specific recombination impose sophisticated regulatory mechanisms on the basic recombinational process to favor one particular outcome of recombination over another (for example, excision over inversion or deletion). Details of the site-specific recombination processes... <s> BIB002 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> The practical realization of DNA data storage is a major scientific goal. Here we introduce a simple, flexible, and robust data storage and retrieval method based on sequence alignment of the genomic DNA of living organisms. Duplicated data encoded by different oligonucleotide sequences was inserted redundantly into multiple loci of the Bacillus subtilis genome. Multiple alignment of the bit data sequences decoded by B. subtilis genome sequences enabled the retrieval of stable and compact data without the need for template DNA, parity checks, or error-correcting algorithms. Combined with the computational simulation of data retrieval from mutated message DNA, a practical use of this alignment-based method is discussed. <s> BIB003 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> Biomineralization, the process by which minerals are deposited by organisms, has attracted considerable attention because this mechanism has shown great potential to inspire bottom-up material syntheses. To understand the mechanism for morphological regulation that occurs during biomineralization, many regulatory proteins have been isolated from various biominerals. However, the molecular mechanisms that regulate the morphology of biominerals remain unclear because there is a lack of in vivo evidence. Magnetotactic bacteria synthesize intracellular magnetosomes that comprise membrane-enveloped single crystalline magnetite (Fe(3)O(4)). These nano-sized magnetite crystals (<100 nm) are bacterial species dependent in shape and size. Mms6 is a protein that is tightly associated with magnetite crystals. Based on in vitro experiments, this protein was first implicated in morphological regulation during nano-sized magnetite biomineralization. In this study, we analyzed the mms6 gene deletion mutant (Δmms6) of Magnetospirillum magneticum (M. magneticum) AMB-1. Surprisingly, the Δmms6 strain was found to synthesize the smaller magnetite crystals with uncommon crystal faces, while the wild-type and complementation strains synthesized highly ordered cubo-octahedral crystals. Furthermore, deletion of mms6 gene led to drastic changes in the profiles of the proteins tightly bound to magnetite crystals. It was found that Mms6 plays a role in the in vivo regulation of the crystal structure to impart the cubo-octahedral morphology to the crystals during biomineralization in magnetotactic bacteria. Magnetotactic bacteria synthesize magnetite crystals under ambient conditions via a highly controlled morphological regulation system that uses biological molecules. <s> BIB004 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems. <s> BIB005 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> The first one-dimensional (1D) assembly of low-toxicity CuInS2/ZnS quantum dots (QDs) embedded in lipid nanotubules, formed from liposomes using the Amphiphysin-BAR (Bin-Amphiphysin-Rvs domain of human amphiphysin) protein to elongate the structure, is reported. The QD-containing lipid nanotubules display a high aspect ratio of ≈500:1 (≈40 nm diameter and 20 μm length) and are stable for more than 20 h. Furthermore, this methodology is extended to the assembly of various nanoparticle species within 1D lipid nanotubules, and includes materials such as CdSe and Au. Encapsulation within the hydrophobic core of the bilayer makes these materials highly biocompatible. The developed methodology and materials with these unique characteristics could be useful for various applications in nanobiotechnology and nanomedicine. <s> BIB006 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> Many Modern Technologies, such as High Density Data Storage, Require Monodispersed Magnetic Nanoparticles (MNPs), which Have a Consistent Magnetic Behavior, Specifically Immobilized onto a Patterned Surface. Current Methods for Synthesizing Uniform Mnps Require High Temperatures and Harsh Chemicals, which Is Not Environmentally Friendly. Also, the Particles Are Expensive to Make and Expensive to Pattern Using Conventional Lithography Methods. Magnetic Bacteria Are Able to Synthesize Consistent Mnps in Vivo Using Biomineralization Proteins inside Magnetosome Vesicles to Control Particle Size and Shape and Make Single Domain Mnps. Mms6 Is a Biomineralization Protein that Is Able to Template Cubo-Octahedral MNP Formation in Vitro. it Is Thought the N-Terminus Helps Integrate the Protein into the Magnetosome Membrane, and the C-Terminus Interacts with Magnetite during Nucleation and/or MNP Growth. by Selectively Attaching Mms6 to a Patterned Self Assembled Monolayer via the N-Terminus, Patterns of Uniform Magnetite Mnps Are Templated in Situ. this Also Requires Careful Selection of the Mineralization Solution Used to Mineralize the Patterned Mms6. here we Evaluate some Low Temperature (room Temperature to < 100°C) Methods of Magnetite Formation to Produce Monodispersed Magnetite Mnps onto Immobilized Mms6. Room Temperature Co-Precipitation (RTCP) Was Found to Be Unsuitable, as the Magnetite Does Not Form on the Immobilized Mms6, but Appears to Form Rapidly as Base Is Added. Partial Oxidation of Ferrous Hydroxide (POFH) Was Found to Be Able to Form Consistent Magnetite Mnps on the Immobilized Mms6, as the Reactants Gradually Mature to Form Magnetite over a few Hours (at 80°C) or a few Days (room Temperature). by Carefully Controlling the Type of Base Used, the Ratio of the Reactants and the Temperature and Duration of the POFH Mineralization Reaction, this System Was Optimized to Produce Consistent Mnps (340 ± 54 Nm, Coercivity 109 Oe) on the Immobilized Mms6, with Scarcely any Mineralization on the Anti-Biofouling Background. the Mnps Are Ferrimagnetic, and Appear to Be Exchange Coupled across Multiple Particles in MFM Measurements. the Specificity of this Method towards Precise Magnetite Mineralization under Relatively Mild Conditions May Be Adapted to Nanoscale Patterning of Multiple Biotemplated Materials, by Using other Biomineralization Proteins or Peptides. this Would Allow the Fabrication of Cheaper, More Environmentally Friendly Components for Devices of the Future. <s> BIB007 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> BACTERIAL HARD DRIVE <s> 4 Magnetic nanoparticles (MNPs) are used in a range of applications, from medical[1] to nanotechnological.[2] Most applications require monodispersed MNPs with both predicable and consistent magnetic behavior,[3] however, synthesizing such MNPs typically requires environmentally harsh conditions.[4] Additionally, technology such as high-density data storage requires MNPs patterned on surfaces, which are conventionally fabricated using top-down methods.[2b] Magnetic bacteria biomineralize morphologically precise MNPs in vivo,[3b,5] where crystallization is controlled by proteins such as Mms6, which is also able to template MNP formation in vitro.[6] Here, the first example of biotemplated magnetic nanoparticle arrays using the commonly available technique of soft-lithography to pattern Mms6 is reported, and it is shown that surface-tethered Mms6 can control mineralization to produce arrays of equidimensional, monodispersed magnetite MNPs. Magnetic force microscopy (MFM) shows the arrays maintain their magnetic orientation at room temperature. This biotemplating method utilizes relatively mild conditions, while the selectivity of different biomineralization proteins offers scope to develop this system to build patterned multi-bionanomaterial architectures. The development of reliable, reproducible nanomaterials is essential to the evolution of dependable nanotechnologies, and nanoscale magnetic materials are no exception. Nanomagnets must respond to an applied field in a known and consistent manner, which requires them to have a uniform size and shape distribution.[1b,2b,3b] Thin films of ferromagnetic materials can be deposited and patterned using expensive top-down techniques to create high-density data storage up to ≈500 Gbit in−2.[2] Magnetite can be patterned onto a substrate using cheaper soft-lithographic techniques,[7] however, such patterns cannot be used for data storage as the particles are too small to maintain a single magnetic domain.[7b] Many organisms, from microscopic bacteria to macroscopic mammals, are able to control and regulate mineral deposition via biomineralizing proteins. Such proteins have evolved over hundreds of millions of years to control the <s> BIB008
J.Cox BIB001 suggested that suitable host to store data in DNA are Bacillus subtilis and Saccharomyces cerevisiae (bakers yeast). Yeast has higher density than bac-teria but it is practically challenging. Bacteria has ability to survive in any condition like nuclear radiation, high temperature, deep under soil and water and in any hazardous condition. Potential bacterium that can be used for data storage are B. subtilis, M.magneticum, D. radiodurans and Mycoplasma genitalium. The idea of using bacteria as storage was pioneered by Masaru Tomita and Yachie BIB003 ] in which they stored famous Einstein relativity equation E MC Square in soil bacteria B.subtillius to repeatedly store message DNA in multiple loci of genomic DNA of bacteria. They could encode 120 bits in 4.2 Mb genome of bacteria and decoded it back by multiple sequence alignment. Remarkable work was done by team of student at Chinese Hong Kong University using E.coli as medium to store the data. It has storage capacity of 4502, 000-gigabyte hard disks per gram of bacteria. This technology has many advantages over the magnetic data storage medium mainly information cannot be hacked and can defend against cyber attacks which points to higher data security than computer storage. An encoding system takes the original data, turns it into a quaternary number, and then encodes it as a DNA sequence by mapping 0,1,2,3 to A,T,C,G respectively with storage capacity of 1 Kb per cell. DNA sequences were compressed using deflate algorithm. This loss less data compression technique is important for two aspects, one is to increase the information storage capacity and other to avoid homo polymer ad repetitive regions in DNA. Information was broken down into fragments which consist of header sequence, message DNA and check sum. To retrieve the data, a novel biological information processing system was develop. Encryption is achieved through DNA sequence shuffling Rci recombination system by using site specific recombination by Recombinase (RCi) gene. They mapped the DNA using restriction enzyme so that data can be addressed just like filing system in magnetic storage. Live bacterial cells are used for data storage and they works like a transistor in the electronic devices which has on and off state. Memory device was designed that instruct the cells when to start the division and stop the division. This kind of devices will be useful in treatment of cancer and other diseases. Storing the data in bacteria was a successful attempt but creating a rewritable storage was still a challenge that was solved by researchers at Stanford University by development of rewritable Recombinase addressable data (RAD) to store and rewrite digital information BIB005 . With the help of enzymes one can modify DNA at specific site and can exchange DNA sequences at specific location. This can be done by enzyme recombinase which allows the strand exchange between site specific DNA sequences BIB002 which mimics the flipping behaviour of a bit by using recombinase-mediated DNA inversion  . RAD module includes inversion of DNA by integrase and excisionase which depicts the bidirectional behaviour of the systems. It has two transcription input signals named set and reset. Set controls the expression of integrase that flips the DNA serving as data register. Other input reset drives the expression of integrase along with excisionase as co-factor that restores the direction of DNA element. This resulted into DNA registers which stores two states like finite automaton which can be flipped on basis of successive input signals. Here the states 0 and 1 are depicted by the green and red fluorescent protein, respectively. Depending upon the orientation of the specific DNA sequences the state of DNA is observed. Tuning and integrating the expression of recombinase, they developed a first reliable and rewritable DNA inversion-based data storage system. Other perspective for bacterial data storage was perceived by researchers at Britains University of Leeds and Japans Tokyo University of Agriculture and Technology. They used bacteria Magnetospirilllum magneticum to organically grow tiny magnets which can store bits of data BIB006 . Magnetic storage devices are built by cutting down the large magnets into tiny magnets and embedding it on to the storage tapes like hard disk and DVD. Instead of cutting magnets, scientist thought of creating tiny magnets out of some natural source that can be used to store the data. This bacteria has capacity to ingest the iron and produce the crystals of mineral magnetite. Researchers studies this mechanism of the bacteria and tried to mimic the same outside the body. They arranged magnetic particle specific iron-binding protein Mms6 BIB007 ] in chess board pattern and dipped in the iron solution BIB004 . This experiment resulted in growth of tiny magnets that may be used as potential material to built the storage devices BIB008 . Each nano cube can store a bit of information with size 20000 nano meters wide much larger than magnetic storage device with 10 nm magnetic pits. The researchers are now working on miniaturizing the size of nano magnets and using alternative magnetic material to develop single array nano magnet that can store one bit of information. In-spite of these success stories for bacterial data storage, there are many problems to be focused. Designing of error models for bacterial data storage, development of error correction codes, modeling of Shannon capacity for bacterial storage are main difficulties.