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Nanomaterials and nanoparticles- sources and toxicity.

Buzea C1, Pacheco II, Robbie K.

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Abstract

This review is presented as a common foundation for scientists interested in nanoparticles, their origin,activity, and biological toxicity. It is written with the goal of rationalizing and informing public health concerns related to this sometimes-strange new science of “nano,” while raising awareness of nanomaterials’ toxicity among scientists and manufacturers handling them. We show that humans have always been exposed to tiny particles via dust storms, volcanic ash, and other natural processes, and that our bodily systems are well adapted to protect us from these potentially harmful intruders. There ticuloendothelial system, in particular, actively neutralizes and eliminates foreign matter in the body,including viruses and nonbiological particles. Particles originating from human activities have existed for millennia, e.g., smoke from combustion and lint from garments, but the recent development of industry and combustion-based engine transportation has profoundly increased an thropogenic particulate pollution. Significantly, technological advancement has also changed the character of particulate pollution, increasing the proportion of nanometer-sized particles–“nanoparticles”–and expanding the variety of chemical compositions. Recent epidemiological studies have shown a strong correlation between particulate air pollution levels, respiratory and cardiovascular diseases, various cancers, and mortality. Adverse effects of nanoparticles on human health depend on individual factors such as genetics and existing disease, as well as exposure, and nanoparticle chemistry, size, shape,agglomeration state, and electromagnetic properties. Animal and human studies show that inhaled nanoparticles are less efficiently removed than larger particles by the macrophage clearance mechanisms in the lungs, causing lung damage, and that nanoparticles can translocate through the circulatory, lymphatic, and nervous systems to many tissues and organs, including the brain. The key to understanding the toxicity of nanoparticles is that their minute size, smaller than cells and cellular organelles, allows them to penetrate these basic biological structures, disrupting their normal function.Examples of toxic effects include tissue inflammation, and altered cellular redox balance toward oxidation, causing abnormal function or cell death. The manipulation of matter at the scale of atoms,”nanotechnology,” is creating many new materials with characteristics not always easily predicted from current knowledge. Within the nearly limitless diversity of these materials, some happen to be toxic to biological systems, others are relatively benign, while others confer health benefits. Some of these materials have desirable characteristics for industrial applications, as nanostructured materials often exhibit beneficial properties, from UV absorbance in sunscreen to oil-less lubrication of motors.A rational science-based approach is needed to minimize harm caused by these materials, while supporting continued study and appropriate industrial development. As current knowledge of the toxicology of “bulk” materials may not suffice in reliably predicting toxic forms of nanoparticles,ongoing and expanded study of “nanotoxicity” will be necessary. For nanotechnologies with clearly associated health risks, intelligent design of materials and devices is needed to derive the benefits of these new technologies while limiting adverse health impacts. Human exposure to toxic nanoparticles can be reduced through identifying creation-exposure pathways of toxins, a study that may someday soon unravel the mysteries of diseases such as Parkinson’s and Alzheimer’s. Reduction in fossil fuel combustion would have a large impact on global human exposure to nanoparticles, as would limiting deforestation and desertification.While nanotoxicity is a relatively new concept to science, this review reveals the result of life’s long history of evolution in the presence of nanoparticles, and how the human body, in particular, has adapted to defend itself against nanoparticulate intruders.

2007 American Vacuum Society.

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Self-assembled bionanostructures–proteins following the lead of DNA nanostructures

Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction.

Keywords:

Self-assembly; Protein nanostructures– DNA nanostructures; Protein origami

Introduction

The versatility of biopolymers can be used to rationally design new molecules and assemblies with structures and functionalities unseen in nature. The ability of biopolymers to self-assemble into complex shapes and structures defined at the nanometer scale, and our competence of sustainable large-scale production using cell factories makes them highly desirable for diverse technological applications. In the rapidly-growing research area of modern nanobiotechnology the natural components polypeptides and nucleic acids have been employed as building blocks for the assembling of new designed nanostructures and nanomaterials. Bionanotechnologists have in the last decades achieved important advances in protein-based and particularly DNA-based responsive nanostructures, which can now be designed to self-assemble into almost any selected shape.

Molecular self-assembly as the main organizing principle of biological systems is also a widely applied strategy in the nanotechnology as the driving force for the assembly of artificial nanostructures. In self-assembly the final structure is encoded by interactions of its building elements defined by their properties and the order of building blocks within the linear polymer. The shapes and functions of both, DNA– and protein-based nanostructures are encoded by the sequence of their constituents, nucleotides and amino acids. Additionally, the architecture of both type of the nanostructures can be affected also by the environmental factors, such as solvent, pH, temperature and building blocks concentration.

DNA nanostructures are based on the Watson-Crick nucleic base complementarity. There are only two different base pairs based on a specific pairwise interaction, where stacking with neighboring pairs underlies the formation of stable double-helical domains that serve as the nanostructural building blocks. Some of the most spectacular examples of the potentials of nanobiotechnology have been demonstrated by DNA-based nanostructures. In the nature the primary function of nucleic acids are the storage, processing and mediation of genetic information; however natural structures such as aptameres, telomeres and partially the ribosome as one of the key and most complex nanodevices are formed by nucleic acids assembled into 3D structures. The relevance of the physiological role of nucleic acids that perform their function in form of self-assembled noncoding RNA transcripts is still unknown. On the other hand artificial rationally designed DNA nanostructures, which utilize a narrower subset of interactions from aptameres, can adopt a huge diversity of 2D or 3D shapes [15].

In contrast to designed DNA nanostructures, the rational design of protein nanostructures is much more complicated due to the complex cooperative interactions between amino acids stabilizing the fold of native proteins. The comparison of some features of self-assembled DNA- and protein nanostructures is presented in Figure 1. Structural folding of most natural proteins still cannot be easily predicted from their primary structure due to contribution of many cooperative and long-range interactions between amino acids, therefore de novo design of completely new protein folds is even more challenging.

Figure 1. Some features of self-assembled DNA– and protein nanostructures.

 Natural proteins comprise 20 amino acid residues with diverse properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. The advantages of protein nanostructures include also cheaper manufacturing of building blocks, as well as the multiple cooperative interactions that govering protein nanostructures.

However, a significant progress has been recently achieved in the development of strategies for building artificial self-assembled bionanostructures, and a range of both, DNA- and protein nanostructures rapidly increased in last two decades. In this review we mainly focus on protein-based nanostructure strategies, while DNA nanotechnology has been discussed in detail in many recent reviews [612].

Designed DNA nanostructures

In 1982, Seeman proposed to use DNA as the structural material for the bottom-up self-assembly [13] and he is accepted as the founder of the field of DNA nanotechnology. Since then, DNA-based self-assembly achieved spectacular results relying on the base-pairing specificity of nucleotides, using DNA synthesis technology, computer based design and, above all, imaginative design. Over the last three decades self-assembled DNA nanostructures have been extensively studied and several different approaches for building DNA nanostructures have been developed. Self-assembled DNA nanostructures range from 3D structures with a well-defined shape [2,4,1417] to a variety of complex dynamic DNA devices [8,1820]. This avenue of research also spawned DNA computing [21,22] and design of dynamic devices [8,23,24], which are however beyond the scope of this review.

DNA self-assembly is a robust and flexible biomimetic strategy for molecular construction that is directed by the information embodied in the nucleotide sequence. Development of DNA nanostructures encompasses several different approaches (Figure 2), where the design of nanostructures is based on the assembly of:

– several medium-sized DNA (few 10–100 nucleotides) oligonucleotides that form finite sized nanostructures [14];

– several medium-sized DNA oligonucleotides that assemble into building blocks that further oligomerize into finite sized structures such as different polyhedra or into lattices [3,25];

– single long DNA scaffold (e.g. encompassing several 1000 nucleotides from the single stranded DNA phage) that is shaped into selected structure by the addition of short oligonucleotide clamps a.k.a. DNA origami technique, invented by Paul Rothemund [26]. This approach can result in complex 2D or 3D shapes such as molecular raster images, box, sphere etc. [2730];

– large number of short DNA bricks (32 or 42 nucleotide long strands that form U-shaped brick) that fill the 2D plane or 3D space, where the selected structure is formed by the omission of appropriate DNA bricks from the assembly mixture. Almost any 2D or 3D shape can be formed by this approach [15,31].

Figure 2. Different approaches for building DNA nanostructures. The design of DNA nanostructure is based on the assembly of several medium-sized oligonucleotides that form either (a) a finite sized nanostructure or (b) assembled building blocks that further oligomerize into a finite sized nanostructure. (c) DNA nanostructure can be assembled from a single long DNA scaffold (blue) and short oligonucleotides (red, green) that hold the scaffold in place. (d) 2D and 3D nanostructures can be constructed by short DNA strands, DNA bricks.

An important advantage of DNA-based nanostructures is that it is possible to address the selected positions within the 2D or 3D nanostructures at approximately 5 nm resolution and introduce oligonucleotides with selected functionalities, such as different organic compounds, fluorophores, metal binding groups, proteins etc. into those positions, thereby functionalizing DNA nanostructures [9,3236].

RNA has the distinct advantage that ssRNA could easily be produced in vivo in order to promote the self-assembly. This property was used to prepare RNA-based scaffolds with attached sites for functional proteins fused to specific sequence RNA binding domains. While those in vivo assembled structures were not well characterized, the scaffold strongly enhanced the reaction yield [37] similar to the DNA-based scaffolded enzymes, where the arrangement of enzymes had been linear [38]. It is hoped that this in vivo approach will be further developed for in vivo applications. ssDNA could also be produced in vivo, demonstrated by the self-assembly of a tetrahedron [39]. Isothermal DNA nanostructure assembly strategy has been developed that could further facilitate future DNA self-assembly in vivo [40].

DNA nanostructures were used to make devices that were functional in the cellular milieu; e.g. drug delivery container that encapsulates cargo, such as therapeutic antibodies, while opening of the container could be controlled by binding of the trigger signals to the aptamer lock that regulates opening of the container only if the triggering signals for both of the two locks are present [41]. DNA origami seems to be stable in vivo indicating that it is relatively protected against nucleases. There are also reports on the use of DNA nanostructures as the constituents of vaccines [4244]. However real applications of DNA nanostructures are at the moment quite rare and essentially all DNA nanostructures are prepared by chemical synthesis, which limits the technological applications due to the cost and scale of production.

Protein nanostructures

Proteins provide masterful examples of complex self-assembling nanostructures with properties and functionalities beyond the reach of any human-made materials. It is estimated that there are only few thousand different protein folds in nature, and recently the number of new determined protein fold basically trickled to a halt despite determination of tens of thousands of new protein structures each year. So far folds of only few small protein domains can be accurately predicted [4548] and design of completely new folds without resemblance to any of the existing native folds represents even a greater challenge [49].

Larger natural proteins have evolved through combinations of several smaller independently folding domains. Protein oligomerization based on the symmetric oligomerization domains is an important source of suprastructured proteins [50]. Existing protein oligomerization domains have been recognized as suitable building blocks for the predictable bottom-up design of artificial protein nanostructures. Strategies that used modified natural domains, or genetically or chemically linked secondary structure elements for self-assembling, and resulted in formation of symmetric intermolecular protein assemblies, lattices and heterogeneous cage-like assemblies, are described in reviews [5153]. Recently we presented a new approach where a single polypeptide chain composed of concatenated coiled-coil-forming peptides self-assembled into a new topological fold, asymmetric tetrahedron-like cage, which is defined and stabilized by the specific pairing of the coiled-coil-forming segments arranged in a precisely defined order rather than cooperative packing of hydrophobic protein core [54].

Assemblies based on linked natural protein oligomerizing domains

The first strategy for the creation of designed protein nanostructures relied on interactions between oligomerizing protein domains which typically comprise 100–200 or more amino acid residues. The domains can self-assemble non-covalently, but specifically into larger superstructures. Attempts in this direction have been pioneered with fusion strategy [55]. Two different oligomerizing domains, one promoting dimerization and another one promoting homo-trimerization were linked by a semi-rigid linker (Figure 3a). Several copies of such a fusion protein were able to self-assemble into symmetric small cage-like but heterogeneous assemblies, or extended fibrils, depending on the length of the helical linker. Recent refinement of the original protein sequence resulted in a homogeneous 12-subunit assembly, confirmed by X-ray crystal structure determination. The structure of this oligomeric nanostructure reveals tetrahedral geometry with 16 nm diameter [56,57].

Figure 3. Design strategies for symmetric domain-based intermolecular protein assemblies. (a) Fusion of natural oligomerizing protein domains. Two different oligomeric protein domains (dimerization domain (pink), trimerization domain (blue)) are genetically fused via helical linker (violet) to obtain a single chain building block which self-assembled into a 12-subunit cage-like structure with tetrahedral shape (4d9j) [56]. (b) Novel protein domain interface design. Computational design of additional interaction surfaces (red) on natural trimerization domain (blue) leads to the formation of 12-subunit assembly with tetrahedral – or 24-subunit assembly with octahedral symmetry (4ddf) [62].

This approach provides the possibility to create smart bionanomaterials by regulating the assembly and disassembly. Self-assembly of the fusion protein composed of the dimerizing gyrase B domain and trimerization domain can be driven by the addition of a small molecule. The addition of pseudo-dimeric gyrase B ligand, coumermycin, induced formation of hexagonal assemblies and its dissociation by the subsequent addition of a monomeric ligand novobiocin, which competes for binding to the same gyrase B site as the pseudodimeric coumermycin [58].

The extended fusion strategy circumvented the problem of connecting two oligomerization domains in a fixed relative orientation which assured well-ordered self-assembled protein nanostructures [59]. They showed that fusion protein can be made by selecting two or more connections between the adjacent oligomers if the two domains are joined along an axis of symmetry that both oligomerization domains share. However this symmetry-matching fusion protein strategy successfully manufactured linear filaments, two-dimensional lattices and large solid aggregates, but is not suitable for designing defined cage-like structures.

Engineering new interaction surfaces into native protein domains

In the strategies described above the range of suitable protein domains is limited by restrictions regarding the symmetry axes of the natural domains. A step further towards the design of artificial protein nanostructures was done by engineering domain surfaces for weak non-covalent interactions in the self-assembling processes. The analysis of natural contact interfaces between protein domains disclosed the rules governing domain association. The contacting surfaces should be complementary and predominantly non-polar. The contribution of hydrogen bonds and salt bridges at the contact rim is negligible. Employing these rules it was demonstrated that a given protein can be engineered to form new contact interfaces that produced a number of novel assemblies [60]. Algorithm Rosetta for modeling protein-protein interactions [61] enables de novo design of interacting interfaces which can drive the self-assembly of designed proteins into a desired symmetric architecture [46,62]. In a recent study, a computational design of protein nanostructures with atomic level accuracy was described [62]. Protein building blocks, based on natural trimeric protein domains were docked together symmetrically to the target packing arrangements and low-energy protein-protein interaction interfaces were designed between building blocks in order to drive the self-assembly (Figure 3b). The designed proteins assembled into cage-like nanostructures with either tetrahedral or octahedral point group symmetry which was confirmed by crystal structures.

Modular approach for de novo designed protein nanostructures

The strategies employing oligomerizing protein domains for designing new protein structures, described above, are limited to homologues of known native protein folds. The next generation engineering approaches are based on modules that can be considerably smaller than the typical protein domain. The modules comprise interacting de novo designed secondary structure elements that are predictably combined with specified partners to form larger assemblies. De novo protein design refers to attempts to construct completely new protein sequences for the prescribed structures based on the principles defining the stability and selectivity of building modules; in de novo design the polypeptide sequence is selected by the designer.

Modularity and orthogonality are two foundation concepts of de novo design and engineering of new protein nanostructures. Instead of optimization of the numerous cooperative interactions that underpin the structures of natural proteins, the use of well-understood structural modules, which could be combined into complex nanostructures, was proposed. α-helices and β-strands represent attractive protein folding motifs to serve as building blocks for well-ordered and defined nanostructures with complex architecture [6367].

The most studied module for building self-assembled protein nanostructures are interacting helical peptides and particularly coiled-coils. They are ubiquitous facilitators of inter- and intramolecular protein-protein interactions and comprise two or more intertwined α-helices that are encoded by the characteristic heptad sequence repeat, where residues are labeled with abcdefg. The non-covalent interactions that drive the formation of coiled-coils are the hydrophobic effects between amino acids at positions a and d that form a hydrophobic core of coiled-coil, and the electrostatic inteactions between the opposite charged residues at positions e and g. The rules governing coiled-coil formation, their oligomerization state and interaction partner specificity have been considerably established over the last decades [68,69]. On the basis of those rules sets of orthogonal designed coiled-coils as the toolkit for the designed protein assemblies were developed [7075]. Engineered coiled-coil polypeptides have been used to assemble different nanomaterials: nanofibres [76,77], membranes [78], nanotubes [79], nanostructured films [80], spherical structures [81], responsive hydrogels [82,83], spheres [84] etc. Homogeneous nanoparticles with regular polyhedral symmetry, about 16 nm in diameter, were prepared from single type of polypeptide chains where the two coiled-coil modules with different oligomerization states were joined by a short linker [85]. In another study two oligomerizing coiled-coil peptides were tethered via disulphide bond close to their center. The self-assembled molecules spontaneously curved into the spherical cage-like particles, with a hexagonal-pattern of the cage surface and about 100 nm in diameter [84]. Another example are discrete circular nanostructures of defined stoichiometry; trimers or tetramers of < 10 nm were observed when linker between two coiled-coil-forming segments comprising 6–10 residues. Larger colloidal-scale assemblies as well as flexible fibers were formed when shorter linkers limited flexibility between peptides [86].

Designed topological protein folds based on interacting coiled-coil modules

Recent innovative approach to construct new engineered self-assembled protein nanostructures is based on the concatenated interacting dimerizing modules, comprise up to 45 amino acid residues [54]. The tetrahedral nanostructure was built from only single polypeptide chain; this strategy may appropriately be called designed protein origami as opposed to native protein structures that fold into a defined 3D structure from a single chain.

Rather than folding the structure based on the interactions between residues in the hydrophobic core as for the native proteins, the modular topological design is based on pairwise interactions between concatenated secondary structure elements (coiled-coil-forming segments), whose folding and orthogonality is engineered independently. Orthogonality of used coiled-coil building modules ensures that each segment preferentially binds to its designated partner segment within the same polypeptide chain. The final topology is defined by the sequential order of coiled-coil segments. The topological fold comprises a cavity bounded by coiled-coil dimers as the edges of the polyhedron. This type of modular self-assembly therefore in many aspects resembles the principles of DNA nanostructures [2,3,26], where polyhedra had been constructed based on the complementary DNA segments.

According to this approach long range non-covalent interactions occur between coiled-coil-forming segments, which dimerize independently of the other segments. The coiled-coil-forming segments are concatenated into a precisely defined order with intervening flexible linkers between each segment, to provide the hinge-like flexibility. In the case of a monomeric tetrahedron, which was constructed to demonstrate the principle, the polypeptide chain is composed of 12 designed coiled-coil dimer- forming segments, each forming an orthogonal coiled-coil dimer with its partner segment within the same polypeptide chain (Figure 4). In this way it forms 6 edges of a tetrahedron, while the flexible linkers were positioned at vertices. The polypeptide was produced in the recombinant form in E. coli and self-assembled by a slow dialysis or temperature annealing into tetrahedral structure, whose edges measure around 5 nm. This direction opens an exciting perspective for the creation of additional entirely new protein folds. The principle of protein assembly can benefit significantly by the application of a mathematical topology theory, which can be used to analyze the number of theoretical solutions and may be in the future applied to optimize the kinetics of the assembly [87]. The results of protein nanocage engineering show that modular design can be used for complex structures, with the potential for applications biocatalysis, targeted drug delivery, vaccination, etc. [88].

Figure 4. Protein origami: modular topological design of protein structure from a single polypeptide chain. A toolbox for constructing tetrahedron-like cage comprised of six orthogonal pairs of coiled-coil-forming peptides, two antiparallel- and four parallel dimers (orientation is denoted by arrow). Twelve peptides were concatenated in a defined order, separated by the tetrapeptide linker. The single polypeptide chain served as a building block that self-assembled into monomeric and asymmetric tetrahedron-like nanostructure [54].

Conclusions and future prospects

The recent successes in the design of new bionanostructures based on DNA and protein demonstrates the potentials of this approach to engineer new functional nanostructures.

While DNA-based nanostructures are clearly ahead of the designed protein nanostructures in terms of the complexity of the designed structures so far they lacked tangible applications. Although it has been demonstrated that DNA-based nanostructures are functional in organisms, use of in vivo produced and assembled nucleic acid-based nanostructures would represent an important step ahead both for the production cost and new biological applications. Functionalization of nucleic acids could combine structural design with precisely addressed functionalities. However, proteins adopt much larger conformational variability than nucleic acids and provide more versatile functionality. De novo design of protein nanostructures has been limited to small number of application cases which predominatly utilizing repurposed natural protein domains. Nevertheless the design of protein assemblies has matured beyond the proof of principles and is ready to face more complex challenges. New emerging paradigms such as the topological protein folds open completely new avenues that seem not to have been adopted or perhaps even tested by nature. Future developments will demonstrate the potentials of different strategies, or their combinations, with respect to the precise engineering of nanostructures and the theoretical limitations of different platforms. The next stage will need to focus on application development. The potentials are numerous, from targeted drug and biomolecule delivery, vaccine design, tissue engineering, senzors design, biocatalysis to bionanomaterials science. The interdisciplinary approach of synthetic biology, combining structural biology, molecular biology, mathematics, engineering and many other disciplines, have the potential to join forces in this exciting opportunity.

 

[F6]oligomer (plural oligomers)

  1. (chemistry) A compound intermediate between a monomer and a polymer, normally having a specified number of units between about five and a hundred.

 

 

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Unregulated Nano Products Flooding Market, Presenting Dangerous Toxicity Potential

 

A vast and rapidly expanding array of engineered nano-products are flooding the consumer market unregulated as evidence of toxicities accumulate.

First cases of nanotoxicity occupational exposure

Seven young women (aged 18–47yrs) working in a paint factory and exposed to nanoparticles for 5–13months fell ill and were admitted to hospital. Two subsequently died. Pathological examinations of the patients’ lung tissue showed nonspecific inflammation, fibrosis and foreign-body granulomas (tumours resulting from inflammation) of the pleura (membrane around the lungs). Transmission electron microscopy revealed nanoparticles of polyacrylate lodged in the cytoplasm and the nucleus of cells and in the chest fluid. The polyacrylate nanoparticles were confirmed in the workplace. These first suspected cases of nanotoxicity from occupational exposure have heightened concerns over the huge and rapidly expanding array of nanotechnology products in the market that remains unregulated despite accumulating evidence that many nano-ingredients, including those most common in commercial use, are indeed toxic.

Common nano-ingredients are toxic

Nanotechnologies are technologies at the scale of nanometres (10-9m), where new quantum effects can alter the chemistry and physics of elements and compounds, offering exciting new possibilities in industrial applications, and for exactly the same reasons, posing unprecedented risks to health and the environment.  It was difficult to separate hype from reality when it all began, and almost no one worried about safety and nanotoxicology became established as a discipline in 2005 (Nanotoxicity: A New Discipline, SiS 28). By then, many serious health impacts had already been observed in laboratory experiments; and more appeared in subsequent years. In 2009, researchers at University of California Los Angeles Jonsson Cancer Center led by Robert Schiest reported that titanium dioxide nanoparticles (TiO2), found in “everything from cosmetics and sunscreens to paint and vitamins” (see Box), caused DNA damage when fed to mice. They induced breaks in DNA, damaged chromosomes, and caused inflammation of tissues; “all of which increase the risk of cancers.” The mice were exposed to the nanoparticles in their drinking water, and genetic damage started showing up on the fifth day, equivalent to occupational exposure in humans of 1.6 years. Once taken into the body, the TiO2 nanoparticles accumulate in different organs because the body cannot eliminate them, and they are so small that they can go everywhere.

These latest findings confirm the results of numerous other studies indicating that nano-TiO2 increases cell death, DNA damage, and genome instability in the short-term and the risk of cancer in the longer term. A team of researchers at several institutes in Taiwan showed that exposing mammalian cells to TiO2 nanoparticles at 10 ppm in the short-term (days) resulted in enhancement of cell growth and survival, and increase in reactive oxygen species (oxidative stress). In the long-term – after 12 weeks – a dramatic increase in transformed (cancerous) cells was observed, resulting from a disturbance of cell division and genome instability. Similar toxicities have been found for other nanoparticles often used with TiO2, such as ZnO2 and SiO2. –Nano-silver, even more widely used than nano-TiO2, is toxic to beneficial bacteria that break down wastes and recycle nutrients in the soil. It also killed half of all zebrafish embryos in laboratory tests at concentrations of 25 to 50 ppm; whereas a solution of ordinary silver ions (Ag+) was non-toxic.  Fullerenes, a new form of carbon in the shape of a football (buckyball) discovered in the mid 1980s, rapidly found applications in electronics, electro-optics and much more besides, including cosmetics. They are being considered for drug delivery and cancer therapy. Fullerenes caused oxidative brain damage (through lipid peroxidation) in juvenile largemouth bass after 48 hours of exposure at 0.5 ppm, mostly likely through the ability of fullerenes to home in on lipid-rich membrane. One main route to the brain is via the olfactory nerve. Fullerenes were also highly toxic to zebrafish embryos at 0.2 ppm. Carbon nanotubes, long thin structures derived from fullerenes and often compared to asbestos, caused inflammation and granulomas when instilled into the lungs of mice. These results have now been confirmed in a study in which the mice inhaled aerosols of multiwall carbon nanotubes. Inflammation and granulomas were found in the lungs even at the lowest concentration of 0.1 mg/m3. Quantum dots are nanosized semi-conductors that generate electron-hole pairs confined in all three dimensions (quantum confinement), and hence behave like giant molecules rather than bulk semiconductors. They have numerous applications in light emitting diodes, transistors, solar cells etc., and are also being developed for drug delivery, cancer therapy and cell imaging. Unfortunately, most quantum dots contain highly toxic metals such as cadmium, which tends to be released when the quantum dots enter the cells or organisms. This was thought to be the main reason why CdSe/ZnSe quantum dots at nanomolar (10-9mol) concentrations were toxic to Daphnia magna, but much less toxic than the equivalent concentration of cadmium ions. However, CdTe quantum dots coated with hydrophilic sodium thioglycolate caused disruption in a cultured monolayer of Caco-2 human intestinal cells and cell-death at 0.1 ppm, which was thought to be caused by the quantum dots, rather than cadmium. In a third study, CdSe/ZnS quantum dots injected intravenously into mice caused marked vascular thrombosis in the lungs at 0.7 to 3.6 nanomol per mouse, especially when the quantum dots had carboxylate surface groups. Three out of four mice injected at the higher concentration died immediately. The injected quantum dots were mainly found in the lungs, liver and blood; and the authors hypothesized that the quantum dots activated the coagulation cascade through contact. In fact, many kinds of nanoparticles enhance the formation of insoluble fibrous protein aggregates (amyloids), which are associated with human diseases including Alzheimer’s, Parkinson’s and Creutzfeld-Jacob disease.

There are now more than 1 000 nanotechnology products on the market (see Box), ranging from microelectronics, solar cells, medicine, to cosmetics, clothing, food, and agriculture.

Nanoparticles, natural, artificial, old and new

What’s new about nanoparticles, as far as risk is concerned, is that many of them are chemically inert as ordinary ions or as larger particles (and hence never had to go through regulatory approval before the nanoparticles were used); but as soon as the particle size reaches nanometre dimensions, they acquire novel physicochemical properties, causing oxidative stress and breaking DNA, and they can get access to every part of the body including the brain, via inhalation and the olfactory nerve.

A comprehensive review by Cristina Buzea and colleagues at Queen’s University, Kingston, Ontario, in Canada, pointed out that human beings have been exposed to natural nanoparticles since the origin of our species, in the form of viruses, dusts from terrestrial and extraterrestrial dust storms, volcanic eruptions, forest fires, and sea salt aerosols (which are largely beneficial). -Nanoparticles have been created by human activities for thousands of years, by burning wood in cooking, and more recently, chemical manufacturing, welding, ore refining and smelting, burning of petrol in vehicles and airplane engines, burning sewage sludge, coal and fuel oil for power generation, all of which are already known to have health impacts. Automobile exhaust particular pollution is linked to heart and lung diseases and childhood cancers. Tobacco smoke is composed of nanoparticles with size ranging from around 10 nm up to 700 nm, with a peak around 150 nm. It has a very complex composition with more than 100 000 chemical components and compounds. First or second hand cigarette smoke is associated with an increased risk of chronic respiratory illness, lung cancer, nasal cancer, and cardiovascular disease, as well as other malignant tumours, such as pancreatic cancer, and genetic alterations. Children exposed to cigarette smoke show an increased risk of sudden infant death syndrome, middle ear disease, lower respiratory tract illnesses, and exacerbated asthma.

Dust from building demolition is an important source of particulate pollution. Older buildings are likely to contain asbestos, fibres, lead, glass, wood, paper and other toxic particles  Natural and artificial nanoparticles overlap. For example, C60 fullerenes have been reported in 10 000-year-old ice core samples.  It is important to distinguish nanoparticles from nano-structured materials that do not exist as free particles during any part of the manufacturing process, which therefore are not expected to present the same hazards.  Nevertheless we are faced with an unprecedented and ever-growing volume and diversity of nanoparticles as nanotechnologies take off in all directions.

Diseases associated with nanoparticles

Nanoparticles may be inhaled, ingested or taken in through contact with the skin. The known possible adverse health impacts include both natural and anthropogenic nanoparticles. Obviously not all nanoparticles are harmful, but without exhaustive tests especially in the case of the newly engineered nanoparticles, it is impossible to tell.
Diseases associated with inhaled nanoparticles include asthma, bronchitis, emphysema, lung cancer, and neurodegenerative diseases, such as Parkinson’s and Alzheimer’s diseases. Nanoparticles in the gastrointestinal tract have been linked to Crohn’s disease and colon cancer. Nanoparticles that enter the circulatory system are implicated  in arteriosclerosis, blood clots, arrhythmia, heart diseases, and ultimately death from heart disease. Nanoparticles entering other organs, such as liver, spleen, etc., may lead to diseases of these organs. Some nanoparticles are associated with autoimmune diseases, such as systemic lupus erythematosus, scleroderma, and rheumatoid arthritis.

Conclusion

There is clearly an urgent need not only to stem but also to reverse the unregulated tide of nanoparticles that are released onto the market. In view of the existing evidence, the following actions should be taken.

  • Engineered nano-ingredients in food, cosmetics and baby products for which toxicity data already exist (e.g., silver, titanium oxide, fullerenes, etc.) should be withdrawn immediately
  • A moratorium should be imposed on the commercialization of nano-products until they are demonstrated safe
  • All consumer products containing nanotechnology should be clearly labelled
  • The Health and Consumer Protection Directorate General (SANCO) of the European Commission should require manufacturers of nano-products to register their products in a database that is publicly available on the SANCO website [12]
  • The voluntary code of conduct for nanotechnology research that the European Commission adopted in 2008 should become mandatory [12]: Nanotechnology research activities must be made comprehensible to the public, performed in a transparent manner, accountable, safe and sustainable, and not pose a threat to the environment
  • A robust regulatory programme on nanotechnology – including characterisation and standardisation of manufacture – should be implemented as soon as possible
  • There should be earmarked funding for research into the hazards of nanotechnology.

 

Now the truth comes out here as to what causes the brain to malfunction

I have been saying for awhile that the amyloid blockage had to be caused by something and now here we are finding out the truth

Dangers of SiO2 nanoparticles

the dangers of SiO2 nanoparticles has been studied pretty well.  I didn’t realize how dangerous this compound is, and that the FDA allows it sprayed on unfinished food and not labeled.  In most people, it doesn’t cause “acute” reactions, but it causes a.  After the obdy gets rid of the SiO2, and it’s introduced into the continuous crystallization inside the body liquid crystalline matrix inside the body, it starts crystallizing to itself, forming larger crystals.  If you don’t believe me, go take a vitamin pill containing amorphous SiO2, wait about 2 hours, then look at your blood under a darkfield microscope.  You’ll see the crystals formingSome are as small as a little dot that will reflect the light), but others are as big as a red blood cell, and are obvious crystals.  When I did some darkfield work, I saw the crystals as well.  I asked what they were (not realizing anything in this email, below), and the guys said “artifacts.”  He also noted that he has been seeing a LOT more artifacts in people’s blood, and don’t really know what they were, or where they are coming from.  Here’s one extract from a book:

When it’s sprayed on food, it acts as a drug delivery system, just like it says aboveIt’s properties allow it to coat proteins, gluten, amino acids, etc… to artificially transport them into the bodyEssentially it acts to force injections into us.  So when you said awhile ago that you speculated there might be forced vaccinations….it already is happening…through the food.  There’s already evidence that TiO2 nano-particles cause iron uptake dysregulation in chicken intestinal cells, and amorphous SiO2 acts the same waySiO2 forces a breakdown in the gut regulation cells, and it does it through ‘disconnecting’ the cells from host. : SiO2 and TiO2 nanoparticles have what is known as ‘light scattering’ properties and electrical insulating properties.  When the SiO2 is ingested, it coats the outsides of the cell walls [the phosphatidylcholine, carbohydrate chains, and proteins (etc)].  When the insulating effect is began, the cell loses connection to what it’s supposed to be doingThis energy originates in the heart, and with every beat we have the heart putting out light energy and epigenetically changing DNA expression (almost instantaneously).  So you can see what happens when you insulate a certain set of cells from receiving that energy with TiO2 or SiO2 nanoparticles; they malfunction.  Also, SiO2 and TiO2, as I alread said, have ‘light scattering’ properties.  This is just another term for a re-direction or, changing the amplitude and wavelength of the energy being passed through it.  It does it very well.  So when our heart and nervous system emit informational instructions, these instructions are either not fully received (as I said before), or they are changed, so the cell gets bad information, and malfunctions.–I learned all this by studying the work and research of Dr. David Jeringan, Dr. Jerry Tennant, Dr. Hal Huggins,  (and from the researchers that they got their info from), and by reading about how you can extract the DNA of living cells, in tissue, and they do not malfunction (but obviously cannot reproduce).  They continue to operate normally until they are removed from their host, which says….the host is controlling the DNA expressions and forcing the cells to function correctly, so something else other than DNA is doing it.  Dr. Jernigan talks about how the light of the body controls DNA expression…so there it was, staring me in the face:  Disrupting energy flow by adding “inert” SiO2 and TiO2 nanoparticles to essentially all the food are the root issues with out food.  Not only that, nano-silicates have a immune-stimulating response when introduced to the immune system (just like the pico-sized aluminum particles in the vaccines), for the reasons I said above (the immune system recognizes a malfunctioning cell, figures out the cell wall is resonating “silicon signatures,” and destroys itThis is called cell mediated immunity to haptens (nanoparticles are the hapten” which induces autoimmunity, TNF-alpha, and interleukin, and cytokine increases).

From the University of Colorado Dept. of Microbiology, Immunology, and Pathologyanything implanted in bone will create an autoimmune response.  The only difference is the  time it takes.”  —-guess what happened to this professor after he proved and released this information?  From the inside info I got, this news release (not the actual link) was unauthorized, and the Professor was “let go.”  He went to Pepperdine after this, and continued research in this category.  I believe he started a business, or joined a business that is researching how to implant the patients own DNA into ceramic and composite compounds for future use inside the body.  Why??  LOL…we already “know” the body is going to form an autoimmunity to metallic implants into any bone structure!  It’s just a matter of time until we find out our nano-silicon implants are really causing some issues.  If the body is “taught” that silica is an antigen, it will get rid of anything that is silicon-based or reject anything that is silicon-coated.  Hence, we get allergic to anything sprayed with nano-silica, or “learn” to get immune response to vitamins when mixed or coated with nano-silica (>90% of supplements).  –Now you see why Codex required capsule fill requirements, and silica was one of the approved fillers.  Also, essentially all the pharmaceutical companies are using one of three immune system modifiers: nano- silicon, alumina, or titaniumMCC and polymers are carcinogenic, just as you said previously.  I looked up the GRAS report on those, and actually read it.  It seems the studies were “stopped” when an increase of organ weights were noticed, and then deemed “GRAS.”  What a crock of dog shit!

Results from realizing this:  I got off everything containing this junk, and perfect health returned.  Feel free to reiterate any of this to anyone you feel it’s important to, or to post wherever you want.  I don’t want any credit, just that these jokers get exposed for inducing rampant [and random] diseases in the population, and convincing younger people that their “genetics are broken,” and “you need to take one of those genetic tests” and take supplements (containing junk that will break your genetics more) to target the”genetic mutations” they have.  Or for the older populations, that “they need to take [______] drug, because they have [______] disease.”    The truth is, the body can NEVER fix the mutations with nanoparticles inside of it, blocking the cells from sensing what they need to do.  Well, I guess it’s pretty ingenious plan if I wanted to steal the wealth from the babyboomers, and steal the future health of the younger generation away from them, get everyone on supplements of some sort (inducing money into the system), bring the entire population to their knees, turning them upside down and circle-jerking the money out of their pockets.

 

XNA- ARTIFICIAL LIFE-ARTIFICIAL INTELLIGENCE or ALIEN LIFE-ALIEN INTELLIGENCE

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XNA- ARTIFICIAL LIFE-ARTIFICIAL INTELLIGENCE or ALIEN LIFE-ALIEN INTELLIGENCE

New research has brought us closer than ever to synthesizing entirely new forms of life. An international team of researchers has shown that artificial nucleic acids – called “XNAs” – can replicate and evolve, just like DNA and RNA.

We spoke to one of the researchers who made this breakthrough, to find out how it can affect everything from genetic research to the search for alien life.

The researchers, led by Philipp Holliger and Vitor Pinheiro, synthetic biologists at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, say their findings have major implications in everything from biotherapeutics, to exobiology, to research into the origins of genetic information itself. This represents a huge breakthrough in the field of synthetic biology.

The “X” Stands for “Xeno”

Every organism on Earth relies on the same genetic building blocks: the the information carried in DNA. But there is another class of genetic building block called “XNA” — a synthetic polymer that can carry the same information as DNA, but with a different assemblage of molecules.

The “X” in XNA stands for “xeno.” Scientists use the xeno prefix to indicate that one of the ingredients typically found in the building blocks that make up RNA and DNA has been replaced by something different from what we find in nature — something “alien,” if you will.

Strands of DNA and RNA are formed by stringing together long chains of molecules called nucleotides. A nucleotide is made up of three chemical components: a phosphate (labeled here in red), a five-carbon sugar group (labeled here in yellow, this can be either a deoxyribose sugar — which gives us the “D” in DNA — or a ribose sugar — hence the “R” in RNA), and one of five standard bases (adenine, guanine, cytosine, thymine or uracil, labeled in blue).

The molecules that piece together to form the six XNAs investigated by Pinheiro and his colleagues (pictured here) are almost identical to those of DNA and RNA, with one exception: in XNA nucleotides, the deoxyribose and ribose sugar groups of DNA and RNA (corresponding to the middle nucleotide component, labeled yellow in the diagram above) have been replaced. Some of these replacement molecules contain four carbons atoms instead of the standard five. Others cram in as many as seven carbons. FANA (pictured top right) even contains a fluorine atom. These substitutions make XNAs functionally and structurally analogous to DNA and RNA, but they also make them alien, unnatural, artificial.

Information Storage vs Evolution

But scientists have been synthesizing XNA molecules for well over a decade. What makes the findings of Pinheiro and his colleagues so compelling isn’t the XNA molecules themselves, it’s what they’ve shown these alien molecules are capable of, namely: replication and evolution.

“Any polymer can store information,” Pinheiro tells io9. What makes DNA and RNA unique, he says, “is that the information encoded in them [in the form of genes, for example] can be accessed and copied.” Information that can be copied from one genetic polymer to another can be propagated; and genetic information that can be propagated is the basis for heredity — the passage of traits from parent to offspring.

In DNA and RNA, replication is facilitated by molecules called polymerases. Using a crafty genetic engineering technique called compartmentalized self-tagging (or “CST”), Pinheiro’s team designed special polymerases that could not only synthesize XNA from a DNA template, but actually copy XNA back into DNA. The result was a genetic system that allowed for the replication and propagation of genetic information.

A simplified analogy reveals the strengths and weaknesses of this novel genetic system: You can think of a DNA strand like a classmate’s lecture notes. DNA polymerase is the pen that lets you copy these notes directly to a new sheet of paper. But let’s say your friend’s notes are written in the “language” of XNA. Ideally, your XNA-based genetic system would have a pen that could copy these notes directly to a new sheet of paper. What Pinheiro’s team did was create two distinct classes of writing utensil — one pen that copies your friend’s XNA-notes into DNA-notes, and a second pen that converts those DNA notes back into XNA-notes.

Is it the most efficient method of replication? No. But it gets the job done. What’s more, it does all this copying to and from DNA with a high degree of accuracy (after all, what good is replication if the copy looks nothing like the original?). The researchers achieved a replication fidelity ranging from 95% in LNA to as high as 99.6% in CeNA — the kind of accuracy Pinheiro says is essential for evolution:

“The potential for evolution is closely tied with how much information is being replicated and the error in that process,” he explains. “The more error-prone… a genetic system is, the less information can be feasibly evolved.” A genetic system as accurate as theirs, on the other hand, should be capable of evolution.

The researchers put this claim to the test by showing that XNA strands made up of the HNA xeno-nucleotides like the one pictured here could evolve into specific sequences capable of binding target molecules (like an RNA molecule, or a protein) tightly and specifically. Researchers call this guided evolution, and they’ve been doing it with natural DNA for some time. The fact that it can also be accomplished in the lab with synthetic DNA indicates that such a system could, in theory, work in a living organism.

“The HNA system we’ve developed,” explains Pinheiro, is “robust enough for meaningful information to be stored, replicated and evolved.”

A Step Toward Novel Lifeforms

The implications of the team’s findings are numerous and far-reaching. For one thing, the study sheds significant light on the origins of life itself. In the past, investigations into XNA have been largely driven by the question of whether simpler genetic systems may have existed before the emergence of RNA and DNA; the fact that these XNAs appear to be capable of evolution adds to an ever-growing body of evidence of a genetic system predating DNA and RNA both.

What mysterious genetic material ruled the world before DNA and RNA?

All living organisms use DNA as the carrier of genetic material and RNA as the messenger molecule… Read more

Practical and therapeutic applications abound, as well. “The methodologies [we’ve developed] are a major step forward in enabling the development of nucleic acid treatments,” says Pinheiro. Natural nucleic acids [i.e. DNA and RNA] can be forced to evolve so that they bind tightly and specifically to specific molecular targets. The problem is that these nucleic acids are unsuitable for therapeutic use because they are rapidly broken down by enzymes called nucleases. As a result, these evolved nucleic acid treatments have a short lifespan and have a difficult time reaching their therapeutic targets.

To get around this, Pinheiro says medicinal chemistry is used to modify evolved DNA sequences in an attempt to create a functional molecule that can still bind to a therapeutic target but resist nuclease degradation. But doing this is tough:

“Overall, this leads to high cost and a high failure rate for potential therapies – there is still only a single licenced [nucleic acid-based] drug on the market (Macugen).”

But all six of the XNAs studied by Pinheiro and his team are stronger than regular DNA or RNA, in that they’re more resistant to degradation by biological nucleases.

As a result, these molecules would need little or no adaptation for therapeutic (or diagnostic) use. “Since these molecules can now be selected directly on XNA, medicinal chemistry should no longer be limiting,” says Pinheiro. You could select a suitable XNA for its biocompatibility and therapeutic potential, and not worry about having it rapidly degrade inside the body.

Pinheiro also says the outcome of the research could even have a strong impact on exobiology:

In my view, exobiology looks for life in regions it cannot physically visit. In that context, it searches for tell tale signs of life that can be remotely monitored but it has only life on Earth as examples to identify such suitable markers. Based on extant biology, DNA and RNA are good candidates for such a search. However, by showing that other nucleic acids can also store information, replicate and evolve, our research may force a rethink as to whether DNA and RNA are the most suitable tell tale signs of life.

Of course, nothing would call the indispensability of DNA- or RNA-based life into question more than the generation of an entirely synthetic, alternative life form, built from the ground up entirely by XNA. Such an organism would require XNA capable of driving its own replication, without the aid of any biological molecules. Pinheiro says that’s still a ways off. “Even in its simplest setup… it would be very challenging to develop an XNA system within a cell.” Such a system would require XNA capable of self-replication, and capable of undergoing evolution in a self-sustained manner.

That said, his team’s work represents a major step in the right direction. As the molecular machinery designed to manipulate XNAs grows, so, too, will the capacity for synthetic genetic systems to stand and operate on their own.

The researchers’ findings are published in today’s issue of Science.
Top image via Shutterstock; XNA moieties via Science; all other images via Wikimedia Commons

One wonders if we’ll ever come across creatures in the universe that evolved and emerged from XNA naturally. Life on earth only uses about 20 amino acids but there are many others so to stands to life elsewhere in the universe might be working in proteins based on a largely different set of amino acids.

There’s a growing body of evidence that suggests TNA (one of the six XNAs examined by Pinheiro’s team) may have been a simple, four-carbon-sugar (threose) precursor to RNA. Alasdair did a good writeup on it a couple of months ago (the ASU researcher Alasdair quotes was a co-author on this latest study, as well).

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XNA-Synthetic DNA That Can Evolve

By swapping sugars in the DNA helix, scientists have created a new kind of genetic code that can function and evolve like regular DNA.

 

Every living thing on Earth uses DNA or RNA to carry its genetic instructions for life. These two nucleic acids have different names because they’re built from different sugars: DNA uses deoxyribose sugars for a backbone of its double helix, while RNA uses ribose. But what if other sugars could be used too?

Now scientists have shown that at least six other types of sugars can form nucleic acid backbonesand they can be used to store and retrieve genetic information. The researchers built DNA molecules from scratch, but replaced the deoxyribose with six other kinds of sugar, including hexitol, threose, and arabinose. The six types of synthetic genetic chains are called XNAs, or xeno-nucleic acids (“xeno” is Greek for “foreign”). And because XNA shows the possibility of heredity—passing down their genetic information—the researchers say these molecules not only could address fascinating questions about the origin of life, but also could open up the possibility of another kind of life based not on DNA and RNA. –Jack Szostak, a geneticist and Nobel laureate at Harvard University, tells PM in an email that the work “is very interesting with respect to the origin of life—in principle, many different polymers could serve the roles of RNA and DNA in living organisms. Why then does modern biology use only RNA and DNA?”

How to Make Synthetic DNA

This isn’t the first time that geneticists have cooked up synthetic nucleic acids in a lab. Some scientists had previously created DNA with new kinds of base pairs beyond the A-T and C-G connections in DNA, and others had already created XNAs that incorporate foreign sugars. John Chaput, a molecular biologist at Arizona State University and an author on the new study in Science, says this work asks a new question: “How can you perform Darwinian evolution on something other than DNA or RNA? Lots of DNA and RNA molecules have been evolved in the laboratory, but going the next step and doing it on other molecules has been very challenging. This is one of the first examples of that.”–To prove that XNAs could evolve, the researchers first had to create a new kind of enzyme to build the XNAs. Although it’s possible to manufacture XNAs by machine, the resulting nucleic acids are short chains that have limited functionality and evolvability. So instead of using the machinated approach, the researchers took thousands of DNA-building enzymes and evolved them into XNA-building enzymes.–That required taking thousands of enzymes and mixing them together with XNA building blocks, as well as DNA strands that served as templates for the scaffolding on which to build XNA molecules. If an enzyme turned out to be good at building XNA strands, it was captured using a filtering process and amplified it for the next round of testing; enzymes that were bad at making XNA were washed away. Over many rounds of filtering, the enzyme population evolved to become more adroit at building XNAs—in fact, they could produce polymers XNA chains that lasted were five times longer than machine-made XNAs.

“They took enzymes that already existed, and evolved mutants of them that are better at making XNAs,” says Floyd Romesberg, a chemist at the Scripps Research Institute, who called the technique “impressive.”–Next, the researchers tried to evolve the XNAs themselves. To do so, they used a similar filtering technique. In this case, the scientists selected for XNAs that could bind to a specific protein; XNAs that did not bind to the proteins were washed away. Those that did bind were transcribed back into DNA so that they could be replicated. After replication, the team transcribed the copies back into XNA. In this way, the XNAs that had evolved to bind the protein were able to pass on that talent to a new generation of XNAs.

Synthetic DNA, Synthetic Life?

Because the XNAs are able to pass genetic information from one generation to the next and can adapt to the constraints of test tube evolution, Chaput says, XNAs could serve as the building blocks for completely new genetic systems.Could you create synthetic life with it? That’s possible, but it’s much further down the road.”-Szostak agrees, saying that “in the longer run, a very interesting implication is that it may be possible to design and build new forms of life that are based on one or more of these non-natural genetic polymers.” But Romesberg emphasized that creating completely new life forms using XNA would be a long and difficult mission. The foremost challenge: Researchers must find an efficient way to reproduce XNAs directly into more XNAs without having to convert them to DNA and back again.—Some folks are nervous that releasing XNA into the biosphere could allow it to intermingle with DNA and RNA with unpredictable results. But scientists such as Steven Benner and Markus Schmidt retort that XNAs are foreign enough to be invisible to natural organisms (read more about this issue here).–Regardless of whether XNAs can or will be used to create new life forms, the researchers have shown that it is possible to expand evolution into systems based not on DNA or RNA. And the XNAs and their enzymes may also lead to some answers about why life as we know it is based on those to molecules only. Are DNA and RNA the best molecules to store genetic information and catalyze biological reactions, or did they become the building blocks of life by sheer happenstance? Now researchers will have the tools to test the true efficiency against lab-created competitors.–Medicine, too, could benefit from XNAs, Romesberg says. Doctors already prescribe biological products such as enzymes and antibodies to treat certain diseases, but these drugs break down quickly in the stomach and the blood stream. Because XNAs are somewhat foreign, they’re not broken down as quickly in the body, as it has not evolved enzymes to digest them.The experiment also has implications for looking for life on other planets. “Maybe if you look hard enough out in space, you might find a life form based on XNA,” Chaput says.

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Towards XNA nanotechnology- new materials from synthetic genetic polymers.

Pinheiro VB1, Holliger P2.

Author information

Abstract

Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry.

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Synthetic genetic polymers capable of heredity and evolution.

Pinheiro VB1, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, Holliger P.

Author information

Abstract

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

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Artificial Cells –Self Repair Self Assembly and Self Production-An EU integrated project in IT- FP6-IST-FET-002035

The European Commission has supported the Integrated Project PACE in its Future Emerging Technologies program from 2004-2008. This is the final public report of results and experience in PACE.—PACE has created the foundation for a new generation of embedded IT using programmable chemical systems that approach artificial cells in their properties of self-repair, self-assembly, self-reproduction and evolvability.

Future projects will build on the technology and experience developed in PACE to build the first artificial chemical cells and apply them to revolutionize complex construction in and outside IT. PACE has established a new hybrid IT technology for programming complex chemical systems. PACE has explored the IT potential of future synthetic chemical cells: addressing both the novel embedded IT required to produce and program them and their technical opportunities, both within IT and to other fields. In contrast with biological approaches to minimize existing cells, applications of these artificial chemical cells will exploit their chemical distinctiveness from biological cells, in particular their ability to function without proteins and below the complexity barrier posed by biological translation machinery.--A consortium of some 13 partners and 2 cooperating groups from 8 European countries, including Switzerland and Lithuania, and several leading USA organizations are pioneering this new approach under the IST-FET section of the EU 6th Framework Program (FP6).

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XNA-Synthetic DNA That Can Evolve

By swapping sugars in the DNA helix, scientists have created a new kind of genetic code that can function and evolve like regular DNA.

 

Every living thing on Earth uses DNA or RNA to carry its genetic instructions for life. These two nucleic acids have different names because they’re built from different sugars: DNA uses deoxyribose sugars for a backbone of its double helix, while RNA uses ribose. But what if other sugars could be used too?

Now scientists have shown that at least six other types of sugars can form nucleic acid backbonesand they can be used to store and retrieve genetic information. The researchers built DNA molecules from scratch, but replaced the deoxyribose with six other kinds of sugar, including hexitol, threose, and arabinose. The six types of synthetic genetic chains are called XNAs, or xeno-nucleic acids (“xeno” is Greek for “foreign”). And because XNA shows the possibility of heredity—passing down their genetic information—the researchers say these molecules not only could address fascinating questions about the origin of life, but also could open up the possibility of another kind of life based not on DNA and RNA. –Jack Szostak, a geneticist and Nobel laureate at Harvard University, tells PM in an email that the work “is very interesting with respect to the origin of life—in principle, many different polymers could serve the roles of RNA and DNA in living organisms. Why then does modern biology use only RNA and DNA?”

How to Make Synthetic DNA

This isn’t the first time that geneticists have cooked up synthetic nucleic acids in a lab. Some scientists had previously created DNA with new kinds of base pairs beyond the A-T and C-G connections in DNA, and others had already created XNAs that incorporate foreign sugars. John Chaput, a molecular biologist at Arizona State University and an author on the new study in Science, says this work asks a new question: “How can you perform Darwinian evolution on something other than DNA or RNA? Lots of DNA and RNA molecules have been evolved in the laboratory, but going the next step and doing it on other molecules has been very challenging. This is one of the first examples of that.”–To prove that XNAs could evolve, the researchers first had to create a new kind of enzyme to build the XNAs. Although it’s possible to manufacture XNAs by machine, the resulting nucleic acids are short chains that have limited functionality and evolvability. So instead of using the machinated approach, the researchers took thousands of DNA-building enzymes and evolved them into XNA-building enzymes.–That required taking thousands of enzymes and mixing them together with XNA building blocks, as well as DNA strands that served as templates for the scaffolding on which to build XNA molecules. If an enzyme turned out to be good at building XNA strands, it was captured using a filtering process and amplified it for the next round of testing; enzymes that were bad at making XNA were washed away. Over many rounds of filtering, the enzyme population evolved to become more adroit at building XNAs—in fact, they could produce polymers XNA chains that lasted were five times longer than machine-made XNAs.

“They took enzymes that already existed, and evolved mutants of them that are better at making XNAs,” says Floyd Romesberg, a chemist at the Scripps Research Institute, who called the technique “impressive.”–Next, the researchers tried to evolve the XNAs themselves. To do so, they used a similar filtering technique. In this case, the scientists selected for XNAs that could bind to a specific protein; XNAs that did not bind to the proteins were washed away. Those that did bind were transcribed back into DNA so that they could be replicated. After replication, the team transcribed the copies back into XNA. In this way, the XNAs that had evolved to bind the protein were able to pass on that talent to a new generation of XNAs.

Synthetic DNA, Synthetic Life?

Because the XNAs are able to pass genetic information from one generation to the next and can adapt to the constraints of test tube evolution, Chaput says, XNAs could serve as the building blocks for completely new genetic systems.Could you create synthetic life with it? That’s possible, but it’s much further down the road.”-Szostak agrees, saying that “in the longer run, a very interesting implication is that it may be possible to design and build new forms of life that are based on one or more of these non-natural genetic polymers.” But Romesberg emphasized that creating completely new life forms using XNA would be a long and difficult mission. The foremost challenge: Researchers must find an efficient way to reproduce XNAs directly into more XNAs without having to convert them to DNA and back again.—Some folks are nervous that releasing XNA into the biosphere could allow it to intermingle with DNA and RNA with unpredictable results. But scientists such as Steven Benner and Markus Schmidt retort that XNAs are foreign enough to be invisible to natural organisms (read more about this issue here).–Regardless of whether XNAs can or will be used to create new life forms, the researchers have shown that it is possible to expand evolution into systems based not on DNA or RNA. And the XNAs and their enzymes may also lead to some answers about why life as we know it is based on those to molecules only. Are DNA and RNA the best molecules to store genetic information and catalyze biological reactions, or did they become the building blocks of life by sheer happenstance? Now researchers will have the tools to test the true efficiency against lab-created competitors.–Medicine, too, could benefit from XNAs, Romesberg says. Doctors already prescribe biological products such as enzymes and antibodies to treat certain diseases, but these drugs break down quickly in the stomach and the blood stream. Because XNAs are somewhat foreign, they’re not broken down as quickly in the body, as it has not evolved enzymes to digest them.The experiment also has implications for looking for life on other planets. “Maybe if you look hard enough out in space, you might find a life form based on XNA,” Chaput says.

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World’s first artificial enzymes created using synthetic biology

Xeno nucleic acid (XNA) is a synthetic alternative to the natural nucleic acids DNA and RNA as information-storing biopolymers that differs in the sugar backbone.[1] As of 2011, at least six types of synthetic sugars have been shown to form nucleic acid backbones that can store and retrieve genetic information. Research is now being done to create synthetic polymerases to transform XNA. The study of its production and application has created a field known as xenobiology.–Although the genetic information is still stored in the four canonical base pairs (unlike other nucleic acid analogues), natural DNA polymerases cannot read and duplicate this information. Thus the genetic information stored in XNA is “invisible” and therefore useless to natural DNA-based organisms.[2]

http://www.cam.ac.uk/research/news/worlds-first-artificial-enzymes-created-using-synthetic-biology#sthash.Hi3SOWu0.dpuf

Enzymes made from artificial molecules which do not occur anywhere in nature have been shown to trigger chemical reactions in the lab, challenging existing views about the conditions that are needed to enable life to happen.–Our assumptions about what is required for biological processes – the ‘secret of life’ – may need some further revision

Alex Taylor –A team of researchers have created the world’s first enzymes made from artificial genetic material.-The synthetic enzymes, which are made from molecules that do not occur anywhere in nature, are capable of triggering chemical reactions in the lab.–The research is published in the journal Nature and promises to offer new insights into the origins of life, as well as providing a potential starting point for an entirely new generation of drugs and diagnostics. In addition, the authors speculate that the study increases the range of planets that could potentially host life.–All life on Earth depends on the chemical transformations that enable cellular function and the performance of basic tasks, from digesting food to making DNA. These are powered by naturally-occurring enzymes which operate as catalysts, kick-starting the process and enabling such reactions to happen at the necessary rate.–For the first time, however, the research shows that these natural biomolecules may not be the only option, and that artificial enzymes could also be used to power the reactions that enable life to occur.–The findings build on previous work in which the scientists, from the MRC Laboratory of Molecular Biology in Cambridge and the University of Cambridge, created synthetic molecules called “XNAs”. These are entirely artificial genetic systems that can store and pass on genetic information in a manner similar to DNA.

Using these XNAs as building blocks, the new research involved the creation of so-called “XNAzymes”. Like naturally occurring enzymes, these are capable of powering simple biochemical reactions.–Dr Alex Taylor, a Post-doctoral Researcher at St John’s College, University of Cambridge, who is based at the MRC Laboratory and was the study’s lead author, said: “The chemical building blocks that we used in this study are not naturally-occurring on Earth, and must be synthesised in the lab. This research shows us that our assumptions about what is required for biological processes – the ‘secret of life’ – may need some further revision. The results imply that our chemistry, of DNA, RNA and proteins, may not be special and that there may be a vast range of alternative chemistries that could make life possible.–Every one of our cells contains thousands of different enzymes, many of which are proteins. In addition, however, nucleic acids – DNA and its close chemical cousin, RNA – can also form enzymes. The ribosome, the molecular machine which manufactures proteins within all cells, is an RNA enzyme. Life itself is widely thought to have begun with the emergence of a self-copying RNA enzyme.–Dr Philipp Holliger, from the MRC Laboratory of Molecular Biology, said: “Until recently it was thought that DNA and RNA were the only molecules that could store genetic information and, together with proteins, the only biomolecules able to form enzymes.”“Our work suggests that, in principle, there are a number of possible alternatives to nature’s molecules that will support the catalytic processes required for life. Life’s ‘choice’ of RNA and DNA may just be an accident of prehistoric chemistry.”“The creation of synthetic DNA, and now enzymes, from building blocks that don’t exist in nature also raises the possibility that if there is life on other planets it may have sprung up from an entirely different set of molecules, and widens the possible number of planets that might be able to host life.”–The group’s previous study, carried out in 2012, showed that six alternative molecules, called XNAs, could store genetic information and evolve through natural selection. Expanding on that principle, the new research identified, for the first time, four different types of synthetic catalyst formed from these entirely unnatural building blocks.-These XNAzymes are capable of catalysing simple reactions, like cutting and joining strands of RNA in a test tube. One of the XNAzymes can even join strands together, which represents one of the first steps towards creating a living system. Because their XNAzymes are much more stable than naturally occurring enzymes, the scientists believe that they could be particularly useful in developing new therapies for a range of diseases, including cancers and viral infections, which exploit the body’s natural processes.—Dr Holliger added: “Our XNAs are chemically extremely robust and, because they do not occur in nature, they are not recognised by the body’s natural degrading enzymes. This might make them an attractive candidate for long-lasting treatments that can disrupt disease-related RNAs.”—Professor Patrick Maxwell, Chair of the MRC’s Molecular and Cellular Medicine Board and Regius Professor of Physic at the University of Cambridge, said: “Synthetic biology is delivering some truly amazing advances that promise to change the way we understand and treat disease. The UK excels in this field, and this latest advance offers the tantalising prospect of using designer biological parts as a starting point for an entirely new class of therapies and diagnostic tools that are more effective and have a longer shelf-life.”-Funders of the research included the MRC, European Science Foundation and the Biotechnology and Biological Sciences Research Council.The text in this work is licensed under a Creative Commons Licence. If you use this content on your site please link back to this page. For image rights, please see the credits associated with each individual image.- See more at: http://www.cam.ac.uk/research/news/worlds-first-artificial-enzymes-created-using-synthetic-biology#sthash.Hi3SOWu0.dpuf

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Breakthrough in synthetic enzymes could lead to the manufacture of organisms

  • Synthetic form of DNA, called XNA, is capable of editing genetic material
  • XNA triggered reactions thought to be crucial for life first starting on Earth
  • Scientists suggest alien life could have evolved using XNA instead of DNA
  • Artificial molecules could also be used to create synthetic life in the lab
  • Researchers believe XNA may lead to a new ways of treating cancers

The world’s first enzymes made from artificial genetic material have been created by scientists in what could be a major step towards generating synthetic life.-The enzymes, which do not occur naturally, were created using a synthetic form of DNA called XNA and were capable of triggering chemical reactions in the lab.-The findings build on previous work that showed six types of XNA molecules were capable of storing and transmitting genetic information in the same way as DNA and RNA.-It had been previously thought that DNA and RNA, which form the basis for all life on Earth, were the only way of storing genetic material.-But now the latest research by synthetic biologists in Cambridge shows that this synthetic genetic material is also capable of performing another crucial biological role – catalysing biochemical reactions that are essential for life.-Using their lab-made XNAs as building blocks, the team were able to create synthetic enzymes, which they have named ‘XNAzymes’, that could cut up and stitch together small chunks of genetic material, just like naturally occurring enzymes.-The suggests that such molecules could be used to replicate some of the earliest steps needed to produce life itself and may even provide clues about what life on other planets may be like.-It is thought that life first began with the evolution of a segment of RNA that was able to copy itself and catalyse reactions. If XNA is also capable of this, then it could also have led to different forms of life on other planets or could be used to create new synthetic forms of life. However, Dr Philipp Holliger, who led the research at the MRC Laboratory of Molecular Biology in Cambridge, said: ‘Our work suggests that, in principle, there are a number of possible alternatives to nature’s molecules that will support the catalytic processes required for life.-‘Until recently, it was thought that DNA and RNA were the only molecules that could store genetic information and, together with proteins, the only biomolecules able to form enzymes.-‘Life’s ‘choice’ of RNA and DNA may just be an accident of prehistoric chemistry.–‘The creation of synthetic DNA, and now enzymes, from building blocks that don’t exist in nature also raises the possibility that if there is life on other planets it may have sprung up from an entirely different set of molecules, and widens the possible number of planets that might be able to host life.’-In 2012 Dr Holliger’s group showed that there were six alternative molecules to the oligonucleotides that form RNA and DNA, which they called XNAs.–They demonstrated that these could store information and could even evolve through natural selection.-In their latest research, which is published in the journal Nature, the team created four different types of synthetic enzyme from strands of XNA.–These XNAzymes were able to perform the role of a polymerase – an enzyme that cuts and joins RNA strands together – in a test tube. One of the XNAzymes they created was also able to join XNA strands together to form longer molecules – a key step towards creating a living system that can replicate itself.–Although it will still be some time before these can be used to create living synthetic organisms, Dr Holliger believes that XNAzymes could also be useful for developing new therapies for range of diseases including cancers and some viral infections.-Dr Holliger added: ‘Our XNAs are chemically extremely robust and, because they do not occur in nature, they are not recognised by the body’s natural degrading enzymes.-‘This might make them an attractive candidate for long-lasting treatments that can disrupt disease-related RNAs.’Professor Patrick Maxwell, chair of the MRC’s Molecular and Cellular Medicine Board, said the work could kick start an entirely new branch of medicine.

Two of the XNA enzymes created by the scientists at the Laboratory of Molecular Biology in Cambridge, which were able to join two strands of XNA together (left) and cut up strands of RNA (right)-Life on other planets outside our own solar system, like this exoplanet, could have evolved from XNA rather than RNA, which could have led to very different forms of life to those we are familiar with here on Earth–He said: ‘Synthetic biology is delivering some truly amazing advances that promise to change the way we understand and treat disease. ‘This latest advance offers the tantalising prospect of using designer biological parts as a starting point for an entirely new class of therapies and diagnostic tools that are more effective and have a longer shelf-life.’-Professor Jack Szostak, a Nobel prize winner at Harvard University who studies the origins of life, added that the research raises some fundamental questions about what life on other planets may be like.He told New Scientist: ‘The possibility that life elsewhere, on exoplanets, could have started with something other than RNA or DNA is quite interesting. ‘But the primordial biopolymer for any form of life must satisfy other constraints as well, such as being something that can be generated by prebiotic chemistry and replicated efficiently.-‘Whether XNA can satisfy these constraints, as well as providing useful functions, remains an open question.’

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Synthetic enzymes hint at life without DNA or RNA

Life might not have to be based on DNA or RNA (Image: Mohamed Sadath/Getty)

Enzymes that don’t exist in nature have been made from genetic material that doesn’t exist in nature either, called XNA, or xeno nucleic acid.–It’s the first time this has been done and the results reinforce the possibility that life could evolve without DNA or RNA, the two self-replicating molecules considered indispensible for life on Earth.–“Our work with XNA shows that there’s no fundamental imperative for RNA and DNA to be prerequisites for life,” says Philipp Holliger of the Laboratory of Molecular Biology in Cambridge, UK, the same laboratory where the structure of DNA was discovered in 1953 by Francis Crick and James Watson.

It’s not all about the base–

Holliger’s team has made XNAs before. Their unnatural XNA contains the same bases – adenine, thymine, guanine, cytosine and uracil – on which DNA and RNA rely for coding hereditary information. What’s different is the sugar to which each base is attached.In DNA and RNA, the sugars are deoxyribose and ribose, respectively. Holliger made new types of genetic material by replacing these with different sugars or other molecules.–Now, they have taken a step closer to mimicking early life on the planet by showing that XNAs can also serve as enzymes – indispensible catalysts for speeding up chemical reactions vital for life.–One of the first steps towards life on Earth is thought to be the evolution of RNA into self-copying enzymes.

Big steps

So by showing that XNAs can act as enzymes, on top of being able to store hereditary information, Holliger has recreated a second major step towards life.–The XNA enzymes can’t yet copy themselves but they can cut and paste RNA, just like natural enzymes do, and even paste together fragments of XNA.–It’s the first demonstration that, like prehistoric RNA, XNA can catalyse reactions on itself, even if it can’t yet copy itself as RNA can.–Holliger argues that RNA and DNA may have come to dominate Earth by chance, simply because they were the best evolutionary materials to hand. “You could speculate that on other planets, XNAs would dominate instead,” he says.

Primal molecules

“This work is another nice step towards demonstrating the functional capabilities of XNAs,” says Nobel prizewinner Jack Szostak of Harvard University, who studies the origins of life on Earth .–“The possibility that life elsewhere, on exoplanets, could have started with something other than RNA or DNA is quite interesting, but the primordial biopolymer for any form of life must satisfy other constraints as well, such as being something that can be generated by prebiotic chemistry and replicated efficiently,” Szostak says. “Whether XNA can satisfy these constraints, as well as providing useful functions, remains an open question.”

Holliger says that XNAs may also have roles to play in medicine. Because they do not occur naturally, they can’t be broken down in the human body. And since they can be designed to break and destroy RNA, they could work as drugs for treating RNA viruses or disabling RNA messages that trigger cancers.-“We’ve made XNA enzymes that cut RNA at specific sites, so you could make therapies for cleaving viral or oncogenic messenger RNA,” says Holliger. “And because they can’t be degraded, they could give long-lasting protection.”

Journal reference: Nature, DOI: 10.1038/nature13982

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Scientists unveil giant leap towards synthetic life

Achievement akin to ‘climbing Mount Everest’ in its complexity

Steve Connor

Friday, 28 March 2014

Scientists have made the first artificial chromosome which is both complete and functional in a milestone development in synthetic biology, which promises to revolutionise medical and industrial biotechnology in the coming century.–The researchers built the artificial chromosome from scratch by stitching synthetic strands of DNA together in a sequence based on the known genome of brewer’s yeast. They predict that a completely synthetic yeast genome comprised of its entire complement of 16 chromosomes could be made within four years.-“Our research moves the needle in synthetic biology from theory to reality. This work represents the biggest step yet in an international effort to construct the full genome of synthetic yeast,” said Jef Boeke of the New York University School of Medicine, a lead author of the study published in the journal Science.-“It is the most extensively altered chromosome ever built. But the milestone that really counts is integrating it into a living yeast cell. We have shown that yeast cells carrying this synthetic chromosome are remarkably normal,” Dr Boeke said.–“They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot [do],” he said.–“Not only can we make designer changes on a computer, but we can make hundreds of changes through a chromosome and we can put that chromosome into yeast and have a yeast that looks, smells and behaves like a regular yeast, but this yeast is endowed with special properties that normal yeasts don’t have,” he explained.–The synthetic yeast chromosome was based on chromosome number 3, but scientists deleted large parts of it that were considered redundant and introduced further subtle changes to its sequence – yet the chromosome still functioned normally and replicated itself in living yeast cells, they said.–“We took tiny snippets of synthetic DNA and fused them together in a complex series of steps to build an essentially computer-designed chromosome 3, one of the 16 chromosomes of yeast. We call it ‘synIII’ because it’s a completely synthetic derivative that has been engineered in a variety of interesting ways to make it different from the normal chromosome,” Dr Boeke said.–The achievement was compared to climbing Mount Everest in its labour-intensive complexity, as it involved stitching together 273,871 individual building blocks of DNA – the nucleotide bases of the yeast’s genes – in the right order, and removing about 50,000 repeating sequences of the chromosome that were considered redundant.–“When you change the genome you’re gambling. One wrong change can kill the cell. We have made over 50,000 changes to the DNA code in the chromosome and our yeast still lived. That is remarkable, it shows that our synthetic chromosome is hardy, and it endows the yeast with new properties,” Dr Boeke said.–Britain is one of several countries involved in the international effort to synthesise all 16 yeast chromosomes. Last year, the Government announced that it will spend £1 million on the yeast project out of a total budget of £60 million it has dedicated to synthetic biology.–Paul Freemont of Imperial College London said that the first complete and functional synthetic yeast chromosome is “a big deal” and significant step forward from the work by DNA scientist Craig Venter, who synthesised the much simpler genome of a bacterium in 2010.–“It opens up a whole new way of thinking about chromosome and genome engineering as it provides a proof of concept that complicated chromosomes can be redesigned, synthesised and made to work in a living cell,” Dr Freemont said.–Artificial chromosomes designed by computer will be vital for the synthetic life-forms that scientists hope to design for a range of applications, such as the breakdown of persistent pollutants in the environment or the industrial manufacture of new kinds of drugs and vaccines for human and animal medicine.–“It could have a lot of practical applications because yeast is used in the biotechnology industry to produce everything from alcohol, which has been produced for centuries, to biofuels and speciality chemicals to nutrients,” Dr Boeke said.–“Yeast is a really interesting microorganism to work on because it has an ancient industrial relationship with man. We’ve domesticated it since the days of the Fertile Crescent and we’ve had this fantastic collaboration to make wine, break and beer,” he said.–“That relationship persists today in a wide range of products that are made with yeast such as vaccines, fuels and specialty chemicals and it’s only going to be growing. Yeast is one of the few microbes that packages its genetic material in a nucleus just like human cells. So it serves as a better model for how human cells work in health and disease,” Dr Boeke added.

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Scientists create ‘alien’ life form with artificial genetic code

 

From left to right, the structures of A-, B- and Z-DNA. Zephyris

Scientists made a substantial breakthrough in understanding how to alter the fundamental nature of life, and they did so by creating for the first time a partially artificial life form that passes along lab-engineered DNA. –The work, published online in the journal Nature on Wednesday, came from the Scripps Research Institute in La Jolla, Calif., and centered around a modified strain of E. coli bacterium that was fused with chemically synthesized nucleotides and was able to replicate its natural and synthetic components during reproduction. -Throughout the entire history of life on Earth, the genetic code of all organisms has been uniform, from the simplest of bacteria all the way up to human beings, meaning our genetic code is composed of the same four nucleotides labeled A, C, T, and G. Those nucleotides join to form base pairs, which are used in the creation of genes that cells use to produce proteins. –Researchers at Scripps created two new nucleotides, X and Y, and fused them into the E. coli bacterium. The organism was able to reproduce normally with six — instead of the standard four — nucleotides, meaning it genetically passed along the first combination of manmade and natural DNA. -“This has very important implications for our understanding of life,” Floyd Romesberg, who headed the Scripps researcher team, told The New York Times. “For so long people have thought that DNA was the way it was because it had to be, that it was somehow the perfect molecule.” –Because this breakthrough could impact more than just biological research, the field — called synthetic biology — is likely to be met with harsh criticism from those who fear that tampering with the building blocks of existence could be a step too far for science. The subset of synthetic biology focusing on creations unfamiliar to nature with expanded genetic alphabets is sometimes referred to as xenobiology. –“The arrival of this unprecedented ‘alien’ life form could in time have far-reaching ethical, legal and regulatory implications,” Jim Thomas of the ETC Group, a Canadian advocacy organization, told The New York Times. “While synthetic biologists invent new ways to monkey with the fundamentals of life, governments haven’t even been able to cobble together the basics of oversight, assessment or regulation for this surging field.”-To create a modified organism that would reproduce, Romesberg’s team had to first create stable enough artificial nucleotides. The creation of X and Y variants came only after 300 types were tried. The X nucleotide pairs with the Y, just as A does with T and C with G in natural DNA. It’s unclear whether a semi-artificial organism could sustain a far more expansive genetic code, meaning many more synethic pairs, and if there is any time-based restraint involved.-As far as worrying about never-before-seen strains of bacteria escaping into the wild, Romesberg stressed that this newly created organism could never infect anything. To continue reproducing the synthetic nucleotides, the researchers had to feed the necessary chemicals to the bacterium or else it would stop producing the X and Y pair. P–Romesberg and his colleagues’ findings follow decades of work in synthetic biology, and the results have long since left the confines of academic research. Romesberg’s company, Synthorx, is trying to design an administering technique for viruses that would rely on the artificial life forms’ inability to reproduce the synthetic nucleotides without the proper chemicals, meaning they could be used to create an immune system response while be inhibited from spreading.

Beyond those immediate applications, the next steps are figuring out if the synthesized nucleotides can be fused into the RNA of living organisms and used to produce new proteins, as well as discovering whether or not genetically engineered cells could be used to help organisms reproduce those synthetic nucleotides on their own.

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Good Bacteria in the Intestine Prevent Diabetes

Good Bacteria in the Intestine Prevent Diabetes, Study Suggests

Jan. 18, 2013 — All humans have enormous numbers of bacteria and other micro-organisms in the lower intestine. In fact our bodies contain about ten times more bacteria than the number of our own cells and these tiny passengers are extremely important for our health. They help us digest our food and provide us with energy and vitamins. These ‘friendly’ commensal bacteria in the intestine help to stop the ‘bad guys’ such as Salmonella that cause infections, taking hold. Even the biochemical reactions that build up and maintain our bodies come from our intestinal bacteria as well as our own cells. -Pretty important that we get along with these little bacterial friends… definitely. But as in all beautiful relationships, things can sometimes turn sour. If the bacteria in the intestine become unbalanced, inflammation and damage can occur at many different locations in the body. The best known of these is the intestine itself: the wrong intestinal bacteria can trigger Crohn’s disease and ulcerative colitis. The[U1]  liver also becomes damaged when intestinal bacteria are unbalanced.—Research groups led by Professor Jayne Danska at the Sick Children’s Hospital of the University of Toronto and Professor Andrew Macpherson in the Clinic for Visceral Surgery and Medicine at the Inselspital and the University of Bern have now shown that the influence of the intestinal bacteria extends even deeper inside the body to influence the likelihood of getting diabetes. In children and young people, diabetes is caused by the immune cells of the body damaging the special cells in the pancreas that produce the hormone insulin. By[U2]  chance, 30 years ago, before the development of genetic engineering techniques, Japanese investigators noticed that a strain of NOD laboratory mice tended to get diabetes. These mice (also by chance) have many of the same genes that make some humans susceptible to the disease. With the help of the special facilities of the University of Bern and in Canada, these teams have been able to show that the intestinal bacteria, especially in male mice, can produce biochemicals and hormones that stop diabetes developing.—Diabetes in young people is becoming more and more frequent, and doctors even talk about a diabetes epidemic. This increase in diabetic disease has happened over the last 40 years as our homes and environment have become cleaner and more hygienic. At the moment, once a child has diabetes, he or she requires life-long treatment.[U3] “We hope that our new understanding of how intestinal bacteria may protect susceptible children from developing diabetes, will allow us to start to develop new treatments to stop children getting the disease,” says Andrew Macpherson of the University Bern.—Story Source-The above story is reprinted from materials provided by University of Bern. —Journal Reference-J. G. M. Markle, D. N. Frank, S. Mortin-Toth, C. E. Robertson, L. M. Feazel, U. Rolle-Kampczyk, M. von Bergen, K. D. McCoy, A. J. Macpherson, J. S. Danska. Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity. Science, 2013; DOI: 10.1126/science.1233521

Toxic Effects of Excessive Consumption of MSG

Toxic Effects of Excessive Consumption of MSG

The toxic effects that occur as a result of excessive consumption of MSG are known as Chinese Restaurant Syndrome.

MSG is known to be more toxic than Glutamic Acid – this is due to MSG being more readily absorbed by the body compared to Glutamic Acid.  The increased toxicity of MSG is also believed to occur from the presence of the D-Glutamic Acid form of Glutamic Acid (as opposed to L-Glutamic Acid).

Digestive System—Excessive consumption of MSG may cause Intestinal Cramps (abdominal Pain).  Excessive consumption of MSG may cause Vomiting.  references

Eyes/Vision–Excessive consumption of MSG may cause Blurred Vision.

Excessive consumption of MSG may damage the Retina (which could lead to Blindness)

Excessive consumption of MSG may cause Sight impairment.

Metabolism—Excessive consumption of MSG may cause atrophy of the Thyroid.

Musculoskeletal  System-Excessive consumption of MSG may contribute to the symptoms of Fibromyalgia and some Fibromyalgia patients may experience symptom relief after discontinuing MSG use.

Excessive consumption of MSG may cause Muscle Tension.

Nervous System–Excessive consumption of MSG may cause Convulsions

Excessive consumption of MSG may cause Headaches.

Excessive consumption of MSG may damage the Hypothalamus.

Excessive consumption of MSG may cause impairment of Long-Term Memory.

Excessive consumption of MSG may trigger Migraines.

Many of the toxic effects of excessive consumption of MSG are due to MSG causing excessive stimulation of the N-Methyl-D-Aspartate (NMDA) Receptors in the Brain.

Excessive consumption of MSG may cause Nausea.

Excessive consumption of MSG may cause atrophy of the Pituitary Gland.

Excessive consumption of MSG may cause Vertigo (dizziness).

Respiratory System-Excessive consumption of MSG may cause Asthma.

Sexual System:  Female Excessive consumption of MSG may cause Female Infertility.  Excessive consumption of MSG may cause cause Male Infertility.

Excessive consumption of MSG may cause atrophy of the Ovaries.

Excessive consumption of MSG may cause atrophy of the Testes.

MSG may Interfere with these Substances

Amino Acids–Excessive consumption of MSG may interfere with Taurine.

Enzymes—MSG may lower Catalase levels.

MSG may lower Glutathione Peroxidase levels.

MSG may lower Glutathione Reductase levels.

MSG may lower Superoxide Dismutase levels.

MSG may Enhance the Function of these Substances

Amino Acids–MSG can be converted within the body to form Glutamic Acid.

MSG can be converted within the body to form Glutamine.

Celery Seed and Benefits

Celery Seed

 Gout sufferers take heart! You may find relief with Celery Seed. Its exceptional diuretic action not only promotes the flow of urine and uric acid excretions from the kidneys, helping to flush kidney stones and gravel, but its antiseptic properties ease urinary inflammation and benefits the overall health of the urinary tract. Celery Seed is also thought to be an especially helpful anti-inflammatory for people who suffer from joint discomforts, such as arthritis and rheumatism.

Botanical: Apium graveolens

Family: Umbelliferae (carrot) – Apiaceae (parsley)Other Common Names: Smallage, Marsh Water Parsley, Wild Celery, Garden Celery, Marsh Parsley

 History:

Celery has been used since earliest times as a food, for flavoring and for medicinal purposes. Of uncertain origin, perhaps the Mediterranean region, the bitter marsh plant grew wild on wet and flooded salt marshes, and it is sometimes called “smallage,” a biennial with stalks that grow from one to two feet. Celery Seed is the dried fruit (tiny brown seed with a celery-like flavor and aroma) of the Apium graveolens. Its botanical genus, the Latin, apium, may be derived from a prehistoric Indo-European word for water. If true, it seems logical that celery’s growth preference is wet soil and marshes. The town of Selinuntein Sicilyderived its name from the Greek word for the plant, selinon (Σέλινο). The ancient Egyptians used the plant for culinary purposes, and Celery leaves were part of the garlands discovered in the tomb of the Egyptian pharoah, Tutankhamun. The Greeks and Romans used Celery for medicinal and culinary purposes, and there was even a popular belief that it was an aphrodisiac. The use of Celery Seed for relieving pain and inflammation was described by Aulus Cornelius Celcus (circa 30 AD). It was also regarded in ancient times to have magical properties and was frequently associated with rites and celebrations of death and the underworld. In the Middle Ages, Italian farmers began to cultivate “smallage,” and once begun, this cultivation steadily improved its quality. When the seeds were first used is not clear, but we know that the English herbalist, Nicholas Culpeper, wrote in 1653 that Celery Seeds would “sweeten and purify the blood.” Celery was introduced to the new world as a vegetable, but in the nineteenth century, it was known that the Shakers grew “smallage” for their medical remedies. The plant grows in North and South America, Europe, Asiaand Africa. It is used in Ayurvedic medicine for asthma, bronchitis, hiccups, flatulence and as a nerve tonic; and in Mainland China, it is taken to reduce hypertension. In temperate countries, Celery is also grown for its seeds, which yield a valuable volatile oil used in the perfume and pharmaceutical industries. Celery Seeds can be used as flavoring or spice either as whole seeds or, ground and mixed with salt, as celery salt. The seeds, harvested after the plant flowers in its second year, are the basis for homeopathic remedies as a diuretic and for urinary tract inflammations. Celery Seeds and stalks contain a sedative compound called phthalide, and the seeds contain essential oils (bergapten, apiole, which is very potent), 3-n-butylphthalide (3-n-B), beta-carotene, beta-sitosterol, fiber, flavonoids (apigenin, rutin, quercetin), calcium, choline, folate, iron, magnesium, manganese, phosphorus, potassium, selenium, copper, chromium, bromine, sulfur, zinc, silicon, stearic acid, thymol, scopoletin, limonene, eugenol, P-coumaric acid, pectin, mannitol, essential fatty acids (linoleic acid, linolenic acid), amino acids, arginine, alanine, tryptophan, tyrosine, B-vitamins and vitamins A, C, E and K. and  andersterone

Beneficial Uses:

Celery Seed is an excellent herbal diuretic that promotes the flow of urine through the kidneys and increases uric acid excretions, helping to clear toxins from the system. This is especially good for gout, where excess uric acid crystals collect in the joints. Its diuretic action may also relieve bladder disorders, cystitis and other kidney problems including stones and gravel. Early herbalists used it as a cleansing tonic after the stagnation of winter, and herbalists in France today use the extract to relieve retention of urine.

Celery Seed may support a healthy heart. Its diuretic properties help to rid the body of excess water through increased urine flow, including the release of fluid surrounding the heart, which helps to reduce the heart’s workload.

Celery Seed is considered beneficial for easing the discomfort and degeneration of the body joints frequently associated with age. Its anti-inflammatory properties also appear to help those who suffer from rheumatoid arthritis, osteoarthritis, gout and neuralgia, and its diuretic qualities help flush impurities (including uric acid and other toxins) from the kidneys, which frequently cause these ailments. Considered a fine anti-inflammatory, the 3-n-butylphthalide content in Celery Seed is said to calm the action of COX-1 and COX-2 enzymes that trigger pain and cause swelling and discomfort, especially in the joints. Moreover, researchers at the University of Chicago Medical Center found that 3-n-B may also help lower blood pressure and improve overall circulation.

Although Celery is said to be a stimulant (particularly in kidney function), it is also known as a sedative that will calm stressed nerves and promote restfulness and sleep.

Celery Seed is thought to have a calming effect on the digestive system, enhancing appetite, relieving gas and indigestion.

In 2009, researchers from Brigham and Women’s Hospital and HarvardMedicalSchoolshowed that increased intake of the flavonoid  apigenin, found in Celery (and parsley and cooked tomato), may reduce the risk of ovarian cancer by twenty percent in a large, population-based study. The mechanism included an inhibitory effect on endogenous estrogen activity or a reduction on circulating estrogen levels via competition for estrogen receptors or suppression of estrogen biosynthesis.

Celery Seed is a popular folk remedy for promoting the onset of menstruation.

Recipe –Combine Celery seed-Rosemary-Parsley—equal parts dried 1 tablespoon of each—and mix in a heated water  2 cup capacity pot or container -or in broths and drink several oz throughout the day—the added benefits of the pther herbs would be again anti-inflammatory and kidney regulating-and the antioxidant profile to further protect the endocrine system as well as the brain liver and blood CAs an Anti Estrogen—for males this will maintain the levels of Testosterone and for Women it will assist in the balancing of the excesses of estrogens and estrogen conversions—Adding iodine to this will increase estriol production further lowering and balancing estradiol—but men and women can benefit from this to minimize estrogenically based cancers—