Synthetic Biology

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My goal is to be able to design a synthetic bio project regarding quorn or corn within three weeks.

Lecture: Tom Ellis - Synthetic Biology

  • the engineering of biology, which displays functions not found in nature
  • hacking the codebooks for life - DNA genomes
  • biology as information science - custom dna sequences to be written chemically
  • classic method (aimed at accelerating biotech and biosciences)
    • standardisation
    • modularity
    • abstraction
    • design rules
    • modelling and simulation
    • opensource innovation
  • example: 10 years ago - edge detection of images - image edge detect to biological process of cells - abstraction w/ logic gate system through E.coli + v fischeri + lambda phase + cyanobacteria
  • iGEM uses biobricks
  • registry of standard parts - open source, modular
    • plasticity - recycling bioreactor, MAPLE)
    • auxin - bacteria promoting revegetation through signals to plant to put down more fibrous roots
    • parasight - bacterial that changes colour if infected with deadly parasite
    • e.chromi - pigmented e.coli
  • real projects right now
    • biofuels
    • antibiotics
    • natural fertilisets
    • rapid printing of vaccines
    • microbes to kill cancer

sc2.0

  • ellis lab: areas of interest - dna assembly, pattern formation, cellular capacity, engineered regulation , intrinsic containment, synthetic genome, the first artificial organization - electronic code - 2010: craig venter institute - a complete synthesis of a million base part bacterial genome from electronic code (w/ watermarks) [most pretentious bacteria, charlie brooker could not help but quip)
  • assembly of synthetic yeast - dd: what are the different types of yeast anyway?
  • Sc2.0 – A Human-made Yeast Genome. Project = Synthetic Yeast 2.0 - http://biostudio.bme.jhu.edu/sc2/.
  • watermark sequences of intergenic sites with cryptic code
  • scientist names, famous quotes, email addresses
  • normal vs synthetic evolution : retrotranposon, subtelometric repetition, introus codon, the code of life, 64 codon, 3 pases, amino acids, scramble tooklet, IxcP, PCR
  • value add - using Sc2.0 to make yeast do things like generate
  • partsregistry.org
  • synbioproject.org/topics/synbiology
  • igem.org
  • nematode worm & memory -??
  • brainbuds/livergrowing experiments
  • what motivates your choice of project? - $ and the interest in the nuts and bolts process

Definition of Synthetic biology

  • Definition from Synthetic Biology: Tools and Applications (2013) by Zhao Huimin: "Synthetic biology is the design, construction, and characterization of improved or novel biological systems using engineering design principles"
  • Definition from Synthetic Biology: Industrial and Environmental Applications (2012) by Markus Schmidt: "Synthetic biology is the design and construction of biological devices and systems for useful purposes."
  • Definition from Synthetic Biology Engineering Research Center (SynBERC): Synthetic biology is the design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems.
  • Definition from ERAsynbio (EU's synthetic biology network): Synthetic Biology is the engineering of biology: the deliberate (re)design and construction of novel biological and biologically based systems to perform new functions for useful purposes, which draws on principles elucidated from biology and engineering.
  • Polish geneticist said in 1974 Wacoaw Syzbalski: "Up to now we are working on the descriptive phase of molecular biology… but the real challenge will start when we enter the synthetic biology phase of research in our field. We will then devise new control elements and add these new modules to the existing genomes or build up wholly new genomes…. a field with unlimited expansion potential and hardly any limitations to building 'new better control circuits' and finally other' synthetic' organisms, like a 'new better mouse'.
  • syn bio is sometimes confused with systems biology or metabolic engineering. the difference is that system biology forces more on the characterisation of complex interactions within biological systems using a more holistic perspective, so sys bio and syn bio are like two sides of the same code. metabolic engineering focuses on engineering of cellular metabolism to product a certain substance using recombinant dna tech. however metabollic engineering is limited to singe cells and to maximise the formation of specific product. the difference between that and synbio is that it deals with a biological system which could be anything from a genome, a cell, a tissue, and an ecosystem. synthetic biologists also address broader issues - and are not limited to recombinant dna technology.
  • key tools for synbio include dna synthesis, construction of large size dna molecules, and bio-orthogonal systems such as the introduction of unnatural amino acids into proteins

various digressions

  • The DNA can be cut with restriction enzymes to look for single nucleotide polymorphisms (SNPs) which can tell the identity of a person. This is how forensics scientists identify a person based on DNA evidence, and also how paternity can be determined (a child will have combination of SNPs from mom and dad) SNPs can also tell you if someone is prone to a certain genetic disease in some cases.
  • DNA can be sequenced - you can get the exact base pair sequence. Again, this can tell you about the persons genetic make up... different versions of different genes they have, etc. In an experimental lab, it can verify that you are working with the DNA that you think you are.
  • DNA can be put through chromation immunoprecipitation assays (ChIP) In this test, you are looking for a protein that bind to a particular sequence of DNA. This is often use to determine transcription factor - promoter interactions...
  • you can cut the DNA with a restriction enzyme and run it through an electrophoresis chamber
  • you could put into a plasmid gene and transfer it to a bacteria

Fish forensics

To identify a piece of fish, AFT staff slice off a tiny sample from a fillet, heat it up to break down the tissue and open up its cells, and spin it in a centrifuge to extract the DNA. They put this genetic material through a technique that uses polymerase chain reactions (PCR) to produce many copies of a particular DNA segments. By amplifying just a few different genes—most often, the COI gene—researchers can readily distinguish similar-looking pieces of fish and determine their species.

Using water in mouth to flush out excess urea (turtles urinate through their mouth, solution for kidney patients?)

Urinating Through Your Mouth Is Great. Ask This Turtle. - See more at: http://inkfish.fieldofscience.com/2012/10/urinating-through-your-mouth-is-great.html#sthash.8lKGOL7k.dpuf http://inkfish.fieldofscience.com/2012/10/urinating-through-your-mouth-is-great.html

Ip writes in the Journal of Experimental Biology that turtles on dry land dunked their heads in water for 20 to 100 minutes at a time. While submerged, they repeatedly "rinsed" their mouths with water while rhythmically pulsing their throats. He discovered that this motion simultaneously pulled oxygen out of the water, so the turtles could keep breathing, and expelled urea into it.

Looking at the turtle's DNA, the researchers found what looked like a gene for a urea transporter, a protein that carries urea molecules across membranes. The gene was active in the turtle's mouth and the gill-like BVPs, but not—as it would be in humans or almost any other vertebrate animal—in the kidneys.

Ip thinks the Chinese soft-shelled turtle's strategy is not, unlike most cases of misplaced urine, an accident. He notes that P. sinensis and other soft-shelled turtles often live in salty marshes and swamps, or even in the sea. If they excreted urea in the usual way, they would need to continuously drink the water around them to make urine. But like human castaways in the ocean, the turtles would be ill-advised to drink this water; their kidneys can't handle that much salt. So instead, P. sinensis—perhaps along with the other soft-shelled turtles—sends urea back toward its mouth after filtering it from its blood. To dispose of the urea, the turtle only has to rinse its mouth with water, not drink it.

Chinese soft-shelled turtles aren't the only animals that know the taste of urea. Cows and other ruminant animals excrete some urea into their saliva. Their reasons are quite different: they use nitrogen in urea to feed the friendly bacteria that live in their guts and help them digest plant matter. By swallowing their urea-carrying saliva, cows send it to their stomach and keep their microbes alive.

You may find this trick unappealing, but to Ip it's inspirational. Hypothetically, he says, doctors could one day treat patients who have kidney failure by turning on genes for urea excretion in their mouths, just as these genes are turned on in turtles. "Urea excretion can still occur through rinsing the mouth with water, just like the soft-shelled turtle," he says, "without having to go through blood dialysis." Then we'll be able to ask them just how great it is. - See more at: http://inkfish.fieldofscience.com/2012/10/urinating-through-your-mouth-is-great.html#sthash.8lKGOL7k.dpuf

Apples which do not brown

To scientifically breed Arctic apples, Okanagan Specialty Fruits’ science team turns down the expression of the apple PPO genes in a process called gene silencing, which utilizes low-PPO genes from other apples. Gene silencing is a natural process that all plants (and animals too) use to control expression of their genes. This apple-to-apple transformation is aided by time-proven biotechnology tools. In the end, Arctic apples produce too little PPO to brown. (For an even more detailed description of Arctic apple science, visit the OSF website.) No frankenfood here, folks – just apples, now with suppressed PPO to stop enzymatic browning. http://www.arcticapples.com/arctic-apples-story/how-we-keep-apples-from-turning-brown

Pigeon which poops soap

Huitlacoche

  • "We had no idea huitlacoche could actually synthesize significant nutrients that don't even exist in corn," says Octavio Paredes-Lopez, one of Mexico's leading food scientists.
  • Loaded with lysine When huitlacoche attacks corn, the insidious-looking pustules that bubble up don't just force the husk to explode, it forces the metabolical process inside the cob to change, creating new, healthier nutrients. Take lysine, one of those "essential amino acids" that the body requires but can't manufacture. We need it to fight infections and strengthen bones. Bodybuilders pound lysine when they want to build muscle, and estheticians recommend it to keep skin looking young. Corn has virtually no lysine; huitlacoche is loaded with it. It also is packed with more beta-glucens — the soluble fiber that gives oatmeal its well-known cholesterol-cutting power — than, well, oatmeal.
  • Their findings: An ear of huitlacoche costs about 41 cents to produce and sells for about $1.20. By comparison, an ear of sweet corn costs about less than a dime, with profits of just a few cents per ear.
  • Still, if fresh huitlacoche has an image problem, the canned product — slimy, black and gooey — has even more to overcome.
  • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1169972/ - Identification of a motor protein required for filamentous growth in Ustilago maydis. - The phytopathogenic fungus Ustilago maydis exists in two stages, the yeast-like haploid form and the filamentous dikaryon. Both pathogenicity and dimorphism are genetically controlled by two mating-type loci, with only the filamentous stage being pathogenic on corn. We have identified two genes (kin1 and kin2) encoding motor proteins of the kinesin family. Kin1 is most similar to the human CENP-E gene product, while Kin2 is most closely related to the conventional kinesin Nkin of Neurospora crassa. Deletion mutants of kin1 had no discernible phenotype; delta kin2 mutants, however, were severely affected in hyphal extension and pathogenicity. The wild-type dikaryon showed rapid tip growth, with all the cytoplasm being moved to the tip compartment. Left behind are septate cell wall tubes devoid of cytoplasm. In delta kin2 mutants, dikaryotic cells were formed after cell fusion, but these hyphal structures remained short and filled with cytoplasm. A functional green fluorescent protein (GFP)-Kin2 fusion was generated and used to determine the localization of the motor protein by fluorescence microscopy. Inspection of the hyphal tips by electron microscopy revealed a characteristic accumulation of darkly stained vesicles which was absent in mutant cells. We suggest that the motor protein Kin2 is involved in organizing this specialized growth zone at the hyphal tip, probably by affecting the vectorial transport of vesicles.

artificial jellyfish from rat's heart

Despite being one of the most alien-looking things on Earth, the mechanism jellyfish use to swim is similar in some ways to the beating human heart. That inspired researchers to build a sort of cyborg jellyfish from the ground up, using heart muscle cells from a rat and silicone polymer. And it's actually only a little more odd-looking than a regular jelly.

The heart cells harvested from the rat were grown onto the silicone. When an electric current is sent through the water, the jellyfish--named "Medusoid"--contracts in a way that mimics a heart. The technique could eventually lead to scientists creating bio-engineered systems for humans, such as a pacemaker that works without batteries. The jellyfish could also make a good vessel for testing heart drugs before they're used on humans.

miracle berry

  • The berry itself has a low sugar content and a mildly sweet tang. It contains a glycoprotein molecule, with some trailing carbohydrate chains, called miraculin.[8][9] When the fleshy part of the fruit is eaten, this molecule binds to the tongue's taste buds, causing sour foods to taste sweet. At neutral pH, miraculin binds and blocks the receptors, but at low pH (resulting from ingestion of sour foods) miraculin binds protons and becomes able to activate the sweet receptors, resulting in the perception of sweet taste.[10] This effect lasts until the protein is washed away by saliva (up to about 60 minutes).
  • Miraculin (MCL) is a homodimeric protein isolated from the fruits of Richadella dulcifica, a shrub native to West Africa. Although it is flat in taste at neutral pH, MCL has taste-modifying activity in which sour stimuli produce a sweet perception. Once MCL enters the mouth, strong sweetness can be detected for more than 1 h each time we taste a sour solution. While the human sweet taste receptor (hT1R2–hT1R3) has been identified, the molecular mechanisms underlying the taste-modifying activity of MCL remain unclear. Recently, experimental evidence has been published demonstrating the successful quantitative evaluation of the acid-induced sweetness of MCL using a cell-based assay system. The results strongly suggested that MCL binds hT1R2–hT1R3 as an antagonist at neutral pH and functionally changes into an agonist at acidic pH. Since sweet-tasting proteins may be used as low-calorie sweeteners because they contain almost no calories, it is expected that MCL will be used in the near future as a new low-calorie sweetener or to modify the taste of sour fruits.

biofactories

  • From miracle fruit to transgenic tomato: mass production of the taste-modifying protein miraculin in transgenic plants. - The utility of plants as biofactories has progressed in recent years. Some recombinant plant-derived pharmaceutical products have already reached the marketplace. However, with the exception of drugs and vaccines, a strong effort has not yet been made to bring recombinant products to market, as cost-effectiveness is critically important for commercialization. Sweet-tasting proteins and taste-modifying proteins have a great deal of potential in industry as substitutes for sugars and as artificial sweeteners. The taste-modifying protein, miraculin, functions to change the perception of a sour taste to a sweet one. This taste-modifying function can potentially be used not only as a low-calorie sweetener but also as a new seasoning that could be the basis of a new dietary lifestyle. However, miraculin is far from inexpensive, and its potential as a marketable product has not yet been fully developed. For the last several years, biotechnological production of this taste-modifying protein has progressed extensively. In this review, the characteristics of miraculin and recent advances in its production using transgenic plants are summarized, focusing on such topics as the suitability of plant species as expression hosts, the cultivation method for transgenic plants, the method of purifying miraculin and future advances required to achieve industrial use.

taste modifying

  • http://en.wikipedia.org/wiki/Thaumatin - haumatin production is induced in katemfe in response to an attack upon the plant by viroid pathogens. Several members of the thaumatin protein family display significant in vitro inhibition of hyphal growth and sporulation by various fungi. The thaumatin protein is considered a prototype for a pathogen-response protein domain. This thaumatin domain has been found in species as diverse as rice and Caenorhabditis elegans. Thaumatins are pathogenesis-related (PR) proteins, which are induced by various agents ranging from ethylene to pathogens, and are structurally diverse and ubiquitous in plants:[2] They include thaumatin, osmotin, tobacco major and minor PR proteins, alpha-amylase/trypsin inhibitor, and P21 and PWIR2 soybean and wheat leaf proteins. The proteins are involved in systematically acquired resistance and stress response in plants, although their precise role is unknown.[2] Thaumatin is an intensely sweet-tasting protein (on a molar basis about 100,000 times as sweet as sucrose[3]) found in the West African shrub Thaumatococcus daniellii: it is induced by attack by viroids, which are single-stranded unencapsulated RNA molecules that do not code for protein. The thaumatin protein I consists of a single polypeptide chain of 207 residues. In the 1970s, Tate and Lyle began extracting thaumatin from the fruit. In 1990, researchers at Unilever reported the isolation and sequencing of the two principal proteins found in thaumatin, which they dubbed thaumatin I and thaumatin II. These researchers were also able to express thaumatin in genetically engineered bacteria.

Biobrick

More notes for later

A stunning corn variety selected by Carl Barnes, a part-Cherokee farmer and breeder, from several traditional corn varieties. Gifted to NS/S by one of his students, Greg Schoen. Produces a diversity of gorgeous translucent, jewel-colored ears, each one unique.

Sweet corn that one eats off the cob is soft when ripe and is a hybrid bred for that purpose from ancestral hard corns. Hard corns are hard when ripe, which is why they are ground into meal or popped (the hard kernel covering prevents water from escaping until it turns to steam and blows the kernel open--the pop)

As it happens, before human selection interfered, corn ears were all multi-coloured.* Kernels are siblings housed on the same ear, meaning that each kernel has its own set of genes, including those that control colour. Livestock feeders prefer vitamin-rich yellow kernels, Southerners like white kernels, and Native Americans favor blue. Years of deliberate selection, careful pollination, and storing of seeds produced these single-color corn ears. [...] Some studies suggest corn pigments promote resistance to insects or fungi that invade an ear of corn.

  • nixtamalization - In the United States, European settlers did not always adopt the nixtamalization process, except in the case of hominy grits, though maize became a staple among the poor of the southern states. This led to endemic pellagra in poor populations throughout the southern US in the early 20th century.[5] Fortification of wheat flour, the other staple food, essentially has eliminated this deficiency.
  • “THE GALLERY SPACE IS NOT A NEUTRAL CONTAINER, BUT A HISTORICAL CONTRUCT”
  • Demo or die - 'Demo or Die' is a dogma. The belief that technical prototyping is the only way of developing an idea quickly becomes a problem when it prevents designers from engaging with technologies beyond their level of ability, budget or means. The result of this dogma for people without the luxury of a lab will always be small scale, craft-like objects: a form of digital craft. There's nothing wrong with this, but sometimes we need to turn our attention to problems and ideas that are bigger and more complex than we can handle individually or make ourselves, these skills are important too.
  • Unlike many other areas of engineering, biology is incredibly non-linear.
  • food which play with my cutlery and create hyper-sensations in my mouth - but are those things actually edible and palatable, or is it just an exercise in making unliving stuff move?
  • Circular Walks Around Rowley Hall - Andrew Lanyon
  • WHy not use wood panelling on everything - There is a part of the story missing. Real wood paneling was expensive and a sign of status. The look became unfashionable because many electronic and furniture manufacturers moved away from real wood veneer toward cheaper wood-looking laminates made of particle board cores and paper, vinyl, or resin/paper top layer combinations (think today's laminate flooring). These laminates could be processed in mass production lines and resulted in everything having a "wooden" look: Cheap TV's, Sound speakers, IKEA furniture, the inside of mobile homes, kitchen cabinets. This trend not only "cheapened" the wood look, but it also gave it a low quality reputation since many of those cheap laminates peeled off or ripped with heavy use. Thus the move away from the wood look to "expensive looking" black plastic.
  • A modern version is known as the "Sheffield rack" or "Sheffield stand" after the city of Sheffield in England where these were pioneered.[7] These consist of a thick metal bar or tube bent into the shape of a square arch. The top part is about level with the top bar of the bicycle frame, and thus supports the bicycle and allows the frame to be secured. The origin of the racks was when the frugal citizens of Sheffield had to decide what to do with some old gas piping. Local cyclists suggested the cycle rack idea and two simple bends later, and a little concrete in the ground, the rack was born. At the time this was a revolution in a world of 'single-point holders' that bent wheels and offered little lockability for frames. A version of this design feature a second, lower horizontal bar to support smaller bikes (this version is also known as “A stand”), and are coated to reduce their surface hardness and to not scratch the bike's paintwork.
  • As you know, ‘experimental’ can live on a fine line between being a true artist and

simply using it as an excuse to avoid the difficulties of plotting a work.

  • Many people respond to the violent destruction of books and libraries with deep emotion. The sadness and fear in eyewitness accounts convey a sense that the destruction of texts signifies not only the immediate breakdown of order and peace but also a compromised future (…)

Popular historian Barbara Tuchman's 1980 address at the library of congress describes the humanist attitude towards books: "Books are the carriers of civilization. Without books, history of silent, literature dumb, science crippled, thought and speculation at a standstill. Without books, the development of civilization would have been impossible. They are engines of change, windows on the world, and (as a poet as said) 'lighthouses erected in the sea of time'. They are companions, teachers, magicians, bankers of the treasures of the mind. Books are humanity in print" (Tuchman 1980, 13). This notion is a cornerstone of twentieth-century humanism. The well-being and future of people is linked with the well-being and future of books and libraries. Like an article of faith, Tuchman's words have emotional and rational resonance. The angst in humanists' accounts of the destruction of libraries carries a sense of personal trauma akin to the accounts of the destruction of groups of people (especially of children). Books, like children, are objects of affection, vessels for society's hope and aspirations, links between past and future, and barriers to morality….

  • Microbes in air - Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches.
  • The leaves of the Coriandrum sativum plant, known as cilantro or coriander, are widely used in many cuisines around the world. However, far from being a benign culinary herb, cilantro can be polarizing---many people love it while others claim that it tastes or smells foul, often like soap or dirt. This soapy or pungent aroma is largely attributed to several aldehydes present in cilantro. Cilantro preference is suspected to have a genetic component, yet to date nothing is known about specific mechanisms. Here we present the results of a genome-wide association study among 14,604 participants of European ancestry who reported whether cilantro tasted soapy, with replication in a distinct set of 11,851 participants who declared whether they liked cilantro. We find a single nucleotide polymorphism (SNP) significantly associated with soapy-taste detection that is confirmed in the cilantro preference group. This SNP, rs72921001, (p=6.4e-9, odds ratio 0.81 per A allele) lies within a cluster of olfactory receptor genes on chromosome 11. Among these olfactory receptor genes is OR6A2, which has a high binding specificity for several of the aldehydes that give cilantro its characteristic odor. We also estimate the heritability of cilantro soapy-taste detection in our cohort, showing that the heritability tagged by common SNPs is low, about 0.087. These results confirm that there is a genetic component to cilantro taste perception and suggest that cilantro dislike may stem from genetic variants in olfactory receptors. We propose that OR6A2 may be the olfactory receptor that contributes to the detection of a soapy smell from cilantro in European populations.
  • In a society masquerading as post-racial, it is still only the white man who can speak authoritatively for every man. People of color, on the other hand, are expected to speak only for themselves. Ideally, the authority of a work of fiction should be judged against the standards of the world that it creates, not by its alignment with a rigid notion of reality.
  • By using a positional cloning technique and molecular markers, McSteen and her colleagues were able to pinpoint the absent gene, which they named vanishing tassel2 or vt2. The gene encodes an enzyme, called tryptophan aminotransferase, important for making auxin, an important growth hormone in plants.

"We know that auxin is critical for determining where cell division and expansion are going to happen to make new organs," said McSteen. "Where auxin is made tells the plant where organs, such as ears, tassels, and leaves, are going to grow." The researchers confirmed that the corn plants lacking the vt2 gene do produce low levels of the hormone. The study is part of a larger effort by McSteen to understand the role auxin plays in organogenesis -- the formation of specific organs in plants -- and to shed light on the largely unknown molecular mechanism that fuels auxin's production in plants. In previous work, McSteen discovered another gene, sparse inflorescence1 or spi1, also involved in making auxin in corn.

  • Cytokinins act in concert with auxin, another plant growth hormone.
  • oxalic acid dryness - There is a compound called oxalic acid in spinach leaves. When it comes in contact with calcium ions in your saliva, it forms an insoluble crystal that deposits on your teeth
  • This delightful account by a Singaporean botanist who is the patron of the Gardening Society makes me want to go on a plant tour with these people, even though they might find an elaborate gong set most irresistible - http://www.gardeningsingapore.org/index.php?option=com_content&view=article&id=53:thailand-foray&catid=36:outings-and-trips&Itemid=53
  • achromatopsia
  • entelechy - (Aristotle) the state of something that is fully realized; actuality as opposed to potentiality / entelechial
  • [F]or the limits to which our thoughts are confined, are small in respect of the vast extent of Nature it self; some parts of it are too large to be comprehended, and some too little to be perceived, and from thence it must follow, that not having a full sensation of the object, we must be very lame and imperfect in our conceptions about it, and in all the propositions which we build upon it; hence we often take the Shadow of things for the substance, small appearances for good similitudes, similitudes for definitions; and even many of those, which we think to be the most solid definitions, are rather expressions of our misguided apprehensions than of the true nature of the things themselves. —Robert Hooke, Micrographia (1665)
  • “In my early twenties, I felt that my life could be one big experiment, and in my mid-twenties I am coming to terms with the fact that no, my life is actually my life,”

"With these purple tomatoes you can get the same compounds that are present in blueberries and cranberries that give them their health benefits - but you can apply them to foods that people actually eat in significant amounts and are reasonably affordable," she said. The purple pigment is the result of the transfer of a gene from a snapdragon plant - the modification triggers a process within the tomato plant allowing the anthocyanin to develop.

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