Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES BIOMIMETICS Biomimetics is the scientific method of learning learning new principles and processes based on systematic study, observation and experimentation with live animals and organisms. Biomimetics is a novel approach to developing developing designs and products or to solving human problems by taking inspiration from nature. Biomimetics at the molecular level: Imitating and learning from nature, based on our understanding of molecular biology and biochemistry will enable innovation and develop designs to solve human problems. THE BIOMOLECULES CARBOHYDRATES Carbohydrates are the most abundant biological molecule and most of them consist of carbon, hydrogen and oxygen in a 1:2:1 ratio (CH 2O)n. Carbohydrates contain either an aldehyde moiety or a ketone moiety with large quantities of hydroxyl groups. The presence of the hydroxyl groups allows carbohydrates to interact with the aqueous environment and to participate in hydrogen bonding, both within and between chains. Cells use carbohydrates as: structural materials transportable forms of energy storage form of energy
Occurrence: Cell walls of bacteria and plants Cell membranes of animals Nucleotides – sugar sugar component Nucleotides –
Major size classes of Carbohydrates: a. MONOSACCHARIDES MONOSACCHARIDES are are the simplest sugars, having the formula (CH2O)n. Monosaccharides can be categorized according to their value of 'n,' as shown below: n 3 4 5 6
Fischer Projection formula of an aldose and ketose:
Category Triose Tetrose Pentose Hexose
ISOMERISM in Carbohydrates Stereoisomerism
H
H
H
OH
H
H
OH
HO
H
OH
H
H D-glyceraldehyde
OH H OH
H L-glyceraldehyde
* D-form monosaccharides are used to construct carbohydrates.
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Enantiomers – Enantiomers – two two molecules that are mirror-images to each other and cannot be superimposed on each other D – dextrorotatory, – dextrorotatory, (+) clockwise rotation, position of hydroxyl group on the reference carbon is on the right of the projection formula L – levorotatory, – levorotatory, (-) counterclockwise rotation, position of the hydroxyl group on the reference carbon is on the left of the projection formula
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
Haworth Projection formula: Cyclic form of aldose and ketose Furanose – five-membered ring Pyranose – six-membered ring
E xample: S tructures of -D-Glucose Fischer Projection
Haworth Projection (planar)
Chair conformation (nonplanar)
H
OH
O
C H
OH
HO
H
H
H
OH
H
OH
H2 C
H OH
OH
HO HO
H
HO
H
H
O H
OH H
OH
OH
H
H
OH
-D-glucopyranose
OH
OH
-D-glucopyranose
D-glucose
Application: Simple monosaccharides are reducing agents. +3 +2 Glucose and other sugars are capable of reducing Fe or Cu and are called reducing sugars. Fehling’s test is a quantitative test to detect presence of reducing sugar (in diagnosis of diabetes mellitus). OH
OH
OH
O H
OH
H
HO
+2
2Cu H
H
H
OH
H
OH
+ 5OH-
O
H OH
H
HO
+
Cu2O
+ 3 H2O
OH H
OH
b. DISACCHARIDES are two monosaccharides joined covalently through Condensation reaction by an O-glycosidic bond and the resultant molecules are called glycosides. Several physiologically important disaccharides are sucrose, lactose and maltose. Sucrose: prevalent in sugar cane and sugar beets, is composed of glucose and fructose through an α(1,2)β-glycosidic bond.
Lactose: is found exclusively in the milk of mammals and consists of galactose and glucose in a -(1,4) glycosidic bond.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES Maltose: the major degradation product of starch, is composed of 2 glucose monomers in an -(1,4) glycosidic bond.
To describe disaccharides or oligosaccharides, the end of a chain that has a free anomeric carbon is called the reducing end. Condensation Reaction is involved in the formation of disaccharides.
c. POLYSACCHARIDES or glycans are polymers of monosaccharide units. Polysaccharides differ in the composition of the monomeric unit, the linkages between them, and the ways in which branches from the chains occur. Homopolysaccharides - made up of only one kind of monomer Heteropolysaccharides - made up of several kinds of monomers HOMOPOLYSACCHARIDES Storage Polysaccharides a. Starch is the major form of stored carbohydrate in plant cells. It is actually a mixture of two compounds, amylose (unbranched with glucose units linked (14) and amylopectin ( (14) links with (1 6) links approximately every 25-30 glucose residues). Unbranched starch is called amylose; branched starch is called amylopectin. The unbranched structure of amylose causes the polymer to exist as a long, coiled helix under conditions when it can be stabilized. One substance that will stabilize an amylose helix is iodine, which fits into the hollow core of the structure. Binding of iodine to amylose helices produces an intense blue color and has long been used as a qualitative test for starch. Polymers consisting solely of glucose are called glucans. Amylopectin is a polymer of glucose. It differs from amylose and resembles the animal storage polysaccharide, glycogen, in containing ( 16) branches in addition to ( 14) links between glucose units. b. Glycogen is a branched polymer of glucose, consisting of main branches of glucose units joined in (14) linkages. Every 7-20 residues, (16) branches of glucose units are also present. It is the primary energy storage material in muscle. Individual glucose units are cleaved from glycogen in a phosphorolytic mechanism catalyzed by glycogen phosphorylase. Glycogen is a very compact structure that results from the coiling of the polymer chains. This compactness allows large amounts of carbon energy to be stored in a small volume, with little effect on cellular osmolarity.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
S truc tural Polys accharides a. Cellulose is a glucan and is the major polysaccharide in woody and fibrous plants. It is the most abundant single polymer in the biosphere. Made up of units of D-glucose linked in the 1-> 4 configuration, cellulose forms a planar structure with individual parallel chains held together by hydrogen bonds. Most animals cannot digest the 1->4 linkages in cellulose. Among the animals, only ruminants (cows, horses, etc.) contain a symbiotic bacterium with an enzyme, cellulase that can break cellulose down to glucose. Fungi too contain cellulases. Cellulose is also used as a structural component of some animal cells, such as the marine invertebrates called tunicates.
Molecular arrangement in cellulose
b. Chitin is a polymer of of N-acetyl- -D-glucosamine. The linkage between individual N-acetyl--Dglucosamine units is -1,4, giving it a structure similar to that of cellulose, except that the hydroxyl on carbon 2 of each residue is replaced by an acetylated amino group. Chitin is widely distributed among the kingdoms of organisms. It is a minor constituent in most fungi and some algae, where it often substitutes for cellulose or other glucans. In dividing yeast cells, chitin is found in the septum that forms between the separating cells. The best known role of chitin, in invertebrate animals is it constitutes a major structural material in the exoskeletons of many arthropods and mollusks. In many of these exoskeletons, chitin forms a matrix on which mineralization takes place.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
LIPIDS - provide energy reserves, predominantly in the form of triacylglycerols. - serve as structural components of biological membranes. - both lipids and lipid derivatives serve as vitamins and hormones. STORAGE LIPIDS a.
FATTY ACIDS
Numerical Symbol
Common Name
Structure
Melting temp., C
14:0 16:0 9 16:1 18:0 9 18:1 9,12 18:2 9,12,15 18:3 5,8,11,14 20:4
Myristic acid Palmitic acid Palmitoleic acid Stearic acid Oleic acid Linoleic acid Linolenic acid Arachidonic acid
CH3(CH2)12COOH CH3(CH2)14COOH CH3(CH2)5CH=CH(CH2)7COOH CH3(CH2)16COOH CH3(CH2)7CH=CH(CH2)7COOH CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH CH3(CH2)3(CH2CH=CH)4(CH2)3COOH
53.9 63.1 – 0.5 69.6 13.4 – 5 – 11 – 49.5
Physical Properties of Fatty acids Length of hydrocarbon chain Degree of unsaturation
Solubility to water - FAs have poor solubility in H 2O
*the longer the FA chain and fewer double bonds, the lower its solubility in water. 9 Ex: Arrange the ff. FAs accdg. to increasing solubility in water: 16:0; 20:0; 18:0; 16:1
Melting point unsaturated FAs have lower MP than saturated FAs. % Fatty Acid
Olive oil Butter Beef fat
State at RT 25C Liquid Solid (soft) Solid (hard)
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C4-C12 <2 11 <2
Saturated C14 C16 <2 13 10 26 <2 29
C18 3 11 21
Unsaturated C16 + C18 80 40 46
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES Triacylglycerols – simplest lipids constructed from FAs which functions as energy storage and insulation. TAG or fats are in form of solids and oil. Fats which are rich in unsaturated fatty acids are typically oils. When lipid-rich foods are exposed too long to air, they become rancid as a result from the oxidative cleavage of their double bonds in the chain.
TAGs yield 2x as much energy as CHOs (stored in adipocytes or fat cells; seeds in plants) TAGs provide insulation: seals, walrus, penguins TAGs have low density: in sperm whales, TAGs allows the animal to match the buoyancy of their bodies to that of their surroundings. Hydrolysis of TAGs produces soaps by heating them with NaOH or KOH. This process is called + + saponification which produces glycerol and Na or K salts of the fatty acids known as the soap. O H2C
O
C
O
O HC
O
C
H2C
R1
OH
K
+
-O
HC
OH
K
+
-O
O H2C
O
C
R1
O
3KOH R2
C
C
R2
O R3
H2C
+
OH
K -O
C
R3
Salts of long-chain carboxylic acids or soap
How do soaps clean dirt and grease? In water, soaps exist in soluble spherical clusters called micelles Micelles have the hydrophilic carboxylate group of the fatty acid salt on the outside exposed to water Soaps clean by incorporating greasy (hydrophobic) dirt molecules into the hydrophobic alkyl portion of micelles The polar carboxylate groups of the soap micelles serve to suspend the micelle in water so that it (with the enclosed dirt molecules) can be washed away.
dirt grease
dirt grease
STRUCTURAL LIPIDS Phospholipids are a class of lipids that are a major component of all cell membranes or plasma membrane as they can form lipid bilayers.
The cell membrane lipid bilayer is semi-permeable. It only allow small nonpolar molecules such as CO 2 and O2 to pass through the membrane. Other molecules need a transporter in order to move across the membrane.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
The Fluid Mosaic Model of the Cell Membrane The cell membrane consists of two layers of phospholipids that arranged in a fashion by which the nonpolar portions are sandwiched in between the polar portions. The lipid bilayer also consists of other biomolecules such as peripheral protein and integral proteins that aid in transport of molecules; carbohydrates for cell recognition; and cholesterol.
Carbohydrates and Lipids in Biomimetics
Chitosan has been used in many medical applications. It serves as biomimetic material of antihemoglobin antibodies to create an imprinted recognition surface of hemoglobin beads.
Chitosan was proved to act as a thickener in cement mixtures.
Glycocalyx-mimetic peptoid is a modified polysaccharide that serves as antifouling agent on surfaces.
Welan gum that exhibits high rheological property is used as admixtures for eco-efficient construction materials e.g. concretes.
Biomimetic membranes may provide an alternative to current reverse osmosis and nanofiltration membranes e.g. for industrial separation and wastewater treatment.
In the creation of biosensors, a lipid layer that mimics the cell membrane served as an impermeable barrier around the wire where a membrane protein (bio-element) can be incorporated.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
AMINO ACIDS Amino acids are the building blocks of proteins. An amino acid consists of an asymmetric carbon (carbon) at the center with four different groups attached to it: an amino group, a carboxyl group, a hydrogen atom and a variable group, R (except for glycine). Thus amino acids have chiral centers.
Essential amino acids Threonine, Thr (T) Valine, Val (V) Methionine, Met (M) Isoleucine, Ile (I) Leucine, Leu (L) Lysine, Lys (K) Phenylalanine, Phe (F) Tryptophan, Trp (W) Histidine, His (H) Arginine, Arg (R)
Non-essential amino acids Alanine, Ala (A) Asparagine, Asn (N) Aspartic acid, Asp (D) Cysteine, Cys (C) Glutamic acid, Glu (E) Glutamine, Gln (Q) Glycine, Gly (G) Proline, Pro (P) Serine, Ser (S) Tyrosine, Tyr (Y)
Stereoisomers of alanine
Essential amino acids are those the body cannot make and must be obtained from dietary sources.
PEPTIDES AND POLYPEPTIDES Peptides are chains of amino acids joined by a peptide bond. The linkage of two amino acids is a dipeptide and the reaction is an example of condensation reaction. When few amino acids are joined, they are called oligopeptide, and thousands of it, they are called polypeptide. Peptides are named from sequence of their constituent amino acids, beginning from the amino terminal residue at the left proceeding toward the carboxyl terminus at the right.
Peptides undergo characteristic chemical reactions: a. Hydrolysis by boiling with either strong acid or base b. Hydrolysis by certain enzymes (proteases) Some biologically important peptides have only few amino acid residues like the commercially synthesized L-Aspartyl-Lphenylalanyl methyl ester or better known as aspartame.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES PROTEIN Proteins are biopolymers (called polypeptides) of L-amino acids. Only L-amino acids are used to make proteins (rare exceptions of proteins in bacterial cell wall, which contain some D-amino acids) The process of putting amino acids together to make proteins is called translation. Translation relies on the genetic code, in which three nucleotides in mRNA specify one amino acid in protein. The difference between a polypeptide and a protein is that the term polypeptide refers simply to a chain of amino acids. The term protein refers to the chain of amino acids after it folds properly and is (in some cases) modified. Proteins may consist of more than one polypeptide chain. Proteins are sometimes described as the "workhorses" of the cell because they do so many things catalyze reactions, provide structural integrity, transport molecules, provide movement, bind molecules, and others. Function of Proteins a. Transport b. Nutrient and storage c. Contraction d. Structure or support
e. f. g.
Defense Regulation of cellular or physiological activity Catalyst
Protein Structure The order or sequence of amino acids distinguishes different proteins from each other. The sequence of amino acids determines the 3-dimensional shape of the protein. Alterations to the amino acid sequence of a protein changes its 3D shape. Primary structure is the most basic level of protein structure. It is the linear sequence of amino acids. The primary structure of a protein is specified by the order of bases in the genomic DNA. Different sequences of the acids along a chain, however, affect the structure of a protein molecule in different ways. Secondary structures are stable and occur widely in proteins (globular and fibrous). Most prominent are the -helix and -conformation. The simplest arrangement the polypeptide chain could assume with its rigid peptide bonds is a helical structure that is right-handed. -Helical structure (right-handed) is predominant in keratin. Secondary structures are stabilized by favorable hydrogen bonding between residues and have been brought into close juxtaposition by folding or coiling of the primary structure. In the -conformation, the backbone of the polypeptide chain is extended into a zigzag manner ( pleated sheets) and the hydrogen bonding can either be intrachain or interchain between peptide linkages of adjacent polypeptide chains. -keratin – right-handed helix; rich in Phe, Ile, Val, Met, and Ala. collagen – left-handed helix; rich in Gly, Ala, Pro and Hyp
Structure-properties of fibrous proteins: -helix cross-linked by disulfide bonds – tough, insoluble protective structures of varying hardness and flexibility ex. -keratin of hair, feathers and nails -Conformation – soft, flexible filaments ex. Fibrion of silk Collagen triple helix – high tensile strength, without stretch ex. Collagen of tendons, bone matrix
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
Tertiary structure (three dimensional arrangement of atoms in protein) is formed when forces cause the molecule to become even more compact, as in globular proteins. Each molecule of a particular protein has the same conformation and this differs from molecules of other proteins. Myoglobin contains a single polypeptide chain folded about a prosthetic group, the heme, which contains the oxygen binding site. The heme in myoglobin is in the form of an iron complexed with protoporphyrin IX. Myoglobin, by contrast with hemoglobin, is an oxygen storage protein. Oxygen transported to tissues must be released for utilization. In tissues, such as muscle, with high oxygen demands, myoglobin provides large oxygen reserves.
Quaternary protein structure refers to the interaction between subunits of oligomeric protein or large protein assemblies as in hemoglobin and some enzymes. Four subunits of hemoglobin exhibit cooperative interactions on oxygen-binding. ENZYMES - Most enzymes are proteins. - They function as catalyst in biological reactions. - Enzymes are globular proteins - their molecules are round in shape. - Each enzyme has a specific catalytic action. - Their normal activity depends on their environment. - Abnormal conditions cause reduced activity How enzymes work. Enzymes have an area - usually thought of as a pocket-shaped gap in the molecule - which is called the active site. Some enzymes are found inside cells (intracellular enzymes), and some - especially digestive enzymes are released so they have their effects outside the cell (extracellular enzymes). (Only) the substrate (or substrates) fits/fit into the active site. The enzyme speeds up the process of conversion of substrates (reactants) into products - usually so much that the reaction does not take place in the absence of enzyme. Although the enzyme obviously joins with the substrate for a short while, the enzyme and substrate split apart afterwards, releasing the enzyme. Thus the enzyme is not used up in the process (unlike the substrate(s)), so it can continue to react if more substrate is provided.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES NUCLEIC ACIDS Nucleic acids are complex structures composed of nucleotide chains that are used to maintain genetic information. Component structures of nucleotide: Pyrimidine and purine bases Sugar Phosphate Pyrimidine bases O
O
NH2 N O
Purine bases
HN O
N
H2N
O
N
N
CH3
HN
O N
HN
HN N
N
N
H2N
H
H
H
H
CYTOSINE (C)
URACIL (U)
THYMINE (T)
N
N
H
ADENINE (A)
GUANINE (G)
Nucleosides: Pyrimidine + sugar O
NH2
NH2
O
HN
N
CH3
HN
O N
N
N
C
HN
C
CH
N
O HO
N
O HO
O
HC O HO
O
OH OH
OH OH
CYTIDINE
URIDINE
N
C
N
N
C
HO
O
O
OH OH
OH OH
OH OH
THYMIDINE
N
N
H2N
HO
O
CH
C
ADENOSINE
GUANOSINE
Nucleotides: Nucleoside + Phosphate C P
O
U P
OH OH
Cytidine monophosphate
O
OH OH
Uridine monophosphate
A
T P
O
OH OH
Thymidine monophosphate
P
G P
O
OH OH
Adenosine monophosphate
O
OH OH
Guanosine monophosphate
Two common Nucleic Acids: 1.
RNA – Ribonucleic acid RNAs are single-stranded polynucleotides that are used to express genetic information. Three types of RNAs: rRNA – ribosomal RNA mRNA – messenger RNA tRNA – transfer RNA
2.
DNA – Deoxyribonucleic acid DNAs are double-stranded polynucleotide helix that carries the genetic information.
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES
Differences in the structure of RNA and DNA RNA type of bases used A, G, C, U sugar used Ribose polynucleotide strand Single
DNA A G, C, T Deoxyribose double
Nucleic acids are formed through linkage of one nucleotide with another by forming a covalent bond called 3’,5’-phosphodiester bond. The next nucleotide to be attached to the growing polynucleotide chain is always added at the 3’-end.
Nucleic acids are constructed starting from the 5’-end going to the 3’-end Example: 5’- ATG CCC GGG AAA GCG TTT CCG……….-3’
James Watson and Francis Crick ’s model of the DNA The DNA molecule consists of 2 strands of polynucleotide held together through hydrogen bonding interaction of the bases contained in the 2 strands. This pairing of bases is called complimentary base pairs: A=T and C G The orientation of the 2 strands is anti-parallel to each other. Cytosine
Guanine
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Thymine
Adenine
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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design School of Chemical Engineering and Chemistry THE BIOMOLECULES A-DNA Parameters Direction of helical rotation Residues per turn of helix Occurence
A Form Right
B Form Right
Z Form Left
11 BP
10 BP
12 BP
Favored at dehydrated condition
Favored at high water concentration
Favored at high salt concentration
B-DNA Z-DNA
Proteins and Nucleic Acids in Biomimetics
Steel-Cable Technology in Muscles: The load-bearing cables in suspension bridges are composed of bundles of strands, just like the human muscles. Fiberglass Technology in Crocodile Skin: A crocodile’s skin has much the same str ucture as fiberglass. Crocodile skin is impervious to arrows, knives and sometimes, even bullets. The substance that gives crocodile skin its special strength is the collagen protein fibers it contains.
DNA-inspired: World's first curved double helix bridge at Marina Bay, Singapore Bridge measures 280 meters long made of a special stainless steel. If all the steel tubes forming the major and minor helix are laid end to end, it will measure 2,250 meters long, and the entire structure weighs about 1,700 tons, which is equivalent to about 1,130 saloon cars.
DNA-inspired: DNA-Shaped Agora Garden Building (Taiwan) The design creates more surface area, and enables suspended open-air gardens to hang from one level to the next, unobtrusively.
References: Yosef Bar Cohen, Biomimetics – Biologically Inspired Technologies, CRC press, 2006. Hyun Ok Ham, et al., J. Am. Chem. Soc., 2013, 135 (35), pp 13015 –13022. Varinder Kaur, Manav B. Bera, Parmjit S. Panesar, Harish Kumar, J.F. Kenned, Int. Journ. of Biological Macromolecule, 2014 M. Lasheras-Zubiate, I. Navarro-Blasco, J. M. Fernández and J. I. Alvarez, Journal of Applied Polymer Science, 2010. Torben Lenau, Biomimetics as a Design Methodology, Int’l Conf. on Engg Des. Stanford Univ., 2009 nd Voet and Voet, Biochemistry 2 ed. Wiley Publication (2004). rd Voet, Voet and Pratt, Biochemistry 3 edition (2008), Wiley and Sons. th Starr and Taggart (2004). Biology. The Unity and Diversity of Life, 10 edition, Wadsworth Group, Thomson Learning, Inc., California
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