Three dimensional scaffolds

Eucaryotes have many more genes and a broader range of specific transcription factors than procaryotes and gene expression is regulated by using sets of these factors in a combinatorial way. Eucaryotes have found several different solutions to the problem of producing a three-dimensional scaffold that allows a protein to interact specifically with DNA. In the next chapter we shall discuss some of the solutions that have no counterpart in procaryotes. However, the procaryotic helix-turn-helix solution to this problem (see Chapter 8) is also exploited in eucaryotes, in homeodomain proteins and some other families of transcription factors. 

Liu C, Xia Z, Czemuszka JT (2007) Design and development of three-dimensional scaffolds for tissue engineering. Trans IChemE, Part A, Chem Eng Res Des 85 1051-1064... 

The cytoplasm of eukaryotic cells is traversed by three-dimensional scaffolding structures consisting of filaments (long protein fibers), which together form the cytoskeleton. These filaments are divided into three groups, based on their diameters microfilaments (6-8 nm), intermediate filaments (ca. 10 nm), and microtubules (ca. 25 nm). All of these filaments are polymers assembled from protein components. 

Fig. 8.3 (A) Human fibroblast stretching across the three-dimensional scaffold composed of Vicryl suture material, a biodegradable sugar polymer. (B) Histological cross-section...

The pore size of the membrane could also be controlled independently of the porosity by altering the size of the salt particles (Fig. 5a). Membranes with high surface area/volume ratios were produced and the ratio was dependent on both salt weight fraction and particle size (Fig. 5b). In addition, the crystallinity of PLLA membranes can be tailored to that desired for each application. These characteristics are all desirable properties of a scaffold for organ regeneration. The major disadvantage of this technique is that it can only be used to produce thin wafers or membranes (up to 2 mm in thickness). A three-dimensional scaffold cannot be directly constructed. This problem may be circumvented however, by membrane lamination. 

Melt molding is an alternative method of constructing three-dimensional scaffolds which has many advantages over membrane lamination. PLGA scaffolds... 

His current activities include the application of polyurethane composites to the development of three-dimensional scaffold for cell growth (bacteria, plant and mammalian). 

Builders of artificial scaffolds aie most concerned with this junction. In a natural environment, the binding is done via an intercellular glue known as extracellular matrix. The matrix is a protein gel produced by the cells and it serves as the basis of three-dimensional cell structure development. In the development of a three-dimensional scaffold, it is advisable that this mechanism be mimicked by some means. 

Our initial foray into microwave chemistry was with a reaction that had proven inaccessible using traditional thermal techniques. The reaction was a simple [3 + 2] cycloaddition reaction between a di-substituted maleimide and a simple azomethine ylide generated in situ (Scheme 8.1)13. The reaction with the unsubstituted maleimide had yielded excellent results for a variety of dipoles however, even simple methyl substitution had dramatic reductions in product yield (Table 8.1). The interest in our group was in generating novel three-dimensional scaffolds for library generation and the di-substituted maleimides would be a key entry point into these compounds, so the need for the products had us attempt these reactions in sealed pressure vessels. While we were pleased to obtain some of the desired product, the extremely low yield had eliminated this class of compounds from consideration. 

It is well established that the same three-dimensional scaffolding in proteins often carries constellations of amino acids with diverse enzymatic functions. A classic example is the large family of a/jS, or TIM, barrel enzymes (Farber and Petsko, 1990 Lesk et ai, 1989). It appears that lipases are no exception to date five other hydrolases with similar overall tertiary folds have been identified. They are AChE from Torpedo calif arnica (Sussman et al., 1991) dienelactone hydrolase, a thiol hydrolase, from Pseudomonas sp. B13 (Pathak and Ollis, 1990 Pathak et al, 1991) haloalkane dehalogenase, with a hitherto unknown catalytic mechanism, from Xanthobacter autotrophicus (Franken et al, 1991) wheat serine carboxypeptidase II (Liao et al, 1992) and a cutinase from Fusa-rium solani (Martinez et al, 1992). Table I gives some selected physical and crystallographic data for these proteins. They all share a similar overall topology, described by Ollis et al (1992) as the a/jS hydrolase... 

Monodisperse oligo(phenylenevinylene)s are assembled to three-dimensional scaffolds in convergent three- or fourfold Homer reactions of a silane core and stilbenoid aldehydes in moderate to good yields. The central silane is sensitive toward nucleophilic attack. Tetrahedral compounds with short side chains form stable amorphous films but trigonal-pyramidal shaped assemblies tend to recrystallize. The connection of the chromophores to a central silicon atom results in a stabilization of the excited states an intense blue-green fluorescence is emitted from solution as well as from transparent films. 

Convergent dendrimers, with their versatile three-dimensional scaffold, may be tailored to mimic, perhaps crudely, some elements of enzymatic structures. Numerous catalytic moieties, including manganese porphyrins,253,254 bis(oxazoline) copper complexes,304 305 tertiary amines,306 binaphthol titanium complexes,285 307 titanium taddolates,292,308 thiazolio-cyclophanes,309 and fullerene-bound bisoxazoline copper complexes,310 have been incorporated at the core of dendritic molecules to determine the effect of dendritic encapsulation on their catalytic activity. 

Li, Y. Yang, S.-T. Effects of three-dimensional scaffolds on cell organization. Biotechnol. Bioprocess Eng. 2001, 6, 311. 

Photolithography and microfabrication are techniques used for the formation of scaffolds of specific shape and with distinct surface properties. Three-dimensional scaffolds are composed of hydrogels like biodegradable lactide/glycolic acid copolymers or nonbiodegradable polydimethylsiloxane. In the case of lactide/glycolic acid copolymers, the polymer is formed into a fibrous... 

Besides being used as adsorbent for gas molecules, both SWCNTs and MWC-NTs can be cast as a random network or a porous thin film on metal electrodes [57-59] or used as a three-dimensional scaffold [41,42] for biosensors. CNTs serve both as large immobilization matrices and as mediators to improve the electron transfer between the active enzyme site and the electrochemical transducer. Various enzymes, such as glucose oxidase and flavin adenine dinucleotide (FAD) can adsorb onto the CNT surface spontaneously and maintain their substrate-specific enzyme activity over prolonged times [57]. Recently, cells have been grown on CNT scaffolds which provide a three-dimensional permeable environment, simulating the natural extracellular matrix in a tissue [60-62]. 

Leong KF, Cheah CM, Chua CK (2003) Solid freeform fabrication of three-dimensional scaffolds for engineering replacement tissues and organs. Biomaterials 24 2363-2378... 

Wang, Y. W. et al. Evaluation of three-dimensional scaffolds made of blends of hydroxyapatite and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) for bone reconstruction 5iomafer 2005, 26(8), 899-904 (a). 

Nanofibrous structures have been extensively smdied as the two- or three-dimensional scaffolds that mimic the cell living environment for tissue regeneration. Nanofibrous structures provide temporary spaces with a mnable porosity in which cells can exchange metabolites and nutrients with their environment so that cellular functionality can be maintained, the reconstruction of tissues can be aided, and the tailored mechanical properties will function as desired, and the wound bed can be protected from collapsing, and mechanical mismatch between scaffolds and host tissues can... 

Futhermore, nanofiber scaffold electrodes based on PEDOT for cell stimulation were recently reported by Bolin et al. [87]. Electronically conductive and electrochemically active three-dimensional scaffolds based on electrospun poly(ethylene terephthalate) (PET) nanofibers were prepared. Vapor-phase polymerization was employed to achieve a uniform and conformal coating of poly(3,4-ethylenedioxythiophene) doped with tosylate (PEDOT tosylate) on the nanofibers. The PEDOT coatings had a large impact on the... 

---