A novel representation of RNA secondary structure based on element-contact graphs-1

Ions are illustrated. (A) Secondary structures of three typical RNAs (miRNA , SAM riboswitch, tRNA). (B) Stem-loop-contact graphs of the three typical RNAs. (C) Stem-contact graphs of the three typical RNAs. (D) Loop-contact graphs of the three typical RNAs.<p><b>Copyright information:</b></p><p>Taken from "A novel representation of RNA secondary structure based on element-contact graphs"</p><p>http://www.biomedcentral.com/1471-2105/9/188</p><p>BMC Bioinformatics 2008;9():188-188.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2373570.</p><p></p

A novel representation of RNA secondary structure based on element-contact graphs-0

Ions are illustrated. (A) Secondary structures of three typical RNAs (miRNA , SAM riboswitch, tRNA). (B) Stem-loop-contact graphs of the three typical RNAs. (C) Stem-contact graphs of the three typical RNAs. (D) Loop-contact graphs of the three typical RNAs.<p><b>Copyright information:</b></p><p>Taken from "A novel representation of RNA secondary structure based on element-contact graphs"</p><p>http://www.biomedcentral.com/1471-2105/9/188</p><p>BMC Bioinformatics 2008;9():188-188.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2373570.</p><p></p

Zinc Ion Coordinated Poly(Ionic Liquid) Antimicrobial Membranes for Wound Healing

Herein, a series of quaternary ammonium (Qa) or imidazolium (Im) cation-based poly­(ionic liquid) (PIL) membranes and their corresponding zinc ion coordinated PIL membranes were synthesized. The effects of chemical structure, including organic cations, alkyl side chain of substitution, and zinc atoms on the antimicrobial activities against <i>Escherichia coli</i>, <i>Staphylococcus aureus</i>, and <i>Candida albicans</i> were investigated. The Zn-containing PIL membranes show higher antibacterial activities compared to those of pristine PIL membranes due to the synergistic attributes of both organic cations (Qa or Im) and zinc atoms. A wound healing test using methicillin-resistant <i>S. aureus</i> infected mouse as the model further demonstrated that zinc ion coordinated PIL membranes were antibacterially active, biologically safe, and may have potential application as an antimicrobial wound dressing in a clinical setting

Nanoprotective Layer-by-Layer Coatings with Epoxy Components for Enhancing Abrasion Resistance: Toward Robust Multimaterial Nanoscale Films

Layer-by-Layer (LbL) assembled films offer many interesting applications (<i>e.g.</i>, in the field of nanoplasmonics), but are often mechanically feeble. The preparation of nanoprotective films of an oligomeric novolac epoxy resin with poly(ethyleneimine) using covalent LbL-assembly is described. The film growth is linear, and the thickness increment per layer pair is easily controlled by varying the polymer concentration and/or the adsorption times. The abrasion resistance of such cross-linked films was tested using a conventional rubbing machine and found to be greatly enhanced in comparison to that of classic LbL-films that are mostly assembled through electrostatic interactions. These robust LbL-films are then used to mechanically protect LbL-films that would completely be removed by a few rubbing cycles in the absence of a protective coating. A 45 nm thick LbL-film composed of gold nanoparticles and poly(allylamine hydrochloride) was chosen as an especially weak example for a functional multilayer system. The critical thickness for the protective LbL-coatings on top of the weak multilayer was determined to be about 6 layer pairs corresponding to about only 10 nm. At this thickness, the whole film withstands at least 25 abrasion cycles with a reduction of the total thickness of only about 2%

Metal-Containing Poly(ionic liquid) Membranes for Antibacterial Applications

Imidazolium-type metal-containing ionic liquid (IL) monomers and their corresponding poly­(ionic liquid) (PIL) membranes coordinated with CuCl₂ (PILM-Cu), FeCl₃ (PILM-Fe), or ZnCl₂ (PILM-Zn) were synthesized. The effect of metal ions on the antimicrobial activities against both <i>Staphylococcus aureus</i> (<i>S. aureus</i>) and <i>Escherichia coli</i> (<i>E. coli</i>) was investigated. Compared with pristine PILM-Br membrane, PILM-Cu, PILM-Fe, and PILM-Zn membranes exhibit enhanced antibacterial activities due to the attributes of both imidazolium cations and metal-containing anions. Furthermore, all of the metal-containing PIL membranes present low hemolysis toward human red blood cell and high long-term antibacterial stability, even after immersion in water for 90 days, demonstrating clinical feasibility in topical applications

Structure–Antibacterial Activity Relationships of Imidazolium-Type Ionic Liquid Monomers, Poly(ionic liquids) and Poly(ionic liquid) Membranes: Effect of Alkyl Chain Length and Cations

The structure–antibacterial activity relationship between the small molecular compounds and polymers are still elusive. Here, imidazolium-type ionic liquid (IL) monomers and their corresponding poly­(ionic liquids) (PILs) and poly­(ionic liquid) membranes were synthesized. The effect of chemical structure, including carbon chain length of substitution at the N3 position and charge density of cations (mono- or bis-imidazolium) on the antimicrobial activities against both <i>Escherichia coli</i> (<i>E. coli</i>) and <i>Staphylococcus aureus</i> (<i>S. aureus</i>) was investigated by determination of minimum inhibitory concentration (MIC). The antibacterial activities of both ILs and PILs were improved with the increase of the alkyl chain length and higher charge density (bis-cations) of imidazolium cations. Moreover, PILs exhibited lower MIC values relative to the IL monomers. However, the antibacterial activities of PIL membranes showed no correlation to those of their analogous small molecule IL monomers and PILs, which increased with the charge density (bis-cations) while decreasing with the increase of alkyl chain length. The results indicated that antibacterial property studies on small molecules and homopolymers may not provide a solid basis for evaluating that in corresponding polymer membranes

Intrinsically Antibacterial Poly(ionic liquid) Membranes: The Synergistic Effect of Anions

The development of materials with intrinsically antimicrobial activities has attracted great interest. Herein, we report the synthesis of free-standing and robust poly­(ionic liquid) (PIL) membranes with high antibacterial activities by in situ photo-cross-linking of an ionic liquid monomer and followed by anion-exchange with an amino acid (l-proline (Pro) or l-tryptophan (Trp)). The resultant PIL-based membranes with excellent robustness exhibit high antimicrobial properties against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus) and present no significant hemolysis and cytotoxicity toward human red blood and skin fibroblast cells, as well as low adsorption of bovine serum albumin. The synthesized PIL-Trp membranes exhibit the highest antibacterial efficiency due to the synergistic attributes of both imidazolium cation and Trp^– anion. Furthermore, all the PIL-based membranes exhibit long-term antibacterial stability, which demonstrates clinical feasibility in topical applications

Assembly of RGD-Modified Hydrogel Micromodules into Permeable Three-Dimensional Hollow Microtissues Mimicking in Vivo Tissue Structures

Fabricated microscale tissues that replicate in vivo architectures have shown huge potential in regenerative medicine and drug discovery. Owing to the spatial organization of cell-encapsulated hydrogel microstructures, three-dimensional (3D) tissue structures have been broadly applied as novel pathological or pharmacological models. However, the spatial reorganization of arbitrary microstructures with tissue-specific shapes into 3D in vitro microtissues that mimic the physiological morphology and nutrient diffusion of native tissues presents a major challenge. Here, we develop a versatile method that engineers permeable 3D microtissues into tissue-specific microscopic architectures. The customized, arbitrarily shaped hollow micromodules are prepared by photocopolymerizing poly­(ethylene glycol) diacrylate (PEGDA) with acryloyl-PEG-Arg-Gly-Asp-Ser (RGDS). These micromodules are spatially reorganized and self-aligned by a facile assembly process based on hydrodynamic interactions, forming an integrated geometry with tissue-specific morphology and a vessel-mimetic lumen. The RGD linkages create cell-adhesive structures in the PEGDA hydrogel, greatly increasing the long-term cell viability in 3D microtissue cultures. Meanwhile, the mechanical properties for fast cell spreading inside the microstructures can be optimized by modulating the PEGDA concentration. The 3D microtissues, with their different geometries and permeable tubular lumens, maintained cell proliferation over 14 days. The cell viabilities exceeded 98%. We anticipate that our method will regenerate complex tissues with physiological importance in future tissue engineering

Dissociation, and not specific actions of Trypsin-EDTA, acts to suppress neurectoderm formation.

<p>(A). EPL cells, formed in aggregates in MEDII, were dissociated with Dispase, Dissociation buffer or Trypsin-EDTA, reaggregated and maintained for a further 4 days before being seeded individually into 48 tissue culture wells and allowed to differentiate. Aggregates were scored for the presence of beating cardiocytes and neural extensions and the peak score for each represented. Outcomes are compared to outcomes from EPL cells that were maintained in aggregates. n = 3 independent experiments. Error bars represent sem. (a) denotes a decrease compared to MEDII⁻/Dissociation⁻ where p<0.01. (B). EPL cells, formed in aggregates in MEDII, were either maintained in medium supplemented with 50% MEDII (control), cultured in unsupplemented medium (no addition) or dissociated with Dispase, Dissociation buffer or Trypsin-EDTA, reaggregated and maintained in suspension culture in unsupplemented medium for a further 6 days. Aggregates were collected and extracted RNA was analyzed for the presence of <i>Sox1</i>, and <i>GAPDH</i> by real-time PCR. n = 3 independent experiments. Error bars represent sem.</p

Tgf-β antagonists suppress mesoderm formation from EPL cells in culture.

<p><i>Mixl1:GFP</i> ES cells were cultured as aggregates in MEDII for 3 days to form EPL cells. Aggregates were transferred to unsupplemented medium or medium supplemented with 50% MEDII, 0.4% DMSO or 10 µM SB431542 (prepared in DMSO) and cultured for a further 2 days before reduction to a single cell suspension. The proportion of GFP⁺ cells present was determined by flow cytometry. n = 3 independent experiments. Error bars represent standard error of the mean. (B). EPL cells were prepared as for (A) and transferred to unsupplemented medium or medium supplemented with 50% MEDII or 77 µM Nona-Arg (prepared in H₂0) and cultured for a further 2 days before reduction to a single cell suspension. The proportion of GFP⁺ cells present was determined by flow cytometry. A representative result is shown. (C). EPL cell aggregates were formed from ES cells and transferred to unsupplemented medium or medium supplemented with MEDII, DMSO, 10 µM SB431542 or 10 µM PD169316 as indicated. Aggregates were maintained in culture for a further 4 days before seeding them individually into 48 tissue culture wells and allowing them to differentiate. Aggregates were scored for the presence of visible red blood cells, beating cardiocytes and neural extensions and the peak score for each represented. n = 3 independent experiments (PD169316). Error bars represent sem. A representative experiment is shown for SB431542.</p