Compatibility of termination mechanisms in bacterial transcription with inference on eukaryotic models.

Transcription termination has evolved to proceed through diverse mechanisms. For several classes of terminators, multiple models have been debatably proposed. Recent single-molecule studies on bacterial terminators have resolved several long-standing controversies. First, termination mode or outcome is twofold rather than single. RNA is released alone before DNA or together with DNA from RNA polymerase (RNAP), i.e. with RNA release for termination, RNAP retains on or dissociates off DNA, respectively. The concomitant release, described in textbooks, results in one-step decomposition of transcription complexes, and this 'decomposing termination' prevails at ρ factor-dependent terminators. Contrastingly, the sequential release was recently discovered abundantly from RNA hairpin-dependent intrinsic terminations. RNA-only release allows RNAP to diffuse on DNA in both directions and recycle for reinitiation. This 'recycling termination' enables one-dimensional reinitiation, which would be more expeditious than three-dimensional reinitiation by RNAP dissociated at decomposing termination. Second, while both recycling and decomposing terminations occur at a hairpin-dependent terminator, four termination mechanisms compatibly operate at a ρ-dependent terminator with ρ in alternative modes and even intrinsically without ρ. RNA-bound catch-up ρ mediates recycling termination first and decomposing termination later, while RNAP-prebound stand-by ρ invokes only decomposing termination slowly. Without ρ, decomposing termination occurs slightly and sluggishly. These four mechanisms operate on distinct timescales, providing orderly fail-safes. The stand-by mechanism is benefited by terminational pause prolongation and modulated by accompanying riboswitches more greatly than the catch-up mechanisms. Conclusively, any mechanism alone is insufficient to perfect termination, and multiple mechanisms operate compatibly to achieve maximum possible efficiency under separate controls.

Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination.

Transcriptional pause is essential for all types of termination. In this single-molecule study on bacterial Rho factor-dependent terminators, we confirm that the three Rho-dependent termination routes operate compatibly together in a single terminator, and discover that their termination efficiencies depend on the terminational pauses in unexpected ways. Evidently, the most abundant route is that Rho binds nascent RNA first and catches up with paused RNA polymerase (RNAP) and this catch-up Rho mediates simultaneous releases of transcript RNA and template DNA from RNAP. The fastest route is that the catch-up Rho effects RNA-only release and leads to 1D recycling of RNAP on DNA. The slowest route is that the RNAP-prebound stand-by Rho facilitates only the simultaneous rather than sequential releases. Among the three routes, only the stand-by Rho's termination efficiency positively correlates with pause duration, contrary to a long-standing speculation, invariably in the absence or presence of NusA/NusG factors, competitor RNAs or a crowding agent. Accordingly, the essential terminational pause does not need to be long for the catch-up Rho's terminations, and long pauses benefit only the stand-by Rho's terminations. Furthermore, the Rho-dependent termination of mgtA and ribB riboswitches is controlled mainly by modulation of the stand-by rather than catch-up termination.

Rho-dependent transcription termination proceeds via three routes.

Rho is a general transcription termination factor in bacteria, but many aspects of its mechanism of action are unclear. Diverse models have been proposed for the initial interaction between the RNA polymerase (RNAP) and Rho (catch-up and stand-by pre-terminational models); for the terminational release of the RNA transcript (RNA shearing, RNAP hyper-translocation or displacing, and allosteric models); and for the post-terminational outcome (whether the RNAP dissociates or remains bound to the DNA). Here, we use single-molecule fluorescence assays to study those three steps in transcription termination mediated by E. coli Rho. We find that different mechanisms previously proposed for each step co-exist, but apparently occur on various timescales and tend to lead to specific outcomes. Our results indicate that three kinetically distinct routes take place: (1) the catch-up mode leads first to RNA shearing for RNAP recycling on DNA, and (2) later to RNAP displacement for decomposition of the transcriptional complex; (3) the last termination usually follows the stand-by mode with displacing for decomposing. This three-route model would help reconcile current controversies on the mechanisms.

Porous calcium phosphate-collagen composite microspheres for effective growth factor delivery and bone tissue regeneration.

Microspheres are beneficial for filling defects of various shapes and provide a large surface area for cell attachment. Porous microspheres have attracted particular attention because they can deliver cells and bioactive molecules such as growth factors. In this study, BCP-collagen composite microspheres were developed for growth factor delivery in bone regeneration. Firstly, porous biphasic calcium phosphate (BCP) microspheres were fabricated by applying a water-in-oil emulsion technique using camphene as a pore generator. Then, porous BCP-collagen composite microspheres were fabricated by repetitively dip coating the microspheres in a collagen solution to effectively deliver growth factor to bone defects. Characterization of the microspheres and in vitro studies were conducted to investigate the effect of collagen infiltration on bone regeneration. In addition, in vitro evaluation demonstrated the sustained bone morphogenetic protein-2 (BMP-2) delivery of the microspheres and the effect of cell differentiation, and in vivo assessment with rabbits revealed that the microspheres filled the defect well and that bone could be regenerated through the microspheres. Moreover, the composite system was more effective for bone regeneration than the bare BCP microspheres because of the drug retention of collagen. These findings indicate that the porous microspheres are effective for tissue regeneration by continuous growth factor delivery.

ATAD5 promotes replication restart by regulating RAD51 and PCNA in response to replication stress.

Maintaining stability of replication forks is important for genomic integrity. However, it is not clear how replisome proteins contribute to fork stability under replication stress. Here, we report that ATAD5, a PCNA unloader, plays multiple functions at stalled forks including promoting its restart. ATAD5 depletion increases genomic instability upon hydroxyurea treatment in cultured cells and mice. ATAD5 recruits RAD51 to stalled forks in an ATR kinase-dependent manner by hydroxyurea-enhanced protein-protein interactions and timely removes PCNA from stalled forks for RAD51 recruitment. Consistent with the role of RAD51 in fork regression, ATAD5 depletion inhibits slowdown of fork progression and native 5-bromo-2'-deoxyuridine signal induced by hydroxyurea. Single-molecule FRET showed that PCNA itself acts as a mechanical barrier to fork regression. Consequently, DNA breaks required for fork restart are reduced by ATAD5 depletion. Collectively, our results suggest an important role of ATAD5 in maintaining genome integrity during replication stress.

Reduced fibrous capsule formation at nano-engineered silicone surfaces via tantalum ion implantation.

Although the design of more biocompatible polymeric implants has been studied for decades, their intended functionality continues to be impaired by the response of the host tissue to foreign bodies at the tissue-implant interface. In particular, the formation and contracture of fibrous capsules prevent the intimate integration of an implant with surrounding tissues, which leads to structural deformation of the implants and persistent discomfort and pain. We report a new surface nano-engineered silicone implant that reduces fibrous capsule formation and improves the biocompatibility of it via sputtering-based plasma immersion ion implantation (S-PIII). This technique can introduce biologically compatible tantalum (Ta) on the silicone surface to produce a Ta-implanted skin layer (<60 nm thick) as well as generate either smooth (Smooth/Ta silicone) or nano-textured (Nano/Ta silicone) surface morphologies. The biologically inert chemical structure and strong hydrophobic surface characteristics of bare silicone are substantially ameliorated after Ta ion implantation. In particular, the Nano/Ta silicone implant's combination of surface nano-texturing as a physical cue and the Ta-implanted layer as a chemical cue was found to be very effective at achieving outstanding hydrophilicity and fibroblast affinity compared to the bare and Smooth/Ta silicone implants. In a mouse in vivo study conducted for 8 weeks, the Nano/Ta silicone implant inhibited fibrous capsule formation and contracture on its surface better than the bare silicone based on an analysis of the number of macrophages, myofibroblast differentiation and activation, collagen density, and thickness of fibrous capsules.

In-vitro blood and vascular compatibility of sirolimus-eluting organic/inorganic hybrid stent coatings.

The surface characteristics of coronary stents play a pivotal role in inhibiting in-stent restenosis and late-stent thrombosis. In this study, a sol-gel-derived silica xerogel-chitosan hybrid coating was applied to Co-Cr stent and was reported, for the first time, as a biocompatible drug delivery tool in vascular stent application. A dense and uniform chitosan-silica xerogel hybrid coating (<1-µm thick) was applied on bare Co-Cr material. Sirolimus was well incorporated into the hybrid coatings without re-crystallization. The chitosan-silica hybrid coating with 30 wt% silica xerogel showed better mechanical stability and good adhesive strength without any cracking or delamination. The chitosan-silica hybrid coated Co-Cr surface exhibited significantly improved wettability and corrosion resistance compared to the chitosan coated Co-Cr surface. In addition, the hybrid coating layer enabled efficient loading of sirolimus, owing to the unique mesoporous structure of silica xerogel, which further allowed the sustained release of sirolimus over 3 weeks. In-vitro tests with human umbilical cord vein endothelial cells and blood platelets confirmed that the chitosan-silica hybrid coating had excellent cytocompatibility and hemocompatibilty. Thus, this study demonstrated that the chitosan-silica hybrid material is a promising material for coating coronary stents, with minimal risk of in-stent restenosis and thrombogenicity.

Enhanced Osseointegration Ability of Poly(lactic acid) via Tantalum Sputtering-Based Plasma Immersion Ion Implantation.

Poly(lactic acid) (PLA) is the most utilized biodegradable polymer in orthopedic implant applications because of its ability to replace regenerated bone tissue via continuous degradation over time. However, the poor osteoblast affinity for PLA results in a high risk of early implant failure, and this issue remains one of the most difficult challenges with this technology. In this study, we demonstrate the use of a new technique in which plasma immersion ion implantation (PIII) is combined with a conventional DC magnetron sputtering. This technique, referred to as sputtering-based PIII (S-PIII), makes it possible to produce a tantalum (Ta)-implanted PLA surface within 30 s without any tangible degradation or deformation of the PLA substrate. Compared to a Ta-coated PLA surface, the Ta-implanted PLA showed twice the surface roughness and substantially enhanced adhesion stability in dry and wet conditions. The strong hydrophobic surface properties and biologically relatively inert chemical structure of PLA were ameliorated by Ta S-PIII treatment, which produced a moderate hydrophilic surface and enhanced cell-material interactions. Furthermore, in an in vivo evaluation in a rabbit distal femur implantation model, Ta-implanted PLA demonstrated significantly enhanced osseointegration and osteogenesis compared with bare PLA. These results indicate that the Ta-implanted PLA has great potential for orthopedic implant applications.

Fluorine-ion-releasing injectable alginate nanocomposite hydrogel for enhanced bioactivity and antibacterial property.

The creation of a moist environment and promotion of cell proliferation and migration together with antibacterial property are critical to the wound-healing process. Alginate (Alg) is an excellent candidate for injectable wound dressing materials because it can form a gel in a mild environment. Taking advantage of its gelation property, an injectable nano composite hydrogel containing nano-sized (about 90 nm) calcium fluoride (CaF2) particles was developed using in-situ precipitation process. The amount of released fluorine (F-) ion from the nanocomposite hydrogel increased with increasing CaF2 content inside the composite hydrogel and the ions stimulated both the proliferation and migration of fibroblast cells in vitro. The antibacterial property of the composite hydrogel against E. coli and S. aureus was confirmed through colony formation test where the number of bacterial colonies significantly decreased compared to Alg hydrogel. The in vivo results based on a full-thickness wound model showed that the nanocomposite hydrogel effectively enhanced the deposition of the extracellular matrix compared to that of the Alg hydrogel. This study demonstrates the potential of this nanocomposite hydrogel as a bioactive injectable wound-dressing material with the ability to inhibit bacterial growth and stimulate cell proliferation and migration for accelerated wound healing.

Use of thioglycerol on porous polyurethane as an effective theranostic capping agent for bone tissue engineering.

Thiolated biodegradable polyurethane (TG-DPU) was synthesized using a one-pot reaction with thioglycerol adopted as a functionalized chain extender. After characterization of the chemical structure of TG-DPU using proton nuclear magnetic resonance spectroscopy, bone morphogenetic protein (BMP-2) was loaded in the TG-DPU under oxidative conditions to form disulfides between the free thiol of TG-DPU and BMP-2. The interaction between TG-DPU and BMP-2, so-called bioconjugates, was investigated using X-ray photoelectron spectroscopy analysis; the appearance of disulfide (S-S) linkage indicated the formation of a polymer/growth factor conjugate system. The covalently linked bioconjugates provided stability with minimal loss during the drug delivery with prolonged release performance in in vitro release tests. The effects of the drugs delivered by TG-DPU were also confirmed by in vitro alkaline phosphatase tests using pre-osteoblasts and in vivo bone regeneration tests. The drugs effectively induced cell differentiation and promoted mature bone recovery.

Chitosan-Based Dressing Materials for Problematic Wound Management.

Wound healing is a complex mechanism involving a variety of factors and is a representative process of tissue growth and regeneration in our body. Surface-based interactions between the dressing material and the wound may significantly influence the healing phase. Advances in understanding the mechanism of wound healing have led to the development of numerous dressing materials that can accelerate the healing process. However, these materials have a passive role in wound healing. It is therefore necessary to develop novel wound dressing materials, especially effective for clinically problematic wounds. Chitosan-based dressing materials are considered suitable for clinically problematic wounds as they exhibit several characteristic features, such as facilitating hemostasis, enhanced wound healing during the inflammatory and proliferative phases, antimicrobial effect, etc. Here, we review the current status of clinically available dressing materials and studies on the biological characteristics of chitosan, and discuss the potential applications of chitosan in multi-functional dressing materials for accelarated wound healing.

Acceleration of the healing process of full-thickness wounds using hydrophilic chitosan-silica hybrid sponge in a porcine model.

In this study, we evaluated the surface characterization of a novel chitosan-silica hybridized membrane and highlighted the substantial role of silica in the wound environment. The chemical coupling of chitosan and silica resulted in a more condensed network compared with pure chitosan, which was eventually able to stably maintain its framework, particularly in the wet state. In addition, we closely observed the wound-healing process along with the surface interaction between chitosan-silica and the wound site using large-surface-area wounds in a porcine model. Our evidence indicates that chitosan-silica exerts a synergetic effect of both materials to promote a remarkable wound-healing process. In particular, the silica in chitosan-silica accelerated wound closure including wound contraction, and re-epithelialization via enhancement of cell recruitment, epidermal maturity, neovascularization, and granulation tissue formation compared with pure chitosan and other commercial dressing materials. This advanced wound dressing material may lead to effective treatment for problematic cutaneous wounds and can be further applied for human skin regeneration.

Effective Wound Healing by Antibacterial and Bioactive Calcium-Fluoride-Containing Composite Hydrogel Dressings Prepared Using in Situ Precipitation.

In this study, we report the development of a hyaluronic acid (HA)-based composite hydrogel containing calcium fluoride (CaF2) with good biocompatibility and antibacterial properties for multifunctional wound dressing applications. CaF2 was newly selected for incorporation within HA because it can release both Ca2+ and F- ions, which are well-known ions for affecting cell proliferation and inhibiting bacterial growth, respectively. In particular, an in situ precipitation process enables easy control over the released amount of F- ions by simply adjusting the precursor solutions (calcium chloride (CaCl2) and ammonium fluoride (NH4F)) used for the CaF2 precipitation. CaF2 particles were uniformly embedded within a HA-based pure hydrogel using an in situ precipitation process. Through variation of the CaCl2 and NH4F concentrations used in the precipitation as well as the precipitation time, composite hydrogels with different ion-release profiles were obtained. By controlling the precipitation time, especially for 10 min and after 30 min, large differences in the ion-release profiles as a function of CaF2 concentration were observed. A shorter precipitation time resulted in faster release of fluoride, whereas for the 30 min and 1 h samples, sustained ion release was achieved. Colony tests and live/dead assays using Escherichia coli and Staphylococcus aureus revealed a lower density of bacteria on the CaF2 composite hydrogels than on the pure hydrogel for both strains. In addition, improved cellular responses such as cell attachment and proliferation were also observed for the CaF2 composite hydrogels compared to those for the pure hydrogel. Furthermore, the composite hydrogels exhibited excellent wound healing efficiency, as evidenced by an in vitro cell migration assay. Finally, monitoring of the wound closure changes using a full-thickness wound in a rat model revealed the accelerated wound healing capability of the CaF2 composite hydrogels compared with that of the pure hydrogel. Based on our findings, these CaF2 composite hydrogels show great potential for application as advanced hydrogel wound dressings with antibacterial properties and accelerated wound-healing capabilities.

Calcium Phosphate-Collagen Scaffold with Aligned Pore Channels for Enhanced Osteochondral Regeneration.

This study reports the development of a bilayered scaffold with aligned channels produced via a sequential coextrusion and unidirectional freezing process to facilitate upward bone-marrow stem-cell migration. The biomimetic scaffold with collagen and biphasic calcium phosphate (BCP) layers is successfully fabricated with matching of the cartilage and bone layers. The aligned structure results in an enhancement of the compressive strength, and the channels enable tight anchoring of the collagen layers on the BCP scaffolds compared with a randomly structured porous scaffold. An in vitro evaluation demonstrates that the aligned channels guide the cells to attach on the surface in highly stretched shapes and migrate upward faster than the random structure. In addition, in vivo assessment reveals that the aligned channels yield superior osteochondral tissue regeneration compared with the random structure. Moreover, the channel diameter greatly affects the tissue regeneration, and the scaffold with a channel diameter of ≈270 µm exhibits the optimal regeneration because of sufficient nutrient supply and adequate tissue ingrowth. These findings indicate that the introduction of aligned channels to a bilayered scaffold provides an effective approach for osteochondral tissue regeneration.

Polyurethane-silica hybrid foams from a one-step foaming reaction, coupled with a sol-gel process, for enhanced wound healing.

Polyurethane (PU)-based dressing foams have been widely used due to their excellent water absorption capability, optimal mechanical properties, and unequaled economic advantage. However, the low bioactivity and poor healing capability of PU limit the applications of PU dressings in complex wound healing cases. To resolve this problem, this study was carried out the hybridization of bioactive silica nanoparticles with PU through a one-step foaming reaction that is coupled with the sol-gel process. The hybridization with silica did not affect the intrinsically porous microstructure of PU foams with silica contents of up to 10wt% and where 5-60nm silica nanoparticles were well dispersed in the PU matrix, despite slight agglomerations. The incorporated silica enhanced the mechanical performance of PU by proffering better flexibility and durability as well as maintaining good water absorption capabilities and the WVTR characteristics of pure PU foam. The silica of PU-10wt% Si foams was gradually dissolved and released under physiological conditions during a 14-day immersion period. The in vitro cell attachment and proliferation tests showed significant improvements in terms of the biocompatibility of PU-Si hybrid foams and demonstrated the effects of silica on cell growth. More significantly, the superior healing capability of PU-Si as a wound dressing in comparison to PU-treated wounds was verified through in vivo animal tests. Full-thickness wounds treated with PU-Si foams exhibited faster wound closure rates as well as accelerated collagen and elastin fiber regeneration in newly formed dermis, which was ultimately completely covered by a new epithelial layer. It is clear that PU-Si hybrid foams have considerable potential as a wound dressing material geared for accelerated, superior wound healing.

The accelerating effect of chitosan-silica hybrid dressing materials on the early phase of wound healing.

Commercialized dressing materials with or without silver have played a passive role in early-phase wound healing, protecting the skin defects from infections, absorbing exudate, and preventing dehydration. Chitosan (CTS)-based sponges have been developed in pure or hybrid forms for accelerating wound healing, but their wound-healing capabilities have not been extensively compared with widely used commercial dressing materials, providing limited information in a practical aspect. In this study, we have developed CTS-silica (CTS-Si) hybrid sponges with water absorption, flexibility, and mechanical behavior similar to those of CTS sponges. In vitro and in vivo tests were performed to compare the CTS-Si sponges with three commercial dressing materials [gauze, polyurethane (PU), and silver-containing hydrofiber (HF-Ag)] in addition to CTS sponges. Both in vitro and in vivo tests showed that CTS-Si sponges promoted fibroblast proliferation, leading to accelerated collagen synthesis, whereas the CTS sponges did not exhibit significant differences in fibroblast proliferation and collagen synthesis from gauze, PU, and HF-Ag sponges. In case of CTS-Si, the inflammatory cells were actively recruited to the wound by the influence of the released silicon ions from CTS-Si sponges, which, in return, led to an enhanced secretion of growth factors, particularly TGF-ß during the early stage. The higher level of TGF-ß likely improved the proliferation of fibroblasts, and as a result, collagen synthesis by fibroblasts became remarkably productive, thereby increasing collagen density at the wound site. Therefore, the CTS-Si hybrid sponges have considerable potential as a wound-dressing material for accelerating wound healing. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1828-1839, 2017.

Biomimetic Coating of Hydroxyapatite on Glycerol Phosphate-Conjugated Polyurethane via Mineralization.

In this study, glycerol phosphate was introduced into polyurethane (PU) to promote the coating stability of hydroxyapatite (HA) during its mineralization on the PU surface. Glycerol phosphate was successfully conjugated with the PU chain during polymerization. Phosphate groups in glycerol phosphate accelerated the nucleation of HA under calcium phosphate ion-rich conditions (concentrated simulated body fluid), resulting in the enhancement of structural stability. The robust interface between HA and PU also improved mechanical properties. Hydrophilic phosphate groups and bioactive HA improved in vitro cellular responses in terms of the attachment and proliferation of L929 fibroblasts and MC3T3-E1 preosteoblasts. Thus, the highly elastic and bioactive PU-gp-HA could be a promising candidate for tissue engineering applications that experience frequent deformation, including diverse cartilage replacements.

Highly oriented gold/nanoclay-polymer nanocomposites for flexible gas barrier films.

Layer-by-layer (LBL) assembly, which uses electronic and ionic intermolecular bonding under nonvacuum conditions, is a promising technology for fabricating gas barrier films owing to its simple processing and easy formation of a multilayer structure. In this research, nanoclay-polymer multilayers of Na(+)-montmorillonite (Na-MMT) were fabricated. Particularly, the addition of AuCl3 on fabricated MMT layers caused a reaction with the surface silanol functional groups (Si-O-H) of the MMT platelets, resulting in the formation of Au2O3 on the MMT-polymer multilayers. The Au2O3 filled the vacancies between the MMT platelets and linked the MMT platelets together, thus forming a gas barrier film that reduced the water vapor transmission rate (WVTR) to 3.2 × 10(-3) g m(-2) day(-1). AuCl3-treated MMT-polymer multilayers thus have the potential to be utilized for manufacturing gas barrier films for flexible electronics on a large scale.

Phage lambda capsids as tunable display nanoparticles.

Nanoparticle technologies provide a powerful tool for the development of reagents for use in both therapeutic and diagnostic, or "theragnostic" biomedical applications. Two broad classes of particles are under development, viral and synthetic systems, each with their respective strengths and limitations. Here we adapt the phage lambda system to construct modular "designer" nanoparticles that blend these two approaches. We have constructed a variety of modified "decoration" proteins that allow site-specific modification of the shell with both protein and nonproteinaceous ligands including small molecules, carbohydrates, and synthetic display ligands. We show that the chimeric proteins can be used to simultaneously decorate the shell in a tunable surface density to afford particles that are physically homogeneous and that can be manufactured to display a variety of ligands in a defined composition. These designer nanoparticles set the stage for development of lambda as a theragnostic nanoparticle system.

In vivo targeting of alveolar macrophages via RAFT-based glycopolymers.

Targeting cell populations via endogenous carbohydrate receptors is an appealing approach for drug delivery. However, to be effective, this strategy requires the production of high affinity carbohydrate ligands capable of engaging with specific cell-surface lectins. To develop materials that exhibit high affinity towards these receptors, we synthesized glycopolymers displaying pendent carbohydrate moieties from carbohydrate-functionalized monomer precursors via reversible addition-fragmentation chain transfer (RAFT) polymerization. These glycopolymers were fluorescently labeled and used to determine macrophage-specific targeting both in vitro and in vivo. Mannose- and N-acetylglucosamine-containing glycopolymers were shown to specifically target mouse bone marrow-derived macrophages (BMDMs) in vitro in a dose-dependent manner as compared to a galactose-containing glycopolymer (30- and 19-fold higher uptake, respectively). In addition, upon macrophage differentiation, the mannose glycopolymer exhibited enhanced uptake in M2-polarized macrophages, an anti-inflammatory macrophage phenotype prevalent in injured tissue. This carbohydrate-specific uptake was retained in vivo, as alveolar macrophages demonstrated 6-fold higher internalization of mannose glycopolymer, as compared to galactose, following intratracheal administration in mice. We have shown the successful synthesis of a class of functional RAFT glycopolymers capable of macrophage-type specific uptake both in vitro and in vivo, with significant implications for the design of future targeted drug delivery systems.