Clofazimine improves clinical outcomes in multidrug-resistant tuberculosis: a randomized controlled trial

OBJECTIVES

We carried out a randomized multicentre study in China to investigate whether the clofazimine would improve the efficacy of the standardized regimen in patients with multidrug-resistant tuberculosis (MDR-TB).

METHODS

Patients with MDR-TB managed in 17 TB specialist hospitals in China between September 2009 and September 2011 were randomly assigned to the treatment groups at enrolment. In the intervention group, 100 mg clofazimine per day was added to the standardized regimen. The primary outcome was the proportion of patients with successful outcomes.

RESULTS

From the 156 patients that were screened, 74 were assigned to the control group and 66 to the clofazimine group. Of the 66 cases analysed for clinical outcome in the clofazimine group, 36 patients were cured, and seven completed treatment, yielding a favourable outcome rate of 65.1%. The proportion of patients with favourable outcomes receiving the control regimen was 47.3% (35/74), which was significantly lower than that in the clofazimine group (p 0.034, relative risk 0.661, 95% CI 0.243-0.949).

CONCLUSIONS

The addition of clofazimine to the standard regimen improved the treatment of MDR-TB.

Hierarchical nanostructures for functional materials

Naturally occurring biomaterials often have amazing functions, such as mechanical, thermal, electromagnetic, biological, optical and acoustic. These superior performances are often due to their hierarchical organizations of natural materials, starting from the nanoscopic scale and extending all the way to the macroscopic level. This topical issue features articles dedicated to understanding, designing and characterizing complex de novo hierarchical materials for a variety of applications. This research area is quickly evolving, and we hope that future work will drive the rational designs of innovative functional materials and generate deep impacts to broad engineering fields that address major societal challenges and needs.

Materials-by-Design: Computation, Synthesis, and Characterization from Atoms to Structures

In the 50 years that succeeded Richard Feynman's exposition of the idea that there is "plenty of room at the bottom" for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

Interlocking Friction Governs the Mechanical Fracture of Bilayer MoS2

A molybdenum disulfide (MoS₂) layered system is a two-dimensional (2D) material, which is expected to provide the next generation of electronic devices together with graphene and other 2D materials. Due to its significance for future electronics applications, gaining a deep insight into the fundamental mechanisms upon MoS₂ fracture is crucial to prevent mechanical failure toward reliable applications. Here, we report direct experimental observation and atomic modeling of the complex failure behaviors of bilayer MoS₂ originating from highly variable interlayer frictions, elucidated with in situ transmission electron microscopy and large-scale reactive molecular dynamics simulations. Our results provide a systematic understanding of the effects that different stacking and loading conditions have on the failure mechanisms and crack-tip behaviors in the bilayer MoS₂ systems. Our findings unveil essential properties in fracture of this 2D material and provide mechanistic insight into its mechanical failure.

Multiscale modeling of keratin, collagen, elastin and related human diseases: Perspectives from atomistic to coarse-grained molecular dynamics simulations

Scleroproteins are an important category of proteins within the human body that adopt filamentous, elongated conformations in contrast with typical globular proteins. These include keratin, collagen, and elastin, which often serve a common mechanical function in structural support of cells and tissues. Genetic mutations alter these proteins, disrupting their functions and causing diseases. Computational characterization of these mutations has proven to be extremely valuable in identifying the intricate structure-function relationships of scleroproteins from the molecular scale up, especially if combined with multiscale experimental analysis and the synthesis of model proteins to test specific structure-function relationships. In this work, we review numerous critical diseases that are related to keratin, collagen, and elastin, and through several case studies, we propose ways of extensively utilizing multiscale modeling, from atomistic to coarse-grained molecular dynamics simulations, to uncover the molecular origins for some of these diseases and to aid in the development of novel cures and therapies. As case studies, we examine the effects of the genetic disease Epidermolytic Hyperkeratosis (EHK) on the structure and aggregation of keratins 1 and 10; we propose models to understand the diseases of Osteogenesis Imperfecta (OI) and Alport syndrome (AS) that affect the mechanical and aggregation properties of collagen; and we develop atomistic molecular dynamics and elastic network models of elastin to determine the role of mutations in diseases such as Cutis Laxa and Supravalvular Aortic Stenosis on elastin's structure and molecular conformational motions and implications for assembly.

IL6 derived from cancer-associated fibroblasts promotes chemoresistance via CXCR7 in esophageal squamous cell carcinoma

Various factors and cellular components in the tumor microenvironment are key drivers associated with drug resistance in many cancers. Here, we analyzed the factors and molecular mechanisms involved in chemoresistance in patients with esophageal squamous cell carcinoma (ESCC). We found that interleukin 6 (IL6) derived mainly from cancer-associated fibroblasts played the most important role in chemoresistance by upregulating C-X-C motif chemokine receptor 7 (CXCR7) expression through signal transducer and activator of transcription 3/nuclear factor-κB pathway. CXCR7 knockdown resulted in the inhibition of IL6-induced proliferation and chemoresistance. In addition, CXCR7 silencing significantly decreased gene expression associated with stemness, chemoresistance and epithelial-mesenchymal transition and suppressed the proliferation ability of ESCC cells in three-dimensional culture systems and angiogenesis assay. In clinical samples, ESCC patients with high expression of CXCR7 and IL6 presented a significantly worse overall survival and progression-free survival upon receiving cisplatin after operation. These results suggest that the IL6-CXCR7 axis may provide a promising target for the treatment of ESCC.

Sub-nanometre channels embedded in two-dimensional materials

Two-dimensional (2D) materials are among the most promising candidates for next-generation electronics due to their atomic thinness, allowing for flexible transparent electronics and ultimate length scaling. Thus far, atomically thin p-n junctions, metal-semiconductor contacts, and metal-insulator barriers have been demonstrated. Although 2D materials achieve the thinnest possible devices, precise nanoscale control over the lateral dimensions is also necessary. Here, we report the direct synthesis of sub-nanometre-wide one-dimensional (1D) MoS₂ channels embedded within WSe₂ monolayers, using a dislocation-catalysed approach. The 1D channels have edges free of misfit dislocations and dangling bonds, forming a coherent interface with the embedding 2D matrix. Periodic dislocation arrays produce 2D superlattices of coherent MoS₂ 1D channels in WSe₂. Using molecular dynamics simulations, we have identified other combinations of 2D materials where 1D channels can also be formed. The electronic band structure of these 1D channels offers the promise of carrier confinement in a direct-gap material and the charge separation needed to access the ultimate length scales necessary for future electronic applications.

Acetic acid lignins from Chinese quince fruit (Chaenomeles sinensis): effect of pretreatment on their structural features and antioxidant activities

In this study, three pretreatment processes were evaluated for their effects on the structural features and antioxidant activities of lignins extracted by the acetosolv process from the fruit of Chinese quince. The three pretreatments included dephenolization, sugar removal, and multiple processes (a combination of both dephenolization and sugar removal). The results showed that after sugar removal pretreatment, the carbohydrate content, the molecular weight and S/G value of the lignin fractions decreased. However, after dephenolization pretreatment, the carbohydrate content and the molecular weight of the lignin fractions increased. After sugar removal and dephenolization, there were increases in the temperatures corresponding to the maximal rate of decomposition (DTG_max) in all lignin fractions. The radical scavenging index of lignin after sugar removal pretreatment was higher compared to other pretreatments and no treatment. The results of these tests showed that sugar removal, as a pretreatment, enhanced lignin extraction, yielding pure and highly functional lignins. Additionally, dephenolization or multiple process were beneficial to the acquisition of macromolecular lignins. All the results provided references for the biorefinery of biomass rich in polyphenol and sugar compounds.

Three pretreatments, including sugar removal, dephenolization and multiple processes, are applied on the lignin extraction from Chinese quince fruits.

Polymorphic regenerated silk fibers assembled through bioinspired spinning

A variety of artificial spinning methods have been applied to produce regenerated silk fibers; however, how to spin regenerated silk fibers that retain the advantages of natural silks in terms of structural hierarchy and mechanical properties remains challenging. Here, we show a bioinspired approach to spin regenerated silk fibers. First, we develop a nematic silk microfibril solution, highly viscous and stable, by partially dissolving silk fibers into microfibrils. This solution maintains the hierarchical structures in natural silks and serves as spinning dope. It is then spun into regenerated silk fibers by direct extrusion in the air, offering a useful route to generate polymorphic and hierarchical regenerated silk fibers with physical properties beyond natural fiber construction. The materials maintain the structural hierarchy and mechanical properties of natural silks, including a modulus of 11 ± 4 GPa, even higher than natural spider silk. It can further be functionalized with a conductive silk/carbon nanotube coating, responsive to changes in humidity and temperature.

Age-related reduction of dermal fibroblast size upregulates multiple matrix metalloproteinases as observed in aged human skin in vivo

BACKGROUND

Fragmentation of collagen fibrils, the major structure protein in skin, is a hallmark of dermal ageing. Matrix metalloproteinases (MMPs) are largely responsible for the fragmentation of collagen fibrils.

OBJECTIVES

To quantify gene expression of all 23 known mammalian MMPs in sun-protected young and aged human skin in vivo and to investigate the potential mechanism underlying age-related alteration of multiple MMPs.

METHODS

MMP mRNA expression levels and MMP activity in sun-protected young and aged human skin in vivo were determined by real-time reverse transcription polymerase chain reaction (RT-PCR) and in situ zymography, respectively. The relative contributions to elevated MMPs in epidermis and dermis were quantified by laser capture microdissection coupled real-time RT-PCR. Dermal fibroblast morphology and collagen fibril fragmentation in human skin in vivo were assessed by second-harmonic generation microscopy and atomic force microscopy, respectively. In vitro cell morphology was assessed by CellTracker® fluorescent dye (Molecular Probes, Eugene, OR, U.S.A.) and phalloidin staining. Protein levels were determined by ProteinSimple capillary electrophoresis immunoassay (ProteinSimple, Santa Clare, CA, U.S.A.).

RESULTS

Multiple MMPs are elevated in aged human skin dermis. Increased MMP activity and collagen fibril fragmentation were observed in aged skin dermis. As dermal fibroblasts are the major MMP-producing cells in the dermis, reduction of dermal fibroblast size, which is observed in aged human skin, contributes to the elevation of age-related multiple MMPs. Reduction of fibroblast size upregulates c-Jun/c-Fos and activates AP-1.

CONCLUSIONS

Combined actions of the wide variety of MMPs that are constitutively elevated in aged dermis may be involved in the progressive degradation of dermal collagen fibrils. Age-related elevations of multiple MMPs are likely to be a result of the reduction of fibroblast size via activation of AP-1.

Experimental and theoretical studies on the morphogenesis of bacterial biofilms

Biofilm morphogenesis not only reflects the physiological state of bacteria but also serves as a strategy to sustain bacterial survival. In this paper, we take the Bacillus subtilis colony as a model system to explore the morphomechanics of growing biofilms confined in a defined geometry. We find that the growth-induced stresses may drive the occurrence of both surface wrinkling and interface delamination in the biofilm, leading to the formation of a labyrinthine network on its surface. The wrinkles are perpendicular to the boundary of the constraint region. The variation in the surface undulations is attributed to the spatial stress field, which is isotropic in the inner regime but anisotropic in the vicinity of the boundary. Our experiments show that the directional surface wrinkles can confer biofilms with anisotropic wetting properties. This study not only highlights the role of mechanics in sculpturing organisms within the morphogenetic context but also suggests a promising route toward desired surfaces at the interface between synthetic biology and materials sciences.

Ultrathin thermoresponsive self-folding 3D graphene

Graphene and other two-dimensional materials have unique physical and chemical properties of broad relevance. It has been suggested that the transformation of these atomically planar materials to three-dimensional (3D) geometries by bending, wrinkling, or folding could significantly alter their properties and lead to novel structures and devices with compact form factors, but strategies to enable this shape change remain limited. We report a benign thermally responsive method to fold and unfold monolayer graphene into predesigned, ordered 3D structures. The methodology involves the surface functionalization of monolayer graphene using ultrathin noncovalently bonded mussel-inspired polydopamine and thermoresponsive poly(N-isopropylacrylamide) brushes. The functionalized graphene is micropatterned and self-folds into ordered 3D structures with reversible deformation under a full control by temperature. The structures are characterized using spectroscopy and microscopy, and self-folding is rationalized using a multiscale molecular dynamics model. Our work demonstrates the potential to design and fabricate ordered 3D graphene structures with predictable shape and dynamics. We highlight applicability by encapsulating live cells and creating nonlinear resistor and creased transistor devices.

Unusually low and density-insensitive thermal conductivity of three-dimensional gyroid graphene

Graphene has excellent mechanical, thermal and electrical properties. However, there are limitations in utilizing monolayers of graphene for mechanical engineering applications due to its atomic thickness and lack of bending rigidity. Synthesizing graphene aerogels or foams is one approach to utilize graphene in three-dimensional bulk forms. Recently, graphene with a gyroidal geometry has been proposed. A gyroid is a triply periodic minimal surface that allows graphene sheets to form a three-dimensional structure. Its light weight and high mechanical strength suggests that the graphene that constitutes this geometry can synergistically contribute to the mechanics of the bulk material. However, it is not clear whether gyroid graphene can preserve the high thermal conductivity of pristine graphene sheets. Here, we investigate the thermal conductivities of gyroid graphene with different porosities by using full-atom molecular dynamics simulations. In contrast to its excellent mechanical properties, we find that the thermal conductivity of gyroid graphene is more than 300 times lower than that of pristine graphene, with a bulk density of only about one-third of that of graphene. We derive a scaling law showing that the thermal conductivity does not vary much with different bulk densities, which contrasts the behavior of conventional porous materials. Our analysis shows that the poor thermal conductivity of gyroid graphene can be attributed to defects and curvatures of graphene, which increase with the density, resulting in the reduction of a phonon mean free path by phonon scattering. Our study shows that three-dimensional porous graphene has potential that may be utilized in designing new lightweight structural materials with low and density-insensitive thermal properties and superior mechanical strength.

Combined Medication of Antiretroviral Drugs Tenofovir Disoproxil Fumarate, Emtricitabine, and Raltegravir Reduces Neural Progenitor Cell Proliferation In Vivo and In Vitro

The application of combination antiretroviral therapy has greatly reduced the death rate from AIDS. However, up to 50% of patients on combination antiretroviral therapy develop HIV-associated neurocognitive disorders (HAND), which is associated with residual neuroinflammation and oxidative injury in the brain. Neural stem cells (NSCs) and progenitors play a vital role in repairing neuronal injuries. Therefore, we hypothesize that combination antiretroviral therapy may adversely affect NSCs/progenitors, contributing to the increasing prevalence of HAND. Here, we show that combined medication of three antiretroviral drugs tenofovir disoproxil fumarate (TDF), emtricitabine (FTC), and raltegravir (RAL) affects NSC homeostasis and progenitor proliferation in the mouse dentate gyrus (DG). Our results also show that TDF/FTC/RAL treatment prohibits proliferation and induces apoptosis of cultured mouse neural progenitor cells (NPCs), resulting in a reduction in the viability of NPCs. Moreover, we find that TDF, among the three drugs used in this combination antiretroviral treatment, accounts for most of the effects on neural progenitors. Together, our results offer a mechanistic explanation for the prevalence of HAND in AIDS patients treated with combination antiretroviral therapy.

Predicting rates of in vivo degradation of recombinant spider silk proteins

Developing fundamental tools and insight into biomaterial designs for predictive functional outcomes remains critical for the field. Silk is a promising candidate as a biomaterial for tissue engineering scaffolds, particularly where high mechanical loads or slow rates of degradation are desirable. Although bioinspired synthetic spider silks are feasible biomaterials for this purpose, insight into how well the degradation rate can be programmed by fine tuning the sequence remains to be determined. Here we integrated experimental approaches and computational modelling to investigate the degradation of two bioengineered spider silk block copolymers, H(AB)₂ and H(AB)₁₂ , which were designed based on the consensus domains of Nephila clavipes dragline silk. The effect of protein chain length and secondary structure on degradation was analysed in vivo. The degradation rate of H(AB)₁₂ , the silk with longer chain length/higher molecular weight, and higher crystallinity, was slower when compared to H(AB)₂ . Using full atomistic modelling, it was determined that the faster degradation of H(AB)₂ was due to the lower folded molecular structure of the silk and the greater accessibility to solvent. Comparison of the specific surface areas of proteins via modelling showed that higher exposure of random coil and lower exposure of ordered domains in H(AB)₂ led to the more reactive silk with a higher degradation rate when compared with H(AB)₁₂ , as validated by the experimental results. The study, based on two simple silk designs demonstrated that the control of sequence can lead to programmable degradation rates for these biomaterials, providing a suitable model system with which to study variables in protein polymer design to predict degradation rates in vivo. This approach should reduce the use of animal screening, while also accelerating translation of such biomaterials for repair and regenerative systems. Copyright © 2016 John Wiley & Sons, Ltd.

Multiscale mechanics of the lateral pressure effect on enhancing the load transfer between polymer coated CNTs

While individual carbon nanotubes (CNTs) are known as one of the strongest fibers ever known, even the strongest fabricated macroscale CNT yarns and fibers are still significantly weaker than individual nanotubes. The loss in mechanical properties is mainly because the deformation mechanism of CNT fibers is highly governed by the weak shear strength corresponding to sliding of nanotubes on each other. Adding polymer coating to the bundles, and twisting the CNT yarns to enhance the intertube interactions are both efficient methods to improve the mechanical properties of macroscale yarns. Here, we perform molecular dynamics (MD) simulations to unravel the unknown deformation mechanism in the intertube polymer chains and also local deformations of the CNTs at the atomistic scale. Our results show that the lateral pressure can have both beneficial and adverse effects on shear strength of polymer coated CNTs, depending on the local deformations at the atomistic scale. In this paper we also introduce a bottom-up bridging strategy between a full atomistic model and a coarse-grained (CG) model. Our trained CG model is capable of incorporating the atomistic scale local deformations of each CNT to the larger scale collect behavior of bundles, which enables the model to accurately predict the effect of lateral pressure on larger CNT bundles and yarns. The developed multiscale CG model is implemented to study the effect of lateral pressure on the shear strength of straight polymer coated CNT yarns, and also the effect of twisting on the pull-out force of bundles in spun CNT yarns.

Ribonucleotide reductase represents a novel therapeutic target in primary effusion lymphoma

Primary effusion lymphoma (PEL) is a highly aggressive B-cell malignancy that is closely associated with one of oncogenic viruses infection, Kaposi's sarcoma-associated herpesvirus (KSHV). PEL prognosis is poor and patients barely survive more than 6 months even following active chemotherapy interventions. There is therefore an urgent need to discover more effective targets for PEL management. We recently found that the ribonucleotide reductase (RR) subunit M2 is potentially regulated by the key oncogenic HGF/c-MET pathway in PEL (Dai et al., Blood. 2015;126(26):2821-31). In the current study, we set to investigate the role of RR in PEL pathogenesis and to evaluate its potential as a therapeutic target. We report that the RR inhibitor 3-AP actively induces PEL cell cycle arrest through inhibiting the activity of the NF-κB pathway. Using a xenograft model, we found that 3-AP effectively suppresses PEL progression in immunodeficient mice. Transcriptome analysis of 3-AP treated PEL cell lines reveals altered cellular genes, most of whose roles in PEL have not yet been reported. Taken together, we propose that RR and its signaling pathway may serve as novel actionable targets for PEL management.

Protein-free formation of bone-like apatite: New insights into the key role of carbonation

The nanometer-sized plate-like morphology of bone mineral is necessary for proper bone mechanics and physiology. However, mechanisms regulating the morphology of these mineral nanocrystals remain unclear. The dominant hypothesis attributes the size and shape regulation to organic-mineral interactions. Here, we present data supporting the hypothesis that physicochemical effects of carbonate integration within the apatite lattice control the morphology, size, and mechanics of bioapatite mineral crystals. Carbonated apatites synthesized in the absence of organic molecules presented plate-like morphologies and nanoscale crystallite dimensions. Experimentally-determined crystallite size, lattice spacing, solubility and atomic order were modified by carbonate concentration. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations predicted changes in surface energy and elastic moduli with carbonate concentration. Combining these results with a scaling law predicted the experimentally observed scaling of size and energetics with carbonate concentration. The experiments and models describe a clear mechanism by which crystal dimensions are controlled by carbonate substitution. Furthermore, the results demonstrate that carbonate substitution is sufficient to drive the formation of bone-like crystallites. This new understanding points to pathways for biomimetic synthesis of novel, nanostructured biomaterials.