Hierarchical assembly of tryptophan zipper peptides into stress-relaxing bioactive hydrogels.

Soft materials in nature are formed through reversible supramolecular assembly of biological polymers into dynamic hierarchical networks. Rational design has led to self-assembling peptides with structural similarities to natural materials. However, recreating the dynamic functional properties inherent to natural systems remains challenging. Here we report the discovery of a short peptide based on the tryptophan zipper (trpzip) motif, that shows multiscale hierarchical ordering that leads to emergent dynamic properties. Trpzip hydrogels are antimicrobial and self-healing, with tunable viscoelasticity and unique yield-stress properties that allow immediate harvest of embedded cells through a flick of the wrist. This characteristic makes Trpzip hydrogels amenable to syringe extrusion, which we demonstrate with examples of cell delivery and bioprinting. Trpzip hydrogels display innate bioactivity, allowing propagation of human intestinal organoids with apical-basal polarization. Considering these extensive attributes, we anticipate the Trpzip motif will prove a versatile building block for supramolecular assembly of soft materials for biotechnology and medicine.

Complex Dispersion of Detonation Nanodiamond Revealed by Machine Learning Assisted Cryo-TEM and Coarse-Grained Molecular Dynamics Simulations.

Understanding the polydispersity of nanoparticles is crucial for establishing the efficacy and safety of their role as drug delivery carriers in biomedical applications. Detonation nanodiamonds (DNDs), 3-5 nm diamond nanoparticles synthesized through detonation process, have attracted great interest for drug delivery due to their colloidal stability in water and their biocompatibility. More recent studies have challenged the consensus that DNDs are monodispersed after their fabrication, with their aggregate formation poorly understood. Here, we present a novel characterization method of combining machine learning with direct cryo-transmission electron microscopy imaging to characterize the unique colloidal behavior of DNDs. Together with small-angle X-ray scattering and mesoscale simulations we show and explain the clear differences in the aggregation behavior between positively and negatively charged DNDs. Our new method can be applied to other complex particle systems, which builds essential knowledge for the safe implementation of nanoparticles in drug delivery.

Insight into Bioactivity of In-situ Trapped Enzyme-Covalent-Organic Frameworks.

Selecting a suitable support material for enzyme immobilization with excellent biocatalytic activity and stability is a critical aspect in the development of functional biosystems. The highly stable and metal-free properties of covalent-organic frameworks (COFs) make them ideal supports for enzyme immobilization. Herein, we constructed three kinds of COFs via a biofriendly and one-pot synthetic strategy at room temperature in aqueous solution. Among the three developed COFs (COF-LZU1, RT-COF-1 and ACOF-1), the horseradish peroxidase (HRP)-incorporated COF-LZU1 is found to retain the highest activity. Structural analysis reveals that a weakest interaction between the hydrated enzyme and COF-LZU1, an easiest accessibility by the COF-LZU1 to the substrate, as well as an optimal conformation of enzyme together promote the bioactivity of HRP-COF-LZU1. Furthermore, the COF-LZU1 is revealed to be a versatile nanoplatform for encapsulating multiple enzymes. The COF-LZU1 also offers superior protection for the immobilized enzymes under harsh conditions and during recycling. The comprehensive understanding of interfacial interactions of COF host and enzyme guest, the substrate diffusion, as well as the enzyme conformation alteration within COF matrices represents an opportunity to design the ideal biocatalysts and opens a broad range of applications of these nanosystems.

On the growth of the soft and hard protein corona of mesoporous silica particles with varying morphology.

The characterization of the protein corona has become an essential part of understanding the biological properties of nanomaterials. This is also important in the case of mesoporous silica particles intended for use as drug delivery excipients. A combination of scattering, imaging and protein characterization techniques is used here to assess the effect of particle shape and growth of the reversible (soft) and strongly bound (hard) corona of three types mesoporous silica particles with different aspect ratios. Notable differences in the protein composition, surface coverage and particle agglomeration of the protein corona-particle complex point to specific protein adsorption profiles highly dependent on exposed facets and aspect ratio. Spherical particles form relatively homogeneous soft and hard protein coronas (approx.10 nm thick) with higher albumin content. In contrast to rod-shaped and faceted particles, which possess soft coronas weakly bound to the external surface and influenced to a greater extent by the particle morphology. These differences are likely important contributors to observed changes in biological properties, such as cell viability and immunological behaviour, with mesoporous silica particle shape.

Modeling of a spray drying method to produce ciprofloxacin nanocrystals inside the liposomes utilizing a response surface methodology: Box-Behnken experimental design.

Spray drying was previously used to modify the physical form of the encapsulated ciprofloxacin drug to produce ciprofloxacin nanocrystals inside the liposomes (CNL). The purpose of the present study was to optimize CNL powder production by evaluating the response surface via design of experiments (DoE). Using the Box-Behnken (BB) design, the study independent variables were the protectant type (sucrose, trehalose or lactose), protectant amount, drying temperature, and spray gas flow. Individual spray drying experiments were performed at various set points for each variable followed by characterization of the produced powders. Liposomal particle size, drug encapsulation efficiency (EE%), liposomal surface zeta potential, and nanocrystal dimensions were the design dependant variables. By applying the least square regression method on the experimental data, mathematical models were developed using the mathematical software package MATLAB R2018b. Model reliability and the significance of the model's factors were estimated using analysis of variance (ANOVA). The generated CNL powders showed spherical to elliptical liposomal vesicles with particle sizes ranging from 98 to 159 nm. The EE (%) ranged from 30 to 95% w/w while the zeta potential varied between -3.5 and -10.5 mV. The encapsulated ciprofloxacin nanocrystals were elongated cylindrical structures with an aspect ratio of 4.0-7.8. Coefficients of determination (R2 > 0.9) revealed a good agreement between the predicted and experimental values for all responses except for the nanocrystal dimensions. Sucrose and lactose were superior to trehalose in protecting the liposomes during spray drying. The amount of sugar significantly affected the characteristics of the CNL powders (p-value < 0.05). In conclusion, the DoE approach using BB design has efficiently modelled the generation of CNL by spray drying. The optimum processing conditions which produced high drug encapsulation (90%) after formation of nanocrystals and a vesicle size of ~125 nm utilized 57% (w/w) sucrose, an 80 °C inlet temperature, and an atomization rate of 742 L/hr.

Quality Assessment and Comparison of Plasma-Derived Extracellular Vesicles Separated by Three Commercial Kits for Prostate Cancer Diagnosis.

INTRODUCTION: Current standard biomarkers in clinic are not specific enough for prostate cancer (PCa) diagnosis. Extracellular vesicles (EVs) are nano-scale vesicles released by most mammalian cells. EVs are promising biomarker source for PCa liquid biopsy due to its minimal invasive approach, rich information and improved accuracy compared to the clinical standard prostate-specific antigen (PSA). However, current EV separation methods cannot separate pure EVs and the quality characteristics from these methods remain largely unknown. In this study, we evaluated the quality characteristics of human plasma-derived EVs by comparing three clinical suitable separation kits. METHODS: We combined EV separation by commercial kits with magnetic beads capture and flow cytometry analysis, and compared three kits including ExoQuick Ultra based on precipitation and qEV35 and qEV70 based on size exclusion chromatography (SEC). RESULTS: Our results indicated that two SEC kits provided higher EV purity and lower protein contamination compared to ExoQuick Ultra precipitation and that qEV35 demonstrated a higher EV yield but lower EV purity compared to qEV70. Particle number correlated very well particularly with CD9/81/63 positive EVs for all three kits, which confirms that particle number can be used as the estimate for EV amount. At last, we found that several EV metrics including total EVs and PSA-specific EVs could not differentiate PCa patients from health controls. CONCLUSION: We provided a systematic workflow for the comparison of three separation kits as well as a general analysis process in clinical laboratories for EV-based cancer diagnosis. Better EV-associated cancer biomarkers need to be explored in the future study with a larger cohort.

Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction.

Sequence overlap between two genes is common across all genomes, with viruses having high proportions of these gene overlaps. Genome modularization and refactoring is the process of disrupting natural gene overlaps to separate coding sequences to enable their individual manipulation. The biological function and fitness effects of gene overlaps are not fully understood, and their effects on gene cluster and genome-level refactoring are unknown. The bacteriophage φX174 genome has ∼26% of nucleotides involved in encoding more than one gene. In this study we use an engineered φX174 phage containing a genome with all gene overlaps removed to show that gene overlap is critical to maintaining optimal viral fecundity. Through detailed phenotypic measurements we reveal that genome modularization in φX174 causes virion replication, stability, and attachment deficiencies. Quantitation of the complete phage proteome across an infection cycle reveals 30% of proteins display abnormal expression patterns. Taken together, we have for the first time comprehensively demonstrated that gene modularization severely perturbs the coordinated functioning of a bacteriophage replication cycle. This work highlights the biological importance of gene overlap in natural genomes and that reducing gene overlap disruption should be an integral part of future genome engineering projects.

Electron Microscopy Studies of Local Structural Modulations in Zeolite Crystals.

Zeolites are widely used in catalysis, gas separation, ion exchange, etc. due to their superior physicochemical properties, which are closely related to specific features of their framework structures. Although more than two hundred different framework types have been recognized, it is of great interest to explore from a crystallographic perspective, the atomic positions, surface terminations, pore connectivity and structural defects that deviate from the ideal framework structures, namely local structural modulation. In this article, we review different types of local modulations in zeolite frameworks using various techniques, especially electron microscopy (EM). The most recent advances in resolving structural information at the atomic level with aberration corrected EM are also presented, commencing a new era of gaining atomic structural information, not only for all tetrahedral atoms including point vacancies in framework but also for extra-framework cations and surface terminations.

Nanoscale Probing of Liposome Encapsulating Drug Nanocrystal Using Atomic Force Microscopy-Infrared Spectroscopy.

Use of liposomes encapsulating drug nanocrystals for the treatment of diseases like cancer and pulmonary infections is gaining attention. The potential therapeutic benefit of these engineered formulations relies on maintaining the physical integrity of the liposomes and the stability of the encapsulated drug. With the significant advancement in the microscopic and analytical techniques, analysis of the size and size distribution of these nanosized vesicles is possible. However, due to the limited spatial resolution of conventional vibrational spectroscopy techniques, the chemical composition of individual nanosized liposome cannot be resolved. To address this limitation, we applied atomic force microscopy infrared spectroscopy (AFM-IR) to assess the chemical composition of individual liposomes encapsulating ciprofloxacin in dissolved and nanocrystalline form. Spatially resolved AFM-IR spectra acquired from individual liposomes confirmed the presence of peaks related to N-H bending vibration, C-N stretching and symmetric, and asymmetric vibration of the carboxyl group present in the ciprofloxacin. Our results further demonstrated the effectiveness of AFM-IR in differentiating the liposome containing ciprofloxacin in dissolved or nanocrystalline form. Spectra acquired from dissolved ciprofloxacin had peaks related to the ionised carboxyl group, i.e., at 1576 and 1392 cm-1, which were either absent or far weaker in intensity in the spectra of liposomal sample containing ciprofloxacin nanocrystals. These findings are highly significant for pharmaceutical scientists to ascertain the stability and physicochemical composition of individual liposomes and will facilitate the design and development of liposomes with greater therapeutic benefits.

Effect of a protein corona on the fibrinogen induced cellular oxidative stress of gold nanoparticles.

The protein corona of nanoparticles is becoming a tool to understand the relation between intrinsic physicochemical properties and extrinsic biological behaviour. A diverse set of characterisation techniques such as transmission electron microscopy, mass spectrometry, dynamic light scattering, zeta-potential measurements and surface enhanced Raman spectroscopy are used to determine the composition and physical properties of the soft and hard corona formed around spherical gold nanoparticles. Advanced characterisation via small angle X-ray scattering and cryo-transmission electron microscopy suggests the presence of a thin hard corona of a few nm on 50 nm gold nanoparticles. The protein corona does not cause changes in cell viability, but inhibits the generation of reactive oxygen species in microglia cells. When a pre-incubated layer of fibrinogen, a protein with high affinity for the gold surface, is present around the nanoparticles before a protein corona is formed in bovine serum, the cellular uptake is significantly increased with an inhibition of ROS. The selective sequential pre-formation of protein complexes prior to incubation in cells is demonstrated as a viable method to alter the biological behaviour of nanoparticles.

Formation of ciprofloxacin nanocrystals within liposomes by spray drying for controlled release via inhalation.

The present study was conducted to harness spray drying technology as a novel method of producing Ciprofloxacin nanocrystals inside liposomes (CNL) for inhalation delivery. Liposomal ciprofloxacin dispersions were spray dried with sucrose as a lyoprotectant in different mass ratios (0.5:1, 1:1 and 2:1 sucrose to lipids), along with 2% w/w magnesium stearate and 5% w/w isoleucine as aerosolization enhancers. Spray drying conditions were: inlet air temperature 50 °C, outlet air temperature 33-35 °C, atomizer rate 742 L/h and aspirator 35 m3/h. After spray drying, the formation of ciprofloxacin nanocrystals inside the liposomes was confirmed by cryo- transmission electron microscopy. The physiochemical characteristics of the spray dried powder (particle size, morphology, crystallinity, moisture content, drug encapsulation efficiency (EE), in vitro aerosolization performance and drug release) were determined. The EE of the liposomes was found to vary between 44 and 87% w/w as the sucrose content was increased from 25 to 57% w/w. The powders contained partially crystalline particles with a volume median diameter of ~1 µm. The powders had low water content (~2% wt.) and were stable at high relative humidity. Aerosol delivery using the Osmohaler® inhaler at a flow rate of 100 L/min produced an aerosol fine particle fraction (% wt. <5 µm) of 58-64%. The formulation with the highest sucrose content (2:1 w/w sucrose to lipid) demonstrated extended ciprofloxacin release from liposomes (80% released within 7 h) in comparison to the original liquid formulation (80% released within 2 h). In conclusion, a stable and inhalable CNL powder with controlled drug release was successfully prepared by spray drying.

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters.

DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.

Ciprofloxacin nanocrystals liposomal powders for controlled drug release via inhalation.

This study was conducted to evaluate the feasibility of developing inhalable dry powders of liposomal encapsulated ciprofloxacin nanocrystals (LECN) for controlled drug release. Dry powders of LECN were produced by freeze-thaw followed by spray drying. The formulations contained sucrose as a lyoprotectant in different weight ratios (0.75:1, 1:1 and 2:1 sucrose to lipids), along with 2% magnesium stearate and 5% isoleucine as aerosolization enhancers. The powder physical properties (particle size, morphology, crystallinity, moisture content), in vitro aerosolization performance, drug encapsulation efficiency and in vitro drug release were investigated. The spray dried powders were comprised of spherical particles with a median diameter of ∼1 µm, partially crystalline, with a low water content (∼2% mass) and did not undergo recrystallization at high relative humidity. When dispersed by an Osmohaler® inhaler at 100 L/min, the powders showed a high aerosol performance with a fine particle fraction (% wt. <5 µm) of 66-70%. After reconstitution of the powders in saline, ciprofloxacin nanocrystals were confirmed by cryo-electron microscopy. The drug encapsulation efficiency of the reconstituted liposomes was 71-79% compared with the stock liquid formulation. Of the three formulations, the one containing a sucrose to lipids wt. ratio of 2:1 demonstrated a prolonged release of ciprofloxacin from the liposomes. In conclusion, ciprofloxacin nanocrystal liposomal powders were prepared that were suitable for inhalation aerosol delivery and controlled drug release.

Swimming behaviour and magnetotaxis function of the marine bacterium strain MO-1.

Magnetotactic bacteria (MTB) have the unique capacity to align and swim along the geomagnetic field lines downward to the oxic-anoxic interface in chemically stratified water columns and sediments. They are most abundant within the first few centimetres of sediments below the water-sediment interface. It is unknown how MTB penetrate into the sediment layer and swim in the pocket water, while their movements are restricted by the alignment along the magnetic field lines. Here we characterized the swimming behaviour of the marine fast-swimming magnetotactic ovoid bacterium MO-1.We found that it rotates around and translates along its short body axis to the magnetic north (northward). MO-1 cells swim forward constantly for a minimum of 1770 µm without apparent stopping. When encountering obstacles, MO-1 cells squeeze through or swim southward to circumvent the obstacles. The distance of southward swimming is short and inversely proportional to the magnetic field strength. Using a magnetic shielding device, we provide direct evidence that magnetotaxis is beneficial to MO-1 growth and becomes essential at low cell density. Environmental implications of the fast-swimming magnetotactic behaviour of magnetococci are discussed.

Architecture of a flagellar apparatus in the fast-swimming magnetotactic bacterium MO-1.

The bacterial flagellum is a motility organelle that consists of a rotary motor and a helical propeller. The flagella usually work individually or by forming a loose bundle to produce thrust. However, the flagellar apparatus of marine bacterium MO-1 is a tight bundle of seven flagellar filaments enveloped in a sheath, and it has been a mystery as to how the flagella rotate smoothly in coordination. Here we have used electron cryotomography to visualize the 3D architecture of the sheathed flagella. The seven filaments are enveloped with 24 fibrils in the sheath, and their basal bodies are arranged in an intertwined hexagonal array similar to the thick and thin filaments of vertebrate skeletal muscles. This complex and exquisite architecture strongly suggests that the fibrils counter-rotate between flagella in direct contact to minimize the friction of high-speed rotation of individual flagella in the tight bundle within the sheath to enable MO-1 cells to swim at about 300 µm/s.

Transient colloidal stability controls the particle formation of SBA-15.

A hypothesis about (transient) colloidal stability as a controlling mechanism for particle formation in SBA-15 is presented. The hypothesis is based on results from both in situ and ex situ investigations, including cryogenic transmission electron microscopy (cryo-TEM), UV-vis spectroscopy, and dynamic light scattering (DLS). Cryo-TEM images show that particles grow via the formation of silica-Pluronic-water "flocs", which coalesce in a seemingly arbitrary manner. Despite this, the final material consists of well-defined particles with a small size distribution. We argue that the interface between the flocs and surrounding media is covered by Pluronic molecules, which provide steric stabilization. As the flocs grow, the coverage of polymers at the interface is increased until a stable size is reached, and that regulates the particle size. By targeting the characteristics of the Pluronic molecules, during the on-going synthesis, the hypothesis is tested. The results are consistent with the concept of (transient) colloidal stability.

Complex spatial organization and flagellin composition of flagellar propeller from marine magnetotactic ovoid strain MO-1.

Marine magnetotactic ovoid bacterium MO-1 is capable of swimming along the geomagnetic field lines by means of its two sheathed flagellar bundles at a speed up to 300 µm/s. In this study, by using electron microscopy, we showed that, in each bundle, six individual flagella were organized in hexagon with a seventh in the middle. We identified 12 flagellin paralogs and 2 putative flagellins in the genome of MO-1. Among them, 13 were tandemly located on an ~ 17-kb segment while the 14th was on a separated locus. Using reverse transcription PCR and quantitative PCR, we found that all the 14 flagellin or putative flagellin genes were transcribed and that 2 of them were more abundantly expressed than others. A nLC (nanoliquid chromatography)-ESI (electrospray ionization)-MS/MS (mass spectrometry/mass spectrometry) mass spectrometry analysis identified all the 12 flagellin proteins in three glycosylated polypeptide bands resolved by one-dimensional denaturing polyacrylamide gel electrophoresis and 10 of them in 21 spots obtained by means of two-dimensional electrophoresis of flagellar extracts. Most spots contained more than one flagellin, and eight of the ten identified flagellins existed in multiple isoforms. Taken together, these results show unprecedented complexity in the spatial organization and flagellin composition of the flagellar propeller. Such architecture is observed only for ovoid-coccoid, bilophotrichously flagellated magnetotactic bacteria living in marine sediments, suggesting a species and environmental specificity.

Formation of two- and three-dimensional hybrid mesostructures from branched siloxane molecules.

We report the design of a new precursor having three branching disiloxane units capable of forming 3D mesostructures with a cubic Pm-3n and its orthorhombic and tetragonal variants Cmmm and P4(2)/mnm, in addition to a conventional 2D hexagonal (p6mm) mesostructure, thus creating a novel research area of mesostructural design in silica-organic nanohybrid materials.

Methodology for synthesizing crystalline metallosilicates with expanded pore windows through molecular alkoxysilylation of zeolitic lamellar precursors.

Postalkoxysilylation with diethoxydimethylsilane has been carried out on the zeolitic lamellar precursors of various topologies such as MWW, FER, CDO and MCM-47 aiming to construct new crystalline structures with expanded pore apertures between the layers. The silylation process and the crystalline and pore structures of the resulting materials have been investigated with the techniques of XRD, IR, (13)C and (29)Si MAS NMR, ICP, SEM, HRTEM, elemental analyses, and N 2 adsorption. In contrast to forming known three-dimensional zeolite structures after direct calcination of the lamellar precursors, the silylation led to new crystalline structures with opener pores, as evidenced by the shift of layer-related diffractions to the lower-angle region in XRD patterns and the enlarged interlayer pores found by HRTEM images. After optimizing the treatment conditions, particularly the amount of silane agent, a maximum and homogeneous silylation was realized, which guaranteed the phase purity in interlayer expanded zeolites. The expanded structures were well preserved after calcination at 823 K or reflux in water for 1 to 2 weeks, indicating a high thermal stability and also a hydrothermal stability. The interlayer expanded zeolites prepared from the metallosilicate precursors of MWW topology exhibited higher catalytic activities in the redox and solid acid-catalyzed reactions of bulky molecules than that of their counterparts with conventional MWW topology.