AND-Logic Cascade Rolling Circle Amplification for Optomagnetic Detection of Dual Target SARS-CoV-2 Sequences.

DNA logic operations are accurate and specific molecular strategies that are appreciated in target multiplexing and intelligent diagnostics. However, most of the reported DNA logic operation-based assays lack amplifiers prior to logic operation, resulting in detection limits at the subpicomolar to nanomolar level. Herein, a homogeneous and isothermal AND-logic cascade amplification strategy is demonstrated for optomagnetic biosensing of two different DNA inputs corresponding to a variant of concern sequence (containing spike L452R) and a highly conserved sequence from SARS-CoV-2. With an "amplifiers-before-operator" configuration, two input sequences are recognized by different padlock probes for amplification reactions, which generate amplicons used, respectively, as primers and templates for secondary amplification, achieving the AND-logic operation. Cascade amplification products can hybridize with detection probes grafted onto magnetic nanoparticles (MNPs), leading to hydrodynamic size increases and/or aggregation of MNPs. Real-time optomagnetic MNP analysis offers a detection limit of 8.6 fM with a dynamic detection range spanning more than 3 orders of magnitude. The accuracy, stability, and specificity of the system are validated by testing samples containing serum, salmon sperm, a single-nucleotide variant, and biases of the inputs. Clinical samples are tested with both quantitative reverse transcription-PCR and our approach, showing highly consistent measurement results.

Polymersomes in Drug Delivery─From Experiment to Computational Modeling.

Polymersomes, composed of amphiphilic block copolymers, are self-assembled vesicles that have gained attention as potential drug delivery systems due to their good biocompatibility, stability, and versatility. Various experimental techniques have been employed to characterize the self-assembly behaviors and properties of polymersomes. However, they have limitations in revealing molecular details and underlying mechanisms. Computational modeling techniques have emerged as powerful tools to complement experimental studies and enabled researchers to examine drug delivery mechanisms at molecular resolution. This review aims to provide a comprehensive overview of the state of the art in the field of polymersome-based drug delivery systems, with an emphasis on insights gained from both experimental and computational studies. Specifically, we focus on polymersome morphologies, self-assembly kinetics, fusion and fission, behaviors in flow, as well as drug encapsulation and release mechanisms. Furthermore, we also identify existing challenges and limitations in this rapidly evolving field and suggest possible directions for future research.

Escape dynamics of active ring polymers in a cylindrical nanochannel.

We explore the escape dynamics of active ring polymers confined in a cylindrical nanochannel using Brownian dynamics. Our simulation results show that the escape time decreases with the increase of the Péclet number, which is not noticeable between the two stages of the escape process, based on whether the center of mass of the polymer is inside or outside the nanochannel. However, the monomer motion trajectory of the active polymer is very different from that of the passive polymer, similar to the snake-like motion with uniform velocity. The passive polymer, however, is in constant fugitive motion with increased velocity at the tail end of the escape. Our work is vital for understanding the escape dynamics of active ring polymers in the confined nanochannel, which provides new perspectives on their characterization and analysis.

Inertial migration of polymer micelles in a square microchannel.

Using a hybrid simulation approach that combines a lattice-Boltzmann method for fluid flow and a molecular dynamics model for polymers, we investigate the inertial migration of star-like and crew-cut polymer micelles in a square microchannel. It is found that they exhibit two types of equilibrium positions, which shift further away from the center of the microchannel when the Reynolds number (Re) increases, as can be observed for soft particles. What differs from the behaviors of soft particles is that here, the blockage ratio is no longer the decisive factor. When the sizes are the same, the star-like micelles are always relatively closer to the microchannel wall as they gradually transition from spherical to disc-like with the increase of Re. In comparison, the crew-cut micelles are only transformed into an ellipsoid. Conversely, when the hydrophobic core sizes are the same, the equilibrium position of the star-like micelles becomes closer to that of the crew-cut micelles. Our results demonstrate that for polymer micelles with a core-shell structure, the equilibrium position is no longer solely determined by their overall dimensions but depends on the core and shell's specific dimensions, especially the hydrophobic core size. This finding opens up a new approach for achieving the separation of micelles in inertial migration.

Self-Assembly of Poly(Amino Acid)s Mediated by Secondary Conformations.

Self-assembly of block copolymers has recently drawn great attention due to its remarkable performance and wide variety of applications in biomedicine, biomaterials, microelectronics, photoelectric materials, catalysts, etc. Poly(amino acid)s (PAAs), formed by introducing synthetic amino acids into copolymer backbones, are able to fold into different secondary conformations when compared with traditional amphiphilic copolymers. Apart from changing the chemical composition and degree of polymerization of copolymers, the self-assembly behaviors of PAAs could be controlled by their secondary conformations, which are more flexible and adjustable for fine structure tailoring. In this article, we summarize the latest findings on the variables that influence secondary conformations, in particular the regulation of order-to-order conformational changes and the approaches used to manage the self-assembly behaviors of PAAs. These strategies include controlling pH, redox reactions, coordination, light, temperature, and so on. Hopefully, we can provide valuable perspectives that will be useful for the future development and use of synthetic PAAs.

Flow-driven translocation of comb-like copolymer micelles through a nanochannel.

Using hybrid lattice-Boltzmann molecular dynamics simulations, we investigate the flow-driven translocation of comb-like copolymer micelles through a nanochannel, in particular, making a detailed comparison with micelles formed by the corresponding diblock copolymers. Our results demonstrate that the critical flow flux of micelles formed by the comb-like copolymers is higher than that of micelles formed by the corresponding diblock copolymers, which is more pronounced with increasing side chain lengths or grafting densities, as evidenced by the free energy computed by self-consistent field theory. Our work indicates that the impact of chain topology on the stability of micelles, especially with the same size, can be well characterized using the critical flow fluxes, which provides a theoretical basis for designing self-assembling micelles for various applications.

Ejection dynamics of spherically confined active polymers through a small pore.

Using Brownian dynamics simulations, we study the ejection dynamics of spherically confined active polymers through a small pore. Although the active force can provide a driving force other than the entropy drive, it also causes the collapse of the active polymer, which in turn reduces the entropy drive. Thus, our simulation results confirm that the active polymer's ejection process can be divided into three stages. In the first stage, the influence of the active force is small, and the ejection is mainly an entropy-driven process. In the second stage, the ejection time satisfies the scaling relationship with the chain length, and the value of obtained scaling exponent is less than 1.0, indicating that the active force accelerates the ejection process. In the third stage, the scaling exponent is maintained at about 1.0, where the active force dominates the ejection process, and the ejection time is inversely proportional to the Péclet number. Furthermore, we find that the ejection velocity of the trailing particles has significant differences at different stages and is the core factor of the ejection mechanism at different stages. Our work helps us understand this non-equilibrium dynamic process and enhances our prediction of the relevant physiological phenomena.

Protein-Inspired Polymers with Metal-Site-Regulated Ordered Conformations.

Metal ions play critical roles in facilitating peptide folding and inducing conformational transitions, thereby impacting on the biological activity of many proteins. However, the effect of metal sites on the hierarchical structures of biopolymers is still poorly understood. Herein, inspired by metalloproteins, we report an order-to-order conformational regulation in synthetic polymers mediated by a variety of metal ions. The copolymers are decorated with clinically available desferrioxamine (DFO) as an exogenous ligand template, which presents a geometric constraint toward peptide backbone via short-range hydrogen bonding interactions, thus dramatically altering the secondary conformations and self-assembly behaviors of polypeptides and allowing for a controllable ß-sheet to α-helix transition modulated by metal-ligand interactions. These metallopolymers could form ferritin-inspired hierarchical structures with high stability and membrane activity for efficient brain delivery across the blood-brain barrier (BBB) and long-lasting magnetic resonance imaging (MRI) in vivo.

[Clinical features and prognosis of childhood B-lineage acute lymphoblastic leukemia expressing the PRAME gene]. / 表达PRAMEåŸºå› çš„å„¿ç«¥æ€¥æ€§Bæ·‹å·´ç»†èƒžç™½è¡€ç— çš„ä¸´åºŠç‰¹ç‚¹åŠé¢„åŽåˆ†æž.

OBJECTIVES: To study the clinical and prognostic significance of the preferentially expressed antigen of melanoma (PRAME) gene in the absence of specific fusion gene expression in children with B-lineage acute lymphoblastic leukemia (B-ALL). METHODS: A total of 167 children newly diagnosed with B-ALL were enrolled, among whom 70 were positive for the PRAME gene and 97 were negative. None of the children were positive for MLL-r, BCR/ABL, E2A/PBX1, or ETV6/RUNX1. The PRAME positive and negative groups were analyzed in terms of clinical features, prognosis, and related prognostic factors. RESULTS: Compared with the PRAME negative group, the PRAME positive group had a significantly higher proportion of children with the liver extending >6 cm below the costal margin (P<0.05). There was a significant reduction in the PRAME copy number after induction chemotherapy (P<0.05). In the minimal residual disease (MRD) positive group after induction chemotherapy, the PRAME copy number was not correlated with the MRD level (P>0.05). In the MRD negative group, there was also no correlation between them (P>0.05). The PRAME positive group had a significantly higher 4-year event-free survival rate than the PRAME negative group (87.5%±4.6% vs 73.5%±4.6%, P<0.05), while there was no significant difference between the two groups in the 4-year overall survival rate (88.0%±4.4% vs 85.3%±3.8%, P>0.05). The Cox proportional-hazards regression model analysis showed that positive PRAME expression was a protective factor for event-free survival rate in children with B-ALL (P<0.05). CONCLUSIONS: Although the PRAME gene cannot be monitored as MRD, overexpression of PRAME suggests a good prognosis in B-ALL.

Flow-driven competition between two capsules passing through a narrow pore.

By incorporating a distance function into the finite element simulation, we investigate the flow-driven competition between two soft capsules passing through a narrow pore, employing the arbitrary Lagrangian-Eulerian formulation to satisfy the boundary conditions for fluid flow and capsule deformation. In our simulations, the motion and deformation of the capsules can be described in an intuitive manner, and the order in which capsules of different sizes pass through a pore can be clearly determined. Meanwhile, when the capsules are near the narrow pore, the change of the flow field is also very interesting and can be expressed intuitively. It is shown that, driven by the Poiseuille flow, the larger capsule has a stronger tendency to pass through the pore than the small one, which can be attributed to the greater resistance and the volume advantage of the larger capsule. In addition, we demonstrate that this tendency can be reversed by changing the inlet velocity and setting the initial position of the smaller capsule closer to the axis of the pore. And as long as the large one passes through first, the small one will offset the axis to the same orientation as the initial, while the large one always moves along the axis.

Structure and dynamics of ions in dipolar solvents: a coarse-grained simulation study.

We employ the coarse-grained molecular dynamics simulation to investigate the fundamental structural and dynamic properties of the ionic solution with and without the application of an external electric field. Our simulations, in which the solvent molecules are treated as Stockmayer fluids and the ions are modeled as spheres, can effectively account for the multi-body correlations between ion-ion, ion-dipole, and dipole-dipole interactions, which are often ignored by the mean-field theories or coarse-grained simulations based on a dielectric continuum. By focusing on the coupling between effects of ion solvation, electrostatic correlations and applied electric field, we highlight some nontrivial microscopic molecular features of the systems, such as the reorganization of the dipolar solvent, clustering of the ions, and diffusions of ions and dipolar solvent molecules. Particularly, our simulation indicates the nonmonotonic dependence of the ionic clustering and ion diffusion rates on the dipolar nature of the solvent molecules, as well as the amplification of these tendencies caused by the electric field application. This work provides insights into the fundamental understanding of physicochemical properties for ion-containing liquids and contributes to the design and development of ion-containing materials.

Characteristics and prognosis of pediatric myeloid sarcoma in the cytogenetic context of t(8;21).

The prognosis of myeloid sarcoma (MS) is controversial. Many reports indicated that orbital-MS has a good prognosis and is closely related to t(8;21), but the prognostic role of MS in pediatric t(8;21) AML is unclear. We retrospectively analyzed data from 127 patients with pediatric t(8;21) AML diagnosed between January 2010 and June 2018. We compared patients with (n = 30) and without MS (n = 97). The median follow-up time was 52.6 months. The proportion of t(8;21) AML patients with MS was 23.6%. Males were more likely to have MS than females. The complete remission rate after the first course of induction chemotherapy and the 3-year relapse-free survival (RFS) among patients with MS were lower than those among patients without MS (60% vs. 78.4%, p = 0.045) (68.8 ± 8.8% vs. 88.0 ± 3.4%, p = 0.004). The female sex and a higher level of RUNX1/RUNX1T1 transcripts after consolidation were risk factors for poor RFS among patients with MS. Our data showed that MS was an independent risk factor in pediatric t(8;21) AML. Close monitoring of measurable residual disease of the bone marrow and extramedullary lesions is needed to guide stratified treatment.

Ordered Conformation-Regulated Vesicular Membrane Permeability.

In nature, the folding and conformation of proteins can control the cell or organelle membrane permeability and regulate the life activities. Here we report the first example of synthetic polypeptide vesicles that regulate their permeability via ordered transition of secondary conformations, in a manner similar to biological systems. The polymersomes undergo a ß-sheet to α-helix transition in response to reactive oxygen species (ROS), leading to wall thinning without loss of vesicular integrity. The change of membrane structure increases the vesicular permeability and enables specific transport of payloads with different molecular weights. As a proof-of-concept, the polymersomes encapsulating enzymes could serve as nanoreactors and carries for glucose-stimulated insulin secretion in vivo inspired by human glucokinase, resulting in safe and effective treatment of type 1 diabetes mellitus in mouse models. This study will help understand the biology of biomembranes and facilitate the engineering of nanoplatforms for biomimicry, biosensing, and controlled delivery applications.

Flow-induced translocation of vesicles through a narrow pore.

We use finite element method to investigate the flow-induced translocation of vesicles through a narrow pore from a dynamic point of view. In order to complete the coupling between fluid flow and the vesicle membranes, we employ the fluid-structure interactions with the arbitrary Lagrangian-Eulerian method. Our results demonstrate that the vesicle shows similar shape change from bullet-like to dumbbell-like, dumbbell-like to bulb-like, and bulb-like to parachute-like if it is pushed by flow field to pass through a narrow pore smaller than its size. We further find that the strain energy exhibits a higher peak and a lower peak in the whole translocation process, where the higher peak corresponds to the dumbbell-like shape and the lower peak corresponds to the parachute-like shape due to more stretching of the membrane for the dumbbell-like shape than that of the parachute-like shape. The translocation time of the vesicle from one side to the other side of the narrow pore decreases with the increase of inlet velocity, but the strain energy exhibits an increase, which implies that the vesicle needs more time to complete the translocation with the lower inlet velocity, but the requirement for the mechanical properties of the membrane is lower. Our work answers the mapping between the positions of the vesicles and deformed states with the stress distribution and change of strain energy, which can provide helpful information on the utilization of vesicles in pharmaceutical, chemical, and physiological processes.

Unusual self-diffusion behaviors of polymer adsorbed on rough surfaces.

We investigate the diffusion dynamics of a single polymer strongly adsorbed on surfaces in an extremely broad chain length and surface roughness by means of molecular dynamics simulations. Our simulations demonstrate that with the increase in chain length, the diffusion dynamics of polymer chains exhibits three regimes: the Rouse dynamics with D ∼ N-1 when the lateral size of polymer chains is smaller than a half of distance between obstacles on rough surfaces; the reptationlike dynamics with D ∼ N-1.5 and τr ∼ N3 when the obstacles inhibit the freely Rouse behavior of polymer chains; and the quasi-Rouse dynamics with D ∼ N-1 and τr ∼ N2.5 when the height of obstacles is smaller than twice the vertical size of polymer chains, where D, N, and τr are the diffusion coefficient, chain length, and end-to-end vector relaxation time of polymer chains, respectively. The long chains have sufficient conformation entropy to form loops to hop over short obstacles, which could dramatically reduce the confinement from obstacles on the rough surfaces and changes the diffusion and relaxation dynamics of polymer chains from the reptationlike dynamics to the quasi-Rouse dynamics. Our results reveal the whole diffusion dynamics of polymer chains strongly adsorbed on rough surfaces and clarify the corresponding transition mechanism, which is significant for the understanding of the physical nature and the development of the corresponding applications.

Conformation-Directed Micelle-to-Vesicle Transition of Cholesterol-Decorated Polypeptide Triggered by Oxidation.

Hierarchical self-assembly of synthetic polypeptides has attracted increasing interests due to its protein-mimetic structure and great potential in nanotechnology and biomedical applications. However, controlling the morphology and function of polymeric nanostructures via secondary structures remains largely unexplored. Here, we report an unusual micelle-to-vesicle transformation of cholesterol-decorated poly(l-cysteine) copolymer assemblies in response to reactive oxygen species (ROS). We found that the interesting morphological transition correlates with the alteration in conformations from ß-sheet to α-helix, which grants an attractive "on-off" switch for triggered release and cellular interaction. We further demonstrated the usefulness of the conformation-regulated assembly strategy both in vitro and in vivo, taking cancer treatment as a model. The work offers a new insight on the folding and hierarchical assembly of polypeptides and a novel approach for the development of smart platforms in biosensing, disease treatment, and diagnostic applications.

Antibacterial and Biocompatible Cross-Linked Waterborne Polyurethanes Containing Gemini Quaternary Ammonium Salts.

A cross-linked waterborne polyurethane (CPTMGPU) with long-term stability was developed from poly(ethylene glycol) (PEG), polyoxytetramethylene glycol (PTMG), isophorone diisocyanate (IPDI), l-lysine, and its derivative diamine consisting of gemini quaternary ammonium salt (GQAS), using ethylene glycol diglycidyl ether (EGDE) as a cross-linker. Weight loss test, X-ray photoelectron spectroscopy (XPS) measurements, and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were performed to prove the surface structure and stability of these CPTMGPU films. Furthermore, the GQAS-bearing CPTMGPUs show repeatable contact-active antibacterial efficacy against both Gram-positive Staphylococcus aureus (S. aureus) and Gram-negative Escherichia coli (E. coli) bacteria and do not show any inhibition effect against fibroblasts in vitro. After subcutaneous implantation in rats, the CPTMGPU films manifest good biocompatibility in vivo, despite the presence of a typical foreign body reaction toward surrounding tissues and mild systematic inflammation reaction that could be eliminated after a short implantation period, as demonstrated by histology and immunohistochemistry combined with interleukin (IL)-1ß, IL-4, IL-6, IL-10, and TNF-α analysis though enzyme-linked immunosorbent assay (ELISA) and real-time quantitative polymerase chain reaction (qRT-PCR). Therefore, these cross-linked waterborne polyurethanes hold great promise for antibacterial applications in vivo.

Simultaneous Improvement of Oxidative and Hydrolytic Resistance of Polycarbonate Urethanes Based on Polydimethylsiloxane/Poly(hexamethylene carbonate) Mixed Macrodiols.

The degradation behaviors including oxidation and hydrolysis of silicone modified polycarbonate urethanes were thoroughly investigated. These polyurethanes were based on polyhexamethylene carbonate (PHMC)/polydimethylsiloxane (PDMS) mixed macrodiols with molar ratio of PDMS ranging from 5% to 30%. It was proved that PDMS tended to migrate toward surface and even a small amount of PDMS could form a silicone-like surface. Macrophages-mediated oxidation process indicated that the PDMS surface layer was desirable to protect the fragile soft PHMC from the attack of degradative species. Hydrolysis process was probed in detail after immersing in boiling buffered water using combined analytical tools. Hydrolytically stable PDMS could act as protective shields for the bulk to hinder the chain scission of polycarbonate carbonyls whereas the hydrolysis of urethane linkages was less affected. Although the promoted phase separation at higher PDMS fractions lead to possible physical defects and mechanical compromise after degradation, simultaneously enhanced oxidation and hydrolysis resistance could be achieved for the polyurethanes with proper PDMS incorporation.

Effects of surface roughness on the self-diffusion dynamics of a single polymer.

We employ molecular dynamics simulations to simulate the diffusion dynamics of a single polymer adsorbed on surfaces with different roughnesses, which are characterized by the separation distance between obstacles and the height of obstacles. Our simulations demonstrate that for strong adsorption and when the confinement of obstacles is strong enough for all chains, the scaling exponent α of the diffusion coefficient on the chain length exhibits three cases with increase of the height of obstacles: a Rouse plateau with α ≈ -1 (the lateral motion of the polymer chains is free), a reptationlike plateau with α ≈ -1.5 (the polymer chains can hardly stride over the obstacles in the perpendicular direction) and a transition from the Rouse plateau to the reptationlike plateau with -1.5 < α < -1 (the obstacles hinder the lateral motion of the polymer chains). However, with increase of the separation distance between obstacles, the confinement from the obstacles exhibits a decrease (more lateral motions of the polymer chains are allowed), which results in a higher plateau (no longer separate reptationlike dynamics). Our results clarify the effects of surface roughness on the diffusion mechanism of polymer chains strongly adsorbed on solid surfaces in dilute solutions and the resulting transition mechanism from the Rouse scaling to the reptationlike scaling, which is significant for the understanding of the physical nature and the development of the corresponding applications.

Flow-induced polymer separation through a nanopore: effects of solvent quality.

Using a hybrid simulation method that combines a lattice-Boltzmann approach for the flow and a molecular dynamics model for the polymer, we investigated the effect of solvent quality on the flow-induced polymer translocation through a nanopore. We demonstrate the nontrivial dependence of the translocation dynamics of polymers on the solvent quality, i.e., the enhancement in the polymer insolubility increases the critical velocity flux and shortens the translocation time. Accordingly, we propose a new strategy to separate polymers with different solubilities via their translocations in the nanopore by adjusting the velocity flux of the flow, which appears to be promising for the design of micro-scaled polymer separation devices.