Discovery of deaminase functions by structure-based protein clustering.

The elucidation of protein function and its exploitation in bioengineering have greatly advanced the life sciences. Protein mining efforts generally rely on amino acid sequences rather than protein structures. We describe here the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected deaminase proteins to analyze and identified many previously unknown properties. We were surprised to find that most proteins in the DddA-like clade were not double-stranded DNA deaminases. We engineered the smallest single-strand-specific cytidine deaminase, enabling efficient cytosine base editor (CBE) to be packaged into a single adeno-associated virus (AAV). Importantly, we profiled a deaminase from this clade that edits robustly in soybean plants, which previously was inaccessible to CBEs. These discovered deaminases, based on AI-assisted structural predictions, greatly expand the utility of base editors for therapeutic and agricultural applications.

An advanced strategy for quality evaluation of Xinyi Biyan Pill by UPLC-DAD fingerprinting combined with multi-components UPLC-MS/MS analysis.

Xinyi Biyan Pill (XBP) is a classical Chinese patent medicine and widely used to treat acute and chronic or allergic rhinitis in clinical practice. This study aimed to establish and validate a comprehensive strategy combining ultra-performance liquid chromatography with diode array detector (UPLC-DAD) fingerprinting and multi-component quantification for quality evaluation of XBP. In the fingerprint analysis, 32 peaks were selected as common peaks and used to evaluate the similarity of 12 batches of XBP. In addition, 141 compounds of XBP were identified or preliminarily characterized in both positive and negative ion modes by coupling with an advanced hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer. Moreover, a rapid quantitative method based on UPLC tandem mass spectrometry (UPLC-MS/MS) has been optimized and validated for simultaneous determination of 10 chemical markers within 15 min, and applied to analyzing 12 batches of XBP. The proposed comprehensive strategy combining UPLC-DAD fingerprinting and multi-component UPLC-MS/MS quantification exhibited satisfactory results with high efficiency, accuracy and reliability, which can be used as a reference for overall quality consistency evaluation of Chinese herbal formulations.

Prime editing using CRISPR-Cas12a and circular RNAs in human cells.

Genome editing with prime editors based on CRISPR-Cas9 is limited by the large size of the system and the requirement for a G/C-rich protospacer-adjacent motif (PAM) sequence. Here, we use the smaller Cas12a protein to develop four circular RNA-mediated prime editor (CPE) systems: nickase-dependent CPE (niCPE), nuclease-dependent CPE (nuCPE), split nickase-dependent CPE (sniCPE) and split nuclease-dependent CPE (snuCPE). CPE systems preferentially recognize T-rich genomic regions and possess a potential multiplexing capacity in comparison to corresponding Cas9-based systems. The efficiencies of the nuclease-based systems are up to 10.42%, whereas niCPE and sniCPE reach editing frequencies of up to 24.89% and 40.75% without positive selection in human cells, respectively. A derivative system, called one-sniCPE, combines all three RNA editing components under a single promoter. By arraying CRISPR RNAs for different targets in one circular RNA, we also demonstrate low-efficiency editing of up to four genes simultaneously with the nickase prime editors niCPE and sniCPE.

Molecular modeling-based inclusion mechanism and stability studies of doxycycline and hydroxypropyl-ß-cyclodextrin complex for ophthalmic delivery.

The aim of the present study was to prepare a stable complex of doxycycline (Doxy) and hydroxypropyl-ß-cyclodextrin (HPßCD) for ophthalmic delivery and investigate the inclusion mechanism and the inclusion effects on the stability of Doxy. The Doxy/HPßCD complex was prepared by solution stirring and then characterized by scanning electron microscopy and ultraviolet spectroscopy. Based on results of nuclear magnetic resonance, molecular model of Doxy/HPßCD complex was established using computational simulation of PM3 method implemented in Gaussian 03. Stabilities of Doxy/HPßCD complex in both aqueous solution and solid state at 25°C were evaluated by HPLC. Finally, in vitro antibacterial activity of the Doxy/HPßCD complex was evaluated by disk diffusion test. It was found that the stabilities of Doxy/HPßCD complex in both aqueous solution and solid state were improved obviously as compared with Doxy alone. This stability enhancement is consistent with the inclusion mechanism between HPßCD and Doxy, which showed that the unstable site of Doxy molecule at 6-CH3 was protected in the hydrophobic cavity of HPßCD, additionally, the chelation of Mg2+ provided a synergetic protection of the other unstable site of Doxy at 4-N(CH3)2. The antibacterial activity results indicated that Doxy/HPßCD complex might have potential for clinical applications.

Intrinsic half-metallicity in two-dimensional Cr2TeX2 (X = I, Br, Cl) monolayers.

Two-dimensional (2D) materials with intrinsic half-metallicity at or above room temperature are important in spin nanodevices. Nevertheless, such 2D materials in experiment are still rarely realized. In this work, a new family of 2D Cr2TeX2 (X = I, Br, Cl) monolayers has been predicted using first-principles calculations. The monolayer is made of five atomic sublayers with ABCAB-type stacking along the perpendicular direction. It is found that the energies for all the ferromagnetic (FM) half-metallic states are the lowest. The phonon spectrum calculations and molecular dynamics simulations both demonstrate that the FM states are stable, indicating the possibility of experimentally obtaining the 2D Cr2TeX2 monolayers with half-metallicity. The Curie temperatures from Monte Carlo simulations are 486, 445, and 451 K for Cr2TeI2, Cr2TeBr2, and Cr2TeCl2 monolayers, respectively, and their half-metallic bandgaps are 1.72, 1.86 and 1.90 eV. The corresponding magnetocrystalline anisotropy energies (MAEs) are about 1185, 502, 899 µeV per Cr atom for Cr2TeX2 monolayers, in which the easy axes are along the plane for the Cr2TeBr2 and Cr2TeCl2 monolayers, but being out of the plane in the Cr2TeI2. Our study implies the potential application of the 2D Cr2TeX2 (X = I, Br, Cl) monolayers in spin nanodevices.

[Improvement of Preparation Method of Rats Platelet-Rich Plasma and Quality Detection].

OBJECTIVE: To optimize the single centrifugation preparation protocol of rat platelet-rich plasma (PRP). METHODS: The arterial blood of rats obtained by carotid artery intubation was collected by heparin sodium anticoagulant tubes, and then the blood divided into sterile EP tubes, adjusting the red blood cell concentration with normal saline, while rat PRP was prepared by centrifugation under different conditions (the centrifugal force was 200×g-240×g, and the centrifugal time was 8-12 min). Subsequently, the blood cell count and quality evaluation of anticoagulat whole blood and PRP were performed by hematology analyzer and flow cytometry, respectively, and the differences between different groups were compared. RESULTS: The red blood cell concentration to (5.5-6.5)×1012/L after anticoagulation of rat whole blood was good for PRP extraction. When the blood samples was centrifuged at 220×g for 10 min, the platelet recovery rate was the highestï¼»(53.52±0.63)%ï¼½. The level of apoptosis and activation of plateles in PRP were not significantly different compared to whole blood(P>0.05), and the release level of growth factor was significantly increased(P<0.05). CONCLUSION: It is a key to improve the PRP extraction efficiency by reducing the amount of mixed red blood cell, and this study successfully modified the preparation method of rat PRP, with platelets high recovery rate and stable quality.

Extracellular Matrix-Mimetic Peptide Scaffolds Prolonged the Hypothermic Preservation of Stem Cells for Storage and Transportation.

Encouraging advances in both regenerative medicine and tissue engineering with stem cells require a short-term preservation protocol to provide enough time for quality control or the transportation of cell products from manufacturing facilities to clinical destinations. The hypothermic preservation of stem cells under refrigerated conditions (2-8 °C) in their specific culture medium provides an alternative and low-cost method for cryopreservation or commercial preservation fluid for short-term storage. However, most stem cells are vulnerable to hypothermia, which might result in cell damage from the cooling process and the lack of extracellular matrix (ECM). Herein, we report a peptide scaffold cell-culture-medium additive for mimicking in vivo ECM to enhance the storage efficiency of mesenchymal stem cells (MSCs) under hypothermic preservation. Peptide scaffolds exhibit protective effects against hypothermic injury by maintaining the viability, proliferation, migration, and differentiation capabilities of cells. The mechanistic study showed that the peptide scaffold was conducive to maintain mitochondrial function by retaining mitochondrial respiration, mitochondrial membrane potential (ΔΨm), and mass to alleviate intracellular and mitochondrial reactive oxygen species (ROS) production. Moreover, the peptide scaffold also prolonged the survival and retained the multipotency of hematopoietic stem and progenitor cells (HSPCs) under hypothermic conditions. In conclusion, these results demonstrate a feasible and convenient preservation system for stem cells that has the potential to promote the clinical application of hematopoietic stem cell therapy.

Dual-sensitized Eu(III)/Tb(III) complexes exhibiting tunable luminescence emission and their application in cellular-imaging.

Two novel dual-photosensitized stable complexes, namely [Eu(dpq)(BTFA)3] (1) and [Tb(dpq)(BTFA)3] (2), have been successfully assembled via a mixed ligand approach using dipyrido[3,2-d:2',3'-f]quinoxaline (dpq) and 3-benzoyl-1,1,1-trifluoroacetone (BTFA). The crystallographic data reveal mononuclear lanthanide cores in both 1 and 2, in which each eight-coordinated Ln(III) ion is located in a slightly distorted dodecahedron (D2d). The room-temperature photoluminescence spectra of complexes 1 and 2 indicate that both BTFA and dpq can effectively sensitize Eu(III) and Tb(III) characteristic luminescence. Moreover, heterometallic Ln-complexes can be synthesized, leading to a new series of differently doped EuxTb1-x complexes. Luminescence experiments on them reveal dual-emission peaks of Eu3+ and Tb3+, which lead to a gradual change in the luminous colour between yellow-green, yellow, orange, orange-red and red upon increasing the Eu3+ content. On the basis of the intrinsic strong emission properties and nontoxic nature of complexes 1 and 2, we explore their potential application as cellular imaging agents. Fluorescence microscopy data suggest the cytosolic and nuclear localization of 1 and 2 in HeLa and MCF-7 cells.

Cobalt-catalyzed Divergent Markovnikov and Anti-Markovnikov Hydroamination.

Catalytic hydroamination of the readily available alkenes is among the most straightforward means to construct diverse alkyl amines. To this end, the facile access to both regioselectivity, i.e., Markovnikov or anti-Markovnikov hydroamination, with minimum reaction-parameter alternation, remains challenging. Herein, we report a cobalt-catalyzed highly selective and divergent Markovnikov and anti-Markovnikov hydroamination of alkenes, in which the switch of regioselectivity is achieved simply by the variation of the addition sequence of 9-BBN.

Injectable, Pore-Forming, Perfusable Double-Network Hydrogels Resilient to Extreme Biomechanical Stimulations.

Biological tissues hinge on blood perfusion and mechanical toughness to function. Injectable hydrogels that possess both high permeability and toughness have profound impacts on regenerative medicine but remain a long-standing challenge. To address this issue, injectable, pore-forming double-network hydrogels are fabricated by orchestrating stepwise gelation and phase separation processes. The interconnected pores of the resulting hydrogels enable direct medium perfusion through organ-sized matrices. The hydrogels are amenable to cell encapsulation and delivery while promoting cell proliferation and spreading. They are also pore insensitive, tough, and fatigue resistant. When tested in biomimetic perfusion bioreactors, the hydrogels maintain physical integrity under prolonged, high-frequency biomechanical stimulations (>6000 000 cycles at 120 Hz). The excellent biomechanical performance suggests the great potential of the new injectable hydrogel technology for repairing mechanically dynamic tissues, such as vocal folds, and other applications, such as tissue engineering, biofabrication, organs-on-chips, drug delivery, and disease modeling.

Efficacy of Aerosol Reduction Measures for Dental Aerosol Generating Procedures.

Aerosol particles generated by dental procedures could facilitate the transmission of infectious diseases and contain carcinogen particles. Such particles can penetrate common surgical masks and reach the lungs, leading to increased risk for dental care professionals. However, the risk of inhaling contaminated aerosol and the effectiveness of aerosol reduction measures in dental offices remain unclear. The present study aimed to quantify aerosols produced by drilling and scaling procedures and to evaluate present recommendations for aerosol reduction. The concentration of aerosol particles released from the mock scaling and drilling procedures on dental mannequin were measured using a TSI Optical Particle Sizer (OPS 3330) during 15-min sessions carried out in a single-patient examination room. Using a drilling procedure as the aerosol source, the aerosol reduction performance of two types of high-volume evacuators (HVEs) and a commercial off-the-shelf air purifier was evaluated in a simulated clinical setting. Using either HVEs or the air purifier individually reduced the aerosol accumulated over the course of a 15-minutes drilling procedure at a reduction rate of 94.8 to 97.6%. Using both measures simultaneously raised the reduction rate to 99.6%. The results show that existing HVEs can effectively reduce aerosol concentration generated by a drilling procedure and can be further improved by using an air purifier. Following current regulatory guidelines can ensure a low risk of inhaling contaminated aerosol for dentists, assistants, and patients.

[Factors Affecting the Preservation of Human Peripheral Blood Mononuclear Cells at 4 ℃].

OBJECTIVE: To analyze the preservation effect and related influencing factors of human peripheral blood mononuclear cells under serum-free condition at 4 ℃. METHODS: Human peripheral blood mononuclear cells were isolated by density gradient centrifugation, and stored at 4 ℃ under different cell concentrations, supplemented with human serum albumin, and glucose. The cell viability, total cell number, viable cell number and cell phenotype were detected during preservation of 72 h. RESULTS: With the prolongation of storage time, the number of human peripheral blood mononuclear cells gradually decreased(r=0.982). Compared with the cell concentration of (5-6)×106 cells/ml, the cell number decreased more slowly when the cell storage concentration was (1-2)×106 cells/ml; Adding human serum albumin and glucose can effectively improve the survival rate of human peripheral blood mononuclear cells, among which 2% human serum albumin has a better preservation effect; Compared with the blank control group, the analysis results of cell subsets showed that the downward trends of NK cells and T cells were significantly slowed after adding albumin and glucose. CONCLUSION: The cell density of (1-2)×106/ml and 2% human serum albumin are more suitable for the preservation of PBMC, and 5% glucose can improve the preservation effect of human peripheral blood mononuclear cells at 4 ℃.

Controlled tough bioadhesion mediated by ultrasound.

Tough bioadhesion has important implications in engineering and medicine but remains challenging to form and control. We report an ultrasound (US)-mediated strategy to achieve tough bioadhesion with controllability and fatigue resistance. Without chemical reaction, the US can amplify the adhesion energy and interfacial fatigue threshold between hydrogels and porcine skin by up to 100 and 10 times. Combined experiments and theoretical modeling suggest that the key mechanism is US-induced cavitation, which propels and immobilizes anchoring primers into tissues with mitigated barrier effects. Our strategy achieves spatial patterning of tough bioadhesion, on-demand detachment, and transdermal drug delivery. This work expands the material repertoire for tough bioadhesion and enables bioadhesive technologies with high-level controllability.

The effect of doxycycline temperature-sensitive hydrogel on inhibiting the corneal neovascularization induced by BFGF in rats.

BACKGROUND: To study the effect of doxycycline temperature-sensitive hydrogel (DTSH) on inhibiting the corneal neovascularization (NV) induced by the basic fibroblast growth factor (bFGF). METHODS: Corneal NV was induced by slow-release polymer pellets containing bFGF, using a rat corneal pocket model. After being implanted with bFGF pellets, the female Sprague-Dawley rats were randomly divided into seven groups (12 rats/group). The grouped rats were given topically normal saline solution and neutralized DTSH at a concentration of 0%, 0.01%, 0.05%, 0.1%, 0.5%, and 1% respectively, and treated for 6 consecutive days. After 6 days of treatment, the cornea was perfused with India ink. The length and area of the corneal vessel were measured and analyzed by Image Pro-Plus 5.1. RESULTS: Compared to the control group given saline solution, the study groups given DTSH at a concentration of 0.05%, 0.1%, 0.5%, and 1% showed significant reduction in the vessel length (respectively, 58%, 60%, 52%, and 37%) and the vessel area (respectively, 61%, 62%, 49%, and 39%) (p < 0.001). However, no such significant reduction was observed in the study group given 0.01% DTSH (p = 0.133 and 0.166 for vessel length and area respectively). Study groups given 0.05% and 0.1% DTSH showed better effects than groups given 0.01% and 1% DTSH with regard to reducing the vessel length and the vessel area (p < 0.05). CONCLUSION: The study results showed that topical DTSH effectively inhibited corneal NV at the ideal concentration of 0.05% and 0.1%. Therefore, topical DTSH could be considered as an alternative treatment for the clinical management of corneal NV.

Needle-free Mental Incisive Nerve Block:In vitro, Cadaveric, and Pilot Clinical Studies.

The present study aimed to optimize Needle-Free Liquid Jet Injection (NFLJI) for Mental Incisive Nerve Blocks (MINB) and evaluate its clinical safety and feasibility. A MINB protocol was developed and optimized by series of NFLJI experiments in soft tissue phantoms and cadavers, then validated in two pilot Randomized Controlled Trials (RCT). The NFLJI penetration depth was found to be directly proportional to the supply pressure and volume. High-pressure NFLJIs (620 kPa or above) created maximum force and total work significantly greater than needle injections. Low-pressure NFLJIs (413 kPa), however, produced results similar to those of needle injections. Additionally, high-pressure NFLJIs created jet impingement pressure and maximum jet penetration pressure higher than low-pressure NFLJIs. Pilot RCTs revealed that high-pressure NFLJI caused a high risk of discomfort (60%) and paresthesia (20%); meanwhile, low-pressure NFLJI was less likely to cause complications (0%). The preliminary success rates of MINB from cadavers using NFLJIs and needles were 83.3% and 87.5%. In comparison, those from RCTs are 60% and 70%, respectively. To conclude, NFLJI supply pressure can be adjusted to achieve effective MINB with minimal complications. Furthermore, the cadaver study and pilot RCTs confirmed the feasibility for further non-inferiority RCT.

Doxycycline enhances the inhibitory effects of bevacizumab on corneal neovascularization and prevents its side effects.

PURPOSE: To investigate the combination therapeutic effects of topical doxycycline temperature-sensitive hydrogel (DTSH) and bevacizumab on corneal neovascularization (CNV) and corneal wound healing (CWH) and to explore the underlying mechanisms of doxycycline on CNV and CWH. METHODS: Rats were treated with a saline solution, topical DTSH (0.1%), topical bevacizumab (2.5 mg/0.1 mL), or a DTSH and bevacizumab combination. For the bFGF-induced CNV model (n = 15/group), the length and area of CNV were measured on day 7. In the alkali burn model (n = 33/group), the length and area of CNV were determined on days 3, 7, 14, and 21 after alkali burn. The activity of matrix metalloproteinase (MMP)-2 and MMP-9 was determined by a fluorogenic peptide substrate. Western blot, real-time PCR, and ELISA were used to analyze the expression of induced nitric oxide synthase (iNOS), VEGF, VEGFRS, MMP-2, MMP-9, and IL-1ß. RESULTS: Combination therapy more effectively inhibited CNV than therapy with topical bevacizumab or DTSH alone. DTSH combined with bevacizumab significantly accelerated delayed CWH caused by topical bevacizumab in the alkali burn model (P = 0.018). Combination therapy showed better inhibitory effects on MMP expression and phosphorylated VEGFR1 and VEGFR2. With DTSH treatment, doxycycline inhibited the activity and expression of MMPs, the expression of VEGF and of phosphorylated VEGFR1 and VEGFR2, and the production of iNOS and IL-1ß in local cornea. CONCLUSIONS: Doxycycline enhances the inhibitory effects of bevacizumab on CNV and prevents its side effects on CWH, possibly by inhibiting the expression and activity of MMPs, the expression of VEGF and of phosphorylated VEGFR1 and VEGFR2, and the production of iNOS and IL-1ß.