An 'activator-repressor' loop controls the anthocyanin biosynthesis in red-skinned pear.

The color of red-skinned pear (Pyrus spp.) is primarily attributed to accumulation of anthocyanins, which provide nutritional benefits for human health and are closely associated with the commercial value of fruits. Here, we reported the functional characterization of a R2R3-MYB repressor PyMYB107, which forms an 'activator-repressor' loop to control anthocyanin accumulation in the red-skinned pear. PyMYB107 overexpression inhibited anthocyanin biosynthesis in both pear calli and fruits, while virus-induced gene silencing of PyMYB107 increased anthocyanin accumulation in pear fruits. Furthermore, ectopic expression of PyMYB107 decreased anthocyanin accumulation in tomato, strawberry and tobacco. PyMYB107 can competitively bind to PybHLH3 with PyMYB10/MYB114, thereby suppressing the transcriptional activation of key anthocyanin biosynthesis genes, PyANS and PyUFGT. Site-directed mutagenesis showed that mutations within the R3 domain and EAR motif of PyMYB107 eliminated its repressive activity. Additionally, PyMYB107 exhibited a comparable expression pattern to PyMYB10/MYB114 and was transcriptionally activated by them. Our finding advanced comprehension of the repression mechanism underlying anthocyanin accumulation, providing valuable molecular insights into improving quality of pear fruits.

Transformation of a Viral Capsid from Nanocages to Nanotubes and Then to Hydrogels: Redirected Self-Assembly and Effects on Immunogenicity.

The ability to manipulate the self-assembly of proteins is essential to understanding the mechanisms of life and beneficial to fabricating advanced nanomaterials. Here, we report the transformation of the MS2 phage capsid from nanocages to nanotubes and then to nanotube hydrogels through simple point mutations guided by interfacial interaction redesign. We demonstrate that site 70, which lies in the flexible FG loop of the capsid protein (CP), is a "magic" site that can largely dictate the final morphology of assemblies. By varying the amino acid at site 70, with the aid of a cysteine-to-alanine mutation at site 46, we achieved the assembly of double-helical or single-helical nanotubes in addition to nanocages. Furthermore, an additional cysteine substitution on the surface of nanotubes mediated their cross-linking to form hydrogels with reducing agent responsiveness. The hierarchical self-assembly system allowed for the investigation of morphology-related immunogenicity of MS2 CPs, which revealed dramatic differences among nanocages, nanotubes, and nanotube hydrogels in terms of immune response types, antibody levels and T cell functions. This study provides insights into the assembly manipulation of protein nanomaterials and the customized design of nanovaccines and drug delivery systems.

Chirality Transfer of Glycopeptide across Scales Defined by the Continuity of Hydrogen Bonds.

In nature, chirality transfer refines biomolecules across all size scales, bestowing them with a myriad of sophisticated functions. Despite recent advances in replicating chirality transfer with biotic or abiotic building blocks, a molecular understanding of the underlying mechanism of chirality transfer remains a daunting challenge. In this paper, the coassembly of two types of glycopeptide molecules differing in capability of forming intermolecular hydrogen bonds enabled the involvement of discontinuous hydrogen bond, which allowed for a nanoscale chirality transfer from glycopeptide molecules to chiral micelles, yet inhibited the micrometer scale chirality transfer toward helix formation, leading to an achiral transfer from chiral micelles to planar monolayer. Upon stacking the monolayer into a bilayer, the nonsuperimposable front and back faces of the chiral micelles involved in the monolayer ribbons lead to the opposite rotation of two layers toward increasing the continuity of H-bonds. The resultant continuity triggered the symmetry breaking of stacked bilayers and thus reactivated the micrometer-scale chirality transfer toward the final helix. This work delineates a promising step toward a better understanding and replicating the naturally occurring chirality transfer events and will be instructive to future chiral material design.

One-Pot Fabrication of Supramolecular Synthetic Protein Hydrogel with Tissue-like Integrated Dynamic Features.

Protein-incorporated soft networks have received remarkable attention during the past several years. They possess desirable properties similar to native tissues and organs and exhibit unique advantages in applications. However, fabrication of protein-based hydrogels usually suffers from complex protein mutation and modification or chemical synthesis, which limited the scale and yield of production. Meanwhile, the lack of rationally designed noncovalent interactions in networks may result in a deficiency of the dynamic features of materials. Therefore, a highly efficient method is needed to include supramolecular interactions into protein hydrogel to generate a highly dynamic hydrogel possessing integrated tissue-like properties. Here, we report the design and construction of native protein-based supramolecular synthetic protein hydrogels through a simple and efficient one-pot polymerization of acrylamide and ligand monomers in the presence of a ligand-binding protein. The supramolecular interactions in the network yield integrated dynamic properties, including remarkable stretchability over 10,000% of their original length, ultrafast self-healing abilities within 3-4 s, tissue-like fast stress relaxation, satisfactory ability of adhesion to different living and nonliving substrates, injectability, and high biocompatibility. Furthermore, this material demonstrated potential as a biosensor to monitor small finger movements. This strategy provides a new avenue for fabricating synthetic protein hydrogels with integrated features.

Single-Molecule Fluorescence Imaging Reveals Coassembly of CTPS and P5CS.

The cellular compartmentation induced by self-assembly of natural proteins has recently attracted widespread attention due to its structural-functional significance. Among them, as a highly conserved metabolic enzyme and one of the potential targets for cancers and parasitic diseases in drug development, CTP synthase (CTPS) has also been reported to self-assemble into filamentous structures termed cytoophidia. To elucidate the dynamical mechanism of cytoophidium filamentation, we utilize single-molecule fluorescence imaging to observe the real-time self-assembly dynamics of CTPS and the coordinated assembly between CTPS and its interaction partner, Δ1-pyrroline-5-carboxylate synthase (P5CS). Significant differences exist in the direction of growth and extension when the two proteins self-assemble. The oligomer state distribution analysis of the CTPS minimum structural subunit under different conditions and the stoichiometry statistics of binding CTPS and P5CS by single-molecule fluorescence photobleach counting further confirm that the CTPS cytoophidia are mainly stacked with tetramers. CTPS can act as the nucleation core to induce the subsequent growth of the P5CS filaments. Our work not only provide evidence from the molecular level for the self-assembly and coordinated assembly (coassembly) of CTPS with its interaction partner P5CS in vitro but also offer new experimental perspectives for the dynamics research of coordinated regulation between other protein polymers.

Supramolecular Hydrogel with Ultra-Rapid Cell-Mediated Network Adaptation for Enhancing Cellular Metabolic Energetics and Tissue Regeneration.

Cellular energetics plays an important role in tissue regeneration, and the enhanced metabolic activity of delivered stem cells can accelerate tissue repair and regeneration. However, conventional hydrogels with limited network cell adaptability restrict cell-cell interactions and cell metabolic activities. In this work, it is shown that a cell-adaptable hydrogel with high network dynamics enhances the glucose uptake and fatty acid ß-oxidation of encapsulated human mesenchymal stem cells (hMSCs) compared with a hydrogel with low network dynamics. It is further shown that the hMSCs encapsulated in the high dynamic hydrogels exhibit increased tricarboxylic acid (TCA) cycle activity, oxidative phosphorylation (OXPHOS), and adenosine triphosphate (ATP) biosynthesis via an E-cadherin- and AMP-activated protein kinase (AMPK)-dependent mechanism. The in vivo evaluation further showed that the delivery of MSCs by the dynamic hydrogel enhanced in situ bone regeneration in an animal model. It is believed that the findings provide critical insights into the impact of stem cell-biomaterial interactions on cellular metabolic energetics and the underlying mechanisms.

A New "Mix and Measure" Method for Rapid Quantitative Determination of Alkalinity Based on Proton Equilibrium and Definite Integral of Buffer Capacity.

Alkalinity is crucial in environmental control of ecosystems, wastewater and drinking water treatment, and industrial process control. In this work, we reported a new equation for calculating alkalinity based on the definition of buffer capacity in acid-base buffer solutions and the quantitative relationship between the buffer capacity and pH changes. A "mix and measure" method was developed using this new equation, involving mixing a solution with unknown alkalinity and a standard solution in a specific volume ratio, followed by measuring the pH after mixing. The alkalinity of the solution can be calculated using the newly developed equation. The "mix and measure" method is much more efficient than traditional titration methods for determination of alkalinity because it is restricted by the titration stoichiometric point. Additionally, we demonstrated the rapid determination of the alkalinity for a series of solutions using a portable detection system. This system exhibited precision and accuracy comparable to those of traditional titration methods. The portable system offers great potential for the on-site and real-time determination of alkalinity for industrial control and environmental monitoring purposes.

Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution.

Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, 'Yunhong No. 1' (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear's primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes ('Cuiguan' and 'Nijisseiki'). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.

Multi-functionalized carbon nanotubes towards green fabrication of heterogeneous catalyst platforms with enhanced catalytic properties under NIR light irradiation.

Metal/carbon nanotubes (CNTs) have been attractive hybrid systems due to their high specific surface area and exceptional catalytic activity, but their challenging synthesis and dispersion impede their extensive applications. Herein, we report a facile and green approach towards the fabrication of metal/CNT composites, which utilizes a versatile glycopeptide (GP) both as a stabilizer for CNTs in water and as a reducing agent for noble metal ions. The abundant hydrogen bonds in GP endow the formed GP-CNTs with excellent plasticity, enabling the availability of polymorphic CNT species from dispersion to viscous paste, gel, and even to dough by increasing their concentration. The GP molecules can reduce metal precursors at room temperature without additional reducing agents, enabling the in situ immobilization of metal nanoparticles (e.g. Au, Ag, Pt, and Pd) on the CNT surface. The combination of the excellent catalytic properties of Pd particles with photothermal conversion capability of CNTs makes the Pd/CNT composite a promising catalyst for the fast degradation of organic pollutants, as demonstrated by a model catalytic reaction using 4-nitrophenol (4-NP). The conversion of 4-NP using the Pd/CNT composite as the catalyst has increased by 1.6-fold under near infrared light illumination, benefiting from the strong light-to-heat conversion effect of CNTs. Our proposed strategy opens a new avenue for the synthesis of CNT composites as a sustainable and versatile catalyst platform.

Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions.

Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.

Self-Assembly of Glycolipid Epimers: Their Supramolecular Morphology Control and Immunoactivation Function.

Although advances have been made in carbohydrate-based macromolecular self-assembly, harnessing epimers of carbohydrates to perform molecular assembly and further investigating the properties of supramolecular materials remain little explored. Herein, two classes of stereoisomeric glycolipid amphiphiles based on d-N-acetylgalactosamine (GalNAc) are reported, and they can aggregate into ribbon-like structures in the aqueous solution due to amphiphilic property, which allow to obtain glycocalyx-mimicking supramolecular materials. The subtle distinction in glycoside configuration of GalNAc-α-SSA and GalNAc-ß-SSA dictates the different molecular packing in self-assembled structures. Since driven by the distinguishing carbohydrate-carbohydrate interactions, the ribbon-like architectures transform into spherical nanostructures via mixing GalNAc-α-SSA and GalNAc-ß-SSA. The resulting spherical micelles fabricated by blending glycolipid epimers can potentiate the macrophage- and dendritic cell-mediated immune responses in vitro. Such glycolipid epimers will pave the way to create glycocalyx-mimicking immune modulators by incorporating stereochemistry into supramolecular self-assembly.

Inorganic phosphate regulated high luminescence NaYF4:Yb3+, Er3+ as an iron ion fluorescent nanoprobe.

The iron ion in industrial circulating cooling water is an important indicator for early warning of equipment corrosion and control level. It is interesting to construct an upconversion luminescence iron ion nanoprobe with a common inorganic phosphate water treatment agent. Herein, inorganic phosphate sodium hexametaphosphate (SHMP) was used to regulate the morphology and functionalization of NaYF4:Yb3+, Er3+ upconversion luminescent nanoprobe (UCNPs) and applied to fluorometric detection of trace Fe(III) in water based on the fluorescence quenching which is caused by the selective coordination between hexametaphosphate on the surface of UCNPs and Fe(III). The structure, morphology, and luminous intensity of UCNPs were regulated by disodium hydrogen phosphate (ADSP), sodium tripolyphosphate (STPP) and sodium hexametaphosphate(SHMP). The UCNPs functionalized with SHMP has high sensitivity and selectivity for Fe(III) detection. The linear range and detection limit are 1.0-50 µM and 0.2 µM, respectively. The method has satisfactory results for the detection of trace Fe(III) in industrial circulating cooling water.

Conjugation of Macrophage-Mimetic Microalgae and Liposome for Antitumor Sonodynamic Immunotherapy via Hypoxia Alleviation and Autophagy Inhibition.

Sonodynamic therapy (SDT) is a noninvasive technique for local antitumor treatment; however, its clinical application is often limited by the low tumor accumulation of SDT agents, tumor's hypoxic microenvironment, and cytoprotective effects of autophagy. To address these issues, herein we developed surface-engineered chlorella (Chl, a green algae) as a targeted drug carrier and sustainable oxygen supplier (via photosynthesis) for significantly improved SDT via hypoxia alleviation as well as autophagy inhibition of chloroquine phosphate. In this design, the macrophage membrane was coated onto Chl to form macrophage-mimetic Chl (MChl) to increase its biocompatibility and targeted tumor accumulation driven by the inflammatory-homing effects of macrophage membranes. In addition, the membrane coating on Chl allowed lipid insertion to yield ß-cyclodextrin (ß-CD) modified MChl (CD-MChl). Subsequently, supramolecular conjugates of MChl-NP were constructed via host-guest interactions between CD-MChl and adamantane (ADA)-modified liposome (ADA-NP), and the anchored liposome went with CD-MChl hand-in-hand to the tumor tissues for co-delivery of Chl, hematoporphyrin, and chloroquine phosphate (loaded in ADA-NP). The synergistic therapy achieved via local oxygenation, SDT, and autophagy inhibition maximally improved the therapeutic efficacy of MChl-CQ-HP-NP against melanoma. Tumor rechallenging results revealed that the changes of tumor microenvironment including hypoxia alleviation, SDT induced immunogenic cell death, and autophagy inhibition collectively induced a strong antitumor immune response and memory.

Nanovaccine Based on a Biepitope Antigen to Potentiate the Immunogenicity of a Neoantigen.

Specific neoantigens are promising candidates for personalized cancer vaccines and immunotherapies, whereas the low immunogenicity and physicochemical variability are the main challenges in clinical trials. Herein, based on the rational design of neoantigens, we developed biepitope nanovaccines via integrating CD4+ with CD8+ T cell epitopes. A class of amphiphilic peptides composed of biepitope and hydrophilic amino acids can form well-defined nanostructures, thus incorporating functional sequences into an artificial platform. Cellular uptake studies demonstrated the enhanced endocytosis of biepitope neoantigens in dendritic cells (DCs). Such designed biepitopes can further stimulate the maturation of DCs, as validated by the upregulation of costimulatory molecules and secreted proinflammatory cytokines, which show the potential ability to prime T cells and evoke specific cellular immunity. The inspiring prophylactic and therapeutic efficacy of biepitope nanovaccines was evaluated in murine colon cancer. In contrast to individual CD8+ T cell epitopes, the rationally designed biepitope nanovaccines can efficiently provoke immune activation and potentiate antitumor immunity both in vitro and in vivo, presenting an alternative strategy for neoantigen vaccines.

Evolution of Protein Assemblies Driven by the Switching of Interplay Mode.

A protein assembly with the ability to switch interplay modes of multiple driving forces has been achieved. Although biomolecular systems driven by multiple driving forces have been exploited, work on such a protein assembly capable of switching the interplay modes at nanoscale has been rarely reported so far as a result of their great fabrication challenge. In this work, two sets of driving forces such as ligand-ligand interaction and protein-protein interaction were leveraged to antagonistically underpin the multilayered stackings and trigger the hollow evolution to afford the well-defined hollow rectangular frame of proteins. While these protein frames further collapsed into aggregates, the ligand-ligand interactions were weakened, and the interplay of two sets of driving forces thereby tended to switch into synergistic mode, converting the protein packing mode from porously loose packing to axially dense packing and thus giving rise to a morphological evolution toward a nanosized protein tube. This strategy not only provides a nanoscale understanding on the mechanism underlying the switch of interplay modes in the context of biomacromolecules but also may provide access for diverse sophisticated biomacromolecular nanostructures that are historically inaccessible for conventional self-assembly strategies.

A real-world pharmacovigilance study of FDA Adverse Event Reporting System (FAERS) events for venetoclax.

BACKGROUND: Venetoclax (VEN) is the first selective small molecule Bcl-2 inhibitor approved by FDA and used in adult chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL) and some acute myeloid leukemia (AML). However, the long-term safety of VEN in large sample population was unknown. This study evaluated the adverse events (AEs) of VEN from FDA Adverse Event Reporting System (FAERS) since its approval in 2016 by data mining. METHODS: The disproportionality analyses, including four algorithms of reporting odd ratio (ROR), proportional reporting ratio (PRR), bayesian configuration promotion neural network (BCPNN), and multi item gamma poisson shrinker (MGPS), were employed to quantify the signals of VEN-associated AEs. RESULTS: From the FAERS database, a total of 8,379,682 reports were collected during the study period. After removing the duplication, the number of reports with VEN as the primary suspect (PS) was 19,107. The 19,107 cases of AEs involved 27 organ systems, 256 significant PTs which conforming to the four algorithms. Unexpected serious AEs, such as pleural effusion, splenic infarction, atrial fibrillation, skin squamous cell carcinoma, etc., have signals. The median time of occurrence of AEs related to VEN was 31 days (inter quartile range [IQR] 7-131 days), and half of the reported AEs occurred within 1 month after administration. CONCLUSION: Our research has found new significant AEs signals of VEN, which improved its safety information in real-world after marketing approval, and contributed to its risk control of use in clinic.

Modular Platform of Carbohydrates-modified Supramolecular Polymers Based on Dendritic Peptide Scaffolds.

Glycopeptide supramolecular polymers displaying multivalent carbohydrates are particularly suitable for immune-relevant biomaterials, due to the important functions of carbohydrates in mediating cell-cell communication and modulating immune responses. However, the diversity and complexity of carbohydrates limited the generation of glycopeptide supramolecular monomers. Thereby, a modular platform of presenting various carbohydrates, especially more complex oligosaccharides, is highly desirable but remains underexplored. Here, we first prepared the linear amphiphilic glycopeptides that self-assembled into spherical nanoparticles and worm-like nanoparticles. Furthermore, the dendritic glycopeptides that self-assembled into uniform nanorods were designed to generate modular supramolecular polymers with variable functionality, via redesigning the molecular backbone. With various functional oligosaccharide-modified supramolecular polymers, the in vitro studies further indicated that these polymers were not cytotoxic to macrophages, and significantly modulated the production of proinflammatory cytokines. These findings provide a promising platform to develop supramolecular glycopeptide biomaterials with potential applications in immunomodulation and immunotherapy.

A real-world pharmacovigilance study of FDA adverse event reporting system (FAERS) events for niraparib.

Niraparib was approved for the treatment of platinum-sensitive recurrent epithelial ovarian cancer, fallopian tube and primary peritoneal cancer. The authors retrospectively investigated niraparib-related adverse events (AEs) through data mining of the US Food and Drug Administration Adverse Event Reporting System (FAERS). Four algorithms were employed to quantify the signals of niraparib associated AEs, using data from the FAERS between 2017 and 2021. MYSQL 8.0, Navicat Premium 15, Microsoft EXCEL 2019 and the GraphPad Prism 8 were used to conduct statistical analysis. There are 7,238,157 reports collected from the FAERS database, of which 11,701 reports listed niraparib as the 'primary suspected (PS)' drug. A total of 97 significant disproportionality PTs conforming to the four algorithms were simultaneously retained. Unexpected significant AEs such as neuropathy peripheral, photosensitivity reaction, gastrooesophageal reflux disease might also occur. The median onset time of niraparib-associated AEs was 18 days (interquartile range [IQR] 4-66 days), and most of the cases occurred within the first months after niraparib initiation. The study found niraparib-associated AEs and might provide important support for clinical monitoring and risk identification of niraparib.

Construction of Active Protein Materials: Manipulation on Morphology of Salmon Calcitonin Assemblies with Enhanced Bone Regeneration Effect.

The effect of protein drugs is always limited by their relatively low stability and fast degradation property; thus, various elegant efforts have been made to improve the bioactivity and biocompatibility of the protein drugs. Here, an alternative way is proposed to solve this problem. By simply adding a limited amount of small-molecular regulator, which tunes the subtle balance of protein-protein interactions (PPIs) and disulfide bond formation, the self-assembly property of the protein drug can be regulated, forming an "active protein material" itself. This means that, the resulting biomaterial is dominated by the protein drug and water, with significantly enhanced bone regeneration effect compared to the virgin protein in vitro and in vivo, through multivalent effect between the protein and receptor and the retarded degradation of the assembled proteins. In this active protein material, the protein drug is not only the active drug, but also the drug carrier, which greatly increases the drug-loading efficiency of the biomaterial, indicating the advantages of the easy preparation, high efficiency, and low cost of the active protein material with a bright future in biomedical applications.

Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials.

The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.