Xuefu Zhuyu decoction promotes synaptic plasticity by targeting miR-191a-5p/BDNF-TrkB axis in severe traumatic brain injury.

BACKGROUND: Xuefu Zhuyu decoction (XFZYD) is a traditional Chinese herbal formula known for its ability to eliminate blood stasis and improve blood circulation, providing neuroprotection against severe traumatic brain injury (sTBI). However, the underlying mechanism is still unclear. PURPOSE: We aim to investigate the neuroprotective effects of XFZYD in sTBI from a novel mechanistic perspective of miRNA-mRNA. Additionally, we sought to elucidate a potential specific mechanism by integrating transcriptomics, bioinformatics, and conducting both in vitro and in vivo experiments. METHODS: The sTBI rat model was established, and the rats were treated with XFZYD for 14 days. The neuroprotective effects of XFZYD were evaluated using a modified neurological severity score, hematoxylin and eosin staining, as well as Nissl staining. The anti-inflammatory effects of XFZYD were explored using quantitative real-time PCR (qRT-PCR), Western blot analysis, and immunofluorescence. Next, miRNA sequencing of the hippocampus was performed to determine which miRNAs were differentially expressed. Subsequently, qRT-PCR was used to validate the differentially expressed miRNAs. Target core mRNAs were determined using various methods, including miRNA prediction targets, mRNA sequencing, miRNA-mRNA network, and protein-protein interaction (PPI) analysis. The miRNA/mRNA regulatory axis were verified through qRT-PCR or Western blot analysis. Finally, morphological changes in the neural synapses were observed using transmission electron microscopy and immunofluorescence. RESULTS: XFZYD exhibited significant neuroprotective and anti-inflammatory effects on subacute sTBI rats' hippocampus. The analyses of miRNA/mRNA sequences combined with the PPI network revealed that the therapeutic effects of XFZYD on sTBI were associated with the regulation of the rno-miR-191a-5p/BDNF axis. Subsequently, qRT-PCR and Western blot analysis confirmed XFZYD reversed the decrease of BDNF and TrkB in the hippocampus caused by sTBI. Additionally, XFZYD treatment potentially increased the number of synaptic connections, and the expression of the synapse-related protein PSD95, axon-related protein GAP43 and neuron-specific protein TUBB3. CONCLUSIONS: XFZYD exerts neuroprotective effects by promoting hippocampal synaptic remodeling and improving cognition during the subacute phase of sTBI through downregulating of rno-miR-191a-5p/BDNF axis, further activating BDNF-TrkB signaling.

Cyclin B1: A potential prognostic and immunological biomarker in pan-cancer.

Cyclin B1 (CCNB1) encodes a regulatory protein essential for the regulation of cell mitosis, particularly in controlling the G2/M transition phase of the cell cycle. Current research has implicated CCNB1 in the progression of various types of cancer, including gastric cancer, breast cancer, and non-small cell lung cancer. In this study, we conducted a pan-cancer analysis of CCNB1 to investigate its prognostic significance and immunological aspects. Our comprehensive investigation covered a wide range of analyses, including gene expression, promoter methylation, genetic alterations, immune infiltration, immune regulators, and enrichment studies. We utilized multiple databases and tools for this purpose, such as The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, the Human Protein Atlas (HPA), the University of Alabama at Birmingham CANcer data analysis Portal (UALCAN), the Gene Expression Profiling Interactive Analysis (GEPIA), the DNA Methylation Interactive Visualization Database (DNMIVD), the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Sangerbox, and cBioPortal. Data analyses were executed using GraphPad Prism software, R software, and various online tools. Our findings demonstrated a significant increase in CCNB1 expression across 28 cancer types. Elevated CCNB1 expression correlated with decreased overall survival (OS) in 11 cancer types and disease-free survival (DFS) in 12 cancer types. Additionally, DNA promoter methylation levels were significantly decreased in 14 cancer types. Furthermore, the study verified a significant association between CCNB1 expression and immune infiltration, immune modulators, microsatellite instability (MSI), and tumor mutational burden (TMB). Enrichment analysis indicated that CCNB1 is involved in multiple cellular pathways. Collectively, our results suggested that CCNB1 has the potential to serve as a valuable prognostic biomarker and may be a promising target for immunotherapy in various cancer types.

Crystal phase and nanoscale size regulation utilizing the in-situ catalytic pyrolysis of bamboo sawdust in the recycling of spent lithium batteries.

Current Li-ion battery (LIB) recycling methods exhibit the disadvantages of low metal recovery efficiencies and high levels of pollution and energy consumption. Here, products generated via the in-situ catalytic pyrolysis of bamboo sawdust (BS) were utilized to regulate the crystal phase and nanoscale size of the NCM cathode to enhance the selective Li extraction and leaching efficiencies of other valuable metals from spent LIBs. The catalytic effect of the NCM cathode significantly promoted the release of gases from BS pyrolysis. These gases (H2, CO, and CH4) finally transformed the crystal phase of the NCM cathode from LiNixCoyMnzO2 into (Ni-Co/MnO/Li2CO3)/C. The size of the spent NCM cathode material was reduced approximately 31.7-fold (from 4.1 µm to 129.2 nm) after roasting. This could be ascribed to the in-situ catalytic decomposition of aromatic compounds generated via the primary pyrolysis of BS into C and H2 on the surface of the cathode material, resulting in the formation of the nanoscale composite (Ni-Co/MnO/Li2CO3)/C. This process enabled the targeted control of the crystal phase and nanoscale size of the material. Water leaching studies revealed a remarkable selective Li extraction efficiency of 99.27 %, and sulfuric acid leaching experiments with a concentration of 2 M revealed high extraction efficiencies of 99.15 % (Ni), 93.87 % (Co), and 99.46 % (Mn). Finally, a novel mechanism involving synergistic thermo-reduction and carbon modification for crystal phase regulation and nanoscale control was proposed. This study provides a novel concept for use in enhancing the recycling of valuable metals from spent LIBs utilizing biomass waste and practices the concept of "treating waste with waste".

Heparin-free veno-arterial extracorporeal membrane oxygenation in lung transplantation: a retrospective cohort study.

BACKGROUND: In lung transplantation (LTx) surgery, veno-arterial extracorporeal membrane oxygenation (VA-ECMO) can provide mechanical circulatory support to patients with cardiopulmonary failure. However, the use of heparin in the administration of ECMO can increase blood loss during LTx. This study aimed to evaluate the safety of heparin-free V-A ECMO strategies. METHODS: From September 2019 to April 2022, patients who underwent lung transplantation at the First Affiliated Hospital of Guangzhou Medical University were retrospectively reviewed. A total of 229 patients were included, including 117 patients in the ECMO group and 112 in the non-ECMO group. RESULT: There was no significant difference in the incidence of thrombus events and bleeding requiring reoperation between the two groups. The in-hospital survival rate after single lung transplantation (SLTx) was 81.08%in the ECMO group and 85.14% in the Non-ECMO group, (P = 0.585). The in-hospital survival rate after double lung transplantation (DLTx) was 80.00% in the ECMO group and 92.11% in the Non-ECMO groups (P = 0.095). CONCLUSIONS: In conclusion, the findings of this study suggest that the heparin-free V-A ECMO strategy in lung transplantation is a safe approach that does not increase the incidence of perioperative thrombotic events or bleeding requiring reoperation.

[Evaluation of the 5-year clinical restoration effect of implants retained complete overdentures with Locator attachments in 48 patients].

PURPOSE: To observe the long-term clinical effect of implants retained complete overdentures with Locator attachments. METHODS: A total of 48 patients with edentulous jaws treated with implants retained complete overdentures with Locator attachments were selected from the Outpatient Department of Peking University School and Hospital of Stomatology from 2016 to 2017. Among them, 21 patients underwent double-maxillary complete overdentures restoration and 27 patients underwent single-maxillary restoration. A total of 230 implants were implanted. The clinical observation indicators included the implant survival rate, peri-implant mucosal bleeding on probing(BOP), the change in the vertical height of alveolar bone absorption around the implants, overdenture base fracture rate, artificial tooth fall off and fracture rate and other complications. The change of the locator attachment retention force of the implant-supported overdentures was evaluated. SPSS 13.0 software package was used for data analysis. RESULTS: During the five-years clinical observation period, 5 implants fell off, 1 narrow dimeter implant in the anterior zone was broken, and 12 implants were lost to follow-up. The implant survival rate was 97.25%. One year after the restoration therapy finished, peri-implant mucosal bleeding on probing (BOP+) was detected in 48 (21.4%) implants. The average BI was 0.21±0.42, which was higher in the anterior zone than that in the posterior zone. The vertical alveolar bone absorption height around the implants was (0.21±0.35) mm, 2 implants-supported complete overdenture bases were broken. After 5 years of restoration, 163(76.89%) implants had peri-implant mucosal bleeding on probing(BOP+). The average BI was 1.00±0.70, and the vertical alveolar bone absorption height around the implants was (0.58±0.85) mm. There was no significant difference between males and females. There was no significant difference in the peri-implant mucosal bleeding index and the alveolar bone vertical absorption height between the anterior zone and the posterior zone(P＞0.05). The mean BI of peri-implant mucosa and the vertical absorption height of peri-implant alveolar bone were significantly different between the 1-year observation period and the 5-year observation period respectively(P＜0.01). There were 17(26.15%) cases with overdenture bases fracture, and the fracture rate of artificial teeth was 16.92%. Most of them occurred in the midline area of the anterior zone and the location of the overdenture base on the locator attachments. The average first replacement time of the locator attachment nylon retainer washer was 34.2±10.3 months. CONCLUSIONS: Implants retained complete overdentures with Locator attachments are effective in long term clinical observation. Complications are mainly found in peri-implant mucosal bleeding on probing and vertical alveolar bone absorption, and tended to increase gradually over time. The fracture of the implant retains complete overdenture bases and the fall off or fracture of the artificial teeth are the second serious complications. Overdenture base with metal frame at the location of the Locator abutment and the midline of the anterior area should be strengthened, and narrow diameter implants should be avoided as far as possible in the anterior zone.

Formation of cation bridges and its promoting mechanism for sorption of sulfamethoxazole by montmorillonite.

The coexistence of metal cations is often accompanied by organic pollution and could affect the environmental fate of organics by mediating the formation of cation bridges. However, the environmental fate and risk of organics in cation co-existing environments are poorly understood due to the lack of accurate identification of cation bridge formation and stability. In this study, the sorption of sulfamethoxazole (SMX) on montmorillonite (MT) with the coexistence of three different valence metal cations (Na+, Ca2+, and Cr3+) was investigated. Ca2+ and Cr3+ can significantly promote the sorption of SMX on MT for about 5∼10 times promotion, respectively, while Na+ bridges displayed little effect on the sorption of SMX. The sorption binding energy of SMX with MT-Ca (-44.01 kcal/mol) and MT-Cr (-64.57 kcal/mol) bridges was significantly lower than that with MT-Na (-38.45 kcal/mol) and MT (-39.39 kcal/mol), indicating that the sorption affinity of SMX on Cr and Ca bridges was much stronger. The higher valence of the cations also resulted in a more stable adsorbed SMX with less desorption fluctuation. In addition, the relatively higher initial concentration of SMX and the valence of cations increased the bonding density of the cation bridges, thus promoting the apparent sorption of SMX on MT to a certain extent. This work reveals the formation and function of cation bridges in the sorption of SMX on MT. It lays a theoretical foundation for further understanding the environmental fate and risk of organics.

Quantifying sodium hypochlorite content in hypochlorite-based disinfectants via phase-conversion headspace technique.

In this work, a novel and efficient approach for sodium hypochlorite analysis is proposed via phase-conversion headspace technique, which is based on the gas chromatography (GC) detection of generated carbon dioxide (CO2) from the redox reaction of sodium hypochlorite with sodium oxalate. The data obtained by the proposed method suggest the high detecting precision and accuracy. In addition, the method has low detection limits (limit of quantification (LOQ) = 0.24 µg/mL), and the recoveries of added standard ranged from 98.33 to 101.27 %. The proposed phase-conversion headspace technique is efficient and automated, thereby offering an efficient strategy for highly efficient analysis of sodium hypochlorite and related products.

Ginkgo biloba and Its Chemical Components in the Management of Alzheimer's Disease.

The pathogenesis of Alzheimer's disease (AD), a degenerative disease of the central nervous system, remains unclear. The main manifestations of AD include cognitive and behavioral disorders, neuropsychiatric symptoms, neuroinflammation, amyloid plaques, and neurofibrillary tangles. However, current drugs for AD once the dementia stage has been reached only treat symptoms and do not delay progression, and the research and development of targeted drugs for AD have reached a bottleneck. Thus, other treatment options are needed. Bioactive ingredients derived from plants are promising therapeutic agents. Specifically, Ginkgo biloba (Gb) extracts exert anti-oxidant, anticancer, neuroplastic, neurotransmitter-modulating, blood fluidity, and anti-inflammatory effects, offering alternative options in the treatment of cardiovascular, metabolic, and neurodegenerative diseases. The main chemical components of Gb include flavonoids, terpene lactones, proanthocyanidins, organic acids, polysaccharides, and amino acids. Gb and its extracts have shown remarkable therapeutic effects on various neurodegenerative diseases, including AD, with few adverse reactions. Thus, high-quality Gb extracts are a well-established treatment option for AD. In this review, we summarize the insights derived from traditional Chinese medicine, experimental models, and emerging clinical trials on the role of Gb and its chemical components in the treatment of the main clinical manifestations of AD.

Artificial intelligence in medicine: mitigating risks and maximizing benefits via quality assurance, quality control, and acceptance testing.

The adoption of artificial intelligence (AI) tools in medicine poses challenges to existing clinical workflows. This commentary discusses the necessity of context-specific quality assurance (QA), emphasizing the need for robust QA measures with quality control (QC) procedures that encompass (1) acceptance testing (AT) before clinical use, (2) continuous QC monitoring, and (3) adequate user training. The discussion also covers essential components of AT and QA, illustrated with real-world examples. We also highlight what we see as the shared responsibility of manufacturers or vendors, regulators, healthcare systems, medical physicists, and clinicians to enact appropriate testing and oversight to ensure a safe and equitable transformation of medicine through AI.

Unlocking the potential of T-cell metabolism reprogramming: Advancing single-cell approaches for precision immunotherapy in tumour immunity.

As single-cell RNA sequencing enables the detailed clustering of T-cell subpopulations and facilitates the analysis of T-cell metabolic states and metabolite dynamics, it has gained prominence as the preferred tool for understanding heterogeneous cellular metabolism. Furthermore, the synergistic or inhibitory effects of various metabolic pathways within T cells in the tumour microenvironment are coordinated, and increased activity of specific metabolic pathways generally corresponds to increased functional activity, leading to diverse T-cell behaviours related to the effects of tumour immune cells, which shows the potential of tumour-specific T cells to induce persistent immune responses. A holistic understanding of how metabolic heterogeneity governs the immune function of specific T-cell subsets is key to obtaining field-level insights into immunometabolism. Therefore, exploring the mechanisms underlying the interplay between T-cell metabolism and immune functions will pave the way for precise immunotherapy approaches in the future, which will empower us to explore new methods for combating tumours with enhanced efficacy.

Advancing Lithium-Magnesium Separation: Pioneering Swelling-Embedded Cation Exchange Membranes Based on Sulfonated Poly(ether ether ketone).

With the continuous advancement of electrodialysis (ED) technology, there arises a demand for improved monovalent cation exchange membranes (CEMs). However, limitations in membrane materials and structures have resulted in the low selectivity of monovalent CEMs, posing challenges in the separation of Li+ and Mg2+. In this investigation, a designed CEM with a swelling-embedded structure was created by integrating a polyelectrolyte containing N-oxide Zwitterion into a sulfonated poly(ether ether ketone) (SPEEK) membrane, leveraging the notable solubility characteristic of SPEEK. The membranes were prepared by using N-oxide zwitterionic polyethylenimine (ZPEI) and 1,3,5-benzenetrlcarbonyl trichloride (TMC). The as-prepared membranes underwent systematic characterization and testing, evaluating their structural, physicochemical, electrochemical, and selective ED properties. During ED, the modified membranes demonstrated notable permeability selectivity for Li+ ions in binary (Li+/Mg2+) systems. Notably, at a constant current density of 2.5 mA cm-2, the modified membrane PEI-TMC/SPEEK exhibited significant permeability selectivity (PMg2+Li+=5.63) in the Li+/Mg2+ system, while ZPEI-TMC/SPEEK outperformed, displaying remarkable permeability selectivity (PMg2+Li+=12.43) in the Li+/Mg2+ system, surpassing commercial monovalent cation-selective membrane commercial monovalent cation-selective membrane (CIMS). Furthermore, in the Li+/Mg2+ binary system, Li+ flux reached 9.78 × 10-9 mol cm-2 s-1 for ZPEI-TMC/SPEEK, while its Mg2+ flux only reached 2.7 × 10-9 mol cm-2 s-1, showing potential for lithium-magnesium separation. In addition, ZPEI-TMC/SPEEK was tested for performance and stability at high current densities. This work offers a straightforward preparation process and an innovative structural approach, presenting methodological insights for the advancement of lithium and magnesium separation techniques.

The role of superoxide anion to Cr(VI) reduction by pine biochar.

It has been reported that Cr(VI) can be reduced by biochar because of its redox activity. Considering the anionic form of Cr(VI), we hypothesize that the reduction in aqueous phase is significant. However, the contribution of different reactive oxygen species in the biochar-Cr(VI) reaction system has not been distinguished. Herein, we quantitatively identified Cr(VI) adsorption and reduction in biochar systems. The reduction content of Cr(VI) was 1.5 times higher in untreated conditions than in anaerobic conditions. The disappearance of·O2- under anaerobic conditions illustrated that·O2- may be involved in the reduction of Cr(VI). Quenching of·O2- resulted in a decrease of Cr(VI) reduction by 34%, while 1O2 was negligible, probably due to the stronger electron-donating capacity of·O2-. The degradation of nitrotetrazolium blue chloride (quenching agent of·O2-) confirmed that the reduction process of·O2- mainly occurred in the liquid-phase. Boehm titration and quantification of·O2- further elucidated the significant correlation (P < 0.05) between phenolic groups and the formation of·O2-, which implied that phenolic groups acted as the primary electron donors in generating·O2-. This study highlights the importance of the liquid-phase reduction process in removing Cr(VI), which provides theoretical support for biochar conversion of Cr(VI).

Identification of Anoikis-Related Genes in Spinal Cord Injury: Bioinformatics and Experimental Validation.

Spinal cord injury (SCI) is a serious disease without effective therapeutic strategies. To identify the potential treatments for SCI, it is extremely important to explore the underlying mechanism. Current studies demonstrate that anoikis might play an important role in SCI. In this study, we aimed to identify the key anoikis-related genes (ARGs) providing therapeutic targets for SCI. The mRNA expression matrix of GSE45006 was downloaded from the Gene Expression Omnibus (GEO) database, and the ARGs were downloaded from the Molecular Signatures Database (MSigDB database). Then, the potential differentially expressed ARGs were identified. Next, correlation analysis, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) analysis were employed for the differentially expressed ARGs. Moreover, miRNA-gene networks were constructed by the hub ARGs. Finally, RNA expression of the top ten hub ARGs was validated in the SCI cell model and rat SCI model. A total of 27 common differentially expressed ARGs were identified at different time points (1, 3, 7, and 14 days) following SCI. The GO and KEGG enrichment analysis of these ARGs indicated several enriched terms related to proliferation, cell cycle, and apoptotic process. The PPI results revealed that most of the ARGs interacted with each other. Ten hub ARGs were further screened, and all the 10 genes were validated in the SCI cell model. In the rat model, only seven genes were validated eventually. We identified 27 differentially expressed ARGs of the SCI through bioinformatic analysis. Seven real hub ARGs (CCND1, FN1, IGF1, MYC, STAT3, TGFB1, and TP53) were identified eventually. These results may expand our understanding of SCI and contribute to the exploration of potential SCI targets.

Immunological parameters of maternal peripheral blood as predictors of future pregnancy outcomes in patients with unexplained recurrent pregnancy loss.

INTRODUCTION: Unexplained recurrent pregnancy loss (URPL), affecting approximately 1%-5% of women, exhibits a strong association with various maternal factors, particularly immune disorders. However, accurately predicting pregnancy outcomes based on the complex interactions and synergistic effects of various immune parameters without an automated algorithm remains challenging. MATERIAL AND METHODS: In this historical cohort study, we analyzed the medical records of URPL patients treated at Xiangya Hospital, Changsha, China, between January 2020 and October 2022. The primary outcomes included clinical pregnancy and miscarriage. Predictors included complement, autoantibodies, peripheral lymphocytes, immunoglobulins, thromboelastography findings, and serum lipids. Least absolute shrinkage and selection operator (LASSO) analysis and logistic regression analysis was performed for model development. The model's performance, discriminatory, and clinical applicability were assessed using area under the curve (AUC), calibration curve, and decision curve analysis, respectively. Additionally, models were visualized by constructing dynamic and static nomograms. RESULTS: In total, 502 patients with URPL were enrolled, of whom 291 (58%) achieved clinical pregnancy and 211 (42%) experienced miscarriage. Notable differences in complement, peripheral lymphocytes, and serum lipids were observed between the two outcome groups. Moreover, URPL patients with elevated peripheral NK cells (absolute counts and proportion), decreased complement levels, and dyslipidemia demonstrated a significantly increased risk of miscarriage. Four models were developed in this study, of which Model 2 demonstrated superior performance with only seven predictors, achieving an AUC of 0.96 (95% CI: 0.93-0.99) and an accuracy of 0.92. A web-based platform was established to visually present model 2 and to facilitate its utilization by clinicians in outpatient settings (available from: https://yingrongli.shinyapps.io/liyingrong/). CONCLUSIONS: Our findings suggest that the implementation of such prediction models could serve as valuable tools for providing comprehensive information and facilitating clinicians in their decision-making processes.

Anisotropic Strain-Tailoring Nonlinear Optical Response in van der Waals NbOI2.

Two-dimensional (2D) NbOI2 demonstrates significant second-harmonic generation (SHG) with a high conversion efficiency. To unlock its full potential in practical applications, it is desirable to modulate the SHG behavior while utilizing the intrinsic lattice anisotropy. Here, we demonstrate direction-specific modulation of the SHG response in NbOI2 by applying anisotropic strain with respect to the intrinsic lattice orientations, where more than 2-fold enhancement in the SHG intensity is achieved under strain along the polar axis. The strain-driven SHG evolution is attributed to the strengthened built-in piezoelectric field (polar axis) and the enlarged Peierls distortions (nonpolar axis). Moreover, we provide quantifications of the correlation between strain and SHG intensity in terms of the susceptibility tensor. Our results demonstrate the effective coupling of orientation-specific strain to the anisotropic SHG response through the intrinsic polar order in 2D nonlinear optical crystals, opening a new paradigm toward the development of functional devices.

The Humanization and Maturation of an Anti-PrPc Antibody.

The cellular prion protein (PrPc) is a cell surface glycoprotein that is highly expressed in a variety of cancer tissues in addition to the nervous system, and its elevated expression is correlated to poor prognosis in many cancer patients. Our team previously found that patients with colorectal cancer (CRC) with high-level PrPc expression had significantly poorer survival than those with no or low-level PrPc expression. Mouse antibodies for PrPc inhibited tumor initiation and liver metastasis of PrPc-positive human CRC cells in mouse model experiments. PrPc is a candidate target for CRC therapy. In this study, we newly cloned a mouse anti-PrPc antibody (Clone 6) and humanized it, then affinity-matured this antibody using a CHO cell display with a peptide antigen and full-length PrPc, respectively. We obtained two humanized antibody clones with affinities toward a full-length PrPc of about 10- and 100-fold of that of the original antibody. The two humanized antibodies bound to the PrPc displayed significantly better on the cell surface than Clone 6. Used for Western blotting and immunohistochemistry, the humanized antibody with the highest affinity is superior to the two most frequently used commercial antibodies (8H4 and 3F4). The two new antibodies have the potential to be developed as useful reagents for PrPc detection and even therapeutic antibodies targeting PrPc-positive cancers.

Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein.

The small ultrared fluorescent protein (smURFP) is a bright near-infrared (NIR) fluorescent protein (FP) that forms a dimer and binds its fluorescence chromophore, biliverdin, at its dimer interface. To engineer a monomeric NIR FP based on smURFP potentially more suitable for bioimaging, we employed protein design to extend the protein backbone with a new segment of two helices that shield the original dimer interface while covering the biliverdin binding pocket in place of the second chain in the original dimer. We experimentally characterized 13 designs and obtained a monomeric protein with a weak fluorescence. We enhanced the fluorescence of this designed protein through two rounds of directed evolution and obtained designed monomeric smURFP (DMsmURFP), a bright, stable, and monomeric NIR FP with a molecular weight of 19.6 kDa. We determined the crystal structures of DMsmURFP both in the apo state and in complex with biliverdin, which confirmed the designed structure. The use of DMsmURFP in in vivo imaging of mammalian systems was demonstrated. The backbone design-based strategy used here can also be applied to monomerize other naturally multimeric proteins with intersubunit functional sites.

Self-Assembly of Heterogeneous Ferritin Nanocages for Tumor Uptake and Penetration.

Well-defined nanostructures are crucial for precisely understanding nano-bio interactions. However, nanoparticles (NPs) fabricated through conventional synthesis approaches often lack poor controllability and reproducibility. Herein, a synthetic biology-based strategy is introduced to fabricate uniformly reproducible protein-based NPs, achieving precise control over heterogeneous components of the NPs. Specifically, a ferritin assembly toolbox system is developed that enables intracellular assembly of ferritin subunits/variants in Escherichia coli. Using this strategy, a proof-of-concept study is provided to explore the interplay between ligand density of NPs and their tumor targets/penetration. Various ferritin hybrid nanocages (FHn) containing human ferritin heavy chains (FH) and light chains are accurately assembled, leveraging their intrinsic binding with tumor cells and prolonged circulation time in blood, respectively. Further studies reveal that tumor cell uptake is FH density-dependent through active binding with transferrin receptor 1, whereas in vivo tumor accumulation and tissue penetration are found to be correlated to heterogeneous assembly of FHn and vascular permeability of tumors. Densities of 3.7 FH/100 nm2 on the nanoparticle surface exhibit the highest degree of tumor accumulation and penetration, particularly in tumors with high permeability compared to those with low permeability. This study underscores the significance of nanoparticle heterogeneity in determining particle fate in biological systems.

De novo design of cavity-containing proteins with a backbone-centered neural network energy function.

The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones without predefined architectures by introducing tailored restraints into the backbone sampling driven by SCUBA (Side Chain-Unknown Backbone Arrangement), a neural network statistical energy function. For 521 out of 5816 designs, the root-mean-square deviations (RMSDs) of the Cα atoms for the AlphaFold2-predicted structures and our designed structures are within 2.0 Å. We experimentally tested 10 designed proteins and determined the crystal structures of two of them. One closely agrees with the designed model, while the other forms a domain-swapped dimer, where the partial structures are in agreement with the designed structures. Our results indicate that data-driven methods such as SCUBA hold great potential for designing de novo proteins with tailored small-molecule-binding function.