Transcriptome analysis revealing the effect of Bupleurum scorzonerifolium Willd association with endophytic fungi CHS3 on the production of saikosaponin D.

Saikosaponin D (SSd) is a naturally active product with strong pharmacological activity found in Bupleurum scorzonerifolium Willd. Studies have shown that endophytic fungi have great potential as sources of natural medicines. Fusarium acuminatum (CHS3), an SSd-producing endophytic fungus, was isolated from B. scorzonerifolium. To elucidate the effect of host plants on the production of SSd in CHS3, CHS3 was co-cultured with suspension cells of B. scorzonerifolium and SSd was detected using high-performance liquid chromatography (HPLC). Transcriptome sequencing (RNA-Seq) of CHS3 before and after co-culture was performed using an Illumina HiSeq 2500 platform. The results indicated that the content of SSd synthesised by CHS3 increased after co-culture with suspension cells of B. scorzonerifolium. Transcriptome analysis of CHS3 with differentially expressed genes (DEGs) showed that 1202 and 1049 genes were upregulated and downregulated, respectively, after co-culture. Thirty genes associated with SSd synthesis and 11 genes related to terpene backbone biosynthesis were annotated to the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Combined with transcriptome data, it was speculated that the mevalonate (MVA) pathway is a possible pathway for SSd synthesis in CHS3, and the expression of key enzyme genes (HMGR, HMGCS, GGPS1, MVK, FDFT1, FNTB) was validated by qRT-PCR. In conclusion, the endophytic fungus CHS3 can form an interactive relationship with its host, thereby promoting SSd biosynthesis and accumulation by upregulating the expression of key enzyme genes in the biosynthesis pathway.

Strong Protein Adhesives through Lanthanide-enhanced Structure Folding and Stack Density.

Generating strong adhesion by engineered proteins has the potential for high technical applications. Current studies of adhesive proteins are primarily limited to marine organisms, e.g., mussel adhesive proteins. Here, we present a modular engineering strategy to generate a type of exotic protein adhesives with super strong adhesion behaviors. In the protein complexes, the lanmodulin (LanM) underwent α-helical conformational transition induced by lanthanides, thereby enhancing the stacking density and molecular interactions of adhesive protein. The resulting adhesives exhibited outstanding lap-shear strength of ≈31.7 MPa, surpassing many supramolecular and polymer adhesives. The extreme temperature (-196 to 200 °C) resistance capacity and underwater adhesion performance can significantly broaden their practical application scenarios. Ex vivo and in vivo experiments further demonstrated the persistent adhesion performance for surgical sealing and healing applications.

Collective cell behaviors manipulated by synthetic DNA nanostructures.

Cellular collective motion in confluent epithelial monolayers is involved in many processes such as embryo development, carcinoma invasion, and wound healing. The development of new chemical strategies to achieve large-scale control of cells' collective motion is essential for biomedical applications. Here a series of DNA nanostructures with different dimensions were synthesized and their influences on cells' collective migration and packing behaviors in epithelial monolayers were investigated. We found that the framed DNA nanoassemblies effectively reduced the cells' speed by increasing the rigidity of cells, while the lipid-DNA micelles had a more pronounced effect on cells' projection area and shape factor. These DNA nanostructures all significantly enhanced the dependence of cells' speed on their shape factor. Our results indicate that cells' mobility in monolayers can be manipulated by chemical intercellular interactions without any genetic intervention. This may provide a new chemical strategy for tissue engineering and tumor therapy.

Highly reliable and efficient encoding systems for hexadecimal polypeptide-based data storage.

Polypeptides consisting of amino acid (AA) sequences are suitable for high-density information storage. However, the lack of suitable encoding systems, which accommodate the characteristics of polypeptide synthesis, storage and sequencing, impedes the application of polypeptides for large-scale digital data storage. To address this, two reliable and highly efficient encoding systems, i.e. RaptorQ-Arithmetic-Base64-Shuffle-RS (RABSR) and RaptorQ-Arithmetic-Huffman-Rotary-Shuffle-RS (RAHRSR) systems, are developed for polypeptide data storage. The two encoding systems realized the advantages of compressing data, correcting errors of AA chain loss, correcting errors within AA chains, eliminating homopolymers, and pseudo-randomized encrypting. The coding efficiency without arithmetic compression and error correction of audios, pictures and texts by the RABSR system was 3.20, 3.12 and 3.53 Bits/AA, respectively. While that using the RAHRSR system reached 4.89, 4.80 and 6.84 Bits/AA, respectively. When implemented with redundancy for error correction and arithmetic compression to reduce redundancy, the coding efficiency of audios, pictures and texts by the RABSR system was 4.43, 4.36 and 5.22 Bits/AA, respectively. This efficiency further increased to 7.24, 7.11 and 9.82 Bits/AA by the RAHRSR system, respectively. Therefore, the developed hexadecimal polypeptide-based systems may provide a new scenario for highly reliable and highly efficient data storage.

In vivo processing of digital information molecularly with targeted specificity and robust reliability.

DNA has attracted increasing interest as an appealing medium for information storage. However, target-specific rewriting of the digital data stored in intracellular DNA remains a grand challenge because the highly repetitive nature and uneven guanine-cytosine content render the encoded DNA sequences poorly compatible with endogenous ones. In this study, a dual-plasmid system based on gene editing tools was introduced into Escherichia coli to process information accurately. Digital data containing large repeat units in binary codes, such as text, codebook, or image, were involved in the realization of target-specific rewriting in vivo, yielding up to 94% rewriting reliability. An optical reporter was introduced as an advanced tool for presenting data processing at the molecular level. Rewritten information was stored stably and amplified over hundreds of generations. Our work demonstrates a digital-to-biological information processing approach for highly efficient data storage, amplification, and rewriting, thus robustly promoting the application of DNA-based information technology.

Preservation and Encryption in DNA Digital Data Storage.

The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.

Molecular Engineered Crown-Ether-Protein with Strong Adhesion over a Wide Temperature Range from -196 to 200 °C.

The inherently tenuous adhesion strength and limited environmental tolerance of supramolecular adhesives severely restrict their application scenarios. It is challenging for the development of robust adhesives with extreme temperature tolerance. Herein, we report a new type of temperature-resistant crown-ether-protein (CEP) adhesive by harnessing synergistic host-guest molecular interactions between engineered crown ether and protein building blocks. The outputs of CEP adhesive demonstrate ultrahigh shearing adhesion strength of ≈22 MPa over a wide temperature range from -196 to 200 °C, superior to other established supramolecular or polymeric adhesives. The temperature-induced phase transition and internal bound water stabilized the system and led to superb adhesion under extreme conditions. Thus, this work pioneers a molecular engineering approach for the generation of adhesives with tailored applications in extreme settings.

DNA-Based Concatenated Encoding System for High-Reliability and High-Density Data Storage.

Information storage based on DNA molecules provides a promising solution with advantages of low-energy consumption, high storage efficiency, and long lifespan. However, there are only four natural nucleotides and DNA storage is thus limited by 2 bits per nucleotide. Here, artificial nucleotides into DNA data storage to achieve higher coding efficiency than 2 bits per nucleotide is introduced. To accommodate the characteristics of DNA synthesis and sequencing, two high-reliability encoding systems suitable for four, six, and eight nucleotides, i.e., the RaptorQ-Arithmetic-LZW-RS (RALR) and RaptorQ-Arithmetic-Base64-RS (RABR) systems, are developed. The two concatenated encoding systems realize the advantages of correcting DNA sequence losses, correcting errors within DNA sequences, reducing homopolymers, and controlling specific nucleotide contents. The average coding efficiencies with error correction and without arithmetic compression by the RALR system using four, six, and eight nucleotides reach 1.27, 1.61, and 1.85 bits per nucleotide, respectively. While the average coding efficiencies by the RABR system are up to 1.50, 2.00, and 2.35 bits per nucleotide, respectively. The coding efficiency, versatility, and tunability of the developed artificial DNA systems might provide significant guidance for high-reliability and high-density data storage.

Highly Plasticized Lanthanide Luminescence for Information Storage and Encryption Applications.

The development of new storage media to meet the demands for diverse information storage scenarios is a great challenge. Here, a series of lanthanide-based luminescent organogels with ultrastrong mechanical performance and outstanding plasticity are developed for patterned information storage and encryption applications. The organogels possessing outstanding mechanical properties and tunable luminescent colors are prepared by electrostatic and coordinative interactions between natural DNA, synthetic ligands, and rare earth (RE) ions. The organogel-REs can be stretched by 180 times and show an ultrastrong breaking strength of 80 MPa. A series of applications with both information storage and encryption, such as self-information pattern, quick response (QR) code, and barcode, are successfully demonstrated by the organogel-REs. The developed information storage systems have various advantages of good processability, high stretchability, excellent stability, and versatile design of information patterns. Therefore, the organogel-RE-based information storage systems are suitable for applications under different scenarios, such as flexible devices under repeating rude operations. The advancements will enable the design and development of luminescent organogel-REs as information storage and encryption media for various scenarios.

Biosynthetic Structural Proteins with Super Plasticity, Extraordinary Mechanical Performance, Biodegradability, Biocompatibility and Information Storage Ability.

Degradable bioplastics have attracted growing interest worldwide. However, it is challenging to develop bioplastics with a simple processing procedure, strong mechanical performance, good biocompatibility, and adjustable physicochemical properties. Herein, we introduced structural proteins as building blocks and developed a simple environmentally friendly approach to fabricate diverse protein-based plastics. A cost-effective and high-level production approach was developed through batch fermentation of Escherichia coli to produce the biomaterials. These bioplastics possess super plasticity, biocompatibility, biodegradability, and high resistance to organic solvents. Their structural and mechanical properties can be precisely controlled. Besides, high density information storage and hemostatic applications were realized in the bioplastic system. The customizable bioplastics have great potential for applications in numerous fields and are capable to scale up to the industrial level.

The emerging chemical patterns applied in predicting human toll-like receptor 8 agonists.

Toll-like receptors (TLRs) are important pattern recognition receptors to human innate immunity, which can recognize pathogen-associated molecular patterns and initiate innate immune responses. As the receptor of single stranded RNA (ssRNA), toll-like receptor 8 (TLR8) has potential in the treatment of tumors, microbial infection, and inflammatory diseases. Herein, an emerging chemical pattern (ECP) method was utilized to predict the key chemical patterns of TLR8 agonists. Based on the ECPs discovered, a robust and predictive ECP model was derived with prediction accuracies of 83.3%, 81.0%, and 80.0% for 132 training samples, 79 validation samples, and 75 test samples, respectively. When the ECP model was applied with a molecular docking method, the hit rate of TLR8 agonists was greatly enhanced. The results of ECP-based hierarchical cluster analysis and Connolly surface analysis of the TLR8 receptor showed that the H-bonding, hydrophilic and hydrophobic potentials as well as the unbalanced degree of property distributions are very important for distinguishing the TLR8 agonists from non-agonists.

Responsiveness of voltage-gated calcium channels in SH-SY5Y human neuroblastoma cells on micropillar substrates.

In this study, poly-L-lactic acid micropillar substrates were fabricated to evaluate the influence of topographic substrates on cell morphological and functional characteristics, such as spreading area, voltage-gated calcium channels (VGCCs) and membrane potential. The proliferation, spreading area, perimeter and circularity of SH-SY5Y cells interfaced with different substrates were first investigated. In addition, the cytoskeleton and focal adhesion of a cell as important manifestations of cell morphology were analyzed by immunofluorescence. VGCC responsiveness was evaluated by measuring the dynamic changes in intracellular Ca2+ evoked by 50 mM extracellular K+. To determine study whether the differences in VGCC responsiveness were caused by the differences in VGCC gene expression, the expression of N/L- type VGCCs was determined by qPCR and fluorescence staining. Notably, improved measurement of the membrane potential with potentiometric fluorescent dye TMRM was applied to determine the membrane potential of SH-SY5Y cells. Results indicated that the SH-SY5Y cells were deformed significantly to adapt to the substrates; however, no distinct effect on the proliferative ability of SH-SY5Y cells was observed. The micropillar substrates markedly influenced VGCC responsiveness, which correlated strongly with cell spreading but not with VGCC expression. The resting membrane potential of SH-SY5Y cells cultured on different substrates also changed, but no effect on responsiveness of VGCC was observed. These results suggest that the effect of the micropillar substrates on cell VGCC responsiveness may be attributed to changes in the functionality of the ion channel itself. Thus, topographic substrates can be used to engineer cell functionality in cell-based drug screening.