Additional file 1: of The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis

Dataset of 35286 ORFs of the Puccinia helianthi transcriptome (XLSX 4749 kb

Additional file 2: of The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis

Dataset of 908 putative secretory proteins (XLSX 129 kb

Drug-Specific Design of Telodendrimer Architecture for Effective Doxorubicin Encapsulation

Designing a versatile nanocarrier platform that can be tailored to deliver specific drug payloads is challenging. In general, effective drug encapsulation, high drug-loading capacity, uniform shape and size distribution, and enhanced stability are among the fundamental attributes of a successful nanocarrier design. These physiochemical features of the nanocarriers are intimately tied to the specific drug payload that they are tasked to deliver. The molecular architecture of the nanocarrier’s scaffold often needs to be tuned for each drug, especially if the target drugs are structurally and chemically distinct as in the case of doxorubicin (DOX) and paclitaxel (PTX). Starting from our previously reported telodendrimeric block copolymer platform optimized for PTX, we analyze three generations of telodendrimer architectures to arrive at the design that is capable of encapsulating another important chemotherapeutic drug, DOX. Multiple long-time-scale self-assembly simulations were performed both in atomistic and coarse-grained resolutions to generate equilibrated DOX-encapsulated nanocarriers. The results show how subtle changes in the molecular architecture of the telodendrimer head groups have profound effects on the nanocarrier size, morphology, and asphericity. The simulation results are in agreement with the experimental data for DOX-encapsulated nanocarriers. This work emphasizes the increasing role of molecular simulations in the rational design of nanocarriers, thereby eliminating the trial and error method that has been prevalent in experimental synthesis. The molecular-level insights gained from the simulations will be used to design the next generation of drug-specific nanocarriers

Fine-Tuning Vitamin E‑Containing Telodendrimers for Efficient Delivery of Gambogic Acid in Colon Cancer Treatment

Certain natural products such as gambogic acid (GA) exhibit potent antitumor effects. Unfortunately, administration of these natural products is limited by their poor solubility in conventional pharmaceutical solvents. In this study, a series of telodendrimers, composed of linear polyethylene glycol (PEG)-blocking-dendritic oligomer of cholic acid (CA) and vitamin E (VE), have been designed with architectures optimized for efficient delivery of GA and other natural anticancer compounds. Two of the telodendrimers with segregated CA and VE domains self-assembled into stable cylindrical and/or spherical nanoparticles (NPs) after being loaded with GA as observed under transmission electron microscopy (TEM), which correlated with the dynamic light scattering (DLS) analysis of sub-30 nm particle sizes. A very high GA loading capacity (3:10 drug/polymer w/w) and sustained drug release were achieved with the optimized telodendrimers. These novel nanoformulations of GA were found to exhibit similar <i>in vitro</i> cytotoxic activity against colon cancer cells as the free drug. Near-infrared fluorescence small animal imaging revealed preferential accumulation of GA-loaded NPs into tumor tissue. The optimized nanoformulation of GA achieved superior antitumor efficacy compared to GA-Cremophor EL formulation at equivalent doses in HT-29 human colon cancer xenograft mouse models. Given the mild adverse effects associated with this natural compound and the enhanced anticancer effects via tumor targeted telodendrimer delivery, the optimized GA nanoformulation is a promising alternative to the traditional chemotherapy in colon cancer treatment

Structure-Based Nanocarrier Design for Protein Delivery

Structure-based nanocarrier design for protein delivery remains challenging and has rarely been documented in the literature. We herein present a facile computer-aided approach for rational and customized design of a unique linear–dendritic telodendrimer that self-assembles into a nanocarrier for therapeutic protein delivery, e.g., insulin. Virtual screening of a small-molecule library was performed to identify optimal protein binding moieties, which were conjugated precisely in the telodendrimer backbone preinstalled with charged moieties. We systematically tested our hypothesis and obtained significant correlations between the computational predictions and experimental results. The d-α-tocopherol (vitamin E)-containing nanocarrier showed strong binding affinity for insulin in both computational prediction and experiments, which led to improved blood glucose control. This study affirms the concept and validates the approach of structure-based nanocarrier design for protein delivery

Table_2_CRISPR/Cas9-mediated targeted mutation of the E1 decreases photoperiod sensitivity, alters stem growth habits, and decreases branch number in soybean.xlsx

The distribution of elite soybean (Glycine max) cultivars is limited due to their highly sensitive to photoperiod, which affects the flowering time and plant architecture. The recent emergence of CRISPR/Cas9 technology has uncovered new opportunities for genetic manipulation of soybean. The major maturity gene E1 of soybean plays a critical role in soybean photoperiod response. Here, we performed CRISPR/Cas9-mediated targeted mutation of E1 gene in soybean cultivar Tianlong1 carrying the dominant E1 to investigate its precise function in photoperiod regulation, especially in plant architecture regulation. Four types of mutations in the E1 coding region were generated. No off-target effects were observed, and homozygous trans-clean mutants without T-DNA were obtained. The photoperiod sensitivity of e1 mutants decreased relative to the wild type plants; however, e1 mutants still responded to photoperiod. Further analysis revealed that the homologs of E1, E1-La, and E1-Lb, were up-regulated in the e1 mutants, indicating a genetic compensation response of E1 and its homologs. The e1 mutants exhibited significant changes in the architecture, including initiation of terminal flowering, formation of determinate stems, and decreased branch numbers. To identify E1-regulated genes related to plant architecture, transcriptome deep sequencing (RNA-seq) was used to compare the gene expression profiles in the stem tip of the wild-type soybean cultivar and the e1 mutants. The expression of shoot identity gene Dt1 was significantly decreased, while Dt2 was significantly upregulated. Also, a set of MADS-box genes was up-regulated in the stem tip of e1 mutants which might contribute to the determinate stem growth habit.</p

Data_Sheet_1_Removing the sporoderm from the sporoderm-broken spores of Ganoderma lucidum improves the anticancer and immune-regulatory activity of the water-soluble polysaccharide.docx

Plant-derived polysaccharides have demonstrated promising anti-cancer effects via immune-regulatory activity. The aim of the current study was to compare the chemical property and the anticancer effects of polysaccharides extracted from the sporoderm-removed spores of the medicinal mushroom Ganoderma lucidum (RSGLP), which removed the sporoderm completely, with polysaccharides extracted from the sporoderm-broken spores of G. lucidum (BSGLP). We found that RSGLP has a higher extraction yield than BSGLP. HPGPC and GC-MS results revealed that both RSGLP and BSGLP are heteropolysaccharides, but RSGLP had a higher molecular weight and a different ratio of monosaccharide composition than BSGLP. MTT and flow cytometry results demonstrated that RSGLP exhibited much higher dose-efficacy in inhibiting cell viability and inducing apoptosis than BSGLP in 8 cancer cell lines representing colon (HCT116 and HT29), liver (HepG2 and Huh-7), breast (MDA-MB-231 and MCF-7), and lung cancers (NCI-H460 and A549). Furthermore, RSGLP is more effective in inhibiting HCT116 and NCI-H460 xenograft tumor growth and inhibiting tumor-induced splenomegaly than BSGLP in nude mice, suggesting a better effect on regulating immunity of RSGLP. Next, we found that RSGLP is more potent in inhibiting the level of serum inflammatory cytokines in nude mice, and in inhibiting the activation of macrophage RAW264.7 and the expression of the inflammatory mediators IL-1β, TNF-α, iNOS, and COX-2 in vitro. This is the first study to compare the chemical properties, anti-cancer, and immune-regulatory effects of RSGLP and BSGLP using multiple cancer cell lines. Our results revealed that the sporoderm-removed spores of G. lucidum (RSGL) and RSGLP may serve as new anticancer agents for their promising immune-regulatory activity.</p

Table_1_CRISPR/Cas9-mediated targeted mutation of the E1 decreases photoperiod sensitivity, alters stem growth habits, and decreases branch number in soybean.docx

The distribution of elite soybean (Glycine max) cultivars is limited due to their highly sensitive to photoperiod, which affects the flowering time and plant architecture. The recent emergence of CRISPR/Cas9 technology has uncovered new opportunities for genetic manipulation of soybean. The major maturity gene E1 of soybean plays a critical role in soybean photoperiod response. Here, we performed CRISPR/Cas9-mediated targeted mutation of E1 gene in soybean cultivar Tianlong1 carrying the dominant E1 to investigate its precise function in photoperiod regulation, especially in plant architecture regulation. Four types of mutations in the E1 coding region were generated. No off-target effects were observed, and homozygous trans-clean mutants without T-DNA were obtained. The photoperiod sensitivity of e1 mutants decreased relative to the wild type plants; however, e1 mutants still responded to photoperiod. Further analysis revealed that the homologs of E1, E1-La, and E1-Lb, were up-regulated in the e1 mutants, indicating a genetic compensation response of E1 and its homologs. The e1 mutants exhibited significant changes in the architecture, including initiation of terminal flowering, formation of determinate stems, and decreased branch numbers. To identify E1-regulated genes related to plant architecture, transcriptome deep sequencing (RNA-seq) was used to compare the gene expression profiles in the stem tip of the wild-type soybean cultivar and the e1 mutants. The expression of shoot identity gene Dt1 was significantly decreased, while Dt2 was significantly upregulated. Also, a set of MADS-box genes was up-regulated in the stem tip of e1 mutants which might contribute to the determinate stem growth habit.</p