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Expansion microscopy (ExM) allows super-resolution imaging on conventional fluorescence microscopes, but has been limited to proteins and nucleic acids. Here we develop click-ExM, which integrates click labeling into ExM to enable a ‘one-stop-shop’ method for nanoscale imaging of various types of biomolecule. By click labeling with biotin and staining with fluorescently labeled streptavidin, a large range of biomolecules can be imaged by the standard ExM procedure normally used for proteins. Using 18 clickable labels, we demonstrate click-ExM on lipids, glycans, proteins, DNA, RNA and small molecules. We demonstrate that click-ExM is applicable in cell culture systems and for tissue imaging. We further show that click-ExM is compatible with signal-amplification techniques and two-color imaging. Click-ExM thus provides a convenient and versatile method for super-resolution imaging, which may be routinely used for cell and tissue samples.Click-ExM uses click-chemistry-based labeling to increase the versatility of expansion microscopy. Click-ExM enables imaging of numerous classes of biomolecules including lipids, glycans, proteins, DNA, RNA and small molecules.

Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per- O -acetylated, which, however, can induce a long-overlooked side reaction, non-enzymatic S-glycosylation. Herein, we develop 1,3-di-esterified N -azidoacetylgalactosamine (GalNAz) as next-generation chemical reporters for metabolic glycan labeling. Both 1,3-di- O -acetylated GalNAz (1,3-Ac 2 GalNAz) and 1,3-di- O -propionylated GalNAz (1,3-Pr 2 GalNAz) exhibit high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying 1,3-Pr 2 GalNAz in mouse embryonic stem cells (mESCs), we identify ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We show that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase at serine 25, which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG. Per- O -acetylated unnatural monosaccharides are popular tools for glycan labeling in live cells but can undergo unwanted side reactions with cysteines. Here, the authors develop unnatural sugars in a partially esterified form that are inert towards cysteines, and use them to probe O-GlcNAcylation in mESCs.

Lung cancers with a mutated epidermal growth factor receptor (EGFR) are a major contributor to cancer fatalities globally. Targeted tyrosine kinase inhibitors (TKIs) have been developed against EGFR and show encouraging results for survival rate and quality of life. However, drug resistance may affect treatment plans and treatment efficacy may be lost after about a year. Predicting the response to EGFR-TKIs for EGFR-mutated lung cancer patients is a key research area. In this study, we propose a personalized drug response prediction model (PDRP), based on molecular dynamics simulations and machine learning, to predict the response of first generation FDA-approved small molecule EGFR-TKIs, Gefitinib/Erlotinib, in lung cancer patients. The patient’s mutation status is taken into consideration in molecular dynamics (MD) simulation. Each patient’s unique mutation status was modeled considering MD simulation to extract molecular-level geometric features. Moreover, additional clinical features were incorporated into machine learning model for drug response prediction. The complete feature set includes demographic and clinical information (DCI), geometrical properties of the drug-target binding site, and the binding free energy of the drug-target complex from the MD simulation. PDRP incorporates an XGBoost classifier, which achieves state-of-the-art performance with 97.5% accuracy, 93% recall, 96.5% precision, and 94% F1-score, for a 4-class drug response prediction task. We found that modeling the geometry of the binding pocket combined with binding free energy is a good predictor for drug response. However, we observed that clinical information had a little impact on the performance of the model. The proposed model could be tested on other types of cancers. We believe PDRP will support the planning of effective treatment regimes based on clinical-genomic information. The source code and related files are available on GitHub at:   https://github.com/rizwanqureshi123/PDRP/ .

The anatomy of the superior mesenteric vessels is complex, yet important, for right-sided colorectal surgery. The usefulness of three-dimensional (3D) printing of these vessels in right hemicolon cancer surgery has rarely been reported. In this prospective clinical study, 61 patients who received laparoscopic surgery for right hemicolon cancer were preoperatively randomized into 3 groups: 3D-printing (20 patients), 3D-image (19 patients), and control (22 patients) groups. Surgery duration, bleeding volume, and number of lymph node dissections were designed to be the primary end points, whereas postoperative complications, post-operative flatus recovery time, duration of hospitalization, patient satisfaction, and medical expenses were designed to be secondary end points. To reduce the influence of including different surgeons in the study, the surgical team was divided into 2 groups based on surgical experience. The duration of surgery for the 3D-printing and 3D-image groups was significantly reduced (138.4 ± 19.5 and 154.7 ± 25.9 min vs. 177.6 ± 24.4 min, P  = 0.000 and P  = 0.006), while the number of lymph node dissections for the these 2 groups was significantly increased (19.1 ± 3.8 and 17.6 ± 3.9 vs. 15.8 ± 3.0, P  = 0.001 and P  = 0.024) compared to the control group. Meanwhile, the bleeding volume for the 3D-printing group was significantly reduced compared to the control group (75.8 ± 30.4 mL vs. 120.9 ± 39.1 mL, P  = 0.000). Moreover, patients in the 3D-printing group reported increased satisfaction in terms of effective communication compared to those in the 3D-image and control groups. Medical expenses decreased by 6.74% after the use of 3D-printing technology. Our results show that 3D-printing technology could reduce the duration of surgery and total bleeding volume and increase the number of lymph node dissections. 3D-printing technology may be more helpful for novice surgeons. Trial registration : Chinese Clinical Trial Registry, ChiCTR1800017161. Registered on 15 July 2018.

MicroRNAs (miRNAs) widely participate in plant growth and development. The miR396 family, one of the most conserved miRNA families, remains poorly understood in sorghum. To reveal the evolution and expression pattern of Sbi-miR396 gene family in sorghum, bioinformatics analysis and target gene prediction were performed on the sequences of the Sbi-miR396 gene family members. The results showed that five Sbi-miR396 members, located on chromosomes 4, 6, and 10, were identified at the whole-genome level. The secondary structure analysis showed that the precursor sequences of all five Sbi-miR396 potentially form a stable secondary stem–loop structure, and the mature miRNA sequences were generated on the 5′ arm of the precursors. Sequence analysis identified the mature sequences of the five sbi-miR396 genes were high identity, with differences only at the 1st, 9th and 21st bases at the 5’ end. Phylogenetic analysis revealed that Sbi-miR396a , Sbi-miR396b , and Sbi-miR396c were clustered into Group I, and Sbi-miR396d and Sbi-miR396e were clustered into Group II, and all five sbi-miR396 genes were closely related to those of maize and foxtail millet. Expression analysis of different tissue found that Sbi-miR396d / e and Sbi-miR396a / b / c were preferentially and barely expressed, respectively, in leaves, flowers, and panicles. Target gene prediction indicates that the growth-regulating factor family members ( SbiGRF1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 10 ) were target genes of Sbi-miR396d / e . Thus, Sbi-miR396d / e may affect the growth and development of sorghum by targeting SbiGRF s. In addition, expression analysis of different tissues and developmental stages found that all Sbi-miR396 target genes, SbiGRF s, were barely expressed in leaves, root and shoot, but were predominantly expressed in inflorescence and seed development stage, especially SbiGRF1 / 5 / 8 . Therefore, inhibition the expression of sbi-miR396d /e may increase the expression of SbiGRF1 / 5 / 8 , thereby affecting floral organ and seed development in sorghum. These findings provide the basis for studying the expression of the Sbi-mir396 family members and the function of their target genes.

WRKY transcription factors are plant-specific, zinc finger-type transcription factors. The WRKY superfamily is involved in abiotic stress responses in many crops including cotton, a major fiber crop that is widely cultivated and consumed throughout the world. Salinity is an important abiotic stress that results in considerable yield losses. In this study, we identified 109 WRKY genes (GarWRKYs) in a salt-tolerant wild cotton species Gossypium aridum from transcriptome sequencing data to elucidate the roles of these factors in cotton salt tolerance. According to their structural features, the predicted members were divided into three groups (Groups I-III), as previously described for Arabidopsis. Furthermore, 28 salt-responsive GarWRKY genes were identified from digital gene expression data and subjected to real-time quantitative RT-PCR analysis. The expression patterns of most GarWRKY genes revealed by this analysis are in good agreement with those revealed by RNA-Seq analysis. RT-PCR analysis revealed that 27 GarWRKY genes were expressed in roots and one was exclusively expressed in roots. Analysis of gene orthology and motif compositions indicated that WRKY members from Arabidopsis, rice and soybean generally shared the similar motifs within the same subgroup, suggesting they have the similar function. Overexpression-GarWRKY17 and -GarWRKY104 in Arabidopsis revealed that they could positively regulate salt tolerance of transgenic Arabidopsis during different development stages. The comprehensive data generated in this study provide a platform for elucidating the functions of WRKY transcription factors in salt tolerance of G. aridum. In addition, GarWRKYs related to salt tolerance identified in this study will be potential candidates for genetic improvement of cultivated cotton salt stress tolerance.

In sorghum [ Sorghum bicolor (L.) Moench], combining ability and heterosis analysis are commonly used to evaluate superior parental lines and to screen for strongly heterotic hybrids, which helps in sorghum variety selection and breeding. In this context, combining ability and heterosis analysis were assessed using 14 restorer lines and seven cytoplasmic male sterile (CMS) lines in 2019 and 2020. The analysis of variance of all cross combinations had highly significant differences for all characters studied, which indicated a wide variation across the parents, lines, testers, and crosses. Combining ability analysis showed that the general combining ability (GCA) and specific combining ability (SCA) of the different parents were differed significantly among different traits. Most combinations with high SCA also showed high GCA in their parent lines. The heritability in the narrow sense of grain weight per panicle and grain yield was relatively low, indicating that the ability of these traits to be directly inherited by offspring was weak, that they were greatly affected by the environment. The better-parent heterosis for plant height, grain weight per panicle, panicle length, and 1000-grain weight was consistent with the order of mid-parent heterosis from strong to weak. The GCA effects of two lines 10480A, 3765A and three testers 0-30R, R111, and JY15R were significant for the majority of the agronomic traits including grain yield and might be used for improving the yield of grains in sorghum as parents of excellent specific combining ability. Seven strongly heterotic F 1 hybrids were screened; of these, hybrids 3765A × R111, 1102A × L2R, and 3765A × JY15R showed significant increases in seed iristectorigenin A content and will feature into the creation of new sorghum varieties rich in iristectorigenin A.

Under salt stress, the plants need to maintain a low Na + concentration and Na + /K + ratio in the cell cytoplasm to keep normal growth and development. High-affinity K + transporter (HKT) genes are known to play an important role in regulating the transportation of Na + and K + in higher plants. However, reports on its potential role in conferring stress tolerance in cotton are rare. In a previous study, we isolated a potassium transporter SbHKT1 from halophyte Salicornia bigelovii . With the intention to assess whether the SbHKT1 gene would improve salt tolerance in cotton, cotton plants overexpressing SbHKT1 were generated by Agrobacterium -mediated transgenic technology. Overexpression of SbHKT1 in cotton increased germination rate and biomass as well as root systems compared with wild-type plants. Transgenic cotton had significantly higher K + content, lower Na + content, and lower Na + /K + ratio than wild-type plants in leaves, stems and roots under salt stress. Moreover, there were significant higher activity of antioxidant enzymes including SOD, POD, and CAT and lower malondialdehyde content which means better cell membrane integrity in transgenic cotton compared to control plants. These results indicated that overexpressing SbHKT1 in cotton improved salt tolerance by increasing the capacity of K + uptake, K + /Na + homeostasis, and the scavenging of reactive oxygen species.

Sorghum bicolor (L.) is one of the oldest crops cultivated by human beings which has been used in food and wine making. To understand the genetic diversity of sorghum breeding resources and further guide molecular-marker-assisted breeding, six yield-related traits were analyzed for 214 sorghum germplasm from all over the world, and 2,811,016 single-nucleotide polymorphisms (SNPs) markers were produced by resequencing these germplasms. After controlling Q and K, QTLs were found to be related to the traits using three algorisms. Interestingly, an important QTL was found which may affect multiple traits in this study. It was the most likely candidate gene for the gene SORBI_3008G116500, which was a homolog of Arabidopsis thaliana gene-VIP5 found by analyzing the annotation of the gene in the LD block. The haplotype analysis showed that the SORBI_3008G116500hap3 was the elite haplotype, and it only existed in Chinese germplasms. The traits were proven to be more associated with the SNPs of the SORBI_3008G116500 promoter through gene association studies. Overall, the QTLs and the genes identified in this study would benefit molecular-assisted yield breeding in sorghum.

Metabolic labeling of glycans with clickable unnatural sugars has enabled glycan analysis in multicellular systems. However, cell-type-specific labeling of glycans in vivo remains challenging. Here we develop genetically encoded metabolic glycan labeling (GeMGL), a cell-type-specific strategy based on a bump-and-hole pair of an unnatural sugar and its matching engineered enzyme. N-pentynylacetylglucosamine (GlcNAl) serves as a bumped analog of N-acetylglucosamine (GlcNAc) that is specifically incorporated into glycans of cells expressing a UDP-GlcNAc pyrophosphorylase mutant, AGX2F383G. GeMGL with the 1,3-di-O-propionylated GlcNAl (1,3-Pr2GlcNAl) and AGX2F383G pair was demonstrated in cell cocultures, and used for specific labeling of glycans in mouse xenograft tumors. By generating a transgenic mouse line with AGX2F383G expressed under a cardiomyocyte-specific promoter, we performed specific imaging of cardiomyocyte glycans in the heart and identified 582 cardiomyocyte O-GlcNAcylated proteins with no interference from other cardiac cell types. GeMGL will facilitate cell-type-specific glycan imaging and glycoproteomics in various tissues and disease models.A genetically encoded metabolic glycan labeling (GeMGL) method based on an orthogonal engineered enzyme–unnatural sugar pair was developed for cell-type-specific glycan labeling in cells and living mice.