Modular chimeric cytokine receptors with leucine zippers enhance the antitumour activity of CAR T cells via JAK/STAT signalling.

The limited availability of cytokines in solid tumours hinders maintenance of the antitumour activity of chimeric antigen receptor (CAR) T cells. Cytokine receptor signalling pathways in CAR T cells can be activated by transgenic expression or injection of cytokines in the tumour, or by engineering the activation of cognate cytokine receptors. However, these strategies are constrained by toxicity arising from the activation of bystander cells, by the suboptimal biodistribution of the cytokines and by downregulation of the cognate receptor. Here we show that replacement of the extracellular domains of heterodimeric cytokine receptors in T cells with two leucine zipper motifs provides optimal Janus kinase/signal transducer and activator of transcription signalling. Such chimeric cytokine receptors, which can be generated for common γ-chain receptors, interleukin-10 and -12 receptors, enabled T cells to survive cytokine starvation without induction of autonomous cell growth, and augmented the effector function of CAR T cells in vitro in the setting of chronic antigen exposure and in human tumour xenografts in mice. As a modular design, leucine zippers can be used to generate constitutively active cytokine receptors in effector immune cells.

A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species.

Leveraging existing resources in studied species to predict gene functions has the potential to rapidly expand understanding of annotated genes in other, less well-studied, species with assembled genomes. However, orthology is not a reliable predictor for the transcriptional responses of genes to stress. Machine learning methods can quantitatively estimate expression patterns and gene functions using known annotations and collections of features describing each gene. In this chapter, we describe a supervised machine learning framework to predict stress-responsive genes across species using only features derived from nucleotide sequences, using the example of cold stress-responsive genes in different Panicoid grass species.

Effect of Nano Nd2O3 on the Microstructure and High-Temperature Resistance of G@Ni Laser Alloying Coatings on Ti-6Al-4V Alloy.

Titanium and its alloys are widely used in high-end manufacturing fields. However, their low high-temperature oxidation resistance has limited their further application. Recently, laser alloying processing has attracted researchers to improve the surface properties of Ti, for which Ni coated graphite system is an excellent prospect due to its outstanding properties and metallurgical bonding between coating and substrate. In this paper, nanoscaled rare earth oxide Nd2O3 addition was added to Ni coated graphite laser alloying materials to research its influence on the microstructure and high-temperature oxidation resistance of the coating. The results proved that nano-Nd2O3 has an outstanding effect on refining coating microstructures, thus the high-temperature oxidation resistance was improved. Furthermore, with the addition of 1. 5 wt.% nano-Nd2O3, more NiO formed in the oxide film, which effectively strengthened the protective effect of the film. After 100 h of 800 °C oxidation, the oxidation weight gain per unit area of the normal coating was 14.571 mg/cm2, while that of the coating with nano-Nd2O3 addition was 6.244 mg/cm2, further proving that the addition of nano-Nd2O3 substantially improved the high-temperature oxidation properties of the coating.

Chinese expert consensus on transradial access in percutaneous peripheral interventions.

Transradial access (TRA) is a safe and comfortable approach and the preferred access for percutaneous coronary intervention. However, TRA is not widely used for peripheral interventions. Currently, there is a lack of data on patient selection, appropriate medical devices, complication prevention, and TRA adoption. Therefore, the Chinese Society of Interventional Oncology of the China Anti-Cancer Association organized nationwide experts to establish a Working Group of China Expert Consensus on TRA in percutaneous peripheral interventions in 2022, and jointly formulated this consensus to better promote the application of TRA in peripheral interventions to guide clinicians on patient selection, technical recommendations, and physician training. This consensus mainly focuses on the current situation, advantages and limitations of TRA in peripheral interventions, anatomical characteristics of the radial artery, patient selection, technical aspects, prevention and management of complications, radiation dose, and learning curve. A consensus was reached through a literature evaluation and by referring to the opinions of the expert group.

ICP-MS based metallomics and GC-MS based metabolomics reveals the physiological and metabolic responses of Dendrobium huoshanense plants exposed to Fe3O4 nanoparticles.

It is found that the growth of Dendrobium huoshanense was dependent on Fe3O4, while the bioavailability of plants to ordinary Fe3O4 was low on the earth. In order to improve the growth, quality and yield of D. huoshanense, we used Fe3O4 NPs (100 or 200 mg/L) that was easily absorbed by plants as nano-fertilizer to hydroponically treat seedlings of D. huoshanense for 3 weeks. Fe3O4 NPs induced not only earlier flowering and increased sugar content and photosynthesis, but also stressed to plants, increased MDA content and related antioxidant enzymes activities. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) revealed that Fe3O4 NPs caused a significant accumulation of Fe and some other nutrient elements (Mn, Co, B, Mo) in stems of D. huoshanense. Metabolomics revealed that the metabolites were reprogrammed in D. huoshanense when under Fe3O4 NPs exposure. Fe3O4 NPs inhibited antioxidant defense-related pathways, demonstrating that Fe3O4 NPs have antioxidant capacity to protect D. huoshanense from damage. As the first study associating Fe3O4 NPs with the quality of D. huoshanense, it provided vital insights into the molecular mechanisms of how D. huoshanense responds to Fe3O4 NPs, ensuring the reasonable use of Fe3O4 NPs as nano-fertilizer.

Influence of Scanning Speed on the Microstructure and Wear Resistance of Laser Alloying Coatings on Ti-6Al-4V Substrate.

Laser alloying has attracted significant attentions due to the advantages of high processing precision, good controllability and low heat effects on the substrate. However, the complexity of laser alloying requires further attentions on its processing parameters. This study aims at improving the wear resistance of the Ti-6Al-4V substrate by means of laser surface alloying with Ni-coated graphite (G@Ni). The effect of laser scanning speed is explored. The result suggests that the coating has a high surface quality and excellent metallurgical bonding with the substrate. NiTi and NiTi2 have a eutectic microstructure as well as in the TiC ceramic-reinforced phase as dendrites distribute in the γ-Ni matrix of the coatings. At higher scanning speeds, the lower energy density and shorter existence time of the molten pool refines the microstructure of the coating, improving its microhardness. At the scanning speed of 15 mm/s, the coating has the lowest wear weight loss due to its high microhardness and dense structure. This paper explores the influence of scanning speed on the microstructure and properties of the coatings, expanding the application of laser alloying on the surface modification of Ti-6Al-4V alloys.

Operator radiation dose during trans-hepatic arterial chemoembolization: different patients' positions via transradial or transfemoral access.

PURPOSE This study aimed to compare the radiation dose received by the operator among different patients' positions via transradial access (TRA) or transfemoral access (TFA) during transarterial chemoembolization (TACE) for hepatocellular carcinoma (HCC). METHODS A total of 120 patients with HCC undergoing TACE for the first time between January and November 2019 were randomized into 4 groups with 30 patients in each group. In group A, patients were placed in the foot-first position with the left upper arm abducted, and TACE was performed via the left radial artery. In group B, patients were placed in the conventional headfirst position with the left hand placed at the left groin, and TACE was performed via the left radial artery. In group C, patients were placed in the conventional head-first position, and TACE was performed via the right radial artery. In group D, patients were placed in the conventional head-first position, and TACE was performed via the right femoral artery. Before each procedure, thermoluminescent dosimeters were taped at 7 different body parts of the operator and the radiation dose was measured and collected after the procedure. The normalized radiation dose was also calculated. Procedural parameters included radiation dose, fluoroscopy time (FT), dose-area product (DAP), and air kerma (AK) were recorded. Patients' demographics, tumor baseline characteristics, radiation dose, and procedural parameters were compared between groups. RESULTS No significant differences were found in patients' demographics, tumor baseline characteristics, as well as in total FT, DAP, and AK. However, significant differences were found in the total radiation dose received by the operator and the doses on the pelvic cavity and the right wrist (P < .05). In group C, the radiation doses received on the pelvic cavity, the right wrist, and the total radiation doses were relatively higher. Significant differences were also found in the normalized radiation doses received by the operator on the thyroid, chest, left wrist, right wrist, and pelvic cavity, and the total normalized doses (all P < .05). Similarly, the radiation doses received by the operator at the aforementioned parts in group C were higher, while those in group A were lower. CONCLUSION No statistically significant differences were observed in the FT, DAP, and AK in TACE via TRA when patients were placed in different positions. However, TACE via the left TRA, with patients in the feet-first position, reduced the radiation dose received by the operator, thereby reducing the radiation risk.

Comparative Proteome and Phosphoproteome Analyses Reveal Different Molecular Mechanism Between Stone Planting Under the Forest and Greenhouse Planting of Dendrobium huoshanense.

The highly esteemed Chinese herb, Dendrobium huoshanense, whose major metabolites are polysaccharides and alkaloids, is on the verge of extinction. The stone planting under the forest (SPUF) and greenhouse planting (GP) of D. huoshanense are two different cultivation methods of pharmaceutical Dendrobium with significantly differences in morphology, metabolites content and composition, and medication efficacy. Here, we conducted proteomics and phosphoproteomics analyses to reveal differences in molecular mechanisms between SPUF and GP. We identified 237 differentially expressed proteins (DEPs) between the two proteomes, and 291 modification sites belonging to 215 phosphoproteins with a phosphorylation level significantly changed (PLSC) were observed. GO, KEGG pathway, protein domain, and cluster analyses revealed that these DEPs were mainly localized in the chloroplast; involved in processes such as posttranslational modification, carbohydrate transport and metabolism, and secondary metabolite biosynthesis; and enriched in pathways mainly including linoleic acid metabolism, plant-pathogen interactions, and phenylpropanoid, cutin, suberin, and wax biosynthesis. PLSC phosphoproteins were mainly located in the chloroplast, and highly enriched in responses to different stresses and signal transduction mechanisms through protein kinase and phosphotransferase activities. Significant differences between SPUF and GP were observed by mapping the DEPs and phosphorylated proteins to photosynthesis and polysaccharide and alkaloid biosynthesis pathways. Phosphorylation characteristics and kinase categories in D. huoshanense were also clarified in this study. We analyzed different molecular mechanisms between SPUF and GP at proteomic and phosphoproteomic levels, providing valuable information for the development and utilization of D. huoshanense.

Comparative proteomics reveals biochemical changes in Salvia miltiorrhiza Bunge during sweating processing.

ETHNOPHARMACOLOGICAL RELEVANCE: Salvia miltiorrhiza Bunge is a bulk medicinal material used in traditional Chinese medicine, that can cure cardiovascular diseases, neurasthenia, and other conditions. Sweating is a frequently used method of processing S. miltiorrhiza for medical applications. We previously demonstrated changes to the metabolic profile of linoleic acid, glyoxylate, and dicarboxylate after Sweating. However, this alteration has not been explained at the molecular level. MATERIALS AND METHODS: Fresh roots of Salvia miltiorrhiza Bunge were treated by the Sweating processing, and then the tandem mass tag technique was used to compare the proteome difference between Sweating S. miltiorrhiza and non-Sweating S. miltiorrhiza. RESULTS: We identified a total of 850 differentially expressed proteins after Sweating treatment in S. miltiorrhiza, including 529 upregulated proteins and 321 downregulated proteins. GO enrichment analysis indicated that these differentially expressed proteins are involved in external encapsulating structure, cell wall, oxidoreductase activity, ligase activity, and others. Further analysis showed that CYP450, the pathogenesis-related protein Bet v 1 family, and the peroxidase domain were the major protein domains. KEGG enrichment identified 18 pathways, of which phenylpropanoid biosynthesis is the most important one related to the metabolite profile and is the principal chemical component of S. miltiorrhiza. CONCLUSION: This study addressed potential molecular mechanisms in S. miltiorrhiza after Sweating, and the findings provide reasons for the changes in biochemical properties and metabolites changes which might cause pharmacological variation at the proteome level.

Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense.

The lysine crotonylation of histone proteins is a newly identified posttranslational modification with diversified cellular functions. However, there are few reports on lysine crotonylation of non-histone proteins in medicinal plant cells. By using high-resolution liquid chromatography-mass spectrometry (LC-MS) coupled with highly sensitive-specific immune-affinity antibody analysis, a whole crotonylation proteome analysis of Dendrobium huoshanense was performed. In total, 1,591 proteins with 4,726 lysine crotonylation sites were identified; among them, 11 conserved motifs were identified. Bioinformatic analyses linked crotonylated proteins to the drought stress response and multiple metabolic pathways, including secondary metabolite biosynthesis, transport and catabolism, energy production and conversion, carbohydrate transport and metabolism, translation, and ribosomal structure and biogenesis. This study contributes toward understanding the regulatory mechanism of polysaccharide biosynthesis at the crotonylation level even under abiotic stress.

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity.

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.).

MAIN CONCLUSION: The Albizia julibrissin chloroplasts have a classical chloroplast genome structure, containing 93 coding genes and 34 non-coding genes. Our research provides basic data for plant phylogenetic evolutionary studies. There is limited genomic information available for the important Chinese herb Albizia julibrissin Durazz. In this study, we constructed the chloroplast (Cp) genome of A. julibrissin. The length of the assembled Cp genome was 175,922 bp consisting of four conserved regions: a 5145 bp small single-copy (SSC) region, a 91,323 bp large single-copy (LSC) region, and two identical length-inverted repeat (IR) regions (39,725 bp). This Cp genome included 34 non-coding RNAs and 93 unique genes, the former contains 30 transfer and 4 ribosomal RNA genes. Gene annotation indicated some of the coding genes (82) in the A. julibrissin Cp genome classified in the Leguminosae family, with some to other related families (11). The results show that low GC content (36.9%) and codon bias towards A- or T-terminal codons may affect the frequency of gene codon usage. The sequence analysis identified 30 forward, 18 palindrome, and 1 reverse repeat > 30 bp length, and 149 simple sequence repeats (SSR). Fifty-five RNA editing sites in the Cp of A. julibrissin were predicted, most of which are C-to-U conversions. Analysis of the reverse repeat expansion or contraction and divergence area between several species, including A. julibrissin, was performed. The phylogenetic tree revealed that A. julibrissin was most closely related to Albizia odoratissima and Albizia bracteata, followed by Samanea saman, forming an evolutionary branch with Mimosa pudica and Leucaena trichandra. The research results are helpful for breeding and genetic improvement of A. julibrissin, and also provide valuable information for understanding the evolution of this plant.

The complete chloroplast genome sequence of Buxus megistophylla Levl. (Buxaceae Dumort.).

Buxus megistophylla Levl. is one of the most common green horticultural plants in the city presently. Here, we assembled and annotated the complete chloroplast (cp) genome of B. megistophylla. The whole length of the genome is 157,611 bp and encodes a total of 124 genes, which contains 89 protein-coding genes, 31 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic tree analysis showed that B. megistophylla is separated from two other species of the same family, but these three species, clustered in one clade, are relatively closer to each other compared to the species in other families. This cp genome sequencing and phylogenetic analysis offer genetic background for conservation and may contribute to further evolutionary studies of this species.

Comprehensive Analysis of Lysine Lactylation in Rice (Oryza sativa) Grains.

Protein lysine lactylation is a new post-translational modification (PTM) prevalently found in fungi and mammalian cells that directly stimulates gene transcription and regulates the glycolytic flux. However, lysine lactylation sites and regulations remain largely unexplored, especially in cereal crops. Herein, we report the first global lactylome profile in rice, which effectively identified 638 lysine lactylation sites across 342 proteins in rice grains. Functional annotations demonstrated that lysine lactylation was enriched in proteins associated with central carbon metabolism and protein biosynthesis. We also observed that proteins serving as nutrition reservoirs in rice grains were frequently targeted by lactylation. Homology analyses indicated that lactylation was conserved on both histone and nonhistone proteins across plants, human cells, and fungi. In addition to lactylation, additional types of acylations could co-occur in many proteins at identical lysine residues, indicating potential cross-talks between these modifications. Our study provided a comprehensive profile of protein lysine lactylation in cereal crop grains.

Comparative Transcriptome Analysis Reveals Genetic Mechanisms of Sugarcane Aphid Resistance in Grain Sorghum.

The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae) (SCA), has become a major pest of grain sorghum since its appearance in the USA. Several grain sorghum parental lines are moderately resistant to the SCA. However, the molecular and genetic mechanisms underlying this resistance are poorly understood, which has constrained breeding for improved resistance. RNA-Seq was used to conduct transcriptomics analysis on a moderately resistant genotype (TAM428) and a susceptible genotype (Tx2737) to elucidate the molecular mechanisms underlying resistance. Differential expression analysis revealed differences in transcriptomic profile between the two genotypes at multiple time points after infestation by SCA. Six gene clusters had differential expression during SCA infestation. Gene ontology enrichment and cluster analysis of genes differentially expressed after SCA infestation revealed consistent upregulation of genes controlling protein and lipid binding, cellular catabolic processes, transcription initiation, and autophagy in the resistant genotype. Genes regulating responses to external stimuli and stress, cell communication, and transferase activities, were all upregulated in later stages of infestation. On the other hand, expression of genes controlling cell cycle and nuclear division were reduced after SCA infestation in the resistant genotype. These results indicate that different classes of genes, including stress response genes and transcription factors, are responsible for countering the physiological effects of SCA infestation in resistant sorghum plants.

Putative genes in alkaloid biosynthesis identified in Dendrobium officinale by correlating the contents of major bioactive metabolites with genes expression between Protocorm-like bodies and leaves.

BACKGROUND: Dendrobium officinale, an endangered Chinese herb, possesses extensive therapeutic effects and contains bioactive ingredients such as major polysaccharides, alkaloids, and minimal flavonoids. We first obtained the protocorm-like bodies (PLBs) of this plant through tissue culture in order to determine the distribution of the main secondary metabolites in each organelle and the PLBs. We then analyzed the correlation between gene expression level from comparative transcriptome sequencing and metabolite content in different organs to identify putative genes encoding enzymes involved in the biosynthesis of polysaccharides, alkaloids, and flavonoids. RESULTS: We used seeds as explants for protocorm induction and PLB propagation of D. officinale. The optimal medium formula for PLB propagation was 1/2 MS + α-NAA 0.5 mg·L- 1 + 6-BA 1.0 mg·L- 1 + 2, 4-D 1.5-2.0 mg·L- 1 + potato juice 100 g·L- 1. Stems, PLBs and leaves of D. officinale had the highest content of polysaccharides, alkaloids and flavonoids, respectively. Naringenin was only produced in stem; however, PLBs with high alkaloid content can replace other organs producing alkaloids. The hot water extraction method outperformed the ultrasound-assisted extraction method for extracting polysaccharides from D. officinale. A comparative transcriptome analysis of PLBs and leaves of D. officinale revealed differential expression of genes encoding enzymes involved in polysaccharide, alkaloid and flavonoid biosynthetic pathways. Putative genes encoding enzymes involved in these biosynthetic pathways were identified. Notably, we identified genes encoding the alkaloid biosynthesis enzymes strictosidine ß-D-Glucosidase, geissoschizine synthase and vinorine synthase in D. officinale. CONCLUSIONS: The identification of candidate genes encoding enzymes involved in metabolite biosynthesis will help to explore and protect this endangered species and facilitate further analysis of the molecular mechanism of secondary metabolite biosynthesis in D. officinale.

Predicting transcriptional responses to cold stress across plant species.

Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification model to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained by using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species provided at least equivalent performance to models trained and tested in a single species and outperformed single-species models in cross-species prediction. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene-expression patterns in related, less-studied species with sequenced genomes.

Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS.

BACKGROUND: The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice. RESULTS: In this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice. CONCLUSIONS: Nearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.