Corrigendum: Association of CT-based delta radiomics biomarker with progression-free survival in patients with colorectal liver metastases undergo chemotherapy.

[This corrects the article DOI: 10.3389/fonc.2022.843991.].

Suppressing ASPARTIC PROTEASE 1 prolongs photosynthesis and increases wheat grain weight.

The elongation of photosynthesis, or functional staygreen, represents a feasible strategy to propel metabolite flux towards cereal kernels. However, achieving this goal remains a challenge in food crops. Here we report the cloning of wheat CO2 assimilation and kernel enhanced 2 (cake2), the mechanism underlying the photosynthesis advantages and natural alleles amenable to breeding elite varieties. A premature stop mutation in the A-genome copy of the ASPARTIC PROTEASE 1 (APP-A1) gene increased the photosynthesis rate and yield. APP1 bound and degraded PsbO, the protective extrinsic member of photosystem II critical for increasing photosynthesis and yield. Furthermore, a natural polymorphism of the APP-A1 gene in common wheat reduced APP-A1's activity and promoted photosynthesis and grain size and weight. This work demonstrates that the modification of APP1 increases photosynthesis, grain size and yield potentials. The genetic resources could propel photosynthesis and high-yield potentials in elite varieties of tetraploid and hexaploid wheat.

Suppression of ZEAXANTHIN EPOXIDASE 1 restricts stripe rust growth in wheat.

Reducing losses caused by pathogens is an effective strategy for stabilizing crop yields. Daunting challenges remain in cloning and characterizing genes that inhibit stripe rust, a devastating disease of wheat (Triticum aestivum) caused by Puccinia striiformis f. sp. tritici (Pst). We found that suppression of wheat zeaxanthin epoxidase 1 (ZEP1) increased wheat defense against Pst. We isolated the yellow rust slower 1 (yrs1) mutant of tetraploid wheat in which a premature stop mutation in ZEP1-B underpins the phenotype. Genetic analyses revealed increased H2O2 accumulation in zep1 mutants and demonstrated a correlation between ZEP1 dysfunction and slower Pst growth in wheat. Moreover, wheat kinase START 1.1 (WKS1.1, Yr36) bound, phosphorylated, and suppressed the biochemical activity of ZEP1. A rare natural allele in the hexaploid wheat ZEP1-B promoter reduced its transcription and Pst growth. Our study thus identified a novel suppressor of Pst, characterized its mechanism of action, and revealed beneficial variants for wheat disease control. This work opens the door to stacking wheat ZEP1 variants with other known Pst resistance genes in future breeding programs to enhance wheat tolerance to pathogens.

HSP90.2 promotes CO2 assimilation rate, grain weight and yield in wheat.

Wheat fixes CO2 by photosynthesis into kernels to nourish humankind. Improving the photosynthesis rate is a major driving force in assimilating atmospheric CO2 and guaranteeing food supply for human beings. Strategies for achieving the above goal need to be improved. Here, we report the cloning and mechanism of CO2 ASSIMILATION RATE AND KERNEL-ENHANCED 1 (CAKE1) from durum wheat (Triticum turgidum L. var. durum). The cake1 mutant displayed a lower photosynthesis rate with smaller grains. Genetic studies identified CAKE1 as HSP90.2-B, encoding cytosolic molecular chaperone folding nascent preproteins. The disturbance of HSP90.2 decreased leaf photosynthesis rate, kernel weight (KW) and yield. Nevertheless, HSP90.2 over-expression increased KW. HSP90.2 recruited and was essential for the chloroplast localization of nuclear-encoded photosynthesis units, for example PsbO. Actin microfilaments docked on the chloroplast surface interacted with HSP90.2 as a subcellular track towards chloroplasts. A natural variation in the hexaploid wheat HSP90.2-B promoter increased its transcription activity, enhanced photosynthesis rate and improved KW and yield. Our study illustrated an HSP90.2-Actin complex sorting client preproteins towards chloroplasts to promote CO2 assimilation and crop production. The beneficial haplotype of Hsp90.2 is rare in modern varieties and could be an excellent molecular switch promoting photosynthesis rate to increase yield in future elite wheat varieties.

Prognostic value of the ratio of pretreatment carcinoembryonic antigen to tumor volume in rectal cancer.

Background: As a commonly used biomarker in rectal cancer (RC), the prognostic value of carcinoembryonic antigen (CEA) remains underexplored. This study aims to evaluate the prognostic value of pretreatment CEA/tumor volume in RC. Methods: This retrospective study included patients who underwent pretreatment magnetic resonance imaging (MRI) with histologically confirmed primary rectal adenocarcinoma from November 2012 to April 2018. Patients were divided into high-risk and low-risk groups according to the median values of CEA/Diapath (CEA to pathological diameter), CEA/DiaMRI (CEA to MRI tumor diameter), and CEA/VolMRI (CEA to MRI tumor volume). Cox regression analysis was utilized to determine the prognostic value of CEA, CEA/Diapath, CEA/DiaMRI, and CEA/VolMRI. Stepwise regression was used to establish nomograms for predicting disease-free survival (DFS) and overall survival (OS). Predictive performance was estimated by using the concordance index (C-index) and area under curve receiver operating characteristic (AUC). Results: A total of 343 patients [median age 58.99 years, 206 (60.06%) males] were included. After adjusting for patient-related and tumor-related factors, CEA/VolMRI was superior to CEA, CEA/Diapath, and CEA/DiaMRI in distinguishing high-risk from low-risk patients in terms of DFS [hazard ratio (HR) =1.83; P=0.010] and OS (HR =1.67; P=0.048). Subanalysis revealed that CEA/VolMRI stratified high death risk in CEA-negative individuals (HR =2.50; P=0.038), and also stratified low recurrence risk in CEA-positive individuals (HR =2.06; P=0.024). In the subanalysis of stage II or III cases, the highest HRs and the smallest P values were observed in distinguishing high-risk from low-risk patients according to CEA/VolMRI in terms of DFS (HR =2.44; P=0.046 or HR =2.41; P=0.001) and OS (HR =1.96; P=0.130 or HR =2.22; P=0.008). The nomograms incorporating CEA/VolMRI showed good performance, with a C-index of 0.72 [95% confidence interval (CI): 0.68-0.79] for DFS and 0.73 (95% CI: 0.68-0.80) for OS. Conclusions: Higher CEA/VolMRI was associated with worse DFS and OS. CEA/VolMRI was superior to CEA, CEA/Diapath, and CEA/DiaMRI in predicting DFS and OS. Pretreatment CEA/VolMRI may facilitate risk stratification and treatment decision-making.

Hormone-response transcriptional landscapes of wheat seedlings and the development of a JA fluorescent reporter.

Wheat is an essential energy and protein source for humans. Climate change brings daunting challenges to wheat yield through environmental stresses, in which phytohormones play critical roles. Nevertheless, the comprehensive understanding of wheat phytohormone responses remains elusive. Here, we investigated the transcriptome response of wheat seedlings to five phytohormones, cytokinin (6-BA), abscisic acid (ABA), gibberellic acid (GA), jasmonate (JA) and salicylic acid (SA). We further selected two JA marker genes and cloned their promoters to drive the expression of 3XEGFP (tandem trimeric enhanced green fluorescent protein) in transgenic lines. The JA fluorescent reporter displayed a fast and stable response to JA treatment as an ideal tool to follow JA dynamics during fungal and cold stresses at a cellular resolution. Overall, this study provided a transcriptional landscape and facilitated generating fluorescent reporters to monitor the dynamics of phytohormones in food crops.

Mild phototherapy mediated by manganese dioxide-loaded mesoporous polydopamine enhances immunotherapy against colorectal cancer.

One of the main challenges in applying the immune checkpoint blockade to treat colorectal cancer (CRC) is the immunosuppressive tumor microenvironment. Owing to its excellent cancer cell killing ability and immune activation, mild photothermal therapy (PTT) has shown bright promise to sensitize tumors to immune checkpoint inhibition through turning the immunologically "cold" tumors into "hot" ones. Herein, a mild photothermal effect-assisted theragnostic nanodrug (MnO2@MPDA-PEG NPs) is developed by incorporating MnO2 into PEGylated-mesoporous polydopamine nanoparticles (MPDA-PEG NPs). The presence of PEG endows the theragnostic nanodrug with high biostability. After accumulation in colorectal tumor, the theragnostic nanodrug responds to the tumor microenvironment, leading to the simultaneous release of Mn2+ which serves as a magnetic resonance imaging (MRI) contrast agent for tumor imaging. The released Mn2+ could also promote mild photothermal treatment-induced immune response, including the maturation of BMDC cells. In vivo antitumor studies on a CT26 model demonstrate that MnO2@MPDA-PEG NPs could be a promising dual-imaging theragnostic nanodrug to potentiate the systemic antitumor immunities.

Association of CT-Based Delta Radiomics Biomarker With Progression-Free Survival in Patients With Colorectal Liver Metastases Undergo Chemotherapy.

Predicting the prognosis of patients in advance is conducive to providing personalized treatment for patients. Our aim was to predict the therapeutic efficacy and progression free survival (PFS) of patients with liver metastasis of colorectal cancer according to the changes of computed tomography (CT) radiomics before and after chemotherapy. Methods: This retrospective study included 139 patients (397 lesions) with colorectal liver metastases who underwent neoadjuvant chemotherapy from April 2015 to April 2020. We divided the lesions into training cohort and testing cohort with a ratio of 7:3. Two - dimensional region of interest (ROI) was obtained by manually delineating the largest layers of each metastasis lesion. The expanded ROI (3 mm and 5 mm) were also included in the study to characterize microenvironment around tumor. For each of the ROI, 1,316 radiomics features were extracted from delineated plain scan, arterial, and venous phase CT images before and after neoadjuvant chemotherapy. Delta radiomics features were constructed by subtracting the radiomics features after treatment from the radiomics features before treatment. Univariate Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression were applied in the training cohort to select the valuable features. Based on clinical characteristics and radiomics features, 7 Cox proportional-hazards model were constructed to predict the PFS of patients. C-index value and Kaplan Meier (KM) analysis were used to evaluate the efficacy of predicting PFS of these models. Moreover, the prediction performance of one-year PFS was also evaluated by area under the curve (AUC). Results: Compared with the PreRad (Radiomics form pre-treatment CT images; C-index [95% confidence interval (CI)] in testing cohort: 0.614(0.552-0.675) and PostRad models (Radiomics form post-treatment CT images; 0.642(0.578-0.707), the delta model has better PFS prediction performance (Delta radiomics; 0.688(0.627-0.749). By incorporating clinical characteristics, CombDeltaRad obtains the best performance in both training cohort [C-index (95% CI): 0.802(0.772-0.832)] and the testing cohort (0.744(0.686-0.803). For 1-year PFS prediction, CombDeltaRad model obtained the best performance with AUC (95% CI) of 0.871(0.828-0.914) and 0.745 (0.651-0.838) in training cohort and testing cohort, respectively. Conclusion: CT radiomics features have the potential to predict PFS in patients with colorectal cancer and liver metastasis who undergo neoadjuvant chemotherapy. By combining pre-treatment radiomics features, post-treatment radiomics features, and clinical characteristics better prediction results can be achieved.

OsRAM2 Function in Lipid Biosynthesis Is Required for Arbuscular Mycorrhizal Symbiosis in Rice.

Arbuscular mycorrhiza (AM) is a mutualistic symbiosis formed between most land plants and Glomeromycotina fungi. During symbiosis, plants provide organic carbon to fungi in exchange for mineral nutrients. Previous legume studies showed that the required for arbuscular mycorrhization2 (RAM2) gene is necessary for transferring lipids from plants to AM fungi (AMF) and is also likely to play a "signaling" role at the root surface. To further explore RAM2 functions in other plant lineages, in this study, two rice (Oryza sativa) genes, OsRAM2 and OsRAM2L, were identified as orthologs of legume RAM2. Examining their expression patterns during symbiosis revealed that only OsRAM2 was strongly upregulated upon AMF inoculation. CRISPR/Cas9 mutagenesis was then performed to obtain three Osram2 mutant lines (-1, -2, and -3). After inoculation by AMF Rhizophagus irregularis or Funneliformis mosseae, all of the mutant lines showed extremely low colonization rates and the rarely observed arbuscules were all defective, thus supporting a conserved "nutritional" role of RAM2 between monocot and dicot lineages. As for the signaling role, although the hyphopodia numbers formed by both AMF on Osram2 mutants were indeed reduced, their morphology showed no abnormality, with fungal hyphae invading roots successfully. Promoter activities further indicated that OsRAM2 was not expressed in epidermal cells below hyphopodia or outer cortical cells enclosing fungal hyphae but instead expressed exclusively in cortical cells containing arbuscules. Therefore, this suggested an indirect role of RAM2 rather than a direct involvement in determining the symbiosis signals at the root surface.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.).

BACKGROUND: GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. RESULTS: In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. CONCLUSIONS: Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.

Molecular mapping of the gene(s) conferring resistance to Soybean mosaic virus and Bean common mosaic virus in the soybean cultivar Raiden.

KEY MESSAGE: In the soybean cultivar Raiden, both a SMV-resistance gene and a BCMV-resistance gene were fine-mapped to a common region within the Rsv1 complex locus on chromosome 13, in which two CC-NBS-LRR resistance genes (Glyma.13g184800 and Glyma.13g184900) exhibited significant divergence between resistant and susceptible cultivars and were subjected to positive selection. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases. To date, few studies have explored soybean resistance against these two viruses simultaneously. In this work, Raiden, a cultivar resistant to both SMV and BCMV, was crossed with a susceptible cultivar, Williams 82, to fine-map the resistance genes. After inoculating ~ 200 F2 individuals with either SMV (SC6-N) or BCMV (HZZB011), a segregation ratio of 3 resistant:1 susceptible was observed, indicating that for either virus, a single dominant gene confers resistance. Bulk segregation analysis (BSA) revealed that the BCMV-resistance gene is also linked to the SMV-resistance Rsv1 complex locus. Genotyping the F2 individuals with 12 simple sequence repeat (SSR) markers across the Rsv1 complex locus then preliminarily mapped the SMV-resistance gene, Rsv1-r, between SSR markers BARCSOYSSR_13_1075 and BARCSOYSSR_13_1161 and the BCMV-resistance gene between BARCSOYSSR_13_1084 and BARCSOYSSR_13_1115. Furthermore, a population of 1009 F2 individuals was screened with markers BARCSOYSSR_13_1075 and BARCSOYSSR_13_1161, and 32 recombinant F2 individuals were identified. By determining the genotypes of these F2 individuals on multiple internal SSR and single nucleotide polymorphism (SNP) markers and assaying the phenotypes of selected recombinant F2:3 lines, both the SMV- and BCMV-resistance genes were fine-mapped to a common region ( ~ 154.5 kb) between two SNP markers: SNP-38 and SNP-50. Within the mapped region, two CC-NBS-LRR genes exhibited significant divergence between Raiden and Williams 82, and their evolution has been affected by positive selection.

An Update on the Evolution of Glucosyltransferase (Gtf) Genes in Streptococcus.

In many caries-promoting Streptococcus species, glucosyltransferases (Gtfs) are recognized as key enzymes contributing to the modification of biofilm structures, disruption of homeostasis of healthy microbiota community and induction of caries development. It is therefore of great interest to investigate how Gtf genes have evolved in Streptococcus. In this study, we conducted a comprehensive survey of Gtf genes among 872 streptococci genomes of 37 species and identified Gtf genes from 364 genomes of 18 species. To clarify the relationships of these Gtf genes, 45 representative sequences were used for phylogenic analysis, which revealed two clear clades. Clade I included 12 Gtf genes from nine caries-promoting species of the Mutans and Downei groups, which produce enzymes known to synthesize sticky, water-insoluble glucans (WIG) that are critical for modifying biofilm structures. Clade II primarily contained Gtf genes responsible for synthesizing water-soluble glucans (WSG) from all 18 species, and this clade further diverged into three subclades (IIA, IIB, and IIC). An analysis of 16 pairs of duplicated Gtf genes revealed high divergence levels at the C-terminal repeat regions, with ratios of the non-synonymous substitution rate (dN) to synonymous substitution rate (dS) ranging from 0.60 to 1.03, indicating an overall relaxed constraint in this region. However, among the clade I Gtf genes, some individual repeat units possessed strong functional constraints by the same criterion. Structural variations in the repeat regions were also observed, with detection of deletions or recent duplications of individual repeat units. Overall, by establishing an updated phylogeny and further elucidating their evolutionary patterns, this work enabled us to gain a greater understanding of the origination and divergence of Gtf genes in Streptococcus.

Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review.

MicroRNAs (MiRNAs) play multiple crucial regulating roles in cell which can regulate one third of protein-coding genes. MiRNAs participate in the developmental and physiological processes of human body, while their aberrant adjustment will be more likely to trigger diseases such as cancers, kidney disease, central nervous system diseases, cardiovascular diseases, diabetes, viral infections and so on. What's worse, for the detection of miRNAs, their small size, high sequence similarity, low abundance and difficult extraction from cells impose great challenges in the analysis. Hence, it's necessary to fabricate accurate and sensitive biosensing platform for miRNAs detection. Up to now, researchers have developed many signal-amplification strategies for miRNAs detection, including hybridization chain reaction, nuclease amplification, rolling circle amplification, catalyzed hairpin assembly amplification and nanomaterials based amplification. These methods are typical, feasible and frequently used. In this review, we retrospect recent advances in signal amplification strategies for detecting miRNAs and point out the pros and cons of them. Furthermore, further prospects and promising developments of the signal-amplification strategies for detecting miRNAs are proposed.

Hydrogen-Rich Saline Ameliorates Hepatic Ischemia-Reperfusion Injury Through Regulation of Endoplasmic Reticulum Stress and Apoptosis.

OBJECTIVE: To evaluate the effect of hydrogen-rich saline (HS) on hepatic ischemia-reperfusion (I/R) injury. METHODS: Forty rats were randomly allocated into five groups: one sham group (control group), one group treated with 20 min of ischemia and normal saline (NS; I/R1 + NS group), one group treated with 20 min of ischemia and HS (I/R1 + HS group), one group treated with 60 min of ischemia and NS (I/R2 + NS group), and one group treated with 60 min of ischemia and HS (I/R2 + HS group). After reperfusion for 6 h, hepatic function, oxidative stress, pathological changes, and apoptosis of hepatic cells were evaluated. Furthermore, the expression levels of endoplasmic reticulum (ER) stress-associated proteins were identified. RESULTS: Serum ALT and AST levels and tissue MDA content in the I/R + HS groups were significantly lower than those in the I/R + NS groups. Pathological changes were also significantly ameliorated in the HS groups compared with those in the NS groups. Moreover, HS appeared to significantly attenuate hepatic I/R-induced ER stress responses, as indicated by the decreased expression of C/EBP homologous protein, protein-kinase-RNA-like ER kinase, and inositol-requiring protein-1α, as well as the increased expression of GRP78 proteins. Finally, the levels of apoptotic markers such as caspase-3 and TUNEL-positive cells were significantly lower in the HS groups than in the NS control groups, whereas the level of Bcl2 protein increased in the HS groups. CONCLUSION: The protective effect of HS can be attributed to ER stress and apoptosis inhibition.

Chitin synthase gene FgCHS8 affects virulence and fungal cell wall sensitivity to environmental stress in Fusarium graminearum.

Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) of wheat and barley and is considered to be one of the most devastating plant diseases worldwide. Chitin is a critical component of the fungal cell wall and is polymerized from UDP-N-acetyl-alpha-D-glucosamine by chitin synthase. We characterized FgCHS8, a new class of the chitin synthase gene in F. graminearum. Disruption of FgCHS8 resulted in reduced accumulation of chitin, decreased chitin synthase activity, and had no effect on conidia growth when compared with the wild-type isolate. ΔFgCHS8 had a growth rate comparable to that of the wild-type isolate in vitro. However, ΔFgCHS8 had reduced growth when grown on agar supplemented with either 0.025% SDS or 0.9 mM salicylic acid. ΔFgCHS8 produced significantly less deoxynivalenol and exhibited reduced pathogenicity in wheat spikes. Re-introduction of a functional FgCHS8 gene into the ΔFgCHS8 mutant strain restored the wild-type phenotypes. Fluorescence microscopy revealed that FgCHS8 protein was initially expressed in the septa zone, and then gradually distributed over the entire cellular membrane, indicating that FgCHS8 was required for cell wall development. Our results demonstrated that FgCHS8 is important for cell wall sensitivity to environmental stress factors and deoxynivalenol production in F. graminearum.