Search

Key message: An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F1, F2, and F2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway. [ABSTRACT FROM AUTHOR]

Background: The heterogeneity limits the effective application of immune checkpoint inhibitors for patients with stomach adenocarcinoma (STAD). Precise immunotyping can help select people who may benefit from immunotherapy and guide postoperative management by describing the characteristics of tumor microenvironment. Methods: Gene expression profiles and clinical information of patients were collected from ACRG and TCGA-STAD datasets. The immune subtypes (ISs) were identified by consensus clustering analysis. The tumor immune microenvironments (TIME) of each IS were characterized using a series of immunogenomics methods and further confirmed by multiplex immunohistochemistry (mIHC) staining in clinical samples. Two online datasets and one in-house dataset were utilized to construct and validate a prognostic immune-related gene (IRG) signature. Results: STAD patients were stratified into five reproducible ISs. IS1 (immune deserve subtype) had low immune infiltration and the highest degree of HER2 gene mutation. With abundant CD8+ T cells infiltration and activated cytotoxicity reaction, patients in the IS2 (immune-activated subtype) had the best overall survival (OS). IS3 and IS4 subtypes were both in the reactive stroma state and indicated the worst prognosis. However, IS3 (immune-inhibited subtype) was characterized by enrichment of FAP+ fibroblasts and upregulated TGF-β signaling pathway, while IS4 (activated stroma subtype) was characterized by enrichment of ACTA2+ fibroblasts. In addition, mIHC staining confirmed that TGF-β upregulated FAP+ fibroblasts were independent risk factor of OS. IS5 (chronic inflammation subtype) displayed moderate immune cells infiltration and had a relatively good survival. Lastly, we developed a nine-IRG signature model with a robust performance on overall survival prognostication. Conclusions: The immunotyping is indicative for characterize the TIME heterogeneity and the prediction of tumor prognosis for STADs, which may provide valuable stratification for the design of future immunotherapy. [ABSTRACT FROM AUTHOR]

Obesity, characterized as a state of low-level inflammation, is a powerful determinant influencing the development of insulin resistance and progression to type 2 diabetes. The purpose of the present study was to investigate the anti-inflammatory activity of fucoxanthin in experimental high-fat-diet-induced obesity in mice and antioxidant activity in PC12 cells under oxidative stress situation. The anti-inflammatory potential of fucoxanthin in the regulation of maleic dialdehyde (MDA), polymorphonuclear cells (PMNs), interleukin-1β (IL-1β), inducible nitric oxide synthase (iNOS), tumor necrosis factor alpha (TNF-α), and cyclooxygenase-2 (COX-2) was determined by ELISA. Fucoxanthin significantly inhibited obesity-induced upregulation of the production of IL-1β, TNF-α, iNOS, and COX-2. Moreover, fucoxanthin suppressed MDA and infiltration of PMNs. The protective effects were associated with lack of hypertrophy and crown-like structures in mammary gland. At the same time, fucoxanthin showed an advantage of antioxidant activity in PC12 cells under oxidative stress situation. These results suggest that supplementation of fucoxanthin is a promising strategy for blocking macrophage-mediated inflammation and inflammation-induced obesity and its associated complications. [ABSTRACT FROM AUTHOR]

A carotenoid gene (crtR-B) from the green alga Haematococcus pluvialis, encoding β-carotene hydroxylase that was able to catalyze the conversion of β-carotene to zeaxanthin and canthaxanthin to astaxanthin, was cloned into Chlamydomonas reinhardtii chloroplast expression vector p64D to yield plasmid p64DcrtR-B. The vector p64DcrtR-B was transferred to the chloroplast genome of C. reinhardtii using micro-particle bombardment. PCR and Southern blot analyses indicated that crtR-B was integrated into the chloroplast genome of the transformants. RT-PCR assays showed that the H. pluvialiscrt R-B gene was expressed in C. reinhardtii transformants. The transformants rapidly synthesized carotenoids in larger quantities than the wild-type upon being transferred from moderate to high-intensity white light. This research provides a foundation for further study to elucidate the possible mechanism of photo-protection by xanthophylls and other carotenoids in high light conditions or through exposure to UV radiation. [ABSTRACT FROM AUTHOR]

In the original publication of this article, the acknowledgement section has been missed to publish. Now the same has been provided in this correction. [ABSTRACT FROM AUTHOR]

The division of diffuse large B-cell lymphoma (DLBCL) into germinal center B-cell-like (GCB) and activated B-cell-like (ABC) subtypes based on gene expression profiling has proved to be a landmark in understanding the pathogenesis of the disease. This study aims to identify a novel biomarker to facilitate the translation of research into clinical practice. Using a training set of 350 patients, we identified a two-gene expression signature, 'LIMD1-MYBL1 Index', which is significantly associated with cell-of-origin subtypes and clinical outcome. This two-gene index was further validated in two additional dataset. Tested against the gold standard method, the LIMD1-MYBL1 Index achieved 81% sensitivity, 89% specificity for ABC group and 81% sensitivity, 87% specificity for GCB group. The ABC group had significantly worse overall survival than the GCB group (hazard ratio = 3.5, P = 0.01). Furthermore, the performance of LIMD1-MYBL1 Index was satisfactory compared with common immunohistochemical algorithms. Thus, the LIMD1-MYBL1 Index had considerable clinical value for DLBCL subtype classification and prognosis. Our results might prompt the further development of this two-gene index to a simple assay amenable to routine clinical practice. [ABSTRACT FROM AUTHOR]

Key message: Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding. [ABSTRACT FROM AUTHOR]

Key message: Two tightly linked genes for rice purple leaf sheath were identified via map-based cloning. Further analysis indicated that these two genes together with OsC1 co-regulating the purple leaf sheath. The purple color of the leaf sheath in rice is dependent on the accumulation of anthocyanins such as cyanidin 3-O-glucoside (C3G) and peonidin 3-O-glucoside (P3G). Although many genes related to leaf sheath color have been mapped, the genetic basis for leaf sheath color is not yet clear. Here, PSH1 (purple leaf sheath 1) was mapped to chromosome 1 using an F2 and a RIL population. Map-based cloning and transformation assays further divided PSH1 as two tightly linked bHLH genes, Rb1 and Rb2. Ectopic expression of these two genes resulted in substantial accumulation of C3G and P3G in the leaf blade, leaf sheath and pericarp. Single gene mutants displayed a faded purple leaf sheath or green leaf sheath in the top half of the leaf sheath, but double mutants displayed a green leaf sheath, indicating that both genes have dosage effects on anthocyanin synthesis. However, overexpression of Rb1 and Rb2 sharply decreased grain filling. A segregation ratio of green to purple was 15:1 observed in the F2 population from parents Minghui 63 and Xizang 2, which both had green leaf sheaths; these results demonstrate that dominant complementary interaction between OsC1 and Rb (Rb1 and Rb2) controls the purple leaf sheath. These findings systematically uncovered the genetic basis of leaf sheath color and provided alternative genes for breeding anthocyanin-rich rice. [ABSTRACT FROM AUTHOR]

Key message: An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci (QTL) analysis of APR and fine mapping were performed on five barley populations derived from a common parent Vlamingh, which expresses APR to scald. Two QTLs, designated QSc.VR4 and QSc.BR7, were detected from a cross between Vlamingh and Buloke. Our data confirmed that QSc.VR4 is an effective and stable APR locus, residing on the short arm of chromosome 4H, and QSc.BR7 derived from Buloke may be an allele of reported Rrs2. High-resolution fine mapping revealed that QSc.VR4 is located in a 0.38 Mb genomic region between InDel markers 4H2282169 and 4H2665106. The gene annotation analysis and sequence comparison suggested that a gene cluster containing two adjacent multigene families encoding leucine-rich repeat receptor kinase-like proteins (LRR-RLKs) and germin-like proteins (GLPs), respectively, is likely contributing to scald resistance. Adult plant resistance (APR) governed by QSc.VR4 may confer partial levels of resistance to the fungus Rhynchosporium commune and, furthermore, be an important resource for gene pyramiding that may contribute broad-based and more durable resistance. [ABSTRACT FROM AUTHOR]

Background: Pituitary tumor-transforming gene-1 (PTTG1) is a transcription factor that can affect transcriptional activity, angiogenesis, and cell senescence. We examined PTTG1 mRNA and protein expression in gastric cancer (GC) cell lines and tissues to determine its value as a biomarker for GC diagnosis and therapy. Methods: PTTG1 mRNA expression from 78 GC cases and paired adjacent normal mucosa (PCR cohort) as well as from five gastric cell lines was assessed using qRT-PCR. Nuclear and cytoplasmic RNA were extracted from two gastric cell lines to determine PTTG1 mRNA localization. PTTG1 protein expression from 98 GC cases, their paired adjacent normal mucosa, and 23 gastric intraepithelial neoplasia (GIN) cases was examined using immunohistochemistry (IHC cohort). The correlation between PTTG1 mRNA and protein expression and GC clinicopathological parameters was analyzed. Results: PTTG1 mRNA expression in GC tissues and cell lines was significantly increased compared with adjacent normal gastric mucosa and normal gastric mucous cell lines ( p < 0.05). PTTG1 expression was nuclear and cytoplasmic, with higher cytoplasmic expression. PTTG1 immunostaining significantly differed in GC (95.66 ± 20.65), GIN (84.00 ± 34.16), and normal adjacent mucosa (28 ± 22.25) ( p < 0.001). Multivariate Cox regression analysis revealed that PTTG1 mRNA and protein expression are independent prognostic factors for GC patient survival. Conclusion: Our results suggest that PTTG1 is a promising target for GC diagnosis and therapy. [ABSTRACT FROM AUTHOR]

Purpose: Gene expression profiling of whole blood is showing great promise for the discovery of novel biomarkers for colorectal cancer (CRC) detection. Given the relatively low incidence rate of CRC in the general population, most blood samples collected prior to a colonoscopy were confirmed to be noncancerous afterward. Previous studies have relied on blood samples collected after a colonoscopy to reach the sufficient number of CRC cases. The present study aimed to determine the colonoscopy-induced variability in the blood transcriptome and its potential impact on biomarker discovery. Methods: Whole blood gene expression profiling was conducted using Affymetrix HG-U133Plus2 arrays. We analyzed 20 paired blood samples collected from healthy controls before and after colonoscopy, and 20 blood samples collected from CRC patients after colonoscopy. Results: Utilizing hierarchical clustering analysis, samples collected before and after colonoscopy from the same subjects were closely clustered together, suggesting that the blood gene expression profiles primarily reflect the heterogeneity within each individual. A total of 914 genes were differentially expressed between controls and CRC patients, while gene expression did not differ between samples collected before and after colonoscopy. Using real-time PCR technology, we further validated six genes from published biomarkers in this study. Our results confirmed that the biomarkers identified in previous studies were not likely to be biased due to the colonoscopy effect. Conclusions: Our results showed that the colonoscopy-induced variations were minute compared to individuals' heterogeneity and disease-induced variations. These findings may serve as a basis for future development of blood-based transcriptomic biomarkers for the diagnosis and treatment of CRC. [ABSTRACT FROM AUTHOR]

CCT domain-containing genes generally control flowering in plants. Currently, only six of the 41 CCT family genes have been confirmed to control flowering in rice. To efficiently identify more heading date-related genes from the CCT family, we compared the positions of heading date QTLs and CCT genes and found that 25 CCT family genes were located in the QTL regions. Association mapping showed that a total of 19 CCT family genes were associated with the heading date. Five of the seven associated genes within QTL regions and two of four associated genes outside of the QTL regions were confirmed to regulate heading date by transformation. None of the seven non-associated genes outside of the QTL regions regulates heading date. Obviously, combination of candidate gene-based association mapping with linkage analysis could improve the identification of functional genes. Three novel CCT family genes, including one non-associated (OsCCT01) and two associated genes (OsCCT11 and OsCCT19) regulated the heading date. The overexpression of OsCCT01 delayed flowering through suppressing the expression of Ehd1, Hd3a and RFT1 under both long day and short day conditions. Potential functions in regulating heading date of some untested CCT family genes were discussed. [ABSTRACT FROM AUTHOR]