Fine mapping of ClLOX, a QTL for powdery mildew resistance in watermelon (Citrullus lanatus L.).

KEY MESSAGE: ClLOX, is located on chromosome 2 and encodes a lipoxygenase gene, which induced watermelon powdery mildew resistance by inhibiting pathogen spread. Powdery mildew is one of the most severe fungal diseases reducing yield and quality of watermelon (Citrullus lanatus L.) and other cucurbit crops. Genes responsible for powdery mildew resistance in watermelon are highly valuable. In this study, we first identified the QTL pm-lox for powdery mildew resistance in watermelon, located within a 0.93 Mb interval of chromosome 2, via XP-GWAS method using two F2 populations. The F2:3 families from one of the F2 populations were then used for fine-mapping the pm-lox locus into a 9,883 bp physical region between 29,581,906 and 29,591,789, containing only two annotated genes. Of these, only ClG42_02g0161300 showed a significant differential expression between the resistant and susceptible lines after powdery mildew inoculation based on RNA sequencing (RNA-seq) and qRT-PCR analysis, and is designated ClLOX. Derived Cleaved Amplified Polymorphic Sequence (dCAPs) markers were developed and validated. In addition, our tests showed that the resistance was anti-spread rather than anti-infection of the pathogen. This study identified a new resistance gene (ClLOX), provided insights into the mechanism of powdery mildew resistance, and developed a molecular marker for watermelon breeding.

Physiological and transcriptomic analysis of a yellow leaf mutant in watermelon.

Leaf color mutants are important materials for studying chloroplast and photomorphogenesis, and can function as basic germplasms for genetic breeding. In an ethylmethanesulfonate mutagenesis population of watermelon cultivar "703", a chlorophyll-deficient mutant with yellow leaf (Yl2) color was identified. The contents of chlorophyll a, chlorophyll b, and carotenoids in Yl2 leaves were lower than those in wild-type (WT) leaves. The chloroplast ultrastructure in the leaves revealed that the chloroplasts in Yl2 were degraded. The numbers of chloroplasts and thylakoids in the Yl2 mutant were lower, resulting in lower photosynthetic parameters. Transcriptomic analysis identified 1292 differentially expressed genes, including1002 upregulated and 290 downregulated genes. The genes involved in chlorophyll biosynthesis (HEMA, HEMD, CHL1, CHLM, and CAO) were significantly downregulated in the Yl2 mutant, which may explain why chlorophyll pigment content was lower than that in the WT. Chlorophyll metabolism genes such as PDS, ZDS and VDE, were upregulated, which form the xanthophyll cycle and may protect the yellow‒leaves plants from photodamage. Taken together, our findings provide insight into the molecular mechanisms of leading to leaf color formation and chloroplast development in watermelon.

A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding.

Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon. Here, we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing the highest completeness and assembly quality to date. The G42 reference genome is 369 321 829 bp in length and contains 24 205 predicted protein-coding genes, with all 22 telomeres and 11 centromeres characterized. Furthermore, we established a pollen-EMS mutagenesis protocol and obtained over 200 000 M1 seeds from G42 . In a sampling pool, 48 monogenic phenotypic mutations, selected from 223 M1 and 78 M2 mutants with morphological changes, were confirmed. The average mutation density was 1 SNP/1.69 Mb and 1 indel/4.55 Mb per M1 plant and 1 SNP/1.08 Mb and 1 indel/6.25 Mb per M2 plant. Taking advantage of the gap-free G42 genome, 8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100% accuracy, whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed. Using this library and the gap-free genome, two genes responsible for elongated fruit shape and male sterility (ClMS1) were identified, both caused by a single base change from G to A. The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.

Genome-Wide Identification and Expression Profiling of CONSTANS-Like Genes in Pepper (Capsicum annuum): Gaining an Insight to Their Phylogenetic Evolution and Stress-Specific Roles.

CONSTANS-like (COL) genes play important regulatory roles in multiple growth and development processes of plants but have rarely been studied in Capsicum annuum. This study explored the evolutionary relationship and expression patterns of COL genes from C. annuum. A total of 10 COL genes were identified in the genome of the cultivated pepper Zunla-1 and were named CaCOL01-10. These genes were unequally distributed among five chromosomes and could be divided into three groups based on differences in gene structure characteristics. During evolutionary history, duplications and retentions were divergent among different groups of COL genes. Tandem duplication caused amplification of group I genes. Genetic distance among COL genes was the largest in group III, suggesting that group III genes undergo more relaxed selection pressure compared with the other groups. Expression patterns of CaCOLs in tissues were significantly different, with CaCOL08 exhibiting the highest expression in stem and leaf. Some COL orthologous genes showed markedly different expression patterns in pepper compared with tomato, such as COL_1 orthologs, which may be involved in fruit development in pepper. In addition, CaCOLs participated in the regulation of abiotic stresses to varying degrees. Five CaCOL genes were induced by cold, and CaCOL02 and CaCOL03 were specifically upregulated by cold and downregulated by heat. This study provides a theoretical basis for the in-depth understanding of the functions of COL genes in pepper and their molecular mechanisms involved in growth and development and responses to abiotic stresses.

Unsupervised learning of cross-modal mappings in multi-omics data for survival stratification of gastric cancer.

Aims: This study presents a survival stratification model based on multi-omics integration using bidirectional deep neural networks (BiDNNs) in gastric cancer. Methods: Based on the survival-related representation features yielded by BiDNNs through integrating transcriptomics and epigenomics data, K-means clustering analysis was performed to cluster tumor samples into different survival subgroups. The BiDNNs-based model was validated using tenfold cross-validation and in two independent confirmation cohorts. Results: Using the BiDNNs-based survival stratification model, patients were grouped into two survival subgroups with log-rank p-value = 9.05E-05. The subgroups classification was robustly validated in tenfold cross-validation (C-index = 0.65 ± 0.02) and in two confirmation cohorts (E-GEOD-26253, C-index = 0.609; E-GEOD-62254, C-index = 0.706). Conclusion: We propose and validate a robust and stable BiDNN-based survival stratification model in gastric cancer.

Plasma miR-1, but not Extracellular Vesicle miR-1, Functions as a Potential Biomarker for Colorectal Cancer Diagnosis.

BACKGROUND: miRNAs have been proved to function as diagnostic biomarkers. Extracellular vesicles (EVs) are carriers of miRNAs. This study aimed to investigate the diagnostic potential of miR-1 in plasma and extracellular vesicles (EVs) for patients with colorectal cancer (CRC). METHODS: Bioinformatics analysis was used to find a target miRNA and its potential functions. miR-1 was then detected in plasma and EV from 49 control samples and 40 CRC samples. Next, the diagnostic potential of plasma and EV miR-1 were compared based on common biomarkers including CEA and CA211. RESULTS: miR-1 was differentially expressed in CRC. Target gene and function analyses showed that it might participate in cell migration and the regulation of mRNA splicing via the spliceosome. Plasma miR-1 levels in CRC samples were significantly higher than those in control samples, whereas EV miR-1 levels were not statistically different. Based on receiver operating characteristic (ROC) curve analysis, comparing their predictive power compared to that of CEA and CA211, plasma miR-1 performed better and EV miR-1 performed worse. CONCLUSIONS: Our data indicate that plasma miR-1, but not EV miR-1, could function as a potential biomarker for CRC diagnosis.

Overexpression of UBE2M through Wnt/ß-Catenin signaling is associated with poor prognosis and chemotherapy resistance in colorectal cancer.

BACKGROUND: The expression of ubiquitin-conjugating enzyme E2 M (UBE2M) is elevated in colorectal carcinoma (CRC). However, the underlying mechanisms and effects of UBE2M on the prognosis and drug resistance in CRC have not been investigated. METHODS: CRC specimens and adjacent normal tissues were collected from 74 patients. The expression of UBE2M was measured by quantitative real-time polymerase chain reaction (PCR) and immunohistochemistry. Multivariable cox regression analysis was used to analyze the risk factors for overall survival in clinical CRC patients. Human colorectal cancer cell lines HCT116 and SW480 were transfected with specific UBE2M small interfering ribonucleic acid (siRNA) or plasmid to either suppress or increase the expression of UBE2M for in vitro experiments. Also, chemotherapy-resistant HCT116 and SW480 cells were established by being treated with increasingly higher concentrations of fluorouracil (5-FU) or oxaliplatin. XAV-939 was used as a wingless/integrated-beta-catenin (Wnt/ß-catenin) signaling inhibitor. RESULTS: According to quantitative real-time PCR and immunohistochemistry, the expression of UBE2M was elevated in CRC tissues compared to normal tissues. Based on cox regression analysis, the overexpression of UBE2M was a risk factor for overall survival of CRC patients. The expression of UBE2M was notably high in 5-FU- and oxaliplatin-resistant cells in in vitro experiments. Also, cells transfected with specific UBE2M siRNA or plasmid induced lower resistance to 5-FU and higher resistance to oxaliplatin. Finally, the expression of ß-catenin was correlated with the expression of UBE2M in transfected cells and treatment with XAV939 decreased the degree of drug resistance in chemotherapy-resistant HCT116 cells. CONCLUSIONS: Overexpression of UBE2M in CRC specimens contributes to a decreased overall survival of patients and mediates 5-FU and oxaliplatin resistance in CRC cells via the Wnt/ß-catenin signaling pathway.

Study on the method of compensation for the heading effect of the rate offset frequency laser inertial measurement unit.

For the rate offset frequency laser inertial measurement unit (IMU), the errors of its three attitude angles, laser gyroscope, and accelerometer are coupled, which will affect the initial alignment result of the IMU and will make the measurement results of the IMU at different positions and angles deviate from the truth value. Meanwhile, with the increase of tilt angle, the heading effect becomes more obvious, and the error value is distributed positively cosine with the heading angle. In order to ensure the adaptability of the IMU to various operating conditions, it is necessary to compensate for the heading effect. The contribution of each error source of IMU to the heading effect is theoretically studied in this paper. We present a new method for compensating for the heading effect of the rate offset frequency laser IMU, in which the normal drift error of the vertical direction laser gyroscope and the zero bias error of the accelerometer under the turntable coordinate system are compensated. Based on the above method, simulation analysis and test verification are carried out. The experimental results show that the compensation method has a remarkable effect. In the case of two horizontal attitude angles tilted 0.0873 rad and 5 min initial alignment, the error of the rate offset frequency laser IMU reduced from 5.02E-04 rad $({3}\sigma)$(3σ) to 1.45E-04 rad $({3}\sigma)$(3σ), and the accuracy increased by 71%. High-precision initial alignment is achieved, which can meet the requirements of high-precision engineering applications.

Association of high-sensitivity C-reactive protein with the increments of BMI and WC in junior high school students / 中国学校卫生

Objective@#To observe the short-term changes of Body Mass Index (BMI) and Waist Circumference (WC) in junior high school students in Harbin, and to explore its association with the changes of high-sensitivity C-reactive protein (hs-CRP) in the same period. Furthermore, to analyze the value of hs-CRP to predict the BMI and WC changes in children and adolescents.@*Methods@#Convenient sampling method was used,and the students in grades 6 and 7 in junior high school in Harbin were selected by stratified clicstering. Physical examination and serum hs-CRP were performed for two consecutive years. According to the results of the two surveys, the subjects were divided into control group (normal → normal), case group (abnormal → abnormal), improved group (abnormal → normal) and progression group (normal → abnormal). The multinomial logistic regression was used to analyze the predictive value of hs-CRP changes for BMI and WC changes.@*Results@#The rate of overweight and obesity among samples from junior high school was 30.6%. The increment of BMI in female was more obvious than that in male(U=17 358.0，P<0.05). Both increments in BMI and WC were positively correlated with increments in hs-CRP(P<0.05). The risk of occurrence of "BMI always abnormal" and "WC always abnormal" increased sequentially in hs-CRP "normal → abnormal", "abnormal → normal" and "abnormal → abnormal", were 3.45 times, 5.98 times and 38.84 times of "BMI is always normal", respectively; and were 3.45 times, 4.26 times and 28.50 times of "WC is always normal", respectively. The risk of "BMI improvement" was 7.70 times more than that of BMI "always normal" when hs-CRP "abnormal → normal".@*Conclusion@#The prevalence of overweight and obesity in junior high school students in Harbin is high. The BMI increases faster in female from junior high school. The trends of change of BMI and WC are consistent with the trend of change of hs-CRP. The “hs-CRP change” has a good predictive value for BMI and WC development.

Protective effects of Atractylodes macrocephala polysaccharide on liver ischemia-reperfusion injury and its possible mechanism in rats.

Atractylodes macrocephala polysaccharide (AMP), a traditional Chinese medicine, is thought to have protective effects against liver injury. Therefore, this study was designed to explore the effects of AMP on hepatic ischemia-reperfusion injury (IRI) and elucidate the possible mechanisms. Ninety-six Sprague-Dawley rats were randomly divided into four groups with 24 rats per group: a normal control group, an IRI group, an AMP-treated group (0.4 g/kg/d) and a bifendate-treated group (100 mg/kg). Rats were treated with AMP or bifendate once daily for seven days by gastric gavage. The normal control group and the IRI model group received an equivalent volume of physiological saline. At 1, 6 and 24 h after surgery, the rats were killed and liver tissue samples were obtained to determine interleukin-1 (IL-1) expression by Western blotting and nuclear factor-κB (NF-κB) expression by immunohistochemistry. Liver morphology was assessed by microscopy and transmission electron microscopy. Blood samples were obtained to measure liver function (alanine aminotransferase, aspartate aminotransferase, total bilirubin and direct bilirubin). AMP significantly reduced the elevated expression of markers of liver dysfunction and the hepatic morphologic changes induced by hepatic IRI in rats. AMP also markedly inhibited IRI-induced lipid peroxidation and altered the activities of the antioxidant enzyme superoxide dismutase and malondialdehyde levels. Moreover, pretreatment with AMP suppressed the expression of interleukin-1ß and NF-kB in IRI-treated rats. These results suggest that AMP exerts protective and therapeutic effects against hepatic IRI in rats, which might be associated with its antioxidant properties and inhibition of NF-κB activation. More studies are needed to better understand the mechanisms underlying the protective effects of AMP on hepatic IRI.

The minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis.

Hepatocellular carcinoma (HCC) is one of the most common human cancers in Asia. Previous studies have shown that in addition to aberrations of the p53 gene on chromosome 17p13.1, other gene(s) on chromosome 17p13.3 may also play a role in HCC. To detect the status of loss of heterozygosity (LOH) in HCC and to determine the minimum region of LOH on 17p13.3, we analyzed 22 paired HCC and non-cancerous liver samples with 14 polymorphic markers plus TP53 (p53 gene) as a comparison. The data revealed a high level of LOH (>68%) in a minimum region between D17S1866 and D17S1574, spanning over a 1.5 Mb region. Genomic library screening using markers in the region has resulted in the isolation of a cluster of BAC/PAC clones. We created a physical map in this region. Using large-scale genome sequencing, gene annotation, cDNA screening, and exon trapping, we identified 17 known genes and 13 novel genes in the minimum region. The function of these genes was analyzed and the possibility of several putative tumor suppressor genes was discussed.