Chromosome-scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis

Melilotus officinalis is an important legume crop with forage and Chinese medicinal value. The unknown genome of M. officinalis restricted the domestication and utilization of the species and its germplasm resource diversity. A chromosome-scale assembly of the M. officinalis genome was assembled and analysed. The 976.27 Mb of genome was divided into eight chromosomes covering 99.16% of the whole genome. A total of 50022 genes were predicted in the genome. M. officinalis and Melilotus albus shared a common ancestor 0.5-5.65 million years ago (MYA). A genome-wide doubling event occurred 68.93 MYA according to the synonymous nucleotide-substitution values. A total of 552102 tandem repeats were predicted, and 46004 SSR primers of TRs with 10 or more base pairs were developed and designed. The elucidation of the M. officinalis genome provides a compelling model system for studying the genetic, evolutionary and biosynthesis of this legume.

A chromosome-scale genome sequence of sudangrass (Sorghum sudanense) highlights the genome evolution and regulation of dhurrin biosynthesis

Sudangrass is more similar to US commercial sorghums than to cultivated sorghums from Africa sequence-wise and contain significantly lower dhurrin than sorghums. CYP79A1 is linked to dhurrin content in sorghum. Sudangrass [Sorghum sudanense (Piper) Stapf] is a hybrid between grain sorghum and its wild relative S. bicolor ssp. verticilliflorum and is grown as a forage crop due to its high biomass production and low dhurrin content compared to sorghum. In this study, we sequenced the sudangrass genome and showed that the assembled genome was 715.95 Mb with 35,243 protein-coding genes. Phylogenetic analysis with whole genome proteomes demonstrated that the sudangrass genome was more similar to US commercial sorghums than to its wild relatives and cultivated sorghums from Africa. We confirmed that at seedling stage, sudangrass accessions contained significantly lower dhurrin as measured by hydrocyanic acid potential (HCN-p) than cultivated sorghum accessions. Genome-wide association study identified a QTL most tightly associated with HCN-p and the linked SNPs were located in the 3' UTR of Sobic.001G012300 which encodes CYP79A1, the enzyme that catalyzes the first step of dhurrin biosynthesis. As in other grasses such as maize and rice, we also found that copia/gypsy long terminal repeat (LTR) retrotransposons were more abundant in cultivated than in wild sorghums, implying that crop domestication in the grasses was accompanied by increased copia/gypsy LTR retrotransposon insertions in the genomes.

An efficient transformation method for tannin-containing sorghum

Background

Tannins are the main bottlenecks restricting the transformation efficiency of plants. Hongyingzi is a special tannin-containing sorghum cultivar used in brewing.

Methods

In this study, a highly efficient microprojectile transformation system for tannin-containing sorghum was successfully exploited using immature embryos (IEs) of Hongyingzi as explants.

Results

Hongyingzi presented two types of calli. Type II calli were found to be the most suitable and effective explants for transformation. After optimization of the geneticin (G418) concentration and tissue culture medium, an average transformation frequency of 27% was achieved. Molecular analyzis showed that all transgenic plants were positive and showed transgenes expression. The inheritance analyzis confirmed that the transgenes could be inherited into the next generation. Thus, we successfully established an efficient transformation system for tannin-containing sorghum and demonstrated the possibility of breaking the restriction imposed by tannins in plants.

Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L

Foxtail millet is commonly used as a food and forage grass. ERECTA (ER) is a receptor-like kinase that can improve plant biomass and stress resistance. The sorghum SbER10_X1 gene was used as a probe to identify ER family genes on the Setaria italica genomes (SiERs), and determine the characteristics of the SiERs family. Herein, the structural features, expression patterns, and thermotolerance of SiERs function were identified by bioinformatics analysis, real-time PCR and transgenesis estimation. Results showed that SiERs had four members: two members were located on chromosome 1 with a total of six copies (SiER1_X1, SiER1_X2, SiER1_X3, SiER1_X4, SiER1_X5, and SiER1_X6), and two were on chromosome 4, namely, SiER4 (SiER4_X1 and SiER4_X2) and SiERL1. Among them, SiER1_X4 and SiER4_X1 were expressed highest in above-ground organs of foxtail millet, and actively responded to treatments with abscisic acid, brassinolide, gibberellin, and indole acetic acid. After overexpression of SiER1_X4 and SiER4_X1 in Arabidopsis, the plant height and biomass of the transgenic Arabidopsis significantly increased. Following high-temperature treatment, transgenic seedlings survived better compared to wild type. Transgenic lines showed higher SOD and POD activities, and expression level of AtHSF1 and AtBl1 genes significantly increased. These results indicated that SiER1_X4 and SiER4_X1 played important regulatory roles in plant growth and thermotolerance. The two genes provide potential targets for conventional breeding or biotechnological intervention to improve the biomass of forage grass and thermotolerance of field crops.

[Study of abnormal lipid metabolism analysis and significance of fatty acid binding protein expression in patients with hepatocellular carcinoma]

Objective: Hepatocellular carcinoma (HCC) is the fourth most dominant cancer in the world and the second leading cause of cancer-related deaths in the China. With the increase in the incidence of metabolic syndrome (MS) in the population, the correlation between MS and HCC has gradually been recognized. MS manifests as non-alcoholic fatty liver disease (shortly known as NAFLD) in the liver. A large number of research results has shown that the development of fatty liver is closely related to the occurrence of HCC, in which lipid metabolism plays a key regulatory role, and lipid metabolism is regulated by fatty acid binding protein (FABP). This study signifies the lipid metabolism analysis and the key FABP expression conditions in HCC. Methods: Data of patients who were first diagnosed with primary HCC between January 2016 to July 2019 were collected, and were divided into two groups according to the etiology, namely the viral and non-viral hepatitis-related HCC group. The relationship between MS-related factors and HCC was analyzed by t-test and chi square test. The expressions of FABP1, FABP4 and FABP5 were detected in cancer and adjacent tissues by immunohistochemistry, and the expressions of FABP1, FABP4 and FABP5 in HCC with fatty liver were detected by immunofluorescence. Finally, the expressional characteristics of the above-mentioned FABPs in HCC patients were analyzed with different clinicopathological features. Results: There were statistically significant differences in the rate of abnormal lipid metabolism and the number of abnormalities in MS-related factors between the viral and non-viral hepatitis-related HCC group. FABP1, FABP4, and FABP5 expression in HCC tissues were lower than the corresponding adjacent tumor tissues. Compared with simple HCC, FABP1, FABP4, FABP5 expression were increased in HCC tissues with steatosis, and the expression of FABP was closely related to the clinical characteristics of patients. Conclusion: Abnormal lipid metabolism is closely related to non-viral hepatitis-related HCC. The expression of lipid metabolism regulatory proteins FABP1, FABP4, and FABP5 are down-regulated in HCC tissues, but up-regulated in HCC with fatty liver, suggesting that the relationship between MS, especially dyslipidemia, and HCC should be paid attention to in clinical practice for early intervention. FABP1, FABP4, FABP5 may regulate HCC occurrence and development.

P–165 Using Artificial Intelligence to Classify Embryo Shape: An International Perspective

Study question

Is a pre-trained machine learning algorithm able to accurately detect cellular arrangement in 4-cell embryos from a different continent?

Summary answer

Artificial Intelligence (AI) analysis of 4-cell embryo classification is transferable across clinics globally with 79% accuracy.

What is known already

Previous studies observing four-cell human embryo configurations have demonstrated that non-tetrahedral embryos (embryos in which cells make contact with fewer than 3 other cells) are associated with compromised blastulation and implantation potential. Previous research by this study group has indicated the efficacy of AI models in classification of tetrahedral and non-tetrahedral embryos with 87% accuracy, with a database comprising 2 clinics both from the same country (Brazil). This study aims to evaluate the transferability and robustness of this model on blind test data from a different country (France).

Study design, size, duration

The study was a retrospective cohort analysis in which 909 4-cell embryo images (“tetrahedral”, n = 749; “non-tetrahedral”, n = 160) were collected from 3 clinics (2 Brazilian, 1 French). All embryos were captured at the central focal plane using Embryoscope™ time-lapse incubators. The training data consisted solely of embryo images captured in Brazil (586 tetrahedral; 87 non-tetrahedral) and the test data consisted exclusively of embryo images captured in France (163 tetrahedral; 72 non-tetrahedral).

Participants/materials, setting, methods

The embryo images were labelled as either “tetrahedral” or “non-tetrahedral” at their respective clinics. Annotations were then validated by three operators. A ResNet–50 neural network model pretrained on ImageNet was fine-tuned on the training dataset to predict the correct annotation for each image. We used the cross entropy loss function and the RMSprop optimiser (lr = 1e–5). Simple data augmentations (flips and rotations) were used during the training process to help counteract class imbalances.

Main results and the role of chance

Our model was capable of classifying embryos in the blind French test set with 79% accuracy when trained with the Brazilian data. The model had sensitivity of 91% and 51% for tetrahedral and non-tetrahedral embryos respectively; precision was 81% and 73%; F1 score was 86% and 60%; and AUC was 0.61 and 0.64. This represents a 10% decrease in accuracy compared to when the model both trained and tested on different data from the same clinics.

Limitations, reasons for caution

Although strict inclusion and exclusion criteria were used, inter-operator variability may affect the pre-processing stage of the algorithm. Moreover, as only one focal plane was used, ambiguous cases were interpoloated and further annotated. Analysing embryos at multiple focal planes may prove crucial in improving the accuracy of the model.

Wider implications of the findings: Though the use of machine learning models in the analysis of embryo imagery has grown in recent years, there has been concern over their robustness and transferability. While previous results have demonstrated the utility of locally-trained models, our results highlight the potential for models to be implemented across different clinics.

Trial registration number

Not applicable

Utility of Contrast-Enhanced T2 FLAIR for Imaging Brain Metastases Using a Half-dose High-Relaxivity Contrast Agent

BACKGROUND AND PURPOSE

Efficient detection of metastases is important for patient' treatment. This prospective study was to explore the clinical value of contrast-enhanced T2 FLAIR in imaging brain metastases using half-dose gadobenate dimeglumine.

MATERIALS AND METHODS

In vitro signal intensity of various gadolinium concentrations was explored by spin-echo T1-weighted imaging and T2 FLAIR. Then, 46 patients with lung cancer underwent nonenhanced T2 FLAIR before administration of half-dose gadobenate dimeglumine and 3 consecutive contrast-enhanced T2 FLAIR sequences followed by 1 spin-echo T1WI after administration of half-dose gadobenate dimeglumine. After an additional dose of 0.05 mmol/kg, 3D brain volume imaging was performed. All brain metastases were classified as follows: solid-enhancing, ≥ 5 mm (group A); ring-enhancing, ≥ 5 mm (group B); and lesion diameter of <5 mm (group C). The contrast ratio of the lesions on 3 consecutive phases of contrast-enhanced T2 FLAIR was measured, and the percentage increase of contrast-enhanced T2 FLAIR among the 3 groups was compared.

RESULTS

In vitro, the maximal signal intensity was achieved in T2 FLAIR at one-eighth to one-half of the contrast concentration needed for maximal signal intensity in T1WI. In vivo, the mean contrast ratio values of metastases on contrast-enhanced T2 FLAIR for the 3 consecutive phases ranged from 63.64% to 83.05%. The percentage increase (PI) values of contrast-enhanced T2 FLAIR were as follows: PI_A < PI_B (P = .001) and PI_A < PI_C (P < .001). The degree of enhancement of brain metastases on contrast-enhanced T2 FLAIR was lower than on 3D brain volume imaging (P < .001) in group A, and higher than on 3D brain volume imaging (P < .001) in group C.

CONCLUSIONS

Small or ring-enhancing metastases can be better visualized on delayed contrast-enhanced T2 FLAIR using a half-dose high-relaxivity contrast agent.

An efficient sorghum protoplast assay for transient gene expression and gene editing by CRISPR/Cas9

Protoplasts are commonly used in genetic and breeding research. In this study, the isolation of sorghum protoplasts was optimized and applied to transient gene expression and editing by CRISPR/Cas9. The protoplast was most viable in 0.5 M mannitol, which was the highest of three concentrations after 48- and 72-hours treatments. Using this method we can derive an average of 1.6×10⁶ cells which vary from 5 to 22 nm in size. The average transfection of the protoplasts was 68.5% using the PEG-mediated method. The subcellular assays located Sobic.002G279100-GFP and GFP proteins in the cell compartments as predicted bioinformatically. Two CRISPR/Cas9 plasmids were transfected into sorghum protoplasts to screen for an appropriate sgRNA for gene editing. One plasmid can correctly edit the target region using a single protoplast cell as template DNA. Our results indicated that the protoplast assays as optimized are suitable for transient gene expression and sgRNA screening in CRISPR/Cas9 gene editing procedures.

Transcriptome analysis reveals candidate genes related to phosphorus starvation tolerance in sorghum

BACKGROUND

Phosphorus (P) deficiency in soil is a worldwide issue and a major constraint on the production of sorghum, which is an important staple food, forage and energy crop. The depletion of P reserves and the increasing price of P fertilizer make fertilizer application impractical, especially in developing countries. Therefore, identifying sorghum accessions with low-P tolerance and understanding the underlying molecular basis for this tolerance will facilitate the breeding of P-efficient plants, thereby resolving the P crisis in sorghum farming. However, knowledge in these areas is very limited.

RESULTS

The 29 sorghum accessions used in this study demonstrated great variability in their tolerance to low-P stress. The internal P content in the shoot was correlated with P tolerance. A low-P-tolerant accession and a low-P-sensitive accession were chosen for RNA-seq analysis to identify potential underlying molecular mechanisms. A total of 2089 candidate genes related to P starvation tolerance were revealed and found to be enriched in 11 pathways. Gene Ontology (GO) enrichment analyses showed that the candidate genes were associated with oxidoreductase activity. In addition, further study showed that malate affected the length of the primary root and the number of tips in sorghum suffering from low-P stress.

CONCLUSIONS

Our results show that acquisition of P from soil contributes to low-P tolerance in different sorghum accessions; however, the underlying molecular mechanism is complicated. Plant hormone (including auxin, ethylene, jasmonic acid, salicylic acid and abscisic acid) signal transduction related genes and many transcriptional factors were found to be involved in low-P tolerance in sorghum. The identified accessions will be useful for breeding new sorghum varieties with enhanced P starvation tolerance.

Association of serum uric acid change with mortality, renal function and diuretic dose administered in treatment of acute heart failure

BACKGROUND AND AIMS

Hyperuricemia is reportedly associated with poor outcome in acute heart failure (AHF). The association between changes in Uric acid (UA) levels with renal function change, diuretic doses, and mortality in patients with AHF were studied.

METHODS AND RESULTS

Consecutive patients hospitalized with AHF were reviewed (n = 535). UA levels were measured at admission and either at discharge or on approximately the seventh day of admission. Patients with an UA change in the top tertile were defined as having an increase (UA-increase) and were compared to those outside the top tertile (non-UA-increase). The endpoint was all-cause mortality, with a mean follow-up duration of 22.2 months. Patients in the UA-increase group presented with greater creatine increase (P < 0.001), and were administered a higher average daily dose of loop diuretic (P = 0.016) compared with the non-UA-increase group. In-hospital UA-increase was associated with higher risk of mortality even after adjusting for confounding variables including creatine change and diuretic dosage [harzard ratio (HR) 1.53, 95% confidence interval (CI) 1.02-2.30, P = 0.042]. In patients with hyperuricemia on admission, UA-increase was associated with increased mortality (adjusted HR 2.21, 95% CI 1.38-3.52, P = 0.001). Whereas, in those without admission hyperuricemia, UA-increase had no significant association with mortality.

CONCLUSIONS

An increase in UA during in-hospital treatment is associated with an increase in creatine levels and daily diuretic dose. Mortality associated with increased UA is restricted to patients who already have hyperuricemia at admission. A combination of UA levels at admission and UA changes on serial assessment during hospitalization may be additional value in the risk stratification of AHF patients.

[Research progress of microRNAs in regulation of lipid metabolism-related proteins for influencing the pathogenesis of hepatocellular carcinoma]

The incidence of metabolic syndrome gradually multiplied with the change of dietary structure of high fat- high sugar in the population, bringing it as independent risk factors for tumors. Liver is an important organ of lipid metabolism. The main manifestations of metabolic syndrome are obesity and abnormal lipid metabolism, which are closely related to hepatocellular carcinoma occurrence. MicroRNA (miRNA) is an endogenous non-coding RNA that participates in the post-transcriptional regulation of target genes by binding to the 3'-UTR of mRNA. Research studies have found that abnormal miRNA expression can influence the pathogenesis of hepatocellular carcinoma via regulating lipid metabolism-related proteins in the liver. This article reviews and discusses the characteristics and pathogenesis of lipid metabolism disorder in hepatocellular carcinoma, and the mechanism by which miRNA regulates the occurrence and development of hepatocellular carcinoma through lipid metabolism-related proteins. Furthermore, it also provides a reliable theoretical foundation for the study of the pathogenesis of hepatocellular carcinoma.

[Mechanism of lung injury of rats induced by inhalation of white smoke from burning smoke pot]

Objective: To explore mechanism of lung injury of rats induced by inhalation of white smoke from burning smoke pot. Methods: Forty-eight Sprague Dawley rats were divided into control group (n=12) and injury group (n=36) according to the random number table. Rats in injury group were placed in smoke-induced injury experimental equipment fulled with white smoke from burning smoke pot for 5 minutes to make lung injury, and rats in control group were placed in smoke-induced injury experimental equipment fulled with air for 5 minutes to make sham injury. Six rats in injury group at post injury hour (PIH) 6, 24, and 72 and six rats in control group at PIH 72 were collected to observe pathological changes of lung tissue and pathological score of rats in the two groups by hematoxylin-eosin staining, to detect expression of nuclear factor-κB (NF-κB) p65 mRNA in lung tissue of rats by reverse transcriptional polymerase chain reaction, and to detect content of tumor necrosis factor α (TNF-α), interleukin 1β (IL-1β), and IL-6 in lung tissue of rats by enzyme-linked immunosorbent assay. Data were processed with one-way analysis of variance and t test. Results: At PIH 72, lung tissue structure of rats in control group was clear and complete, with no inflammatory cell infiltration. At PIH 6, there was edema, hemorrhage, and inflammatory cell infiltration in lung tissue of rats in injury group. At PIH 24, edema, hemorrhage, and inflammatory cell infiltration in lung tissue of rats in injury group aggravated. At PIH 72, area of edema in lung tissue of rats in injury group was enlarged, with obvious hemorrhage and inflammatory cell infiltration. At PIH 6, 24, and 72, pathological score of lung tissue of rats in injury group was (3.43±0.86), (5.39±0.93), and (9.99±0.84) points, respectively, obviously higher than that of rats in control group at PIH 72 [(2.11±0.20) points, t=3.659, 8.450, 22.355, P<0.05]. As time post injury prolonged, pathological scores of lung tissue of rats in injury group were significantly increased (F=121.244, P<0.01). At PIH 6, 24, and 72, expression of NF-κB p65 mRNA in lung tissue of rats in injury group was 15.5±4.3, 25.9±1.8, 30.9±3.5 respectively, significantly higher than that of rats in control group at PIH 72 (7.8±0.8, t=4.315, 20.445, 14.408, P<0.01). As time post injury prolonged, expression of NF-κB p65 mRNA in lung tissue of rats in injury group gradually increased (F=32.691, P<0.01). At PIH 6, 24, and 72, content of TNF-α, IL-1β, and IL-6 in lung tissue of rats in injury group was significantly higher than that of rats in control group at PIH 72, respectively (t=7.650, 8.968, 6.827, 6.726, 8.978, 3.460, 5.420, 13.289, 16.438, P<0.01). At PIH 24, content of TNF-α and IL-1β in lung tissue of rats in injury group was higher than that of rats in the same group at PIH 6 and 72, respectively (t=3.409, -2.549, 4.047, -4.100, P<0.05). At PIH 24 and 72, content of IL-6 in lung tissue of rats in injury group was respectively higher than that of rats in the same group at PIH 6 (t=8.273, 9.711, P<0.05). Conclusions: After inhaling white smoke from burning smoke pot, rats are inflicted with lung injury by increasing expression of NF-κB p65 mRNA and content of TNF-α, IL-1β, and IL-6, and induce pathological changes of edema, hemorrhage, and inflammatory cell infiltration of lung tissue.

Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum (Sorghum bicolor L.)

Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and phenotypic data were applied to multi-locus genome-wide association studies (GWAS) with the mrMLM software. A total of 42 SNPs were identified to be associated with the five forage quality-related traits. Moreover, three and two quantitative trait nucleotides (QTNs) were simultaneously detected among them by three and two multi-locus methods, respectively. One QTN on chromosome 5 was found to be associated simultaneously with CP, NDF, and ADF. Furthermore, 3, 2, 2, 5, and 2 candidate genes were identified to be responsible for CP, NDF, ADF, HC, and CL contents, respectively. These results provided insightful information of the forage quality-related traits and would facilitate the genetic improvement of sorghum forage quality in the future.

[A retrospective analysis of clinical characteristics and outcomes of heart failure patients with different left ventricular ejection fractions]

Objective: To compare the clinical characteristics, and outcomes of patients with heart failure with different left ventricular ejection fractions (LVEF). Methods: A total of 1 182 hospitalized patients with heart failure (HF) were enrolled and retrospectively studied in the present study. The patients were stratified by LVEF as reduced (HFrEF, LVEF<40%, n=313), mid-range (HFmrEF, 40% ≤LVEF <50%, n=287) and preserved (HFpEF, LVEF≥50%, n=582) ejection fraction groups. Among the 1 182 cases, 941 of them (81.3%, 84.9%, and 84.0% inHFrEF, HFmrEF and HFpEF groups, respectively) were followed up for an median duration of 27.3 months. Results: (1) Among the study patients, 26.5% were in HFrEF, 24.3% in HFmrEF, and 49.2% in HFpEF groups. (2) Ischemic heart disease with HFmrEF was more frequent than that in patients with HFrEF. The average age, percentage of female subjects, systolic blood pressure, uric acid, N terminal B-type natriuretic peptide precursor (NT-proBNP), hemoglobin, and the incidence of hypertensive heart disease, anemia, atrial fibrillation in patients with HFmrEF were higher than those in patients with HFrEF, but lower than those in patients with HFpEF (all P<0.01). (3) The all-cause cumulative mortality was 10.8% at 1 year, 20.6% at 2 years and 35.9% at 5 years. No difference was observed in the all-cause cumulative mortality at 1 year, 2 years, 5 years among the three groups (all P>0.05). Conclusions: The HFmrEF patients, as a new and distinct group, were with many intermediate characteristics compared with HFrEF and HFpEF subjects. However, the all-cause mortality was not significantly different among HF patients with different LVEF.

Piccolo mediates EGFR signaling and acts as a prognostic biomarker in esophageal squamous cell carcinoma

The presynaptic cytomatrix protein Piccolo, encoded by PCLO, is frequently mutated and amplified in esophageal squamous cell carcinoma (ESCC), but its exact roles in ESCC remain unclear. Here we report that Piccolo expression correlates significantly with clinical stage, patient survival and tumor embolus. Functional studies demonstrate that PCLO knockdown remarkably attenuates ESCC malignancy in vitro and in vivo, and ectopic EGFR expression partially compensates for Piccolo loss. PCLO knockdown promotes ubiquitination and degradation of EGFR, which is associated with the negative regulatory effect of Piccolo on E3 ligase Siah1. An anti-Piccolo monoclonal antibody inhibited tumor proliferation in a mouse model of ESCC. These results demonstrate that Piccolo contributes to tumor aggressiveness in ESCC, likely by stabilizing EGFR and promoting EGFR-dependent signaling. Our results further suggest that Piccolo may represent a novel prognostic biomarker and therapeutic target for patients with ESCC.

Cloning and expression analysis of cinnamoyl-CoA reductase (CCR) genes in sorghum

Cinnamoyl-CoA reductase (CCR) is the first enzyme in the monolignol-specific branch of the lignin biosynthetic pathway. In this research, three sorghum CCR genes including SbCCR1, SbCCR2-1 and SbCCR2-2 were cloned and characterized. Analyses of the structure and phylogeny of the three CCR genes showed evolutionary conservation of the functional domains and divergence of function. Transient expression assays in Nicotiana benthamiana leaves demonstrated that the three CCR proteins were localized in the cytoplasm. The expression analysis showed that the three CCR genes were induced by drought. But in 48 h, the expression levels of SbCCR1 and SbCCR2-2 did not differ between CK and the drought treatment; while the expression level of SbCCR2-1 in the drought treatment was higher than in CK. The expression of the SbCCR1 and SbCCR2-1 genes was not induced by sorghum aphid [Melanaphis sacchari (Zehntner)] attack, but SbCCR2-2 was significantly induced by sorghum aphid attack. It is suggested that SbCCR2-2 is involved in the process of pest defense. Absolute quantitative real-time PCR revealed that the three CCR genes were mainly expressed in lignin deposition organs. The gene copy number of SbCCR1 was significantly higher than those of SbCCR2-1 and SbCCR2-2 in the tested tissues, especially in stem. The results provide new insight into the functions of the three CCR genes in sorghum.

Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense

Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species.

Upregulation of long noncoding RNA ZEB1-AS1 promotes tumor metastasis and predicts poor prognosis in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. Despite progress in diagnostics and treatment of HCC, its prognosis remains poor. Emerging studies showed that long noncoding RNAs (lncRNAs) have crucial regulatory roles in cancer biology. In the current study, differentially expressed lncRNAs between HCC and paired non-tumor tissues were identified using microarrays. The effects of a specific differentially expressed lncRNA (termed ZEB1-AS1) on tumor progression were investigated in vitro and in vivo. We found that ZEB1-AS1 is frequently upregulated in HCC samples, especially in metastatic tumor tissues. DNA methylation analysis shows a tumor-specific ZEB1-AS1 promoter hypomethylation. Aberrant methylation is tightly correlated with overexpression of ZEB1-AS1 in HCC. Patients with ZEB1-AS1 hypomethylation or with high ZEB1-AS1 expression have poor recurrence-free survival. Functionally, ZEB1-AS1 promotes tumor growth and metastasis, acts as an oncogene in HCC. The ZEB1-AS1 gene is located in physical contiguity with ZEB1 and positively regulates the ZEB1 expression. ZEB1 inhibition partially abrogates ZEB1-AS1-induced epithelial to mesenchymal transition (EMT) and cancer metastasis. Our results provide novel insights into the function of lncRNA-driven hepatocarcinogenesis, highlight the important role of ZEB1-AS1 and ZEB1 in HCC progression, and indicate that ZEB1-AS1 may be served as a valuable prognostic biomarker for HCC.

Platelet-activating factor receptor-mediated PI3K/AKT activation contributes to the malignant development of esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies worldwide and occurs at a relatively high frequency in China, yet the mechanisms underlying its devastating outcome remain unclear. Here we report that platelet-activating factor receptor (PAFR), a type of G-protein-coupled receptor, was upregulated in ESCC tumors and cell lines, compared with controls; PAFR levels were positively correlated with ESCC clinical stages and survival time. Overexpression of PAFR promoted the malignant development of ESCC in vitro and in vivo, whereas depletion of PAFR suppressed these effects. Interestingly, PAFR was observed to activate PI3K/AKT (phosphatidylinositol 3-kinase/AKT) through the upregulation of FAK kinase activity. AKT-triggered nuclear factor-κB transcriptionally activated PAFR expression. This mutual positive regulation between PAFR and AKT was required for the aggressiveness of ESCC cells both in vitro and in vivo. Furthermore, treating mice bearing ESCC tumors with cholesterol-conjugated PAFR small interfering RNA effectively inhibited tumor progression and the expression of AKT-mediated oncogenic proteins. Taken together, we made the first demonstration that dysregulation of PAFR and the positive regulatory loop between PAFR and pAKT contribute to malignant progression of ESCC.

A case-control study indicates that the TRIB1 gene is associated with pancreatic cancer

Pancreatic cancer is a malignant neoplasm originating from transformed cells arising in tissues that form the pancreas. To investigate whether the tribbles homolog 1 (Drosophila) gene (TRIB1) is associated with pancreatic cancer in the Chinese Han population, we conducted this case-control study and genotyped 3 single nucleotide polymorphisms (rs2980879, rs2980874, and rs2235108) of the TRIB1 gene in 182 patients and 359 normal controls of Chinese Han origin and analyzed their association. The results showed that the rs2980879 polymorphism was associated with pancreatic cancer [allele: P = 0.023434, genotype: P = 0.03005; odds ratio (OR) and 95% confidence interval (CI) = 0.727788 (0.552664-0.958404)], whereas the rs2980874 polymorphism had no association with pancreatic cancer [allele: P = 0.749885, genotype: P = 0.699533; OR and 95%CI = 1.041981 (0.809196-1.341734)], and the rs2235108 polymorphism was not associated with the disease [allele: P = 0.629475, genotype: P = 0.547534, OR and 95%CI = 1.128290 (0.690829-1.842770)]. Haplotype analyses and linkage disequilibrium tests were also conducted, and the results showed that these 3 loci are not in the same block. In conclusion, our study indicated that the TRIB1 gene is associated with pancreatic cancer. More studies with larger samples are needed in order to support this finding.