Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites.

BACKGROUND: Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions. RESULTS: An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a "phenotype" to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols. CONCLUSIONS: We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding.

BSA-Seq and Transcriptomic Analysis Provide Candidate Genes Associated with Inflorescence Architecture and Kernel Orientation by Phytohormone Homeostasis in Maize.

The developmental plasticity of the maize inflorescence depends on meristems, which directly affect reproductive potential and yield. However, the molecular roles of upper floral meristem (UFM) and lower floral meristem (LFM) in inflorescence and kernel development have not been fully elucidated. In this study, we characterized the reversed kernel1 (rk1) novel mutant, which contains kernels with giant embryos but shows normal vegetative growth like the wild type (WT). Total RNA was extracted from the inflorescence at three stages for transcriptomic analysis. A total of 250.16-Gb clean reads were generated, and 26,248 unigenes were assembled and annotated. Gene ontology analyses of differentially expressed genes (DEGs) detected in the sexual organ formation stage revealed that cell differentiation, organ development, phytohormonal responses and carbohydrate metabolism were enriched. The DEGs associated with the regulation of phytohormone levels and signaling were mainly expressed, including auxin (IAA), jasmonic acid (JA), gibberellins (GA), and abscisic acid (ABA). The transcriptome, hormone evaluation and immunohistochemistry observation revealed that phytohormone homeostasis were affected in rk1. BSA-Seq and transcriptomic analysis also provide candidate genes to regulate UFM and LFM development. These results provide novel insights for understanding the regulatory mechanism of UFM and LFM development in maize and other plants.

Genome-wide association analysis reveals a novel QTL CsPC1 for pericarp color in cucumber.

BACKGROUND: Cucumber is an important melon crop in the world, with different pericarp colors. However, the candidate genes and the underlying genetic mechanism for such an important trait in cucumber are unknown. In this study, a locus controlling pericarp color was found on chromosome 3 of cucumber genome. RESULTS: In this study, the light green inbred line G35 and the dark green inbred line Q51 were crossed to produce one F2 population. Consequently, we identified a major locus CsPC1 (Pericarp color 1). Next, we mapped the CsPC1 locus to a 94-kb region chromosome 3 which contains 15 genes. Among these genes, Csa3G912920, which encodes a GATA transcription factor, was expressed at a higher level in the pericarp of the NIL-1334 line (with light-green pericarp) than in that of the NIL-1325 line (with dark-green pericarp). This study provides a new allele for the improvement of cucumber pericarp color. CONCLUSION: A major QTL that controls pericarp color in cucumber, CsPC1, was identified in a 94-kb region that harbors the strong candidate gene CsGATA1.

A high-continuity and annotated tomato reference genome.

BACKGROUND: Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. RESULTS: Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. CONCLUSION: Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.

Report: Bacterial susceptibility and resistance analysis of traumatic osteomyelitis.

With the rapid development of industry, agriculture and transportation, the high energy trauma happened accordingly, thus greatly increased the incidence of traumatic osteomyelitis. The clinical traumatic osteomyelitis was mainly the local bone tissue inflammation caused by bacteria infection as trauma or iatrogenic causes. The delaying recovery could cause bone defection or bone nonunion. The purpose of this paper was to contribute new reference for the clinical prevention and treatment through tremendous of disease-causing bacteria susceptibility and resistance analysis of osteomyelitis.

miRNA-646 suppresses osteosarcoma cell metastasis by downregulating fibroblast growth factor 2 (FGF2).

MicroRNAs are short regulatory RNAs that play crucial roles in cancer development and progression. MicroRNA-646 (miR-646) is downregulated in many human cancers, and increasing evidence indicates that it functions as a tumor suppressor. However, the role of miR-646 in osteosarcoma remains unclear. Expression levels of miR-646 in osteosarcoma cell lines and patient tissues were evaluated by quantitative real-time PCR (qRT-PCR), and the clinicopathological significance of the resultant data was later analyzed. Next, we investigated the role of miR-646 to determine its potential roles on osteosarcoma cell proliferation, migration, and invasion in vitro. A luciferase reporter assay was conducted to confirm the target gene of miR-646, and the results were validated in the osteosarcoma cell line. In this study, we found that miR-646 was downregulated in osteosarcoma cell lines and osteosarcoma tissues compared with normal osteoblast cell line NHOst and paired adjacent nontumor tissue. We found that a lower expression of miR-646 was associated with metastasis. In osteosarcoma cells, overexpression of miR-646 inhibited cell proliferation, migration, and invasion. In contrast, downregulation of miR-646 expression promoted osteosarcoma cell proliferation, migration, and invasion. Next, we identified that the FGF2 gene is a novel direct target of miR-646 in osteosarcoma cells. Moreover, enforced expression of FGF2 partially reversed the inhibition of cell proliferation, migration, and invasion that was caused by miR-646. Our study demonstrated that miR-646 might be a tumor suppressor in osteosarcoma via the regulation of FGF2, which provided a potential prognostic biomarker and therapeutic target.

miR-155 promotes the growth of osteosarcoma in a HBP1-dependent mechanism.

Osteosarcoma (OS) is a type of malignant tumor arising from soft-tissues of bone and displays poor prognosis in most cases. However, the molecular mechanism by which OS initiates and progresses is still not completely elucidated. miR-155 has been shown to be overexpressed in OS specimen and cell lines. Our study is intended to explore the role of miR-155 in OS etiology. The data confirmed that miR-155 abundance is higher in OS samples than non-cancerous bone tissue. Inhibition of miR-155 suppressed the proliferation of OS cells and cell cycle progression in vitro, and the growth of OS xenografts in vivo. Wnt pathway was suppressed in OS cells by miR-155 inhibitors. HMG-box transcription factor 1 (HBP1), a strong Wnt pathway suppressor, was found to be a target of miR-155. Restoration of HBP1 abolished the effect of miR-155 on OS cells. Finally, miR-155 levels in OS tissues and serum are both inversely associated with the survival of OS patients. Collectively, miR-155 was identified to be among the list of OS-related oncogenic miRNAs, and HBP1-mediated Wnt signaling is involved with the role of miR-155 in OS progression.

Effects of psoralen on chondrocyte degeneration in lumbar intervertebral disc of rats.

Discuss the internal mechanism of delaying degeneration of lumber intervertebral disc. The cartilage of lumbar intervertebral disc of SD rats was selected in vitro, then cultured by tissue explant method, and identified by HE staining, toluidine blue staining and immunofluorescence. The optimal concentration of psoralen was screened by cell proliferation assay and RT-PCR method. The cells in third generation with good growth situation is selected and placed in 6-well plate at concentration of 1×10(5)/well and its expression was tested. Compared to concentration of 0, the mRNA expression of Col2al (Collagen Ⅱ) secreted by was up regulated chondrocyte of lumbar intervertebral disc at the concentration of 12.5 and 25µM (P<0.0 or P<0.01). The aggrecan mRNA of psoralen group was higher than blank control group (P<0.01); compared with IL-1ß induced group, the mRNA expression of Col2al was significantly increased but the mRNA expression of ADAMTS-5 was significantly decreased in psoralen group (P<0.01). These findings suggest that, psoralen can remit the degeneration of lumbar intervertebral disc induced by IL-1ß to some extent, and affect the related factors of IL-1ß signaling pathway.

Clinical curative effect observation of therapy of Chinese drug iontophoresis in treatment of degenerative osteoarthropathy.

Degenerative osteoarthropathy is a kind of arthrosis induced by various factors, with main pathological feature of articular cartilage and syndesmophyte formation. In recent years, its morbidity increases year by year and tend to appear more among young people. Its curative effect has yet to be improved. This paper mainly discussed the clinical curative effect of therapy of Chinese drug iontophoresis in degenerative osteoarthropathy. A total of 296 cases of degenerative osteoarthropathy was randomly divided into two groups (with no consideration on gender): Chinese drug iontophoresis group: joint was treated by therapy of Chinese drug iontophoresis and MTZ-F experiment; frequency electrotherapy group: joint was only treated by medium frequency electrotherapy. Two groups were both treated for 30 min for one time, 1 time for a day, total for 4 weeks. Result of the study found that, total effective rate of medium frequency electrotherapy group was 74.3%, Chinese medicine iontophoresis group was 93.2%; curative effect of Chinese medicine iontophoresis group was superior to electrotherapy group. It indicates that, Chinese medicine iontophoresis has good clinical effect in the treatment of osteoarthropathy and deserves to be popularized and applied.

The association of XPG and MMS19L polymorphisms response to chemotherapy in osteosarcoma.

OBJECTIVE: To assess the role of XPG, XPC, CCNH and MMS19L polymorphisms response to chemotherapy in osteosarcoma, and the clinical outcome of osteosarcoma. METHODS: One hundred and sixty eight osteosarcoma patients who were histologically confirmed were enrolled in our study between January 2007 and March 2009. Genotyping of XPG, XPC, CCNH and MMS19L was performed in a 384-well plate format on the MassARRAY® platform. RESULTS: Individuals with rs2296147 TT genotype showed a better response as compared with CC genotype, with the OR (95% CI) of 3.89(1.49-10.95). Those carrying rs29001322 TT genotype presented better response to chemotherapy, and the OR (95% CI) was as high as 12.25(2.63-121.84). Patients carrying TT genotype of XPG rs2296147 and MMS19L rs29001322 showed a significantly longer overall survival than CC genotype, they had 0.37 and 0.31-fold risk of death when compared with wide-type of this gene. CONCLUSIONS: XPG rs2296147 and MMS19L rs29001322 are correlated with response to chemotherapy and prognosis of osteosarcoma. Our findings would provide important evidence for prognostic and therapeutic implications in osteosarcoma.

[Correlation of the expression of NF-κB p65 and hepatic fibrosis in hepatitis patients].

OBJECTIVE: To explore the relationship between the expression of NF-κB p65 and hepatic fibrosis in chronic hepatitis B (CHB) patients. METHODS: Sixty CHB patients with hepatic fibrosis underwent liver biopsy to determine the stages of liver fibrosis (S0-S4). The distribution and expression of collagens I, III and NF-κB p65 in different stages of fibrosis in liver tissue were observed by immunohistochemistry and the results analyzed statistically. RESULTS: The expression of NF-κB p65 was positively correlated with the stage of hepatic fibrosis. That was S4 > S3 > S2 > S1 (S0) (P < 0.01). And it was also positively correlated with the expression of collagens I and III (P < 0.01). CONCLUSION: The elevated expression of NF-κB p65 is closely associated with the occurrence and development of hepatic fibrosis. Its mechanism is probably related with the increased secretion of collagens I and III after the activation of hepatic stellate cell.

The High Immunity Induced by the Virus-Like Particles of Foot-and-Mouth Disease Virus Serotype O.

Foot-and-mouth disease (FMD), caused by FMD virus (FMDV), is a highly contagious and economically devastating viral disease of cloven-hoofed animals worldwide. In this study, the coexpression of small ubiquitin-like modifier (SUMO)-fused capsid proteins of FMDV serotype O by single plasmid in Escherichia coli was achieved with an optimal tandem permutation (VP0-VP3-VP1), showing a protein yield close to 1:1:1. After SUMO removal at a low level of protease activity (5 units), the assembled FMDV virus-like particles (VLPs) could expose multiple epitopes and have a size similar to the naive FMDV. Immunization of pigs with the FMDV VLPs could induce FMDV-specific humoral and cellular immune responses effectively, in a dose-dependent manner. These data suggested that the stable FMDV VLPs with multiple epitope exposure were effective for the induction of an immune response in pigs, which laid a foundation for the further development of the FMDV subunit vaccine.

Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers.

Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year. The association panel was sorted into two subpopulations. Linkage disequilibrium ranged from 3.0 to 47.2 Mb across 12 chromosomes. A set of 102 markers significantly (p < 1.19-1.30 × 10-4) associated with SSC, FW, fruit shape, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The associations were compared with the known gene/QTLs for the same traits. Genetic analysis using F2 populations detected 14 and 4 markers significantly (p < 0.05) associated with SSC and FW, respectively. Some loci were commonly detected by both association and linkage analysis. Particularly, one novel locus for FW on chromosome 4 detected by association analysis was also identified in F2 populations. The results demonstrated that association mapping using limited number of InDel markers and a relatively small population could not only complement and enhance previous QTL information, but also identify novel loci for marker-assisted selection of fruit traits in tomato.

Wogonin inhibits osteoclast differentiation by inhibiting NFATc1 translocation into the nucleus.

The aim of the present study was to identify a natural product with the ability to inhibit nuclear factor of activated T cells c1 (NFATc1) translocation from the cytoplasm to the nucleus by high-throughput screening, and to investigate the effect of the natural product upon osteoclast differentiation and its underlying mechanism. An NFATc1 antagonist redistribution assay was performed in U2OS-NFATc1 cells against a natural product library, and Wogonin was found to have the ability to inhibit the NFATc1 translocation from the cytoplasm to the nucleus. The effect of Wogonin on NFATc1 transcription activation was further determined by luciferase assay. An osteoclast differentiation assay was executed to evaluate the effect of Wogonin on osteoclast differentiation. The effect of Wogonin upon the vital genes in osteoclast differentiation was investigated using fluorescent quantitative polymerase chain reaction analysis. The natural product Wogonin significantly inhibited the translocation of NFATc1 from the cytoplasm to the nucleus and its transcriptional activation activity. Wogonin also significantly inhibited osteoclast differentiation and decreased the transcription of osteoclast-associated immunoglobulin-like receptor, tartrate-resistant acid phosphatase and calcitonin receptor. In conclusion, the natural product Wogonin inhibited osteoclast differentiation through the inhibition of NFATc1 translocation from the cytoplasm to the nucleus, and thus the downregulation of genes associated with osteoclast differentiation, which marked Wogonin as a potential treatment for osteoporosis.

Increased expression of lncRNA HULC indicates a poor prognosis and promotes cell metastasis in osteosarcoma.

INTRODUCTION: Long non-coding RNAs (lncRNAs) are aberrantly expressed in many diseases including cancer. LncRNA HULC (highly up-regulated in liver cancer) has recently been revealed to be involved in hepatocellular carcinoma development and progression. However, the role and function of HULC in human osteosarcoma remains unknown. METHODS: LncRNA HULC expression in osteosarcoma tissues and cell lines was detected by quantitative real-time PCR. Then, the association of HULC level with survival of osteosarcoma patients was performed by the Kaplan-Meier and Cox proportional regression analyses. Furthermore, the effects of HULC on tumorigenicity of osteosarcoma cells were evaluated by in vitro assays. RESULTS: In the present study, we demonstrated that HULC was significantly up-regulated in osteosarcoma tissues and cell lines compared with normal controls, and over-expression of HULC was correlated with clinical stage and distant metastasis. Moreover, higher HULC expression was associated with shorter overall survival of osteosarcoma patients. Furthermore, decreased expression of HULC markedly suppressed osteosarcoma cell proliferation, migration, and invasion. CONCLUSIONS: Our results indicated that HULC is a novel molecule involved in osteosarcoma progression, which may provide a new marker of poor prognosis and a potential therapeutic target for osteosarcoma intervention.

Rocaglamide-A Potentiates Osteoblast Differentiation by Inhibiting NF-κB Signaling.

Rheumatoid arthritis is a chronic inflammatory disease that leads to bone and cartilage erosion. The inhibition of osteoblast differentiation by the inflammatory factor TNF-α is critical for the pathogenesis of rheumatoid arthritis. To modulate TNF-α mediated inhibition of osteoblast differentiation is required to improve therapeutic efficacy of rheumatoid arthritis. Here, we explored the potential role of rocaglamide-A, a component of Aglaia plant, in osteoblast differentiation. Rocaglamide-A prevented TNF-α mediated inhibition of osteoblast differentiation, and promoted osteoblast differentiation directly, in both C2C12 and primary mesenchymal stromal cells. Mechanistically, Rocaglamide-A inhibited the phosphorylation of NF-κB component p65 protein and the accumulation of p65 in nucleus, which resulted in the diminished NF-κB responsible transcriptional activity. Oppositely, overexpression of p65 reversed rocaglamide-A's protective effects on osteoblast differentiation. Collectively, rocaglamide-A protected and stimulated osteoblast differentiation via blocking NF-κB pathway. It suggests that rocaglamide-A may be a good candidate to develop as therapeutic drug for rheumatoid arthritis associated bone loss diseases.