Transcriptome profiling reveals key genes related to astringency during cucumber fruit development

The goal of this study was to provide quantitative data on the catechin contents and underlying molecular regulatory mechanisms in cucumber during fruit development. The dynamic changes in the total catechin contents and RNA-seq-based transcriptome profiling of the flesh and peel of the cucumber cultivar 'YanBai', which is strongly astringent, were examined at three key developmental stages 3, 6 and 9 days post-pollination. The total catechin content decreased as cucumber fruit developed and was significantly lower in the flesh than in the peel. In total, 5092 and 4004 genes were found to be differently expressed in the peel and flesh, respectively. Based on a functional annotation, eight structural genes encode enzymes involved in the catechin biosynthesis pathway. Three genes encoding 4-coumarate-CoA ligases, two genes encoding chalcone isomerases, two genes encoding dihydroflavonol-4-reductase and one gene each encoding a phenylalanine ammonia-lyase, flavanone 3-hydroxylase and cinnamate 4-hydroxylase were identified as affecting the catechin content of cucumber. The transcriptome data also revealed the significance of transcription factors, including WD40-repeat proteins, MYB and bHLH, in regulating catechin biosynthesis. These findings help increase our understanding of the molecular mechanisms controlling catechin biosynthesis and astringency development in cucumber fruit.

Integrating transcriptome-wide association study and mRNA expression profiling identified candidate genes and pathways associated with osteomyelitis

Objective: Osteomyelitis (OM) is an acute or chronic inflammatory process, characterized by severe inflammation and progressive bone destruction. Limited efforts have been made to explore the genetic basis of OM.Method: The genome-wide association study data set of OM was obtained from the UK Biobank. A transcriptome-wide association study (TWAS) of OM was conducted by the FUSION tool using the gene expression reference weights of lymphocytes and blood. The OM-associated genes identified by TWAS were subjected to gene ontology (GO) enrichment analysis to explore OM-related gene sets. The TWAS results of OM were finally compared with a genome-wide mRNA expression profiling of OM to detect common genes and gene sets.Results: TWAS of OM detected 86 genes for lymphocytes and 387 genes for blood. Comparing the genes identified by TWAS and mRNA expression profiling detected eight common genes for OM, including VWF (p_TWAS = 0.0030, p_mRNA = 3.44 × 10^-9), CCDC50 (p_TWAS = 0.0130, p_mRNA = 0.0003), and TPD52 (p_TWAS = 0.0180, p_mRNA = 1 × 10^-6). GO analysis of the genes identified by TWAS detected multiple OM-associated GO terms, e.g. peroxisomal matrix (p_TWAS = 0.0082), extracellular exosome (p_TWAS = 0.0248), and monooxygenase activity (p_TWAS = 0.0040). Further comparing the GO results of TWAS and mRNA expression profiling detected one common GO term, named extracellular exosome (p_TWAS = 0.0248, p_mRNA = 0.0027).Conclusion: This integrative study of TWAS and mRNA expression profiling detected multiple candidate genes and GO terms for OM. Our results provide novel clues for understanding the pathogenesis of OM.

[Overview of logistic regression model analysis and application]

Logistic regression is a kind of multiple regression method to analyze the relationship between a binary outcome or categorical outcome and multiple influencing factors, including multiple logistic regression, conditional logistic regression, polytomous logistic regression, ordinal logistic regression and adjacent categorical logistic regression. This paper illustrates the basic principle, independent variable selection and assignment, applied condition, model evaluation and diagnosis for multiple logistic regression model. Moreover, the principle and application for polytomous logistic regression and ordinal logistic regression models were also introduced. By providing SAS codes and detailed explanations of the result for an example of obesity, readers could be able to better understand logistic regression model, and apply this method correctly to their research and daily work, so as to improve their capacity of the data analysis.

Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity

Lytic polysaccharide monooxygenases (LPMOs) are key enzymes in both the natural carbon cycle and the biorefinery industry. Understanding the molecular basis of LPMOs acting on polysaccharide substrates is helpful for improving industrial cellulase cocktails. Here we analyzed the sequences, structures, and substrate binding modes of LPMOs to uncover the factors that influence substrate specificity and regioselectivity. Our results showed that the different compositions of a motif located on L2 affect the electrostatic potentials of substrate binding surfaces, which in turn affect substrate specificities of AA10 LPMOs. A conserved Asn at a distance of 7 Å from the active center Cu might, together with the conserved Ser immediately before the second catalytic His, determine the localization of LPMOs on substrate, and thus contribute to C4-oxidizing regioselectivity. The findings in this work provide an insight into the molecular basis of substrate specificity and regioselectivity of LPMOs.

[Overview of multivariate regression model analysis and application]

Analyses of the multivariate regression model are ued very widely in the medical research. Analytical methods of the mutivariate regression model including multiple linear regression, logistic regression, Poisson regression and Cox proportional hazard model were introduced in this article. The contents of the article covered the application conditions of regression models, analytical procedures, strategies of selecting independent variables, extended discussions of regression models and application notes. It is expected that authors could understand the principle of the mutivariate regression model, accurately use these analytical methods in their research, improve the efficiency of data utilization, and enhance the level of statistical analyses.

Integrating transcriptome-wide association study and mRNA expression profiling identifies novel genes associated with bone mineral density

To scan novel candidate genes associated with osteoporosis, a two-stage transcriptome-wide association study (TWAS) of bone mineral density (BMD) was conducted. The BMD-associated genes identified by TWAS were then compared with the gene expression profiling of BMD in bone cells, B cells, and mesenchymal stem cells. We identified multiple candidate genes and gene ontology (GO) terms associated with BMD.

INTRODUCTION

Osteoporosis (OP) is a metabolic bone disease characterized by decrease in BMD. Our objective is to scan novel candidate genes associated with OP.

METHODS

A transcriptome-wide association study (TWAS) was performed by integrating the genome-wide association study (GWAS) summary of bone mineral density (BMD) with two pre-computed mRNA expression weights of peripheral blood and muscle skeleton. Then, another independent GWAS data of BMD was used to verify the discovery results. The BMD-associated genes identified between discovery and replicate TWAS were further subjected to gene ontology (GO) analysis implemented by DAVID. Finally, the BMD-associated genes and GO terms were further compared with the mRNA expression profiling results of BMD to detect the common genes and GO terms shared by both DNA-level TWAS and mRNA expression profile analysis.

RESULTS

TWAS identified 95 common genes with permutation P value < 0.05 for peripheral blood and muscle skeleton, such as TMTC4 in muscle skeleton and DDX17 in peripheral blood. Further comparing the genes detected by discovery-replicate TWAS with the differentially expressed genes identified by mRNA expression profiling of OP patients found 18 overlapped genes, such as MUL1 in muscle skeleton and SPTBN1 in peripheral blood. GO analysis of the genes identified by discovery-replicate TWAS detected 12 BMD-associated GO terms, such as negative regulation of cell growth and regulation of glycogen catabolic process. Further comparing the GO results of discovery-replicate TWAS and mRNA expression profiles found 6 overlapped GO terms, such as membrane and cell adhesion.

CONCLUSION

Our study identified multiple candidate genes and GO terms for BMD, providing novel clues for understanding the genetic mechanism of OP.

Detection sensitivity of laser feedback interferometry using a terahertz quantum cascade laser

We report on the high detection sensitivity of a laser feedback interferometry scheme based on a terahertz frequency quantum cascade laser (QCL). We show that variations on the laser voltage induced by optical feedback to the laser can be resolved with the reinjection of powers as low as ∼-125  dB of the emitted power. Our measurements demonstrate a noise equivalent power of ∼1.4  pW/√Hz, although, after accounting for the reinjection losses, we estimate that this corresponds to only ∼1  fW/√Hz being coupled to the QCL active region.

Waterlogging-induced adventitious root formation in cucumber is regulated by ethylene and auxin through reactive oxygen species signalling

Development of adventitious roots (ARs) at the base of the shoot is an important adaptation of plants to waterlogging stress; however, its physiological mechanisms remain unclear. Here, we investigated the regulation of AR formation under waterlogged conditions by hormones and reactive oxygen species (ROS) in Cucumis sativus L., an agriculturally and economically important crop in China. We found that ethylene, auxin, and ROS accumulated in the waterlogged cucumber plants. On the other hand, application of the ethylene receptor inhibitor 1-methylcyclopropene (1-MCP), the auxin transport inhibitor 1-naphthylphthalamic acid (NPA), or the NADPH oxidase inhibitor diphenyleneiodonium (DPI) decreased the number of ARs induced by waterlogging. Auxin enhanced the expression of ethylene biosynthesis genes, which led to ethylene entrapment in waterlogged plants. Both ethylene and auxin induced the generation of ROS. Auxin-induced AR formation was inhibited by 1-MCP, although ethylene-induced AR formation was not inhibited by NPA. Both ethylene- and auxin-induced AR formation were counteracted by DPI. These results indicate that auxin-induced AR formation is dependent on ethylene, whereas ethylene-induced AR formation is independent of auxin. They also show that ROS signals mediate both ethylene- and auxin-induced AR formation in cucumber plants.

Effects of organic zinc on tibia quality, mineral deposit, and metallothionein expression level of aged hens

The study aimed to determine the effects of methionine hydroxy analog chelate zinc on the tibia quality, mineral deposit, apparent retention of nutrients, and liver metallothionein (MT) expression level of aged laying hens. A total of 960 layers (Hy-Line Grey, 57 wk old) were randomly assigned into 4 groups, and each group had 8 replicates of 30 hens. During the first 2 wk, groups were fed a basal diet without extra zinc (Zn: 35.08 mg/kg). During the ensuing 14 wk, 4 levels of Zn (inorganic Zn: 80 mg/kg; organic Zn: 20, 40, 80 mg/kg) were added to the diet. The results indicated that both the Zn source and level did influence tibia strength and calcium (Ca) and Zn concentrations of tibia (P < 0.05), whereas there were no differences in the copper (Cu) and phosphorus (P) concentrations of the tibia and the tibia length (P > 0.05). Moreover, dietary supplementation with 40 or 80 mg/kg of organic Zn showed higher Zn and Ca concentrations in the tibia and higher tibia strength. The Cu concentration in the liver showed no difference among the 4 treatments, whereas the Zn concentration in the liver increased with the increasing Zn level. The apparent retention of P, iron (Fe), and manganese (Mn) was not affected by the Zn level or source (P > 0.05). However, the organic Zn group increased the apparent retention of Cu, Zn, Ca, crude protein (CP), and energy, and the group supplemented with 40 or 80 mg/kg of organic Zn obtained significant effects (P < 0.05). Moreover, dietary supplementation with 40 or 80 mg/kg organic Zn increased the MT mRNA expression of the liver at week 72, whereas 20 mg/kg of organic Zn decreased it (P < 0.05). In conclusion, this study suggested that an optimum dietary (40 mg/kg) organic Zn level plays a key role in promoting the apparent retention of minerals and nutrients, trace element deposit, and MT mRNA expression.

[Effect of a novel cold atmospheric plasma jet treatment with different temperatures on resin-dentin bonding]

OBJECTIVE

To investigate the effect of different treatment temperatures of a novel cold atmospheric plasma jet treatment on the resin-dentin bonding.

METHODS

(1) Fifty-two freshly extracted, non-carious and intact third molars were collected. The occlusal one-third of the crown was removed by means of a water-cooled low-speed Isomet saw. One dentin disc [(900 ±100) μm] was prepared for each tooth. The fifty-two dentin discs were randomly divided into control group and experimental groups, of which four were in control group, and forty-eight were divided into four experimental groups according to the different treatment temperatures (4 °C, 10 °C, 20 °C and 30 °C) of the novel radio-frequency atmospheric-pressure glow discharge (RF-APGD) plasma jet, twelve in each group. Each experimental group was divided into three subgroups according to different treatment time (10 s, 20 s and 30 s), with four in each subgroup. The occlusal one-third of the crown was removed by means of a water-cooled low-speed Isomet saw. The morphology of demineralized dentin surfaces was analyzed using field emission scanning electron microscopy. (2) Twenty unerupted, non-carious and intact third molars were randomly divided into five groups, four in each group: control group, untreated; 4 °C, 10 °C, 20 °C and 30 °C experimental groups, each group was treated with the RF-APGD plasma jet for 20 s. The micro-tensile resin dentin bond strength was tested after 20 s RF-APGD plasma jet treatment with different temperatures, using a universal mechanical machine.

RESULTS

(1) The field emission scanning electron microscopy results indicated that when compared with the control group, a 10 s RF-APGD plasma jet treatment with 30 °C and 20 °C collapsed the collagen scaffold. Collagen fibrils maintained an uncollapsed three-dimensional structure after the 4 °C RF-APGD plasma jet treatment for even 30 s treatment. (2) The microtensile resin dentin bond strength results of the 4 °C RF-APGD plasma jet treatment group (57.8±0.7) MPa were significantly higher than that of the control group [(47.4±0.5) MPa] and 10 s, 20 s and 30 s RF-APGD plasma treatment group [(51.9±0.7) MPa,(29.7±1.0) MPa and (22.2±1.5) MPa] with statistically significant difference (P<0.05). Compared with the control group, the micro-tensile bond strength increased about 21.9% and 9.5% after 4 °C and 10 °C RF-APGD plasma jet treatment, respectively.

CONCLUSION

Compared with other treatment temperatures, this novel RF-APGD plasma jet treatment with the temperature of 4 °C can preserve the three-dimensional morphology of demineralized dentin better, and can improve the resin-dentin bonding.

Abstract P3-03-01: Comparison of sentinel lymph node detection performances using methylene blue in conjunction with indocyanine green or radioisotope in breast cancer patients: A prospective single-center cohort study

Aim: This cohort study aimed to compare the clinical efficacies between the novel dual tracer composed of indocyanine green (ICG) and blue dye (BD) and the conventional dual tracer composed of radioisotope and BD for sentinel lymph node (SLN) mapping in breast cancer patients.

Methods: This study enrolled 471 clinically lymph node-negative patients with primary breast cancer. All the patients received mastectomy, while, for the sentinel lymph node biopsy (SLNB), they were randomized to receive BD plus radioisotope or BD plus ICG. Two hundred and twenty-seven patients received radioisotope plus BD (Control, RB group) for SLNB, while, 200 patients underwent the ICG plus BD (IB group) for SLNB. The detection performances on SLN identification rate, positive SLN counts, detection sensitivity, and false-negative rate were compared between the two groups. Following SLNB, axillary lymph node dissection (ALND) was performed only on patients with metastatic SLNs. Injection safety and potential side-effects of the two dual tracers were evaluated by a 24-month follow-up after the SLNB procedure.

Results: In the IB group, 97% (194/200) of the patients who underwent the ICG and BD dual tracer injection showed fluorescent-positive lymphatic vessels within 2-5 minutes. The identification rate of SLNs was comparable between the IB group (99.0%, 198/200) and the RB group (99.6%, 270/271) (P=0.79). No significant differences were observed in identification rate of metastatic SLNs (22.5% versus 22.9%, P&gt;0.05, RB group versus IB group, the same below), positive SLN counts (3.72±2.28 versus 3.91±2.13, P&gt;0.05), positive metastatic SLN counts (0.38±0.84 versus 0.34±0.78, P&gt;0.05), SLNB detection sensitivity (94.4% vs. 92.5%, P&gt;0.05), or false-negative rate (5.6% versus 7.5%, P&gt;0.05) between the two groups. No obvious allergic reaction or anaphylaxis, infection at the injection sites, skin necrosis or distal metastasis was reported in either group during the 24-month follow-up.

Conclusions: ICG can be used as a promising alternative tracer for radioisotope in SLN mapping, and when it is combined with BD in lymphangiography, it offers comparable detection sensitivity compared to the conventional lymphatic mapping strategies that are widely used in clinical practice.

Efficacy of indocyanine green vs. radioisotope + blue dye for sentinel lymph node mapping in breast cancer patients.Parameters99Tcm-Dx+BD(N=271)ICG+BD (N=200)P-valueSLN identification rate (%)99.6(270/271)99.0(198/200)0.79SLN counts3.91±2.133.72±2.280.09Metastatic SLN rate (%)22.9(62/271)25.5(51/200)0.51Metastatic SLN counts0.34±0.780.38±0.840.46Sensitivity92.5(62/67)94.4(51/54)0.96False-negative rate (%)7.5(5/67)5.6(3/54) 

Citation Format: Qi X, Yuan L, Zhang Y, Jiang J. Comparison of sentinel lymph node detection performances using methylene blue in conjunction with indocyanine green or radioisotope in breast cancer patients: A prospective single-center cohort study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-03-01.

Comparative proteomic analysis of cucumber powdery mildew resistance between a single-segment substitution line and its recurrent parent

Powdery mildew (PM) is considered a major cause of yield losses and reduced quality in cucumber worldwide, but the molecular basis of PM resistance remains poorly understood. A segment substitution line, namely, SSL508-28, was developed with dominant PM resistance in the genetic background of PM-susceptible cucumber inbred line D8. The substituted segment contains 860 genes. An iTRAQ-based comparative proteomic technology was used to map the proteomes of PM-inoculated and untreated (control) D8 and SSL508-28. The number of differentially regulated proteins (DRPs) in SSL508-28 was almost three times higher than that in D8. Fourteen DRPs were located in the substituted segment interval. Comparative gene expression analysis revealed that nodulin-related protein 1 (NRP1) may be a good candidate for PM resistance. Gene Ontology enrichment analysis showed that DRPs functioning in tetrapyrrole biosynthetic process, sulfur metabolic process and cell redox homeostasis were specifically enriched in the resistant line SSL508-28. DRPs categorized in the KEGG term photosynthesis increased in both lines upon PM infection, suggesting that the strategies used by cucumber may be different from those used by other crops to react to PM attacks at the initial stage. The measurement of hydrogen peroxide and superoxide anion production and net photosynthetic rate were consistent with the changes in protein abundance, suggesting that the proteomic results were reliable. There was a poor correlation between DRPs measured by iTRAQ and the corresponding gene expression changes measured by RNA-seq with the same experimental design. Taken together, these findings improve the understanding of the molecular mechanisms underlying the response of cucumber to PM infection.

Clinical significance of angiopoietin-like protein 3 expression in patients with glioblastoma

There is strong evidence that angiopoietin-like peptide family is involved in the invasiveness and metastasis of cancer. Angiopoietin-like protein 3 (ANGPTL3) is proven to be involved in angiogenesis and tumor development. However, there is no published data on the role ANGPLT3 plays in glioblastomas. The present study was conducted to examine ANGPLT3 proteins expression and its association with clinicopathological factors and prognosis in human glioblastomas. Immunohistochemistry was used to evaluate the expression of ANGPTL3, EGFR and VEGFR. We found that 33 cases (57.9%) that showed strong immunostaining for ANGPTL3 proteins. However, there was no significant difference between the expression of ANGPTL3 and the proangiogenic factors, including EGFR or VEGFR. Patients with high/moderate expression of ANGPTL3 had a significantly shorter survival time (6.3 months) than those (median survival time 13.8 months) with low/negative expression. The overall survival (OS) was also investigated and analyzed by the Kaplan-Meier method, which showed a significant difference (P=0.0045, Breslow test). The present data leads to new insights into the role of ANGPTL3 in glioblastomas and provides an independent predictive factor.