Analysis of alterations to the transcriptome of Loquat (Eriobotrya japonica Lindl.) under low temperature stress via de novo sequencing

Loquat (Eriobotrya japonica Lindl.), which originates from the cooler hill regions of southwestern China, is a typical subtropical evergreen tree. Loquat is one of the most important economic crops in China, but the available genomic information is very limited. Here, we present the first deep transcriptomic analysis of loquat. De novo assembly generated 116,723 contigs and 64,814 unigenes using Illumina sequencing technology. A total of 45,739 unigenes were annotated by Nr, GO, and COG datasets. In addition, we analyzed the gene expression profiles of loquat fruit under low temperature stress and 4017 differential expressed genes were identified. We found that the unigenes involved in the brassinosteroid biosynthesis and phosphatidylinositol signaling systems were upregulated, indicating that they have an important role in the resistance of plants to low temperature. Our results provide an invaluable resource for identification of specific genes and proteins involved in loquat development and response to low temperatures.

RNF126 promotes homologous recombination via regulation of E2F1-mediated BRCA1 expression

RNF126 is an E3 ubiquitin ligase. The deletion of RNF126 gene was observed in a wide range of human cancers and is correlated with improved disease-free and overall survival. These data highlights the clinical relevance of RNF126 in tumorigenesis and cancer therapy. However, the specific functions of RNF126 remain largely unknown. Homologous recombination (HR)-mediated DNA double-strand break repair is important for tumor suppression and cancer therapy resistance. Here, we demonstrate that RNF126 facilitates HR by promoting the expression of BRCA1, in a manner independent of its E3 ligase activity but depending on E2F1, a well-known transcription factor of BRCA1 promoter. In support of this result, RNF126 promotes transactivation of BRCA1 promoter by directly binding to E2F1. Most importantly, an RNF126 mutant lacking 11 amino acids that is responsible for the interaction with E2F1 has a dominant-negative effect on BRCA1 expression and HR by suppressing E2F1-mediated transactivation of BRCA1 promoter and blocking the enrichment of E2F1 on BRCA1 promoter. Lastly, RNF126 depletion leads to the increased sensitivity to ionizing radiation (IR) and poly (ADP-ribose) polymerase (PARP) inhibition. Collectively, our results suggest a novel role of RNF126 in promoting HR-mediated repair through positive regulation on BRCA1 expression by direct interaction with E2F1. This study not only offers novel insights into our current understanding of the biological functions of RNF126 but also provides a potential therapeutic target for cancer treatment.

Transcription factor myocyte enhancer factor 2D regulates interleukin-10 production in microglia to protect neuronal cells from inflammation-induced death

BACKGROUND

Neuroinflammatory responses have been recognized as an important aspect in the pathogenesis of Parkinson's disease (PD). Transcriptional regulation plays a critical role in the process of inflammation. Transcription factor myocyte enhancer factor 2D (MEF2D) is identified as a central factor in transmission of extracellular signals and activation of the genetic programs in response to a wide range of stimuli in several cell types, including neurons. But its presence and function in microglia have not been reported. We therefore investigated the effect of MEF2D in activated microglia on the progress of neuroinflammation and the survival of neurons.

METHODS

BV2 cells and primary cultured glial cells were stimulated with lipopolysaccharide (LPS). Samples from cells were examined for MEF2D expression, interleukin-10 (IL-10), and tumor necrosis factor alpha (TNF-α) by immunoblotting, quantitative real-time PCR (qPCR) or enzyme-linked immunosorbent assay (ELISA). The activity of MEF2D was examined by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation assay (ChIP). Recombinant lentivirus expressing shRNA specific to MEF2D was used to silence MEF2D expression in BV2 cells. The role of IL-10 transcriptionally induced by MEF2D on neuronal survival was assessed by anti-IL-10 neutralizing antibody. The survival of neurons was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining. Male C57bl/6 mice were used to establish an acute PD model. Brain sections and cell slides were tested by immunofluorescence.

RESULTS

We demonstrated that MEF2D was present in microglia. Activation of microglia was associated with an increase in MEF2D level and activity in response to different stimuli in vivo and in vitro. MEF2D bound to a MEF2 consensus site in the promoter region of IL-10 gene and stimulated IL-10 transcription. Silencing MEF2D decreased the level of IL-10, increased the TNF-α mRNA, and promoted inflammation-induced cytotoxicity, consistent with the result of inhibiting IL-10 activity with an anti-IL-10 neutralizing antibody.

CONCLUSIONS

Our study identifies MEF2D as a critical regulator of IL-10 gene expression that negatively controls microglia inflammation response and prevents inflammation-mediated cytotoxicity.

Clinical and laboratory characteristics of systemic sclerosis patients with pulmonary arterial hypertension in China

OBJECTIVES

Pulmonary arterial hypertension (PAH) is associated with significant morbidity and mortality, especially in systemic sclerosis (SSc). Since there was no published study regarding PAH in the Chinese SSc population, we aimed to describe a cohort to provide some data for early diagnosis.

METHODS

We evaluated 236 systemic sclerosis patients prospectively registered in the EUSTAR (European League Against Rheumatism Scleroderma Trial and Research Group) database from the Peking Union Medical College Hospital from 2009 to 2012. Among them, 33 individuals received right heart catheterisations (RHC) while the remaining patients were grouped by echocardiographic data. These patients were classified into two groups, PAH and non-PAH group. Their clinical and laboratory features were statistically analysed to identify possible risk factors for PAH in Chinese SSc population.

RESULTS

The possible prevalence of PAH in SSc patients was approximately 11% in our study. Digital ulcers (52.0% vs. 31.2%), telangiectasias (64.0% vs. 37.6%) and gastroesophageal reflux disease (GERD) (60.0% vs. 36.2%) were more common in SSc patients with PAH. Some laboratory results were also proved to be significantly correlated with it. Logistic regression analysis showed that telangiectasias (OR=2.888, 95% CI=1.176-7.093), presence of GERD (OR=2.592, 95% CI=1.067-6.296), anti-RNP positivity (OR=24.384, 95% CI=1.978-36.651), IgA level elevation (OR=8.745, 95% CI 4.838-122.896) and FVC/TLCO ratio (OR=97.067, 95% CI 12.475-755.271) were associated with an increased odds for PAH in SSc patients.

CONCLUSIONS

This study described possible predictors of PAH in Chinese SSc population, which have been supported by similar studies in other ethnic groups.

Variability in free 25(OH) vitamin D levels in clinical populations

Our goal was to determine total and directly measured free 25-hydroxy vitamin D (25(OH)D) serum levels in humans with a range of 25(OH)D levels and clinical conditions associated with low and high vitamin D binding protein levels. Serum samples and clinical data were collected from 106 subjects: 62 without cirrhosis or pregnancy, 24 cirrhotic patients with albumin <2.9g/dL, and 20 pregnant women. Total 25(OH)D (LC/MS/MS) and "free" 25(OH)D (immunoassay) were measured. Total 25(OH)D was significantly lower in liver disease patients but free 25(OH)D concentrations were significantly higher in this group (p<.001). Neither total nor free 25(OH)D concentrations were significantly different in pregnant women vs. the comparator group. There were significant direct positive relationships between free 25(OH)D and total 25(OH)D concentrations for the entire dataset and for each group (p<.0001), however slopes of relationships differed in the cirrhotic group compared to pregnant women or the comparator group. In cirrhotics: y (free 25(OH)D)=2.52+0.29×X(total 25 (OH)D), r(2)=.51, p<.001; y=1.45+0.09×X; r(2)=.77, p<.0001 for pregnant women; and y=1.11+0.12×X; r(2)=.72, p<.0001 for the comparator group).

CONCLUSIONS

directly measured free 25(OH)D serum concentrations and relationships between total and free 25(OH)D vary with clinical conditions, and may differ from those predicted by indirect estimation methods. This article is part of a Special Issue entitled 'Vitamin D Workshop'.

Measurements of fusion reactions of low-intensity radioactive carbon beams on 12C and their implications for the understanding of X-ray bursts

The interaction between neutron-rich nuclei plays an important role for understanding the reaction mechanism of the fusion process as well as for the energy production through pycnonuclear reactions in the crust of neutron stars. We have performed the first measurements of the total fusion cross sections in the systems (10,14,15)C+(12)C using a new active target-detector system. In the energy region accessible with existing radioactive beams, a good agreement between the experimental and theoretical cross sections is observed. This gives confidence in our ability to calculate fusion cross sections for systems which are outside the range of today's radioactive beam facilities.

A comparison of measured and calculated free 25(OH) vitamin D levels in clinical populations

OBJECTIVE

Our goal was to compare direct quantitation of circulating free 25-hydroxyvitamin D (25(OH)D)levels to calculated free 25(OH)D levels and their relationships to intact PTH (iPTH), a biomarker of 25(OH)D effect, in humans with a range of clinical conditions.

PATIENTS AND METHODS

Serum samples and clinical data were collected from 155 people: 111 without cirrhosis or pregnancy (comparison group), 24 cirrhotic patients with albumin <2.9 g/dL, and 20 pregnant women (second and third trimester). Total 25(OH)D (LC/MS/MS), free 25(OH)D (immunoassay), vitamin D binding protein (DBP) (immunoassay), albumin, and iPTH (immunoassay) were measured.

RESULTS

Total 25(OH)D, DBP, and albumin were lowest in patients with cirrhosis, but measured free 25(OH)D was highest in this group (P < .001). DBP was highest in pregnant women (P < .001), but measured free 25(OH)D did not differ from the comparison group. Calculated free 25(OH)D was positively correlated with measured free 25(OH)D (P < .0001) but explained only 13% of the variability with calculated values higher than measured. African Americans had lower DBP than other ethnic populations within all clinical groups (P < .03), and differences between measured and calculated free 25(OH)D were greatest in African Americans (P < .001). Measured free 25(OH)D was correlated with total 25(OH)D (P < .0001; r(2) = 0.51), but calculated free 25(OH)D was not. Similarly, both measured free 25(OH)D (P < .02) and total 25(OH)D (P < .05) were correlated with iPTH, but calculated free 25(OH)D was not.

CONCLUSIONS

Calculated free 25(OH)D levels varied considerably from direct measurements of free 25(OH)D with discrepancies greatest in the data for African Americans. Differences in DBP binding affinity likely contributed to estimation errors between the races. Directly measured free 25(OH)D concentrations were related to iPTH, but calculated estimates were not. Current algorithms to calculate free 25(OH)D may not be accurate. Further evaluation of directly measured free 25(OH)D levels to determine its role in research and clinical management of patients is needed.

Noise temperature improvement for magnetic fusion plasma millimeter wave imaging systems

Significant progress has been made in the imaging and visualization of magnetohydrodynamic and microturbulence phenomena in magnetic fusion plasmas [B. Tobias et al., Plasma Fusion Res. 6, 2106042 (2011)]. Of particular importance have been microwave electron cyclotron emission imaging and microwave imaging reflectometry systems for imaging T(e) and n(e) fluctuations. These instruments have employed heterodyne receiver arrays with Schottky diode mixer elements directly connected to individual antennas. Consequently, the noise temperature has been strongly determined by the conversion loss with typical noise temperatures of ~60,000 K. However, this can be significantly improved by making use of recent advances in Monolithic Microwave Integrated Circuit chip low noise amplifiers to insert a pre-amplifier in front of the Schottky diode mixer element. In a proof-of-principle design at V-Band (50-75 GHz), significant improvement of noise temperature from the current 60,000 K to measured 4000 K has been obtained.

Covalent amphiphilic polyoxometalates for the design of biphasic microemulsion systems

Unprecedented stabilization of a Winsor I microemulsion has been achieved using a covalent polyoxotungstate amphiphile.

Gene expression signature analysis and protein-protein interaction network construction of spinal cord injury

BACKGROUND

The aim of this study was to investigate the gene expression profile of thoracic propriospinal neurons between post-injury rat and controls.

MATERIALS AND METHODS

Microarray dataset GSE20907 was downloaded from GEO database, including 12 Spinal Cord Injury (SCI) rat and 12 controls. Student's t test was employed to identified differentially expressed genes with a fold-change > 1.2. Then, we used DAVID to perform functional enrichment analysis to uncover dysfunctional biological processes and molecular signatures database (MsigDB) to find any potential relationship between SCI gene expression signature and other published gene expression signature. Protein-Protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. Functional analysis of the hub protein was performed by BinGO.

RESULTS

The maximum change of gene expression profile was found at 3-days post injury and immune response was found upregulated all tested time points. Interestingly, genes upregulated 2-weeks post injury was found significantly overlapped with genes upregulated in brains from Alzheimer's disease patients. Protein interaction network analysis found that LYN, PTPN6 and SMAD1 could be of great value for further investigation.

CONCLUSIONS

It could be inferred that understanding the underlying molecular mechanism post injury, especially at early moment, may provide novel insight for development of therapeutics strategy.

Vulval cancer incidence, mortality and survival in England: age-related trends

OBJECTIVE

To explore the trends and age characteristics of vulval cancer incidence, mortality, survival and stage of disease.

DESIGN

Retrospective population-based observational study based on cancer registry and Office for National Statistics data.

SETTING

England.

POPULATION

All women diagnosed with vulval cancer, defined by the site of the tumour (ICD-10 code C51).

METHODS

Including all C51 cases, Poisson regression was used to test for trends in incidence and mortality rates, and generalised linear modelling was used to test for trends in relative survival. Excluding women with melanomas, basal cell carcinomas and Paget disease, stage was investigated as a percentage of staged data by age.

MAIN OUTCOME MEASURES

Age-standardised incidence and mortality rates, relative survival rates and stage of disease at diagnosis.

RESULTS

From 1990, there was a statistically significant increase in overall incidence (P = 0.018) and decrease in mortality (P < 0.001). In addition, there were statistically significant increases in overall survival (1-year, P < 0.001; 5-year, P < 0.001). However, from 1990, incidence increased in women aged 20-39 years (P = 0.002), 40-49 and 50-59 years (both P < 0.001) and 60-69 years (P = 0.030) and decreased in women aged 80 years and above (P < 0.001). There were statistically significant decreases in mortality in women aged ≥60 years (P < 0.001), and statistically significant increases in 1-year survival in women aged ≥40 years (P ≤ 0.047) and in 5-year survival in women aged 40-49 and ≥60 years (P ≤ 0.011). Stage patterns by age highlight diagnosis at an earlier stage in younger women and more advanced stage diagnosis in older women.

CONCLUSION

Survival from vulval cancer has improved and mortality has decreased since 1990. The overall incidence of disease has increased as a result of more new diagnoses in the under 70-year age group.

Dietary patterns as compared with physical activity in relation to metabolic syndrome among Chinese adults

AIMS

To examine the nationally-representative dietary patterns and their joint effects with physical activity on the likelihood of metabolic syndrome (MS) among 20,827 Chinese adults.

METHODS AND RESULTS

CNNHS was a nationally representative cross-sectional observational study. Metabolic syndrome was defined according to the Joint Interim Statement definition. The "Green Water" dietary pattern, characterized by high intakes of rice and vegetables and moderate intakes in animal foods was related to the lowest prevalence of MS (15.9%). Compared to the "Green Water" dietary pattern, the "Yellow Earth" dietary pattern, characterized by high intakes of refined cereal products, tubers, cooking salt and salted vegetable was associated with a significantly elevated odds of MS (odds ratio 1.66, 95%CI: 1.40-1.96), after adjustment of age, sex, socioeconomic status and lifestyle factors. The "Western/new affluence" dietary pattern characterized by higher consumption of beef/lamb, fruit, eggs, poultry and seafood also significantly associated with MS (odds ratio: 1.37, 95%CI: 1.13-1.67). Physical activity showed significant interactions with the dietary patterns in relation to MS risk (P for interaction = 0.008). In the joint analysis, participants with the combination of sedentary activity with the "Yellow Earth" dietary pattern or the "Western/new affluence" dietary pattern both had more than three times (95%CI: 2.8-6.1) higher odds of MS than those with active activity and the "Green Water" dietary pattern.

CONCLUSIONS

Our findings from the large Chinese national representative data indicate that dietary patterns affect the likelihood of MS. Combining healthy dietary pattern with active lifestyle may benefit more in prevention of MS.

[Association between cancer related fatigue and social support in patients after breast cancer chemotherapy in Changsha]

OBJECTIVE

To explore the association between the cancer related fatigue and social support in breast cancer patients after chemotherapy.

METHODS

According to the uniform inclusive and exclusive criteria, 396 breast cancer patients after chemotherapy were sampled randomly from 4 hospitals in Changsha and investigated on the spot by cancer fatigue scale and social support scale.

RESULTS

The levels of social support, subjective support, Objective support, and utilization of support of the breast cancer patients after chemotherapy were 36.63±7.80, 21.05±4.67, 8.45±3.06, and 7.13±2.10, respectively, which were lower than the normal level, with significant difference(P<0.001). There was a negative correlation between each fatigue dimension and social support, subjective support, Objective support, and utilization of support (P<0.05 or P<0.001).

CONCLUSION

The social support system in patients with breast cancer after chemotherapy is poor. There is a negative correlation between the social support system and cancer related fatigue.