Associations of microRNA single nucleotide polymorphisms and disease risk and pathophysiology

Single nucleotide polymorphisms (SNPs) are genetic variations that contribute to human phenotypes associated with various diseases. SNPs are involved in the regulation of a broad range of physiological and pathological processes, such as cellular senescence, apoptosis, inflammation, and immune response, by upregulating the expression of classical inflammation markers. Recent studies have suggested that SNPs located in gene-encoding microRNAs (miRNAs) affect various aspects of diseases by regulating the expression or activity of miRNAs. In the last few years, miRNA polymorphisms that increase and/or reduce the risk of developing many diseases, such as cancers, autoimmune diseases, and cardiovascular diseases, have attracted increasing attention not only because of their involvement in the pathophysiology of diseases but also because they can be used as prognostic biomarkers for a variety of diseases. In this review, we summarize the relationships between miRNA SNPs and the pathophysiology and risk of diseases.

Allergic rhinitis and allergy are risk factors for otitis media with effusion: A meta-analysis

OBJECTIVE/HYPOTHESIS

We systematically reviewed the associations between allergic rhinitis or allergy and otitis media with effusion, by reference to published data.

STUDY DESIGN

A meta-analysis of case-controlled studies.

DATA SOURCE

Five databases (Pubmed, Highwire, Medline, Wanfang, and China National Knowledge Infrastructure) were searched for relevant studies in the English language published prior to November 12, 2015.

STUDIES CHOSEN

Studies with clearly defined experimental and control groups, in which the experimental groups had otitis media with effusion together with allergic rhinitis or allergy, were selected.

METHODS

We performed a meta-analysis on data from the identified cross-sectional and case-controlled studies using fixed- or random-effects models (depending on heterogeneity). We used Reviewer Manager 5.3 software to this end.

RESULTS

Seven studies met the inclusion criteria. The prevalence of allergic rhinitis in patients with otitis media with effusion and the control groups differed significantly in three studies (P<0.00001), as did the prevalence of allergy (in six studies; P=0.003).

CONCLUSION

Allergic rhinitis and allergy appear to be risk factors for otitis media with effusion.

TATA Box Insertion Provides a Selection Mechanism Underpinning Adaptations to Fe Deficiency

Intraspecific genetic variation is essential for the responses and adaption of plants to evolutionary challenges, such as changing environmental conditions. The development of the Earth's aerobic atmosphere has increased the demand for iron (Fe) in organisms, and Fe deficiency has become a limiting environmental factor for plant growth. Here, we demonstrate that genus Malus adapt to Fe deficiency through modification of the Iron-Regulated Transporter1 (IRT1) promoter. Specifically, an IRT1 mutant allele with a TATA-box insertion in the promoter region upstream of the coding region exhibited increased IRT1 expression. The altered IRT1 promoter is responsible for enhancing Fe uptake. Increasing the number of synthetic repeat TATA-boxes correlates with increased promoter activity. Furthermore, we demonstrate that the insertion of the TATA-box correlates with an increase in transcriptional activation via specific binding of the transcription factor IID (MDP0000939369). Taken together, these results indicate that an allelic insertion of a TATA-box in a gene promoter has allowed apple to adapt to the selective pressure posed by Fe deficiency. More broadly, this study reveals a new mechanism for enhancing gene expression to help plants adapt to different environments, providing new insights into molecular genetic divergence in plants.

Linking genomic reorganization to tumor initiation via the giant cell cycle

To investigate the mechanisms underlying our recent paradoxical finding that mitotically incapacitated and genomically unstable polyploid giant cancer cells (PGCCs) are capable of tumor initiation, we labeled ovarian cancer cells with α-tubulin fused to green fluorescent protein, histone-2B fused to red fluorescent protein and FUCCI (fluorescent ubiquitination cell cycle indicator), and tracked the spatial and time-dependent change in spindle and chromosomal dynamics of PGCCs using live-cell fluorescence time-lapse recording. We found that single-dose (500 nm) treatment with paclitaxel paradoxically initiated endoreplication to form PGCCs after massive cell death. The resulting PGCCs continued self-renewal via endoreplication and further divided by nuclear budding or fragmentation; the small daughter nuclei then acquired cytoplasm, split off from the giant mother cells and acquired competency in mitosis. FUCCI showed that PGCCs divided via truncated endoreplication cell cycle (endocycle or endomitosis). Confocal microscopy showed that PGCCs had pronounced nuclear fragmentation and lacked expression of key mitotic proteins. PGCC-derived daughter cells were capable of long-term proliferation and acquired numerous new genome/chromosome alterations demonstrated by spectral karyotyping. These data prompt us to conceptualize a giant cell cycle composed of four distinct but overlapping phases, initiation, self-renewal, termination and stability. The giant cell cycle may represent a fundamental cellular mechanism to initiate genomic reorganization to generate new tumor-initiating cells in response to chemotherapy-induced stress and contributes to disease relapse.

[Value of single-source dual-energy CT (ssDECT) in differentiating lipid-poor adrenal adenomas from metastatic lesions]

Objective: To evaluate the value of single-source dual-energy CT (ssDECT) in differentiating lipid-poor adenomas from metastases in adrenal glands. Methods: From August 2011 to Oct 2014, 63 patients with 73 adrenal nodules (53 metastases proven by 5-6 months follow-up, and 20 histopathologically proven adenomas, CT value > 10 HU) underwent ssDECT scanning. The CT values of conventional polychromatic CT and virtual monochromatic images (40-140 keV) , fat-water density images and effective atomic number (eff-Z) were reconstructed on an ADW4.5 workstation and ROC curves were then constructed to evaluate the effectiveness of each parameter. The slope of spectral curve was measured and divided into 3 types: increment curve (K>0.1), straight curve (-0.1≤K≤0.1) and decrement curve (K< -0.1) according to the slope (the value of K) of spectral curve, and the curve patterns in the two groups were compared statistically. Results: There was no statistical difference between the mean CT values of metastases (35.12±5.29)HU and lipid-poor adenomas (32.48±6.94)HU by conventional polychromatic CT (P>0.05). The range of single-energy CT values of metastases [from (53.00±15.12) HU to (33.38±5.67) HU] was significantly higher than that of lipid-poor adenomas [from (26.90±26.94) HU to (28.77±10.66) HU] at energy levels ranging from 40 to 80 keV (P<0.05). There was no significant difference between the single-energy CT value of metastases and lipid-poor adenomas at energy levels ranging from 90 to 140 keV (P>0.05). The median fat-water concentration of metastases was -164.61 μg/cm^3, significantly lower than that of lipid-poor adenomas (114.32 μg/cm^3,P<0.05). The eff-Z of metastases (7.76±0.15) was also significantly higher than that of lipid-poor adenomas (7.50±0.25, P<0.05). When the threshold of fat-water concentration was -143.89 μg/cm^3, the sensitivity, specificity and accuracy rate of metastasis diagnosis was 70.0%, 66.0%, and 76.7%, respectively. When the threshold of eff-Z was 7.63, the sensitivity, specificity and accuracy rate of metastasis diagnosis was 83.0%, 65.0%, and 80.4%, respectively. The lower the energy, the higher the diagnostic accuracy at energy levels ranging from 40 to 80 keV, and that of 40 keV was the highest. The spectral curves of metastases included 2 (3.8%) ascending curves, 9 (17.0%) straight curves and 42 (79.2%) descending curves, while in the 20 lipid-poor adenomas, there were 9 (45.0%) ascending curves, 4 (20.0%) straight curves and 7 (35.0%) descending curves, showing significant differences between the two groups (P<0.05). Conclusions: Single-source dual-energy CT provides an effective multi-parameter approach for differentiating lipid-poor adrenal adenomas from metastases.

Surface-sensitive diamond photonic crystals for high-performance gas detection

Diamond slotted photonic crystal (PhC) cavities were fabricated and used for gas detection. They exhibit wavelength sensitivity reaching a 350 nm per unit change of the refractive index of the gaseous environment of the PhC. With a simple oxidized surface termination, diamond PhCs display an ultrahigh sensitivity to the surface adsorption of polar molecules. Gaseous concentrations as low as 80 parts per million (ppm) of hexanol vapor in nitrogen are probed, and a detection limit in the ppm range is inferred, demonstrating a high interest of such devices for trace sensing.

Extract from Arca granosa L. Inhibits Proliferation of Human Tumour Cell Lines with Kidney and Lung Origin

Marine organisms are being considered increasingly as sources of anti-tumour agents. The extract from Arca granosa L. has been shown to decrease the growth of tumours and this study was undertaken to determine its ability and mechanism of inhibition. The extract inhibited the proliferation of six human tumour cell lines from different origins with varying sensitivity. The cell lines Ketr-3, A549 and NCI-H460 with kidney or lung origins were more sensitive to the extract than those of the HepG-2, MCF-7 and MGC-803 cells from other origins. In the three sensitive cell lines (Ketr-3, A549 and NCI-H460) the extract was shown to block different phases of the cell cycle progression and inhibit DNA synthesis in a concentration-dependent manner. It was concluded that the extract from A. granosa is potentially a novel anti-tumour agent, especially on kidney and lung tumour cell lines.

Occurrence and exposure assessment of multiple mycotoxins in dried fruits based on liquid chromatography-tandem mass spectrometry

A reliable analytical method based on liquid chromatography-tandem mass spectrometry was developed for simultaneous determination of aflatoxin B1 (AFB1), aflatoxin B2 (AFB2), aflatoxin G1, aflatoxin G2, ochratoxin A (OTA), deoxynivalenol, T-2 and HT-2 toxin, and zearalenone (ZEA) in various dried fruits. A simple one-step sample extraction without using clean-up cartridges made the established method less labour consuming and less expensive, while optimisation of the several important MS/MS parameters, i.e. the scan time and run segments, ensured its sensitivity and selectivity. After careful validation of the method by determining the linearity (R2>0.99), recovery (77.8-115.9%), precision (relative standard deviation ≤19.5%) and sensitivity (limits of quantification in the range of 0.1-10 μg/kg), a survey of 125 dried fruit samples including 25 pistachios, 28 dried longans, 32 raisins and 40 dried dates randomly collected from different markets in Shanghai, China, was performed. Results revealed that 32.0% of samples were contaminated with different mycotoxins, among which, OTA was the most frequent contaminant with the incidence of 29.6% attaining the concentration levels in the range of 0.4-212.6 μg/kg. ZEA was positively found in 2 pistachio samples with the concentrations of 84.9 μg/kg and 426.9 μg/kg. Trace amounts of AFB1 (0.8 μg/kg) and AFB2 (0.2 μg/kg) were also observed in one pistachio sample and one dried longan sample, respectively. To the best of our knowledge, this is the first report to reveal the real situations of mycotoxin contaminations in various dried fruits in China.

HLA-B allele dropout in PCR sequence-specific oligonucleotide probe typing due to intronic polymorphism in the novel B*58:01:01:02 allele

Currently, Luminex technology based on the PCR sequence-specific oligonucleotide (SSO) probe method has been widely used for HLA genotyping in the immunogenetics laboratories. Here, we reported a case with HLA-B allele dropout by Luminex technology. The initial HLA-B result of the Luminex method with a commercial agent kit was inconclusive, and then, the result of PCR-SBT technology indicated the dropout as a HLA-B*58 allele. Subsequently, the full-length sequence of HLA-B allele was determined by TOPO-TA cloning, and a novel allele B*58:01:01:02 was identified in the individual. Compared with HLA-B*58:01:01:01, the novel allele showed some nucleotides difference at 509 C>T, 521 T>G and CCC insertion in position 503 of intron 2. According to the full-length sequence, the new mutations of intron 2 were contributed to HLA-B locus allele dropout in the sample. Our results indicated multiplatform should be used to improve the HLA typing accuracy when a conclusive HLA genotype cannot be determined.

HLA-A, -B and -DRB1 allele and haplotype frequencies of 8333 Chinese Han from the Zhejiang province, China

The distribution of human leucocyte antigen (HLA) allele and haplotype is varied among different ethnic populations. In this study, HLA-A, -B and -DRB1 allele and haplotype frequencies were determined in 8333 volunteer bone marrow donors of Zhejiang Han population using the polymerase chain reaction sequence-based typing. A total of 52 HLA-A, 96 HLA-B and 61 HLA-DRB1 alleles were found. Of these, the top three frequent alleles in HLA-A, HLA-B and HLA-DRB1 loci, respectively, were A*11:01 (24.53%), A*24:02 (17.35%), A*02:01 (11.58%); B*40:01 (15.67%), B*46:01 (11.87%), B*58:01 (9.05%); DRB1*09:01 (17.54%),DRB1*12:02 (9.64%) and DRB1*08:03 (8.65%). A total of 171 A-B-DRB1 haplotypes with a frequency of >0.1% were presented and the five most common haplotypes were A*33:03-B*58:01- DRB1*03:01, A*02:07-B*46:01-DRB1*09:01, A*30:01-B*13:02-DRB1*07:01, A*33:03-B*58:01-RB1*13:02 and A*11:01-B*15:02-DRB1*12:02. The information will be useful for selecting unrelated bone marrow donors and for anthropology studies and pharmacogenomics analysis.

Efficient oxygen electroreduction over ordered mesoporous Co–N-doped carbon derived from cobalt porphyrin

High-performance self-supported Co–N-doped carbon electrocatalyst for ORR with comparable activity to Pt/C in both acidic and alkaline media was prepared.

Hybrid graphene plasmonic waveguide modulators

The unique optical and electronic properties of graphene make possible the fabrication of novel optoelectronic devices. One of the most exciting graphene characteristics is the tunability by gating which allows one to realize active optical devices. While several types of graphene-based photonic modulators have already been demonstrated, the potential of combining the versatility of graphene with subwavelength field confinement of plasmonic waveguides remains largely unexplored. Here we report fabrication and study of hybrid graphene-plasmonic waveguide modulators. We consider several types of modulators and identify the most promising one for telecom applications. The modulator working at the telecom range is demonstrated, showing a modulation depth of >0.03 dB μm(-1) at low gating voltages for an active device area of just 10 μm(2), characteristics which are already comparable to those of silicon-based waveguide modulators while retaining the benefit of further device miniaturization. Our proof-of-concept results pave the way towards on-chip realization of efficient graphene-based active plasmonic waveguide devices for optical communications.