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.

Nitric oxide signaling is involved in the response to iron deficiency in the woody plant Malus xiaojinensis

To cope with iron (Fe) deficiency, plants have evolved a wide range of adaptive responses from changes in morphology to altered physiological responses. Recent studies have demonstrated that nitric oxide (NO) is involved in the Fe-deficiency response through hormonal signaling pathways. Here, we report that NO plays a significant role in Malus xiaojinensis, an Fe-efficient woody plant. Fe deficiency triggered significant accumulation of NO in the root system, predominantly in the outer cortical and epidermal cells of the elongation zone. The NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide potassium salt (cPTIO) completely arrested Fe deficiency-induced root hair formation, blocked the increase in root ferric-chelate reductase activity and in root H⁺ excretion, further reduced the active iron content in young leaves and roots, and prevented the upregulation of the critical Fe-related genes, FIT, MxFRO2-like, and MxIRT1. These conditions were restored under Fe deficiency by treatment with the NO donor, sodium nitroprusside (SNP). Additionally, chlorophyll content and relative expression levels of the genes chlorophyll a deoxygenase (MxCAO) and polyamine oxidase (MxPAO) were not changed significantly following Fe deficiency for 6 d; however, SNP treatment increased MxHEMA gene expression. Interestingly, the Fv/Fm ratio, the maximum quantum yield of photosystem II (PSII), decreased significantly following cPTIO treatment. We observed more severe chlorosis under Fe deficiency with cPTIO treatment for 9 d. These results strongly suggest that NO mediates a range of responses to Fe deficiency in M. xiaojinensis, from morphological changes to the regulation of physiological processes and gene expression.

[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.

Reactive Oxygen Species Function to Mediate the Fe Deficiency Response in an Fe-Efficient Apple Genotype: An Early Response Mechanism for Enhancing Reactive Oxygen Production

Reactive oxygen species (ROS) are important signaling molecules in plants that contribute to stress acclimation. This study demonstrated that ROS play a critical role in Fe deficiency-induced signaling at an early stage in Malus xiaojinensis. Once ROS production has been initiated, prolonged Fe starvation leads to activation of ROS scavenging mechanisms. Further, we demonstrated that ROS scavengers are involved in maintaining the cellular redox homeostasis during prolonged Fe deficiency treatment. Taken together, our results describe a feedback repression loop for ROS to preserve redox homeostasis and maintain a continuous Fe deficiency response in the Fe-efficient woody plant M. xiaojinensis. More broadly, this study reveals a new mechanism in which ROS mediate both positive and negative regulation of plant responses to Fe deficiency stress.

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.

A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality

Background

Genetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions.

Methods

A total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR.

Results

A high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity.

Conclusions

We demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.

Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves

Sorbitol is a major product of photosynthesis in apple (Malus domestica) that is involved in carbohydrate metabolism and stress tolerance. However, little is known about how the global transcript levels in apple leaves respond to decreased sorbitol synthesis. In this study we used RNA sequencing (RNA-seq) profiling to characterize the transcriptome of leaves from transgenic lines of the apple cultivar 'Greensleeves' exhibiting suppressed expression of aldose-6-phosphate reductase (A6PR) to gain insights into sorbitol function and the consequences of decreased sorbitol synthesis on gene expression. We observed that, although the leaves of the low sorbitol transgenic lines accumulate higher levels of various primary metabolites, only very limited changes were found in the levels of transcripts associated with primary metabolism. We suggest that this is indicative of post-transcriptional and/or post-translational regulation of primary metabolite accumulation and central carbon metabolism. However, we identified significantly enriched gene ontology terms belonging to the 'stress related process' category in the antisense lines (P-value < 0.05). These include genes involved in the synthesis/degradation of abscisic acid, salicylic acid and jasmonic acid, nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes and ATP-binding cassette (ABC) transporter genes. This suggests that sorbitol plays a role in the responses of apple trees to abiotic and biotic stresses.