Comparative analysis of cytokinin response factors in Brassica diploids and amphidiploids and insights into the evolution of Brassica species

Background

Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many genes, including cytokinin response factors (CRFs). Although CRFs take vital part in the growth of Arabidopsis thaliana and Solanum lycopersicum, little information of the CRFs in the Brassica U-triangle species has been known yet.

Results

We identified and compared 141 CRFs in the diploids and amphidiploids of Brassica species, including B. rapa, B. oleracea, B. nigra, B. napus, and B. juncea. For all the 141 CRFs, the sequence and structure analysis, physiological and biochemical characteristics analysis were performed. Meanwhile, the Ka/Ks ratios of orthologous and paralogous gene pairs were calculated, which indicated the natural selective pressure upon the overall length or a certain part of the CRFs. The expression profiles of CRFs in different tissues and under various stresses were analyzed in B. oleracea, B. nigra, and B. napus. The similarities and differences in gene sequences and expression profiles among the homologous genes of these species were discussed. In addition, AtCRF11 and its ortholog BrCRF11a were identified to be related to primary root growth in Arabidopsis.

Conclusion

This study performed a genome-wide comparative analysis of the CRFs in the diploids and amphidiploids of the Brassica U-triangle species. Many similarities and differences in gene sequences and expression profiles existed among the CRF homologous genes of these species. In the bioinformatics analysis, we found the close relativity of the CRF homologous genes in the Brassica A and C genomes and the distinctiveness of those in the B genome, and the CRF homologous genes in B subgenome were considerably influenced by the A subgenome of B. juncea. In addition, we identified a new function of the Clade V CRFs related to root growth, which also clarified the functional conservation between Arabidopsis and B. rapa. These results not only offer useful information on the functional analysis of CRFs but also provide new insights into the evolution of Brassica species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5114-y) contains supplementary material, which is available to authorized users.

Increased serum periostin concentrations are associated with the presence of diabetic retinopathy in patients with type 2 diabetes mellitus

PURPOSE

To determine the association between serum periostin and the presence of diabetic retinopathy (DR).

METHODS

Serum periostin was detected in 114 healthy subjects, 122 patients with type 2 diabetes mellitus (T2DM) and 159 patients with DR and compared among groups. Clinical data and other laboratory measurements such as glycated hemoglobin (HbA1c), lipid profiles, serum creatinine (Cr) and high-sensitivity CRP (hsCRP) were also collected and compared among groups. For subgroup analysis, patients with DR were divided into a non-proliferated diabetic retinopathy (NPDR) group and a proliferated diabetic retinopathy (PDR) group. Multivariate analysis was performed using logistic regression models.

RESULTS

The serum periostin level was significantly higher in patients with diabetic retinopathy compared with healthy subjects and patients with T2DM (both P < 0.001, respectively). Also, the periostin level was significantly higher in the PDR group compared to the NPDR group (P = 0.044). Multivariate logistic regression revealed that serum periostin was independently associated with the presence of DR in patients with T2DM (P < 0.001). The receiver operating characteristic (ROC) curves for DR development using serum periostin showed that the area under the receiver operating characteristic curves (AUC) was 0.838 (P < 0.001).

CONCLUSIONS

The current study demonstrated that serum periostin is significantly associated with the presence of DR in patients with T2DM and is an independent risk factor of DR.

Diffusivity of Carbon Dioxide in Aqueous Solutions under Geologic Carbon Sequestration Conditions

Accurate assessment of the long-term security of geologic carbon sequestration requires knowledge of the mobility of carbon dioxide in brines under pressure and temperature conditions that prevail in subsurface aquifers. Here, we report Raman spectroscopic measurements of the rate of CO₂ diffusion in water and brines as a function of pressure, salinity, and concentration of CO₂. In pure water at 50 ± 2 °C and 90 ± 2 bar, we find the diffusion coefficient, D, to be (3.08 ± 0.03) × 10^-9 m²/s, a value that is consistent with a recent microfluidic study but lower than earlier PVT measurements. Under reservoir conditions, salinity affects the mobility of CO₂ significantly and D decreased by 45% for a 4 M solution of NaCl. We find significant differences of diffusivity of CO₂ in brines (0-4 M NaCl), in both the absolute values and the trend compared to the Stokes-Einstein prediction under our experimental conditions. We observe that D decreases significantly at the high CO₂ concentrations expected in subsurface aquifers (∼15% reduction at 0.55 mol/kg of CO₂) and provides an empirical correction to the commonly reported D values that assume a tracer concentration dependence on diffusivity.

[Association between the ratio of early diastolic transmitral velocity to early diastolic mitral annular velocity and invasive measured left atrial pressure in patients with atrial fibrillation and preserved left ventricular ejection fraction]

Objective: To evaluate the association between the ratio of early diastolic transmitral velocity to early diastolic mitral annular velocity (E/E') and left atrial pressure (LAP) estimated from invasive catheter measurements in patients with atrial fibrillation (AF). Methods: A total of 46 consecutive patients with non-valvular AF and preserved left ventricular ejection fraction (LVEF) admitted in our department to receive the first radiofrequency ablation from May to July 2017 were included. All patients underwent echocardiography at 24-48 hours before radiofrequency ablation, and LAP was invasively measured during the ablation procedure. According to mean LAP, patients were divided into 2 groups of normal LAP (LAP≤12 mmHg(1 mmHg=0.133 kPa, n=31) and elevated LAP (LAP>12 mmHg, n=15). Linear correlation analysis was used to evaluate the relationship between E/E' and LAP. Results: E/E' correlated well with LAP (septal E/E' (E/E'(sep)), r= 0.397, P=0.006; lateral E/E' (E/E'(lat)), r=0.433, P=0.003; mean E/E' (E/E'(mean)), r=0.431, P=0.003). Using receiver operating characteristic analysis, the optimal cut-off for E/E'(sep) was 12.5 (sensitivity 73.3%, specificity 67.7%), E/E'(lat) was 10.8 (sensitivity 80.0%, specificity 77.4%), E/E'(mean) was 11.0 (sensitivity 86.7%, specificity 64.5%) to predict mean LAP>12 mmHg. Conclusion: E/E', especially the E/E'(lat), is positively correlated with LAP in patients with AF and preserved LVEF, and may be used to estimate the diastolic function in AF patients with preserved LVEF.

Nicotine inhibits osteogenic differentiation of human periodontal ligament cells under cyclic tensile stress through canonical Wnt pathway and α7 nicotinic acetylcholine receptor

BACKGROUND AND OBJECTIVES

Nicotine, the main psychoactive component of tobacco, affects cell metabolism, proliferation, adhesion and, importantly, the osteogenic differentiation of fibroblasts. Approximately 15% of all orthodontic patients are adults among who one-fifth are smokers. Hence, it is necessary to have insight into the effects of nicotine on the osteogenic differentiation of hPDLCs during orthodontic tooth movement. This study aimed to investigate the effects and mechanisms of nicotine on the osteogenic differentiation of human periodontal ligament cells (hPDLCs) under the application of cyclic tensile stress.

MATERIAL AND METHODS

hPDLCs were obtained from donor third molars. The hPDLCs were treated with nicotine and/or cyclic tensile stress that was applied with a cell stress plus unit. The effect of nicotine on cell viability was analyzed using the MTT assay. The osteogenic differentiation of hPDLCs was detected by alkaline phosphatase staining, Alizarin Red S staining, quantitative real-time polymerase chain reaction and western blotting.

RESULTS

In combination with cyclic tensile stress, nicotine prevented the tensile stress-induced increase in alkaline phosphatase activity, formation of mineralization nodules and the upregulation of mRNA and protein expression of Runt-related transcription factor 2, transcription factor Sp7 and collagen type I; however, canonical Wnt pathway was activated. Furthermore, the addition of Dickkopf-related protein 1 and α-bungarotoxin counteracted the negative effect of nicotine and rescued the osteogenic differentiation of hPDLCs, respectively.

CONCLUSION

These results indicate that nicotine prevents the increased osteogenic potential of hPDLCs induced by cyclic tensile stress by binding to an α7 nicotinic acetylcholine receptor and activating the canonical Wnt pathway.

Analysis of the correlation between non-alcoholic fatty liver disease and bone metabolism indicators in healthy middle-aged men

OBJECTIVE

To investigate the relationship between bone metabolic indicators and non-alcoholic fatty liver disease (NAFLD) in healthy middle-aged men.

PATIENTS AND METHODS

The bone metabolic indicators of 232 healthy middle-age men with NAFLD (NAFLD group) and 308 healthy controls without fatty liver (Control group) were measured, including non-collagenous osteocalcin, the procollagen type 1 N-terminal propeptide (P1NP), beta-C-terminal telopeptide of type I collagen (β-CTX). The Student's t-test was used to analyze the differences in the bone metabolic indicators, age, clinical data, biochemical indicators, and the indicators of glucose and lipid metabolism between the two groups. The correlation of fatty liver-related indicators was detected using the logistic regression analysis.

RESULTS

The body mass index (BMI), diastolic blood pressure, and heart rate in NAFLD group were significantly higher than those in Control group. Among the indicators of glucose and lipid metabolism in NAFLD group, the levels of blood glucose [fasting plasma glucose, postprandial blood glucose and hemoglobin A1c (HbA1c)] were significantly higher than those in Control group. In addition, the insulin resistance and secretion indexes were also significantly higher than those in Control group. The levels of lipid metabolic indicators such as triglyceride were higher, but high-density lipoprotein cholesterol was lower than that in Control group. From logistic regression analysis, the BMI, Homeostasis model assessment (HOMA)-β, HOMA-IR, HbA1c and P1NP were positively associated with the occurrence of NAFLD.

CONCLUSIONS

The bone metabolic indicator P1NP might be a potential predicator for the diagnosis of NAFLD in clinical application.

[Primary investigation of immunoglobulin A synthesis and secretion in human mesangial cells]

OBJECTIVE

To investigate the expression of immunoglobulin A (IgA) in human mesangial cells (HMCs).

METHODS

The HMCs were cultured. The subcellular location of IgA was detected by immunofluorescence staining; the transcripts of Igα,Igκ and IgΛ constant region were detected by reverse transcription-polymerase chain reaction (RT-PCR) and further analyzed by DNA sequencing. The expressions of Igα and IgΛ were detected at transcription level by Western blot after the cytoplasmic protein extraction. The culture supernatant was collected to explore whether IgA could be secreted out of the cell and the protein was further analyzed by mass spectrometry after being purified by affinity chromato-graphy with jacalin-sepharose. The results of DNA sequencing and mass spectrometry were aligned with the mRNA and amino acid sequences in the National Center of Biotechnology Information (NCBI) database.

RESULTS

By immunofluorescence staining, we detected the presence of IgA heavy chain Igα, light chain, both Igκ and IgΛ in expressions of transcripts of Igα1, Igα2, Igκ and IgΛ in the HMCs and the alignment of the sequences of the RT-PCR products with those of the IgCα1, IgCα2, Igκ and IgΛ mRNA in the NCBI database exhibited that the similarities were 99%, 97%, 98% and 97%, respectively. Western blot showed Igα and IgΛ expressions in the cell lysate and secretion of Igα1 and Igα2 heavy chains in cell culture supernatant. To further explore the protein that secreted into the supernatant, after supernatant affinity chromatography with jacalin-sepharose, the proteins were separated by sodium dodecyl sulfonate-polyacrylamide gel electrophoresis (SDS-PAGE) and the band approximating to 65 000 was cut and sent to mass spectrometry. The results were aligned with the amino acid sequences of Igα1 and Igα2 constant region in NCBI database, showing that amino acids between No.52 and No.104, amino acids between No.154 and No.221, amino acids between No.276 and No.327 from IgCα1 and amino acids between No.52 and No.113, amino acids between No.151 and No.204, amino acids between No.251 and No.314 from IgCα2 were the same with those derived from B cells.

CONCLUSION

Our fin-dings suggested that HMCs could synthesize and secret IgA.

Effects of Fe plaque and organic acids on metal uptake by wetland plants under drained and waterlogged conditions

This study aims to assess the role of Fe plaque in metal uptake and translocation by different wetland plants and examine the effects of organic acids on metal detoxification in wetland plants. It was found that although exposed to a similar level of metals in rhizosphere soil solution, metal uptake by shoots of Cypercus flabelliformis and Panicum paludosum was greatly reduced, consequently leading to a better growth under flooded than under drained conditions. This may be related to the enhanced Fe plaque in the former, but due to the decreased root permeability in the latter under anoxic conditions. The Fe plaque on root surface has potential to sequester metals and then reduce metal concentrations and translocation in shoot tissues. However, whether the Fe plaque acts as a barrier to metal uptake and translocation may also be dependent on the root anatomy. Although metal tolerance in wetland plants mainly depends upon their metal exclusion ability, the higher-than-toxic-level of metal concentrations in some species indicates that internal metal detoxification might also exist. It was suggested that malic or citric acid in shoots of P. paludosum and C. flabelliformis may account for their internal detoxification for Zn.

Plasma vascular endothelial growth factor B levels are increased in patients with newly diagnosed type 2 diabetes mellitus and associated with the first phase of glucose-stimulated insulin secretion function of β-cell

PURPOSE

To detect plasma vascular endothelial growth factor B (VEGF-B) in individuals with different glucose tolerance and investigate the relationship between plasma VEGF-B levels and the first phase of glucose-stimulated insulin secretion.

METHODS

A cross-sectional study was conducted involving 45 patients with newly diagnosed type 2 diabetes mellitus (T2DM), 37 patients with impaired glucose regulation (IGR), and 39 Normal glucose tolerance (NGT) subjects, all of whom underwent intravenous glucose tolerance test. Plasma VEGF-B levels were assayed by ELISA. The first phase of insulin secretion was evaluated by acute insulin response (AIR), the area under the curve of the first-phase (0-10 min) insulin secretion (AUC) and glucose disposition index (GDI).

RESULTS

The T2DM and IGR groups had higher plasma VEGF-B levels than the NGT group (P < 0.01). Plasma VEGF-B levels were negatively correlated with AIR, AUC, GDI, HOMA-β (P < 0.01), and positively correlated with plasma glucose, HbA1c, triglyceride, free fatty acid (FFA), fasting insulin, and HOMA-IR (P < 0.01). Logistic regression analysis revealed that higher VEGF-B levels [145.59-180.07 pg/ml, OR 3.55 (95% CI 1.05-12.02) and >180.07 pg/ml, OR 3.64 (95% CI 1.16-11.42)] were related to a greater probability of β-cell hypofunction, compared with low VEGF-B levels (<145.59 pg/ml). After adjusting for triglyceride or FFA, the association between VEGF-B levels and β-cell hypofunction disappeared (P > 0.05).

CONCLUSIONS

Our study provides evidence that plasma VEGF-B levels were higher in patients with newly diagnosed T2DM, and were strongly associated with glucose and lipid metabolism and the first-phase insulin secretion function of β-cells. VEGF-B may be involved in the mechanism of β-cell dysfunction in T2DM.

Polyketides with different post-modifications from desert endophytic fungus Paraphoma sp

Three new polyketides 4,6,8-trihydroxy-5-methyl-3,4-dihydronaphthalen-1(2H)-one (1), 5,7-dihydroxy-3-(1-hydroxyethyl)-3,4-dimethylisobenzofuran-1(3H)-one (2) and 1-(4-hydroxy-6-methoxy-1,7-dimethyl-3-oxo-1,3-dihydroisobenzofuran-1-yl) ethyl acetate (3) together with seven known analogues (4-10) were isolated from desert endophytic fungus Paraphoma sp. The structures of these compounds were elucidated by analysis of NMR data. The absolute configuration of (1-3) was established on the basis of CD experiments. The possible biosynthetic pathway of compounds (1-10) was suggested, which implied that these secondary metabolites might be originated from polyketide biosynthesis with different post-modification reactions. Compounds 2, and 5-8 were evaluated for bioactivities against plant pathogen A. solani, whereas none of them displayed any biological effects. In addition, compounds 1, 2 and 5-10 were also tested for cytotoxic activities against three human cancer cell lines (HepG2 cells, MCF-7 cells and Hela cells) without biological effects.

Acceleration of sub-relativistic electrons with an evanescent optical wave at a planar interface

We report on a theoretical and experimental study of the energy transfer between an optical evanescent wave, propagating in vacuum along the planar boundary of a dielectric material, and a beam of sub-relativistic electrons. The evanescent wave is excited via total internal reflection in the dielectric by an infrared (λ = 2 μm) femtosecond laser pulse. By matching the electron propagation velocity to the phase velocity of the evanescent wave, energy modulation of the electron beam is achieved. A maximum energy gain of 800 eV is observed, corresponding to the absorption of more than 1000 photons by one electron. The maximum observed acceleration gradient is 19 ± 2 MeV/m. The striking advantage of this scheme is that a structuring of the acceleration element's surface is not required, enabling the use of materials with high laser damage thresholds that are difficult to nano-structure, such as SiC, Al₂O₃ or CaF₂.

Alteration and Erosion of Rock Matrix Bordering a Carbonate-Rich Shale Fracture

A novel reactive transport model has been developed to examine the processes that affect fracture evolution in a carbonate-rich shale. An in situ synchrotron X-ray microtomography experiment, flowing CO₂ saturated water through a single fracture mini-core of Niobrara Shale provided the experimental observations for the development and testing of the model. The phenomena observed included the development of a porous altered layer, flow channeling, and increasingly limited calcite dissolution. The experimental observations cannot be explained by models that consider only mineral dissolution and development of an altered layer. The difference between the fracture volume change recorded by the microtomography images and what would be expected from mineral dissolution alone suggest that there is erosion of the altered layer as it develops. The numerical model includes this additional mechanism, with the erosion rate based on the thickness of the altered layer, and successfully captures the evolution of the geochemical reactions and morphology of the fracture. The findings imply that the abundance (with a threshold of approximately 35%) and reactivity of the rapidly reacting mineral control the development and erodibility of the altered layer on the fracture surfaces, and therefore fracture opening.

Genetic analysis of PITX3 variants in patients with essential tremor

BACKGROUND

A clinical overlap between essential tremor (ET) and Parkinson's disease (PD) has prompted investigation whether these disorders share common genetic factors. The paired-like homeodomain transcription factor 3 gene (PITX3) has been shown to play an important role for the differentiation and survival of midbrain dopaminergic neurons in the substantia nigra pars compacta. The preferential degeneration of those dopaminergic neurons is the pathological hallmark in PD.

AIMS OF THE STUDY

The purpose of this study was to evaluate whether PITX3 variants are related to susceptibility of ET in Chinese Han population.

METHODS

Genetic analysis of two variants rs3758549 and rs4919621 of the PITX3 gene was conducted in 200 Chinese Han patients with ET and 426 controls.

RESULTS

We did not identify any statistically significant difference in either genotypic or allelic frequencies of variants between the ET patients and control cohort (all P > 0.05). Haplotype analysis of two variants in the PITX3 gene showed no potential association between the haplotypes and risk of ET (all P > 0.05).

CONCLUSIONS

Our data suggest that PITX3 variants rs3758549 and rs4919621 are not associated with ET in Chinese Han population.

Optical gating and streaking of free electrons with sub-optical cycle precision

The temporal resolution of ultrafast electron diffraction and microscopy experiments is currently limited by the available experimental techniques for the generation and characterization of electron bunches with single femtosecond or attosecond durations. Here, we present proof of principle experiments of an optical gating concept for free electrons via direct time-domain visualization of the sub-optical cycle energy and transverse momentum structure imprinted on the electron beam. We demonstrate a temporal resolution of 1.2±0.3 fs. The scheme is based on the synchronous interaction between electrons and the near-field mode of a dielectric nano-grating excited by a femtosecond laser pulse with an optical period duration of 6.5 fs. The sub-optical cycle resolution demonstrated here is promising for use in laser-driven streak cameras for attosecond temporal characterization of bunched particle beams as well as time-resolved experiments with free-electron beams.