Genome-wide identification and expression analysis of GRAS gene family in Eucalyptus grandis.

BACKGROUND: The GRAS gene family is a class of plant-specific transcription factors with important roles in many biological processes, such as signal transduction, disease resistance and stress tolerance, plant growth and development. So far, no information available describes the functions of the GRAS genes in Eucalyptus grandis. RESULTS: A total of 82 GRAS genes were identified with amino acid lengths ranging from 267 to 817 aa, and most EgrGRAS genes had one exon. Members of the GRAS gene family of Eucalyptus grandis are divided into 9 subfamilies with different protein structures, while members of the same subfamily have similar gene structures and conserved motifs. Moreover, these EgrGRAS genes expanded primarily due to segmental duplication. In addition, cis-acting element analysis showed that this family of genes was involved involved in the signal transduction of various plant hormones, growth and development, and stress response. The qRT-PCR data indicated that 18 EgrGRAS genes significantly responded to hormonal and abiotic stresses. Among them, the expression of EgrGRAS13, EgrGRAS68 and EgrGRAS55 genes was significantly up-regulated during the treatment period, and it was hypothesised that members of the EgrGRAS family play an important role in stress tolerance. CONCLUSIONS: In this study, the phylogenetic relationship, conserved domains, cis-elements and expression patterns of GRAS gene family of Eucalyptus grandis were analyzed, which filled the gap in the identification of GRAS gene family of Eucalyptus grandis and laid the foundation for analyzing the function of EgrGRAS gene in hormone and stress response.

Comparison of multiple imputation and other methods for the analysis of imputed genotypes.

BACKGROUND: Analysis of imputed genotypes is an important and routine component of genome-wide association studies and the increasing size of imputation reference panels has facilitated the ability to impute and test low-frequency variants for associations. In the context of genotype imputation, the true genotype is unknown and genotypes are inferred with uncertainty using statistical models. Here, we present a novel method for integrating imputation uncertainty into statistical association tests using a fully conditional multiple imputation (MI) approach which is implemented using the Substantive Model Compatible Fully Conditional Specification (SMCFCS). We compared the performance of this method to an unconditional MI and two additional approaches that have been shown to demonstrate excellent performance: regression with dosages and a mixture of regression models (MRM). RESULTS: Our simulations considered a range of allele frequencies and imputation qualities based on data from the UK Biobank. We found that the unconditional MI was computationally costly and overly conservative across a wide range of settings. Analyzing data with Dosage, MRM, or MI SMCFCS resulted in greater power, including for low frequency variants, compared to unconditional MI while effectively controlling type I error rates. MRM andl MI SMCFCS are both more computationally intensive then using Dosage. CONCLUSIONS: The unconditional MI approach for association testing is overly conservative and we do not recommend its use in the context of imputed genotypes. Given its performance, speed, and ease of implementation, we recommend using Dosage for imputed genotypes with MAF [Formula: see text] 0.001 and Rsq [Formula: see text] 0.3.

Genome-Wide Identification and Expression Analysis of Nitrate Transporter (NRT) Gene Family in Eucalyptus grandis.

Eucalyptus grandis is an important planted hardwood tree worldwide with fast growth and good wood performance. The nitrate transporter (NRT) gene family is a major core involved in nitrogen (N) absorption and utilization in plants, but the comprehensive characterization of NRT genes in E. grandis remains mostly elusive. In this study, a total of 75 EgNRT genes were identified from the genome of E. grandis that were distributed unevenly across ten chromosomes, except Chr9. A phylogenetic analysis showed that the EgNRT proteins could be divided into three classes, namely NRT1, NRT2 and NRT3, which contained 69, 4 and 2 members, respectively. The cis-regulatory elements in the promoter regions of EgNRT genes were mainly involved in phytohormone and stress response. The transcriptome analysis indicated that the differentially expressed genes of leaf and root in E. grandis under different N supply conditions were mainly involved in the metabolic process and plant hormone signal transduction. In addition, the transcriptome-based and RT-qPCR analysis revealed that the expression of 13 EgNRT genes, especially EgNRT1.3, EgNRT1.38, EgNRT1.39 and EgNRT1.52, was significantly upregulated in the root under low-N-supply treatment, suggesting that those genes might play a critical role in root response to nitrate deficiency. Taken together, these results would provide valuable information for characterizing the roles of EgNRTs and facilitate the clarification of the molecular mechanism underlying EgNRT-mediated N absorption and distribution in E. grandis.

The genetic contribution of the X chromosome in age-related hearing loss.

Age-related (AR) hearing loss (HL) is the most common sensory impairment with heritability of 55%. The aim of this study was to identify genetic variants on chromosome X associated with ARHL through the analysis of data obtained from the UK Biobank. We performed association analysis between self-reported measures of HL and genotyped and imputed variants on chromosome X from ∼460,000 white Europeans. We identified three loci associated with ARHL with a genome-wide significance level (p < 5 × 10-8), ZNF185 (rs186256023, p = 4.9 × 10-10) and MAP7D2 (rs4370706, p = 2.3 × 10-8) in combined analysis of males and females, and LOC101928437 (rs138497700, p = 8.9 × 10-9) in the sex-stratified analysis of males. In-silico mRNA expression analysis showed MAP7D2 and ZNF185 are expressed in mice and adult human inner ear tissues, particularly in the inner hair cells. We estimated that only a small amount of variation of ARHL, 0.4%, is explained by variants on the X chromosome. This study suggests that although there are likely a few genes contributing to ARHL on the X chromosome, the role that the X chromosome plays in the etiology of ARHL may be limited.

Rare-variant association analysis reveals known and new age-related hearing loss genes.

Age-related (AR) hearing loss (HL) is a prevalent sensory deficit in the elderly population. Several studies showed that common variants increase ARHL susceptibility. Here, we demonstrate that rare-variants play a crucial role in ARHL etiology. We analyzed exome and imputed data from white-European UK Biobank volunteers, performing both single-variant and rare-variant aggregate association analyses using self-reported ARHL phenotypes. We identified and replicated associations between ARHL and rare-variants in KLHDC7B, PDCD6, MYO6, SYNJ2, and TECTA. PUS7L and EYA4 also revealed rare-variant associations with ARHL. EYA4, MYO6, and TECTA are all known to underline Mendelian nonsyndromic HL. PDCD6, a new HL gene, plays an important role in apoptosis and has widespread inner ear expression, particularly in the inner hair cells. An unreplicated common variant association was previously observed for KHLDC7B, here we demonstrate that rare-variants in this gene also play a role in ARHL etiology. Additionally, the first replicated association between SYNJ2 and ARHL was detected. Analysis of common variants revealed several previously reported, i.e., ARHGEF28, and new, i.e., PIK3R3, ARHL associations, as well as ones we replicate here for the first time, i.e., BAIAP2L2, CRIP3, KLHDC7B, MAST2, and SLC22A7. It was also observed that the odds ratios for rare-variant ARHL associations, were higher than those for common variants. In conclusion, we demonstrate the vital role rare-variants, including those in Mendelian nonsyndromic HL genes, play in the etiology of ARHL.

Integrated Metabolome and Transcriptome Analyses Reveal Dissimilarities in the Anthocyanin Synthesis Pathway Between Different Developmental Leaf Color Transitions in Hopea hainanensis (Dipterocarpaceae).

Changes in plant leaf color during development are directly related to the accumulation or degradation of certain phytochemicals such as anthocyanins. Since some anthocyanins can be beneficial to human health and provide insights into the biology of leaves, the underlying processes and timing by which plants produce these molecules has been the focus of numerous studies. The tree species Hopea hainanensis generally produces green leaves at all growth stages; however, a few explored individuals have been identified possessing red leaves on the top of the seedlings at a young stage. While the phenomenon of leaf color varying with age has been studied in several species, the underlying mechanisms are largely unknown in H. hainanensis. Using a metabolomics approach, the young red leaves in H. hainanensis were found to contain higher levels of anthocyanins and flavonoids than the young green-leaved individuals. Among anthocyanins, pelargonidin and cyanidin were the most likely candidates contributing to the red color of the young leaves. Transcriptome results indicated the genes related to the production of these anthocyanins were significantly upregulated, leading to greater accumulation of red pigments. Specifically, the expression of several MYB and bHLH genes in young red leaf lines was significantly higher than that in the young green leaf lines, especially HhMYB66, HhMYB91, HhMYB6, and HhbHLH70. As such these four transcription factors are probably the main regulatory genes resulting in young red leaves in H. hainanensis. From these results, comparative analyses with other species can be made to better understand the evolution of pigment biosynthesis and how anthocyanins function in plant metabolism and evolution/adaptation.

Hypothetical Interventions for Falls Among Older Adults: An Application of the Parametric G-Formula.

Introduction: Falls, which have a higher incidence and mortality due to accidental injuries, are a major global health challenge. The effects of lifestyle factor, health indicator, psychological condition, and functional status interventions on the risk of falls are unknown and the conventional regression model would not adjust for the confounders. This study aimed to evaluate the 4-year risk of falls on the basis of these hypothetical interventions among Chinese older adults. Methods: Data were obtained from 9,692 aged 65 years and over older adults in the China Health and Retirement Longitudinal Study wave, from 2011 to 2015. We used the parametric g-formula to evaluate the risk of falls on the basis of independent hypothetical interventions of sleep duration, social activities, smoking status, drinking status, body mass index (BMI), systolic blood pressure (SBP), vision, depression, activities of daily living (ADL), and their different joint intervention combinations. Results: During the follow-up of 4 years, we documented 1,569 falls. The observed risk of falls was 23.58%. The risk ratios (95% confidence intervals [CIs]) of falls under the intensive hypothetical interventions on increasing sleep duration, participating in more social activities, quit smoking and drinking, reducing BMI and SBP, better vision, alleviating depressive symptoms, and improving ADL capability were 0.93 (0.87-0.96), 0.88 (0.79-0.92), 0.98 (0.95-1.03), 0.97 (0.95-1.02), 0.92 (0.86-1.03), 0.93 (0.87-1.04), 0.86 (0.74-0.91), 0.91 (0.85-0.96), and 0.79 (0.74-0.85), respectively. The feasible and intensive joint hypothetical intervention reduced the 4-year fall risk by 22% (95% CI: 0.52-0.91) and 33% (95% CI: 0.56-0.72), respectively. Conclusions: Hypothetical interventions for increasing sleep duration, participating in more social activities, better vision, alleviating depressive symptoms, and improving ADL capability help protect older adults from falls. Our findings suggest that a combination of lifestyle factors, health indicators, psychological conditions, and functional status may prove to be an effective strategy for preventing falls among older adults.

MicroRNA-124-5p delays the progression of cerebral aneurysm by regulating FoxO1.

Cerebral aneurysm (CA) is a common brain disease, and the development of cerebral aneurysm is driven by inflammation and hemodynamic stress. MicroRNA (miR)-124-5p is reported to be associated with inflammatory response in brain disease such as cerebral ischemia-reperfusion injury. However, the function and molecular mechanism of miR-124-5p in CA are not clear, thus, the effects of miR-124-5p on inflammatory response in CA were explored. Firstly, the expression of miR-124-5p in the peripheral blood of patients with CA and the control group was detected by reverse transcription-quantitative PCR. Then, the human umbilical vein endothelial cells (HUVECs) were used as an in vitro model system and stimulated with interleukin (IL)-1ß to simulate the inflammatory environment of CA, and the expression of miR-124-5p was detected. Next, the effect of miR-124-5p on the migration and invasion of HUVECs was detected using Transwell assays. Meanwhile, the function of miR-124-5p on various inflammatory factors was determined by western blotting and enzyme-linked immunosorbent assay (ELISA). Next, the TargetScan website was used to predict FoxO1 as a target gene of miR-124-5p, and this target association was validated by double luciferase reporter assay and western blotting. Finally, the interaction of miR-124-5p with FoxO1 in CA was measured by Transwell western blotting and ELISA assays. The results showed that the expression level of miR-124-5p in the peripheral blood of patients with CA was lower compared with that of control group, and the miR-124-5p in HUVECs stimulated by IL-1ß was less compared with that in normal HUVECs. Besides, miR-124-5p could inhibit the migration and invasion abilities of HUVECs and the release of inflammatory factors. Additionally, the overexpression of miR-124-5p was able to inhibit the expression of FoxO1. miR-124-5p-inhibitor promoted the migration and invasion of HUVECs, as well as inflammatory response, which was weakened following the introduction of FoxO1 small interfering RNA. Overall, the present study demonstrated that miR-124-5p could prevent the occurrence and development of cerebral aneurysm by downregulating the expression of FoxO1.

Characterization of cupric glutamate extinguishing mechanism of Alexandrium sp. LC3 with two-dimensional electrophoresis and MALDI-TOF MS.

Mechanisms by which cupric glutamate, a novel algicide, extinguishes Alexandrium sp. LC3 are shown in this study. We show that cupric glutamate not only stimulated the production of malonaldehyde (MDA) and dramatically promoted cell plasma membrane permeability (p < 0.01) but also remarkably reduced sulfhydryl (SH) group content (p < 0.01). Analysis of protein expression profiles by two-dimensional electrophoresis (2-DE) indicated that only 47 protein spots were detected in both control and cupric glutamate treated cells. Three reliable spots were identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) as ribulose-bisphosphate carboxylase large subunit precursor, RNA polymerase beta chain, and hypothetical protein, which can be well correlated with cupric glutamate stress. Based on above results, we hypothesize that the extinguishing mechanisms include (1) the cell membrane being damaged by cupric glutamate; (2) cupric glutamate probably induced denaturation and disintegration of intracellular protein, which led to inhibition of cell growth.

Optimization of cold-active protease production by the psychrophilic bacterium Colwellia sp. NJ341 with response surface methodology.

Culture conditions were optimized for an extracellular cold-active protease production by the psychrophilic bacterium Colwellia sp. NJ341. Response surface methodology was applied for the most significant fermentation parameters (casein, citrate sodium, temperature and Tween-80) identified earlier by one-factor-at-a-time approach. A 2(4) full factorial central composite design was employed to determine the maximum protease production. Using this methodology, the quadratic regression model of producing cold-active protease was built and the optimal combinations of media constituents for maximum protease production (183.21 U/mL) were determined as casein 5.18 g/L, citrate sodium 3.84 g/L, temperature 7.96 degrees C, Tween-80 0.23 g/L. Protease production obtained experimentally coincident with the predicted value and the model was proven to be adequate.

Promotion of hexadecyltrimethyleamine bromide to the damage of Alexandrium sp. LC3 by cupric glutamate.

The effect of hexadecyltrimethyleamine bromide (HDTMAB) on the removal of Alexandrium sp. LC3 under cupric glutamate stress was investigated. Toxic effect of cupric glutamate on A lexandrium sp. LC3 was significantly promoted in the presence of HDTMAB, especially at 3.0 cmc of HDTMAB. It was found that the sulfhydryl group content of the cell decreased, while the malonaldehyde content and membrane permeability increased when Alexandrium sp. LC3 was treated with HDTMAB and cupric glutamate complex, compared with cupric glutamate alone. The data suggest that HDTMAB might stimulate the damage of Alexandrium sp. LC3 by enhancing the membrane permeability.

Effects of exogenous Ca2+ on the membrane permeability, MDA and SH group content of Alexandrium sp. LC3 under surfactant stress.

The effect of Ca2+ on the removal of Alexandrium sp. LC3 under HDTMAB stress was investigated. The results showed that the toxic effect of HDTMAB on Alexandrium sp. LC3 was significantly reduced in the presence of Ca2 , especially under 4 mmol/L of Ca2+. To understand the underlying mechanism, the SH group and MDA content of the cell membrane and membrane permeability were measured. It was found that the SH content of cell member increased, the MDA content and membrane permeability decreased when Alexandrium sp. was treated with Ca2+ and HDTMAB complex, compared with using HDTMAB only. The data suggested that Ca2+ might promote HDTMAB stress resistance of Alexandrium sp. LC3 by reducing the permeability and increasing the stability of cell membrane.

Effect of Cd on GSH and GSH-related enzymes of Chlamydomonas sp. ICE-L existing in Antarctic ice.

Glutathione (GSH) and GSH-related enzymes play a great role in protecting organisms from oxidative damage. The GSH level and GSH-related enzymes activities were investigated as well as the growth yield and malonyldialdehyde (MDA) content in the Antarctic ice microalga Chlamydomonas sp. ICE-L exposure to the different cadmium concentration in this paper. The results showed that the higher concentration Cd inhibited the growth of ICE-L significantly and Cd would induce formation of MDA. At the same time, it is clear that GSH level, glutathione peroxidases (GPx) activity and glutathione S-transferases (GST), activity were higher in ICE-L exposed to Cd than the control. But GR activity dropped notably when ICE-L were cultured in the medium containing Cd. Increase of GSH level, GPx and GST activities acclimate to oxidative stress induced by Cd and protect Antarctic ice microalga Chlamydomonas sp. ICE-L from toxicity caused by Cd exposure. These parameters may be used to assess the biological impact of Cd in the Antarctic pole region environment.

[Physiological effects of taurine on the growth of wheat (Triticum aestivum L.) seedlings].

Wheat (Triticum aestivum L.) seedlings were grown in taurine solution at concentrations of 10, 100, 500, 1000 and 5000 mg/L, and the photochemistry efficiency, the relative permeability of membrane, membrane lipid peroxidation and the growth indexes in wheat seedlings were determined. The results showed that taurine treatments distinctly promoted the growth of wheat seedlings and increased root length, plant height, dry weight and fresh weight single plant of wheat seedlings. In addition, the photochemistry efficiency in the leaf was also increase, and the membrane relative permeability and the content of membrane lipid peroxidation product MDA were decreased, with an optimum treatment concentration at about 500 mg/L. It suggests that taurine has protective effects on the cell membrane of wheat seedlings to the certain extent.

SURFACTANT PROMOTION OF THE INHIBITORY EFFECTS OF CUPRIC GLUTAMATE ON THE DINOFLAGELLATE ALEXANDRIUM(1).

We studied cupric glutamate as a novel algicide for marine harmful algae and hexadecyltrimethyleamine bromide (HDTMAB) as an accelerant. Cupric glutamate had an excellent ability to inhibit the growth of Alexandrium sp. LC3, but the inhibition efficiency did not increase with higher cupric glutamate concentration. The studies on the inhibition ofAlexandrium sp. LC3 by cupric sulfate or cupric glutamate showed that cupric glutamate had a higher inhibition rate than cupric sulfate (P < 0.05). HDTMAB could significantly enhance the inhibition by cupric glutamate (P < 0.05). Ultrastructural changes of Alexandrium sp. LC3 under cupric sulfate, cupric glutamate, and cupric glutamate-HDTMAB combined treatment were studied with TEM. Under these stresses, the integrity of the cell plasma membranes (cell plasma membrane, chloroplast and mitochondria membranes) was destroyed. The degree of damage under cupric glutamate-HDTMAB combined treatment was more severe than under the other stresses. These results indicated that mechanistically cupric glutamate inhibits algal growth by destroying the cell membranes, and that HDTMAB promotes this process, which induced mass extravasation of intracellular components and more copper ion entry into the plasma.

Involvement of VAMP-2 in exocytosis of IL-1 beta in turbot (Scophthalmus maximus) leukocytes after Vibrio anguillarum infection.

Vibrio anguillarum is a major pathogen threatening the fish aquaculture in China. Infection of cultivated turbot (Scophthalmus maximus) with V. anguillarum induced rapid synthesis and secretion of IL-1beta, which initiates the innate immune response. SNARE proteins are known to regulate vesicular trafficking and fusion in all eukaryotes. Here, we determined whether SNARE proteins, specifically vesicle-associated membrane protein-2 (VAMP-2), are involved in regulated exocytosis of IL-1beta of leukocytes in marine fish. We show that VAMP-2 is present in turbot blood leukocytes, with nucleotide sequence identity of 88.2% and 93.0% to those of zebra fish and sea bass, respectively. After Vibrio infection, turbot leukocyte VAMP-2 was increased at the levels of transcription and translation in a temporal pattern coinciding with leukocyte IL-1beta secretion. Confocal microscopy localized VAMP-2 to vesicle structures in leukocytes. Taken together, our results suggest that VAMP-2 is involved in regulated exocytosis of cytokines in immunocytes in fish.

Purification and characterization of a cold-active iron superoxide dismutase from a Psychrophilic Bacterium, Marinomonas sp. NJ522.

Marinomonas sp. NJ522, isolated from Antarctic sea ice, produces a cold-active iron superoxide dismutase (SOD; EC 1.15.1.1). The purified SOD was dimeric and had an approx. Mr of 48 kDa. Highest activity was detected from pH 8 to 10 and at 40 degrees C (assayed over 10 min). Activity at 0 degree C was nearly 35% of the maximum activity.

Purification and characterization of an extracellular cold-active serine protease from the psychrophilic bacterium Colwellia sp. NJ341.

Colwellia sp. NJ341, isolated from Antarctic sea ice, secreted a cold-active serine protease. The purified protease had an apparent Mr of 60 kDa by SDS-PAGE and MALDI-TOF MS. It was active from pH 5-12 with maximum activity at 35 degrees C (assayed over 10 min). Activity at 0 degrees C was nearly 30% of the maximum activity. It was completely inhibited by phenylmethylsulfonyl fluoride.